Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 31
Found at i:1151714 original size:21 final size:21
Alignment explanation
Indices: 1151688--1151729 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1151678 ATTTAGGGTC
1151688 TAATTAAAATTT-TAATAAATT
1 TAATTAAAATTTCTAA-AAATT
*
1151709 TAATTAAATTTTCTAAAAATT
1 TAATTAAAATTTCTAAAAATT
1151730 GTGAGAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATTAAAATTTCTAAAAATT
Found at i:1154921 original size:2 final size:2
Alignment explanation
Indices: 1154914--1154942 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1154904 ATAAAATCTA
1154914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1154943 GTAATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1156074 original size:24 final size:24
Alignment explanation
Indices: 1156044--1156101 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
1156034 TTAACCGATC
*
1156044 TGATATTGACTCGCTCAATCAATA
1 TGATATTAACTCGCTCAATCAATA
1156068 TGATATTAACTCGCTCAATCAATA
1 TGATATTAACTCGCTCAATCAATA
1156092 TGATATTAAC
1 TGATATTAAC
1156102 CTAACCCGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (24 bp):
TGATATTAACTCGCTCAATCAATA
Found at i:1166588 original size:21 final size:21
Alignment explanation
Indices: 1166562--1166614 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1166552 ACACTGCATG
1166562 AACCGATTCCCTATGAGGGGC
1 AACCGATTCCCTATGAGGGGC
*
1166583 AACCGATTCCCTATGAGGGGG
1 AACCGATTCCCTATGAGGGGC
*
1166604 TACCGATTCCC
1 AACCGATTCCC
1166615 CCCACGCTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGGGGC
Found at i:1174598 original size:20 final size:20
Alignment explanation
Indices: 1174570--1174613 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1174560 AACAAAATGT
*
1174570 CCAGAGGGTACAGATTCCCC
1 CCAGAGGGTACAGATTACCC
* *
1174590 CCAGGGGGTACCGATTACCC
1 CCAGAGGGTACAGATTACCC
1174610 CCAG
1 CCAG
1174614 TTTAACAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.36, G:0.27, T:0.14
Consensus pattern (20 bp):
CCAGAGGGTACAGATTACCC
Found at i:1178250 original size:2 final size:2
Alignment explanation
Indices: 1178238--1178272 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1178228 GACGCCTTAT
*
1178238 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1178273 GGGTTGTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1184293 original size:15 final size:15
Alignment explanation
Indices: 1184261--1184298 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1184251 TCCAGACCCT
1184261 AAAAATATAATACCA
1 AAAAATATAATACCA
*
1184276 AAAAAGTATAATA-TA
1 AAAAA-TATAATACCA
1184291 AAAAATAT
1 AAAAATAT
1184299 TAAACACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 11 0.52
16 7 0.33
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAAATATAATACCA
Found at i:1185302 original size:6 final size:6
Alignment explanation
Indices: 1185286--1185318 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1185276 TCTTTTCTTT
*
1185286 GGGGT- GGGGTG GGGGTG GGGGTG GGGGAG GGGG
1 GGGGTG GGGGTG GGGGTG GGGGTG GGGGTG GGGG
1185319 CGGCGGCAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.03, C:0.00, G:0.85, T:0.12
Consensus pattern (6 bp):
GGGGTG
Found at i:1191999 original size:20 final size:21
Alignment explanation
Indices: 1191950--1192000 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1191940 GTCGCATGGT
1191950 AATAGATGATGACTTGTGAAA
1 AATAGATGATGACTTGTGAAA
1191971 AATAGATGATGACTTGTGAAA
1 AATAGATGATGACTTGTGAAA
1191992 AATA-ATGAT
1 AATAGATGAT
1192001 TGCAAAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (21 bp):
AATAGATGATGACTTGTGAAA
Found at i:1192470 original size:5 final size:6
Alignment explanation
Indices: 1192455--1192480 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1192445 CTCTGCCACA
1192455 TTTTTC TTTTTC TTTTTC TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TT
1192481 CCGTTTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:1199908 original size:22 final size:22
Alignment explanation
Indices: 1199880--1199959 Score: 151
Period size: 22 Copynumber: 3.6 Consensus size: 22
1199870 TGCTCCATCA
1199880 TGTTGTTGGTTAGAAAATTACG
1 TGTTGTTGGTTAGAAAATTACG
1199902 TGTTGTTGGTTAGAAAATTACG
1 TGTTGTTGGTTAGAAAATTACG
*
1199924 TGTTGTTGGTTAGAAAATTACA
1 TGTTGTTGGTTAGAAAATTACG
1199946 TGTTGTTGGTTAGA
1 TGTTGTTGGTTAGA
1199960 GAACGAAATG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.26, C:0.04, G:0.28, T:0.42
Consensus pattern (22 bp):
TGTTGTTGGTTAGAAAATTACG
Found at i:1203724 original size:15 final size:14
Alignment explanation
Indices: 1203676--1203727 Score: 86
Period size: 14 Copynumber: 3.6 Consensus size: 14
1203666 GATGAACATT
1203676 TTTGCATCTTTTCA
1 TTTGCATCTTTTCA
1203690 TTTGCATCTTTTCA
1 TTTGCATCTTTTCA
*
1203704 TTTGCATCTTTACA
1 TTTGCATCTTTTCA
1203718 TTTTGCATCT
1 -TTTGCATCT
1203728 GCATTTCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
14 27 0.75
15 9 0.25
ACGTcount: A:0.15, C:0.21, G:0.08, T:0.56
Consensus pattern (14 bp):
TTTGCATCTTTTCA
Found at i:1206514 original size:21 final size:19
Alignment explanation
Indices: 1206490--1206547 Score: 73
Period size: 18 Copynumber: 3.0 Consensus size: 19
1206480 ATGTTTAATG
*
1206490 AAAAACATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
*
1206509 ACAAAATGATATCAATTGTT-
1 A-AAAA-GATACCAATTGTTA
1206529 AAAAAGATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
1206548 CCAATTGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 12 0.36
19 5 0.15
20 5 0.15
21 11 0.33
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:1209532 original size:21 final size:21
Alignment explanation
Indices: 1209498--1209537 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1209488 AGTCTTATAT
*
1209498 AGCCGTTGGGGATG-TTTTGG
1 AGCCGTTGGAGATGATTTTGG
1209518 AGCCGTTTGGAGATGATTTT
1 AGCCG-TTGGAGATGATTTT
1209538 TCTGCTCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTGGAGATGATTTTGG
Found at i:1209751 original size:20 final size:20
Alignment explanation
Indices: 1209723--1209789 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 20
1209713 TACTATTCAT
* * *
1209723 TACTGTTCACACAGTATTGG
1 TACTATTCACACAGTATCGA
* *
1209743 TACTATTCATACATTATCGA
1 TACTATTCACACAGTATCGA
* *
1209763 TACTATTCATACA-TA-CAA
1 TACTATTCACACAGTATCGA
1209781 TACTATTCA
1 TACTATTCA
1209790 TAAAAACATT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.27
19 2 0.05
20 28 0.68
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.37
Consensus pattern (20 bp):
TACTATTCACACAGTATCGA
Found at i:1213656 original size:32 final size:32
Alignment explanation
Indices: 1213620--1213736 Score: 189
Period size: 32 Copynumber: 3.7 Consensus size: 32
1213610 AACAACGATG
1213620 GCATCTTTGAAGATTCAACATCAAATGTTGGA
1 GCATCTTTGAAGATTCAACATCAAATGTTGGA
1213652 GCATCTTTGAAGATTCAACATCAAATGTTGGA
1 GCATCTTTGAAGATTCAACATCAAATGTTGGA
* * *
1213684 GCATCTTTGGAGATTCAACATCAAATATTGGG
1 GCATCTTTGAAGATTCAACATCAAATGTTGGA
**
1213716 GCATCTTTGGGGATTCAACAT
1 GCATCTTTGAAGATTCAACAT
1213737 TCTAATACGA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 81 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (32 bp):
GCATCTTTGAAGATTCAACATCAAATGTTGGA
Found at i:1213984 original size:66 final size:66
Alignment explanation
Indices: 1213865--1214006 Score: 160
Period size: 66 Copynumber: 2.1 Consensus size: 66
1213855 TTTTCTTAAA
* * * **
1213865 AAACAAAATTTTGTCTATTTTAAGACAATTTCTTTGGAACAAAAATCTTTGAGTTTGTTTCTTTG
1 AAACAAAATTTTGTCTATTTTAAGACAACTTATTTGGAACAAAAATCTCTGAGTAGGTTTCTTTG
1213930 G
66 G
* * * **
1213931 AAACAAAATTTTGTCTCTTTTGAGACAACTTATTTTGAAGC-ATCATCTCTGAGTAGGTTTCTTT
1 AAACAAAATTTTGTCTATTTTAAGACAACTTATTTGGAA-CAAAAATCTCTGAGTAGGTTTCTTT
*
1213995 TG
65 GG
1213997 AAACCAAAAT
1 AAA-CAAAAT
1214007 CCTTAGATGG
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
66 56 0.89
67 7 0.11
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (66 bp):
AAACAAAATTTTGTCTATTTTAAGACAACTTATTTGGAACAAAAATCTCTGAGTAGGTTTCTTTG
G
Found at i:1214237 original size:82 final size:82
Alignment explanation
Indices: 1214142--1214306 Score: 276
Period size: 82 Copynumber: 2.0 Consensus size: 82
1214132 CCTAAGATGG
* * *
1214142 CATGTCGTCCTCATCACATAGGAACCATGTCATCACCCGACTAGATCTTTTCATTATGTAGGAGC
1 CATGTCGTCCTCATCACATAGGAACCATGTCATCACCCGACCAGATCTCTTCATTATGTAGGAAC
1214207 TATGTCAACCCAGATAA
66 TATGTCAACCCAGATAA
* *
1214224 CATGTCGTCCTCATCACGTAGGAACCGTGTCATCACCCGACCAGATCTCTTCATTATGTAGGAAC
1 CATGTCGTCCTCATCACATAGGAACCATGTCATCACCCGACCAGATCTCTTCATTATGTAGGAAC
*
1214289 TGTGTCAACCCAGATAA
66 TATGTCAACCCAGATAA
1214306 C
1 C
1214307 TAGAACTCTT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (82 bp):
CATGTCGTCCTCATCACATAGGAACCATGTCATCACCCGACCAGATCTCTTCATTATGTAGGAAC
TATGTCAACCCAGATAA
Found at i:1214295 original size:40 final size:40
Alignment explanation
Indices: 1214160--1214288 Score: 111
Period size: 40 Copynumber: 3.2 Consensus size: 40
1214150 CCTCATCACA
* *
1214160 TAGGAACCATGTCATCACCCGACTAGATCTTTTCATTATG
1 TAGGAACCATGTCATCACCCGACCAGATCTCTTCATTATG
* * * * * *
1214200 TAGGAGCTATGTCA--ACCCAGATAACATG-TCGTCCTCATCACG
1 TAGGAACCATGTCATCACCC-G--ACCA-GATC-TCTTCATTATG
*
1214242 TAGGAACCGTGTCATCACCCGACCAGATCTCTTCATTATG
1 TAGGAACCATGTCATCACCCGACCAGATCTCTTCATTATG
1214282 TAGGAAC
1 TAGGAAC
1214289 TGTGTCAACC
Statistics
Matches: 66, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
38 4 0.06
39 1 0.02
40 28 0.42
41 9 0.14
42 19 0.29
43 1 0.02
44 4 0.06
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (40 bp):
TAGGAACCATGTCATCACCCGACCAGATCTCTTCATTATG
Found at i:1217394 original size:40 final size:41
Alignment explanation
Indices: 1217330--1217410 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 41
1217320 GATCCTTGGA
1217330 GTATTATAAATTAATAATTATATAAAATTAAAAATATAACT
1 GTATTATAAATTAATAATTATATAAAATTAAAAATATAACT
* *
1217371 GTATT-TAAATTAATAATTCTATAAAATTACAAATATAACT
1 GTATTATAAATTAATAATTATATAAAATTAAAAATATAACT
1217411 ATGACAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 33 0.87
41 5 0.13
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (41 bp):
GTATTATAAATTAATAATTATATAAAATTAAAAATATAACT
Found at i:1225703 original size:20 final size:20
Alignment explanation
Indices: 1225662--1225703 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1225652 ATATAACATA
*
1225662 TATAAATATGACAAAACTGG
1 TATAAATATGACAAAACCGG
*
1225682 TATAAATATGACATAACCGG
1 TATAAATATGACAAAACCGG
1225702 TA
1 TA
1225704 AAGTGCTACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (20 bp):
TATAAATATGACAAAACCGG
Found at i:1225746 original size:182 final size:181
Alignment explanation
Indices: 1225439--1225925 Score: 681
Period size: 182 Copynumber: 2.7 Consensus size: 181
1225429 ATACATTTTT
* * *
1225439 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCGGTATC
1 ATACTTTATAAAAATGTATCGATCCATAACGATATAACATGTAAAAATATGA-AAAACTGGTATC
* * * *
1225504 GAAAA-GACAAAACCGGTAATGCGCTATCGGATCTGTTGAAAGTGTTGATACATTAATATAAGTA
65 -AAAATGACAAAACCGGTAAAGCGCTACCGGATCTGTTGAAAGTGTCGATACTTTAATATAAGTA
* *
1225568 TCGAAACTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCAATAAAGTGTCG
129 TAGAAACTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCAATAAAATGTCG
* *
1225621 ATACTTTATAAAAATGTATCGATCCATAACGATATAACATATATAAATATGACAAAACTGGTAT-
1 ATACTTTATAAAAATGTATCGATCCATAACGATATAACATGTAAAAATATGA-AAAACTGGTATC
* *
1225685 AAATATGACATAACCGGTAAAGTGCTACCGGATCTGTTGAAAGTGTCGATACTTTAATATAAGTA
65 AAA-ATGACAAAACCGGTAAAGCGCTACCGGATCTGTTGAAAGTGTCGATACTTTAATATAAGTA
* * *
1225750 TAGACACTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAATGTTG
129 TAGAAACTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCAATAAAATGTCG
* * * *
1225803 ATACTTTATAAAAATGTATCGAGCCATAATGATATAACATGTAAAAATATGAAAAAATCGGTCTC
1 ATACTTTATAAAAATGTATCGATCCATAACGATATAACATGTAAAAATATGAAAAACT-GGTATC
* ** * * *
1225868 GAAATGACAAAACCGGTAAAGCATTACCGGATATATTGAAAGTGTCTATACTTTAATA
65 AAAATGACAAAACCGGTAAAGCGCTACCGGATCTGTTGAAAGTGTCGATACTTTAATA
1225926 AGTACGTGTA
Statistics
Matches: 270, Mismatches: 31, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
180 3 0.01
181 6 0.02
182 259 0.96
183 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (181 bp):
ATACTTTATAAAAATGTATCGATCCATAACGATATAACATGTAAAAATATGAAAAACTGGTATCA
AAATGACAAAACCGGTAAAGCGCTACCGGATCTGTTGAAAGTGTCGATACTTTAATATAAGTATA
GAAACTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCAATAAAATGTCG
Found at i:1227936 original size:22 final size:23
Alignment explanation
Indices: 1227885--1227940 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
1227875 AACGTTTTTG
* *
1227885 TTTTTTTATATAAAATGATAGTA
1 TTTTATTATATAAAATGATAGAA
*
1227908 TAGTTATTATATAAAATGATA-AA
1 T-TTTATTATATAAAATGATAGAA
1227931 TTTTATTATA
1 TTTTATTATA
1227941 AATGAAGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.29
23 3 0.11
24 17 0.61
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (23 bp):
TTTTATTATATAAAATGATAGAA
Found at i:1230804 original size:199 final size:201
Alignment explanation
Indices: 1230201--1231075 Score: 1344
Period size: 201 Copynumber: 4.4 Consensus size: 201
1230191 TATAATTTTG
* *
1230201 TATA-CGGTTTTATGTGAGAATAGGTCTACATAATGTATCAACACTTTTTAAATGATGTGTGTCG
1 TATACCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACACTTTTTAAAT--T-TGTGTCG
* *
1230265 ATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCAAGAATAAAATGTCGATACATTTATAAA
63 ATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACGAATAAAGTGTCGATACATTTATAAA
* *
1230330 AAGTATCGATTCGAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAAC
128 AAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAAC
1230395 CGATATAAA
193 CGATATAAA
* * * *
1230404 TATACTGGTTTTATGAGAGAATAGGTCTATATAATGTATCGACAATTTTTAAATTTATGTCGATA
1 TATACCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATA
* * *
1230469 CTTTTTGTCTAGAATAAATGCCCAAACTAGGTGCACGTATAAAGTGTCGATACATTTATAAACAA
66 CTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACGAATAAAGTGTCGATACATTTATAAA-AA
1230534 -TATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCG
130 GTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCG
*
1230598 GTATAAA
195 ATATAAA
* * * * *
1230605 TATACCAGTTTTATGAGATAATAGGTCTATATAATGTATCAACACTTTTTAAATTTGTATCGATA
1 TATACCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATA
*
1230670 CTTTTTGTCCAGAATGAATGCCC-AACTAGGT-CACGGATAAAGTGTCGATACATTTATAAAAAG
66 CTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAG
* **
1230733 TATCAATCCCAAAAACATTAAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGA
131 TATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGA
1230798 TATAAA
196 TATAAA
* *
1230804 TATACCGATTTTATGAGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCAATA
1 TATACCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATA
* * * * *
1230869 CTTTTTGTCCAAAATGAATGCCCAAACTAGGTGTACGCATAAAGTGTTGATACATTAATAAAAAG
66 CTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAG
* * *
1230934 TATCGATCCCAAAAACATTGAAACCCATAATTATAATGTAATAGATAATTTTTCAATGTAACCGG
131 TATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGA
1230999 TATAAA
196 TATAAA
* * * * *
1231005 TATATCGGTTTTATGAGATAATATGTCTACATAATGTATCGATAGTTTTTAAATTTGTGTCGATA
1 TATACCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATA
1231070 CTTTTT
66 CTTTTT
1231076 TAAATTTCCC
Statistics
Matches: 616, Mismatches: 51, Indels: 12
0.91 0.08 0.02
Matches are distributed among these distances:
198 2 0.00
199 175 0.28
200 16 0.03
201 372 0.60
202 3 0.00
203 4 0.01
204 44 0.07
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (201 bp):
TATACCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATA
CTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAG
TATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGA
TATAAA
Found at i:1230923 original size:400 final size:402
Alignment explanation
Indices: 1230207--1231075 Score: 1384
Period size: 400 Copynumber: 2.2 Consensus size: 402
1230197 TTTGTATACG
* *
1230207 GTTTTATGTGAGAATAGGTCTACATAATGTATCAACACTTTTTAAATGATGTGTGTCGATACTTT
1 GTTTTATGAGATAATAGGTCTACATAATGTATCAACACTTTTTAAAT--T-TGTGTCGATACTTT
1230272 TTGTCCAGAATGAATGCCCAAACTAGGTGCAAGAATAAAATGTCGATACATTTATAAAAAGTATC
63 TTGTCCAGAATGAATGCCCAAACTAGGTGCAAGAATAAAATGTCGATACATTTATAAAAAGTATC
* * * *
1230337 GATTCGAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGATATA
128 AATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGATATA
* * * *
1230402 AATATACTGGTTTTATGAGAGAATAGGTCTATATAATGTATCGACAATTTTTAAATTTATGTCGA
193 AATATACCGATTTTATGAGAGAATAGGTCTACATAATGTATCGACAATTTTTAAATTTATGTCAA
* * * *
1230467 TACTTTTTGTCTAGAATAAATGCCCAAACTAGGTGCACGTATAAAGTGTCGATACATTTATAAAC
258 TACTTTTTGTCCAAAATAAATGCCCAAACTAGGTGCACGCATAAAGTGTCGATACATTAATAAA-
*
1230532 AA-TATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAAC
322 AAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGATAATTTTTCAATGTAAC
1230596 CGGTATAAATATACCA
387 CGGTATAAATATACCA
* *
1230612 GTTTTATGAGATAATAGGTCTATATAATGTATCAACACTTTTTAAATTTGTATCGATACTTTTTG
1 GTTTTATGAGATAATAGGTCTACATAATGTATCAACACTTTTTAAATTTGTGTCGATACTTTTTG
* * *
1230677 TCCAGAATGAATGCCC-AACTAGGT-CACGGATAAAGTGTCGATACATTTATAAAAAGTATCAAT
66 TCCAGAATGAATGCCCAAACTAGGTGCAAGAATAAAATGTCGATACATTTATAAAAAGTATCAAT
*
1230740 CCCAAAAACATTAAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGATATAAAT
131 CCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGATATAAAT
* *
1230805 ATACCGATTTTATGAGAGAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCAATAC
196 ATACCGATTTTATGAGAGAATAGGTCTACATAATGTATCGACAATTTTTAAATTTATGTCAATAC
* * *
1230870 TTTTTGTCCAAAATGAATGCCCAAACTAGGTGTACGCATAAAGTGTTGATACATTAATAAAAAGT
261 TTTTTGTCCAAAATAAATGCCCAAACTAGGTGCACGCATAAAGTGTCGATACATTAATAAAAAGT
*
1230935 ATCGATCCCAAAAACATTGAAACCCATAATTATAATGTAATAGATAATTTTTCAATGTAACCGGT
326 ATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGATAATTTTTCAATGTAACCGGT
* *
1231000 ATAAATATATCG
391 ATAAATATACCA
* * * *
1231012 GTTTTATGAGATAATATGTCTACATAATGTATCGATAGTTTTTAAATTTGTGTCGATACTTTTT
1 GTTTTATGAGATAATAGGTCTACATAATGTATCAACACTTTTTAAATTTGTGTCGATACTTTTT
1231076 TAAATTTCCC
Statistics
Matches: 428, Mismatches: 35, Indels: 7
0.91 0.07 0.01
Matches are distributed among these distances:
399 2 0.00
400 341 0.80
401 8 0.02
402 32 0.07
403 1 0.00
405 44 0.10
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (402 bp):
GTTTTATGAGATAATAGGTCTACATAATGTATCAACACTTTTTAAATTTGTGTCGATACTTTTTG
TCCAGAATGAATGCCCAAACTAGGTGCAAGAATAAAATGTCGATACATTTATAAAAAGTATCAAT
CCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGATATAAAT
ATACCGATTTTATGAGAGAATAGGTCTACATAATGTATCGACAATTTTTAAATTTATGTCAATAC
TTTTTGTCCAAAATAAATGCCCAAACTAGGTGCACGCATAAAGTGTCGATACATTAATAAAAAGT
ATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGATAATTTTTCAATGTAACCGGT
ATAAATATACCA
Found at i:1232312 original size:9 final size:9
Alignment explanation
Indices: 1232298--1232323 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1232288 CAATGATGTA
1232298 AGAAGCTCC
1 AGAAGCTCC
1232307 AGAAGCTCC
1 AGAAGCTCC
1232316 AGAAGCTC
1 AGAAGCTC
1232324 TAGGTGGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.31, G:0.23, T:0.12
Consensus pattern (9 bp):
AGAAGCTCC
Found at i:1233377 original size:24 final size:24
Alignment explanation
Indices: 1233326--1233378 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1233316 TTTCATACGT
* * *
1233326 AATTGGAGTTTAAATTTAAATTTC
1 AATTTGAGTTTAAATTTAAATATA
* *
1233350 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTAAATTTAAATATA
1233374 AATTT
1 AATTT
1233379 CGGCTTCACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTAAATTTAAATATA
Found at i:1234921 original size:22 final size:21
Alignment explanation
Indices: 1234895--1234938 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1234885 AAAATAGGTA
1234895 TACATAATGTATTGACACTTTT
1 TACAT-ATGTATTGACACTTTT
* * *
1234917 TACATTTGTGTTGATACTTTT
1 TACATATGTATTGACACTTTT
1234938 T
1 T
1234939 GTCCGAGCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.52
Consensus pattern (21 bp):
TACATATGTATTGACACTTTT
Found at i:1235138 original size:203 final size:203
Alignment explanation
Indices: 1234776--1236143 Score: 1178
Period size: 203 Copynumber: 6.7 Consensus size: 203
1234766 TTAACAAACA
* ** *
1234776 TGTCGATGCATTTATTAAAAGTATTAATCCCAAAAACATAGAAACCGATAATTATAATGTAATAG
1 TGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
*
1234841 GTAAATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGTATACATAATGTA
66 GTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAAAATAGGTATACATAATGTA
* * * *
1234906 TTGACACTTTTTACATTTGTGTTGATACTTTTTGTCCGAGCCTTTGTTTGCTCAACGAGATACAC
131 TCGACACTTTTTACATTTGTGTCGATACTTTTTGTCCGAGCCTTTGTTTGCTCAACGAGGTGCAC
*
1234971 ACATAAAG
196 GCATAAAG
* ** *
1234979 TGTCAATACATTTATTAAAAGTATCGATCCCAAAAACATAAAAACTGATAATTATAATGTAATAG
1 TGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
* * *
1235044 GTAAATTTACAAGGTAACCGGTATAAATATACCGATTTTATAAGAAAATAGGTATACATAAAGTA
66 GTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAAAATAGGTATACATAATGTA
* ** *
1235109 TCGACACTATTTACATTTGTGTCGATACTTTTTGTTGGAGCCTTTGTTTGCTCAACAAGGTGCAC
131 TCGACACTTTTTACATTTGTGTCGATACTTTTTGTCCGAGCCTTTGTTTGCTCAACGAGGTGCAC
*
1235174 ACATAAAG
196 GCATAAAG
* * * *
1235182 TGTTGATACATTTATT-AAAGTATCGA-CCCCAAAACATCGAAATCGATAATTATAATGCAATAG
1 TGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
* ** * * * * * *
1235245 GTAAAGTTACAATGTAATTGGTA-AAGT-TA-CAATGTAATCG-GTATAA-A--TATAC-TGATT
66 GTAAATTTACAATGTAACCGGTATAAATATACCGATTTTAT-GAG-AAAATAGGTATACAT-AAT
* * * * * * * * * * **
1235302 TTATAAGAAAATAGGTATACATAATGTATCGACACTTTTTACATTTGTGTCGATAC-TT-TTTG-
128 GTAT-CGACACT--TTTTACAT-TTGTGTCGATAC---TT---TTTGT-CCGAGCCTTTGTTTGC
*** ***
1235364 TCGGAAC-CTTTGTTTGC-TCAACGAGG
182 TC--AACGAGGTGCACGCAT-AA--A-G
* * * * * ** *
1235390 TGCACGCATAAAGTGTCGA-TACATTTATTAAAAGTATCGATCTCCAAAACATCGAAACCGATAA
1 TG-TCG-ATACA-T-T-TATTA-A--AAGT-ATCG-ATC---C-CAAAAACATCGAAACCGATAA
* * *
1235454 TTATAATGTAATAGGTAAATTTACAATGTAACCGGTACAAATATACCAATTTTATGAGAAAATAA
52 TTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAAAATAG
* * * *
1235519 GTATACATAATGTATCGACACTTTTTACATCTATGTCAATACTTTTTGTCCAAGCCTTTGTTTGC
117 GTATACATAATGTATCGACACTTTTTACATTTGTGTCGATACTTTTTGTCCGAGCCTTTGTTTGC
*
1235584 TCAACGAGGTGCACGCATAAAA
182 TCAACGAGGTGCACGCATAAAG
* *
1235606 TATCGATACATTTATTAAAAGTATCGATCCCATAAACATCGAAACCGATAATTATAATGTAATAG
1 TGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
* * * *
1235671 GTAAATTTATAATGTAAACGGTATAAATATACCGGTTTTATGAGAAAATAGATATACATAATGTA
66 GTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAAAATAGGTATACATAATGTA
* ** ** * *
1235736 TCGACACTTTTTACATTTGTGTCGATA-TTTTT-TCTCTAG--AATGAATGTTCAACGAGGTTCA
131 TCGACACTTTTTACATTTGTGTCGATACTTTTTGTC-CGAGCCTTTGTTTGCTCAACGAGGTGCA
1235797 CGCATAAAG
195 CGCATAAAG
* * *
1235806 TGTCGATACATTTA--AAATTGTATCGATCCTAAAAACATCGAAACCCATAATTATAATGTAATA
1 TGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * *
1235869 GGTAATTTTGCAATGTAACCGGTATAAATATACCTG-TTTAATTAGAAAACAGGTCA-ACATAAT
65 GGTAAATTTACAATGTAACCGGTATAAATATACC-GATTTTATGAGAAAATAGGT-ATACATAAT
* * * ** ** *
1235932 GTATCGACACTTTTTAAATATGTGTCGATATTTTTTGTCC-AG--AATGAATG-ACAACGAGGTG
128 GTATCGACACTTTTTACATTTGTGTCGATACTTTTTGTCCGAGCCTTTGTTTGCTCAACGAGGTG
*
1235993 CACGTATAAAG
193 CACGCATAAAG
** * *
1236004 TGTCGATACATTTA--AATTTGTATCGATCCCAAAAACATCGAAACCCATAATTATAATATAATA
1 TGTCGATACATTTATTAA-AAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * * *
1236067 CGTAAATTTATAATATAACCGGTATAAATATACC-AGTTTTATGAGAGAATATGTCTACATAATG
65 GGTAAATTTACAATGTAACCGGTATAAATATACCGA-TTTTATGAGAAAATAGGTATACATAATG
1236131 TATCGACACTTTT
129 TATCGACACTTTT
1236144 AAAATTTATG
Statistics
Matches: 948, Mismatches: 157, Indels: 125
0.77 0.13 0.10
Matches are distributed among these distances:
195 1 0.00
196 9 0.01
197 4 0.00
198 152 0.16
199 141 0.15
200 57 0.06
201 54 0.06
202 18 0.02
203 316 0.33
204 4 0.00
205 9 0.01
206 10 0.01
207 8 0.01
208 5 0.01
209 3 0.00
210 4 0.00
211 3 0.00
212 5 0.01
213 2 0.00
214 5 0.01
215 2 0.00
216 3 0.00
217 6 0.01
218 11 0.01
219 11 0.01
220 3 0.00
221 2 0.00
222 1 0.00
223 53 0.06
224 10 0.01
225 12 0.01
226 9 0.01
227 4 0.00
228 10 0.01
229 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (203 bp):
TGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAAAATAGGTATACATAATGTA
TCGACACTTTTTACATTTGTGTCGATACTTTTTGTCCGAGCCTTTGTTTGCTCAACGAGGTGCAC
GCATAAAG
Found at i:1235267 original size:20 final size:20
Alignment explanation
Indices: 1235244--1235287 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1235234 TAATGCAATA
*
1235244 GGTAAAGTTACAATGTAATT
1 GGTAAAGTTACAATGTAATC
1235264 GGTAAAGTTACAATGTAATC
1 GGTAAAGTTACAATGTAATC
1235284 GGTA
1 GGTA
1235288 TAAATATACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (20 bp):
GGTAAAGTTACAATGTAATC
Found at i:1235345 original size:22 final size:21
Alignment explanation
Indices: 1235319--1235362 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1235309 AAAATAGGTA
1235319 TACATAATGTATCGACACTTTT
1 TACAT-ATGTATCGACACTTTT
* * *
1235341 TACATTTGTGTCGATACTTTT
1 TACATATGTATCGACACTTTT
1235362 T
1 T
1235363 GTCGGAACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (21 bp):
TACATATGTATCGACACTTTT
Found at i:1235417 original size:221 final size:223
Alignment explanation
Indices: 1235034--1235484 Score: 744
Period size: 221 Copynumber: 2.0 Consensus size: 223
1235024 TGATAATTAT
*
1235034 AATGTAATAGGTAAATTTACAAGGTAACCGGTATAAATATACCGATTTTATAAGAAAATAGGTAT
1 AATGTAATAGGTAAAGTTACAAGGTAACCGGTATAAATATACCGATTTTATAAGAAAATAGGTAT
* *
1235099 ACATAAAGTATCGACACTATTTACATTTGTGTCGATACTTTTTGTTGGAGCCTTTGTTTGCTCAA
66 ACATAAAGTATCGACACTATTTACATTTGTGTCGATACTTTTTGTCGGAACCTTTGTTTGCTCAA
* *
1235164 CAAGGTGCACACATAAAGTGTTGATACATTTATT-AAAGTATCGA-CCCCAAAACATCGAAATCG
131 CAAGGTGCACACATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCCAAAACATCGAAACCG
1235227 ATAATTATAATGCAATAGGTAAAGTTAC
196 ATAATTATAATGCAATAGGTAAAGTTAC
* * * *
1235255 AATGTAATTGGTAAAGTTACAATGTAATCGGTATAAATATACTGATTTTATAAGAAAATAGGTAT
1 AATGTAATAGGTAAAGTTACAAGGTAACCGGTATAAATATACCGATTTTATAAGAAAATAGGTAT
* *
1235320 ACATAATGTATCGACACTTTTTACATTTGTGTCGATACTTTTTGTCGGAACCTTTGTTTGCTCAA
66 ACATAAAGTATCGACACTATTTACATTTGTGTCGATACTTTTTGTCGGAACCTTTGTTTGCTCAA
* * *
1235385 CGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCTCCAAAACATCGAAACCG
131 CAAGGTGCACACATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCCAAAACATCGAAACCG
* *
1235450 ATAATTATAATGTAATAGGTAAATTTAC
196 ATAATTATAATGCAATAGGTAAAGTTAC
1235478 AATGTAA
1 AATGTAA
1235485 CCGGTACAAA
Statistics
Matches: 212, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
221 152 0.72
222 10 0.05
223 50 0.24
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (223 bp):
AATGTAATAGGTAAAGTTACAAGGTAACCGGTATAAATATACCGATTTTATAAGAAAATAGGTAT
ACATAAAGTATCGACACTATTTACATTTGTGTCGATACTTTTTGTCGGAACCTTTGTTTGCTCAA
CAAGGTGCACACATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCCAAAACATCGAAACCG
ATAATTATAATGCAATAGGTAAAGTTAC
Found at i:1235619 original size:424 final size:416
Alignment explanation
Indices: 1234830--1235972 Score: 1462
Period size: 424 Copynumber: 2.8 Consensus size: 416
1234820 CCGATAATTA
* * *
1234830 TAATGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGTA
1 TAATGTAATTGGTAAA-TTACAATGTAAACGGTATAAATATACCGATTTTATGAGAAAATAGGTA
* * * *
1234895 TACATAATGTATTGACACTTTTTACATTTGTGTTGATACTTTTTGTCCGAGCCTTTGTTTGCTCA
65 TACATAATGTATCGACACTTTTTACATTTGTGTCGATACTTTTTGTCAGAACCTTTGTTTGCTCA
* * * ** *
1234960 ACGAGATACACACATAAAGTGTCAATACATTTATTAAAAGTATCGATCCCAAAAACATAAAAACT
130 ACGAGGTACACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCC-AAAACATCGAAACC
* *
1235025 GATAATTATAATGTAATAGGTAAATTTACAAGGTAACCGGTATAAATATACCGATTTTATAAGAA
194 GATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCAATTTTATAAGAA
* * * ***
1235090 AATAGGTATACATAAAGTATCGACACTATTTACATTTGTGTCGATACTTTTTGTTGGAGCCTTTG
259 AATAGGTATACATAATGTATCGACACTTTTTACATATGTGTCGATACTTTTTGTCCAAGCCTTTG
* * *
1235155 TTTGCTCAACAAGGTGCACACATAAAGTGTTGATACATTTATT-AAAGTATCGACCCCA-AAACA
324 TTTGCTCAACAAGGTGCACACATAAAATATCGATACATTTATTAAAAGTATCGACCCCATAAACA
*
1235218 TCGAAATCGATAATTATAATGCAATAGGTAAAG
389 TCGAAACCGATAATTATAATGCAATA-G----G
* * *
1235251 TTACAATGTAATTGGTAAAGTTACAATGTAATCGGTATAAATATACTGATTTTATAAGAAAATAG
1 -T--AATGTAATTGGTAAA-TTACAATGTAAACGGTATAAATATACCGATTTTATGAGAAAATAG
*
1235316 GTATACATAATGTATCGACACTTTTTACATTTGTGTCGATACTTTTTGTCGGAACCTTTGTTTGC
62 GTATACATAATGTATCGACACTTTTTACATTTGTGTCGATACTTTTTGTCAGAACCTTTGTTTGC
*
1235381 TCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCTCCAAAACATCGAA
127 TCAACGAGGTACACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATC-CCAAAACATCGAA
* *
1235446 ACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTACAAATATACCAATTTTATGA
191 ACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCAATTTTATAA
* * * *
1235511 GAAAATAAGTATACATAATGTATCGACACTTTTTACATCTATGTCAATACTTTTTGTCCAAGCCT
256 GAAAATAGGTATACATAATGTATCGACACTTTTTACATATGTGTCGATACTTTTTGTCCAAGCCT
* * *
1235576 TTGTTTGCTCAACGAGGTGCACGCATAAAATATCGATACATTTATTAAAAGTATCGATCCCATAA
321 TTGTTTGCTCAACAAGGTGCACACATAAAATATCGATACATTTATTAAAAGTATCGACCCCATAA
*
1235641 ACATCGAAACCGATAATTATAATGTAATAGG
386 ACATCGAAACCGATAATTATAATGCAATAGG
* *
1235672 T-A---AATT--T--A-T--AATGTAAACGGTATAAATATACCGGTTTTATGAGAAAATAGATAT
1 TAATGTAATTGGTAAATTACAATGTAAACGGTATAAATATACCGATTTTATGAGAAAATAGGTAT
* * ** *
1235726 ACATAATGTATCGACACTTTTTACATTTGTGTCGATATTTTTTCTCTAGAA----TGAATGTTCA
66 ACATAATGTATCGACACTTTTTACATTTGTGTCGATACTTTTTGTC-AGAACCTTTGTTTGCTCA
* * *
1235787 ACGAGGTTCACGCATAAAGTGTCGATACATTTA--AAATTGTATCGATCCTAAAAACATCGAAAC
130 ACGAGGTACACGCATAAAGTGTCGATACATTTATTAAA-AGTATCGATCC-CAAAACATCGAAAC
* * * ** * *
1235850 CCATAATTATAATGTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCTGTTTAATTAGA
193 CGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCAATTTTATAAGA
* * *
1235915 AAACAGGTCA-ACATAATGTATCGACACTTTTTAAATATGTGTCGATATTTTTTGTCCA
258 AAATAGGT-ATACATAATGTATCGACACTTTTTACATATGTGTCGATACTTTTTGTCCA
1235973 GAATGAATGA
Statistics
Matches: 645, Mismatches: 67, Indels: 38
0.86 0.09 0.05
Matches are distributed among these distances:
401 4 0.01
402 128 0.20
403 40 0.06
406 84 0.13
407 3 0.00
408 1 0.00
410 1 0.00
412 1 0.00
414 4 0.01
417 1 0.00
420 1 0.00
421 1 0.00
422 1 0.00
424 329 0.51
425 17 0.03
426 29 0.04
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (416 bp):
TAATGTAATTGGTAAATTACAATGTAAACGGTATAAATATACCGATTTTATGAGAAAATAGGTAT
ACATAATGTATCGACACTTTTTACATTTGTGTCGATACTTTTTGTCAGAACCTTTGTTTGCTCAA
CGAGGTACACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAACATCGAAACCGA
TAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCAATTTTATAAGAAAA
TAGGTATACATAATGTATCGACACTTTTTACATATGTGTCGATACTTTTTGTCCAAGCCTTTGTT
TGCTCAACAAGGTGCACACATAAAATATCGATACATTTATTAAAAGTATCGACCCCATAAACATC
GAAACCGATAATTATAATGCAATAGG
Found at i:1239507 original size:245 final size:245
Alignment explanation
Indices: 1239077--1239534 Score: 844
Period size: 245 Copynumber: 1.9 Consensus size: 245
1239067 ATAGGCATAA
1239077 TTGGTCGACCATACAAATTATCTTTGTATGTTGTGTCAAACGCAATTACATCACCGAAGCATGTG
1 TTGGTCGACCATACAAATTATCTTTGTATGTTGTGTCAAACGCAATTACATCACCGAAGCATGTG
1239142 TAATCTGATCTCGATGTAGAATCCGACAAAATAAGATTATGCAATGCCACTGATTCATCTACCGA
66 TAATCTGATCTCGATGTAGAATCCGACAAAATAAGATTATGCAATGCCACTGATTCATCTACCGA
*
1239207 GTATGTCATAAAAAACTCGGGATCATCATGTTTCTTATAATCAAAGTAAGCAATAAGCACATTCA
131 GTATGTCATAAAAAACCCGGGATCATCATGTTTCTTATAATCAAAGTAAGCAATAAGCACATTCA
1239272 CATCCCCATCGACGATTTCCTTTGTTTTACCTCTTTGAAGTGCATTGTAG
196 CATCCCCATCGACGATTTCCTTTGTTTTACCTCTTTGAAGTGCATTGTAG
*
1239322 TTGGTCGACCATACAAATTATCTTTGTATGTTGTGTCGAACGCAATTACATCACCGAAGCATGTG
1 TTGGTCGACCATACAAATTATCTTTGTATGTTGTGTCAAACGCAATTACATCACCGAAGCATGTG
* * **
1239387 TAATCTGATCTCGATGTAGAATCCGACAAAATAAGATTATGCAATGCCCCTGATTCGTCTTTCGA
66 TAATCTGATCTCGATGTAGAATCCGACAAAATAAGATTATGCAATGCCACTGATTCATCTACCGA
* *
1239452 GTATGTCATAAAAAACCCGGGCTCATCATGTTTCTTATAATCAAAGTAAGCAATAAGCGCATTCA
131 GTATGTCATAAAAAACCCGGGATCATCATGTTTCTTATAATCAAAGTAAGCAATAAGCACATTCA
1239517 CATCCCCATCGACGATTT
196 CATCCCCATCGACGATTT
1239535 TGTTTGCTGC
Statistics
Matches: 205, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
245 205 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (245 bp):
TTGGTCGACCATACAAATTATCTTTGTATGTTGTGTCAAACGCAATTACATCACCGAAGCATGTG
TAATCTGATCTCGATGTAGAATCCGACAAAATAAGATTATGCAATGCCACTGATTCATCTACCGA
GTATGTCATAAAAAACCCGGGATCATCATGTTTCTTATAATCAAAGTAAGCAATAAGCACATTCA
CATCCCCATCGACGATTTCCTTTGTTTTACCTCTTTGAAGTGCATTGTAG
Found at i:1240608 original size:201 final size:197
Alignment explanation
Indices: 1240241--1240952 Score: 927
Period size: 198 Copynumber: 3.6 Consensus size: 197
1240231 ACCTAAATAT
* * *
1240241 GTGTCGATACATTT-TCTAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATGT-AT
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTACAATGTAAT
* * * * * * * *
1240304 AGG-GAATTCACAATGTAACCGATATAAATATACCAGTTAATTAAAAAACAGGTCAACATAATGT
65 AGGTAAATTTACAATGT-ACCGATAGAAATATACCGGTTTATGAGAAAATAGGTCAACATAATGT
* ** *
1240368 ATCGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGAATGAATGCTCAAACGAGGTGCATG
129 ATCGACACTTTTTAAATTTGTGTCGATACTT-TTGTCCAGAATGAATGC-CAAACGAGGTGCACG
1240433 CATAAA
192 CATAAA
*
1240439 GTGTCGATACATTTATTAAAAGTATTGATCCCAAAAACATCGAAACCGATAATTACAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTACAATGTAATA
*
1240504 GGTAAATTTACAATGTACTCGATAGAAATATATCGGTTTTATGAGAAAATAGGTCAACATAATGT
66 GGTAAATTTACAATGTAC-CGATAGAAATATACCGG-TTTATGAGAAAATAGGTCAACATAATGT
* *
1240569 ATCGACACTTTTTAAATTTGTGTCGATACATTTTGTCCAGAATGAATGCCAAACGGGGAGCACGC
129 ATCGACACTTTTTAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCAAACGAGGTGCACGC
1240634 ATAAA
193 ATAAA
1240639 GTGTCGATACATTTATTAAAA--ATCGATCCCAAAAACATCGAAACCGATAATTACAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTACAATGTAATA
* * * *
1240702 GATAAATTTACAATGTACCTTATTGAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGT
66 GGTAAATTTACAATGTACC-GATAGAAATATACCGG-TTTATGAGAAAATAGGTCAACATAATGT
* * * *
1240767 ATCGACACTTTTTAAGTTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAACGAGATGCACGCA
129 ATCGACACTTTTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCA
1240832 TAAA
194 TAAA
* * * * *
1240836 TTGTCGATACATTTA--AAATTGTATCGATCCCAAAAATATC-AAACCGATAATTATAATATAAT
1 GTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTACAATGTAAT
* * * * *
1240898 AGGTAAATTTACAATGTTACTGGTATAAATATACAGGTTTAGTTAGAAAATAGGT
65 AGGTAAATTTACAATG-TACCGATAGAAATATACCGGTTTA-TGAGAAAATAGGT
1240953 TAATATAAGT
Statistics
Matches: 458, Mismatches: 44, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
195 3 0.01
196 4 0.01
197 108 0.24
198 202 0.44
199 8 0.02
200 64 0.14
201 67 0.15
202 2 0.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (197 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTACAATGTAATA
GGTAAATTTACAATGTACCGATAGAAATATACCGGTTTATGAGAAAATAGGTCAACATAATGTAT
CGACACTTTTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCATA
AA
Found at i:1241002 original size:23 final size:23
Alignment explanation
Indices: 1240946--1241002 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1240936 TTAGTTAGAA
* *
1240946 AATAGGTTAATATAAGTGCTACCT
1 AATACGTT-ATATAAGCGCTACCT
* *
1240970 ATTACATTATATAAGCGCTACCT
1 AATACGTTATATAAGCGCTACCT
*
1240993 AATATGTTAT
1 AATACGTTAT
1241003 TGTACTTGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (23 bp):
AATACGTTATATAAGCGCTACCT
Found at i:1254879 original size:41 final size:41
Alignment explanation
Indices: 1254815--1255234 Score: 304
Period size: 41 Copynumber: 10.3 Consensus size: 41
1254805 TAGCGGCATT
* * *
1254815 TTTAGTGGCGTTTTTGA-ACAAACGCCGGTAAATACTCGTAC
1 TTTAGTGGCATTTTT-ATATAAACGCCGCTAAATACTCGTAC
* *
1254856 TTTAGTGGCGTTTTTATTTAAACGCCTG-TAAATTA-TC-TAC
1 TTTAGTGGCATTTTTATATAAACGCC-GCTAAA-TACTCGTAC
* * * * *
1254896 TTTAGTGGCATTTTTTTACAAATGCCGCTAAAGACTCGTAT
1 TTTAGTGGCATTTTTATATAAACGCCGCTAAATACTCGTAC
* * **
1254937 TTTAGTGGCATTTTGATATAAGCGCCGCTAAATA-TTATAC
1 TTTAGTGGCATTTTTATATAAACGCCGCTAAATACTCGTAC
* * * * *
1254977 TTTATTGGCATTTTTCGA-ACAAACACCGGTAAATACTCGTCC
1 TTTAGTGGCATTTTT--ATATAAACGCCGCTAAATACTCGTAC
* * * * *
1255019 TTTAGAGGCA-TTTTATATAAACACTGCTAAATA-TTGCAC
1 TTTAGTGGCATTTTTATATAAACGCCGCTAAATACTCGTAC
* * * *
1255058 TTTAGTGG--TTTTGTTTACAAACACCGCTAAATACTCGTAT
1 TTTAGTGGCATTTT-TATATAAACGCCGCTAAATACTCGTAC
* * * * * *
1255098 TTTAATAGCGTTTTTATATAAATGTCGCTAAATA-TTGTAC
1 TTTAGTGGCATTTTTATATAAACGCCGCTAAATACTCGTAC
* * ** *
1255138 TTTAGTGGCATTTTTTTCAAAAATACCGGTAAATACTCGTAC
1 TTTAGTGGCATTTTTAT-ATAAACGCCGCTAAATACTCGTAC
* * * * *
1255180 TTTAGTGGCGTTTTTATATAAACGCTGCTAAAGACTTGAAC
1 TTTAGTGGCATTTTTATATAAACGCCGCTAAATACTCGTAC
1255221 TTTAGTGGCATTTT
1 TTTAGTGGCATTTT
1255235 AAGCACAAAC
Statistics
Matches: 291, Mismatches: 71, Indels: 34
0.73 0.18 0.09
Matches are distributed among these distances:
38 3 0.01
39 30 0.10
40 87 0.30
41 132 0.45
42 39 0.13
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (41 bp):
TTTAGTGGCATTTTTATATAAACGCCGCTAAATACTCGTAC
Found at i:1254969 original size:81 final size:80
Alignment explanation
Indices: 1254815--1255234 Score: 416
Period size: 81 Copynumber: 5.2 Consensus size: 80
1254805 TAGCGGCATT
* ** * *
1254815 TTTAGTGGCGTTTTTGAACAAACGCCGGTAAATACTCGTACTTTAGTGGCGTTTTTATTTAAACG
1 TTTAGTGGCATTTTTTTACAAACACCGGTAAATACTCGTACTTTAGTGGCGTTTTTATATAAACG
*
1254880 CCTG-TAAATTATCTAC
66 CC-GCTAAA-TATTTAC
** * * * * * *
1254896 TTTAGTGGCATTTTTTTACAAATGCCGCTAAAGACTCGTATTTTAGTGGCATTTTGATATAAGCG
1 TTTAGTGGCATTTTTTTACAAACACCGGTAAATACTCGTACTTTAGTGGCGTTTTTATATAAACG
1254961 CCGCTAAATATTATAC
66 CCGCTAAATATT-TAC
* ** * * *
1254977 TTTATTGGCATTTTTCGAACAAACACCGGTAAATACTCGTCCTTTAGAGGC-ATTTTATATAAAC
1 TTTAGTGGCATTTTT-TTACAAACACCGGTAAATACTCGTACTTTAGTGGCGTTTTTATATAAAC
* * *
1255041 ACTGCTAAATATTGCAC
65 GCCGCTAAATATT-TAC
* * * * *
1255058 TTTAGTGG--TTTTGTTTACAAACACCGCTAAATACTCGTATTTTAATAGCGTTTTTATATAAAT
1 TTTAGTGGCATTTT-TTTACAAACACCGGTAAATACTCGTACTTTAGTGGCGTTTTTATATAAAC
*
1255121 GTCGCTAAATATTGTAC
65 GCCGCTAAATATT-TAC
* *
1255138 TTTAGTGGCATTTTTTTCAAAAATACCGGTAAATACTCGTACTTTAGTGGCGTTTTTATATAAAC
1 TTTAGTGGCATTTTTTT-ACAAACACCGGTAAATACTCGTACTTTAGTGGCGTTTTTATATAAAC
* * *
1255203 GCTGCTAAAGACTTGAAC
65 GCCGCTAAATA-TT-TAC
1255221 TTTAGTGGCATTTT
1 TTTAGTGGCATTTT
1255235 AAGCACAAAC
Statistics
Matches: 275, Mismatches: 55, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
79 31 0.11
80 37 0.13
81 110 0.40
82 78 0.28
83 19 0.07
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (80 bp):
TTTAGTGGCATTTTTTTACAAACACCGGTAAATACTCGTACTTTAGTGGCGTTTTTATATAAACG
CCGCTAAATATTTAC
Found at i:1255097 original size:161 final size:162
Alignment explanation
Indices: 1254815--1255234 Score: 496
Period size: 161 Copynumber: 2.6 Consensus size: 162
1254805 TAGCGGCATT
* * *
1254815 TTTAGTGGCGTTTTT-GAACAAACGCCGGTAAATACTCGTACTTTAGTGGCGTTTTTATTTAAAC
1 TTTAGTGGCATTTTTCGAACAAACACCGGTAAATACTCGTACTTTAGTGGCGTTTTTATATAAAC
* **
1254879 GCCTG-TAAAT-TAT-CTACTTTAGTGGCATTTTTTTACAAATGCCGCTAAAGACTCGTATTTTA
66 -ACTGCTAAATAT-TGC-ACTTTAGTGG-ATTTTTTTACAAACACCGCTAAAGACTCGTATTTTA
* * *
1254941 GTGGCATTTTGATATAAGCGCCGCTAAATATTATAC
127 ATAGCATTTTGATATAAACGCCGCTAAATATTATAC
* * * *
1254977 TTTATTGGCATTTTTCGAACAAACACCGGTAAATACTCGTCCTTTAGAGGC-ATTTTATATAAAC
1 TTTAGTGGCATTTTTCGAACAAACACCGGTAAATACTCGTACTTTAGTGGCGTTTTTATATAAAC
*
1255041 ACTGCTAAATATTGCACTTTAGTGG-TTTTGTTTACAAACACCGCTAAATACTCGTATTTTAATA
66 ACTGCTAAATATTGCACTTTAGTGGATTTT-TTTACAAACACCGCTAAAGACTCGTATTTTAATA
* * * * *
1255105 GCGTTTTTATATAAATGTCGCTAAATATTGTAC
130 GCATTTTGATATAAACGCCGCTAAATATTATAC
*
1255138 TTTAGTGGCATTTTTTTC-AA-AAATACCGGTAAATACTCGTACTTTAGTGGCGTTTTTATATAA
1 TTTAGTGGCA--TTTTTCGAACAAACACCGGTAAATACTCGTACTTTAGTGGCGTTTTTATATAA
* * *
1255201 ACGCTGCTAAAGACTTGAACTTTAGTGGCATTTT
64 ACACTGCTAAATA-TTGCACTTTAGTGG-ATTTT
1255235 AAGCACAAAC
Statistics
Matches: 220, Mismatches: 27, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
160 4 0.02
161 96 0.44
162 63 0.29
163 53 0.24
165 4 0.02
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (162 bp):
TTTAGTGGCATTTTTCGAACAAACACCGGTAAATACTCGTACTTTAGTGGCGTTTTTATATAAAC
ACTGCTAAATATTGCACTTTAGTGGATTTTTTTACAAACACCGCTAAAGACTCGTATTTTAATAG
CATTTTGATATAAACGCCGCTAAATATTATAC
Found at i:1257112 original size:52 final size:50
Alignment explanation
Indices: 1257017--1257133 Score: 114
Period size: 51 Copynumber: 2.3 Consensus size: 50
1257007 AATAAATATG
* * * *
1257017 AAAAATAAAAATATTAATATAATAATAGTAATAAAATAAATGAAAAAAGGAA
1 AAAAATAAAAATATAAATATAATAAAAATAATAAAAGAAATG-AAAAA-GAA
* *
1257069 AAAAATAAAAATA-AAAT-TAAGTAAAAATAATAAAAGATGATGAAATAGAA
1 AAAAATAAAAATATAAATATAA-TAAAAATAATAAAAGA-AATGAAAAAGAA
*
1257119 TAAAATAAAAA-ATAA
1 AAAAATAAAAATATAA
1257134 GGTTAAGTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
49 1 0.02
50 18 0.33
51 20 0.36
52 16 0.29
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (50 bp):
AAAAATAAAAATATAAATATAATAAAAATAATAAAAGAAATGAAAAAGAA
Found at i:1258749 original size:39 final size:38
Alignment explanation
Indices: 1258513--1258974 Score: 409
Period size: 39 Copynumber: 12.1 Consensus size: 38
1258503 AGTATTATAT
*
1258513 AAAAATATTTTCAAAAACTATATA--ATATAT-ATTTTC
1 AAAAATGTTTT-AAAAACTATATATTATATATAATTTTC
*** *
1258549 AATTTTTTTTTAAAAAACTATATA--ATATAT-ATTTTC
1 AAAAATGTTTT-AAAAACTATATATTATATATAATTTTC
1258585 AAAAACTGTTTTTAAAAACTATATA--ATATAT-ATTTTC
1 AAAAA-TG-TTTTAAAAACTATATATTATATATAATTTTC
*
1258622 -AAAATGTTTT-AAAACTATATATTATATATAAGTTTTT
1 AAAAATGTTTTAAAAACTATATATTATATATAA-TTTTC
* **
1258659 AAAAATATTTTTAAAAACTATATAATATATATATTTTTTTC
1 AAAAAT-GTTTTAAAAACTATAT-AT-TATATATAATTTTC
1258700 AAAAATGTTTTAAAAACTATATATTATATATAAGTTTTC
1 AAAAATGTTTTAAAAACTATATATTATATATAA-TTTTC
*
1258739 AAAAATGTTTTAAAAACTATATATTGTATATATATTTTC
1 AAAAATGTTTTAAAAACTATATATTATATATA-ATTTTC
** * *
1258778 AAAAAAATTTAAAAAACTATATA--ATATATATTTTTGC
1 AAAAATGTTTTAAAAACTATATATTATATATAATTTT-C
* * * *
1258815 --AATTTTTTTAAAAACTATATATTATGTATAAGTTTTT
1 AAAAATGTTTTAAAAACTATATATTATATATAA-TTTTC
*
1258852 AAAAATATTTTAAAAACTATATATTATATAT-ATTTTC
1 AAAAATGTTTTAAAAACTATATATTATATATAATTTTC
*
1258889 -AAAATGTTTTAAAAATTATAATATATATATATATATATATTC
1 AAAAATGTTTTAAAAACTAT-ATAT-TATATATA-AT-T-TTC
* * * * * *
1258931 AAAAATAATTTTCAAAGCTATATAATATATATATTTTTT
1 AAAAAT-GTTTTAAAAACTATATATTATATATAATTTTC
1258970 AAAAA
1 AAAAA
1258975 CCGATTTTTT
Statistics
Matches: 356, Mismatches: 43, Indels: 51
0.79 0.10 0.11
Matches are distributed among these distances:
33 11 0.03
34 4 0.01
35 25 0.07
36 59 0.17
37 50 0.14
38 28 0.08
39 100 0.28
40 29 0.08
41 14 0.04
42 18 0.05
43 8 0.02
44 10 0.03
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (38 bp):
AAAAATGTTTTAAAAACTATATATTATATATAATTTTC
Found at i:1258847 original size:193 final size:185
Alignment explanation
Indices: 1258513--1258967 Score: 530
Period size: 193 Copynumber: 2.4 Consensus size: 185
1258503 AGTATTATAT
* *** *
1258513 AAAAATATTTTCAAAAACTATATA--ATATAT-ATTTTCAATTTTTTTTTAAAAAACTATATA--
1 AAAAATGTTTT-AAAAACTATATATTATATATAATTTTCAAAAATATTTT-AAAAACTATATATT
** *
1258573 ATATATATTTTCAAAAACTGTTTTTAAAAACTATATAATATATATTTTCAAAATGTTTTAAAACT
64 ATATATATTTTCAAAAAC-AATTTAAAAAACTATATAATATATATTTTCAAAATGTTTTAAAACT
*
1258638 ATATATTATATATAAGTTTTTAAAAATATTTTTAAAAACTATATAATATATATATTTTTTTC
128 ATATATTATATATAAGTTTTTAAAAATA-TTTTAAAAACTATAT-AT-TATATA-TATTTTC
*
1258700 AAAAATGTTTTAAAAACTATATATTATATATAAGTTTTCAAAAATGTTTTAAAAACTATATATTG
1 AAAAATGTTTTAAAAACTATATATTATATATAA-TTTTCAAAAATATTTTAAAAACTATATA-T-
* *
1258765 TATATATATTTTCAAAAA-AATTTAAAAAACTATATAATATATATTTTTGC-AATTTTTTTAAAA
63 TATATATATTTTCAAAAACAATTTAAAAAACTATATAATATATA-TTTT-CAAAATGTTTT-AAA
*
1258828 ACTATATATTATGTATAAGTTTTTAAAAATATTTTAAAAACTATATATTATATATATTTTC
125 ACTATATATTATATATAAGTTTTTAAAAATATTTTAAAAACTATATATTATATATATTTTC
* * *
1258889 -AAAATGTTTTAAAAATTATAATATATATATATATATATATTCAAAAATAATTTTCAAAGCTATA
1 AAAAATGTTTTAAAAACTAT-ATAT-TATATATA-AT-T-TTCAAAAAT-ATTTTAAAAACTATA
*
1258953 TAATATATATATTTT
60 TATTATATATATTTT
1258968 TTAAAAACCG
Statistics
Matches: 234, Mismatches: 17, Indels: 30
0.83 0.06 0.11
Matches are distributed among these distances:
186 12 0.05
187 10 0.04
188 24 0.10
189 23 0.10
190 27 0.12
191 38 0.16
192 35 0.15
193 65 0.28
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (185 bp):
AAAAATGTTTTAAAAACTATATATTATATATAATTTTCAAAAATATTTTAAAAACTATATATTAT
ATATATTTTCAAAAACAATTTAAAAAACTATATAATATATATTTTCAAAATGTTTTAAAACTATA
TATTATATATAAGTTTTTAAAAATATTTTAAAAACTATATATTATATATATTTTC
Found at i:1258862 original size:11 final size:11
Alignment explanation
Indices: 1258848--1258904 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
1258838 ATGTATAAGT
1258848 TTTTAAAAATA
1 TTTTAAAAATA
1258859 TTTTAAAAACTA
1 TTTTAAAAA-TA
* *
1258871 TATATTATATATA
1 T-T-TTAAAAATA
* *
1258884 TTTTCAAAATG
1 TTTTAAAAATA
1258895 TTTTAAAAAT
1 TTTTAAAAAT
1258905 TATAATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
11 23 0.64
12 4 0.11
13 4 0.11
14 5 0.14
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:1259084 original size:2 final size:2
Alignment explanation
Indices: 1259077--1259113 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1259067 CACTATATTA
*
1259077 AT AT AT AT AT AT AT AT AT AT AT AT AA AT A- AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1259114 AAAAAAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1259953 original size:85 final size:85
Alignment explanation
Indices: 1259861--1260970 Score: 1359
Period size: 85 Copynumber: 13.0 Consensus size: 85
1259851 CAAGCTAATC
* * * * * *
1259861 TGTAAATTTGTTATGCCCTTGAGTTGAATGTAATCGAACTCGAAGGTCATTGTTGGCAGATAACC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACC
* *
1259926 CTTATCGCCTTGAGCTATGA
66 CTTCTCGCCTTGAGTTATGA
* * * * * *
1259946 TGCAAATTTGATATGCCTTTGAGCTAAATGTAGTCGAACTCAAAGGTCTTTATTGACAGATAACC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACC
*
1260011 CTTCTTGCCTTGAGTTAT-A
66 CTTCTCGCCTTGAGTTATGA
* *
1260030 CTGTAAATTTGATATGCCTTTGAGCTGAGTTTAATCGAACTAGAAGGTCTTTGTTGACAGATAAC
1 -TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAAC
**
1260095 CCTTCTCGTATTGAGTTAT-A
65 CCTTCTCGCCTTGAGTTATGA
* *
1260115 CTGTAAA-TTGAATATGCCTTTGAGCTGAATGTAATTGAACTCGAAGGTCTTTGTTGACAGATAA
1 -TGTAAATTTG-ATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAA
* *
1260179 CCCTTCTCACCTTGAGTTATGC
64 CCCTTCTCGCCTTGAGTTATGA
* * * * **
1260201 TGTAAATTGGATATGCCTTTGAGATGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAGTC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACC
* * *
1260266 ATTCTCGCCTTGAGCTATGT
66 CTTCTCGCCTTGAGTTATGA
* * * *
1260286 TGTAAATTTGACATGCCTTTGAGCTGAATGTAATTGAACTCGAAGGTCTTGGTTGACAGATAACC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACC
*
1260351 CTTCTTGCCTTGAGTTATGA
66 CTTCTCGCCTTGAGTTATGA
* * * * *
1260371 TGTAAATTTTATATG--TTTAAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAAATAACT
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACC
*
1260434 CTTCTCGCCTTGAGTTATGC
66 CTTCTCGCCTTGAGTTATGA
* ** *
1260454 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATTGAACTTAAAGGTCGTTTGTTGACAGATAGC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAAC
* * * *
1260519 CATTCTCACCTTGAGCTATGC
65 CCTTCTCGCCTTGAGTTATGA
* * * *
1260540 TGTAAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAAATCGAAGGTCTTGGTTGACAGATAACC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACC
* *
1260605 CTTATCGCCTTGAGTTATGC
66 CTTCTCGCCTTGAGTTATGA
* * *
1260625 TGTAAATTTGATATGCCTTTGAGTTGAGTGTAATCGAACTCGAAGATCTTTTATTGACAGATAGA
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATA-A
* *
1260690 -CCTTCTCGCCTTGAGCTATGC
64 CCCTTCTCGCCTTGAGTTATGA
* * * * * *
1260711 TATGAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACC
*** *
1260776 CTTCTCGTAATGAGTTATGT
66 CTTCTCGCCTTGAGTTATGA
*
1260796 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGATAGATAAC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAAC
* *
1260861 CCTTCTCGCCTTGAGCTATGT
65 CCTTCTCGCCTTGAGTTATGA
* * * * * * * *
1260882 TGTAAATTCGATGTGCCTTTAAGCTGAATGTAATCGAACTCGAAGGTCTTGGTGGAAATATAACC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACC
*
1260947 CTTCTCGCCTTGAGTTATGT
66 CTTCTCGCCTTGAGTTATGA
1260967 TGTA
1 TGTA
1260971 TTTGATCCGT
Statistics
Matches: 884, Mismatches: 130, Indels: 22
0.85 0.13 0.02
Matches are distributed among these distances:
83 75 0.08
84 4 0.00
85 583 0.66
86 221 0.25
87 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (85 bp):
TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACC
CTTCTCGCCTTGAGTTATGA
Found at i:1260615 original size:171 final size:170
Alignment explanation
Indices: 1259860--1260970 Score: 1413
Period size: 171 Copynumber: 6.5 Consensus size: 170
1259850 TCAAGCTAAT
* * * * * *
1259860 CTGTAAATTTGTTATGCCCTTGAGTTGAATGTAATCGAACTCGAAGGTCATT-GTTGGCAGATAA
1 CTGTAAATTCGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGACAGATAA
* * * * * * *
1259924 CCCTTATCGCCTTGAGCTATGATGCAAATTTGATATGCCTTTGAGCTAAATGTAGTCGAACTCAA
65 CCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGA
* * * *
1259989 AGGTCTTTATTGACAGATAACCCTTCTTGCCTTGAGTTATA
130 AGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* * * *
1260030 CTGTAAATTTGATATGCCTTTGAGCTGAGTTTAATCGAACTAGAAGGTCTTTGTTGACAGATAAC
1 CTGTAAATTCGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAAC
** * *
1260095 CCTTCTCGTATTGAGTTATACTGTAAA-TTGAATATGCCTTTGAGCTGAATGTAATTGAACTCGA
66 CCTTCTCGCCTTGAGTTATGCTGTAAATTTG-ATATGCCTTTGAGCTGAATGTAATCGAACTCGA
* *
1260159 AGGTCTTTGTTGACAGATAACCCTTCTCACCTTGAGTTATG
130 AGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* * * * * **
1260200 CTGTAAATTGGATATGCCTTTGAGATGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAGT
1 CTGTAAATTCGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAAC
* * * * *
1260265 CATTCTCGCCTTGAGCTATGTTGTAAATTTGACATGCCTTTGAGCTGAATGTAATTGAACTCGAA
66 CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAA
* * *
1260330 GGTCTTGGTTGACAGATAACCCTTCTTGCCTTGAGTTATG
131 GGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* ** * *
1260370 ATGTAAATTTTATATG--TTTAAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAAATAAC
1 CTGTAAATTCGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAAC
* * * **
1260433 TCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATTGAACTTAAA
66 CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAA
* * *
1260498 GGTCGTTTGTTGACAGATAGCCATTCTCACCTTGAGCTATG
131 GGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* *
1260539 CTGTAAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAAATCGAAGGTCTTGGTTGACAGATAAC
1 CTGTAAATTCGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAAC
* * *
1260604 CCTTATCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGTTGAGTGTAATCGAACTCGAA
66 CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAA
* *
1260669 GATCTTTTATTGACAGATAGA-CCTTCTCGCCTTGAGCTATG
131 GGTC-TTTGTTGACAGATA-ACCCTTCTCGCCTTGAGCTATG
* * * *
1260710 CTATGAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGC
1 CTGTAAATTCGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAAC
*** * *
1260775 CCTTCTCGTAATGAGTTATGTTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAA
66 CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAA
*
1260840 GGTCTTTTGTTGATAGATAACCCTTCTCGCCTTGAGCTATG
131 GGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* * * * * * *
1260881 TTGTAAATTCGATGTGCCTTTAAGCTGAATGTAATCGAACTCGAAGGTCTTGGTGGAAATATAAC
1 CTGTAAATTCGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAAC
*
1260946 CCTTCTCGCCTTGAGTTATGTTGTA
66 CCTTCTCGCCTTGAGTTATGCTGTA
1260971 TTTGATCCGT
Statistics
Matches: 824, Mismatches: 109, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
168 100 0.12
169 47 0.06
170 303 0.37
171 374 0.45
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (170 bp):
CTGTAAATTCGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAAC
CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAA
GGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
Found at i:1266960 original size:20 final size:20
Alignment explanation
Indices: 1266935--1266983 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1266925 TGTGTGTGTT
1266935 TGTGTTTGGTATTTCCAATG
1 TGTGTTTGGTATTTCCAATG
1266955 TGTGTTTGGTATTTCCAATG
1 TGTGTTTGGTATTTCCAATG
*
1266975 TGTTTTTGG
1 TGTGTTTGG
1266984 CTTTCTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.08, G:0.27, T:0.53
Consensus pattern (20 bp):
TGTGTTTGGTATTTCCAATG
Found at i:1267517 original size:23 final size:23
Alignment explanation
Indices: 1267490--1267539 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1267480 ACAAAAATAC
1267490 AAAAATAAGTAA-AAACAT-ATAAT
1 AAAAA-AAGTAATAAA-ATAATAAT
*
1267513 AAAAAAATTAATAAAATAATAAT
1 AAAAAAAGTAATAAAATAATAAT
1267536 AAAA
1 AAAA
1267540 GTATTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAAAAAGTAATAAAATAATAAT
Found at i:1267524 original size:12 final size:12
Alignment explanation
Indices: 1267485--1267553 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
1267475 AACAAACAAA
*
1267485 AATACAAAAA-T
1 AATAAAAAAATT
*
1267496 AAGTAAAAACATAT
1 AA-TAAAAAAAT-T
1267510 AATAAAAAAATT
1 AATAAAAAAATT
*
1267522 AATAAAATAA-T
1 AATAAAAAAATT
**
1267533 AATAAAAGTATT
1 AATAAAAAAATT
1267545 ATATAAAAA
1 A-ATAAAAA
1267554 TATTTTCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
11 11 0.24
12 18 0.39
13 14 0.30
14 3 0.07
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (12 bp):
AATAAAAAAATT
Found at i:1267545 original size:23 final size:24
Alignment explanation
Indices: 1267508--1267552 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1267498 GTAAAAACAT
1267508 ATAATAAAAAAATTA-ATAAAATA
1 ATAATAAAAAAATTATATAAAATA
**
1267531 ATAATAAAAGTATTATATAAAA
1 ATAATAAAAAAATTATATAAAA
1267553 ATATTTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (24 bp):
ATAATAAAAAAATTATATAAAATA
Found at i:1267615 original size:40 final size:36
Alignment explanation
Indices: 1267587--1267967 Score: 324
Period size: 40 Copynumber: 9.9 Consensus size: 36
1267577 ATATTTTGAA
*
1267587 AAAAAATGTTTTTTAAAAACTATATAATATATATATTC
1 AAAAAATG-TTTTTAAAAACTATATAATATATAT-TTT
1267625 AAAAAATGTTTTTAAAAACTATATATTATATATAAGTTTT
1 AAAAAATGTTTTTAAAAACTATATA--ATATAT-A-TTTT
*
1267665 CAAAAATGTTTTTAAAAACTATATATTATATATAAGTTTT
1 AAAAAATGTTTTTAAAAACTATATA--ATATAT-A-TTTT
*
1267705 CAAAAATGTTTTTAAAAACTATATAATTTATATATTTTT
1 AAAAAATGTTTTTAAAAACTATATAA--TATATA-TTTT
*
1267744 AAAAAAT-ATTTTAAAAACTATATATTATATATAAGTTTT
1 AAAAAATGTTTTTAAAAACTATATA--ATATAT-A-TTTT
*
1267783 CAAAAATG-TTTTAAAAACTATATATTATATATATATTT
1 AAAAAATGTTTTTAAAAACTATATA--ATATATAT-TTT
** *
1267821 TTAAAATGTTTTAAAAAACTATATAATATTTATATTTT
1 AAAAAATGTTTTTAAAAACTATATAATA--TATATTTT
*
1267859 CAAAAATG--TTTAAAAACTATATATTTATATATAAGTTTT
1 AAAAAATGTTTTTAAAAACTATATA---ATATAT-A-TTTT
* * *
1267898 TAAAAATG-TTTTAAAGACTATATATTATATATATTT
1 AAAAAATGTTTTTAAAAACTATATAATATATAT-TTT
**
1267934 CCAAAATG-TTTTAAAAACTATAATATATATATAT
1 AAAAAATGTTTTTAAAAACTAT-ATA-ATATATAT
1267968 ATATATATAT
Statistics
Matches: 300, Mismatches: 20, Indels: 46
0.82 0.05 0.13
Matches are distributed among these distances:
35 1 0.00
36 36 0.12
37 32 0.11
38 57 0.19
39 86 0.29
40 87 0.29
41 1 0.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (36 bp):
AAAAAATGTTTTTAAAAACTATATAATATATATTTT
Found at i:1267658 original size:39 final size:38
Alignment explanation
Indices: 1267588--1267969 Score: 451
Period size: 39 Copynumber: 9.9 Consensus size: 38
1267578 TATTTTGAAA
*
1267588 AAAAATGTTTTTTAAAAACTATATA--ATATATATATTC
1 AAAAATG-TTTTTAAAAACTATATATTATATATATTTTC
1267625 AAAAAATGTTTTTAAAAACTATATATTATATATAAGTTTTC
1 -AAAAATGTTTTTAAAAACTATATATTATATAT-A-TTTTC
1267666 AAAAATGTTTTTAAAAACTATATATTATATATAAGTTTTC
1 AAAAATGTTTTTAAAAACTATATATTATATAT-A-TTTTC
*
1267706 AAAAATGTTTTTAAAAACTATATAATT-TATATATTTTTA
1 AAAAATGTTTTTAAAAACTATAT-ATTATATATA-TTTTC
*
1267745 AAAAAT-ATTTTAAAAACTATATATTATATATAAGTTTTC
1 AAAAATGTTTTTAAAAACTATATATTATATAT-A-TTTTC
*
1267784 AAAAATG-TTTTAAAAACTATATATTATATATATATTTT
1 AAAAATGTTTTTAAAAACTATATATTATATATAT-TTTC
* * * *
1267822 TAAAATGTTTTAAAAAACTATATAATATTTATATTTTC
1 AAAAATGTTTTTAAAAACTATATATTATATATATTTTC
*
1267860 AAAAATG--TTTAAAAACTATATATTTATATATAAGTTTTT
1 AAAAATGTTTTTAAAAACTATATA-TTATATAT-A-TTTTC
*
1267899 AAAAATG-TTTTAAAGACTATATATTATATATA-TTTC
1 AAAAATGTTTTTAAAAACTATATATTATATATATTTTC
*
1267935 CAAAATG-TTTTAAAAACTATAATATATATATATAT
1 AAAAATGTTTTTAAAAACTAT-ATAT-TATATATAT
1267970 ATATATATAT
Statistics
Matches: 306, Mismatches: 21, Indels: 33
0.85 0.06 0.09
Matches are distributed among these distances:
36 35 0.11
37 31 0.10
38 56 0.18
39 94 0.31
40 83 0.27
41 7 0.02
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (38 bp):
AAAAATGTTTTTAAAAACTATATATTATATATATTTTC
Found at i:1267963 original size:2 final size:2
Alignment explanation
Indices: 1267952--1267983 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1267942 TTTTAAAAAC
1267952 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1267984 TCAAAAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1268007 original size:52 final size:48
Alignment explanation
Indices: 1267916--1268025 Score: 141
Period size: 50 Copynumber: 2.2 Consensus size: 48
1267906 TTTTAAAGAC
* *
1267916 TATATAT-TATATATATTTCCAAAATGTTTTAAAAACTATAATATATATA
1 TATATATATATATATATTTCAAAAATATTTTAAAAACTAT-ATA-ATATA
* *
1267965 TATATATATATATATATATTCAAAAATCATTTTCAAAGCTATATAATATA
1 TATATATATATATATAT-TTCAAAAAT-ATTTTAAAAACTATATAATATA
1268015 TATATATATAT
1 TATATATATAT
1268026 TAAAAACTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
49 7 0.13
50 25 0.46
51 11 0.20
52 11 0.20
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (48 bp):
TATATATATATATATATTTCAAAAATATTTTAAAAACTATATAATATA
Found at i:1274903 original size:31 final size:32
Alignment explanation
Indices: 1274865--1274930 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 32
1274855 CTACATAGCG
*
1274865 TCTGTAACAAGATTCCGACTC-GTAGAAATCA
1 TCTGTAACAAGAGTCCGACTCGGTAGAAATCA
1274896 TCTGTAACAAGAGTCCGACTCGGTAGAAATCA
1 TCTGTAACAAGAGTCCGACTCGGTAGAAATCA
1274928 TCT
1 TCT
1274931 TTCGAGGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 20 0.61
32 13 0.39
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (32 bp):
TCTGTAACAAGAGTCCGACTCGGTAGAAATCA
Found at i:1275222 original size:15 final size:15
Alignment explanation
Indices: 1275202--1275235 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1275192 ATTATCAATG
1275202 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1275217 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1275232 AATT
1 AATT
1275236 AGAATTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1276497 original size:23 final size:23
Alignment explanation
Indices: 1276467--1276522 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1276457 TAATTATGCA
*
1276467 TTTATGACATGTATTCT-TCTATC
1 TTTATGACACGT-TTCTCTCTATC
* *
1276490 TTTATGACACGTTTTTCTCTGTC
1 TTTATGACACGTTTCTCTCTATC
1276513 TTTATGACAC
1 TTTATGACAC
1276523 ATCTTCGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 3 0.10
23 26 0.90
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.50
Consensus pattern (23 bp):
TTTATGACACGTTTCTCTCTATC
Found at i:1284966 original size:64 final size:65
Alignment explanation
Indices: 1284897--1285052 Score: 172
Period size: 65 Copynumber: 2.4 Consensus size: 65
1284887 AAACCCTAAT
* * * *
1284897 TCGAATGCATTTTGTGTACCGATGCA-TAACCATGCATTGATGCACTCCT-GATTTTATTAAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATACACTCCTGGATCTT-TTAAAAC
1284960 A
65 A
* ** * *
1284961 TCGAATGCATTTTATGTATAGATGCACAAACCATGCATCGATACACTCCTGGCTCTTTTCAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATACACTCCTGGATCTTTTAAAACA
* * * *
1285026 TCGAATGTAATTAGTGTGCCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
1285053 CCCAAGTGTA
Statistics
Matches: 74, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
64 23 0.31
65 47 0.64
66 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATACACTCCTGGATCTTTTAAAACA
Found at i:1298777 original size:21 final size:21
Alignment explanation
Indices: 1298747--1298869 Score: 94
Period size: 23 Copynumber: 5.7 Consensus size: 21
1298737 TTTGTGCATT
1298747 GTGCATCGATACACTATGAAA
1 GTGCATCGATACACTATGAAA
* *
1298768 GTGTATCGATGCATCCCT-TGAATA
1 GTGCATCGAT--A-CACTATGAA-A
1298792 -TGCATCGATACACTATG-AA
1 GTGCATCGATACACTATGAAA
* *
1298811 GTTGCACCGATACATGCCT-TGAAT
1 G-TGCATCGATACA---CTATGAAA
*
1298835 GTGCATCGATACACTAT-ACA
1 GTGCATCGATACACTATGAAA
1298855 GTGCATCGATACACT
1 GTGCATCGATACACT
1298870 CGTCGGGTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 25
0.70 0.08 0.22
Matches are distributed among these distances:
19 1 0.01
20 22 0.27
21 24 0.30
23 26 0.32
24 8 0.10
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (21 bp):
GTGCATCGATACACTATGAAA
Found at i:1298831 original size:44 final size:43
Alignment explanation
Indices: 1298748--1298867 Score: 161
Period size: 44 Copynumber: 2.7 Consensus size: 43
1298738 TTGTGCATTG
* *
1298748 TGCATCGATACACTATGAAAGTGTATCGATGCATCCCTTGAATA
1 TGCATCGATACACTATG-AAGTGCATCGATACATCCCTTGAATA
* * *
1298792 TGCATCGATACACTATGAAGTTGCACCGATACATGCCTTGAATG
1 TGCATCGATACACTATGAAG-TGCATCGATACATCCCTTGAATA
1298836 TGCATCGATACACTAT-ACAGTGCATCGATACA
1 TGCATCGATACACTATGA-AGTGCATCGATACA
1298868 CTCGTCGGGT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
43 15 0.22
44 53 0.78
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (43 bp):
TGCATCGATACACTATGAAGTGCATCGATACATCCCTTGAATA
Found at i:1301183 original size:12 final size:13
Alignment explanation
Indices: 1301157--1301185 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1301147 TGGAGTAGTA
1301157 ATTTCAAAAATTG
1 ATTTCAAAAATTG
1301170 ATTTCAAAAA-TG
1 ATTTCAAAAATTG
1301182 ATTT
1 ATTT
1301186 TTCAAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
ATTTCAAAAATTG
Found at i:1301609 original size:64 final size:64
Alignment explanation
Indices: 1301531--1301706 Score: 198
Period size: 65 Copynumber: 2.7 Consensus size: 64
1301521 ACACCCTAAT
* *
1301531 TCGAATGAATTTTATGTACCGATGCACAGCCATGTATCGATGCACT-CTTGATTTTATTGAAACA
1 TCGAATGAATTTTATGTACCGATGCACAGCCATGTATCGATGCACTCCTTGATCTT-TTCAAACA
* * * *
1301595 TCGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATACACTCCTTGCTCTTTTCAAACA
1 TCGAATGAATTTTATGTACCGATGCACAG-CCATGTATCGATGCACTCCTTGATCTTTTCAAACA
* *
1301660 TCGAATGTAA--TTAGTGTATCGATGCAC-CCCAAGTGTATCGATGCACT
1 TCGAATG-AATTTTA-TGTACCGATGCACAGCC-A-TGTATCGATGCACT
1301707 AGGTCTTATA
Statistics
Matches: 95, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
63 2 0.02
64 32 0.34
65 53 0.56
66 8 0.08
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (64 bp):
TCGAATGAATTTTATGTACCGATGCACAGCCATGTATCGATGCACTCCTTGATCTTTTCAAACA
Found at i:1303019 original size:76 final size:76
Alignment explanation
Indices: 1302882--1303040 Score: 293
Period size: 76 Copynumber: 2.1 Consensus size: 76
1302872 CTGAATTTTG
*
1302882 TTTAAT-ATTGAGTAAATGCTTCGGAATAGCTGTAGAGGGACACTTGTCTTTGCCGTAGCATTGC
1 TTTAATAATTGAGTAAATGCTTCGGAATAGCTGTAGAGGGACACTTATCTTTGCCGTAGCATTGC
1302946 CTGAAACTCTC
66 CTGAAACTCTC
*
1302957 TTTAATAATTGAGTAAATGCTTCGGAATAGCTGTAGAGGGACACTTATCTTTGCCGTGGCATTGC
1 TTTAATAATTGAGTAAATGCTTCGGAATAGCTGTAGAGGGACACTTATCTTTGCCGTAGCATTGC
1303022 CTGAAACTCTC
66 CTGAAACTCTC
1303033 TTTAATAA
1 TTTAATAA
1303041 ATGGTAGCCA
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
75 6 0.07
76 75 0.93
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (76 bp):
TTTAATAATTGAGTAAATGCTTCGGAATAGCTGTAGAGGGACACTTATCTTTGCCGTAGCATTGC
CTGAAACTCTC
Found at i:1304122 original size:22 final size:22
Alignment explanation
Indices: 1304096--1304152 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 22
1304086 ACCAGAAGGG
*
1304096 GTATCGATACCATAGTGTAGAA
1 GTATCGATACCATAGGGTAGAA
* *
1304118 GTATCGGTA-C-TAGGGTAGTA
1 GTATCGATACCATAGGGTAGAA
*
1304138 GTATCGATACTATAG
1 GTATCGATACCATAG
1304153 AGCCAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 16 0.57
21 1 0.04
22 11 0.39
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (22 bp):
GTATCGATACCATAGGGTAGAA
Found at i:1304960 original size:68 final size:68
Alignment explanation
Indices: 1304814--1305002 Score: 218
Period size: 68 Copynumber: 2.8 Consensus size: 68
1304804 AATTCTGATT
*
1304814 TGATAGAAATGTGTCATTTATGCCAATTAGATGAAAGGCTAAATGCCTTTGAGGCCTAACTGTGC
1 TGATAGAAAGGTGTCATTTATGCCAATTAGATGAAAGGCTAAATGCCTTTGAGGCCTAACTGTGC
*
1304879 TTA
66 ATA
* * * * * *
1304882 TGACATAAAGGTGTCATTTAAGCCATTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAATTGTGC
1 TGATAGAAAGGTGTCATTTATGCCAATTAGATGAAAGGCTAAATGCCTTTGAGGCCTAACTGTGC
1304947 A-A
66 ATA
* * * * * * * *
1304949 TTGGTAGAAAGGTGTCAATTATGCCAGTTCGATGAATGGTTAAATACCGTTGAG
1 -TGATAGAAAGGTGTCATTTATGCCAATTAGATGAAAGGCTAAATGCCTTTGAG
1305003 TAAAAGAATA
Statistics
Matches: 100, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
67 1 0.01
68 99 0.99
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (68 bp):
TGATAGAAAGGTGTCATTTATGCCAATTAGATGAAAGGCTAAATGCCTTTGAGGCCTAACTGTGC
ATA
Found at i:1305069 original size:81 final size:81
Alignment explanation
Indices: 1304934--1305169 Score: 373
Period size: 81 Copynumber: 2.9 Consensus size: 81
1304924 GTGCCTTTGA
* * *
1304934 GGCCTAATTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAGTTCGATGAATGGTTAAATACCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGACAATTATGCCAGTTAGATGAATGGTTAAATACCGT
1304999 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * *
1305015 GGCCTAACTGTGCAATTGGTAGAAAGGTGCCAACTATGCCAGTTAGATGAATGGTTAAATACCTT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGACAATTATGCCAGTTAGATGAATGGTTAAATACCGT
*
1305080 TGAGTAATAGAATAAT
66 TGAGTAAAAGAATAAT
* * * *
1305096 GGCCTAACTATGCAATTGGTAGAAAGGTGACAATTATGCCAGTTAGATGAACGGTTAAACACTGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGACAATTATGCCAGTTAGATGAATGGTTAAATACCGT
1305161 TGAGTAAAA
66 TGAGTAAAA
1305170 ACGAAAAGTT
Statistics
Matches: 141, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 141 1.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (81 bp):
GGCCTAACTGTGCAATTGGTAGAAAGGTGACAATTATGCCAGTTAGATGAATGGTTAAATACCGT
TGAGTAAAAGAATAAT
Found at i:1305263 original size:109 final size:109
Alignment explanation
Indices: 1305067--1305509 Score: 663
Period size: 109 Copynumber: 4.1 Consensus size: 109
1305057 TTAGATGAAT
* * *
1305067 GGTTAAATACCTTTGAGTAATAGAATAATGGCCTAACTATGCAATTGGTAGAAAGGTGACAATTA
1 GGTTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTATGCAATTGGTAGAAAGGTGCCAATTA
1305132 TGCCAGTTAGATGAACGGTTAAACACTGTTGAGTAAAAACGAAA
66 TGCCAGTTAGATGAACGGTTAAACACTGTTGAGTAAAAACGAAA
* * * * *
1305176 AGTTCAATACCGTTGAGTAAAAGAATAATGGCCTAACTGTGTAATTGGTAGAAAGGTGTCAATTA
1 GGTTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTATGCAATTGGTAGAAAGGTGCCAATTA
* * *
1305241 TGCCAGTTAGGTGAATGGTTAAACATTGTTGAGTAAAAACGAAA
66 TGCCAGTTAGATGAACGGTTAAACACTGTTGAGTAAAAACGAAA
* * * * * *
1305285 GGTTAAATACCGTTGGGAAAAAGAAAAATGGCCTAACTATGCAATTGGTATAAATGCGCCAATTA
1 GGTTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTATGCAATTGGTAGAAAGGTGCCAATTA
* *
1305350 TGCCAGTTAGATGAACGATTAAACACTATTGAGTAAAAACGAAA
66 TGCCAGTTAGATGAACGGTTAAACACTGTTGAGTAAAAACGAAA
* * *
1305394 GGTTAAATACCGCTGAGTAAAATAATAATGGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTA
1 GGTTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTATGCAATTGGTAGAAAGGTGCCAATTA
*
1305459 TGCTAGTTAGATGAACGGTTAAACACTGTAT-AGTAAAAACGAAA
66 TGCCAGTTAGATGAACGGTTAAACACTGT-TGAGTAAAAACGAAA
1305503 GGTTAAA
1 GGTTAAA
1305510 CACTGTTTAA
Statistics
Matches: 295, Mismatches: 38, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
109 294 1.00
110 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (109 bp):
GGTTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTATGCAATTGGTAGAAAGGTGCCAATTA
TGCCAGTTAGATGAACGGTTAAACACTGTTGAGTAAAAACGAAA
Found at i:1305582 original size:109 final size:109
Alignment explanation
Indices: 1305090--1305582 Score: 387
Period size: 109 Copynumber: 4.5 Consensus size: 109
1305080 TGAGTAATAG
* * ** * * * * *
1305090 AATAATGGCCTAACTATGCAATTGGTAGAAAGGTGACAATTATGCCAGTTAGATGAACGGTTAAA
1 AATAATGGACTAACTGTGCAATTGACAGAAAAGTGCCAAATATGCAAGTTAGATGAACGATTAAA
* * * * * * *
1305155 CACTGTTGAGTAAAAACGAAAAGTTCAATACCGTTGAGTAAAAG
66 CACTATTGAGTAAAAACGAAAGGTTAAACACCGCTGAATAAAAT
* * ** * * * * * * *
1305199 AATAATGGCCTAACTGTGTAATTGGTAGAAAGGTGTCAATTATGCCAGTTAGGTGAATGGTTAAA
1 AATAATGGACTAACTGTGCAATTGACAGAAAAGTGCCAAATATGCAAGTTAGATGAACGATTAAA
* * * * * *
1305264 CATTGTTGAGTAAAAACGAAAGGTTAAATACCGTTGGGA-AAAAG
66 CACTATTGAGTAAAAACGAAAGGTTAAACACCGCT-GAATAAAAT
* * * ** * * * * *
1305308 AAAAATGGCCTAACTATGCAATTGGTATAAATGCGCCAATTATGCCAGTTAGATGAACGATTAAA
1 AATAATGGACTAACTGTGCAATTGACAGAAAAGTGCCAAATATGCAAGTTAGATGAACGATTAAA
* *
1305373 CACTATTGAGTAAAAACGAAAGGTTAAATACCGCTGAGTAAAAT
66 CACTATTGAGTAAAAACGAAAGGTTAAACACCGCTGAATAAAAT
* ** * * * *
1305417 AATAATGGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGCTAGTTAGATGAACGGTTAAA
1 AATAATGGACTAACTGTGCAATTGACAGAAAAGTGCCAAATATGCAAGTTAGATGAACGATTAAA
* * * *
1305482 CACTGTAT-AGTAAAAACGAAAGGTTAAACACTGTTTAATAAAAT
66 CACTAT-TGAGTAAAAACGAAAGGTTAAACACCGCTGAATAAAAT
* * ** * * *
1305526 AATGATGGATTAGTTGTGCATTTGACAGAAAAGTGTCAAATATGCAAGTTAAATGAA
1 AATAATGGACTAACTGTGCAATTGACAGAAAAGTGCCAAATATGCAAGTTAGATGAA
1305583 AAGCTAAATA
Statistics
Matches: 329, Mismatches: 52, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
108 1 0.00
109 326 0.99
110 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.27
Consensus pattern (109 bp):
AATAATGGACTAACTGTGCAATTGACAGAAAAGTGCCAAATATGCAAGTTAGATGAACGATTAAA
CACTATTGAGTAAAAACGAAAGGTTAAACACCGCTGAATAAAAT
Found at i:1308392 original size:21 final size:21
Alignment explanation
Indices: 1308367--1308409 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1308357 TTACTTGTTC
*
1308367 AATTATGTATAATTTCACATT
1 AATTACGTATAATTTCACATT
*
1308388 AATTACGTATAATTTTACATT
1 AATTACGTATAATTTCACATT
1308409 A
1 A
1308410 CTCACAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (21 bp):
AATTACGTATAATTTCACATT
Found at i:1309615 original size:118 final size:118
Alignment explanation
Indices: 1309440--1309759 Score: 361
Period size: 118 Copynumber: 2.8 Consensus size: 118
1309430 TAGAATTGAA
* * *
1309440 CTAAGGTTGAATAAGTTATTCTTATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATT
1 CTAAGGTTGAATAAGTTCTTCTCATTATGAATTTCTTCTCCCTCATCGGATGAGTTCTTCTCATT
* **
1309505 ACGAAACCTTCCATTAGAAATGTTGATCCACCTT-CTTCTATGATGGAATCAAG
66 ACGAACCCTTCCATTAGAAATGTTGATCCA-CTTCCTTCTATGATAAAATCAAG
* *
1309558 CTAAGGTTGAATAAGTTCTTCTCATTATGAATTTCTTCTCCCTTATCGGGTGAGTTCTTCTCATT
1 CTAAGGTTGAATAAGTTCTTCTCATTATGAATTTCTTCTCCCTCATCGGATGAGTTCTTCTCATT
** * * *
1309623 GTGAACCCTTTCATT-GAAAATGTTGATCCACTTCCTTCTGTGATAAAATCGAG
66 ACGAACCCTTCCATTAG-AAATGTTGATCCACTTCCTTCTATGATAAAATCAAG
* * ** *
1309676 CT---TTTGAA-CAGTTCTTCTCATTATGAACTCTT-TT-TTACTCATTGGATGAGTTCTTCTCA
1 CTAAGGTTGAATAAGTTCTTCTCATTATGAA-T-TTCTTCTCCCTCATCGGATGAGTTCTTCTCA
* *
1309735 TTACGAACCCCTCC-TCAGAAATGTT
64 TTACGAACCCTTCCATTAGAAATGTT
1309760 TGGTCCATCT
Statistics
Matches: 172, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
113 8 0.05
114 49 0.28
115 8 0.05
116 2 0.01
117 4 0.02
118 101 0.59
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (118 bp):
CTAAGGTTGAATAAGTTCTTCTCATTATGAATTTCTTCTCCCTCATCGGATGAGTTCTTCTCATT
ACGAACCCTTCCATTAGAAATGTTGATCCACTTCCTTCTATGATAAAATCAAG
Found at i:1319654 original size:2 final size:2
Alignment explanation
Indices: 1319647--1319671 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1319637 ATAAAAATGA
1319647 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1319672 CACATACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1325076 original size:21 final size:21
Alignment explanation
Indices: 1325035--1325077 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1325025 AATAACTTTT
*
1325035 AAAATAAAACTAATACAATTA
1 AAAATAAAACTAACACAATTA
*
1325056 AAAATAATAA-TAACACTATTA
1 AAAATAA-AACTAACACAATTA
1325077 A
1 A
1325078 TTTAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATAAAACTAACACAATTA
Found at i:1325843 original size:2 final size:2
Alignment explanation
Indices: 1325838--1325876 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1325828 TATAACTATG
1325838 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1325877 TATTGAAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1326365 original size:24 final size:24
Alignment explanation
Indices: 1326338--1326388 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1326328 TAAAAGGTGG
1326338 TTATGGGCTTTCAAGAAGATATAT
1 TTATGGGCTTTCAAGAAGATATAT
*
1326362 TTATGGTCTTTCAAGAAGATATAT
1 TTATGGGCTTTCAAGAAGATATAT
1326386 TTA
1 TTA
1326389 CTCTCGTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (24 bp):
TTATGGGCTTTCAAGAAGATATAT
Found at i:1328261 original size:70 final size:70
Alignment explanation
Indices: 1328148--1328285 Score: 233
Period size: 70 Copynumber: 2.0 Consensus size: 70
1328138 CCACAAAGTT
* *
1328148 AAGAGCCTTGCGCTCTACCAACTGAGCTGGACAGGCAATCTCTACATGATATATATGCATGTTAT
1 AAGAGCCTTGCGCTCTACCAACTGAGCTAGACAGGCAATCTCTACAGGATATATATGCATGTTAT
1328213 TACGG
66 TACGG
*
1328218 AAGAGCCTTGCGCTCTACCAACTGAGCTAGAC-GAGTAATCTCTACAGGATATATATGCATGTTA
1 AAGAGCCTTGCGCTCTACCAACTGAGCTAGACAG-GCAATCTCTACAGGATATATATGCATGTTA
1328282 TTAC
65 TTAC
1328286 TGAGCTGGAC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 1 0.02
70 63 0.98
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (70 bp):
AAGAGCCTTGCGCTCTACCAACTGAGCTAGACAGGCAATCTCTACAGGATATATATGCATGTTAT
TACGG
Found at i:1328514 original size:2 final size:2
Alignment explanation
Indices: 1328507--1328535 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1328497 CCATAACCTA
1328507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1328536 AAACTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1328965 original size:2 final size:2
Alignment explanation
Indices: 1328958--1328982 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1328948 ATAGATCATA
1328958 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1328983 ACCTCATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1329232 original size:22 final size:22
Alignment explanation
Indices: 1329190--1329251 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
1329180 AATTAGAATG
*
1329190 TAATTATTTAAT-TA-TATAGA
1 TAATAATTTAATATATTATAGA
1329210 TAATAATTTAGA-ATATTATAGA
1 TAATAATTTA-ATATATTATAGA
1329232 TAATAATTTAATATATTATA
1 TAATAATTTAATATATTATA
1329252 ATATACAGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 9 0.24
21 4 0.11
22 24 0.65
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
TAATAATTTAATATATTATAGA
Found at i:1329302 original size:2 final size:2
Alignment explanation
Indices: 1329295--1329324 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1329285 ATAGAAATCG
1329295 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1329325 TGAGGATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1330778 original size:80 final size:81
Alignment explanation
Indices: 1330544--1330921 Score: 389
Period size: 80 Copynumber: 4.7 Consensus size: 81
1330534 AACAAGTCAA
* * * * *
1330544 AGCTTAAATT-ATGAAACAAATGGGGAAACAAATAATATAATGATTCCATAGATA-T-T-A-TTA
1 AGCTTAAATTAAGGAAACAAGTGGAGAAACAAATATTATAATGATTCCATATATATTATAATTTA
1330604 AAAACTAAACACCATACG-T
66 AAAACT-AA-ACC--ACGAT
* * * * **
1330623 AGCTTTAATT-AGG-GA-AAGTTGAGAAACAAATATTATAATGATTCCATATATTATAATCAACA
1 AGCTTAAATTAAGGAAACAAGTGGAGAAACAAATATTATAATGATTCCATATA-TATTAT-AATT
*
1330685 AAAAAACTAAACCACGAT
64 TAAAAACTAAACCACGAT
* *
1330703 AGCTTAAATTAAGGAAACAAGTAGAGAAACAAATATTATAATGATTCTATATATATTATAA-TTA
1 AGCTTAAATTAAGGAAACAAGTGGAGAAACAAATATTATAATGATTCCATATATATTATAATTTA
*
1330767 AAAACTAAACCACTAT
66 AAAACTAAACCACGAT
* **
1330783 AACTTAAATTAAGGAAACAAGTGGAGAAACAAATATTATAATGAATCTATATATATATTATAATT
1 AGCTTAAATTAAGGAAACAAGTGGAGAAACAAATATTATAATG-AT-TCCATATATATTATAA-T
* *
1330848 TTAAAAAATTAAACCACTAT
63 TT-AAAAACTAAACCACGAT
* * *
1330868 AGCTTAAATTAAAGAAACAAGTGGAGAAACAAATAATATACTGATTCCATATAT
1 AGCTTAAATTAAGGAAACAAGTGGAGAAACAAATATTATAATGATTCCATATAT
1330922 TTAAAAAAAC
Statistics
Matches: 255, Mismatches: 29, Indels: 26
0.82 0.09 0.08
Matches are distributed among these distances:
77 30 0.12
78 3 0.01
79 14 0.05
80 68 0.27
81 10 0.04
82 24 0.09
83 47 0.18
84 4 0.02
85 55 0.22
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.29
Consensus pattern (81 bp):
AGCTTAAATTAAGGAAACAAGTGGAGAAACAAATATTATAATGATTCCATATATATTATAATTTA
AAAACTAAACCACGAT
Found at i:1330897 original size:165 final size:159
Alignment explanation
Indices: 1330544--1330921 Score: 442
Period size: 165 Copynumber: 2.3 Consensus size: 159
1330534 AACAAGTCAA
* * * *
1330544 AGCTTAAATT-ATGAAACAAATGGGGAAACAAATAATATAATGATTCCATAGATATTATTAAAAA
1 AGCTTAAATTAAAGAAACAAGTGGAGAAACAAATAATATAATGATTCCATATATATTATTAAAAA
* * * * *
1330608 CTAAACACCATACGTAGCTTTAATTAGGGAAAGTTGAGAAACAAATATTATAATGATTCCATATA
66 CTAAACACCATAC-TAACTTAAATTAGGAAAAGTGGAGAAACAAATATTATAATGAATCCATATA
1330673 TTATAATCAACAAAAAAACTAAACCACGAT
130 TTATAATCAACAAAAAAACTAAACCACGAT
* * * *
1330703 AGCTTAAATTAAGGAAACAAGTAGAGAAACAAATATTATAATGATTCTATATATATTATAATTAA
1 AGCTTAAATTAAAGAAACAAGTGGAGAAACAAATAATATAATGATTCCATATATA-T-T-ATTAA
1330768 AAACT-AA-ACCACTA-TAACTTAAATTAAGGAAACAAGTGGAGAAACAAATATTATAATGAATC
63 AAACTAAACACCA-TACTAACTTAAATT-AGG-AA-AAGTGGAGAAACAAATATTATAATGAATC
* * ** * *
1330830 TATATATATATTAT-AATTTTAAAAAATTAAACCACTAT
124 CATATAT-TATAATCAA--CAAAAAAACTAAACCACGAT
*
1330868 AGCTTAAATTAAAGAAACAAGTGGAGAAACAAATAATATACTGATTCCATATAT
1 AGCTTAAATTAAAGAAACAAGTGGAGAAACAAATAATATAATGATTCCATATAT
1330922 TTAAAAAAAC
Statistics
Matches: 185, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
159 10 0.05
160 46 0.25
161 8 0.04
162 6 0.03
163 45 0.24
164 5 0.03
165 65 0.35
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.29
Consensus pattern (159 bp):
AGCTTAAATTAAAGAAACAAGTGGAGAAACAAATAATATAATGATTCCATATATATTATTAAAAA
CTAAACACCATACTAACTTAAATTAGGAAAAGTGGAGAAACAAATATTATAATGAATCCATATAT
TATAATCAACAAAAAAACTAAACCACGAT
Found at i:1336075 original size:12 final size:12
Alignment explanation
Indices: 1336058--1336082 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1336048 TGTTTTCGTA
1336058 AGTTACTGTAGC
1 AGTTACTGTAGC
1336070 AGTTACTGTAGC
1 AGTTACTGTAGC
1336082 A
1 A
1336083 TGAACATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (12 bp):
AGTTACTGTAGC
Found at i:1337990 original size:20 final size:20
Alignment explanation
Indices: 1337965--1338002 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1337955 ACATTAACAT
1337965 TAATAATAATAATAATATAG
1 TAATAATAATAATAATATAG
* *
1337985 TAATAATATTTATAATAT
1 TAATAATAATAATAATAT
1338003 TTTTTTAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
TAATAATAATAATAATATAG
Found at i:1338980 original size:36 final size:36
Alignment explanation
Indices: 1338933--1339565 Score: 429
Period size: 39 Copynumber: 17.4 Consensus size: 36
1338923 GCTTTAAGAA
* * **
1338933 AAACCATCTCAAGTGAGATAAATTTTGTTTCAAAAG
1 AAACTATCTCAAGTGAGATAAAATTTGTTTCAAGGG
* * * *
1338969 AAACTGTCTCAAGGGAGAGAAAATTCGTTTCAAGGG
1 AAACTATCTCAAGTGAGATAAAATTTGTTTCAAGGG
* **
1339005 AAAC-ATTCTCAA---AG-T---TTTGTGTTTCAAGAT
1 AAACTA-TCTCAAGTGAGATAAAATT-TGTTTCAAGGG
* * *
1339035 AAACTATATCAAGGGAGA-AAAATTTGTTTCAATGG
1 AAACTATCTCAAGTGAGATAAAATTTGTTTCAAGGG
* *
1339070 AAACTATCTTAAGAT-AGACAAAATTTGTTTCAAGGG
1 AAACTATCTCAAG-TGAGATAAAATTTGTTTCAAGGG
* * *
1339106 AAACGT-TTTCAA---AG-T---TTTGTGTTTCAAGAG
1 AAAC-TATCTCAAGTGAGATAAAATT-TGTTTCAAGGG
* * * *
1339136 AAACTATCTCAAGGGAGACAAAATTTGTTTAAAGGA
1 AAACTATCTCAAGTGAGATAAAATTTGTTTCAAGGG
* * *
1339172 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
1 AAACTATCTCAAGTGAGATAAAATTTGTTTCAAGGG
* * * * *
1339208 AAACTGTCTCAAGGGAGACAAAATTCGTTTAAAGGG
1 AAACTATCTCAAGTGAGATAAAATTTGTTTCAAGGG
* * *
1339244 AAACTGTCTCAAGAGAGATAAAATTTGTTTCGAGGG
1 AAACTATCTCAAGTGAGATAAAATTTGTTTCAAGGG
** *
1339280 AAACTATCTCAAGCAAGATAAAATTTTATGTTTCGAGGG
1 AAACTATCTCAAGTGAGATAAAA--TT-TGTTTCAAGGG
* * *
1339319 AAACTATCTCAAGCGAGATAAAATCTTATATTTCGAGGG
1 AAACTATCTCAAGTGAGATAAAA--TT-TGTTTCAAGGG
**
1339358 AAACTATCTCAAGTGAGATAAAATCTTTTGTTTTGAGGG
1 AAACTATCTCAAGTGAGATAAAA---TTTGTTTCAAGGG
*
1339397 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGTGAGATAAAA--TT-TGTTTCAAGGG
*
1339436 AAACTATCTCAAGTGAGATAAAATCTTCTATTTCAAGGG
1 AAACTATCTCAAGTGAGATAAAA--TT-TGTTTCAAGGG
** * *
1339475 AAACTATCTCAAGAAAGACAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGTGAGATAAAA--TT-TGTTTCAAGGG
* ** **
1339514 AAACTCTCTCAAGCAAGATAAAATCTTTTGTTTTGAGGG
1 AAACTATCTCAAGTGAGATAAAA---TTTGTTTCAAGGG
1339553 AAACTATCTCAAG
1 AAACTATCTCAAG
1339566 CAAGACAAAT
Statistics
Matches: 495, Mismatches: 74, Indels: 53
0.80 0.12 0.09
Matches are distributed among these distances:
29 5 0.01
30 36 0.07
31 1 0.00
33 8 0.02
35 22 0.04
36 188 0.38
37 3 0.01
38 4 0.01
39 224 0.45
40 4 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (36 bp):
AAACTATCTCAAGTGAGATAAAATTTGTTTCAAGGG
Found at i:1339073 original size:101 final size:101
Alignment explanation
Indices: 1338941--1339219 Score: 382
Period size: 101 Copynumber: 2.7 Consensus size: 101
1338931 AAAAACCATC
* * * * * * *
1338941 TCAAGTGAGATAAATTTTGTTTCAAAAGAAACTGTCTCAAGGGAGAGAAAATTCGTTTCAAGGGA
1 TCAAGGGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGA
*
1339006 AACATTCTCAAAGTTTTGTGTTTCAAGATAAACTATA
66 AAC-TTCTCAAAGTTTTGTGTTTCAAGAGAAACTATA
* * * *
1339043 TCAAGGGAGA-AAAATTTGTTTCAATGGAAACTATCTTAAGATAGACAAAATTTGTTTCAAGGGA
1 TCAAGGGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGA
* *
1339107 AACGTTTTCAAAGTTTTGTGTTTCAAGAGAAACTATC
66 AAC-TTCTCAAAGTTTTGTGTTTCAAGAGAAACTATA
1339144 TCAAGGGAGACAAAATTTGTTT-AAAGGAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
1 TCAAGGGAGACAAAATTTGTTTCAAAGG-AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
1339208 AAACTGTCTCAA
65 AAACT-TCTCAA
1339220 GGGAGACAAA
Statistics
Matches: 155, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
101 93 0.60
102 62 0.40
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (101 bp):
TCAAGGGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGA
AACTTCTCAAAGTTTTGTGTTTCAAGAGAAACTATA
Found at i:1339204 original size:21 final size:21
Alignment explanation
Indices: 1339144--1339205 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1339134 AGAAACTATC
*
1339144 TCAAGGGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
1339165 T-AA-AG-G--AAAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
1339180 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
1339201 TCAAG
1 TCAAG
1339206 GGAAACTGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 12
0.64 0.11 0.26
Matches are distributed among these distances:
15 4 0.13
16 6 0.20
17 2 0.07
18 2 0.07
19 1 0.03
20 6 0.20
21 9 0.30
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:1339377 original size:78 final size:76
Alignment explanation
Indices: 1339125--1339565 Score: 475
Period size: 78 Copynumber: 5.8 Consensus size: 76
1339115 CAAAGTTTTG
* * * * * *
1339125 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA--TTTGTTTAAAGGAAAACTGTCTCAAGAGA
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATTTTTGTTTAAAGGGAAACTATCTCAAGAGA
*
1339188 GACAAAA--TT
66 GATAAAATCTT
* * * * * *
1339197 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA--TTCGTTTAAAGGGAAACTGTCTCAAGAGA
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATTTTTGTTTAAAGGGAAACTATCTCAAGAGA
1339260 GATAAAA--TT
66 GATAAAATCTT
* ** *
1339269 TGTTTCGAGGGAAACTATCTCAAGCAAGATAAAATTTTATGTTTCGAGGGAAACTATCTCAAGCG
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATTTT-TGTTTAAAGGGAAACTATCTCAAGAG
1339334 AGATAAAATCTT
65 AGATAAAATCTT
* * ** *
1339346 ATATTTCGAGGGAAACTATCTCAAGTGAGATAAAATCTTTTGTTTTGAGGGAAACTATCTCAAGT
1 -TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT-TTTTGTTTAAAGGGAAACTATCTCAAGA
1339411 GAGATAAAATCTT
64 GAGATAAAATCTT
* * * *
1339424 CTGTTTCGAGGGAAACTATCTCAAGTGAGATAAAATCTTCTATTTCAAGGGAAACTATCTCAAGA
1 -TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT-TTTTGTTTAAAGGGAAACTATCTCAAGA
* *
1339489 AAGACAAAATCTT
64 GAGATAAAATCTT
* * **
1339502 CTGTTTCGAGGGAAACTCTCTCAAGCAAGATAAAATCTTTTGTTTTGAGGGAAACTATCTCAAG
1 -TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT-TTTTGTTTAAAGGGAAACTATCTCAAG
1339566 CAAGACAAAT
Statistics
Matches: 326, Mismatches: 36, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
72 96 0.29
74 2 0.01
75 29 0.09
77 2 0.01
78 194 0.60
79 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (76 bp):
TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATTTTTGTTTAAAGGGAAACTATCTCAAGAGA
GATAAAATCTT
Found at i:1339416 original size:117 final size:112
Alignment explanation
Indices: 1339127--1339566 Score: 494
Period size: 117 Copynumber: 3.9 Consensus size: 112
1339117 AAGTTTTGTG
* * ** * * *
1339127 TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACTGTCTCAAG-AGAGAC
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCGAGGGAAACTATCTCAAGCA-AGAT
* * * * **
1339191 AAAA--TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA--TTCG
65 AAAATTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTA
* * *
1339235 TTTAAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCGAGGGAAACTATCTCAAGCAAGATA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCGAGGGAAACTATCTCAAGCAAGATA
1339300 AAATTTTATGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTATA
66 AAATTTT-TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTT-TA
* * * * **
1339349 TTTCGAGGGAAACTATCTCAAGTGAGATAAAATCTTTTGTTTTGAGGGAAACTATCTCAAGTGAG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA---TTTGTTTCGAGGGAAACTATCTCAAGCAAG
* *
1339414 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGTGAGATAAAATCTTCTA
63 ATAAAAT-TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTT-TA
* *
1339466 TTTCAAGGGAAACTATCTCAAGAAAGACAAAATCTTCTGTTTCGAGGGAAACTCTCTCAAGCAAG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA--TT-TGTTTCGAGGGAAACTATCTCAAGCAAG
*
1339531 ATAAAATCTTTTGTTTTGAGGGAAACTATCTCAAGC
63 ATAAAAT-TTTTGTTTCGAGGGAAACTATCTCAAGC
1339567 AAGACAAATC
Statistics
Matches: 281, Mismatches: 39, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
108 56 0.20
109 1 0.00
110 2 0.01
111 30 0.11
113 2 0.01
114 28 0.10
116 2 0.01
117 158 0.56
118 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (112 bp):
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCGAGGGAAACTATCTCAAGCAAGATA
AAATTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTA
Found at i:1339747 original size:75 final size:75
Alignment explanation
Indices: 1339559--1339747 Score: 242
Period size: 75 Copynumber: 2.5 Consensus size: 75
1339549 AGGGAAACTA
* * *
1339559 TCTCAAGCAAGACAAATCTTGTTTTAAGAAAAACAA-CATGTAGTAAAATGAAATGTCTTGTTTT
1 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGTAGTAAAATGAAATGTCTTCTTTT
*
1339623 GAATAAAACTG
66 G-ATAAAACAG
* *
1339634 TCCCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTG-AGTTAAATGAAATGTCTTCTTTC
1 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGTAGTAAAATGAAATGTCTTCTTT-
1339698 ATG-TAAAACAG
65 -TGATAAAACAG
* *
1339709 TCTCAAGTGAGACAAAGTC-TGTTTTAAGAAAAGCAATCT
1 TCTCAAGCGAGACAAA-TCTTGTTTTAAGAAAAACAATCT
1339748 CTAGTGAGAT
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
75 94 0.93
76 5 0.05
77 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (75 bp):
TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGTAGTAAAATGAAATGTCTTCTTTT
GATAAAACAG
Found at i:1344384 original size:11 final size:11
Alignment explanation
Indices: 1344370--1344398 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1344360 TTAAAAAAAA
1344370 CAAAAAAAGGC
1 CAAAAAAAGGC
1344381 C-AAAAAAGGC
1 CAAAAAAAGGC
1344391 CAAAAAAA
1 CAAAAAAA
1344399 ACAAAAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.69, C:0.17, G:0.14, T:0.00
Consensus pattern (11 bp):
CAAAAAAAGGC
Found at i:1352554 original size:16 final size:16
Alignment explanation
Indices: 1352533--1352564 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1352523 TTAAAAATAA
1352533 GTTTAGTGGATGTTTG
1 GTTTAGTGGATGTTTG
*
1352549 GTTTAGTGGATTTTTG
1 GTTTAGTGGATGTTTG
1352565 ATTGCTGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.34, T:0.53
Consensus pattern (16 bp):
GTTTAGTGGATGTTTG
Found at i:1352883 original size:20 final size:20
Alignment explanation
Indices: 1352858--1352895 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1352848 TTAACATTAA
1352858 TAATAATAATAATAATATAG
1 TAATAATAATAATAATATAG
* *
1352878 TAATAATATTTATAATAT
1 TAATAATAATAATAATAT
1352896 TTTTTTAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
TAATAATAATAATAATATAG
Found at i:1353037 original size:48 final size:48
Alignment explanation
Indices: 1352973--1353205 Score: 337
Period size: 48 Copynumber: 4.9 Consensus size: 48
1352963 CAATCGGGGC
* * * *
1352973 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTTGAGAAGAT
1 AGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAAAG
* *
1353021 AGA-TCTGTTCCGCTTACTCTGAAGGGAATATCAAATCTT-GATAAGAG
1 AGACT-TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAAAG
** *
1353068 AGA-TATGTTCTTCTTACTTTGAAGGGAATATCAAATCTTGGAGAAAAG
1 AGACT-TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAAAG
1353116 AGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAAAG
1 AGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAAAG
*
1353164 AGACTTGTTCCGCTTACTCCGAAGGGAATATCAAATCTTGGA
1 AGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGA
1353206 TTTGCTTTAC
Statistics
Matches: 169, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
47 42 0.25
48 126 0.75
49 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (48 bp):
AGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAAAG
Found at i:1353141 original size:95 final size:96
Alignment explanation
Indices: 1352973--1353205 Score: 337
Period size: 95 Copynumber: 2.4 Consensus size: 96
1352963 CAATCGGGGC
* * * *
1352973 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTTGAGAAGATAGATCTGTTCCGCTTAC
1 AGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAAAGAGATCTGTTCCGCTTAC
* *
1353038 TCTGAAGGGAATATCAAATCTT-GATAAGAG
66 TCTGAAGGGAATATCAAATCTTGGAGAAAAG
** *
1353068 AGA-TATGTTCTTCTTACTTTGAAGGGAATATCAAATCTTGGAGAAAAGAGA-CTTGTTCCGCTT
1 AGACT-TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAAAGAGATC-TGTTCCGCTT
1353131 ACTCTGAAGGGAATATCAAATCTTGGAGAAAAG
64 ACTCTGAAGGGAATATCAAATCTTGGAGAAAAG
*
1353164 AGACTTGTTCCGCTTACTCCGAAGGGAATATCAAATCTTGGA
1 AGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGA
1353206 TTTGCTTTAC
Statistics
Matches: 122, Mismatches: 12, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
94 2 0.02
95 77 0.63
96 42 0.34
97 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (96 bp):
AGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAGAAAAGAGATCTGTTCCGCTTAC
TCTGAAGGGAATATCAAATCTTGGAGAAAAG
Found at i:1353245 original size:37 final size:37
Alignment explanation
Indices: 1353204--1353347 Score: 225
Period size: 37 Copynumber: 3.9 Consensus size: 37
1353194 TCAAATCTTG
* * * *
1353204 GATTTGCTTTACTACTTTTTCGTGAAGGCTTAAGATT
1 GATTTGCTTCACTACTCTTTGGTGAAGGCTTAAAATT
*
1353241 GATTTGCTTCACTACTCTTTGGTGAAGGCTTAAAATG
1 GATTTGCTTCACTACTCTTTGGTGAAGGCTTAAAATT
* *
1353278 GATTTGCTTCACTACACTTTGGTGGAGGCTTAAAATT
1 GATTTGCTTCACTACTCTTTGGTGAAGGCTTAAAATT
1353315 GATTTGCTTCACTACTCTTTGGTGAAGGCTTAA
1 GATTTGCTTCACTACTCTTTGGTGAAGGCTTAA
1353348 GATGGCCTAG
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (37 bp):
GATTTGCTTCACTACTCTTTGGTGAAGGCTTAAAATT
Found at i:1357377 original size:12 final size:12
Alignment explanation
Indices: 1357347--1357378 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1357337 AACAACACTG
*
1357347 TGAACAATACCA
1 TGAACAGTACCA
1357359 TGAACAGTACCA
1 TGAACAGTACCA
1357371 TGAACAGT
1 TGAACAGT
1357379 GAAATATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.19
Consensus pattern (12 bp):
TGAACAGTACCA
Found at i:1357425 original size:21 final size:21
Alignment explanation
Indices: 1357401--1357444 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1357391 ATATCAATTA
* *
1357401 TGCATCGATGCATTGCTACAG
1 TGCATCGATACACTGCTACAG
1357422 TGCATCGATACACTGCTACAG
1 TGCATCGATACACTGCTACAG
1357443 TG
1 TG
1357445 ACTTCGGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (21 bp):
TGCATCGATACACTGCTACAG
Found at i:1358787 original size:20 final size:21
Alignment explanation
Indices: 1358762--1358817 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
1358752 CGAAATATCC
*
1358762 ATGCATCGTTGCACCT-CTTA
1 ATGCATCGATGCACCTCCTTA
1358782 ATGCATCGATGCA-CTCCTTA
1 ATGCATCGATGCACCTCCTTA
*
1358802 ATGTATCGATGCACCT
1 ATGCATCGATGCACCT
1358818 TCAAAATTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (21 bp):
ATGCATCGATGCACCTCCTTA
Found at i:1363526 original size:2 final size:2
Alignment explanation
Indices: 1363519--1363543 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1363509 CCCTAACCTA
1363519 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1363544 AATTTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1364253 original size:9 final size:8
Alignment explanation
Indices: 1364236--1364332 Score: 63
Period size: 8 Copynumber: 12.1 Consensus size: 8
1364226 AATATATACC
1364236 AAATATAT
1 AAATATAT
1364244 AAATAT-T
1 AAATATAT
*
1364251 ATATAT-T
1 AAATATAT
** *
1364258 CCATATAG
1 AAATATAT
1364266 AAATCGATAT
1 AAAT--ATAT
*
1364276 ATATATAT
1 AAATATAT
*
1364284 ATATATAT
1 AAATATAT
*
1364292 ATATATAT
1 AAATATAT
*
1364300 ATATATAT
1 AAATATAT
*
1364308 ATATATAT
1 AAATATAT
*
1364316 ATATATAT
1 AAATATAT
*
1364324 ATATATAT
1 AAATATAT
1364332 A
1 A
1364333 TGAGGATTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
7 11 0.14
8 61 0.78
10 6 0.08
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (8 bp):
AAATATAT
Found at i:1364279 original size:2 final size:2
Alignment explanation
Indices: 1364272--1364333 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1364262 ATAGAAATCG
1364272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1364314 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1364334 GAGGATTAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1367448 original size:31 final size:31
Alignment explanation
Indices: 1367410--1367472 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1367400 CTTTAATCAA
1367410 TTGATAACGTACACACATCATGTACAAGTTT
1 TTGATAACGTACACACATCATGTACAAGTTT
*
1367441 TTGATAACGTACACACATCCTGTACAAGTTT
1 TTGATAACGTACACACATCATGTACAAGTTT
1367472 T
1 T
1367473 GGATGACATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (31 bp):
TTGATAACGTACACACATCATGTACAAGTTT
Found at i:1368704 original size:29 final size:29
Alignment explanation
Indices: 1368661--1368823 Score: 121
Period size: 29 Copynumber: 5.6 Consensus size: 29
1368651 AATTGTTGTT
* * *
1368661 AGGTGATATTCTGGGAAATATTTCGATAA
1 AGGTGACATTTTGGGAAATATTTCGAAAA
* *
1368690 AGGTGACATTTTGGGAATTATTTTGAAAA
1 AGGTGACATTTTGGGAAATATTTCGAAAA
* * *
1368719 AGGTGCCATTATGAGAAATATTTC-AAAA
1 AGGTGACATTTTGGGAAATATTTCGAAAA
* * * * *
1368747 CAAGTAACATATTGGGAATTATTTCGTAAA
1 -AGGTGACATTTTGGGAAATATTTCGAAAA
* * * * **
1368777 AGGTGACACTCTGTGAATTATTTAAAAAAA
1 AGGTGACATTTTGGGAAATATTT-CGAAAA
*
1368807 AAGTGACATTTTGGGAA
1 AGGTGACATTTTGGGAA
1368824 TTTTCAAATG
Statistics
Matches: 100, Mismatches: 31, Indels: 5
0.74 0.23 0.04
Matches are distributed among these distances:
28 4 0.04
29 77 0.77
30 19 0.19
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.33
Consensus pattern (29 bp):
AGGTGACATTTTGGGAAATATTTCGAAAA
Found at i:1368799 original size:58 final size:59
Alignment explanation
Indices: 1368695--1368825 Score: 156
Period size: 58 Copynumber: 2.2 Consensus size: 59
1368685 GATAAAGGTG
* * * * *
1368695 ACATTTTGGGAATTATTTTGAAAAAGGTGCCATTATGAGAAATATTT-CAAAACAAGTA
1 ACATTTTGGGAATTATTTCGAAAAAGGTGACACTATGAGAAATATTTAAAAAAAAAGTA
* * * * * *
1368753 ACATATTGGGAATTATTTCGTAAAAGGTGACACTCTGTGAATTATTTAAAAAAAAAGTG
1 ACATTTTGGGAATTATTTCGAAAAAGGTGACACTATGAGAAATATTTAAAAAAAAAGTA
1368812 ACATTTTGGGAATT
1 ACATTTTGGGAATT
1368826 TTCAAATGTT
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
58 39 0.65
59 21 0.35
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (59 bp):
ACATTTTGGGAATTATTTCGAAAAAGGTGACACTATGAGAAATATTTAAAAAAAAAGTA
Found at i:1375296 original size:31 final size:29
Alignment explanation
Indices: 1375231--1375396 Score: 170
Period size: 29 Copynumber: 5.7 Consensus size: 29
1375221 AATTGTTGTT
* * * *
1375231 AGGTGATATTCTGGGAAATATTTCGATAA
1 AGGTGACATTTTGGGAATTATTTCGAAAA
*
1375260 AGGTGACATTTTGGGAATTATTTTGAAAAAA
1 AGGTGACATTTTGGGAATTATTTCG--AAAA
* *
1375291 AGGTGACATTATGGGAAATATTTCGAAAA
1 AGGTGACATTTTGGGAATTATTTCGAAAA
* * *
1375320 AGGTAACATATTGGGAATTATTTCGTAAA
1 AGGTGACATTTTGGGAATTATTTCGAAAA
* * **
1375349 AGGTGACACTCTGGGAATTATTTTTAAAA
1 AGGTGACATTTTGGGAATTATTTCGAAAA
**
1375378 AAATGACATTTTGGGAATT
1 AGGTGACATTTTGGGAATT
1375397 TTCAAATGTT
Statistics
Matches: 111, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
29 86 0.77
31 25 0.23
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (29 bp):
AGGTGACATTTTGGGAATTATTTCGAAAA
Found at i:1375306 original size:60 final size:58
Alignment explanation
Indices: 1375231--1375396 Score: 197
Period size: 60 Copynumber: 2.8 Consensus size: 58
1375221 AATTGTTGTT
* * *
1375231 AGGTGATATTCTGGGAAATATTTCGATAAAGGTGACATTTTGGGAATTATTTTGAAAAAA
1 AGGTGACATTCTGGGAAATATTTCGAAAAAGGTGACATTTTGGGAATTATTTCG--AAAA
* * * *
1375291 AGGTGACATTATGGGAAATATTTCGAAAAAGGTAACATATTGGGAATTATTTCGTAAA
1 AGGTGACATTCTGGGAAATATTTCGAAAAAGGTGACATTTTGGGAATTATTTCGAAAA
* * ** **
1375349 AGGTGACACTCTGGGAATTATTTTTAAAAAAATGACATTTTGGGAATT
1 AGGTGACATTCTGGGAAATATTTCGAAAAAGGTGACATTTTGGGAATT
1375397 TTCAAATGTT
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
58 42 0.47
60 48 0.53
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (58 bp):
AGGTGACATTCTGGGAAATATTTCGAAAAAGGTGACATTTTGGGAATTATTTCGAAAA
Found at i:1376594 original size:609 final size:611
Alignment explanation
Indices: 1375494--1376719 Score: 2267
Period size: 609 Copynumber: 2.0 Consensus size: 611
1375484 TCCTGACAGT
*
1375494 TTTCGACGTCCTGAATCCGTTTTTGGGGTCCGTTTCACCAAATTCAAACTCGAAAGTCTCTAAAT
1 TTTCGACGTCCCGAATCCGTTTTTGGGGTCCGTTTCACCAAATTCAAACTCGAAAGTCTCTAAAT
*
1375559 CGATGGTCAAAGTGGTTGACTTTGACTTTGAAAGAATTTGAATTTTTGAAAAGTCATACTTTATG
66 CGACGGTCAAAGTGGTTGACTTTGAC--T---AGAATTTGAATTTTTGAAAAGTCATACTTTATG
1375624 TTTATCGACGTCCTGATTCCGATTCCACAATATGTTTGGCCAAATTCAGACTCGAAATACCCCAA
126 TTTATCGACGTCCTGATTCCGATTCCACAATATGTTTGGCCAAATTCAGACTCGAAATACCCCAA
*
1375689 ATTGATAATCAAACCCAGAAAATGTTTATATACTTAAGAAGTCTAGCTTTGAACAATTAAGTAAG
191 ATTGATAATCAAACCCAGAAAATGCTTATATACTTAAGAAGTCTAGCTTTGAACAATTAAGTAAG
* *
1375754 ATTTGGGACTGATAGATTATTATTGTTTGAAGGTACAAGAGACTCTCCGGATCGTTCGACAGCTC
256 ATTTGGGACTGATAGATTATTATTGTTTGAAGGTACAAGAGACTCTCCGGATCGTTCGACAACTA
1375819 GACCCAACTCTTCTAGATCTGTTAAACCACGTATACCAGTATTCACCCGTTCGAAAACTGTAACA
321 GACCCAACTCTTCTAGATCTGTTAAACCACGTATACCAGTATTCACCCGTTCGAAAACTGTAACA
1375884 AAGCGTGATAAAACCAGCAATCAGTAGATCTACTATCTGAACCCATTATCGAGGTGTGTTCTTGT
386 AAGCGTGATAAAACCAGCAATCAGTAGATCTACTATCTGAACCCATTATCGAGGTGTGTTCTTGT
1375949 TTACTACATAATGGTTTTATATGTTTTGAAATATGGTACATTGAAATCTATGGTTTATTATTGTT
451 TTACTACATAATGGTTTTATATGTTTTGAAATATGGTACATTGAAATCTATGGTTTATTATTGTT
*
1376014 GGTACACCGATTTATTGTTGATGATTTATGGACTTTGATGACTGGTATGTGGATATTGATTTTGG
516 GGTACACCGATTTATTGTTGATGATTTATGGACTTTGATGACTGGTATATGGATATTGATTTTGG
1376079 GATAGATTGAACTACAATTGTATAGCTCTGA
581 GATAGATTGAACTACAATTGTATAGCTCTGA
* *
1376110 TTTCGATGTCCCGAATCCGTTTTTGGGGTCCGTTTCACCAAATTCGAACTCGAAAGTCTCTAAAT
1 TTTCGACGTCCCGAATCCGTTTTTGGGGTCCGTTTCACCAAATTCAAACTCGAAAGTCTCTAAAT
1376175 CGACGGTCAAAGTGGTTGACTTTGAC-AGAATTTGAATTTTTGAAAAGTCATACTTTATGTTTAT
66 CGACGGTCAAAGTGGTTGACTTTGACTAGAATTTGAATTTTTGAAAAGTCATACTTTATGTTTAT
*
1376239 CGACGTCCTGA-TCCGATTCCACAATATGTTTGGCTAAATTCAGACTCGAAATACCCCAAATTGA
131 CGACGTCCTGATTCCGATTCCACAATATGTTTGGCCAAATTCAGACTCGAAATACCCCAAATTGA
* *
1376303 TAATCGAACCTAGAAAATGCTTATATACTTAAGAAGTCTAGCTTTGAACAATTAAGTAAGATTTG
196 TAATCAAACCCAGAAAATGCTTATATACTTAAGAAGTCTAGCTTTGAACAATTAAGTAAGATTTG
1376368 GGACTGATAGATTATTATTGTTTGAAGGTACAAGAGACTCTCCGGATCGTTCGACAACTAGACCC
261 GGACTGATAGATTATTATTGTTTGAAGGTACAAGAGACTCTCCGGATCGTTCGACAACTAGACCC
*
1376433 AACTCTTCTAGATCTGTTAAACCACGTATACCAGTATTCACCCGTTCGAAAACTGTAACAGAGCG
326 AACTCTTCTAGATCTGTTAAACCACGTATACCAGTATTCACCCGTTCGAAAACTGTAACAAAGCG
* *
1376498 TGGTGAAACCAGCAATCAGTAGATCTACTATCTGAACCCATTATCGAGGTGTGTTCTTGTTTACT
391 TGATAAAACCAGCAATCAGTAGATCTACTATCTGAACCCATTATCGAGGTGTGTTCTTGTTTACT
1376563 ACATAATGGTTTTATATGTTTTGAAATATGGTACATTGAAATCTATGGTTTATTATTGTTGGTAC
456 ACATAATGGTTTTATATGTTTTGAAATATGGTACATTGAAATCTATGGTTTATTATTGTTGGTAC
1376628 ACCGATTTATTGTTGATGATTTATGGACTTTGATGACTGGTATATGGATATTGATTTTGGGATAG
521 ACCGATTTATTGTTGATGATTTATGGACTTTGATGACTGGTATATGGATATTGATTTTGGGATAG
1376693 ATTGAACTACAATTGTATAGCTCTGA
586 ATTGAACTACAATTGTATAGCTCTGA
1376719 T
1 T
1376720 CAAGTTAATA
Statistics
Matches: 596, Mismatches: 14, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
609 460 0.77
610 49 0.08
616 87 0.15
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (611 bp):
TTTCGACGTCCCGAATCCGTTTTTGGGGTCCGTTTCACCAAATTCAAACTCGAAAGTCTCTAAAT
CGACGGTCAAAGTGGTTGACTTTGACTAGAATTTGAATTTTTGAAAAGTCATACTTTATGTTTAT
CGACGTCCTGATTCCGATTCCACAATATGTTTGGCCAAATTCAGACTCGAAATACCCCAAATTGA
TAATCAAACCCAGAAAATGCTTATATACTTAAGAAGTCTAGCTTTGAACAATTAAGTAAGATTTG
GGACTGATAGATTATTATTGTTTGAAGGTACAAGAGACTCTCCGGATCGTTCGACAACTAGACCC
AACTCTTCTAGATCTGTTAAACCACGTATACCAGTATTCACCCGTTCGAAAACTGTAACAAAGCG
TGATAAAACCAGCAATCAGTAGATCTACTATCTGAACCCATTATCGAGGTGTGTTCTTGTTTACT
ACATAATGGTTTTATATGTTTTGAAATATGGTACATTGAAATCTATGGTTTATTATTGTTGGTAC
ACCGATTTATTGTTGATGATTTATGGACTTTGATGACTGGTATATGGATATTGATTTTGGGATAG
ATTGAACTACAATTGTATAGCTCTGA
Found at i:1386352 original size:24 final size:22
Alignment explanation
Indices: 1386302--1386357 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
1386292 ATCTCATCCA
* *
1386302 TTCA-CTTCATCACCACATGAT
1 TTCATCTTCATCACAACATCAT
1386323 TT-ATCTTCATCACAACCATCAGT
1 TTCATCTTCATCACAA-CATCA-T
1386346 TTCATCTTCATC
1 TTCATCTTCATC
1386358 TCATCCATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 12 0.41
22 4 0.14
23 3 0.10
24 9 0.31
ACGTcount: A:0.27, C:0.32, G:0.04, T:0.38
Consensus pattern (22 bp):
TTCATCTTCATCACAACATCAT
Found at i:1386406 original size:15 final size:15
Alignment explanation
Indices: 1386386--1386418 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1386376 TACATCACTA
1386386 CCATCATC-TCCATCT
1 CCATCATCAT-CATCT
1386401 CCATCATCATCATCT
1 CCATCATCATCATCT
1386416 CCA
1 CCA
1386419 CCACCACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.24, C:0.45, G:0.00, T:0.30
Consensus pattern (15 bp):
CCATCATCATCATCT
Found at i:1386422 original size:3 final size:3
Alignment explanation
Indices: 1386416--1386443 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1386406 ATCATCATCT
1386416 CCA CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA C
1386444 TGTCACAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:1390448 original size:30 final size:30
Alignment explanation
Indices: 1390412--1390472 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1390402 CTAATTCTTG
*
1390412 CTCTCTTTCTCACTCTGCAGGAGCACGTAA
1 CTCTCTTTCTCAATCTGCAGGAGCACGTAA
1390442 CTCTCTTTCTCAATCTGCAGGAGCACGTAA
1 CTCTCTTTCTCAATCTGCAGGAGCACGTAA
1390472 C
1 C
1390473 AATGGTAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.21, C:0.33, G:0.16, T:0.30
Consensus pattern (30 bp):
CTCTCTTTCTCAATCTGCAGGAGCACGTAA
Found at i:1392476 original size:28 final size:28
Alignment explanation
Indices: 1392444--1392525 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
1392434 AATCTTTGTT
* * *
1392444 AACATTATG-TTGTCGAGTCAGTGCTTGA
1 AACATTATGCTGGT-GAGTCAATGCTTAA
1392472 AACATTATGCTGGTGAGTCAATGCTTAA
1 AACATTATGCTGGTGAGTCAATGCTTAA
* *
1392500 AACATTATGCTAGTGAGCCAATGCTT
1 AACATTATGCTGGTGAGTCAATGCTT
1392526 GAAAGCAACG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 45 0.94
29 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (28 bp):
AACATTATGCTGGTGAGTCAATGCTTAA
Found at i:1392757 original size:3 final size:3
Alignment explanation
Indices: 1392749--1392796 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1392739 TACCCAGTTA
1392749 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1392797 TTGCTTCTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1393339 original size:9 final size:9
Alignment explanation
Indices: 1393325--1393355 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1393315 GCATCTTCAA
1393325 TAAATAAAT
1 TAAATAAAT
1393334 TAAATAAAT
1 TAAATAAAT
1393343 TAAATTAAAT
1 TAAA-TAAAT
1393353 TAA
1 TAA
1393356 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAATAAAT
Found at i:1394009 original size:36 final size:35
Alignment explanation
Indices: 1393969--1394037 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
1393959 TTGGTTTTTC
*
1393969 GGAAAATGAATTACTAGAATTTGAATTATTGGAACT
1 GGAAAATGAACTACTAGAATTTGAATTA-TGGAACT
*
1394005 GGAAAATGAACTACTGGAATTTGAATTATGGAA
1 GGAAAATGAACTACTAGAATTTGAATTATGGAA
1394038 AATGAATTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 5 0.16
36 26 0.84
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (35 bp):
GGAAAATGAACTACTAGAATTTGAATTATGGAACT
Found at i:1394043 original size:14 final size:15
Alignment explanation
Indices: 1394002--1394047 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1393992 AATTATTGGA
*
1394002 ACTGGAAAATGAACT
1 ACTGGAAAATGAATT
**
1394017 ACTGGAATTTGAATT
1 ACTGGAAAATGAATT
1394032 A-TGGAAAATGAATT
1 ACTGGAAAATGAATT
1394046 AC
1 AC
1394048 ATTTCTGAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (15 bp):
ACTGGAAAATGAATT
Found at i:1394434 original size:23 final size:24
Alignment explanation
Indices: 1394390--1394453 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
1394380 AGTGTTATAT
*
1394390 TATATTTTAAAAATATTAATT-AA
1 TATATTTTAAATATATTAATTAAA
* *
1394413 TATATTTTAAATATCTTTATTAAAA
1 TATATTTTAAATATATTAATT-AAA
*
1394438 TATAATTTAAATATAT
1 TATATTTTAAATATAT
1394454 AAATAATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 18 0.53
25 16 0.47
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TATATTTTAAATATATTAATTAAA
Found at i:1394502 original size:29 final size:29
Alignment explanation
Indices: 1394444--1394608 Score: 103
Period size: 29 Copynumber: 5.7 Consensus size: 29
1394434 AAAATATAAT
1394444 TTAAATATATAAA-TAATATTAT-TCATTA
1 TTAAATATATAAATTAATATTATAT-ATTA
**
1394472 TTAAATATATAAATTTTTATTATATATTA
1 TTAAATATATAAATTAATATTATATATTA
*
1394501 TTAAA-ATAAAAATATAATATCT-TATATTA
1 TTAAATATATAAAT-TAATAT-TATATATTA
** * *
1394530 TTATAATATAATTGATT-ATTTTATATAATA
1 TTA-AATAT-ATAAATTAATATTATATATTA
* * *
1394560 TTATAA-ATATTATATTATTA-TAAATATTA
1 TTA-AATATA-TAAATTAATATTATATATTA
* *
1394589 ATAAATAAATAAA-TAATATT
1 TTAAATATATAAATTAATATT
1394609 TTGATGAAAA
Statistics
Matches: 105, Mismatches: 20, Indels: 24
0.70 0.13 0.16
Matches are distributed among these distances:
27 4 0.04
28 27 0.26
29 48 0.46
30 20 0.19
31 3 0.03
32 3 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (29 bp):
TTAAATATATAAATTAATATTATATATTA
Found at i:1394562 original size:15 final size:16
Alignment explanation
Indices: 1394524--1394582 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 16
1394514 ATAATATCTT
1394524 ATATTATTATAATATA
1 ATATTATTATAATATA
*
1394540 ATTGATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
1394557 ATATTA-TA-AATATT
1 ATATTATTATAATATA
1394571 ATATTATTATAA
1 ATATTATTATAA
1394583 ATATTAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 11 0.31
15 6 0.17
16 4 0.11
17 8 0.23
18 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:1394573 original size:17 final size:17
Alignment explanation
Indices: 1394553--1394588 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1394543 GATTATTTTA
1394553 TATAATATTATAAATAT
1 TATAATATTATAAATAT
*
1394570 TATATTATTATAAATAT
1 TATAATATTATAAATAT
1394587 TA
1 TA
1394589 ATAAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATAATATTATAAATAT
Done.