Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007173.1 Hibiscus syriacus cultivar Beakdansim tig00018827_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: 1357898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1217070 original size:32 final size:33
Alignment explanation
Indices: 1217021--1217124 Score: 129
Period size: 33 Copynumber: 3.1 Consensus size: 33
1217011 TTTTTCCTTT
* *
1217021 AAAAATTATATAATATATTTTCCAAAATGTTTTTG
1 AAAACTTATATTATATATTTT-CAAAATG-TTTTG
* *
1217056 AAAAC-TATATTATATATTTTAAAAATGTTTTC
1 AAAACTTATATTATATATTTTCAAAATGTTTTG
* *
1217088 AAAACTTATTTTATATGTTTTCAAAATGTTTTG
1 AAAACTTATATTATATATTTTCAAAATGTTTTG
1217121 AAAA
1 AAAA
1217125 AACTATATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 9 0.15
33 33 0.55
34 14 0.23
35 4 0.07
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (33 bp):
AAAACTTATATTATATATTTTCAAAATGTTTTG
Found at i:1217086 original size:33 final size:32
Alignment explanation
Indices: 1217022--1217139 Score: 128
Period size: 33 Copynumber: 3.5 Consensus size: 32
1217012 TTTTCCTTTA
*
1217022 AAAATTATATAATATATTTTCCAAAATGTTTTTG
1 AAAACTATATAATATATTTT-CAAAATG-TTTTG
* * *
1217056 AAAACTATATTATATATTTTAAAAATGTTTTC
1 AAAACTATATAATATATTTTCAAAATGTTTTG
* * *
1217088 AAAACTTATTTTATATGTTTTCAAAATGTTTTG
1 AAAAC-TATATAATATATTTTCAAAATGTTTTG
1217121 AAAAAACTATATAATATAT
1 --AAAACTATATAATATAT
1217140 ACACTTTCGA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
32 9 0.13
33 29 0.41
34 27 0.39
35 5 0.07
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (32 bp):
AAAACTATATAATATATTTTCAAAATGTTTTG
Found at i:1217200 original size:2 final size:2
Alignment explanation
Indices: 1217193--1217232 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1217183 TCAAAAATTG
*
1217193 TA TA TA TA TA TA TA TA TA -A TA -A TA AA 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
1217233 AACAAAATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1220775 original size:44 final size:45
Alignment explanation
Indices: 1220561--1220782 Score: 330
Period size: 43 Copynumber: 5.0 Consensus size: 45
1220551 TGCAACTTTC
* * *
1220561 TTACCAATATACATATCATTTA-TCCTATAAGCTCGTAAGCTTTTT
1 TTACCAATATACTTACCATTTATTCC-ATAAGCTCGTAAGCTTATT
*
1220606 TTATCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTT-ATTCCATAAGCTCGTAAGCTTATT
1220652 TTACC-A-ATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1220695 TTACCAATAT--TTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
* *
1220738 TTACCAATATACTTGCCA-TTATTTCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1220782 T
1 T
1220783 GCATGCTTAC
Statistics
Matches: 164, Mismatches: 7, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
43 72 0.44
44 40 0.24
45 26 0.16
46 23 0.14
47 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (45 bp):
TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
Found at i:1220778 original size:87 final size:88
Alignment explanation
Indices: 1220577--1220782 Score: 312
Period size: 87 Copynumber: 2.3 Consensus size: 88
1220567 ATATACATAT
* *
1220577 CATTTA-TCCTATAAGCTCGTAAGCTTTTTTTATCAATATACTTACCATTTAATTCCATAAGCTC
1 CATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA-TTACCATTTAATTCCATAAGCTC
1220641 GTAAGCTTATTTTACCAATACTTAC
64 GTAAGCTTATTTTACCAATACTTAC
1220666 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATAT-TTACCATTT-ATTCCATAAGCTCGT
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATATTACCATTTAATTCCATAAGCTCGT
*
1220729 AAGCTTATTTTACCAATATACTTGC
66 AAGCTTATTTTACC-A-ATACTTAC
*
1220754 CA-TTATTTCATAAGCTCGTAAGCTTATTT
1 CATTTATTCCATAAGCTCGTAAGCTTATTT
1220783 GCATGCTTAC
Statistics
Matches: 110, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
86 29 0.26
87 36 0.33
88 9 0.08
89 33 0.30
90 3 0.03
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.42
Consensus pattern (88 bp):
CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATATTACCATTTAATTCCATAAGCTCGT
AAGCTTATTTTACCAATACTTAC
Found at i:1222710 original size:30 final size:30
Alignment explanation
Indices: 1222670--1222748 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 30
1222660 TTTTTTAAAA
* *
1222670 TTATATTTTGGTCCCTAAACTTT-TCAAAGT
1 TTATAATTTGGTCCCTAAACTTTACCAAA-T
1222700 TTA-AACTTTGGTCACC-AAACTTTACCAAAT
1 TTATAA-TTTGGTC-CCTAAACTTTACCAAAT
*
1222730 TTATAATTTGGTCACTAAA
1 TTATAATTTGGTCCCTAAA
1222749 TAAATCCATT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
29 2 0.05
30 31 0.76
31 8 0.20
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.41
Consensus pattern (30 bp):
TTATAATTTGGTCCCTAAACTTTACCAAAT
Found at i:1223138 original size:82 final size:84
Alignment explanation
Indices: 1223042--1223229 Score: 231
Period size: 82 Copynumber: 2.3 Consensus size: 84
1223032 AAATGGTAAA
* * *
1223042 TTTAGCGGTGTTTTTATACAAATGTCGCAAT-GGAGTTCATATATAGTGGTGT-TTTTTCAACAA
1 TTTAGCGGTGTTTTTATACAAATATCGCAATAGG-GTTCATATATAGTGGTGTCGTTAT-AACAA
*
1223105 ACGATGCAACAGA-GAGTAC-
64 ACGATGCAACAGATAAGTACT
* **
1223124 TTTAGCGGTATTTTTATACAAATATCTTAATAGGGTTCATATATAGTGGTGTCGTTATAACAAAC
1 TTTAGCGGTGTTTTTATACAAATATCGCAATAGGGTTCATATATAGTGGTGTCGTTATAACAAAC
* *
1223189 GCTGCAATAGATAAGTACT
66 GATGCAACAGATAAGTACT
**
1223208 TTTAGTAGTGTTTTTATACAAA
1 TTTAGCGGTGTTTTTATACAAA
1223230 CGCCGCAACA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
82 61 0.68
83 10 0.11
84 19 0.21
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (84 bp):
TTTAGCGGTGTTTTTATACAAATATCGCAATAGGGTTCATATATAGTGGTGTCGTTATAACAAAC
GATGCAACAGATAAGTACT
Found at i:1223229 original size:42 final size:42
Alignment explanation
Indices: 1223178--1223262 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
1223168 AGTGGTGTCG
* *
1223178 TTATAACAAACGCTGCAATA-GATAAGTACTTTTAGTAGTGTTT
1 TTATAACAAACGCCGCAACAGGAT-AGTAC-TTTAGTAGTGTTT
* *
1223221 TTAT-ACAAACGCCGCAACAGGGTAGTACTTTAGTGGTGTTT
1 TTATAACAAACGCCGCAACAGGATAGTACTTTAGTAGTGTTT
1223262 T
1 T
1223263 CTGCAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
41 13 0.35
42 18 0.49
43 6 0.16
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (42 bp):
TTATAACAAACGCCGCAACAGGATAGTACTTTAGTAGTGTTT
Found at i:1223634 original size:41 final size:41
Alignment explanation
Indices: 1223574--1223684 Score: 118
Period size: 41 Copynumber: 2.7 Consensus size: 41
1223564 GCTATAGACT
* * * *
1223574 TGTACTTGAGTGGCGTTTTTGT-TCAAACACCACAATATTCA
1 TGTACTTTAGTGGCTTTTTTGTAT-AAACACAACAATAATCA
1223615 TGTACTTTAGTGGCTTTTTT-TAATAAACACAACAATAATCA
1 TGTACTTTAGTGGCTTTTTTGT-ATAAACACAACAATAATCA
* * *
1223656 TGTAATTTTGTGGTTTTTTTGTAATAAAC
1 TGTACTTTAGTGGCTTTTTTGT-ATAAAC
1223685 GCCGCAATAG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
40 1 0.02
41 50 0.83
42 9 0.15
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (41 bp):
TGTACTTTAGTGGCTTTTTTGTATAAACACAACAATAATCA
Found at i:1223701 original size:42 final size:41
Alignment explanation
Indices: 1223598--1223684 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
1223588 GTTTTTGTTC
* * *
1223598 AAACACCACAATATTCATGTACTTTAGTGGCTTTTTTTAAT
1 AAACACAACAATAATCATGTAATTTAGTGGCTTTTTTTAAT
* *
1223639 AAACACAACAATAATCATGTAATTTTGTGGTTTTTTTGTAAT
1 AAACACAACAATAATCATGTAATTTAGTGGCTTTTTT-TAAT
1223681 AAAC
1 AAAC
1223685 GCCGCAATAG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 32 0.80
42 8 0.20
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (41 bp):
AAACACAACAATAATCATGTAATTTAGTGGCTTTTTTTAAT
Found at i:1224701 original size:3 final size:3
Alignment explanation
Indices: 1224693--1224733 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
1224683 CTATTTAATT
*
1224693 TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1224734 CAAATTTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1224719 original size:23 final size:23
Alignment explanation
Indices: 1224690--1224733 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1224680 TTTCTATTTA
*
1224690 ATTTTATTATTATTATTATTATT
1 ATTTTATTAATATTATTATTATT
1224713 ATTTTATTAATATTATTATTA
1 ATTTTATTAATATTATTATTA
1224734 CAAATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTTATTAATATTATTATTATT
Found at i:1224721 original size:20 final size:20
Alignment explanation
Indices: 1224696--1224733 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1224686 TTTAATTTTA
*
1224696 TTATTATTATTATTATTATT
1 TTATTAATATTATTATTATT
1224716 TTATTAATATTATTATTA
1 TTATTAATATTATTATTA
1224734 CAAATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTAATATTATTATTATT
Found at i:1228041 original size:30 final size:31
Alignment explanation
Indices: 1228006--1228068 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1227996 ATCTTATTTG
*
1228006 TACTAACTCA-TTTTTCTC-TTGTGTTTGTGT
1 TACTAACTCATTTTTTCTCATT-TGGTTGTGT
1228036 TACTAACTCATTTTTTCTCATTTGGTTGTGT
1 TACTAACTCATTTTTTCTCATTTGGTTGTGT
1228067 TA
1 TA
1228069 TTTTTCATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 10 0.33
31 18 0.60
32 2 0.07
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.56
Consensus pattern (31 bp):
TACTAACTCATTTTTTCTCATTTGGTTGTGT
Found at i:1232228 original size:36 final size:36
Alignment explanation
Indices: 1232138--1232279 Score: 146
Period size: 36 Copynumber: 3.9 Consensus size: 36
1232128 ATGTTGTTTC
* * *
1232138 TCTTGAAACA-AAATGTCGTCTCGCTAT-AGACAACTT
1 TCTTGAAAAACAAATTTTGTCTCGCT-TGAGACAA-TT
* *
1232174 CTTTTGAAAAACAAATTTTTTCTCGCTTGAGACAATT
1 -TCTTGAAAAACAAATTTTGTCTCGCTTGAGACAATT
* * *
1232211 TCTCT-CAAAACAAATTTTGTCTCGTTTGAGATAATT
1 TCT-TGAAAAACAAATTTTGTCTCGCTTGAGACAATT
*
1232247 TCTTGAAAAACAAATTTCGTCTCGCTTGAGACA
1 TCTTGAAAAACAAATTTTGTCTCGCTTGAGACA
1232280 TTTTTCCTTT
Statistics
Matches: 87, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
35 1 0.01
36 56 0.64
37 12 0.14
38 18 0.21
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (36 bp):
TCTTGAAAAACAAATTTTGTCTCGCTTGAGACAATT
Found at i:1232393 original size:34 final size:36
Alignment explanation
Indices: 1232348--1232416 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 36
1232338 TTGAGATCGT
* *
1232348 TTTCTCAAAAAA-AACTT-TGTCTCGCTTGAGACAA
1 TTTCTCAAAAAACAAATTCTATCTCGCTTGAGACAA
* *
1232382 TTTCTCTAAAAACAAATTCTATCTCTCTTGAGACA
1 TTTCTCAAAAAACAAATTCTATCTCGCTTGAGACA
1232417 TTTTTCCACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 11 0.38
35 4 0.14
36 14 0.48
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (36 bp):
TTTCTCAAAAAACAAATTCTATCTCGCTTGAGACAA
Found at i:1235191 original size:16 final size:15
Alignment explanation
Indices: 1235166--1235195 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1235156 CCTTTAGGCA
1235166 AATATATATATTTTG
1 AATATATATATTTTG
1235181 AATATTATATATTTT
1 AATA-TATATATTTT
1235196 CATGTAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
AATATATATATTTTG
Found at i:1237907 original size:14 final size:15
Alignment explanation
Indices: 1237888--1237926 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1237878 AGTGAAAGAA
1237888 TTATATAATTA-TAG
1 TTATATAATTATTAG
*
1237902 TTATATAATTATTTG
1 TTATATAATTATTAG
1237917 TTATATAATT
1 TTATATAATT
1237927 TTGTTATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (15 bp):
TTATATAATTATTAG
Found at i:1238506 original size:14 final size:14
Alignment explanation
Indices: 1238487--1238514 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1238477 AAGTGAAAGA
1238487 ATAGTTATATAATT
1 ATAGTTATATAATT
1238501 ATAGTTATATAATT
1 ATAGTTATATAATT
1238515 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:1239550 original size:38 final size:38
Alignment explanation
Indices: 1239485--1239604 Score: 135
Period size: 38 Copynumber: 3.3 Consensus size: 38
1239475 TTTTCAAAAC
* *
1239485 TATA-TATATATTTTCAAAAATCAATTTTATAAAAAGTA
1 TATATTATATATTTTTAAAAA-CTATTTTATAAAAAGTA
* *
1239523 TATATTATATGTTTTTAAAAACTATTTTCTAAAAAGTA
1 TATATTATATATTTTTAAAAACTATTTTATAAAAAGTA
*
1239561 TATATTA-ATTTTTTTAAAAA-TATTTTCA-AAAAA-T-
1 TATATTATATATTTTTAAAAACTATTTT-ATAAAAAGTA
1239595 TATATTATAT
1 TATATTATAT
1239605 TAATATATAT
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
34 7 0.10
35 3 0.04
36 11 0.15
37 12 0.16
38 26 0.36
39 14 0.19
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (38 bp):
TATATTATATATTTTTAAAAACTATTTTATAAAAAGTA
Found at i:1240718 original size:29 final size:29
Alignment explanation
Indices: 1240628--1240735 Score: 78
Period size: 29 Copynumber: 3.7 Consensus size: 29
1240618 AAAGGAATTA
* * * *
1240628 AAATGGTAAGAACAGAAACTTAAAAGACT
1 AAATAGTAAAAACATAAACTTAAGAGACT
* * * *
1240657 AAAACAGTTAAAACAAAAATTTAA-AGACAT
1 -AAATAGTAAAAACATAAACTTAAGAGAC-T
*
1240687 AAATAGTAAAAACATAAACTTAAGTGACT
1 AAATAGTAAAAACATAAACTTAAGAGACT
1240716 AAA-A-TAAAATAACATAAACT
1 AAATAGT-AAA-AACATAAACT
1240736 AAAGTGTCAA
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.02
28 4 0.06
29 37 0.59
30 21 0.33
ACGTcount: A:0.60, C:0.10, G:0.09, T:0.20
Consensus pattern (29 bp):
AAATAGTAAAAACATAAACTTAAGAGACT
Found at i:1241627 original size:3 final size:3
Alignment explanation
Indices: 1241619--1241758 Score: 172
Period size: 3 Copynumber: 45.3 Consensus size: 3
1241609 GTATGTTTTA
*
1241619 AAT AAT AAT AAT AAT AAT AAAT AAT ACT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
1241665 AAT AAT AAT AAT AAT AAT AAT AAAT ACT ACT ACT ACT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
* * *
1241711 AAT AAT AAAT AAT ACT AAT ATT AAT AAT AAT AAT AAT ATTT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
1241758 A
1 A
1241759 TTTTTTCGAC
Statistics
Matches: 123, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
3 112 0.91
4 11 0.09
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1242061 original size:46 final size:45
Alignment explanation
Indices: 1242002--1242324 Score: 203
Period size: 46 Copynumber: 7.4 Consensus size: 45
1241992 GTGATGACCT
* *
1242002 GGTTCCTATGTGATGAGGACGGCAGGTCATCTAAGGGTGATAACAC
1 GGTTCCTACGTGATGAGGACGACAGGTCATCT-AGGGTGATAACAC
* * *
1242048 GGTTCCTACGTGATGAGGACGACTGGTTATCTTA-GGT--TGACAC
1 GGTTCCTACGTGATGAGGACGACAGGTCATC-TAGGGTGATAACAC
* * * *
1242091 GGCTCCTACGTGATGAGGA-GATCAAG---TC--GGATGATGACAC
1 GGTTCCTACGTGATGAGGACGA-CAGGTCATCTAGGGTGATAACAC
* * * * ** * * *
1242131 GATTCCTATGTTATGAGGATGGTAGGCCATCTAAAGGTGATAATAC
1 GGTTCCTACGTGATGAGGACGACAGGTCATCT-AGGGTGATAACAC
* * * * * *
1242177 GGTTCCTATGTGATGAGGACGACTGATTATCT-GGG-GTTTACAC
1 GGTTCCTACGTGATGAGGACGACAGGTCATCTAGGGTGATAACAC
* *
1242220 GGCTCCTACGTGATGAGGA-GATCAGG---TC--GGGTGATGACAC
1 GGTTCCTACGTGATGAGGACGA-CAGGTCATCTAGGGTGATAACAC
* * * *
1242260 GGTTCCTACGTGATGAGGATGACAAGCCATCTAAAGGTGATAACAC
1 GGTTCCTACGTGATGAGGACGACAGGTCATCT-AGGGTGATAACAC
1242306 GGTTCCTACGTGATGAGGA
1 GGTTCCTACGTGATGAGGA
1242325 TGGCTAGTTA
Statistics
Matches: 213, Mismatches: 43, Indels: 42
0.71 0.14 0.14
Matches are distributed among these distances:
38 2 0.01
39 3 0.01
40 54 0.25
41 3 0.01
42 4 0.02
43 53 0.25
44 2 0.01
45 3 0.01
46 88 0.41
47 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (45 bp):
GGTTCCTACGTGATGAGGACGACAGGTCATCTAGGGTGATAACAC
Found at i:1242182 original size:129 final size:129
Alignment explanation
Indices: 1241952--1242407 Score: 603
Period size: 129 Copynumber: 3.5 Consensus size: 129
1241942 GGTCGTCTAA
* * *
1241952 AGGTTGACATGACTCTTACGTGATGAGGAGATCAAGTCGGGTGATGAC-CTGGTTCCTATGTGAT
1 AGGTTGACACGGCTCCTACGTGATGAGGAGATCAAGTCGGGTGATGACAC-GGTTCCTATGTGAT
* * *
1242016 GAGGACGGCAGGTCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTT
65 GAGGATGGCAGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTT
* * *
1242081 AGGTTGACACGGCTCCTACGTGATGAGGAGATCAAGTCGGATGATGACACGATTCCTATGTTATG
1 AGGTTGACACGGCTCCTACGTGATGAGGAGATCAAGTCGGGTGATGACACGGTTCCTATGTGATG
* * * * *
1242146 AGGATGGTAGGCCATCTAAAGGTGATAATACGGTTCCTATGTGATGAGGACGACTGATTATCTG
66 AGGATGGCAGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTT
* * * *
1242210 GGGTTTACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATG
1 AGGTTGACACGGCTCCTACGTGATGAGGAGATCAAGTCGGGTGATGACACGGTTCCTATGTGATG
* * * * *
1242275 AGGATGACAAGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTAGTTATC-T
66 AGGATGGCAGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTT
* ** ** *
1242338 GGAGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGAGG-GATGACATAGTTCCTACGTGA
1 AG-GTTGACACGGCTCCTACGTGATGAGGAGATCAAGTCG-GGTGATGACACGGTTCCTATGTGA
1242402 TGAGGA
64 TGAGGA
1242408 CGAAAGGCCA
Statistics
Matches: 289, Mismatches: 35, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
128 2 0.01
129 284 0.98
130 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (129 bp):
AGGTTGACACGGCTCCTACGTGATGAGGAGATCAAGTCGGGTGATGACACGGTTCCTATGTGATG
AGGATGGCAGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTT
Found at i:1242233 original size:43 final size:43
Alignment explanation
Indices: 1242175--1242407 Score: 137
Period size: 40 Copynumber: 5.5 Consensus size: 43
1242165 AGGTGATAAT
* * * *
1242175 ACGGTTCCTATGTGATGAGGACGACTGATTATCTGGGGTTTAC
1 ACGGTTCCTACGTGATGAGGATGACTGATTATCTGGGGATGAC
* * **
1242218 ACGGCTCCTACGTGATGAGGA-GA-TCA-GGTC-GGGTGATGAC
1 ACGGTTCCTACGTGATGAGGATGACTGATTATCTGGG-GATGAC
* ** * *
1242258 ACGGTTCCTACGTGATGAGGATGACAAGCCATCTA-AAGGTGATAAC
1 ACGGTTCCTACGTGATGAGGATGAC-TG--AT-TATCTGGGGATGAC
* * *
1242304 ACGGTTCCTACGTGATGAGGATGGCT-AGTTATCTGGAGTTGAC
1 ACGGTTCCTACGTGATGAGGATGACTGA-TTATCTGGGGATGAC
* *
1242347 ACGGCTCCTACGTGATGAGGA-GATCTG---GTC-GAGGGATGAC
1 ACGGTTCCTACGTGATGAGGATGA-CTGATTATCTG-GGGATGAC
**
1242387 ATAGTTCCTACGTGATGAGGA
1 ACGGTTCCTACGTGATGAGGA
1242408 CGAAAGGCCA
Statistics
Matches: 146, Mismatches: 30, Indels: 31
0.71 0.14 0.15
Matches are distributed among these distances:
39 4 0.03
40 52 0.36
41 4 0.03
42 6 0.04
43 48 0.33
45 1 0.01
46 29 0.20
47 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.25
Consensus pattern (43 bp):
ACGGTTCCTACGTGATGAGGATGACTGATTATCTGGGGATGAC
Found at i:1242594 original size:36 final size:36
Alignment explanation
Indices: 1242573--1242974 Score: 308
Period size: 36 Copynumber: 11.6 Consensus size: 36
1242563 AGAGGAAATA
* *
1242573 GTCTCAAGTGAGACAAAATTTGTTTCAAGAGAAATT
1 GTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACT
* * * *
1242609 GTCTCTAGTGAGACAAAATATGTTTCAAGGGAAACT
1 GTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACT
*
1242645 GTCTCAAGAGAGACGAAATTTGTTTCAAGA-AAACT
1 GTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACT
* *
1242680 GTCTCAAGAGAGACGAAATTTGTTTCAAGTGAAACAT
1 GTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAC-T
* * *
1242717 AT-TC-----A-AC-GATTTTGTTTCAAG-GAAACT
1 GTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACT
*
1242744 GTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAATT
1 GTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACT
* * * *
1242781 ATCTCAAGGGAGACAAAATTTGTTT-AAGGGGAACT
1 GTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACT
* * *
1242816 GTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAAC-
1 GTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACT
*
1242851 GTTCTC-A-A-AG------TTTACGTTTCAAGAGGAACT
1 G-TCTCAAGAGAGACAAAATTT--GTTTCAAGAGAAACT
* * *
1242881 ATCTCAAAAGAGACAAAACTTGTTTCAAGAGAAACT
1 GTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACT
* * * * * *
1242917 ATCTCAAGCA-AGATAAAATCTAGTTTTAAGAAAAATT
1 GTCTCAAG-AGAGACAAAAT-TTGTTTCAAGAGAAACT
*
1242954 GTCTCAAGGGAGACAAAATTT
1 GTCTCAAGAGAGACAAAATTT
1242975 AAAATCGTGG
Statistics
Matches: 294, Mismatches: 43, Indels: 58
0.74 0.11 0.15
Matches are distributed among these distances:
27 4 0.01
28 7 0.02
29 28 0.10
30 3 0.01
31 2 0.01
32 2 0.01
33 3 0.01
34 2 0.01
35 67 0.23
36 122 0.41
37 52 0.18
38 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
GTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACT
Found at i:1242600 original size:21 final size:21
Alignment explanation
Indices: 1242576--1242637 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1242566 GGAAATAGTC
1242576 TCAAGTGAGACAAAATTTGTT
1 TCAAGTGAGACAAAATTTGTT
*
1242597 TCAA--GAG---AAA-TTGTC
1 TCAAGTGAGACAAAATTTGTT
* *
1242612 TCTAGTGAGACAAAATATGTT
1 TCAAGTGAGACAAAATTTGTT
1242633 TCAAG
1 TCAAG
1242638 GGAAACTGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 12
0.64 0.11 0.26
Matches are distributed among these distances:
15 7 0.23
16 3 0.10
17 3 0.10
19 3 0.10
20 3 0.10
21 11 0.37
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (21 bp):
TCAAGTGAGACAAAATTTGTT
Found at i:1242672 original size:21 final size:21
Alignment explanation
Indices: 1242648--1242708 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1242638 GGAAACTGTC
1242648 TCAAGAGAGACGAAATTTGTT
1 TCAAGAGAGACGAAATTTGTT
* *
1242669 TC---A-AGA--AAA-CTGTC
1 TCAAGAGAGACGAAATTTGTT
1242683 TCAAGAGAGACGAAATTTGTT
1 TCAAGAGAGACGAAATTTGTT
1242704 TCAAG
1 TCAAG
1242709 TGAAACATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 5 0.17
15 3 0.10
17 4 0.14
18 4 0.14
20 3 0.10
21 10 0.34
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACGAAATTTGTT
Found at i:1242788 original size:136 final size:135
Alignment explanation
Indices: 1242591--1242974 Score: 436
Period size: 136 Copynumber: 2.8 Consensus size: 135
1242581 TGAGACAAAA
* * * * * *
1242591 TTTGTTTCAAGAGAAATTGTCTCTAGTGAGACAAAA-TATGTTTCAAGGGAAACTGTCTCAAGAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAGAG
* * * *
1242655 AGACGAAATTTGTTTCAAGAAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGTGAAACATAT-
66 AGACAAAATTTGTTT-AAGAAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAT-TC
*
1242719 TCAACGAT
129 TCAAAG-T
* *
1242727 TTTGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAATTATCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAGAG
** * *
1242791 AGACAAAATTTGTTTAAGGGGAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACGTTCT
66 AGACAAAATTTGTTTAA-GAAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACATTCT
1242856 CAAAGT
130 CAAAGT
* * * *
1242862 TTACGTTTCAAGAGGAACTATCTCAAAAGAGACAAAAC-TTGTTTCAAGAGAAACTATCTCAAGC
1 TT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAG-
* * *
1242926 A-AGATAAAATCTAGTTTTAAGAAAAATTGTCTCAAGGGAGACAAAATTT
64 AGAGACAAAAT-TTG-TTTAAG-AAAACTGTCTCAAGGGAGACAAAATTT
1242975 AAAATCGTGG
Statistics
Matches: 210, Mismatches: 29, Indels: 16
0.82 0.11 0.06
Matches are distributed among these distances:
135 27 0.13
136 130 0.62
137 25 0.12
138 28 0.13
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (135 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTATCTCAAGAG
AGACAAAATTTGTTTAAGAAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACATTCTC
AAAGT
Found at i:1242915 original size:65 final size:64
Alignment explanation
Indices: 1242802--1242923 Score: 158
Period size: 65 Copynumber: 1.9 Consensus size: 64
1242792 GACAAAATTT
* * ** *
1242802 GTTTAAGGGGAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACGT-TCTCAAAGTTTAC
1 GTTTAAGAGGAACTATCTCAAAAGAGACAAAATTCGTTTCAAGAGAAAC-TATCTCAAAGTTTAC
1242866 GTTTCAAGAGGAACTATCTCAAAAGAGACAAAACTT-GTTTCAAGAGAAACTATCTCAA
1 GTTT-AAGAGGAACTATCTCAAAAGAGACAAAA-TTCGTTTCAAGAGAAACTATCTCAA
1242924 GCAAGATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
64 5 0.10
65 43 0.86
66 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (64 bp):
GTTTAAGAGGAACTATCTCAAAAGAGACAAAATTCGTTTCAAGAGAAACTATCTCAAAGTTTAC
Found at i:1242972 original size:37 final size:37
Alignment explanation
Indices: 1242866--1242972 Score: 99
Period size: 37 Copynumber: 2.9 Consensus size: 37
1242856 CAAAGTTTAC
** ** *
1242866 GTTTCAAGAGGAACTATCTCAAAAGAGACAAAA-CTT
1 GTTTCAAGAAAAACTATCTCAAGCGAGACAAAATCTA
* * *
1242902 GTTTCAAGAGAAACTATCTCAAGCAAGATAAAATCTA
1 GTTTCAAGAAAAACTATCTCAAGCGAGACAAAATCTA
* * * *
1242939 GTTTTAAGAAAAATTGTCTCAAGGGAGACAAAAT
1 GTTTCAAGAAAAACTATCTCAAGCGAGACAAAAT
1242973 TTAAAATCGT
Statistics
Matches: 57, Mismatches: 13, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
36 28 0.49
37 29 0.51
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (37 bp):
GTTTCAAGAAAAACTATCTCAAGCGAGACAAAATCTA
Found at i:1244035 original size:32 final size:32
Alignment explanation
Indices: 1243998--1244072 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 32
1243988 ATTGAATTCC
* *
1243998 CAAAGATGCCCCGATATTCGATGTTGAATC-T
1 CAAAGATGCCCCAACATTCGATGTTGAATCTT
* *
1244029 CAAAAGATGCCCTAACATTTGATGTTGAATCTT
1 C-AAAGATGCCCCAACATTCGATGTTGAATCTT
1244062 CAAAGATGCCC
1 CAAAGATGCCC
1244073 GCTATTGCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 1 0.03
32 35 0.92
33 2 0.05
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (32 bp):
CAAAGATGCCCCAACATTCGATGTTGAATCTT
Found at i:1245120 original size:12 final size:13
Alignment explanation
Indices: 1245103--1245137 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1245093 CTTCTTATCC
1245103 TTTTTTCTTTG-T
1 TTTTTTCTTTGCT
1245115 TTTTTTCTTTGCT
1 TTTTTTCTTTGCT
*
1245128 TCTTTTCTTT
1 TTTTTTCTTT
1245138 TTTATTCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (13 bp):
TTTTTTCTTTGCT
Found at i:1245159 original size:20 final size:22
Alignment explanation
Indices: 1245114--1245165 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1245104 TTTTTCTTTG
*
1245114 TTTTTTTCTTTGCTTCTTTTCT
1 TTTTTTTCTTTGCTTCTTTACT
1245136 TTTTTATTC-TTG-TTCTTTACT
1 TTTTT-TTCTTTGCTTCTTTACT
*
1245157 TTTCTTTCT
1 TTTTTTTCT
1245166 GCTTTGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.12
21 12 0.46
22 8 0.31
23 3 0.12
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTTTTTCTTTGCTTCTTTACT
Found at i:1248506 original size:31 final size:29
Alignment explanation
Indices: 1248460--1248566 Score: 74
Period size: 31 Copynumber: 3.5 Consensus size: 29
1248450 AGATCTAGCA
1248460 AAAACATG-AACTTAAAGGATTAAAAATGGT
1 AAAACA-GAAACTTAAAGGA-TAAAAATGGT
* *
1248490 AAGAACAGAAACTTAAAAGACTAAAACA-GTT
1 AA-AACAGAAACTTAAAGGA-TAAAA-ATGGT
* * * * *
1248521 AAAACAAAAATTTAAAGGACATAAATAGT
1 AAAACAGAAACTTAAAGGATAAAAATGGT
1248550 AAAAACAGAAAACTTAA
1 -AAAACAG-AAACTTAA
1248567 GTGGCTAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
28 1 0.02
29 4 0.07
30 23 0.39
31 30 0.51
32 1 0.02
ACGTcount: A:0.60, C:0.09, G:0.12, T:0.19
Consensus pattern (29 bp):
AAAACAGAAACTTAAAGGATAAAAATGGT
Found at i:1248764 original size:32 final size:32
Alignment explanation
Indices: 1248728--1248810 Score: 112
Period size: 32 Copynumber: 2.6 Consensus size: 32
1248718 CACCGACGCT
* ** * *
1248728 GTACCGCCGCGCTGCCACCGCCGACCGTCGTC
1 GTACCACCGCGCCACCACCACCAACCGTCGTC
1248760 GTACCACCGCGCCACCACCACCAACCGTCGTC
1 GTACCACCGCGCCACCACCACCAACCGTCGTC
*
1248792 GTGCCACCGCGCCACCACC
1 GTACCACCGCGCCACCACC
1248811 GTCACCGGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.16, C:0.53, G:0.22, T:0.10
Consensus pattern (32 bp):
GTACCACCGCGCCACCACCACCAACCGTCGTC
Found at i:1249182 original size:145 final size:146
Alignment explanation
Indices: 1248918--1249195 Score: 375
Period size: 145 Copynumber: 1.9 Consensus size: 146
1248908 TGTTCTAAAA
* * *
1248918 AGGCCAAAAACCGTTCGGATTTATTTTCTCTGATCCACCGTCGTCCACCGTCTGATCGTCCTGAT
1 AGGCCAAAAACCGTTCGGACTTATTTTCTCTGATCCACCGTCGTCCACCGTCCGATCGTCCTGAA
* * * * * *
1248983 TTTTTAGTTTGTTGTTCGTGTTGGTATCACGCAACGTTTCATCGTTTGGAATGTTGATC-GCAGA
66 TTTTCAGTATGTTGTTCATGATGGTATCACGCAACGTTTCACCGTTCGGAATGTTGATCAG-AGA
1249047 TCCCGATCGCTGGCAAG
130 TCCCGATCGCTGGCAAG
*
1249064 AGGCCAAAAACCGTTCGG-CTTATTTTCT-TCGATCCATCGTCGTCCACCGTCCGATCGTCCTGA
1 AGGCCAAAAACCGTTCGGACTTATTTTCTCT-GATCCACCGTCGTCCACCGTCCGATCGTCCTGA
* * * *
1249127 ATTTTCAGTATGTTTTTCATGATGG-ACTTACGCAACTTTTGACCGTTCGGAATGTTGATCAGAG
65 ATTTTCAGTATGTTGTTCATGATGGTA-TCACGCAACGTTTCACCGTTCGGAATGTTGATCAGAG
1249191 ATCCC
129 ATCCC
1249196 AATCACCAGC
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
144 2 0.02
145 94 0.82
146 19 0.17
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (146 bp):
AGGCCAAAAACCGTTCGGACTTATTTTCTCTGATCCACCGTCGTCCACCGTCCGATCGTCCTGAA
TTTTCAGTATGTTGTTCATGATGGTATCACGCAACGTTTCACCGTTCGGAATGTTGATCAGAGAT
CCCGATCGCTGGCAAG
Found at i:1249524 original size:3 final size:3
Alignment explanation
Indices: 1249516--1249582 Score: 71
Period size: 3 Copynumber: 21.3 Consensus size: 3
1249506 GCAGGTTTTA
* * *
1249516 AAT AAT AAT AAT AAT AAAT AAT ACT AAT ACT AAT AAT AAT AAT ATTT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
*
1249563 AAT AAT AAT ATTT AAT AAT A
1 AAT AAT AAT A-AT AAT AAT A
1249583 TTTTTTCGAT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
3 46 0.87
4 7 0.13
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:1249535 original size:16 final size:16
Alignment explanation
Indices: 1249514--1249572 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 16
1249504 TGGCAGGTTT
1249514 TAAATAATAATAATAA
1 TAAATAATAATAATAA
* *
1249530 TAAATAATACTAATAC
1 TAAATAATAATAATAA
*
1249546 T-AATAATAATAATAT
1 TAAATAATAATAATAA
*
1249561 TTAATAATAATA
1 TAAATAATAATA
1249573 TTTAATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
15 13 0.34
16 25 0.66
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAATAATAATAATAA
Found at i:1249537 original size:13 final size:13
Alignment explanation
Indices: 1249519--1249582 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
1249509 GGTTTTAAAT
1249519 AATAATAATAATA
1 AATAATAATAATA
*
1249532 AATAATACTAATA
1 AATAATAATAATA
1249545 CTAATAATAATAATA
1 --AATAATAATAATA
**
1249560 TTTAATAATAATA
1 AATAATAATAATA
**
1249573 TTTAATAATA
1 AATAATAATA
1249583 TTTTTTCGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
13 33 0.73
15 12 0.27
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:1258757 original size:17 final size:17
Alignment explanation
Indices: 1258722--1258755 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1258712 TATGCCTAAA
1258722 TATTTATTTCTATTATT
1 TATTTATTTCTATTATT
1258739 TATTTATTT-TATTATT
1 TATTTATTTCTATTATT
1258755 T
1 T
1258756 TAGAAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTATTTCTATTATT
Found at i:1258977 original size:34 final size:34
Alignment explanation
Indices: 1258928--1259063 Score: 143
Period size: 33 Copynumber: 4.0 Consensus size: 34
1258918 ATGTTTTAAG
1258928 GAAAAA-AATCTCAAGTGAGATAATTTTTTTTTA
1 GAAAAACAATCTCAAGTGAGATAATTTTTTTTTA
* *
1258961 GAAAAACAATCTCAAGTGAG-TAAATTTGTTTTA
1 GAAAAACAATCTCAAGTGAGATAATTTTTTTTTA
* * *
1258994 -AGAAAACAATCTCAAGTGAGACGAAATTTATTTTAA
1 GA-AAAACAATCTCAAGTGAGA--TAATTTTTTTTTA
* * *
1259030 GAAAAAGAATCTTAAGTGAGATAATATTTCTTTT
1 GAAAAACAATCTCAAGTGAGATAAT-TTTTTTTT
1259064 GAGTAAAATG
Statistics
Matches: 83, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
32 1 0.01
33 35 0.42
34 16 0.19
35 5 0.06
36 25 0.30
37 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (34 bp):
GAAAAACAATCTCAAGTGAGATAATTTTTTTTTA
Found at i:1259179 original size:35 final size:35
Alignment explanation
Indices: 1259140--1259217 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
1259130 AAACAATCTT
*
1259140 AAGTGAGATAAAATATGTTTTAAGAAAAAAAACTC
1 AAGTGAGATAAAATATGTTTAAAGAAAAAAAACTC
** *
1259175 AAGTGAGATAAAATATGTTTAAAGAAAACGATCTC
1 AAGTGAGATAAAATATGTTTAAAGAAAAAAAACTC
1259210 AAGTGAGA
1 AAGTGAGA
1259218 CAATAAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.24
Consensus pattern (35 bp):
AAGTGAGATAAAATATGTTTAAAGAAAAAAAACTC
Found at i:1259412 original size:44 final size:42
Alignment explanation
Indices: 1259292--1259412 Score: 134
Period size: 44 Copynumber: 2.8 Consensus size: 42
1259282 TCAAACAAGA
* * *
1259292 TGATGTTGATCTAACTCCTTATGTGATGGAATTGAGTGATAG
1 TGATGTTGATCCAACTCCTTATGTGATGGAATCGAGCGATAG
* * * * *
1259334 TGATGCTAATCCAACTCCTTATGCGATAGAATCGAGCGAAATGG
1 TGATGTTGATCCAACTCCTTATGTGATGGAATCGAGCG--ATAG
* *
1259378 TGATGTTGGTCCAACTCCTTATGTGATGGTATCGA
1 TGATGTTGATCCAACTCCTTATGTGATGGAATCGA
1259413 ATATGAAAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
42 31 0.49
44 32 0.51
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (42 bp):
TGATGTTGATCCAACTCCTTATGTGATGGAATCGAGCGATAG
Found at i:1262064 original size:19 final size:20
Alignment explanation
Indices: 1262040--1262077 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1262030 TCCTTGTACT
1262040 TATTTTAT-TTTCTATTTTC
1 TATTTTATGTTTCTATTTTC
*
1262059 TATTTTATGTTTTTATTTT
1 TATTTTATGTTTCTATTTT
1262078 TTTGTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (20 bp):
TATTTTATGTTTCTATTTTC
Found at i:1262089 original size:2 final size:2
Alignment explanation
Indices: 1262084--1262124 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1262074 TTTTTTTGTT
1262084 TA 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 TA T
1262125 TTTAATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1262834 original size:13 final size:12
Alignment explanation
Indices: 1262807--1262842 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1262797 GTCCTTGTAC
1262807 TTATTTTATTTT
1 TTATTTTATTTT
1262819 TTATTTTATGTTT
1 TTATTTTAT-TTT
1262832 TTA-TTTATTTT
1 TTATTTTATTTT
1262843 GTTTTTCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.13
12 14 0.61
13 6 0.26
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.81
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:1263570 original size:19 final size:20
Alignment explanation
Indices: 1263546--1263583 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1263536 TCCTTGTACT
1263546 TATTTTAT-TTTCTATTTTC
1 TATTTTATGTTTCTATTTTC
*
1263565 TATTTTATGTTTTTATTTT
1 TATTTTATGTTTCTATTTT
1263584 TTTTGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (20 bp):
TATTTTATGTTTCTATTTTC
Found at i:1264349 original size:26 final size:29
Alignment explanation
Indices: 1264292--1264363 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 29
1264282 GTCCTTGTAC
* *
1264292 TTATTTTATTTTATTTTCTATTTTATGTTT
1 TTATTTT-TTTTATTATATATTTTATGTTT
1264322 TTATTTTTTTTA-TATATATTTT-TGTTT
1 TTATTTTTTTTATTATATATTTTATGTTT
* * *
1264349 TAATTATTTTAATTA
1 TTATTTTTTTTATTA
1264364 AGTTTATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 14 0.39
28 10 0.28
29 5 0.14
30 7 0.19
ACGTcount: A:0.22, C:0.01, G:0.03, T:0.74
Consensus pattern (29 bp):
TTATTTTTTTTATTATATATTTTATGTTT
Found at i:1265050 original size:13 final size:12
Alignment explanation
Indices: 1265023--1265067 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
1265013 GTCCTTTTAC
1265023 TTATTTTATTTT
1 TTATTTTATTTT
1265035 TTATTTTATGTTT
1 TTATTTTAT-TTT
1265048 TTA-TTTATTTT
1 TTATTTTATTTT
1265059 GTT-TTTTAT
1 -TTATTTTAT
1265068 ATATAGTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.10
12 21 0.70
13 6 0.20
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:1265054 original size:17 final size:16
Alignment explanation
Indices: 1265023--1265067 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
1265013 GTCCTTTTAC
*
1265023 TTATTTTATTTTTTATT
1 TTATTTT-TTATTTATT
1265040 TTATGTTTTTATTTATT
1 TTAT-TTTTTATTTATT
*
1265057 TTGTTTTTTAT
1 TTATTTTTTAT
1265068 ATATAGTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.28
17 15 0.60
18 3 0.12
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (16 bp):
TTATTTTTTATTTATT
Found at i:1265108 original size:22 final size:24
Alignment explanation
Indices: 1265058--1265110 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
1265048 TTATTTATTT
*
1265058 TGTTTTTTATATATAGTTCTTTAA
1 TGTTTTTAATATATAGTTCTTTAA
1265082 T-TTTTTAAT-TA-AGTT-TTTAAA
1 TGTTTTTAATATATAGTTCTTT-AA
1265103 TGTTTTTA
1 TGTTTTTA
1265111 CATAGCTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 8 0.31
23 7 0.27
24 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.64
Consensus pattern (24 bp):
TGTTTTTAATATATAGTTCTTTAA
Found at i:1265984 original size:733 final size:736
Alignment explanation
Indices: 1262108--1267833 Score: 9542
Period size: 739 Copynumber: 7.8 Consensus size: 736
1262098 TATATATATA
* * *
1262108 TATATATATATATATATTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAAT
1 TATATATATATTTTTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAAT
1262173 TCTTAGATTTTAGTTTTAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTT
66 TCTTAGATTTTAGTTTTAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTT
*
1262238 AGTTATGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCCAATACTTAATTTTCCTCTT
131 AGTTATGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTT
*
1262303 TTTCCAAGTCAATTTGTTTC-TGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATA
196 TTTCCATGTCAATTTG-TTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATA
*
1262367 AGCATAACTCAATCGATTTCATAATTGGATTAAAAGTAGTATTTATTTATTTTAAAATATTAAGA
260 AGCATAACTCAATCGATTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGA
* * * * ** * *
1262432 AAGGATTATCTTAAAGTAACTAGATGTCCTATTATGATATTTTAAAATAAATAAATACCCTATTA
325 AATGACTGTATTAAAGTAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTA
* * * *
1262497 GAAAACCCTAAAAAAATCGCGTATGCCTAAAATTAAAATTAAAAGGAAATGGAAATATTCGCTTA
390 GAAAACCCT-AAAAAATCACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTA
1262562 TTTAAACTTATCGAGACAATTC-ATCTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAA
454 TTTAAACTTATCGAGACAATTCGA-CTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAA
*
1262626 TTGAACATCCCTTACCTTTTCCAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTT
518 TTGAACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTT
* * * *
1262691 GGTCGAATCAAATTATTCATTTTAGTCACTTTTTAATTTCGGATTTAATTACTATCTTTTATTTT
583 GGTCAAATCAAATTATTCATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTT
1262756 CTTGCATTTTAGTCAATGTAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTATTTT-T
648 CTTGCATTTTAGTCAATGTAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTATTTTAT
* *
1262820 TATTTTATGTTT-TTATTTATTTTGTT
713 T-TTCTAT-TTTATTTTTTATTTT-TT
* *
1262846 TTTCACATATATTTGTTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTA
1 TAT-ATATATATTT-TTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTA
* *
1262911 ATTCTTAGACTTTAGTTTTAAATTAGATTAACATTCAGATCAAACTTAGAAATTAGGATTTCACT
64 ATTCTTAGATTTTAGTTTTAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACT
* * * * *
1262976 TTATTTATGTTCATACTAGGTATATTGTAATATTACATTTAATTTGCTAATAATTAATTTTCCTC
129 TTAGTTATGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTC
1263041 TTTTTCCATGTCAATTTGTTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCAT
194 TTTTTCCATGTCAATTTGTTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCAT
* *
1263106 AAGCTTAACTCAATCGATTTCATAATTGGATTAAATGTAGTATTTATTTATTTTAAAATATTAAG
259 AAGCATAACTCAATCGATTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAG
* * *
1263171 AAATGACTTTATTAAAGTAACTAGATGTCTTATTCCGATATTTTAAAATGAAAAAATACCCTACT
324 AAATGACTGTATTAAAGTAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACT
* *
1263236 AGAAAACCATAAAAAA-CTGCGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTT
389 AGAAAACCCTAAAAAATC-ACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTT
* *
1263300 ATTTAAACTTATCGAGACAATTCGACTAATTTTATTAGGGATTAGGTGTTGATAATTTTGAATAA
453 ATTTAAACTTATCGAGACAATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAA
*
1263365 TTGAACATCCCTTACCTTTTCTAATTTAATATGTAATTGGGA-TAATTAGCTTCTTTTTTCATTT
518 TTGAACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTT
* * *
1263429 GGTCAAATCAAATTATTCATTTTAGTCACTTTGTAATTTCGGATTTAACTACTATCTTTTATTTT
583 GGTCAAATCAAATTATTCATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTT
* *
1263494 CTTTCATTTTAGTCAATGTAATTATATTTTATTGAAATTAGGTCCTTGTACTTATTTTATTTTCT
648 CTTGCATTTTAGTCAATGTAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTA-TTT-T
1263559 ATTTTCTATTTTATGTTTTTATTTTTTTTGTTTT
711 ATTTTCTATTTTAT-TTTTTA------TT-TTTT
1263593 TATATATATATTTTTTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAA
1 TATATATATA-TTTTTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAA
1263658 TTCTTAGATTTTAGTTTTAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTT
65 TTCTTAGATTTTAGTTTTAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTT
* *
1263723 TAGTTTTGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCTAATAATTAATTTTCCTCT
130 TAGTTATGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCT
*
1263788 TTTTCCATGTCAATTTGTTCGTGCATATAGATCTAGACATTTCAAATATGTATGAAAGCCTCATA
195 TTTTCCATGTCAATTTGTTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATA
*
1263853 AGCTTAACTCAATCGATTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGA
260 AGCATAACTCAATCGATTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGA
1263918 AATGACTGTATTAAAGTAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTA
325 AATGACTGTATTAAAGTAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTA
*
1263983 TAAAACCCTAAAAAATCACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTAT
390 GAAAACCCTAAAAAATCACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTAT
*
1264048 TTAAACTTATCGAGACAATTCGACTAATTTTATGAGGGATTAGGTCTTGATATTTTTGAATAATT
455 TTAAACTTATCGAGACAATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATT
1264113 GAACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGG
520 GAACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGG
*
1264178 TCAAATCAAATTATTCATTTTAGTCACTTTGTAATTTTGGATTTAACTACTAGCTTTTATTTTCT
585 TCAAATCAAATTATTCATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCT
*
1264243 TGCATTTTAGTCAATGTAATTATATTTTATTGAAATTAGGTCCTTGTACTTATTTTATTTTATTT
650 TGCATTTTAGTCAATGTAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTATTTTATTT
1264308 TCTATTTTATGTTTTTATTTTTT
715 TCTATTTTAT-TTTTTATTTTTT
1264331 T-TATATATATTTTTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAAT
1 TATATATATATTTTTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAAT
*
1264395 TCTTAGATTTTAGTTTTAAATTAGATTAACATTCTGATCAAGCTTAGAAATTAGGATTTCACTTT
66 TCTTAGATTTTAGTTTTAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTT
1264460 AGTTATGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTT
131 AGTTATGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTT
* *
1264525 TTTCTATGTCAATTTGTTTGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAA
196 TTTCCATGTCAATTTGTTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAA
1264590 GCATAACTCAATCGATTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAA
261 GCATAACTCAATCGATTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAA
* * * * ** * * *
1264655 AGGATTGTCTTAAAGTAACTAGATATCCTATTATGATATTTTAAAATAAATAAACACCCTATTAG
326 ATGACTGTATTAAAGTAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAG
*
1264720 AAAACCCTAAAAAAATCGCGTATGCCTAAAATTAAAATTAAAA-G----G-AAATATTTGCTTAT
391 AAAACCCT-AAAAAATCACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTAT
* *
1264779 TTAAACTTATCGAGACAATTCGTCTAATTTTATTAGGGATTAGGTGTTGATATTTTTGAATAATT
455 TTAAACTTATCGAGACAATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATT
1264844 GAACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGG
520 GAACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGG
* *
1264909 TCGAATCAAATTATTCATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCATTTATTTTCT
585 TCAAATCAAATTATTCATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCT
*
1264974 TGCATTTTAGTCAATGTAATTATATTTTATTGCAATTAGGTCCTTTTACTTATTTTATTTT-TTA
650 TGCATTTTAGTCAATGTAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTATTTTATT-
* *
1265038 TTTTATGTTT-TTATTTATTTTGTT
714 TTCTAT-TTTATTTTTTATTTT-TT
* ** * *
1265062 T-TTTATATATAGTT-CTTTAATT-TTTTAATTAAGTTT-TTAAATGTTTTTACATAGC-TTAAT
1 TATATATATATTTTTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAAT
1265122 TCTTAGATTTTAGTTTTAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTT
66 TCTTAGATTTTAGTTTTAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTT
*
1265187 AGTTTTGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTT
131 AGTTATGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTT
*
1265252 TTTCCATGTCAATTTGTTCGTGCATATAGATCTAGACATTTCAAATATGTATGAAAGCCTCATAA
196 TTTCCATGTCAATTTGTTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAA
* *
1265317 GCTTAACTCAATCAATTTCATAATTGGATTAAAGGTAGT-TTTATTTATTTTAAAATATTAAGAA
261 GCATAACTCAATCGATTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAA
*
1265381 ATGACTGTATTAAAGTAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAT
326 ATGACTGTATTAAAGTAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAG
1265446 AAAACCCTAAAAAATCACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATT
391 AAAACCCTAAAAAATCACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATT
*
1265511 TAAACTTATCGAGACAATTCGACTAATTTTATGAGGGATTAGGTCTTGATATTTTTGAATAATTG
456 TAAACTTATCGAGACAATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTG
1265576 AACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCA-TTGGT
521 AACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGT
*
1265640 C-AATCAAA-TATTCATTTTAGTCACTTTGTAATTTTGGATTTAACTACTAGCTTTTATTTTCTT
586 CAAATCAAATTATTCATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCTT
*
1265703 GCATTTTAGTCAATGTAATTATATTTTATTGAAATTAGGTCCTTGTACTTATTTTATTTTATTTT
651 GCATTTTAGTCAATGTAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTATTTTATTTT
1265768 CTATTTTATGTTTTTATTTTTT
716 CTATTTTAT-TTTTTATTTTTT
*
1265790 TATATATATATTTTTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCAATAGCTTTAAT
1 TATATATATATTTTTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAAT
*
1265855 TCTTAGATTTTAGTTTTAAATTAGATTAACATTCTGATCAAGCTTAGAAATTAGGATTTCACTTT
66 TCTTAGATTTTAGTTTTAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTT
1265920 AGTTATGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTT
131 AGTTATGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTT
* *
1265985 TTTCTATGTCAATTTGTTTGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAA
196 TTTCCATGTCAATTTGTTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAA
1266050 GCATAACTCAATCGATTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAA
261 GCATAACTCAATCGATTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAA
* * * * ** * * *
1266115 AGGATTGTCTTAAAGTAACTAGATATCCTATTATGATATTTTAAAATTAATAAACACCCTATTAG
326 ATGACTGTATTAAAGTAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAG
*
1266180 AAAACCCTAAAAAAATCGCGTATGCCTAAAATTAAAATTAAAA-G----G-AAATATTTGCTTAT
391 AAAACCCT-AAAAAATCACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTAT
* *
1266239 TTAAACTTATCGAGACAATTCGTCTAATTTTATTAGGGATTAGGTGTTGATATTTTTGAATAATT
455 TTAAACTTATCGAGACAATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATT
1266304 GAACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGG
520 GAACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGG
* *
1266369 TCGAATCAAATTATTCATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCATTTATTTTCT
585 TCAAATCAAATTATTCATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCT
*
1266434 TGCATTTTAGTCAATGTAATTATATTTTATTGCAATTAGGTCCTTTTACTTATTTTATTTTTTAT
650 TGCATTTTAGTCAATGTAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTA--TTTTAT
* *
1266499 TTTATGTTTTTATTTATTT-TGTTTTT
713 TTTCT-ATTTTATTT-TTTAT-TTTTT
* * *
1266525 TATATATAT-TTGTTCTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTACATAGCTTTAAT
1 TATATATATATTTTTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAAT
*
1266589 TCTTAGATTTTAGTTTTAAATTAGATTAACATTAAGATCAAGCTTAGAAATTAGGATTTCACTTT
66 TCTTAGATTTTAGTTTTAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTT
* *
1266654 ATTTATGTTCATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTT
131 AGTTATGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTT
*
1266719 TTTCCATGTCAATTTGTTCGTGGATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAA
196 TTTCCATGTCAATTTGTTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAA
1266784 GCATAACTCAATCGATTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAA
261 GCATAACTCAATCGATTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAA
*
1266849 ATGACTTTATTAAAGTAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAG
326 ATGACTGTATTAAAGTAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAG
1266914 AAAACCCTAAAAAATCACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATT
391 AAAACCCTAAAAAATCACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATT
*
1266979 TAAACTTATCGAGACAATTCGACTAATTTTATTAGGGATTTGGTCTTGATATTTTTGAATAATTG
456 TAAACTTATCGAGACAATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTG
1267044 AACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGT
521 AACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGT
1267109 CAAATCAAATTATTCATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCTT
586 CAAATCAAATTATTCATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCTT
* *
1267174 GCATTTTAGTCAATATAATTATATTTTATTGCAATTAGGTCCTTTTACTTATTTTACTTAATTTA
651 GCATTTTAGTCAATGTAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTA--T--TTTA
1267239 TTTTACTTATTTTATTTTATT-TTGTTTT
712 TTTT-C-TATTTTATTTT-TTATT-TTTT
*
1267267 T-TATATATATTTGTTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATATCTTTAA
1 TATATATATATTT-TTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAA
* *
1267331 TTCTTAGATTTTAGTTTTAAATTAGATTAACATCCAAATCAAGCTTAGAAATTAGGATTTCACTT
65 TTCTTAGATTTTAGTTTTAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTT
*
1267396 TAGTTATGTTCATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCT
130 TAGTTATGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCT
*
1267461 TTTTCCATGTCAATTTGTTTGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATA
195 TTTTCCATGTCAATTTGTTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATA
1267526 AGCATAACTCAATCGATTTCATAATTGGATTAAAGGTAG----TATTTATTTTAAAATATTAAGA
260 AGCATAACTCAATCGATTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGA
* * * * *
1267587 AATGATTGTCTTAAAGTAACTAAATGTCCTATTTCGATATTTTAAAATGAATAAATAACCTACTA
325 AATGACTGTATTAAAGTAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTA
* * *
1267652 GAAAACCCTAAAAAATCACTTATGCC------TAAAATTAAAAGGAAAAGGAAATATTCGCTTAT
390 GAAAACCCTAAAAAATCACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTAT
* *
1267711 TTAAACTTATCGAGACAATTTGTCTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATT
455 TTAAACTTATCGAGACAATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATT
1267776 GAACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTT
520 GAACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTT
1267834 TTTTTCATTT
Statistics
Matches: 4715, Mismatches: 211, Indels: 129
0.93 0.04 0.03
Matches are distributed among these distances:
725 33 0.01
726 89 0.02
727 235 0.05
728 138 0.03
729 178 0.04
730 39 0.01
731 438 0.09
732 128 0.03
733 416 0.09
734 470 0.10
735 56 0.01
736 372 0.08
737 41 0.01
738 150 0.03
739 537 0.11
740 365 0.08
741 24 0.01
742 18 0.00
743 277 0.06
745 22 0.00
746 534 0.11
747 153 0.03
748 2 0.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (736 bp):
TATATATATATTTTTGTTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAAT
TCTTAGATTTTAGTTTTAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTT
AGTTATGTTTATAGTAGATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTT
TTTCCATGTCAATTTGTTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAA
GCATAACTCAATCGATTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAA
ATGACTGTATTAAAGTAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAG
AAAACCCTAAAAAATCACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATT
TAAACTTATCGAGACAATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTG
AACATCCCTTACCTTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGT
CAAATCAAATTATTCATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCTT
GCATTTTAGTCAATGTAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTATTTTATTTT
CTATTTTATTTTTTATTTTTT
Found at i:1266510 original size:13 final size:12
Alignment explanation
Indices: 1266483--1266527 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
1266473 GTCCTTTTAC
1266483 TTATTTTATTTT
1 TTATTTTATTTT
1266495 TTATTTTATGTTT
1 TTATTTTAT-TTT
1266508 TTA-TTTATTTT
1 TTATTTTATTTT
1266519 GTT-TTTTAT
1 -TTATTTTAT
1266528 ATATATTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.10
12 21 0.70
13 6 0.20
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:1266514 original size:17 final size:16
Alignment explanation
Indices: 1266483--1266553 Score: 61
Period size: 17 Copynumber: 4.2 Consensus size: 16
1266473 GTCCTTTTAC
*
1266483 TTATTTTATTTTTTATT
1 TTATTTT-TTATTTATT
1266500 TTATGTTTTTATTTATT
1 TTAT-TTTTTATTTATT
* *
1266517 TTGTTTTTTATATATAT
1 TTATTTTTTATTTAT-T
* *
1266534 TTGTTCTTTTAATTATT
1 TTATT-TTTTATTTATT
1266551 TTA
1 TTA
1266554 ATTAAGTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
16 10 0.22
17 24 0.53
18 11 0.24
ACGTcount: A:0.20, C:0.01, G:0.04, T:0.75
Consensus pattern (16 bp):
TTATTTTTTATTTATT
Found at i:1266526 original size:16 final size:16
Alignment explanation
Indices: 1266477--1266552 Score: 68
Period size: 16 Copynumber: 4.8 Consensus size: 16
1266467 AATTAGGTCC
* *
1266477 TTTTACTTATTTTATT
1 TTTTATTTATTTTGTT
*
1266493 TTTTA-TT-TTATG-T
1 TTTTATTTATTTTGTT
1266506 TTTTATTTATTTTGTT
1 TTTTATTTATTTTGTT
*
1266522 TTTTATATATATTTGTT
1 TTTTATTTAT-TTTGTT
*
1266539 CTTTTAATTATTTT
1 -TTTTATTTATTTT
1266553 AATTAAGTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
13 6 0.12
14 5 0.10
15 6 0.12
16 15 0.31
17 9 0.18
18 8 0.16
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.75
Consensus pattern (16 bp):
TTTTATTTATTTTGTT
Found at i:1267226 original size:739 final size:739
Alignment explanation
Indices: 1262124--1267833 Score: 9675
Period size: 746 Copynumber: 7.8 Consensus size: 739
1262114 TATATATATA
1262124 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAATTCTTAGATTTTAGTTT
1 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAATTCTTAGATTTTAGTTT
1262189 TAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTATGTTTATAGTA
66 TAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTATGTTTATAGTA
* *
1262254 GATATATTGTAATATTACATTTAATTTGCCAATACTTAATTTTCCTCTTTTTCCAAGTCAATTTG
131 GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCCATGTCAATTTG
1262319 TTTC-TGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGA
196 -TTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGA
* * * *
1262383 TTTCATAATTGGATTAAAAGTAGTATTTATTTATTTTAAAATATTAAGAAAGGATTATCTTAAAG
260 TTTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAAATGATTGTATTAAAG
** * *
1262448 TAACTAGATGTCCTATTATGATATTTTAAAATAAATAAATACCCTATTAGAAAACCCTAAAAAAA
325 TAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAGAAAACCCT-AAAAAA
* * * *
1262513 TCGCGTATGCCTAAAATTAAAATTAAAAGGAAATGGAAATATTCGCTTATTTAAACTTATCGAGA
389 TCACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATTTAAACTTATCGAGA
1262578 CAATTC-ATCTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTGAACATCCCTTACC
454 CAATTCGA-CTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTGAACATCCCTTACC
* *
1262642 TTTTCCAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGTCGAATCAAATTAT
518 TTTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGTCAAATCAAATTAT
* * *
1262707 TCATTTTAGTCACTTTTTAATTTCGGATTTAATTACTATCTTTTATTTTCTTGCATTTTAGTCAA
583 TCATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCTTGCATTTTAGTCAA
1262772 TGTAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTATTTTTTATTTTATGTTTTTATT
648 TGTAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTATTTTTTATTTTATGTTTTTATT
* *
1262837 TATTTTGTTTTTCACATATATTTGTTG
713 TATTTTGTTTTTTATATATATTTGTTG
*
1262864 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAATTCTTAGACTTTAGTTT
1 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAATTCTTAGATTTTAGTTT
* * * *
1262929 TAAATTAGATTAACATTCAGATCAAACTTAGAAATTAGGATTTCACTTTATTTATGTTCATACTA
66 TAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTATGTTTATAGTA
* *
1262994 GGTATATTGTAATATTACATTTAATTTGCTAATAATTAATTTTCCTCTTTTTCCATGTCAATTTG
131 GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCCATGTCAATTTG
*
1263059 TTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCTTAACTCAATCGAT
196 TTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGAT
*
1263124 TTCATAATTGGATTAAATGTAGTATTTATTTATTTTAAAATATTAAGAAATGACTT-TATTAAAG
261 TTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAAATGA-TTGTATTAAAG
* * *
1263188 TAACTAGATGTCTTATTCCGATATTTTAAAATGAAAAAATACCCTACTAGAAAACCATAAAAAA-
325 TAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAGAAAACCCTAAAAAAT
*
1263252 CTGCGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATTTAAACTTATCGAGA
390 C-ACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATTTAAACTTATCGAGA
* *
1263317 CAATTCGACTAATTTTATTAGGGATTAGGTGTTGATAATTTTGAATAATTGAACATCCCTTACCT
454 CAATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTGAACATCCCTTACCT
*
1263382 TTTCTAATTTAATATGTAATTGGGA-TAATTAGCTTCTTTTTTCATTTGGTCAAATCAAATTATT
519 TTTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGTCAAATCAAATTATT
* * * *
1263446 CATTTTAGTCACTTTGTAATTTCGGATTTAACTACTATCTTTTATTTTCTTTCATTTTAGTCAAT
584 CATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCTTGCATTTTAGTCAAT
*
1263511 GTAATTATATTTTATTGAAATTAGGTCCTTGTACTTATTTTATTTTCTATTTTCTATTTTATGTT
649 GTAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTA-----T-TTTT-TATTTTATGTT
* *
1263576 TTTATTTTTTTTGTTTTTATATATATATTTTTTG
707 TTTATTTATTTTGTTTTT-TATATATATTTGTTG
1263610 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAATTCTTAGATTTTAGTTT
1 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAATTCTTAGATTTTAGTTT
*
1263675 TAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTTTGTTTATAGTA
66 TAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTATGTTTATAGTA
*
1263740 GATATATTGTAATATTACATTTAATTTGCTAATAATTAATTTTCCTCTTTTTCCATGTCAATTTG
131 GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCCATGTCAATTTG
* *
1263805 TTCGTGCATATAGATCTAGACATTTCAAATATGTATGAAAGCCTCATAAGCTTAACTCAATCGAT
196 TTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGAT
*
1263870 TTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAAATGACTGTATTAAAGT
261 TTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAAATGATTGTATTAAAGT
*
1263935 AACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTATAAAACCCTAAAAAATC
326 AACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAGAAAACCCTAAAAAATC
1264000 ACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATTTAAACTTATCGAGACA
391 ACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATTTAAACTTATCGAGACA
*
1264065 ATTCGACTAATTTTATGAGGGATTAGGTCTTGATATTTTTGAATAATTGAACATCCCTTACCTTT
456 ATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTGAACATCCCTTACCTTT
1264130 TCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGTCAAATCAAATTATTCA
521 TCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGTCAAATCAAATTATTCA
*
1264195 TTTTAGTCACTTTGTAATTTTGGATTTAACTACTAGCTTTTATTTTCTTGCATTTTAGTCAATGT
586 TTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCTTGCATTTTAGTCAATGT
* * *
1264260 AATTATATTTTATTGAAATTAGGTCCTTGTACTTATTTTA--TTTTATTTTCT-ATTTTATGTT-
651 AATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTATTTTTTATTTTATGTTTTTAT-TTA
*
1264321 TTTATTTTTTTTATATATATTT-TTG
715 TTT-TGTTTTTTATATATATTTGTTG
1264346 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAATTCTTAGATTTTAGTTT
1 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAATTCTTAGATTTTAGTTT
*
1264411 TAAATTAGATTAACATTCTGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTATGTTTATAGTA
66 TAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTATGTTTATAGTA
*
1264476 GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCTATGTCAATTTG
131 GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCCATGTCAATTTG
*
1264541 TTTGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGAT
196 TTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGAT
* *
1264606 TTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAAAGGATTGTCTTAAAGT
261 TTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAAATGATTGTATTAAAGT
* ** * * *
1264671 AACTAGATATCCTATTATGATATTTTAAAATAAATAAACACCCTATTAGAAAACCCTAAAAAAAT
326 AACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAGAAAACCCT-AAAAAAT
*
1264736 CGCGTATGCCTAAAATTAAAATTAAAA-G----G-AAATATTTGCTTATTTAAACTTATCGAGAC
390 CACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATTTAAACTTATCGAGAC
* *
1264795 AATTCGTCTAATTTTATTAGGGATTAGGTGTTGATATTTTTGAATAATTGAACATCCCTTACCTT
455 AATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTGAACATCCCTTACCTT
*
1264860 TTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGTCGAATCAAATTATTC
520 TTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGTCAAATCAAATTATTC
*
1264925 ATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCATTTATTTTCTTGCATTTTAGTCAATG
585 ATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCTTGCATTTTAGTCAATG
*
1264990 TAATTATATTTTATTGCAATTAGGTCCTTTTACTTATTTTATTTTTTATTTTATGTTTTTATTTA
650 TAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTATTTTTTATTTTATGTTTTTATTTA
1265055 TTTTGTTTTTTATATATA---GTT-
715 TTTTGTTTTTTATATATATTTGTTG
* *
1265076 CTTTAATT-TTTTAATTAAGTTT-TTAAATGTTTTTACATAGC-TTAATTCTTAGATTTTAGTTT
1 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAATTCTTAGATTTTAGTTT
*
1265138 TAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTTTGTTTATAGTA
66 TAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTATGTTTATAGTA
1265203 GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCCATGTCAATTTG
131 GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCCATGTCAATTTG
* * *
1265268 TTCGTGCATATAGATCTAGACATTTCAAATATGTATGAAAGCCTCATAAGCTTAACTCAATCAAT
196 TTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGAT
*
1265333 TTCATAATTGGATTAAAGGTAGT-TTTATTTATTTTAAAATATTAAGAAATGACTGTATTAAAGT
261 TTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAAATGATTGTATTAAAGT
*
1265397 AACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTATAAAACCCTAAAAAATC
326 AACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAGAAAACCCTAAAAAATC
1265462 ACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATTTAAACTTATCGAGACA
391 ACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATTTAAACTTATCGAGACA
*
1265527 ATTCGACTAATTTTATGAGGGATTAGGTCTTGATATTTTTGAATAATTGAACATCCCTTACCTTT
456 ATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTGAACATCCCTTACCTTT
1265592 TCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCA-TTGGTC-AATCAAA-TATTCA
521 TCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGTCAAATCAAATTATTCA
*
1265654 TTTTAGTCACTTTGTAATTTTGGATTTAACTACTAGCTTTTATTTTCTTGCATTTTAGTCAATGT
586 TTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCTTGCATTTTAGTCAATGT
* * *
1265719 AATTATATTTTATTGAAATTAGGTCCTTGTACTTATTTTA--TTTTATTTTCT-ATTTTATGTT-
651 AATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTATTTTTTATTTTATGTTTTTAT-TTA
*
1265780 TTTAT-TTTTTTATATATATATTTTTG
715 TTT-TGTTTTTTATATATAT-TTGTTG
*
1265806 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCAATAGCTTTAATTCTTAGATTTTAGTTT
1 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAATTCTTAGATTTTAGTTT
*
1265871 TAAATTAGATTAACATTCTGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTATGTTTATAGTA
66 TAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTATGTTTATAGTA
*
1265936 GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCTATGTCAATTTG
131 GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCCATGTCAATTTG
*
1266001 TTTGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGAT
196 TTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGAT
* *
1266066 TTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAAAGGATTGTCTTAAAGT
261 TTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAAATGATTGTATTAAAGT
* ** * * *
1266131 AACTAGATATCCTATTATGATATTTTAAAATTAATAAACACCCTATTAGAAAACCCTAAAAAAAT
326 AACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAGAAAACCCT-AAAAAAT
*
1266196 CGCGTATGCCTAAAATTAAAATTAAAA-G----G-AAATATTTGCTTATTTAAACTTATCGAGAC
390 CACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATTTAAACTTATCGAGAC
* *
1266255 AATTCGTCTAATTTTATTAGGGATTAGGTGTTGATATTTTTGAATAATTGAACATCCCTTACCTT
455 AATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTGAACATCCCTTACCTT
*
1266320 TTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGTCGAATCAAATTATTC
520 TTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGTCAAATCAAATTATTC
*
1266385 ATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCATTTATTTTCTTGCATTTTAGTCAATG
585 ATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCTTGCATTTTAGTCAATG
*
1266450 TAATTATATTTTATTGCAATTAGGTCCTTTTACTTATTTTATTTTTTATTTTATGTTTTTATTTA
650 TAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTATTTTTTATTTTATGTTTTTATTTA
*
1266515 TTTTGTTTTTTATATATATTTGTTC
715 TTTTGTTTTTTATATATATTTGTTG
*
1266540 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTACATAGCTTTAATTCTTAGATTTTAGTTT
1 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAATTCTTAGATTTTAGTTT
* * *
1266605 TAAATTAGATTAACATTAAGATCAAGCTTAGAAATTAGGATTTCACTTTATTTATGTTCATAGTA
66 TAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTATGTTTATAGTA
1266670 GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCCATGTCAATTTG
131 GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCCATGTCAATTTG
*
1266735 TTCGTGGATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGAT
196 TTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGAT
1266800 TTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAAATGACTT-TATTAAAG
261 TTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAAATGA-TTGTATTAAAG
1266864 TAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAGAAAACCCTAAAAAAT
325 TAACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAGAAAACCCTAAAAAAT
1266929 CACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATTTAAACTTATCGAGAC
390 CACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATTTAAACTTATCGAGAC
*
1266994 AATTCGACTAATTTTATTAGGGATTTGGTCTTGATATTTTTGAATAATTGAACATCCCTTACCTT
455 AATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTGAACATCCCTTACCTT
1267059 TTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGTCAAATCAAATTATTC
520 TTCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGTCAAATCAAATTATTC
*
1267124 ATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCTTGCATTTTAGTCAATA
585 ATTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCTTGCATTTTAGTCAATG
* *
1267189 TAATTATATTTTATTGCAATTAGGTCCTTTTACTTATTTTACTTAATTTATTTTACT-TATTTTA
650 TAATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTA-TT-TTTTATTTTA-TGT-TTTTA
1267253 TTTTATTTTGTTTTTTATATATATTTGTTG
711 -TTTATTTTGTTTTTTATATATATTTGTTG
*
1267283 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATATCTTTAATTCTTAGATTTTAGTTT
1 TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAATTCTTAGATTTTAGTTT
* * *
1267348 TAAATTAGATTAACATCCAAATCAAGCTTAGAAATTAGGATTTCACTTTAGTTATGTTCATAGTA
66 TAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTATGTTTATAGTA
1267413 GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCCATGTCAATTTG
131 GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCCATGTCAATTTG
*
1267478 TTTGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGAT
196 TTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGAT
*
1267543 TTCATAATTGGATTAAAGGTAG----TATTTATTTTAAAATATTAAGAAATGATTGTCTTAAAGT
261 TTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAAATGATTGTATTAAAGT
* * *
1267604 AACTAAATGTCCTATTTCGATATTTTAAAATGAATAAATAACCTACTAGAAAACCCTAAAAAATC
326 AACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAGAAAACCCTAAAAAATC
* * *
1267669 ACTTATGCC------TAAAATTAAAAGGAAAAGGAAATATTCGCTTATTTAAACTTATCGAGACA
391 ACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATTTAAACTTATCGAGACA
* *
1267728 ATTTGTCTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTGAACATCCCTTACCTTT
456 ATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTGAACATCCCTTACCTTT
1267793 TCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTT
521 TCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTT
1267834 TTTTTCATTT
Statistics
Matches: 4712, Mismatches: 196, Indels: 131
0.94 0.04 0.03
Matches are distributed among these distances:
725 55 0.01
726 102 0.02
727 232 0.05
728 125 0.03
729 159 0.03
730 28 0.01
731 417 0.09
732 125 0.03
733 442 0.09
734 478 0.10
735 58 0.01
736 369 0.08
737 53 0.01
738 160 0.03
739 521 0.11
740 358 0.08
741 12 0.00
742 6 0.00
743 303 0.06
744 4 0.00
745 29 0.01
746 532 0.11
747 144 0.03
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (739 bp):
TTTTAATTATTTTAATTAAGTTTATTAAATGTTTTTCCATAGCTTTAATTCTTAGATTTTAGTTT
TAAATTAGATTAACATTCAGATCAAGCTTAGAAATTAGGATTTCACTTTAGTTATGTTTATAGTA
GATATATTGTAATATTACATTTAATTTGCTAATACTTAATTTTCCTCTTTTTCCATGTCAATTTG
TTCGTGCATATAGATCTAGACATTTCGAATATGTATGAAAGCCTCATAAGCATAACTCAATCGAT
TTCATAATTGGATTAAAGGTAGTATTTATTTATTTTAAAATATTAAGAAATGATTGTATTAAAGT
AACTAGATGTCCTATTCCGATATTTTAAAATGAATAAATACCCTACTAGAAAACCCTAAAAAATC
ACGTATGCCTAAAATTAAAATTAAAAGGAAAAGAAAATATTTGCTTATTTAAACTTATCGAGACA
ATTCGACTAATTTTATTAGGGATTAGGTCTTGATATTTTTGAATAATTGAACATCCCTTACCTTT
TCTAATTAAATATGTAATTGGGATTAATTAGCTTCTTTTTTCATTTGGTCAAATCAAATTATTCA
TTTTAGTCACTTTTTAATTTTGGATTTAACTACTAGCTTTTATTTTCTTGCATTTTAGTCAATGT
AATTATATTTTATTGCAATTAGGTCCTTGTACTTATTTTATTTTTTATTTTATGTTTTTATTTAT
TTTGTTTTTTATATATATTTGTTG
Found at i:1267241 original size:14 final size:14
Alignment explanation
Indices: 1267222--1267257 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1267212 GTCCTTTTAC
1267222 TTATTTTACTTAAT
1 TTATTTTACTTAAT
*
1267236 TTATTTTACTTATT
1 TTATTTTACTTAAT
1267250 TTATTTTA
1 TTATTTTA
1267258 TTTTGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTTTACTTAAT
Found at i:1270441 original size:18 final size:19
Alignment explanation
Indices: 1270393--1270441 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1270383 TTGGACCCTT
*
1270393 AGTGCATCGGTGCACTAAG
1 AGTGCATCGATGCACTAAG
1270412 AGTGCATCGATGCA-TAA-
1 AGTGCATCGATGCACTAAG
1270429 AGTGCATTCGATG
1 AGTGCA-TCGATG
1270442 TTTCAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 9 0.32
19 13 0.46
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAG
Found at i:1272114 original size:21 final size:22
Alignment explanation
Indices: 1272058--1272145 Score: 88
Period size: 23 Copynumber: 3.9 Consensus size: 22
1272048 GCATGGTAGT
1272058 GTGCATCGATGCACATTCAAGAA
1 GTGCATCGATGCACATTCAAG-A
* * *
1272081 GTGCATCGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAAGA
* *
1272102 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGA
1272125 GATGCATCGATGCACTATTCA
1 G-TGCATCGATGCAC-ATTCA
1272146 GTGTATCGAT
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
21 15 0.28
22 2 0.04
23 19 0.36
24 13 0.25
25 4 0.08
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGA
Found at i:1272150 original size:44 final size:43
Alignment explanation
Indices: 1272062--1272158 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 43
1272052 GGTAGTGTGC
* *
1272062 ATCGATGCACATTCAAGAAGTGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGAAGTGCATCGATGCACATTCA-GGTGT
*
1272106 ATCGATGCACATTCAA-AGGGATGCATCGATGCACTATTCA-GTGT
1 ATCGATGCACATTCAAGA-AG-TGCATCGATGCAC-ATTCAGGTGT
1272150 ATCGATGCA
1 ATCGATGCA
1272159 TTAAGCACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
43 1 0.02
44 30 0.64
45 12 0.26
46 4 0.09
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (43 bp):
ATCGATGCACATTCAAGAAGTGCATCGATGCACATTCAGGTGT
Found at i:1277832 original size:21 final size:21
Alignment explanation
Indices: 1277806--1277853 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1277796 TTGGGAGCGT
1277806 CTGGTGCATCGATGCATAGGG
1 CTGGTGCATCGATGCATAGGG
1277827 CTGGTGCATCGATGCATAGGG
1 CTGGTGCATCGATGCATAGGG
1277848 CTGGTG
1 CTGGTG
1277854 TATTGGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.17, C:0.19, G:0.40, T:0.25
Consensus pattern (21 bp):
CTGGTGCATCGATGCATAGGG
Found at i:1278009 original size:64 final size:62
Alignment explanation
Indices: 1277923--1278085 Score: 175
Period size: 65 Copynumber: 2.5 Consensus size: 62
1277913 TGAACTAAGA
* * * * *
1277923 GTGCATCGATGCATGAAGTGCATTCGATGCTTCAAACAAGCC-AGAGTGCATCGATGCATGGTCT
1 GTGCATCAATGCATAAAATGCATTCGATG-TTCAAA-AA-CCTAGAGTGCATCGATGCATGCTAT
* *
1277987 GTGCATCAATGCATAAAATGCATTTGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGCTAT
1 GTGCATCAATGCATAAAATGCATTCGATG--TTCA-AAAACCTAGAGTGCATCGATGCATGCTAT
* * *
1278052 GTACATCAATGAATAAAATGCATTCAATGTTCAA
1 GTGCATCAATGCATAAAATGCATTCGATGTTCAA
1278086 TTTATTCAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
62 1 0.01
63 4 0.05
64 27 0.32
65 50 0.60
66 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (62 bp):
GTGCATCAATGCATAAAATGCATTCGATGTTCAAAAACCTAGAGTGCATCGATGCATGCTAT
Found at i:1281487 original size:136 final size:128
Alignment explanation
Indices: 1281240--1281546 Score: 377
Period size: 136 Copynumber: 2.4 Consensus size: 128
1281230 AAGGATAATG
* * * * *
1281240 GTTTCAAGAGAAACTAACTCGAAGATGA--TGCTTCAAGAGAAGCTATCTCAAGAGACAAACTTG
1 GTTTCAAGAGAAACAAACTCAAAGATGATGTGTTTCAAGAGAAACTATCTCAAGAGAAAAACTTG
* ** *
1281303 TTTCAAGGGAAACATACTCAGATTTTTGTTTCAAGAGAAACTGTCTCAATAGAGACAAAATTT
66 TTTCAAGGGAAACAGACTCAGATTTTTGTTTCAAGAGAAACTACCTCAAGAGAGACAAAATTT
* *
1281366 GTTTCAAGGGAAACAATCTCAAAGATGATGGTGTTTCAAGAGAAACTATCTCAAGGCAGATAAAA
1 GTTTCAAGAGAAACAAACTCAAAGATGAT-GTGTTTCAAGAGAAACTATCTCAA-G-AGA-AAAA
* * *
1281431 CTTTGTTTCAAGAGG-AACAGACTCAAAGGTTTTGTGTTTCTAGAGAAACTACCTCAAGGGAGAC
62 C-TTGTTTCAAG-GGAAACAGACTC--AGATTTT-TGTTTCAAGAGAAACTACCTCAAGAGAGAC
1281495 AAAATTT
122 AAAATTT
*
1281502 GTTTCAAGAGAAACAAACTCAAAGATGATGTGTTTCAATAGAAAC
1 GTTTCAAGAGAAACAAACTCAAAGATGATGTGTTTCAAGAGAAAC
1281547 AATTTCTAAA
Statistics
Matches: 153, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
126 24 0.16
129 21 0.14
130 1 0.01
131 3 0.02
132 4 0.03
133 18 0.12
134 2 0.01
135 21 0.14
136 59 0.39
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (128 bp):
GTTTCAAGAGAAACAAACTCAAAGATGATGTGTTTCAAGAGAAACTATCTCAAGAGAAAAACTTG
TTTCAAGGGAAACAGACTCAGATTTTTGTTTCAAGAGAAACTACCTCAAGAGAGACAAAATTT
Found at i:1281534 original size:67 final size:67
Alignment explanation
Indices: 1281240--1281546 Score: 324
Period size: 68 Copynumber: 4.7 Consensus size: 67
1281230 AAGGATAATG
* * * * *
1281240 GTTTCAAGAGAAACTAACTCGAAGATGA--TGCTTCAAGAGAAGCTATCTCAA--GAGAC-AAAC
1 GTTTCAAGAGAAACAAACTCAAAGATGATGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAT
1281300 TT
66 TT
* * * * * **
1281302 GTTTCAAGGGAAACATACTC--AGAT-TTTTGTTTCAAGAGAAACTGTCTCAATAGAGACAAAAT
1 GTTTCAAGAGAAACAAACTCAAAGATGATGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAT
1281364 TT
66 TT
* * * *
1281366 GTTTCAAGGGAAACAATCTCAAAGATGATGGTGTTTCAAGAGAAACTATCTCAAGGCAGATAAAA
1 GTTTCAAGAGAAACAAACTCAAAGATGAT-GTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA
1281431 CTTT
65 -TTT
* * * ** * *
1281435 GTTTCAAGAGGAACAGACTCAAAGGTTTTGTGTTTCTAGAGAAACTACCTCAAGGGAGACAAAAT
1 GTTTCAAGAGAAACAAACTCAAAGATGATGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAT
1281500 TT
66 TT
*
1281502 GTTTCAAGAGAAACAAACTCAAAGATGATGTGTTTCAATAGAAAC
1 GTTTCAAGAGAAACAAACTCAAAGATGATGTGTTTCAAGAGAAAC
1281547 AATTTCTAAA
Statistics
Matches: 200, Mismatches: 35, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
60 4 0.02
61 20 0.10
62 17 0.09
63 5 0.03
64 23 0.12
66 4 0.02
67 42 0.21
68 60 0.30
69 25 0.12
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (67 bp):
GTTTCAAGAGAAACAAACTCAAAGATGATGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAT
TT
Found at i:1281536 original size:31 final size:31
Alignment explanation
Indices: 1281365--1281548 Score: 98
Period size: 31 Copynumber: 5.5 Consensus size: 31
1281355 AGACAAAATT
* * *
1281365 TGTTTCAAGGGAAACAATCTCAAAGATGATGG
1 TGTTTCAAGAGAAACAAACTCAAAGATAAT-G
* * *
1281397 TGTTTCAAGAGAAACTATCTCAAGGCAGATAAAACTT
1 TGTTTCAAGAGAAACAAACTCAA---AGAT--AA-TG
* * * **
1281434 TGTTTCAAGAGGAACAGACTCAAAGGTTTTG
1 TGTTTCAAGAGAAACAAACTCAAAGATAATG
* * * * *
1281465 TGTTTCTAGAGAAACTACCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACAAACTCAA---AG--ATAATG
*
1281501 TGTTTCAAGAGAAACAAACTCAAAGATGATG
1 TGTTTCAAGAGAAACAAACTCAAAGATAATG
*
1281532 TGTTTCAATAGAAACAA
1 TGTTTCAAGAGAAACAA
1281549 TTTCTAAATT
Statistics
Matches: 112, Mismatches: 29, Indels: 23
0.68 0.18 0.14
Matches are distributed among these distances:
31 38 0.34
32 21 0.19
33 2 0.02
34 5 0.04
35 4 0.04
36 21 0.19
37 20 0.18
38 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (31 bp):
TGTTTCAAGAGAAACAAACTCAAAGATAATG
Found at i:1283389 original size:2 final size:2
Alignment explanation
Indices: 1283384--1283429 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1283374 CACAGTGCAA
*
1283384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1283426 AT AT
1 AT AT
1283430 TGGGTAAACG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1285555 original size:27 final size:27
Alignment explanation
Indices: 1285517--1285572 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
1285507 TGTTATGCAG
*
1285517 AATGTAAAGATGTATATGGAGATACAA
1 AATGCAAAGATGTATATGGAGATACAA
* *
1285544 AATGCAAAGATGTATATGTAGATGCAA
1 AATGCAAAGATGTATATGGAGATACAA
1285571 AA
1 AA
1285573 ATATTGATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.25
Consensus pattern (27 bp):
AATGCAAAGATGTATATGGAGATACAA
Found at i:1287775 original size:30 final size:29
Alignment explanation
Indices: 1287740--1288019 Score: 250
Period size: 29 Copynumber: 9.7 Consensus size: 29
1287730 CAAAAGGGAT
* *
1287740 TAAAATAGAACAATAAAATATTTAAAGGAC
1 TAAAATAGAAAAATAAAA-ACTTAAAGGAC
* ** * **
1287770 CAAAATATGATTAACAAAAA-TTTGAGGAC
1 TAAAATA-GAAAAATAAAAACTTAAAGGAC
* * *
1287799 AAAAATAG-AAAATAAAAACTTAAGGGAA
1 TAAAATAGAAAAATAAAAACTTAAAGGAC
* *
1287827 TAAAATAGCAAAAATAGAAACTTAAAGGAT
1 TAAAATAG-AAAAATAAAAACTTAAAGGAC
*
1287857 TAAAATCACG-AAAATAAAAACTTAAGGGAC
1 TAAAAT-A-GAAAAATAAAAACTTAAAGGAC
1287887 TAAAATAGTAAAAATAGAAAA-TTAAAGGAC
1 TAAAATAG-AAAAATA-AAAACTTAAAGGAC
*
1287917 -AAAATAGAAAAATAGAAACTTAAAGGAC
1 TAAAATAGAAAAATAAAAACTTAAAGGAC
* * *
1287945 TAAAATAGAAAAATAGACATTTAAAGGAC
1 TAAAATAGAAAAATAAAAACTTAAAGGAC
* * *
1287974 TAAAATAGCAAAATAGAAACTTAAGGGAC
1 TAAAATAGAAAAATAAAAACTTAAAGGAC
*
1288003 T-AAATA-ATAAATAAAAA
1 TAAAATAGAAAAATAAAAA
1288020 TACTTTAGAG
Statistics
Matches: 207, Mismatches: 32, Indels: 25
0.78 0.12 0.09
Matches are distributed among these distances:
27 18 0.09
28 35 0.17
29 73 0.35
30 67 0.32
31 13 0.06
32 1 0.00
ACGTcount: A:0.61, C:0.07, G:0.13, T:0.19
Consensus pattern (29 bp):
TAAAATAGAAAAATAAAAACTTAAAGGAC
Found at i:1287831 original size:29 final size:29
Alignment explanation
Indices: 1287794--1288006 Score: 261
Period size: 29 Copynumber: 7.3 Consensus size: 29
1287784 CAAAAATTTG
* *
1287794 AGGACAAAAATAG-AAAATAAAAACTTAA
1 AGGACTAAAATAGAAAAATAGAAACTTAA
* *
1287822 GGGAATAAAATAGCAAAAATAGAAACTTAA
1 AGGACTAAAATAG-AAAAATAGAAACTTAA
* *
1287852 AGGATTAAAATCACG-AAAATAAAAACTTAA
1 AGGACTAAAAT-A-GAAAAATAGAAACTTAA
* *
1287882 GGGACTAAAATAGTAAAAATAGAAAATTAA
1 AGGACTAAAATAG-AAAAATAGAAACTTAA
1287912 AGGAC-AAAATAGAAAAATAGAAACTTAA
1 AGGACTAAAATAGAAAAATAGAAACTTAA
* *
1287940 AGGACTAAAATAGAAAAATAGACATTTAA
1 AGGACTAAAATAGAAAAATAGAAACTTAA
*
1287969 AGGACTAAAATAGCAAAATAGAAACTTAA
1 AGGACTAAAATAGAAAAATAGAAACTTAA
*
1287998 GGGACTAAA
1 AGGACTAAA
1288007 TAATAAATAA
Statistics
Matches: 159, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
28 31 0.19
29 63 0.40
30 63 0.40
31 1 0.01
32 1 0.01
ACGTcount: A:0.61, C:0.08, G:0.15, T:0.17
Consensus pattern (29 bp):
AGGACTAAAATAGAAAAATAGAAACTTAA
Found at i:1287862 original size:117 final size:115
Alignment explanation
Indices: 1287736--1288002 Score: 297
Period size: 117 Copynumber: 2.3 Consensus size: 115
1287726 CAAGCAAAAG
* ** **
1287736 GGATTAAAATAGAACAATAAAATATTTAAAGGACCAAAATA-TGATTAACA-AAAATTTGAGGAC
1 GGATTAAAATAGAA-AATAAAA-ACTTAAAGGACCAAAATAGT-AAAAACAGAAAATTAAAGGAC
*
1287799 AAAAATAG-AAAATAAAAACTTAAGGGAATAAAATAGCAAAAATAGAAACTTAAA
63 -AAAATAGAAAAATAAAAACTTAAAGGAATAAAATAG-AAAAATAGAAACTTAAA
* * *
1287853 GGATTAAAATCACGAAAATAAAAACTTAAGGGACTAAAATAGTAAAAATAGAAAATTAAAGGACA
1 GGATTAAAAT-A-GAAAATAAAAACTTAAAGGACCAAAATAGTAAAAACAGAAAATTAAAGGACA
* * * *
1287918 AAATAGAAAAATAGAAACTTAAAGGACTAAAATAGAAAAATAGACATTTAAA
64 AAATAGAAAAATAAAAACTTAAAGGAATAAAATAGAAAAATAGAAACTTAAA
* * *
1287970 GGACTAAAATAGCAAAATAGAAACTTAAGGGAC
1 GGATTAAAATAG-AAAATAAAAACTTAAAGGAC
1288003 TAAATAATAA
Statistics
Matches: 129, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
115 1 0.01
116 20 0.16
117 60 0.47
118 45 0.35
119 3 0.02
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.19
Consensus pattern (115 bp):
GGATTAAAATAGAAAATAAAAACTTAAAGGACCAAAATAGTAAAAACAGAAAATTAAAGGACAAA
ATAGAAAAATAAAAACTTAAAGGAATAAAATAGAAAAATAGAAACTTAAA
Found at i:1290717 original size:32 final size:32
Alignment explanation
Indices: 1290681--1290757 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 32
1290671 CCAAAGTTTA
*
1290681 CGATAATTGAAATACTTAAATACTTCCAAGTT
1 CGATAATTGAAATACTTAAAAACTTCCAAGTT
* * *
1290713 CGATAAATTCAAATATTTAAAAACTTCCCAGTT
1 CGAT-AATTGAAATACTTAAAAACTTCCAAGTT
1290746 CGATAATTGAAA
1 CGATAATTGAAA
1290758 CAAAGTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 11 0.28
33 28 0.72
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (32 bp):
CGATAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:1291177 original size:19 final size:19
Alignment explanation
Indices: 1291153--1291189 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1291143 ATGACCAACA
*
1291153 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1291172 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1291190 CAGTATCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1291258 original size:41 final size:42
Alignment explanation
Indices: 1291206--1291287 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 42
1291196 CGTAAATCAG
* * * *
1291206 TTTCCAGATTCGCGTTGCGATTTTG-ACTATCGCATTGCGAT
1 TTTCCAAATTCGCGTTGCAATTTTGTACAATCGCAATGCGAT
1291247 TTTCCAAATTCGCGTTGCAATTTTGTACAATCGCAATGCGA
1 TTTCCAAATTCGCGTTGCAATTTTGTACAATCGCAATGCGA
1291288 ATATGTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.64
42 13 0.36
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (42 bp):
TTTCCAAATTCGCGTTGCAATTTTGTACAATCGCAATGCGAT
Found at i:1291264 original size:21 final size:21
Alignment explanation
Indices: 1291206--1291270 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1291196 CGTAAATCAG
*
1291206 TTTCCAGATTCGCGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
* * *
1291227 TTT--GACTATCGCATTGCGAT
1 TTTCCAAAT-TCGCGTTGCGAT
*
1291247 TTTCCAAATTCGCGTTGCAAT
1 TTTCCAAATTCGCGTTGCGAT
1291268 TTT
1 TTT
1291271 GTACAATCGC
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 1 0.03
20 14 0.42
21 16 0.48
22 2 0.06
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (21 bp):
TTTCCAAATTCGCGTTGCGAT
Found at i:1291280 original size:21 final size:20
Alignment explanation
Indices: 1291215--1291280 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
1291205 GTTTCCAGAT
*
1291215 TCGCGTTGCGATTTTGACTA
1 TCGCGTTGCGATTTTGACAA
* *
1291235 TCGCATTGCGATTTT-CCAAA
1 TCGCGTTGCGATTTTGAC-AA
*
1291255 TTCGCGTTGCAATTTTGTACAA
1 -TCGCGTTGCGATTTTG-ACAA
1291277 TCGC
1 TCGC
1291281 AATGCGAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 17 0.47
22 2 0.06
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTGACAA
Found at i:1291319 original size:20 final size:20
Alignment explanation
Indices: 1291296--1291343 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1291286 GAATATGTAA
1291296 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1291316 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1291336 GTCGCAAC
1 ATCGCAAC
1291344 ACTGAATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1292191 original size:24 final size:24
Alignment explanation
Indices: 1292164--1292217 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1292154 GTATTCGAAA
1292164 TTTGATCTTAGTCAATACACGGAC
1 TTTGATCTTAGTCAATACACGGAC
* * * *
1292188 TTTGATCTTGGTTAATACTCGGAT
1 TTTGATCTTAGTCAATACACGGAC
1292212 TTTGAT
1 TTTGAT
1292218 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTAGTCAATACACGGAC
Found at i:1292433 original size:14 final size:14
Alignment explanation
Indices: 1292404--1292440 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1292394 AGAAGAAAAA
1292404 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
1292419 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
1292433 GAAGAAAA
1 GAAGAAAA
1292441 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:1294091 original size:22 final size:23
Alignment explanation
Indices: 1294063--1294118 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
1294053 GATGGAGATA
1294063 GACGGATTTCGCT-GGAGATGGG
1 GACGGATTTCGCTCGGAGATGGG
*
1294085 GACGGATTTTG-TCGGAGATGGG
1 GACGGATTTCGCTCGGAGATGGG
* *
1294107 GATGGATGTCGC
1 GACGGATTTCGC
1294119 CGTAGAGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.18, C:0.12, G:0.45, T:0.25
Consensus pattern (23 bp):
GACGGATTTCGCTCGGAGATGGG
Found at i:1294307 original size:20 final size:20
Alignment explanation
Indices: 1294279--1294431 Score: 107
Period size: 20 Copynumber: 7.6 Consensus size: 20
1294269 ATTTTGTATT
1294279 ATCGCGTTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAAA
* * **
1294299 ATCGTGTTGTGATTATGT-ATT
1 ATCGCGTTGCGA-TA-GTCAAA
*
1294320 ATCGAGTTGCGATAGTC-AA
1 ATCGCGTTGCGATAGTCAAA
**
1294339 ATCGCGTTGCGATTATGT-ATT
1 ATCGCGTTGCGA-TA-GTCAAA
*
1294360 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAAA
* * *
1294380 ATTGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAAA
* *
1294400 TTCGCATTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAAA
*
1294420 ATCGAGTTGCGA
1 ATCGCGTTGCGA
1294432 ATCTGGAAAC
Statistics
Matches: 100, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
19 16 0.16
20 54 0.54
21 28 0.28
22 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAAA
Found at i:1294318 original size:41 final size:41
Alignment explanation
Indices: 1294255--1294431 Score: 216
Period size: 40 Copynumber: 4.4 Consensus size: 41
1294245 TGGCGCTTTG
* * *
1294255 AAAATCGCATTGCAATTTTGTATTATCGCGTTGCGATAGTC
1 AAAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTC
* * *
1294296 AAAATCGTGTTGTGATTATGTATTATCGAGTTGCGATAGTC
1 AAAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTC
1294337 -AAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTC
1 AAAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTC
* * ** *
1294377 AGAATTGCGTTGCGATT-TACA-TATTCGCATTGCGATAGTC
1 AAAATCGCGTTGCGATTATGTATTA-TCGCGTTGCGATAGTC
*
1294417 AAAATCGAGTTGCGA
1 AAAATCGCGTTGCGA
1294432 ATCTGGAAAC
Statistics
Matches: 117, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
39 2 0.02
40 66 0.56
41 49 0.42
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (41 bp):
AAAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTC
Found at i:1294323 original size:21 final size:21
Alignment explanation
Indices: 1294258--1294372 Score: 96
Period size: 21 Copynumber: 5.6 Consensus size: 21
1294248 CGCTTTGAAA
* * *
1294258 ATCGCATTGCAATTTTGTATT
1 ATCGCGTTGCGATTATGTATT
**
1294279 ATCGCGTTGCGA-TA-GTCAAA
1 ATCGCGTTGCGATTATGT-ATT
* *
1294299 ATCGTGTTGTGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
* *
1294320 ATCGAGTTGCGA-TA-GTCA-A
1 ATCGCGTTGCGATTATGT-ATT
1294339 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
1294360 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
1294373 AGTCAGAATT
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
19 15 0.21
20 18 0.25
21 38 0.52
22 2 0.03
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:1294422 original size:81 final size:82
Alignment explanation
Indices: 1294255--1294431 Score: 218
Period size: 81 Copynumber: 2.2 Consensus size: 82
1294245 TGGCGCTTTG
* * * * * **
1294255 AAAATCGCATTGCAATTTTGTATTATCGCGTTGCGATAGTCAAAATCGTGTTGTGATTATGTATT
1 AAAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAAAATCGCGTTGCGATTACATATT
1294320 ATCGAGTTGCGATAGTC
66 ATCGAGTTGCGATAGTC
* *
1294337 -AAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATTGCGTTGCGATTTACATA-
1 AAAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAAAATCGCGTTGCGA-TTACATAT
1294400 T-TCGCA-TTGCGATAGTC
65 TATCG-AGTTGCGATAGTC
*
1294417 AAAATCGAGTTGCGA
1 AAAATCGCGTTGCGA
1294432 ATCTGGAAAC
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
80 14 0.17
81 63 0.77
82 5 0.06
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (82 bp):
AAAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAAAATCGCGTTGCGATTACATATT
ATCGAGTTGCGATAGTC
Found at i:1294481 original size:19 final size:19
Alignment explanation
Indices: 1294457--1294493 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1294447 TTCGATACTG
*
1294457 GAGATCACGTTGCGATTTA
1 GAGATCACATTGCGATTTA
*
1294476 GAGATCGCATTGCGATTT
1 GAGATCACATTGCGATTT
1294494 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCACATTGCGATTTA
Found at i:1294740 original size:2 final size:2
Alignment explanation
Indices: 1294733--1294770 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1294723 ATAAATTTTA
*
1294733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1294771 TCTAAATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1295181 original size:54 final size:54
Alignment explanation
Indices: 1295121--1295229 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
1295111 GGAAAAATAT
*
1295121 TATATAGATAATTAAACATTAAAAACTAGTTAAAGTTTTAATTTATAACTAAAA
1 TATATAGATAATTAAACATTAAAAACTAGTTAAAATTTTAATTTATAACTAAAA
* *
1295175 TATATAGATAATTAAACATTAAAACCTAGTTAAAATTTTATTTTATAACTAAAA
1 TATATAGATAATTAAACATTAAAAACTAGTTAAAATTTTAATTTATAACTAAAA
1295229 T
1 T
1295230 TTTCATTTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (54 bp):
TATATAGATAATTAAACATTAAAAACTAGTTAAAATTTTAATTTATAACTAAAA
Found at i:1295728 original size:12 final size:12
Alignment explanation
Indices: 1295711--1295744 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1295701 ATGTAAAATA
1295711 ATTTTTTTTAAT
1 ATTTTTTTTAAT
**
1295723 ATTTTTAATAAT
1 ATTTTTTTTAAT
1295735 ATTTTTTTTA
1 ATTTTTTTTA
1295745 TCAATTTTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
ATTTTTTTTAAT
Found at i:1295752 original size:24 final size:22
Alignment explanation
Indices: 1295707--1295753 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1295697 TGTCATGTAA
*
1295707 AATAATTTTTTTTAATATTTTT
1 AATAATTTTTTTTAATAATTTT
*
1295729 AATAATATTTTTTTTATCAATTTT
1 AATAAT-TTTTTTTAAT-AATTTT
1295753 A
1 A
1295754 TTAAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 9 0.43
24 6 0.29
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
AATAATTTTTTTTAATAATTTT
Found at i:1295763 original size:32 final size:33
Alignment explanation
Indices: 1295727--1295794 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
1295717 TTTAATATTT
**
1295727 TTAATAATATTTTTTTTATCAATT-TTATTAAA
1 TTAATAATATTTGATTTATCAATTATTATTAAA
* * *
1295759 TTAATTATATTTGATTTATCTATTATTTTTAAA
1 TTAATAATATTTGATTTATCAATTATTATTAAA
1295792 TTA
1 TTA
1295795 TATTTTTACT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 20 0.67
33 10 0.33
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.60
Consensus pattern (33 bp):
TTAATAATATTTGATTTATCAATTATTATTAAA
Found at i:1296462 original size:182 final size:182
Alignment explanation
Indices: 1296255--1296733 Score: 676
Period size: 181 Copynumber: 2.6 Consensus size: 182
1296245 ATTTATTTAT
* * * *
1296255 AATTAAAATATATAACTTCAAACATAATTTTTCACCAAAACTTTAAATCTCAATATTTGTTGTGA
1 AATTAAAATATATAACTACAAACATAATTTGTCACCAAAAATTTGAATCTCAATATTTGTTGTGA
* * *
1296320 TAATTTTTTCTATAACAATAATTATAAGTTATAGTTACAAAACATGTTATTTTATAAATTTTGTT
66 TAATTTTTTCTATAACAATAATTATAAGTTATAGTTACAAAACATGTCACTCTATAAATTTTGTT
* * *
1296385 TTTGCGCCAAAAATTGGAGGAAAACATTTGTGACTATACATTTTGTCACTAC
131 TTTGCGCCAAAAACTGGAAGAAAACATTTGTGACTATACATTTTGTCACCAC
*
1296437 AATTAAAATATATAACTACAAACATAATTTGTCACCAAAAATTTGAATTTCAATATTTGTTGTGA
1 AATTAAAATATATAACTACAAACATAATTTGTCACCAAAAATTTGAATCTCAATATTTGTTGTGA
* *
1296502 TAA-TTTTTCAATAACAATAATTATAAGTTATAGTTACAAAACATGTCACTCTATAACTTTTGTT
66 TAATTTTTTCTATAACAATAATTATAAGTTATAGTTACAAAACATGTCACTCTATAAATTTTGTT
* * *
1296566 TTTGCGCCAAAAACTGGAAGAAAAGATTTGTGACTATACATTTTTTCACCAT
131 TTTGCGCCAAAAACTGGAAGAAAACATTTGTGACTATACATTTTGTCACCAC
* * ** * *
1296618 AATTAAAATATATAACTACAAACAAAACTTGTCATAAAAAAATTGAATCTCATTATTTGTTGTGA
1 AATTAAAATATATAACTACAAACATAATTTGTCACCAAAAATTTGAATCTCAATATTTGTTGTGA
** * * *
1296683 TAATTTTTTCT-TGTC-ATAATTACTAAACTTATAGTCACAAAACTTGTCACT
66 TAATTTTTTCTATAACAATAATTA-T-AAGTTATAGTTACAAAACATGTCACT
1296734 ATATGTCATA
Statistics
Matches: 265, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
180 7 0.03
181 166 0.63
182 92 0.35
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.39
Consensus pattern (182 bp):
AATTAAAATATATAACTACAAACATAATTTGTCACCAAAAATTTGAATCTCAATATTTGTTGTGA
TAATTTTTTCTATAACAATAATTATAAGTTATAGTTACAAAACATGTCACTCTATAAATTTTGTT
TTTGCGCCAAAAACTGGAAGAAAACATTTGTGACTATACATTTTGTCACCAC
Found at i:1297884 original size:40 final size:40
Alignment explanation
Indices: 1297840--1297992 Score: 179
Period size: 40 Copynumber: 3.8 Consensus size: 40
1297830 TACGATTTTC
*
1297840 CAAATTCGCAACGCGAATCTGT-AAA-TCGCAACACAGAAGT
1 CAAATTCGCAACGCG-AT-AGTCAAATTCGCAACACAGAAGT
* * *
1297880 CAAATTCGCAACGCGATAGTCAAATTCTCAATACAAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAGAAGT
*
1297920 CAAATTCGCAACGCGATAGTCAAATTCGCAACGC-GATAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAGA-AGT
*
1297960 CAAATTCGCAACGCGGA-ATTTCAAATTCGCAAC
1 CAAATTCGCAACGC-GATA-GTCAAATTCGCAAC
1297993 TAGATTTTCA
Statistics
Matches: 99, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
38 2 0.02
39 6 0.06
40 76 0.77
41 15 0.15
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACAGAAGT
Found at i:1297888 original size:20 final size:21
Alignment explanation
Indices: 1297840--1298012 Score: 150
Period size: 20 Copynumber: 8.6 Consensus size: 21
1297830 TACGATTTTC
*
1297840 CAAATTCGCAACGC-GAATCTGT
1 CAAATTCGCAACGCAG-AT-AGT
*
1297862 -AAA-TCGCAACACAGA-AGT
1 CAAATTCGCAACGCAGATAGT
1297880 CAAATTCGCAACGC-GATAGT
1 CAAATTCGCAACGCAGATAGT
* ** *
1297900 CAAATTCTCAATACA-AAAGT
1 CAAATTCGCAACGCAGATAGT
1297920 CAAATTCGCAACGC-GATAGT
1 CAAATTCGCAACGCAGATAGT
1297940 CAAATTCGCAACGC-GATAGT
1 CAAATTCGCAACGCAGATAGT
* *
1297960 CAAATTCGCAACGCGGA-ATTT
1 CAAATTCGCAACGCAGATA-GT
* **
1297981 CAAATTCGCAAC-TAGATTTT
1 CAAATTCGCAACGCAGATAGT
1298001 CAAATTCGCAAC
1 CAAATTCGCAAC
1298013 ACAAATTTAA
Statistics
Matches: 127, Mismatches: 15, Indels: 20
0.78 0.09 0.12
Matches are distributed among these distances:
18 2 0.02
19 5 0.04
20 101 0.80
21 19 0.15
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (21 bp):
CAAATTCGCAACGCAGATAGT
Found at i:1298029 original size:19 final size:19
Alignment explanation
Indices: 1298005--1298055 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1297995 GATTTTCAAA
1298005 TTCGCAACACAAATTTAAT
1 TTCGCAACACAAATTTAAT
*** *
1298024 TTCGCAACA-TGTTTTAGT
1 TTCGCAACACAAATTTAAT
1298042 TTCGCAACACAAAT
1 TTCGCAACACAAAT
1298056 GTTTTGGGTA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (19 bp):
TTCGCAACACAAATTTAAT
Found at i:1298840 original size:12 final size:12
Alignment explanation
Indices: 1298819--1298852 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1298809 ACCACATTTC
*
1298819 CAATACCAAACA
1 CAATATCAAACA
1298831 CAATATCAAACA
1 CAATATCAAACA
*
1298843 CAATCTCAAA
1 CAATATCAAA
1298853 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1299004 original size:24 final size:24
Alignment explanation
Indices: 1298976--1299031 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1298966 CCTTATTCGA
*
1298976 AATTTGATCTTGGTCAATACCCAG
1 AATTTGATATTGGTCAATACCCAG
*
1299000 AATTTGATATTGGTCAATACTCAG
1 AATTTGATATTGGTCAATACCCAG
*
1299024 ATTTTGAT
1 AATTTGAT
1299032 GATGTGATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (24 bp):
AATTTGATATTGGTCAATACCCAG
Found at i:1299220 original size:9 final size:9
Alignment explanation
Indices: 1299206--1299230 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1299196 ATATAACCCT
1299206 AAAGAAGAA
1 AAAGAAGAA
1299215 AAAGAAGAA
1 AAAGAAGAA
1299224 AAAGAAG
1 AAAGAAG
1299231 TCCCCGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:1301318 original size:18 final size:18
Alignment explanation
Indices: 1301295--1301330 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1301285 AAACAAAAGG
*
1301295 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1301313 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1301331 CAACCGGCTT
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:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1301757 original size:42 final size:42
Alignment explanation
Indices: 1301710--1301791 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
1301700 TCGCAAAACG
* *
1301710 AAAATCGCAACGCGAATTTGACTTTCGCATTGCGAATTTGAC
1 AAAATCACAACGCGAATTTGACTTTCGCATTACGAATTTGAC
* *
1301752 AAAATCACAACGCGAATTTTACTTTCGCGTTACGAATTTG
1 AAAATCACAACGCGAATTTGACTTTCGCATTACGAATTTG
1301792 TACCTTCAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (42 bp):
AAAATCACAACGCGAATTTGACTTTCGCATTACGAATTTGAC
Found at i:1301900 original size:38 final size:38
Alignment explanation
Indices: 1301857--1301994 Score: 122
Period size: 38 Copynumber: 3.5 Consensus size: 38
1301847 CAAATCAACT
1301857 TTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTA
1 TTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTA
* * *
1301895 TTTACACATCAAATTAAACAAATCAACTTTTACAAATCAA--C-T-
1 TTTACAAATC-AATTAAAC-AAGCAA-----AAAAAT-AATTCTTA
1301937 TTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTA
1 TTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTA
* **
1301975 TTTCCTCATCAATTAAACAA
1 TTTACAAATCAATTAAACAA
1301995 ATCAACTTTC
Statistics
Matches: 79, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
34 2 0.03
35 5 0.06
36 1 0.01
37 1 0.01
38 26 0.33
39 8 0.10
40 10 0.13
41 8 0.10
42 9 0.11
43 1 0.01
44 1 0.01
45 5 0.06
46 2 0.03
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.30
Consensus pattern (38 bp):
TTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTA
Found at i:1301927 original size:28 final size:28
Alignment explanation
Indices: 1301895--1301948 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1301885 ATAATTCTTA
*
1301895 TTTACACATCAAATTAAACAAATCAACT
1 TTTACAAATCAAATTAAACAAATCAACT
* **
1301923 TTTACAAATCAACTTTTACAAATCAA
1 TTTACAAATCAAATTAAACAAATCAA
1301949 TTAAACAAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAACT
Found at i:1301929 original size:14 final size:14
Alignment explanation
Indices: 1301912--1301948 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1301902 ATCAAATTAA
1301912 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1301926 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1301940 ACAAATCAA
1 ACAAATCAA
1301949 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1301985 original size:80 final size:79
Alignment explanation
Indices: 1301846--1302003 Score: 289
Period size: 80 Copynumber: 2.0 Consensus size: 79
1301836 ATTTAAAACA
1301846 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATTA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATTA
1301911 AACAAATCAACTTTT
65 AACAAATCAACTTTT
* *
1301926 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTCCTCATCAATTAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAA
1301991 ACAAATCAACTTT
66 ACAAATCAACTTT
1302004 CAATGTAAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
79 19 0.25
80 57 0.75
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.30
Consensus pattern (79 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAA
ACAAATCAACTTTT
Found at i:1303409 original size:21 final size:20
Alignment explanation
Indices: 1303385--1303462 Score: 59
Period size: 21 Copynumber: 3.8 Consensus size: 20
1303375 ACGGGCGGGA
1303385 CCTCTTGAAAGATGACAGGGG
1 CCTCTTGAAAGATGA-AGGGG
* *
1303406 CCTCTT-AAATGGTGGGAGGGG
1 CCTCTTGAAA-GAT-GAAGGGG
* **
1303427 CCTCTTGAATGATAGAAGACG
1 CCTCTTGAAAGAT-GAAGGGG
*
1303448 CCTCTTGAATGATGA
1 CCTCTTGAAAGATGA
1303463 TAGGTGCATC
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
20 5 0.11
21 38 0.83
22 3 0.07
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (20 bp):
CCTCTTGAAAGATGAAGGGG
Found at i:1306181 original size:20 final size:20
Alignment explanation
Indices: 1306156--1306213 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1306146 TAATATTGCA
1306156 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
1306176 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* **
1306196 TATCGTATTGCGAATTTG
1 TTTCGCGTTGCGAATTTG
1306214 GAAACTGGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:1308822 original size:11 final size:11
Alignment explanation
Indices: 1308808--1308833 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1308798 AAACACTTAA
1308808 AAAATAATAAT
1 AAAATAATAAT
1308819 AAAATAATAAT
1 AAAATAATAAT
1308830 AAAA
1 AAAA
1308834 ATAAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:1308836 original size:17 final size:19
Alignment explanation
Indices: 1308810--1308852 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
1308800 ACACTTAAAA
* *
1308810 AATAATAATAAA-ATAAT-
1 AATAAAAATAAACAAAATG
1308827 AATAAAAATAAACAAAATG
1 AATAAAAATAAACAAAATG
1308846 AATAAAA
1 AATAAAA
1308853 TGTTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.50
18 4 0.18
19 7 0.32
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAACAAAATG
Found at i:1309112 original size:40 final size:41
Alignment explanation
Indices: 1309068--1309152 Score: 95
Period size: 39 Copynumber: 2.1 Consensus size: 41
1309058 AATATAATAT
1309068 ATATAAATAAATAAAAACA-AAAATAGAATATTAAGA-AAAA
1 ATAT-AATAAATAAAAACATAAAATAGAATATTAAGAGAAAA
* *** *
1309108 ATAT-ATATATAAACGTATAAAATATAATATTAAGAGAAAA
1 ATATAATAAATAAAAACATAAAATAGAATATTAAGAGAAAA
1309148 ATATA
1 ATATA
1309153 TATACATAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
38 9 0.24
39 16 0.43
40 12 0.32
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (41 bp):
ATATAATAAATAAAAACATAAAATAGAATATTAAGAGAAAA
Found at i:1309239 original size:23 final size:23
Alignment explanation
Indices: 1309195--1309258 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
1309185 CTATACATAT
**
1309195 ATATATATATATATAATGATATAAG
1 ATATATATA-ATA-AAAAATATAAG
*
1309220 ATATATATAATAAAAAATATAAT
1 ATATATATAATAAAAAATATAAG
*
1309243 ATAAATA-AATAAAAAA
1 ATATATATAATAAAAAA
1309259 AGAGGAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.26
23 14 0.40
24 3 0.09
25 9 0.26
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (23 bp):
ATATATATAATAAAAAATATAAG
Found at i:1309259 original size:23 final size:23
Alignment explanation
Indices: 1309213--1309296 Score: 73
Period size: 23 Copynumber: 3.5 Consensus size: 23
1309203 ATATATAATG
* *
1309213 ATATAAGATATATATAAT-AAAAA
1 ATATAATATAAATA-AATAAAAAA
1309236 ATATAATATAAATAAATAAAAAA
1 ATATAATATAAATAAATAAAAAA
* *
1309259 AGAGGAATATAGTAAATAAATAAAAAA
1 ATA--TA-ATA-TAAATAAATAAAAAA
1309286 ATATAAT-TAAA
1 ATATAATATAAA
1309297 AATATATATA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
22 7 0.14
23 19 0.38
24 2 0.04
25 2 0.04
26 3 0.06
27 17 0.34
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (23 bp):
ATATAATATAAATAAATAAAAAA
Found at i:1309299 original size:24 final size:24
Alignment explanation
Indices: 1309231--1309300 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 24
1309221 TATATATAAT
1309231 AAAAAATATAA-TATAAATAAATA
1 AAAAAATATAATTATAAATAAATA
* *
1309254 AAAAAAGAGGAATATAGTAAATAAATA
1 AAAAAATA-TAAT-TA-TAAATAAATA
*
1309281 AAAAAATATAATTAAAAATA
1 AAAAAATATAATTATAAATA
1309301 TATATAGGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 7 0.18
24 7 0.18
25 2 0.05
26 5 0.13
27 17 0.45
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (24 bp):
AAAAAATATAATTATAAATAAATA
Found at i:1310092 original size:12 final size:13
Alignment explanation
Indices: 1310077--1310143 Score: 65
Period size: 12 Copynumber: 5.5 Consensus size: 13
1310067 TTTTCTTCAA
1310077 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
1310089 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
1310101 ATTTTCTCTTTGCTT
1 -TTTTCTCTTTG-TT
*
1310116 TTTTCTC---ATT
1 TTTTCTCTTTGTT
1310126 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
1310138 TTTTCT
1 TTTTCT
1310144 GATTGAATCT
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
10 9 0.19
12 15 0.32
13 14 0.30
14 7 0.15
15 2 0.04
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:1310127 original size:27 final size:25
Alignment explanation
Indices: 1310076--1310143 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 25
1310066 TTTTTCTTCA
*
1310076 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCATTTT
1310101 ATTTTCTCTTTGCTTTTTTCTCATTTT
1 ATTTTC-CTTTG-TTTTTTCTCATTTT
*
1310128 -TTCT-CTTT-TTTTTTCT
1 ATTTTCCTTTGTTTTTTCT
1310144 GATTGAATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
22 8 0.21
24 4 0.10
25 6 0.15
26 8 0.21
27 13 0.33
ACGTcount: A:0.04, C:0.18, G:0.03, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCATTTT
Found at i:1311380 original size:8 final size:7
Alignment explanation
Indices: 1311349--1311382 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
1311339 TGAAATGTAG
1311349 ATGCAAA
1 ATGCAAA
1311356 ATGCAAA
1 ATGCAAA
1311363 ATGCAAA
1 ATGCAAA
1311370 ATGCAAAA
1 ATGC-AAA
1311378 ATGCA
1 ATGCA
1311383 TGAAATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGCAAA
Found at i:1313512 original size:38 final size:38
Alignment explanation
Indices: 1313424--1313518 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 38
1313414 AGTATTTACT
* * *
1313424 AAAAAAA-TAAAAAATAAATAAATATATAATACTAAGT
1 AAAAAAAGTAAAAAATAAAGAAATACATAATACTAAGA
* * * *
1313461 AAAACAAGTAAAAAATAAAGATATACATGATATTAAGA
1 AAAAAAAGTAAAAAATAAAGAAATACATAATACTAAGA
*
1313499 AAAAAAAGAAAAAAATAAAG
1 AAAAAAAGTAAAAAATAAAG
1313519 TAAAAATATA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
37 6 0.12
38 42 0.88
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (38 bp):
AAAAAAAGTAAAAAATAAAGAAATACATAATACTAAGA
Found at i:1313654 original size:8 final size:8
Alignment explanation
Indices: 1313641--1313705 Score: 62
Period size: 8 Copynumber: 8.4 Consensus size: 8
1313631 ATAAAAATTA
*
1313641 ATACATCT
1 ATACATAT
1313649 ATACATAT
1 ATACATAT
*
1313657 ATATATAT
1 ATACATAT
*
1313665 ATATATAT
1 ATACATAT
*
1313673 ATATATAT
1 ATACATAT
*
1313681 ATATATAT
1 ATACATAT
1313689 ATA-ATAT
1 ATACATAT
*
1313696 A-AGATAT
1 ATACATAT
1313703 ATA
1 ATA
1313706 TAATAAAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
6 1 0.02
7 10 0.19
8 42 0.79
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (8 bp):
ATACATAT
Found at i:1313660 original size:2 final size:2
Alignment explanation
Indices: 1313648--1313707 Score: 88
Period size: 2 Copynumber: 31.0 Consensus size: 2
1313638 TTAATACATC
*
1313648 TA TA CA 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
*
1313690 TA -A TA TA -A GA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1313708 ATAAAAATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1319467 original size:15 final size:16
Alignment explanation
Indices: 1319447--1319479 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1319437 AATCCAATAT
*
1319447 ACAAAATCGACC-CAA
1 ACAAAATCAACCTCAA
1319462 ACAAAATCAACCTCAA
1 ACAAAATCAACCTCAA
1319478 AC
1 AC
1319480 CCAACTATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.55, C:0.33, G:0.03, T:0.09
Consensus pattern (16 bp):
ACAAAATCAACCTCAA
Found at i:1321443 original size:10 final size:10
Alignment explanation
Indices: 1321420--1321485 Score: 75
Period size: 10 Copynumber: 6.6 Consensus size: 10
1321410 AATCTACGTG
1321420 GACCTCGTCT
1 GACCTCGTCT
1321430 GACCATCGTC-
1 GACC-TCGTCT
1321440 GACCTCGTCT
1 GACCTCGTCT
1321450 GACCATCGTC-
1 GACC-TCGTCT
*
1321460 GACCTCATCT
1 GACCTCGTCT
1321470 GACCATCGTC-
1 GACC-TCGTCT
1321480 GACCTC
1 GACCTC
1321486 AATCTCACCG
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
9 11 0.22
10 24 0.49
11 14 0.29
ACGTcount: A:0.17, C:0.41, G:0.18, T:0.24
Consensus pattern (10 bp):
GACCTCGTCT
Found at i:1321445 original size:20 final size:20
Alignment explanation
Indices: 1321420--1321485 Score: 123
Period size: 20 Copynumber: 3.3 Consensus size: 20
1321410 AATCTACGTG
1321420 GACCTCGTCTGACCATCGTC
1 GACCTCGTCTGACCATCGTC
1321440 GACCTCGTCTGACCATCGTC
1 GACCTCGTCTGACCATCGTC
*
1321460 GACCTCATCTGACCATCGTC
1 GACCTCGTCTGACCATCGTC
1321480 GACCTC
1 GACCTC
1321486 AATCTCACCG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.17, C:0.41, G:0.18, T:0.24
Consensus pattern (20 bp):
GACCTCGTCTGACCATCGTC
Done.