Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009081.1 Hibiscus syriacus cultivar Beakdansim tig00112523_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: 1718667
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1162894 original size:41 final size:41
Alignment explanation
Indices: 1162804--1162901 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 41
1162794 GAGATTTTGG
* * ***
1162804 ACTATCGCATTGCGATTTACATATTCGCGTTGCGATTTTGG
1 ACTATCGCATTGCGATTTACATATTCGCATTGCGATGTCCA
1162845 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCA
1 ACTATCGCATTGCGATTTACATATTCGCATTGCGAT-GTCCA
* *
1162887 AGT-TCGCATTACGAT
1 ACTATCGCATTGCGAT
1162902 AATCGAAGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
41 46 0.94
42 3 0.06
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.36
Consensus pattern (41 bp):
ACTATCGCATTGCGATTTACATATTCGCATTGCGATGTCCA
Found at i:1174108 original size:13 final size:13
Alignment explanation
Indices: 1174090--1174114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1174080 CGACCTAGCA
1174090 TCTTATTCTAATC
1 TCTTATTCTAATC
1174103 TCTTATTCTAAT
1 TCTTATTCTAAT
1174115 TTTTTTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (13 bp):
TCTTATTCTAATC
Found at i:1174517 original size:67 final size:68
Alignment explanation
Indices: 1174405--1174547 Score: 182
Period size: 67 Copynumber: 2.1 Consensus size: 68
1174395 GTTATCTATT
* * * *
1174405 TTTATCTTCATTCTCTTCTAACTTCTGAAACTAATCAAAACTGATATTCAAATTAATTTGACCTT
1 TTTATTTTCATTCTCTTCTAACTTCCGAAACCAATCAAAACTGATATTCAAATTAATTTGACATT
1174470 AAA
66 AAA
* * *
1174473 TTTATTTTCATTTTCTT-TAAAC-TCCGAAACCAATCAAGATTGATATTCAAATTAATTTGACAT
1 TTTATTTTCATTCTCTTCT-AACTTCCGAAACCAATCAAAACTGATATTCAAATTAATTTGACAT
*
1174536 TATA
65 TAAA
*
1174540 TTTTTTTT
1 TTTATTTT
1174548 TTAAATATAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
67 47 0.72
68 18 0.28
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (68 bp):
TTTATTTTCATTCTCTTCTAACTTCCGAAACCAATCAAAACTGATATTCAAATTAATTTGACATT
AAA
Found at i:1176926 original size:2 final size:2
Alignment explanation
Indices: 1176919--1176981 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1176909 AACCCACAAT
1176919 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1176961 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1176982 TACGGGAAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1177291 original size:14 final size:14
Alignment explanation
Indices: 1177272--1177298 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1177262 ATTTTTAAAT
1177272 TTAAATTATTTATC
1 TTAAATTATTTATC
1177286 TTAAATTATTTAT
1 TTAAATTATTTAT
1177299 ATATTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAATTATTTATC
Found at i:1183212 original size:22 final size:22
Alignment explanation
Indices: 1183187--1183230 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1183177 ATGTTGACGT
1183187 AACGATCAACAATGGTTGATAA
1 AACGATCAACAATGGTTGATAA
1183209 AACGATCAACAATGGTTGATAA
1 AACGATCAACAATGGTTGATAA
1183231 CGTATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (22 bp):
AACGATCAACAATGGTTGATAA
Found at i:1185215 original size:31 final size:31
Alignment explanation
Indices: 1185137--1185218 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
1185127 ATATTAATTT
*
1185137 TTAAAAAATTATAAAAGAATCTTTAAATACA
1 TTAAAAAATTATAAAATAATCTTTAAATACA
*** * * *
1185168 TTAATTTATTACAAAATAATCTTTATATTCA
1 TTAAAAAATTATAAAATAATCTTTAAATACA
*
1185199 TTAAACAATTATAAAATAAT
1 TTAAAAAATTATAAAATAAT
1185219 TCTTAGATTT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (31 bp):
TTAAAAAATTATAAAATAATCTTTAAATACA
Found at i:1185233 original size:31 final size:31
Alignment explanation
Indices: 1185137--1185233 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 31
1185127 ATATTAATTT
* * * * *
1185137 TTAAAAAATTATAAAAGAATCTTTAAATACA
1 TTAAACAATTACAAAATAATCTTTAGATTCA
*** *
1185168 TTAATTTATTACAAAATAATCTTTATATTCA
1 TTAAACAATTACAAAATAATCTTTAGATTCA
* *
1185199 TTAAACAATTATAAAATAAT-TCTTAGATTTA
1 TTAAACAATTACAAAATAATCT-TTAGATTCA
1185230 TTAA
1 TTAA
1185234 GTTATGATAA
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 1 0.02
31 51 0.98
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (31 bp):
TTAAACAATTACAAAATAATCTTTAGATTCA
Found at i:1186015 original size:2 final size:2
Alignment explanation
Indices: 1186008--1186038 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1185998 CATATTTCTT
1186008 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 T
1186039 CTACTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1189037 original size:12 final size:12
Alignment explanation
Indices: 1189004--1189038 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1188994 TATTTCTCTA
*
1189004 ATTAAAGACCAG
1 ATTAAAGACTAG
1189016 ATTAAAGACTAG
1 ATTAAAGACTAG
1189028 ATTAAAGACTA
1 ATTAAAGACTA
1189039 AATATCCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.23
Consensus pattern (12 bp):
ATTAAAGACTAG
Found at i:1189211 original size:15 final size:15
Alignment explanation
Indices: 1189159--1189210 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
1189149 ATATTTAGTT
*
1189159 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
1189174 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
*
1189189 GGGCGGGTGGATGCG
1 GGGCGGGCGGATGCG
1189204 GGGCGGG
1 GGGCGGG
1189211 TAATGTCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.06, C:0.15, G:0.69, T:0.10
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:1200228 original size:42 final size:42
Alignment explanation
Indices: 1200168--1200266 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
1200158 CCCCCCACTT
* * *
1200168 CGAGAGCCATCACCTGATCGAGCCGATTCTATAACTCCACAC
1 CGAGAGCCATCACCTGATCGAGCCAATTATACAACTCCACAC
* *
1200210 TGAGAGCCATCACCTGATCGAGCCAATTATACACCTCCACAC
1 CGAGAGCCATCACCTGATCGAGCCAATTATACAACTCCACAC
1200252 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
1200267 ACTCCATGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.29, C:0.36, G:0.16, T:0.18
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCAATTATACAACTCCACAC
Found at i:1200409 original size:21 final size:21
Alignment explanation
Indices: 1200385--1200430 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1200375 GGGGAGTTAT
*
1200385 GTGATGAGGTC-AGTACTTTGC
1 GTGATGAGGTCGA-TACTTTAC
1200406 GTGATGAGGTCGATACTTTAC
1 GTGATGAGGTCGATACTTTAC
1200427 GTGA
1 GTGA
1200431 CGACAATGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.22, C:0.13, G:0.33, T:0.33
Consensus pattern (21 bp):
GTGATGAGGTCGATACTTTAC
Found at i:1200471 original size:21 final size:21
Alignment explanation
Indices: 1200447--1200497 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1200437 TGGTGCATGG
1200447 CGTGATGAGGTA-CGGT-CTTTA
1 CGTGATGAGGTATC--TACTTTA
*
1200468 CGTGGTGAGGTATCTACTTTA
1 CGTGATGAGGTATCTACTTTA
1200489 CGTGATGAG
1 CGTGATGAG
1200498 ATAGCCGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.20, C:0.14, G:0.33, T:0.33
Consensus pattern (21 bp):
CGTGATGAGGTATCTACTTTA
Found at i:1200621 original size:4 final size:4
Alignment explanation
Indices: 1200612--1200657 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
1200602 ATTTTCGACA
* * * *
1200612 TTAT TTAT TTAT TTAT TTAT TTAC TAAT TTAT ATAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1200658 TTAGCGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:1200834 original size:21 final size:21
Alignment explanation
Indices: 1200802--1200899 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
1200792 GATTCACCTG
*
1200802 TCATCATTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1200823 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
1200844 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1200865 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
1200886 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
1200900 CCCGATTCAT
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 1 0.01
21 70 0.97
22 1 0.01
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1202747 original size:18 final size:18
Alignment explanation
Indices: 1202724--1202759 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1202714 AAGCCGGTTG
*
1202724 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1202742 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1202760 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1205088 original size:24 final size:24
Alignment explanation
Indices: 1205037--1205088 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1205027 ATCTAAGTAT
* * *
1205037 TGACTAAGATCAAAGTCCGAGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
1205061 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
1205085 TGAC
1 TGAC
1205089 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:1205848 original size:14 final size:15
Alignment explanation
Indices: 1205812--1205849 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1205802 GAAATCATTG
1205812 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1205827 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1205842 AAAAATTA
1 AAAAATTA
1205850 GAGATAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1206032 original size:20 final size:20
Alignment explanation
Indices: 1206007--1206074 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
1205997 AAATAAAAGT
1206007 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
1206027 TGTTGCG-AATTCGAAAA-TCG
1 TGTTGCGAAATT--AAAATTCG
* * **
1206047 AGTTACGAAAACAAAATTCG
1 TGTTGCGAAATTAAAATTCG
1206067 TGTTGCGA
1 TGTTGCGA
1206075 TTTAGAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 8 0.21
20 24 0.63
21 6 0.16
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:1206063 original size:40 final size:39
Alignment explanation
Indices: 1206019--1206115 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 39
1206009 TTGCGAAATT
*
1206019 AAAATTCGTGTTGCGAATTCGAAAATCGAGTTACGAAAA
1 AAAATTCGTGTTGCGAATTAGAAAATCGAGTTACGAAAA
* **
1206058 CAAAATTCGTGTTGCGATTTAGAAAATCTTGTTACGAAAA
1 -AAAATTCGTGTTGCGAATTAGAAAATCGAGTTACGAAAA
1206098 AGAAACTT-GTGTTGCGAA
1 A-AAA-TTCGTGTTGCGAA
1206116 AAAGAAATCC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
39 1 0.02
40 47 0.94
41 2 0.04
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (39 bp):
AAAATTCGTGTTGCGAATTAGAAAATCGAGTTACGAAAA
Found at i:1206101 original size:20 final size:20
Alignment explanation
Indices: 1206078--1206122 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1206068 GTTGCGATTT
1206078 AGAAAATCT-TGTTACGAAAA
1 AGAAAAT-TGTGTTACGAAAA
* *
1206098 AGAAACTTGTGTTGCGAAAA
1 AGAAAATTGTGTTACGAAAA
1206118 AGAAA
1 AGAAA
1206123 TCCGCGTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.49, C:0.09, G:0.20, T:0.22
Consensus pattern (20 bp):
AGAAAATTGTGTTACGAAAA
Found at i:1208250 original size:134 final size:135
Alignment explanation
Indices: 1207964--1208298 Score: 465
Period size: 135 Copynumber: 2.5 Consensus size: 135
1207954 GAAACGGAGT
* * * *
1207964 AACATAATGATCATGATCATGAAAACGAATATCCCACACTACCAAAAAGACCACCATCACCATCG
1 AACATAATGATCATGATAAAGAAGACGAAAATCCCACACTACCAAAAAGACCACCATCACCATCG
* *
1208029 GTTGCGAGGAGGACCACATTGTTAACGATGAGACAGTACCCTGAAATGGAGAATTCTGAGCAGGG
66 GTTGCGAGGAGGACCACATTGTAAACGATGAGACAGTACCCTGAAATGGAGAATTCCGAGCAGGG
*
1208094 TTAGG
131 TAAGG
* * * *
1208099 AACATAATGATCATGATAAAGAAGGCGAACATCCCACACTACCGAAAAGACCACCATCACCGTCG
1 AACATAATGATCATGATAAAGAAGACGAAAATCCCACACTACCAAAAAGACCACCATCACCATCG
* * *
1208164 GTTGCGAGGAGGACCGCGTTG-AAACGATGAGGCAGTACCCTGAAATGGAGAATTCCGAGCAGGG
66 GTTGCGAGGAGGACCACATTGTAAACGATGAGACAGTACCCTGAAATGGAGAATTCCGAGCAGGG
1208228 TAAGG
131 TAAGG
* * * *
1208233 TACATAACGATCATGATAAAAGAAGTCCAAAATCCCACACTTGGACCAAAAAGACCACCATCACC
1 AACATAATGATCATGAT-AAAGAAGACGAAAATCCCACAC-T--ACCAAAAAGACCACCATCACC
1208298 A
62 A
1208299 ATACAGACGA
Statistics
Matches: 176, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
134 59 0.34
135 96 0.55
136 1 0.01
138 20 0.11
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (135 bp):
AACATAATGATCATGATAAAGAAGACGAAAATCCCACACTACCAAAAAGACCACCATCACCATCG
GTTGCGAGGAGGACCACATTGTAAACGATGAGACAGTACCCTGAAATGGAGAATTCCGAGCAGGG
TAAGG
Found at i:1208675 original size:189 final size:189
Alignment explanation
Indices: 1208348--1208775 Score: 525
Period size: 189 Copynumber: 2.2 Consensus size: 189
1208338 CATTACAAGG
* * * ** * **
1208348 AACATAATGATCATGATAAAGAAAACGAACAATCTGCACCAAGACCATCGAGATTACCATCAGTG
1 AACATAATGATCATGATAAAGAAAACGAACAATCCGCACCAAGACCATCAAGATCAAAACCAGCA
* * * * *
1208413 TTACCAACGATAACGACGAAGGTGAGAATGAGCGTGTCGATGGCGAATTTGAAGTTGTGTTCGGA
66 TTACCAACAACAACGACGAAGATGAGAATGAGCGTGTCGATGACGAATTTGAAGTTGTGCTCGGA
*
1208478 AATGGAGGATTCTGAGCAGGGTAAGAAACAAAAACCAACGGATTCAACACATCATGACA
131 AATGGAGGATTCTGAGCAAGGTAAGAAACAAAAACCAACGGATTCAACACATCATGACA
* * * * *
1208537 AACATAGTGATCATGATAAAGATATCGATCAATCCGCACCAAGACTATCAAGATCAAAACCAGCA
1 AACATAATGATCATGATAAAGAAAACGAACAATCCGCACCAAGACCATCAAGATCAAAACCAGCA
* * *
1208602 TTACCAGCAACAATGACGATGATGAGAATGAGC-TCGTCGATGACGAATTTGAAGTTGTGCTCGG
66 TTACCAACAACAACGACGAAGATGAGAATGAGCGT-GTCGATGACGAATTTGAAGTTGTGCTCGG
* * *
1208666 AAATGGAGGATTCTGAGCAAGGTAAGAAACAGAAACCAATGGATTCAACACGTCATGACAA
130 AAATGGAGGATTCTGAGCAAGGTAAGAAACAAAAACCAACGGATTCAACACATCATGAC-A
* * * * * * *
1208727 GGAACGTAAAGACCATGATAAAGAAATCAAACAATCTGCACCCAGACCA
1 --AACATAATGATCATGATAAAGAAAACGAACAATCCGCACCAAGACCA
1208776 CCACCGTTAC
Statistics
Matches: 200, Mismatches: 35, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
188 1 0.00
189 161 0.81
190 1 0.00
192 37 0.19
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (189 bp):
AACATAATGATCATGATAAAGAAAACGAACAATCCGCACCAAGACCATCAAGATCAAAACCAGCA
TTACCAACAACAACGACGAAGATGAGAATGAGCGTGTCGATGACGAATTTGAAGTTGTGCTCGGA
AATGGAGGATTCTGAGCAAGGTAAGAAACAAAAACCAACGGATTCAACACATCATGACA
Found at i:1209061 original size:165 final size:161
Alignment explanation
Indices: 1208772--1209079 Score: 458
Period size: 165 Copynumber: 1.9 Consensus size: 161
1208762 CTGCACCCAG
* *
1208772 ACCACCACCGTTACCAGCAACAAAGACAACAATGAAATGTTCAGAAATGGAGGATTCTGATCAAG
1 ACCACCACCGTTACCACCAACAAAGACAACAATGAAATGTTCAGAAATGGAGGATTCCGATCAAG
*
1208837 GTGAGAAAAAGGAACCAACGGAATCAACACATGATTACAAGGAAGAACATAAAGATGATGATAAA
66 GTGAGAAAAAGGAACCAACGGAATCAACACATGATGACAA-GAAGAACATAAAGATGATG---AA
*
1208902 GAAAGTGAACAACCCGAGCCAAGGCCATCAGGATC
127 GAAAGGGAACAACCCGAGCCAAGGCCATCAGGATC
* * *
1208937 ACCATCACCGTTACCACCAACAATGACAACAATGGAATGTTCAGAAATGGAGGATTCCGATCAAG
1 ACCACCACCGTTACCACCAACAAAGACAACAATGAAATGTTCAGAAATGGAGGATTCCGATCAAG
* *
1209002 GTGAGAAAAAGGAACCAACGGATTCAACACATGATGA-AA-AGGAACATAAAGATGATGATGAAG
66 GTGAGAAAAAGGAACCAACGGAATCAACACATGATGACAAGAAGAACAT-AA-A-GATGATGAAG
1209065 AAAGGGAACAACCCG
128 AAAGGGAACAACCCG
1209080 CACCAGGATC
Statistics
Matches: 131, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
162 24 0.18
163 2 0.02
164 3 0.02
165 102 0.78
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (161 bp):
ACCACCACCGTTACCACCAACAAAGACAACAATGAAATGTTCAGAAATGGAGGATTCCGATCAAG
GTGAGAAAAAGGAACCAACGGAATCAACACATGATGACAAGAAGAACATAAAGATGATGAAGAAA
GGGAACAACCCGAGCCAAGGCCATCAGGATC
Found at i:1209297 original size:129 final size:129
Alignment explanation
Indices: 1209114--1209431 Score: 429
Period size: 129 Copynumber: 2.5 Consensus size: 129
1209104 CAGAAACAAC
* * * * *
1209114 GAGCTCGGAAACGGAGGACCATGATCAAGATAAGAAACATGAACCAACGGATTCAACAGATGATA
1 GAGCTTGGAAACGGAGGACCATGAGCAAGGTAAGAAACAGGAACCAACGGATTCAACACATGATA
* * * * * * *
1209179 AAGAAAGTGAACAACCGGCTCCAGGATCACCCTCTCCGTTACCGGAAACAACGACGATGAAGGA
66 AAGAAACTGAACAACCGGCGCCAGGATCACCATCACCGTTACCGGAAACAACAACGATAAACGA
* *
1209243 GAGCTTGGAAATGGAGGACCATGAGCAAGGTAAGAAACAGGAACCAACGGATTCAGCACATGATA
1 GAGCTTGGAAACGGAGGACCATGAGCAAGGTAAGAAACAGGAACCAACGGATTCAACACATGATA
* *
1209308 AAGAAACTGAACAACCGGCGCCAGGATCACCATCACCGTTACCGGCAACAGCAACGATAAACGA
66 AAGAAACTGAACAACCGGCGCCAGGATCACCATCACCGTTACCGGAAACAACAACGATAAACGA
* * * ** * *
1209372 GTGCTTGGAACCGAAGGATAATGAGCAAGGTAAGAAACAGGAACCAATGGATTTAACACA
1 GAGCTTGGAAACGGAGGACCATGAGCAAGGTAAGAAACAGGAACCAACGGATTCAACACA
1209432 ACATAACAAG
Statistics
Matches: 164, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
129 164 1.00
ACGTcount: A:0.40, C:0.22, G:0.25, T:0.13
Consensus pattern (129 bp):
GAGCTTGGAAACGGAGGACCATGAGCAAGGTAAGAAACAGGAACCAACGGATTCAACACATGATA
AAGAAACTGAACAACCGGCGCCAGGATCACCATCACCGTTACCGGAAACAACAACGATAAACGA
Found at i:1209709 original size:6 final size:6
Alignment explanation
Indices: 1209678--1209708 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1209668 CGACGGAGAG
*
1209678 GTCGAT GTCGAT GTCGAT GTCGAT GACGAT G
1 GTCGAT GTCGAT GTCGAT GTCGAT GTCGAT G
1209709 AAAGAGTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.16, G:0.35, T:0.29
Consensus pattern (6 bp):
GTCGAT
Found at i:1214478 original size:12 final size:12
Alignment explanation
Indices: 1214461--1214485 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1214451 AGGAGTTAGT
1214461 AAATGAATTTTG
1 AAATGAATTTTG
1214473 AAATGAATTTTG
1 AAATGAATTTTG
1214485 A
1 A
1214486 CTTGTCATAT
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
AAATGAATTTTG
Found at i:1215734 original size:21 final size:21
Alignment explanation
Indices: 1215701--1215770 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
1215691 TTCTACGCGA
* *
1215701 TCCTTCGGGACATATATGTGG
1 TCCTTTGGAACATATATGTGG
* ***
1215722 TCCTTTGGAACATTTCTACACGG
1 TCCTTTGGAACA--TATATGTGG
*
1215745 TCCTTTGGAAAATATATGTGG
1 TCCTTTGGAACATATATGTGG
1215766 TCCTT
1 TCCTT
1215771 CGGGACATTC
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
21 20 0.56
23 16 0.44
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (21 bp):
TCCTTTGGAACATATATGTGG
Found at i:1216034 original size:120 final size:120
Alignment explanation
Indices: 1215794--1216034 Score: 360
Period size: 120 Copynumber: 2.0 Consensus size: 120
1215784 ATGGCACTCA
* * * *
1215794 GTGCAAATTAGATGAGCTGTGGTGACAGCATTTGTGCACAACCTTAATACACTCATATAACTTAA
1 GTGCAAATTAGACGAGCTGTGGTGACAACATTTGTGCACAACCTCAATACACTCACATAACTTAA
* *
1215859 GTTCTCAGAAGTGTATCATGGGCAACTAAAAGACATAACCTAAAATAAACAGTGT
66 GTTCTCAGAAGTGTACCATCGGCAACTAAAAGACATAACCTAAAATAAACAGTGT
* * * * *
1215914 GTGCAAATTATACGAGTTGTGGTGACAACATTTGTGCACAACCTCAATGCACTCGCATACCTTAA
1 GTGCAAATTAGACGAGCTGTGGTGACAACATTTGTGCACAACCTCAATACACTCACATAACTTAA
*
1215979 GTTCTCAGAAGTGTACCA-CGGCAATTAAAAGACATAACCT-AAATAAACAGTGT
66 GTTCTCAGAAGTGTACCATCGGCAACTAAAAGACATAACCTAAAATAAACAGTGT
1216032 GTG
1 GTG
1216035 ATGTAATGTG
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
118 16 0.15
119 20 0.18
120 73 0.67
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (120 bp):
GTGCAAATTAGACGAGCTGTGGTGACAACATTTGTGCACAACCTCAATACACTCACATAACTTAA
GTTCTCAGAAGTGTACCATCGGCAACTAAAAGACATAACCTAAAATAAACAGTGT
Found at i:1230232 original size:12 final size:12
Alignment explanation
Indices: 1230215--1230251 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
1230205 ATTTGCCGGA
1230215 TTTTGTTTATTT
1 TTTTGTTTATTT
1230227 TTTTGTTTATGTT
1 TTTTGTTTAT-TT
1230240 TTTT-TTTATTT
1 TTTTGTTTATTT
1230251 T
1 T
1230252 GAGTTTAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 3 0.12
12 15 0.62
13 6 0.25
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (12 bp):
TTTTGTTTATTT
Found at i:1244193 original size:57 final size:57
Alignment explanation
Indices: 1244071--1244183 Score: 149
Period size: 57 Copynumber: 2.0 Consensus size: 57
1244061 TAATTATTTG
*
1244071 TAACTTTTAATAATAGAAGGACTTAAAAAACAACATCCTATATTAGAGATCATTTTA
1 TAACTTTTAATAATAGAAGGACTTAAAAAACAACATCCTATATTAGAGACCATTTTA
* * *
1244128 TAACTTTTAATAGTCGAAGGAC-TAAAAAACAACA-CTCTATAGTTGGGAGACCATTT
1 TAACTTTTAATAATAGAAGGACTTAAAAAACAACATC-CTATA-TT-AGAGACCATTT
1244184 GTGTATTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
55 1 0.02
56 17 0.35
57 22 0.45
58 9 0.18
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (57 bp):
TAACTTTTAATAATAGAAGGACTTAAAAAACAACATCCTATATTAGAGACCATTTTA
Found at i:1244347 original size:17 final size:18
Alignment explanation
Indices: 1244322--1244355 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1244312 TTTCTTAAAT
1244322 TATAAAAAATT-TAAAAG
1 TATAAAAAATTCTAAAAG
*
1244339 TATATAAAATTCTAAAA
1 TATAAAAAATTCTAAAA
1244356 AATCTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
TATAAAAAATTCTAAAAG
Found at i:1245680 original size:29 final size:29
Alignment explanation
Indices: 1245640--1245745 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 29
1245630 CTTTTTTATT
* * *
1245640 TAAGTACCTAAAATATTTTTTTATAAAAA
1 TAAGTACTTAAAGTATTTTTTTATCAAAA
* *
1245669 TAAGTAGTTAAAGTTATCTTTTTAGTCAAAA
1 TAAGTACTTAAAG-TATTTTTTTA-TCAAAA
* *
1245700 TAAGTACCTAAAGTATTTTTTGATCAAAA
1 TAAGTACTTAAAGTATTTTTTTATCAAAA
*
1245729 TAAGTATTTAAAGTATT
1 TAAGTACTTAAAGTATT
1245746 CAATTTTTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 31 0.48
30 17 0.27
31 16 0.25
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (29 bp):
TAAGTACTTAAAGTATTTTTTTATCAAAA
Found at i:1245872 original size:28 final size:28
Alignment explanation
Indices: 1245835--1245910 Score: 116
Period size: 28 Copynumber: 2.7 Consensus size: 28
1245825 GTTTGAATGG
* * *
1245835 TTTAGATACTTATTTTGACATAAAATAC
1 TTTAGGTACTTATTTTGACAAAAAATAA
*
1245863 TTTAGGTACTTATTTTAACAAAAAATAA
1 TTTAGGTACTTATTTTGACAAAAAATAA
1245891 TTTAGGTACTTATTTTGACA
1 TTTAGGTACTTATTTTGACA
1245911 CTGGTTTCGC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.43
Consensus pattern (28 bp):
TTTAGGTACTTATTTTGACAAAAAATAA
Found at i:1248464 original size:12 final size:12
Alignment explanation
Indices: 1248447--1248473 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1248437 CCTAAATTTC
1248447 AGACTGCTTCCT
1 AGACTGCTTCCT
1248459 AGACTGCTTCCT
1 AGACTGCTTCCT
1248471 AGA
1 AGA
1248474 ACGCTAGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (12 bp):
AGACTGCTTCCT
Found at i:1252042 original size:3 final size:3
Alignment explanation
Indices: 1252029--1252067 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1252019 TCCCGACTGA
1252029 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1252068 TTATCATGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1254763 original size:60 final size:60
Alignment explanation
Indices: 1254641--1254778 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
1254631 AACATAATGA
* * * * **
1254641 ATAGTCAAGTGG-TCATTTTGTAAATTTTAATAGTTGAAGAACTTAATAAAGCAATATTCT
1 ATAGTCAAG-GGACCATTTTATAAATTTTAATAGTCGAAGAACTTAATAAAACAATACCCT
* * * *
1254701 ATAGTTGAA-GGACCATTTTATAACTTTTAATAGTCGAAGGACTTAATAAAACATTACCCT
1 ATAG-TCAAGGGACCATTTTATAAATTTTAATAGTCGAAGAACTTAATAAAACAATACCCT
1254761 ATAGTCAAGGGACCATTT
1 ATAGTCAAGGGACCATTT
1254779 GCTTACTTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
59 5 0.08
60 56 0.88
61 3 0.05
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (60 bp):
ATAGTCAAGGGACCATTTTATAAATTTTAATAGTCGAAGAACTTAATAAAACAATACCCT
Found at i:1259236 original size:29 final size:29
Alignment explanation
Indices: 1259202--1259260 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1259192 CCTAAATTAA
*
1259202 TTTGATGTCATTGTTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
1259231 TTTGATGTTATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1259260 T
1 T
1259261 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.53
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1263915 original size:29 final size:29
Alignment explanation
Indices: 1263881--1263939 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1263871 CCTAAATTAA
1263881 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1263910 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1263939 T
1 T
1263940 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1267803 original size:23 final size:23
Alignment explanation
Indices: 1267777--1267821 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1267767 CACCACAGCT
*
1267777 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1267800 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1267822 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1267964 original size:25 final size:25
Alignment explanation
Indices: 1267936--1268004 Score: 129
Period size: 25 Copynumber: 2.8 Consensus size: 25
1267926 TATATATATA
1267936 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
1267961 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
*
1267986 TCCCGAATGACCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
1268005 CCCTCTACTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.19
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:1269418 original size:21 final size:21
Alignment explanation
Indices: 1269394--1269438 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1269384 TGTTGTTCGT
* *
1269394 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
1269415 TTGAATGGGTGCCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1269436 TTG
1 TTG
1269439 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1272888 original size:25 final size:25
Alignment explanation
Indices: 1272860--1272928 Score: 138
Period size: 25 Copynumber: 2.8 Consensus size: 25
1272850 TATATATATA
1272860 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
1272885 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
1272910 TCCCGAAGGACCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
1272929 CCCTCTACTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:1274362 original size:21 final size:21
Alignment explanation
Indices: 1274338--1274382 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1274328 TGTTGTTCGT
* *
1274338 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
1274359 TTGAATGGGTGCCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1274380 TTG
1 TTG
1274383 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1282247 original size:3 final size:3
Alignment explanation
Indices: 1282239--1282934 Score: 593
Period size: 3 Copynumber: 231.7 Consensus size: 3
1282229 TTTAATCTCC
* * * * *
1282239 TCT TCT TCT TCT TCT CCT TCT CCT TCT CCT TCT TCT CCT TCT CCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * *
1282287 TC- CCT TCT TC- TCAT TCT TCT CCT TCT CCT TCT TCT CCT TCT CCT
1 TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * *
1282331 TCT CCT TCT CCT TCT CCT TC- TCAT TCTT TCT TCT TCT CCT TCT CCT
1 TCT TCT TCT TCT TCT TCT TCT TC-T TC-T TCT TCT TCT TCT TCT TCT
* * * * * * *
1282377 CCT TCT CCT TCT CCT TCT TCT CCT TCT CCT TCT TCT CCT TCT CCT TC-
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
1282424 TCT CCT TCT CCT TCT TCT CCT TCCT TCT TCT TCT CCT TCT T-T CTCTT
1 TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT -TC-T
* * * * *
1282471 TCT TCT TCT TCT CCT TCT CTCT CCT TCT TCT CCT TCT CCT CCT TCT
1 TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * * * * * * * *
1282517 CCT CCT TCT CCT CCT TCT CCT CCT TCT CCT CCT TCT CCT CCT TCT CCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * * * * *
1282565 CCT TCT CCT CCT TCT CCT CCT TCT CCT TCT TCT CCT TCT TCT CCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * *
1282613 TCT CCT TCT TCT CCT TCT TCT TCT CCT TCT CCT TCCT TCT CCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT
* * * * * *
1282659 CCT CCT TC- TCT CCT TCT TCT CCT TCT TCT TCT TCT CCT TCT TCT CCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * *
1282706 TCT TCT CCT TCT TCT CCT TCT TCT CCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
1282754 TCT TCT TC- TCT TCT TC- TCT TCT TTT TCT TCT TCTT TCT CCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT
* *
1282798 TCT TCT CCT TC- TCT TCT TCTT TCT TCT TC- TCT TCT TCT TCT CCT
1 TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT
* *
1282842 TCT TCT CCT TCT TCT CCT TCT TCT CTCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT
1282888 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1282935 ACGCTAAAAG
Statistics
Matches: 554, Mismatches: 119, Indels: 40
0.78 0.17 0.06
Matches are distributed among these distances:
2 18 0.03
3 508 0.92
4 27 0.05
5 1 0.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (3 bp):
TCT
Found at i:1310560 original size:13 final size:13
Alignment explanation
Indices: 1310542--1310567 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1310532 GATCTGTCTC
1310542 GTCGCATTTACAA
1 GTCGCATTTACAA
1310555 GTCGCATTTACAA
1 GTCGCATTTACAA
1310568 CCTTATTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
GTCGCATTTACAA
Found at i:1310628 original size:19 final size:20
Alignment explanation
Indices: 1310605--1310649 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1310595 TTATATTTTT
1310605 TAAAATAATTTAAAAATAAA
1 TAAAATAATTTAAAAATAAA
** *
1310625 -AAAATCGTTTATAAATAAA
1 TAAAATAATTTAAAAATAAA
1310644 TAAAAT
1 TAAAAT
1310650 TCATTAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
TAAAATAATTTAAAAATAAA
Found at i:1316780 original size:33 final size:33
Alignment explanation
Indices: 1316738--1316804 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1316728 TATCTAAGGA
1316738 TGACAATTTAACTCATATTTAAGGATGGTAATT
1 TGACAATTTAACTCATATTTAAGGATGGTAATT
*
1316771 TGACAATTTAACTCATATTTAAGGATTGTAATT
1 TGACAATTTAACTCATATTTAAGGATGGTAATT
1316804 T
1 T
1316805 AACCCGAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (33 bp):
TGACAATTTAACTCATATTTAAGGATGGTAATT
Found at i:1319318 original size:58 final size:58
Alignment explanation
Indices: 1319249--1319388 Score: 169
Period size: 58 Copynumber: 2.4 Consensus size: 58
1319239 AGTCGAGTAC
* * *
1319249 CATTTTATAACTTTTAATAGTTGAGGAACTCAACAAA-CAACACTCC-ATAGTCGAAGGAT
1 CATTTTGTAACTTTTAATAGTCGAAGAACTCAACAAAGCAACAC-CCTATAGTCG--GGAT
* * *
1319308 TA-TTTGTAACTTTTAATAGTCGAAGAACTCAATAAAGCAATACCCTATAGTCGGGAT
1 CATTTTGTAACTTTTAATAGTCGAAGAACTCAACAAAGCAACACCCTATAGTCGGGAT
*
1319365 CATTTTGTAATTTTTAATAGTCGA
1 CATTTTGTAACTTTTAATAGTCGA
1319389 GAGACTTAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
57 5 0.07
58 52 0.74
59 13 0.19
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (58 bp):
CATTTTGTAACTTTTAATAGTCGAAGAACTCAACAAAGCAACACCCTATAGTCGGGAT
Found at i:1326100 original size:30 final size:29
Alignment explanation
Indices: 1326051--1326118 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
1326041 TATATGTATC
*
1326051 ATATATCATGTCATTATCTTA-AGTGACATG
1 ATATAT-ATGTCATAATCTTATA-TGACATG
* *
1326081 TTATATATGATCATAATCTTATATGATATG
1 ATATATATG-TCATAATCTTATATGACATG
1326111 ATATATAT
1 ATATATAT
1326119 TATATTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 3 0.09
30 28 0.88
31 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (29 bp):
ATATATATGTCATAATCTTATATGACATG
Found at i:1328492 original size:184 final size:184
Alignment explanation
Indices: 1328277--1328687 Score: 431
Period size: 185 Copynumber: 2.2 Consensus size: 184
1328267 AAGCCGTCAA
* * * *
1328277 TTATAAAGGTAAAAAGTATGGACTATTTTATAAAATTTA-AAAA-TTATG-GGCCCTTAGTTATA
1 TTATAAAAGTAAAAAGTAGGGACTATTTTATAAAA-TTAGAAAAGTGA-GAGACCCTTAGTTATA
* * *
1328339 AACCTCGA-TCGAAAACTCAAAAAATA-TCTTATAGAACGAAAATATATTATATTATTTTTGAAA
64 AACCTCGAGT-GAAAACTC-AAAAATAGCCTTATAGAACGAAAATAAACTATATTA-TTTTG-AA
* **
1328402 AAACTAATGTAATATTACATTAATGAACCATAG-AAAATAATTAAATTATAGCCCCTTAG
125 AAACTAATGTAATATCACATTAACAAACCATAGAAAAATAATTAAATTATAGCCCCTTAG
* * *
1328461 TTATAAAAGTAGAATGTAGGGACTATTTTATAAAATTAGAAAAGTGAGAGATCCTTAGTTATAAA
1 TTATAAAAGTAAAAAGTAGGGACTATTTTATAAAATTAGAAAAGTGAGAGACCCTTAGTTATAAA
* * * * * *
1328526 TCTTGAGTGAAAACTCAAAACTAGGCCTTATAGAACGAAAATAAACTATGTTATTTTGAACAATT
66 CCTCGAGTGAAAACTCAAAAATA-GCCTTATAGAACGAAAATAAACTATATTATTTTGAAAAACT
* * * *** * *
1328591 AATTTAATATCACATTAACAAATCATAGAAAAATGATTAAATTATAGTTTCTCAA
130 AATGTAATATCACATTAACAAACCATAGAAAAATAATTAAATTATAGCCCCTTAG
* * * *
1328646 TTATAAAAATAAAAAATAAGGATTATTTTATAAAATTA-AAAA
1 TTATAAAAGTAAAAAGTAGGGACTATTTTATAAAATTAGAAAA
1328688 CTTTAGGGCC
Statistics
Matches: 187, Mismatches: 33, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
183 3 0.02
184 74 0.40
185 85 0.45
186 25 0.13
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (184 bp):
TTATAAAAGTAAAAAGTAGGGACTATTTTATAAAATTAGAAAAGTGAGAGACCCTTAGTTATAAA
CCTCGAGTGAAAACTCAAAAATAGCCTTATAGAACGAAAATAAACTATATTATTTTGAAAAACTA
ATGTAATATCACATTAACAAACCATAGAAAAATAATTAAATTATAGCCCCTTAG
Found at i:1330438 original size:20 final size:19
Alignment explanation
Indices: 1330413--1330451 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1330403 TAAATTATGT
1330413 TTAAATAATTGTTTTAGTCA
1 TTAAATAA-TGTTTTAGTCA
*
1330433 TTAAATTATGTTTTAGTCA
1 TTAAATAATGTTTTAGTCA
1330452 CTAACTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
TTAAATAATGTTTTAGTCA
Found at i:1341896 original size:64 final size:63
Alignment explanation
Indices: 1341821--1341941 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 63
1341811 ATTGTTCAAG
* * *
1341821 GTGTATCGATGCACAAGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATACCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATACCATCA
* *
1341885 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAATA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATA
1341942 GAATTTATGC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
63 17 0.33
64 35 0.67
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATACCATCA
Found at i:1341960 original size:63 final size:64
Alignment explanation
Indices: 1341829--1341982 Score: 168
Period size: 63 Copynumber: 2.4 Consensus size: 64
1341819 AGGTGTATCG
* * * * * * * *
1341829 ATGCACAAGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATACCATCAGTGTATCG
1 ATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACAATCAGTGCACCA
* * *
1341893 ATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATACAAACATCGAATAGAATTTA-TGCACCA
1 ATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACAA-TCAGTGCACCA
* *
1341956 ATGCATAAATAGTGCATCGATGCACCC
1 ATGCACAAGTAGTGCATCGATGCACCC
1341983 GTCAAGGGAT
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
63 47 0.62
64 29 0.38
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (64 bp):
ATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACAATCAGTGCACCA
Found at i:1342655 original size:26 final size:24
Alignment explanation
Indices: 1342626--1342677 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
1342616 GATTATTTGA
*
1342626 ATATGTAGCATAAACTATATATATAT
1 ATATATAG-ATAAACTATATAT-TAT
* *
1342652 ATATATAGGTAAATTATATATTAT
1 ATATATAGATAAACTATATATTAT
1342676 AT
1 AT
1342678 GATTTAAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 5 0.22
25 11 0.48
26 7 0.30
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (24 bp):
ATATATAGATAAACTATATATTAT
Found at i:1343583 original size:23 final size:23
Alignment explanation
Indices: 1343543--1343601 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
1343533 ATCTTATATC
* *
1343543 GCACTTCGGAGCATTTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
* * *
1343566 GCACTACGGTGCAATTCTATGTG
1 GCACTTCGGTGCAATTCTACGCG
1343589 GCACTTCGGTGCA
1 GCACTTCGGTGCA
1343602 TTTATACGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:1348176 original size:18 final size:18
Alignment explanation
Indices: 1348127--1348178 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 18
1348117 TAATATTTTT
* * *
1348127 TAATTAAAAAATAGTTTA
1 TAATTATAAAATAATATA
*
1348145 TAATTAATTTAAATAATATA
1 TAATT-A-TAAAATAATATA
1348165 TAATTATAAAATAA
1 TAATTATAAAATAA
1348179 AAATTTTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 12 0.44
19 2 0.07
20 13 0.48
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TAATTATAAAATAATATA
Found at i:1348283 original size:187 final size:185
Alignment explanation
Indices: 1347933--1348296 Score: 604
Period size: 187 Copynumber: 2.0 Consensus size: 185
1347923 ATAAAAATTA
1347933 AATATTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAATAAAAAAT
1 AATATTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAATAAAAAAT
*
1347998 TCAGATAAATTTTTTAATTAATTAATATTGATTAGGTTTAAAAGTTATTGGATCTTAAATTATTA
66 TCAGATAAATTTTTTAATTAATTAATATTGATTAGGTTTAAAAGTTATTGAATCTTAAATTATTA
* * * *
1348063 ATTGAGTTTTAAATGGTTTGGGCTTATCCCATATGTTATATATAATAATATATTT
131 ATTAAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTACATATAATAATATATTT
*
1348118 AATATTTTTTAATT-AAAAAATAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AATA-TTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAATTAT-AAATAAAAA
* * * *
1348182 TTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGAATCTTAAATTA
64 ATTCAGATAAATTTTTTAATTAATTAATATTGA-TTAGGTTTAAAAGTTATTGAATCTTAAATTA
1348247 TTAATTAAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTACATATAATA
128 TTAATTAAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTACATATAATA
1348297 TATTTAAAAT
Statistics
Matches: 166, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
185 43 0.26
186 47 0.28
187 76 0.46
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (185 bp):
AATATTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAATAAAAAAT
TCAGATAAATTTTTTAATTAATTAATATTGATTAGGTTTAAAAGTTATTGAATCTTAAATTATTA
ATTAAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTACATATAATAATATATTT
Found at i:1355287 original size:27 final size:26
Alignment explanation
Indices: 1355249--1355336 Score: 108
Period size: 27 Copynumber: 3.4 Consensus size: 26
1355239 TCCTACAGTG
* *
1355249 GATGCTCCAGAAGGGACAACTGCAGCA
1 GATGCTCCAGAAGGAAAAACT-CAGCA
*
1355276 GATGCTCTAGAAGGAAAAACT--GCA
1 GATGCTCCAGAAGGAAAAACTCAGCA
*
1355300 GATGCTCCAGAAGGAAAAACTACAACA
1 GATGCTCCAGAAGGAAAAACT-CAGCA
1355327 GATGCTCCAG
1 GATGCTCCAG
1355337 GGGAGACGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
24 23 0.43
27 30 0.57
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.14
Consensus pattern (26 bp):
GATGCTCCAGAAGGAAAAACTCAGCA
Found at i:1355305 original size:24 final size:24
Alignment explanation
Indices: 1355249--1355320 Score: 90
Period size: 24 Copynumber: 2.9 Consensus size: 24
1355239 TCCTACAGTG
* *
1355249 GATGCTCCAGAAGGGACAACTGCAGCA
1 GATGCTCCAGAAGGAAAAACT---GCA
*
1355276 GATGCTCTAGAAGGAAAAACTGCA
1 GATGCTCCAGAAGGAAAAACTGCA
1355300 GATGCTCCAGAAGGAAAAACT
1 GATGCTCCAGAAGGAAAAACT
1355321 ACAACAGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
24 23 0.56
27 18 0.44
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (24 bp):
GATGCTCCAGAAGGAAAAACTGCA
Found at i:1357468 original size:32 final size:32
Alignment explanation
Indices: 1357403--1357490 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
1357393 GGTCACCCTT
* * * *
1357403 GGTAGGCTCTTAGGCCCCGAGATGCTCCATTG
1 GGTAGACTCTTAGGCCCCAAGGTACTCCATTG
*
1357435 GGTAGATTCTTAGGCCCCAAGGTACT-CACTTG
1 GGTAGACTCTTAGGCCCCAAGGTACTCCA-TTG
* *
1357467 GGTAGGCTCTAAGGCCCCAAGGTA
1 GGTAGACTCTTAGGCCCCAAGGTA
1357491 TTCTTTAGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 2 0.04
32 45 0.96
ACGTcount: A:0.20, C:0.26, G:0.30, T:0.24
Consensus pattern (32 bp):
GGTAGACTCTTAGGCCCCAAGGTACTCCATTG
Found at i:1357505 original size:31 final size:32
Alignment explanation
Indices: 1357446--1357521 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
1357436 GTAGATTCTT
*
1357446 AGGCCCCAAGGTACTCACTTGGGTAGGCTCTA
1 AGGCCCCAAGGTACTCACTTAGGTAGGCTCTA
* * *
1357478 AGGCCCCAAGGTATTC-TTTAGGTAGGCTTTA
1 AGGCCCCAAGGTACTCACTTAGGTAGGCTCTA
* *
1357509 AGACCGCAAGGTA
1 AGGCCCCAAGGTA
1357522 GTCCCTTATG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 23 0.61
32 15 0.39
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (32 bp):
AGGCCCCAAGGTACTCACTTAGGTAGGCTCTA
Found at i:1361295 original size:39 final size:39
Alignment explanation
Indices: 1361232--1361307 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
1361222 TTACTTCCTC
* *
1361232 ATGAAGAAGATTATTTACCGCCCTCCGATGAAGGAGCTG
1 ATGAAGAAGATTATTCACCACCCTCCGATGAAGGAGCTG
* * * *
1361271 ATGAAGAAGATTCTTCATCACCCTCCGCTGAGGGAGC
1 ATGAAGAAGATTATTCACCACCCTCCGATGAAGGAGC
1361308 ATCGCTACTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (39 bp):
ATGAAGAAGATTATTCACCACCCTCCGATGAAGGAGCTG
Found at i:1365667 original size:23 final size:23
Alignment explanation
Indices: 1365641--1365709 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
1365631 CACCACAGCT
*
1365641 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1365664 CGTAGAATTGCACCGGAGTGCCGA
1 CGTAGAATTGCACCGAAGTGCC-A
*
1365688 -ATAGAATTGCACCGTAA-TGCCA
1 CGTAGAATTGCACCG-AAGTGCCA
1365710 TATAATAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.03
23 37 0.93
24 2 0.05
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1371121 original size:20 final size:20
Alignment explanation
Indices: 1371096--1371141 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1371086 TTAGACAAGT
1371096 AGTATCGATATTGTTCTTAC
1 AGTATCGATATTGTTCTTAC
1371116 AGTATCGATATTGTTCTTAC
1 AGTATCGATATTGTTCTTAC
1371136 AGTATC
1 AGTATC
1371142 AATACATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
AGTATCGATATTGTTCTTAC
Found at i:1379441 original size:13 final size:13
Alignment explanation
Indices: 1379419--1379448 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1379409 ACTAAACACC
1379419 TTTC-ACATACCT
1 TTTCAACATACCT
1379431 TTTCAACATACCT
1 TTTCAACATACCT
1379444 TTTCA
1 TTTCA
1379449 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:1384775 original size:18 final size:19
Alignment explanation
Indices: 1384752--1384790 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1384742 ATTTTAATTA
*
1384752 ATTTTT-ATTATATAAAAT
1 ATTTTTAATTATAAAAAAT
1384770 ATTTTTACATTATAAAAAAT
1 ATTTTTA-ATTATAAAAAAT
1384790 A
1 A
1384791 AAAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTTAATTATAAAAAAT
Found at i:1393886 original size:17 final size:16
Alignment explanation
Indices: 1393843--1393886 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1393833 CATAATAATA
1393843 TTTTTAATTTTAAAAT
1 TTTTTAATTTTAAAAT
* *
1393859 TTTGTATATTTTAAAGT
1 TTTTTA-ATTTTAAAAT
1393876 TTTATTAATTT
1 TTT-TTAATTT
1393887 AATTTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 5 0.22
17 16 0.70
18 2 0.09
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTTAATTTTAAAAT
Found at i:1394647 original size:16 final size:17
Alignment explanation
Indices: 1394626--1394665 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
1394616 ATTTACCGAT
*
1394626 GATTTATATATTTATC-
1 GATTTATATATTGATCA
1394642 GATTTA-ATATTGATCA
1 GATTTATATATTGATCA
1394658 GA-TTATAT
1 GATTTATAT
1394666 TTTTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (17 bp):
GATTTATATATTGATCA
Found at i:1394937 original size:17 final size:18
Alignment explanation
Indices: 1394901--1394941 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1394891 ATAGTATGTA
*
1394901 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
1394919 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
1394936 TTTACT
1 TTTACT
1394942 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:1396620 original size:23 final size:23
Alignment explanation
Indices: 1396594--1396661 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
1396584 TGCTCGTTTA
*
1396594 TTTATTCTTCGCGAACATGTTCG
1 TTTATTCTTCACGAACATGTTCG
* * * *
1396617 TTTAATGTTCATGAGCATGTTCG
1 TTTATTCTTCACGAACATGTTCG
* *
1396640 TTTATATGTTCAAGAACATGTT
1 TTTAT-TCTTCACGAACATGTT
1396662 TATTTAGCGT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 22 0.61
24 14 0.39
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.44
Consensus pattern (23 bp):
TTTATTCTTCACGAACATGTTCG
Found at i:1396690 original size:23 final size:23
Alignment explanation
Indices: 1396606--1396690 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
1396596 TATTCTTCGC
1396606 GAACATGTTCGTTTAATGTTCAT
1 GAACATGTTCGTTTAATGTTCAT
* *
1396629 GAGCATGTTCGTTTATATGTTCAA
1 GAACATGTTCGTTTA-ATGTTCAT
** **
1396653 GAACATGTTTATTTAGCGTTCAT
1 GAACATGTTCGTTTAATGTTCAT
*
1396676 GAACGTGTTCGTTTA
1 GAACATGTTCGTTTA
1396691 TCGTCCTTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
23 31 0.62
24 19 0.38
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (23 bp):
GAACATGTTCGTTTAATGTTCAT
Found at i:1398609 original size:30 final size:30
Alignment explanation
Indices: 1398575--1398648 Score: 148
Period size: 30 Copynumber: 2.5 Consensus size: 30
1398565 ACTTTAGATG
1398575 CAAATATTTATATAATTATTTTATAATAAT
1 CAAATATTTATATAATTATTTTATAATAAT
1398605 CAAATATTTATATAATTATTTTATAATAAT
1 CAAATATTTATATAATTATTTTATAATAAT
1398635 CAAATATTTATATA
1 CAAATATTTATATA
1398649 CAAATATGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
CAAATATTTATATAATTATTTTATAATAAT
Found at i:1401749 original size:21 final size:20
Alignment explanation
Indices: 1401720--1401760 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1401710 TTATCGGTTT
*
1401720 GGGTATCGGGCCGGGTATTA
1 GGGTATCGGGCCGGGGATTA
*
1401740 GGGTAATCGGGGCGGGGATTA
1 GGGT-ATCGGGCCGGGGATTA
1401761 CCAAACACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.17, C:0.12, G:0.49, T:0.22
Consensus pattern (20 bp):
GGGTATCGGGCCGGGGATTA
Found at i:1402550 original size:30 final size:30
Alignment explanation
Indices: 1402510--1402577 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
1402500 TTAGTCCTTA
*
1402510 AGCTTCAACTATAAATACCCTAACCCATTT
1 AGCTTTAACTATAAATACCCTAACCCATTT
*
1402540 AGCTTTAACTATAAATACCCTAACTCATTT
1 AGCTTTAACTATAAATACCCTAACCCATTT
1402570 AGCTTTAA
1 AGCTTTAA
1402578 AACCATCCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (30 bp):
AGCTTTAACTATAAATACCCTAACCCATTT
Found at i:1405920 original size:20 final size:20
Alignment explanation
Indices: 1405895--1405962 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
1405885 TTCGTGGATG
1405895 GATGCACAGCAGGATGCATC
1 GATGCACAGCAGGATGCATC
* **
1405915 GATGCACAACCTTGATGCATC
1 GATGCAC-AGCAGGATGCATC
*
1405936 GATGCACAGAAGGATGCATC
1 GATGCACAGCAGGATGCATC
1405956 GATGCAC
1 GATGCAC
1405963 TAATTGCATT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 23 0.57
21 17 0.43
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (20 bp):
GATGCACAGCAGGATGCATC
Found at i:1406075 original size:22 final size:21
Alignment explanation
Indices: 1405983--1406082 Score: 80
Period size: 22 Copynumber: 4.7 Consensus size: 21
1405973 CGGTATTTGA
*
1405983 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
* *
1406003 ATGCATCGATGCACT--AGTGCAG
1 GTGCATGGATGCACTGCAG-G--G
* *
1406025 GTGCATAGATGCACTGTAGGG
1 GTGCATGGATGCACTGCAGGG
*
1406046 ATGCATGGATGCACTGCAGGGG
1 GTGCATGGATGCACTGCA-GGG
*
1406068 GTGCATGGATACACT
1 GTGCATGGATGCACT
1406083 TTGACACCCT
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.02
20 13 0.21
21 16 0.25
22 30 0.48
23 1 0.02
24 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:1407644 original size:18 final size:18
Alignment explanation
Indices: 1407621--1407668 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1407611 GTTGACTACT
1407621 TCATCTTCATCATTGGAA
1 TCATCTTCATCATTGGAA
1407639 TCATCTTCATCATTGGAA
1 TCATCTTCATCATTGGAA
*
1407657 TCATCTTTATCA
1 TCATCTTCATCA
1407669 CTCCAAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (18 bp):
TCATCTTCATCATTGGAA
Found at i:1408888 original size:32 final size:34
Alignment explanation
Indices: 1408847--1408916 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
1408837 ACCTTACAAC
* *
1408847 TCCCTAGTTTTT-C-CGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTTACACAGGATAAACTAGAACCTT
*
1408879 TCCCTAGTTTTTACACAGGATAAGCTAGAACCTT
1 TCCCTAGTTTTTACACAGGATAAACTAGAACCTT
1408913 TCCC
1 TCCC
1408917 ATTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 12 0.36
33 1 0.03
34 20 0.61
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (34 bp):
TCCCTAGTTTTTACACAGGATAAACTAGAACCTT
Found at i:1409405 original size:43 final size:42
Alignment explanation
Indices: 1409317--1409416 Score: 123
Period size: 43 Copynumber: 2.4 Consensus size: 42
1409307 CGGTATTTGA
*
1409317 GTGCATGGATGCACTGCATGATGCATCGATGCACTAGTGTAG
1 GTGCATGGATGCACTGCAGGATGCATCGATGCACTAGTGTAG
* * *
1409359 GTGCATAGATGCACTGCAGGGATGCATGGATGCACTGCAG-G-GG
1 GTGCATGGATGCACTGCA-GGATGCATCGATGCACT--AGTGTAG
1409402 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1409417 TTGACACCCT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
42 17 0.34
43 30 0.60
44 1 0.02
45 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (42 bp):
GTGCATGGATGCACTGCAGGATGCATCGATGCACTAGTGTAG
Found at i:1409409 original size:22 final size:21
Alignment explanation
Indices: 1409317--1409416 Score: 98
Period size: 22 Copynumber: 4.7 Consensus size: 21
1409307 CGGTATTTGA
*
1409317 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
* *
1409337 ATGCATCGATGCACT--AGTGTAG
1 GTGCATGGATGCACTGCAG-G--G
*
1409359 GTGCATAGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
1409380 ATGCATGGATGCACTGCAGGGG
1 GTGCATGGATGCACTGCA-GGG
1409402 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1409417 TTGACACCCT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
18 1 0.02
20 13 0.20
21 17 0.26
22 31 0.48
23 1 0.02
24 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:1409517 original size:29 final size:29
Alignment explanation
Indices: 1409496--1409553 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
1409486 AAACTTTGAA
1409496 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
1409525 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
1409554 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:1409543 original size:30 final size:30
Alignment explanation
Indices: 1409496--1409555 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
1409486 AAACTTTGAA
1409496 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
1409525 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1409556 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1412044 original size:108 final size:108
Alignment explanation
Indices: 1411853--1412056 Score: 320
Period size: 108 Copynumber: 1.9 Consensus size: 108
1411843 GATTCAAATT
* * * * *
1411853 GGGTTCACCCACAGCCATCGTTTGGTCATGCTAATGATGAAGTAAATTGTACCGCTGTCACTGAT
1 GGGTTCACCCACAGCCATCGGTTGGTCATACTAATGACGAAGTAAATTGTACCACCGTCACTGAT
*
1411918 GCTGATGTATATAGTTCCCCTACATGCGTGGGGTTCACAAGTG
66 GCTGATGTATATACTTCCCCTACATGCGTGGGGTTCACAAGTG
*
1411961 GGGTTCACCCACAGCCATTGGTTGGTCATACTAATGACGAAGTAAATTGTACCACCGTCACTGAT
1 GGGTTCACCCACAGCCATCGGTTGGTCATACTAATGACGAAGTAAATTGTACCACCGTCACTGAT
*
1412026 GCTGATGCT-TATACTTCCCCTACATGTGTGG
66 GCTGATG-TATATACTTCCCCTACATGCGTGG
1412057 TTAATACTGA
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 86 0.99
109 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (108 bp):
GGGTTCACCCACAGCCATCGGTTGGTCATACTAATGACGAAGTAAATTGTACCACCGTCACTGAT
GCTGATGTATATACTTCCCCTACATGCGTGGGGTTCACAAGTG
Found at i:1415996 original size:21 final size:21
Alignment explanation
Indices: 1415971--1416034 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1415961 TATATTGAGA
*
1415971 CCTTTCTTAAAAGGATCGATC
1 CCTTTCGTAAAAGGATCGATC
* **
1415992 CCTTTAGGCAAAGGATCGATC
1 CCTTTCGTAAAAGGATCGATC
* *
1416013 CCTCTCGTAAAAGGATTGATC
1 CCTTTCGTAAAAGGATCGATC
1416034 C
1 C
1416035 TAAACCTAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (21 bp):
CCTTTCGTAAAAGGATCGATC
Found at i:1417493 original size:36 final size:36
Alignment explanation
Indices: 1417447--1417529 Score: 148
Period size: 36 Copynumber: 2.3 Consensus size: 36
1417437 CCACTAGGCT
*
1417447 TCGATGCGACCTAAATATTTAGAGTATAAATTTGAC
1 TCGACGCGACCTAAATATTTAGAGTATAAATTTGAC
1417483 TCGACGCGACCTAAATATTTAGAGTATAAATTTGAC
1 TCGACGCGACCTAAATATTTAGAGTATAAATTTGAC
*
1417519 TCGACCCGACC
1 TCGACGCGACC
1417530 CGATATAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (36 bp):
TCGACGCGACCTAAATATTTAGAGTATAAATTTGAC
Found at i:1419494 original size:66 final size:66
Alignment explanation
Indices: 1419383--1419710 Score: 349
Period size: 66 Copynumber: 5.0 Consensus size: 66
1419373 GTGTTGGATA
* * * ** * *
1419383 AAAGCTCTGATGGTCAGGTGAAAAAGAAGAGTTCAGATGAAGTTTTTCCATCTGGCGCTCAGTCT
1 AAAGCTCTGACGGTCAAGTGAAAGAGAAGAACTCAAATGAAGTTTTTCCATCTGGTGCTCAGTCT
1419448 G
66 G
* ** * *
1419449 AAAGTTCTGACGGTCAAGTGAAAGAGAAGAACAAAAAAGAAGTTTTCCCATCTGGTGCTCAGTCT
1 AAAGCTCTGACGGTCAAGTGAAAGAGAAGAACTCAAATGAAGTTTTTCCATCTGGTGCTCAGTCT
1419514 G
66 G
* * * *
1419515 AAAGCTCCGACTGTCAAGTGAAAGAGAAGAGCTCAAACGAAG-TTTT-C-TCTGGTGCTCAGTCT
1 AAAGCTCTGACGGTCAAGTGAAAGAGAAGAACTCAAATGAAGTTTTTCCATCTGGTGCTCAGTCT
1419577 G
66 G
* * * * *
1419578 AAAGCTCTGATGCTCAAGTTGAAA-AGAAGAGCGCAAATGAAGTTTATCCATCTGGTGCTCAGTC
1 AAAGCTCTGACGGTCAAG-TGAAAGAGAAGAACTCAAATGAAGTTTTTCCATCTGGTGCTCAGTC
1419642 TG
65 TG
* * * * * * ** *
1419644 ATAGCTCTGATGGCCAAGTAAAAAAGACGAACTCAAATGAAGTTTCCCCATCTGGTGCTAAGTCT
1 AAAGCTCTGACGGTCAAGTGAAAGAGAAGAACTCAAATGAAGTTTTTCCATCTGGTGCTCAGTCT
1419709 G
66 G
1419710 A
1 A
1419711 GCTTTTGAAG
Statistics
Matches: 220, Mismatches: 37, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
63 46 0.21
64 9 0.04
65 8 0.04
66 157 0.71
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (66 bp):
AAAGCTCTGACGGTCAAGTGAAAGAGAAGAACTCAAATGAAGTTTTTCCATCTGGTGCTCAGTCT
G
Found at i:1419586 original size:21 final size:21
Alignment explanation
Indices: 1419561--1419601 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1419551 ACGAAGTTTT
*
1419561 CTCTGGTGCTC-AGTCTGAAAG
1 CTCTGATGCTCAAGT-TGAAAG
1419582 CTCTGATGCTCAAGTTGAAA
1 CTCTGATGCTCAAGTTGAAA
1419602 AGAAGAGCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
CTCTGATGCTCAAGTTGAAAG
Found at i:1419595 original size:129 final size:132
Alignment explanation
Indices: 1419395--1419710 Score: 347
Period size: 129 Copynumber: 2.4 Consensus size: 132
1419385 AGCTCTGATG
* * * * *
1419395 GTCAGGTGAAAAAGAAGAGTTCAGATGAAGTTTTTCCATCTGGCGCTCAGTCTGAAAGTTCTGAC
1 GTCAAGTGAAAAAGAAGAGCTCAAACGAAGTTTTTCCATCTGGCGCTCAGTCTGAAAGCTCTGAC
*
1419460 GGTCAAG-TGAAAGAGAAGAACAAAAAAGAAGTTT-TCCCATCTGGTGCTCAGTCTGAAAGCTCC
66 GCTCAAGTTGAAA-AGAAGAACAAAAAAGAAGTTTAT-CCATCTGGTGCTCAGTCTGAAAGCTCC
1419523 GACT
129 GACT
* * *
1419527 GTCAAGTGAAAGAGAAGAGCTCAAACGAAG-TTTT-C-TCTGGTGCTCAGTCTGAAAGCTCTGAT
1 GTCAAGTGAAAAAGAAGAGCTCAAACGAAGTTTTTCCATCTGGCGCTCAGTCTGAAAGCTCTGAC
* ** * * *
1419589 GCTCAAGTTGAAAAGAAGAGCGCAAATGAAGTTTATCCATCTGGTGCTCAGTCTGATAGCTCTGA
66 GCTCAAGTTGAAAAGAAGAACAAAAAAGAAGTTTATCCATCTGGTGCTCAGTCTGAAAGCTCCGA
1419654 -T
131 CT
* * * * * ** * *
1419655 GGCCAAGTAAAAAAGACGAACTCAAATGAAGTTTCCCCATCTGGTGCTAAGTCTGA
1 -GTCAAGTGAAAAAGAAGAGCTCAAACGAAGTTTTTCCATCTGGCGCTCAGTCTGA
1419711 GCTTTTGAAG
Statistics
Matches: 154, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
128 1 0.01
129 98 0.64
130 9 0.06
131 5 0.03
132 41 0.27
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (132 bp):
GTCAAGTGAAAAAGAAGAGCTCAAACGAAGTTTTTCCATCTGGCGCTCAGTCTGAAAGCTCTGAC
GCTCAAGTTGAAAAGAAGAACAAAAAAGAAGTTTATCCATCTGGTGCTCAGTCTGAAAGCTCCGA
CT
Found at i:1420501 original size:21 final size:21
Alignment explanation
Indices: 1420472--1420518 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1420462 TATCAGTACC
*
1420472 TTATCCAGAGCACAATAGCTA
1 TTATTCAGAGCACAATAGCTA
1420493 TTATTCAGAGCACAATAGCTA
1 TTATTCAGAGCACAATAGCTA
1420514 TTATT
1 TTATT
1420519 ATCAGTTCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (21 bp):
TTATTCAGAGCACAATAGCTA
Found at i:1425085 original size:21 final size:21
Alignment explanation
Indices: 1425061--1425100 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1425051 TGTTATGGAG
*
1425061 TTATGATTTAGGGTTTAAGAA
1 TTATGATTTAGGATTTAAGAA
1425082 TTATGATTTAGGATTTAAG
1 TTATGATTTAGGATTTAAG
1425101 TTAGAATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.45
Consensus pattern (21 bp):
TTATGATTTAGGATTTAAGAA
Found at i:1425401 original size:3 final size:3
Alignment explanation
Indices: 1425386--1425424 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1425376 TATTCTCTCT
*
1425386 TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1425425 AAGCATTGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1427523 original size:29 final size:30
Alignment explanation
Indices: 1427481--1427541 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1427471 GTAATTTATA
1427481 GTTGAAAAGAAAGG-TGAAT-TAGGTTGTGTT
1 GTTGAAAAGAAAGGCT-AATGTA-GTTGTGTT
*
1427511 GTTG-AAAGGAAGGCTAATGTAGTTGTGTT
1 GTTGAAAAGAAAGGCTAATGTAGTTGTGTT
1427540 GT
1 GT
1427542 ACTCTTTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.30, C:0.02, G:0.34, T:0.34
Consensus pattern (30 bp):
GTTGAAAAGAAAGGCTAATGTAGTTGTGTT
Found at i:1429489 original size:2 final size:2
Alignment explanation
Indices: 1429477--1429525 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1429467 ATTCAAAACT
*
1429477 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1429519 TA TA TA T
1 TA TA TA T
1429526 TGGGATTGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1432917 original size:31 final size:30
Alignment explanation
Indices: 1432842--1432946 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 30
1432832 AATTCAGGGG
* * * *
1432842 GTCAAATTGATATTTTATTTAAAGTTTAGT
1 GTCAAATTAATATTTTATCTAAAGTTCAAT
* * *
1432872 GGTTAAAATGATATTTTTATCTAAAGTTCAAT
1 -GTCAAATTAATA-TTTTATCTAAAGTTCAAT
** * *
1432904 GTCAAATTAATATTCAATCCAAAGTTCAAAA
1 GTCAAATTAATATTTTATCTAAAGTTC-AAT
1432935 GTCAAATTAATA
1 GTCAAATTAATA
1432947 ATTAATCTCT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
30 12 0.20
31 33 0.55
32 15 0.25
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (30 bp):
GTCAAATTAATATTTTATCTAAAGTTCAAT
Found at i:1436485 original size:17 final size:17
Alignment explanation
Indices: 1436455--1436492 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1436445 CAAATTTTTG
1436455 TTTTTGATCCACATAAA
1 TTTTTGATCCACATAAA
* *
1436472 TTTTTTATCTACATAAA
1 TTTTTGATCCACATAAA
1436489 TTTT
1 TTTT
1436493 CATTCCCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTTTGATCCACATAAA
Found at i:1437886 original size:6 final size:6
Alignment explanation
Indices: 1437875--1438419 Score: 1016
Period size: 6 Copynumber: 91.8 Consensus size: 6
1437865 TGAGGTGAAA
1437875 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1437923 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1437971 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1438019 GTATAT G--TAT GTATAT GTATAT GTATAT GTATAT GTATAT G--TAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1438063 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1438111 GTATAT GTATAT GTATAT G--TAT GTATAT GTATGTAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTA--TAT GTATAT GTATAT
1438159 GTATAT GTATAT GTATAT G--TAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1438205 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1438253 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1438301 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1438349 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1438397 GTATAT GTATAT GTATAT GTATA
1 GTATAT GTATAT GTATAT GTATA
1438420 ACTCCTTGAA
Statistics
Matches: 529, Mismatches: 0, Indels: 20
0.96 0.00 0.04
Matches are distributed among these distances:
4 16 0.03
6 507 0.96
8 6 0.01
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:1438522 original size:20 final size:20
Alignment explanation
Indices: 1438481--1438523 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1438471 TCTAAGAGCC
*
1438481 CATTTAGGACTATTTAGATG
1 CATTTAGGACTATATAGATG
*
1438501 CATTTAGGAGC-ATATAGTTG
1 CATTTAGGA-CTATATAGATG
1438521 CAT
1 CAT
1438524 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGGACTATATAGATG
Found at i:1445231 original size:6 final size:6
Alignment explanation
Indices: 1445220--1445383 Score: 274
Period size: 6 Copynumber: 27.3 Consensus size: 6
1445210 ACAGCGGACA
1445220 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1445268 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* * * * **
1445316 TATATG TATATG TATACG TATACG TATACG TATACG TATATG TATACA
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1445364 TATATG TATATG TATATG TA
1 TATATG TATATG TATATG TA
1445384 CTTCAAAATT
Statistics
Matches: 152, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 152 1.00
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (6 bp):
TATATG
Found at i:1446989 original size:13 final size:13
Alignment explanation
Indices: 1446971--1446998 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1446961 TACTGGAACA
1446971 TTAACATAATGTT
1 TTAACATAATGTT
1446984 TTAACATAATGTT
1 TTAACATAATGTT
1446997 TT
1 TT
1446999 GACAGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (13 bp):
TTAACATAATGTT
Found at i:1449788 original size:30 final size:31
Alignment explanation
Indices: 1449752--1449817 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
1449742 AGGATATCCC
* *
1449752 CAAACTATGACCCCATTCTATATCAGTC-CT
1 CAAACTATGACCCCACTCTAAATCAGTCACT
*
1449782 CAAACTATGACTCCACTCTAAATCAGTCACT
1 CAAACTATGACCCCACTCTAAATCAGTCACT
1449813 -AAACT
1 CAAACT
1449818 TTAAAATGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.35, C:0.32, G:0.06, T:0.27
Consensus pattern (31 bp):
CAAACTATGACCCCACTCTAAATCAGTCACT
Found at i:1457871 original size:11 final size:11
Alignment explanation
Indices: 1457855--1457879 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1457845 CTTAAATCTA
1457855 ATAGTTTATTT
1 ATAGTTTATTT
1457866 ATAGTTTATTT
1 ATAGTTTATTT
1457877 ATA
1 ATA
1457880 ATTGATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (11 bp):
ATAGTTTATTT
Found at i:1460234 original size:31 final size:31
Alignment explanation
Indices: 1460199--1460265 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
1460189 AACTTTATAA
1460199 TCCCTCAATATTTAGTCCGTTTACAATATGG
1 TCCCTCAATATTTAGTCCGTTTACAATATGG
*
1460230 TCCCTCAATATTTAGTCCGTTTGCAATATGG
1 TCCCTCAATATTTAGTCCGTTTACAATATGG
1460261 TCCCT
1 TCCCT
1460266 GACGTAACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.39
Consensus pattern (31 bp):
TCCCTCAATATTTAGTCCGTTTACAATATGG
Found at i:1461223 original size:54 final size:52
Alignment explanation
Indices: 1461139--1461253 Score: 149
Period size: 54 Copynumber: 2.2 Consensus size: 52
1461129 TAATGACGGA
* * * *
1461139 TGACCAAAATATAATGAAATATAACGTTAAGTATGATTTAAAAAAACTATTAGTG
1 TGACC-AAATACAATGAAATATAACATTAAGTACGATTT-AAAAAA-TATTAGAG
* *
1461194 TGACCAAATACAATGAAATATAACATTAAGTACGATTTAGAAAATATTTGAG
1 TGACCAAATACAATGAAATATAACATTAAGTACGATTTAAAAAATATTAGAG
1461246 TGACCAAA
1 TGACCAAA
1461254 ATAGAAACAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
52 14 0.26
53 5 0.09
54 30 0.56
55 5 0.09
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.29
Consensus pattern (52 bp):
TGACCAAATACAATGAAATATAACATTAAGTACGATTTAAAAAATATTAGAG
Found at i:1462978 original size:21 final size:20
Alignment explanation
Indices: 1462892--1463049 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1462882 AAATGACCAA
**
1462892 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1462911 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1462931 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1462951 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1462972 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1462993 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1463013 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
* *
1463034 GAAAATCACAACGCGA
1 CAAAATCGCAACGCGA
1463050 ACACATAAAT
Statistics
Matches: 103, Mismatches: 30, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 47 0.46
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1463040 original size:20 final size:19
Alignment explanation
Indices: 1463014--1463068 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1463004 TGCGATTTTC
*
1463014 CAAAATCGCAACGCGAATA
1 CAAAATCGCAACGCGAACA
* *
1463033 TGAAAATCACAACGCGAACA
1 -CAAAATCGCAACGCGAACA
1463053 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
1463069 TATCCGTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.45, C:0.27, G:0.16, T:0.11
Consensus pattern (19 bp):
CAAAATCGCAACGCGAACA
Found at i:1463078 original size:20 final size:20
Alignment explanation
Indices: 1463055--1463208 Score: 220
Period size: 20 Copynumber: 7.7 Consensus size: 20
1463045 CGCGAACACA
1463055 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1463075 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
**
1463095 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
1463115 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1463135 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1463155 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* *
1463175 TAAATCGCAACGAGAATCCG
1 TAAATCGCAACGCGTATCCG
1463195 TAAATCGCAACGCG
1 TAAATCGCAACGCG
1463209 ATATTTAAAG
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
19 1 0.01
20 117 0.99
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:1463080 original size:40 final size:39
Alignment explanation
Indices: 1463016--1463209 Score: 199
Period size: 40 Copynumber: 4.9 Consensus size: 39
1463006 CGATTTTCCA
* ** * * *
1463016 AAATCGCAACGCGAATATGAAAATCACAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CGT
* *
1463056 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCGT
** * *
1463096 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCGT
* **
1463136 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCGT
* *
1463176 AAATCGCAACGAGAATCCGTAAATCGCAACGCGA
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1463210 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 125 0.98
41 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCGT
Found at i:1463100 original size:60 final size:59
Alignment explanation
Indices: 1463016--1463208 Score: 215
Period size: 60 Copynumber: 3.2 Consensus size: 59
1463006 CGATTTTCCA
* ** * * *
1463016 AAATCGCAACGCGAATATGAAAATCACAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAACGCGTATCCGT
* *** *
1463076 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCGTAAATCGCAACGCGTATCCGT
* ** * *
1463136 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAACGCGTATCCGT
1463196 AAATCGCAACGCG
1 AAATCGCAACGCG
1463209 ATATTTAAAG
Statistics
Matches: 109, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
59 1 0.01
60 107 0.98
61 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (59 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCGTAAATCGCAACGCGTATCCGT
Found at i:1463631 original size:33 final size:33
Alignment explanation
Indices: 1463591--1463661 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1463581 TTCACTTAGA
*
1463591 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1463624 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1463657 TTTCA
1 TTTCA
1463662 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1463785 original size:20 final size:20
Alignment explanation
Indices: 1463739--1463850 Score: 112
Period size: 21 Copynumber: 5.8 Consensus size: 20
1463729 TTTGCAGAAG
*
1463739 AATCGCAACGAGATAAATGAA
1 AATCGCAACGAGA-GAATGAA
*
1463760 AATCGCAACGAGAGAATGAC
1 AATCGCAACGAGAGAATGAA
**
1463780 TGTCGCAACGAGAGAAATGAA
1 AATCGCAACGAGAG-AATGAA
1463801 AATCGCAAC--GAG-A-G--
1 AATCGCAACGAGAGAATGAA
*
1463815 AATCGCAACGCGA-AATGAA
1 AATCGCAACGAGAGAATGAA
1463834 AATCGCAACGAGAGAAT
1 AATCGCAACGAGAGAAT
1463851 CGCAACGCGA
Statistics
Matches: 75, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.20
20 20 0.27
21 25 0.33
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (20 bp):
AATCGCAACGAGAGAATGAA
Found at i:1463820 original size:14 final size:14
Alignment explanation
Indices: 1463801--1463857 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1463791 GAGAAATGAA
1463801 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1463815 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1463834 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1463848 AATCGCAACG
1 AATCGCAACG
1463858 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1463833 original size:33 final size:33
Alignment explanation
Indices: 1463737--1463873 Score: 148
Period size: 33 Copynumber: 3.8 Consensus size: 33
1463727 AATTTGCAGA
1463737 AGAATCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATCGCAACGAG--AAATGAAAATCGCAACGAG
1463772 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AG-A--A---TCGCAAC--GAGAAATGAAAATCGCAACGAG
*
1463813 AGAATCGCAACGCGAAATGAAAATCGCAACGAG
1 AGAATCGCAACGAGAAATGAAAATCGCAACGAG
* **
1463846 AGAATCGCAACGCGAAACCAAAATCGCA
1 AGAATCGCAACGAGAAATGAAAATCGCA
1463874 TTGCGATTTT
Statistics
Matches: 91, Mismatches: 3, Indels: 18
0.81 0.03 0.16
Matches are distributed among these distances:
33 47 0.52
35 9 0.10
36 1 0.01
38 2 0.02
40 1 0.01
41 28 0.31
43 3 0.03
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
AGAATCGCAACGAGAAATGAAAATCGCAACGAG
Found at i:1463891 original size:19 final size:19
Alignment explanation
Indices: 1463869--1463966 Score: 99
Period size: 19 Copynumber: 5.7 Consensus size: 19
1463859 GAAACCAAAA
*
1463869 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1463888 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1463902 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1463921 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1463935 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1463954 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1463967 CTCTCATTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
16 6 0.09
17 6 0.09
19 32 0.50
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1463910 original size:14 final size:14
Alignment explanation
Indices: 1463891--1463980 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
1463881 TTTCATTTCG
1463891 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1463905 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1463924 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1463938 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1463957 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1463971 CATTGCGATT
1 CGTTGCGATT
1463981 TTCATTTCAA
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
14 29 0.48
16 6 0.10
17 6 0.10
19 20 0.33
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1463916 original size:33 final size:33
Alignment explanation
Indices: 1463874--1463988 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
1463864 CAAAATCGCA
1463874 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1463907 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1463940 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1463973 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1463989 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 81 1.00
ACGTcount: A:0.10, C:0.23, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1465919 original size:93 final size:93
Alignment explanation
Indices: 1465685--1466338 Score: 1285
Period size: 93 Copynumber: 7.1 Consensus size: 93
1465675 TAGATTGCTT
1465685 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1465750 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1465777 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1465842 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1465870 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1465935 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1465963 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1466028 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1466056 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1466121 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1466149 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1466214 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1466242 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1466307 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1466334 AGTAA
1 AGTAA
1466339 TGCAATCCAT
Statistics
Matches: 559, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
92 81 0.14
93 478 0.86
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1466426 original size:19 final size:19
Alignment explanation
Indices: 1466386--1466514 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1466376 TAGTTTACTT
* *
1466386 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1466406 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1466425 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1466444 TCGCAA--CG--A-CATAA
1 TCGCAACGCGAAACCAAAA
1466458 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1466477 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1466491 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1466510 TCGCA
1 TCGCA
1466515 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1466465 original size:33 final size:32
Alignment explanation
Indices: 1466422--1466514 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1466412 CGCGAAACCA
**
1466422 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1466454 ATAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1466487 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1466515 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Done.