Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 102 of 199
Found at i:31037924 original size:51 final size:50
Alignment explanation
Indices: 31037793--31037975 Score: 169
Period size: 51 Copynumber: 3.6 Consensus size: 50
31037783 AAAGTGATGG
* ** * *
31037793 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGATGGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCCAAATGATCGA
* * * *
31037843 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTA-CCAAATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCCAAAT-G-ATCGA
*
31037894 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGCTGGAAATG---G-
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATC--C---AAATGATCGA
*
31037945 TCACATGTGTAGTACTATGTGCAGGCTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA
31037976 TGTGAACCGG
Statistics
Matches: 111, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
49 4 0.04
50 34 0.31
51 65 0.59
52 2 0.02
54 1 0.01
56 1 0.01
57 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCCAAATGATCGA
Found at i:31043376 original size:11 final size:12
Alignment explanation
Indices: 31043344--31043377 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
31043334 AGTATCCAAA
31043344 ATCTTTACTTAT
1 ATCTTTACTTAT
31043356 ATCTTTACTTAT
1 ATCTTTACTTAT
31043368 ATC-TTACTTA
1 ATCTTTACTTA
31043378 CTTATATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (12 bp):
ATCTTTACTTAT
Found at i:31043380 original size:15 final size:13
Alignment explanation
Indices: 31043347--31043387 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 13
31043337 ATCCAAAATC
31043347 TTTACTTATATC-
1 TTTACTTATATCT
31043359 TTTACTTATATCT
1 TTTACTTATATCT
31043372 TACTTACTTATATCT
1 T--TTACTTATATCT
31043387 T
1 T
31043388 GTTAGAATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.46
13 1 0.04
15 13 0.50
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTACTTATATCT
Found at i:31045387 original size:27 final size:27
Alignment explanation
Indices: 31045325--31045389 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
31045315 TTCTCTCAAT
* * * *
31045325 GTTCACCATACGCACTATTTCTTTAGA
1 GTTCACCATATGCAATATTCCTTCAGA
** *
31045352 GTTTTCCATATGTAATATTCCTTCAGA
1 GTTCACCATATGCAATATTCCTTCAGA
31045379 GTTCACCATAT
1 GTTCACCATAT
31045390 CTATCATTCT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (27 bp):
GTTCACCATATGCAATATTCCTTCAGA
Found at i:31045505 original size:28 final size:27
Alignment explanation
Indices: 31045473--31045526 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
31045463 AATGCACCAA
*
31045473 AAAAGCGTT-CATTTCCATAGATTGCCAT
1 AAAAGC-TTCCATTT-CAAAGATTGCCAT
31045501 AAAAGCTTCCATTTCAAAGATTGCCA
1 AAAAGCTTCCATTTCAAAGATTGCCA
31045527 CAAAGAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (27 bp):
AAAAGCTTCCATTTCAAAGATTGCCAT
Found at i:31046047 original size:18 final size:18
Alignment explanation
Indices: 31046024--31046061 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31046014 GATCTATTCC
31046024 TCTTTTATTTATTTATTT
1 TCTTTTATTTATTTATTT
* *
31046042 TCTTTTCTTTCTTTATTT
1 TCTTTTATTTATTTATTT
31046060 TC
1 TC
31046062 CTTCCTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (18 bp):
TCTTTTATTTATTTATTT
Found at i:31046069 original size:18 final size:18
Alignment explanation
Indices: 31046035--31046069 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31046025 CTTTTATTTA
* *
31046035 TTTATTTTCTTTTCTTTC
1 TTTATTTTCCTTCCTTTC
31046053 TTTATTTTCCTTCCTTT
1 TTTATTTTCCTTCCTTT
31046070 TGAAACTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTCCTTCCTTTC
Found at i:31046784 original size:3 final size:3
Alignment explanation
Indices: 31046778--31046891 Score: 76
Period size: 3 Copynumber: 38.7 Consensus size: 3
31046768 TTAGTAGCAA
* * * * *
31046778 TAT TAT T-T ATAT TAT TAA TAG TAT TAT TAT TAT TAT TAA TGT CAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
31046823 CAT TAC TA- TAG TAT TAT TACC T-T TAT TAC T-T TAT TACT T-T TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA-T TAT TAT
31046866 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
31046892 CTACTACTAC
Statistics
Matches: 88, Mismatches: 15, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
2 7 0.08
3 77 0.88
4 4 0.05
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:31046790 original size:24 final size:24
Alignment explanation
Indices: 31046756--31046808 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
31046746 TATGTTATCG
* *
31046756 TTATTTTTATTATTAGTAGCAATA
1 TTATTTATATTATTAATAGCAATA
* *
31046780 TTATTTATATTATTAATAGTATTA
1 TTATTTATATTATTAATAGCAATA
31046804 TTATT
1 TTATT
31046809 ATTATTAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
TTATTTATATTATTAATAGCAATA
Found at i:31046814 original size:24 final size:23
Alignment explanation
Indices: 31046760--31046817 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
31046750 TTATCGTTAT
*
31046760 TTTTATTATTAGTAGCAATATTA
1 TTTTATTATTAATAGCAATATTA
31046783 TTTATATTATTAATAG---TATTA
1 TTT-TATTATTAATAGCAATATTA
31046804 TTATTATTATTAAT
1 TT-TTATTATTAAT
31046818 GTCATCATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 17 0.53
22 1 0.03
23 3 0.09
24 11 0.34
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTTATTATTAATAGCAATATTA
Found at i:31050763 original size:14 final size:14
Alignment explanation
Indices: 31050746--31050792 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
31050736 GTTCAGACTC
31050746 AAAAAAAATAACAAA
1 AAAAAAAATAAC-AA
*
31050761 AAAACAAAAAAACAA
1 AAAA-AAAATAACAA
31050776 AAACAAAAATAA-AA
1 AAA-AAAAATAACAA
31050790 AAA
1 AAA
31050793 TCGAAGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 5 0.18
15 15 0.54
16 8 0.29
ACGTcount: A:0.87, C:0.09, G:0.00, T:0.04
Consensus pattern (14 bp):
AAAAAAAATAACAA
Found at i:31050766 original size:8 final size:8
Alignment explanation
Indices: 31050749--31050778 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
31050739 CAGACTCAAA
31050749 AAAAATAAC
1 AAAAA-AAC
31050758 AAAAAAAC
1 AAAAAAAC
31050766 AAAAAAAC
1 AAAAAAAC
31050774 AAAAA
1 AAAAA
31050779 CAAAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.87, C:0.10, G:0.00, T:0.03
Consensus pattern (8 bp):
AAAAAAAC
Found at i:31050822 original size:24 final size:23
Alignment explanation
Indices: 31050760--31050838 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 23
31050750 AAAATAACAA
* *
31050760 AAAAACAAAAAAAC--A-AAAAC
1 AAAAAGAAAAAAACGAAGAAAAG
*
31050780 AAAAATAAAAAAATCGAAGTCAAAA-
1 AAAAAGAAAAAAA-CGAAG--AAAAG
31050805 AAAAGAGAAAAAAA-GAAGAAAAG
1 AAAA-AGAAAAAAACGAAGAAAAG
31050828 AAAAAGAAAAA
1 AAAAAGAAAAA
31050839 GGAGAGGTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
20 12 0.24
21 1 0.02
22 11 0.22
23 5 0.10
24 4 0.08
25 4 0.08
26 12 0.24
ACGTcount: A:0.80, C:0.06, G:0.10, T:0.04
Consensus pattern (23 bp):
AAAAAGAAAAAAACGAAGAAAAG
Found at i:31051688 original size:7 final size:8
Alignment explanation
Indices: 31051669--31051697 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
31051659 TTTGAGTCAA
31051669 AAAAAATG
1 AAAAAATG
31051677 AAAAAATG
1 AAAAAATG
31051685 AAAAAATG
1 AAAAAATG
31051693 AAAAA
1 AAAAA
31051698 GTAAAAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (8 bp):
AAAAAATG
Found at i:31051704 original size:16 final size:16
Alignment explanation
Indices: 31051668--31051704 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
31051658 CTTTGAGTCA
31051668 AAAAAAATGAAAAAAT
1 AAAAAAATGAAAAAAT
* *
31051684 GAAAAAATGAAAAAGT
1 AAAAAAATGAAAAAAT
31051700 AAAAA
1 AAAAA
31051705 TGGAGAGGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (16 bp):
AAAAAAATGAAAAAAT
Found at i:31052991 original size:88 final size:88
Alignment explanation
Indices: 31052838--31053643 Score: 1065
Period size: 88 Copynumber: 9.2 Consensus size: 88
31052828 CCTAATCACT
*
31052838 AGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAACGATCTTGCCTTCCT
1 AGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCT
* *
31052903 GCATTGACAGTGAAGCAAGTCGA
66 GCATTGACAGCGAAGCAGGTCGA
*
31052926 AGATACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCT
1 AGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCT
*
31052991 GTATTGACAGCGAAGCAGGTCGA
66 GCATTGACAGCGAAGCAGGTCGA
* *
31053014 AGACACAGACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAAACAAAAGATCTTGCCTTCCT
1 AGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCT
*
31053079 GTATTGACAGCGAAGCAGGTCGA
66 GCATTGACAGCGAAGCAGGTCGA
* *
31053102 AGACACAAACCTTGCCGCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCT
1 AGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCT
31053167 GCATTGACAGCGAAGCAGGTCGA
66 GCATTGACAGCGAAGCAGGTCGA
* *
31053190 AGATACAGACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCT
1 AGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCT
** * *
31053255 ATATTGATAGCGAAGTAGGTCGA
66 GCATTGACAGCGAAGCAGGTCGA
* *
31053278 AGATACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCTTTCCT
1 AGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCT
* * *
31053343 GTATTGACAGCAAAGTAGGTCGA
66 GCATTGACAGCGAAGCAGGTCGA
* *
31053366 AGACGCAAACCTTGCCTCTCTCAGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCT
1 AGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCT
* * *
31053431 ACATTAACAGCGAAGCAGATCGA
66 GCATTGACAGCGAAGCAGGTCGA
* * * * **
31053454 A-A-ACAAAGCTTTGCCT-TCATTGGTTG-CAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCCTT
1 AGACACAAA-CCTTGCCTCTC-TCGGTTGTGA-TGGAGCTGGTTGAAGACAAAAGATCTTGCCTT
* * *
31053514 CCTGCATTAACAGTGAAGCAGATCGA
63 CCTGCATTGACAGCGAAGCAGGTCGA
* * * * ** *
31053540 AAACA-AAAGCCTTGCCT-TCATTGGTTG-CAGTGGAGCTGGTTAAAGA-AGCAGATCTTGTCTT
1 AGACACAAA-CCTTGCCTCTC-TCGGTTGTGA-TGGAGCTGGTTGAAGACAAAAGATCTTGCCTT
* * *
31053601 CCTGCATTAACAGTGAAGCAGATCGA
63 CCTGCATTGACAGCGAAGCAGGTCGA
*
31053627 AAACA-AAAGCCTTGCCT
1 AGACACAAA-CCTTGCCT
31053644 TCATTGGTTG
Statistics
Matches: 665, Mismatches: 48, Indels: 11
0.92 0.07 0.02
Matches are distributed among these distances:
86 45 0.07
87 126 0.19
88 494 0.74
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (88 bp):
AGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCT
GCATTGACAGCGAAGCAGGTCGA
Found at i:31053554 original size:44 final size:44
Alignment explanation
Indices: 31053506--31053645 Score: 126
Period size: 44 Copynumber: 3.2 Consensus size: 44
31053496 AGAAGCAGAT
31053506 CTTGCCTTCCTGCATTAACAGTGAAGCAGATCGAAAACAAAAGC
1 CTTGCCTTCCTGCATTAACAGTGAAGCAGATCGAAAACAAAAGC
* * * * * * * ** *
31053550 CTTGCCTTCATTG-GTT-GCAGTGGAGCTGGT-TAAAGA-AGCAGAT
1 CTTGCCTTC-CTGCATTAACAGTGAAGCAGATCGAAA-ACAAAAG-C
*
31053593 CTTGTCTTCCTGCATTAACAGTGAAGCAGATCGAAAACAAAAGC
1 CTTGCCTTCCTGCATTAACAGTGAAGCAGATCGAAAACAAAAGC
31053637 CTTGCCTTC
1 CTTGCCTTC
31053646 ATTGGTTGCA
Statistics
Matches: 67, Mismatches: 22, Indels: 14
0.65 0.21 0.14
Matches are distributed among these distances:
42 8 0.12
43 21 0.31
44 30 0.45
45 8 0.12
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (44 bp):
CTTGCCTTCCTGCATTAACAGTGAAGCAGATCGAAAACAAAAGC
Found at i:31053705 original size:55 final size:56
Alignment explanation
Indices: 31053615--31053734 Score: 215
Period size: 55 Copynumber: 2.2 Consensus size: 56
31053605 CATTAACAGT
31053615 GAAGCAGATCGAAAACAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
1 GAAGCAGATCGAAAACAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
* *
31053671 GAAGTAGATCGAAAACAAAA-CCTTGCCTTCATTGGTTGCTGTGGAGCTGGTTAAA
1 GAAGCAGATCGAAAACAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
31053726 GAAGCAGAT
1 GAAGCAGAT
31053735 TTTGCCTTCC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
55 42 0.69
56 19 0.31
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.24
Consensus pattern (56 bp):
GAAGCAGATCGAAAACAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
Found at i:31053716 original size:142 final size:142
Alignment explanation
Indices: 31053528--31053822 Score: 466
Period size: 142 Copynumber: 2.1 Consensus size: 142
31053518 CATTAACAGT
31053528 GAAGCAGATCGAAAACAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
1 GAAGCAGATCGAAAACAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
* ** *
31053593 CTTGTCTTCCTGCATTAACAGTGAAGCAGATCGAAAACAAAAGCCTTGCCTTCATTGGTTGCAGT
66 CTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAA-CCTTGCCTTCATCGGTTGCAGT
* *
31053658 GGAGCTGGTTAAA
130 GGAACTGGGTAAA
* *
31053671 GAAGTAGATCGAAAACAAAA-CCTTGCCTTCATTGGTTGCTGTGGAGCTGGTTAAAGAAGCAGAT
1 GAAGCAGATCGAAAACAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
* *
31053735 TTTGCCTTCCTGCATTAACAACGAAGCAGATTGAAAACAAAACCTTGCCTTCATCGGTTGCAGTG
66 CTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAACCTTGCCTTCATCGGTTGCAGTG
31053800 GAACTGGGTAAA
131 GAACTGGGTAAA
*
31053812 GATAACAGATC
1 GA-AGCAGATC
31053823 TTGCCTTCCT
Statistics
Matches: 139, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
141 34 0.24
142 86 0.62
143 19 0.14
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (142 bp):
GAAGCAGATCGAAAACAAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
CTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAACCTTGCCTTCATCGGTTGCAGTG
GAACTGGGTAAA
Found at i:31055204 original size:50 final size:50
Alignment explanation
Indices: 31053868--31055212 Score: 1106
Period size: 50 Copynumber: 27.1 Consensus size: 50
31053858 AAACCATAGT
*
31053868 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGCA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
** * * * *
31053918 TTATAGTGGAACAA-ATTGAAGCTACAACAGCGGATCTTACTTCCCGGACA
1 TTGCAAT-TAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
31053968 TTGCAATTAAAAAGATTGAAGCTACAACAGTGGATCTTACTTTCCT-AGCA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* ** *
31054018 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
31054068 TTGCAATTAAAAAGATTGAAGCTATAACAGCGGATCTTACTTTCCT-AGCA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* * ** * * *
31054118 TTACAGTGGAATAGGTTGAAGCTACAACCGCGGATCTTACTTCCCTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
31054168 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGCG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* ** * *
31054218 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCACTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
31054268 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGCG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* * ** *
31054318 TTACAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* ** *
31054368 TTGCAATTAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTTCT-AGCG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* ** * *
31054418 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCACTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
31054468 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGCG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* ** *** *
31054518 TTGCAGTGGAGTGGATTGAAGCTACAACAGTGGATCTTACTTCCCTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * * *
31054568 TTGTAATTAAAAAGATTAAAGCTACAACAGCGGATCTTATTTCCCAGGCA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* **** * * ** * **
31054618 ATGCAGCGGAACAGATTGAAGCCACAATGGCGAATCTTACTTCCCCAACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * ** * * *
31054668 TTGCAACTCAAAAGATTGAAGCCACAATGGCGAATCTTACTTCCCAGGCA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * ** ** * * ** *
31054718 GTATAGC-A--GAATAGATTGAAGCTACAATGGCAAATCTCATTTTTTCTGATA
1 -T-T-GCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTA-CTTCCCTGACA
* * * * * * * * *
31054769 TTGCAATT-GAAAGATTGAGGCCACGACGGTGAATCTTACTTTCCT-AGCG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* ** * *
31054818 TTGCAGTGGAATAGATTGAAGCTACAACAGTGGATCTTACTTCCCTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
31054868 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGCG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* ** * **
31054918 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTGTTTCCC---C-
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * * **
31054964 -GGCAGTTAAAAAGATTGAAGCTACAACAGTGGATCTTACTTTCCT-AGTG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
*** * * * **
31055013 TTGCAGCGGAACAA-ATTGAAGCTACAACAGTGGATTTTGTTTCCC---C-
1 TTGCA-ATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * **
31055059 -GGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGTG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* ** *
31055108 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* **
31055158 TTGCAATTAAAAAGATTGAAGCTACAACAGCAGATCTTACCCCCCTGACA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
31055208 TTGCA
1 TTGCA
31055213 GTGGAATAGA
Statistics
Matches: 1028, Mismatches: 228, Indels: 78
0.77 0.17 0.06
Matches are distributed among these distances:
44 4 0.00
45 65 0.06
47 1 0.00
48 3 0.00
49 24 0.02
50 904 0.88
51 23 0.02
52 2 0.00
53 2 0.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (50 bp):
TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
Found at i:31055218 original size:100 final size:100
Alignment explanation
Indices: 31053868--31055197 Score: 1810
Period size: 100 Copynumber: 13.4 Consensus size: 100
31053858 AAACCATAGT
* ** *
31053868 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTATAGTGGAACAAA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
*
31053933 TTGAAGCTACAACAGCGGATCTTACTTCCCGGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
31053968 TTGCAATTAAAAAGATTGAAGCTACAACAGTGGATCTTACTTTCCTAGCATTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
31054033 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * * *
31054068 TTGCAATTAAAAAGATTGAAGCTATAACAGCGGATCTTACTTTCCTAGCATTACAGTGGAATAGG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
*
31054133 TTGAAGCTACAACCGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
31054168 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
*
31054233 TTGAAGCTACAACAGCGGATCTTACTTCACTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
*
31054268 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTACAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
31054333 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
31054368 TTGCAATTAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTTCTAGCGTTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
*
31054433 TTGAAGCTACAACAGCGGATCTTACTTCACTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
***
31054468 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAGTGGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
*
31054533 TTGAAGCTACAACAGTGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * ** *
31054568 TTGTAATTAAAAAGATTAAAGCTACAACAGCGGATCTTA-TTTCCCAGGCAATGCAGCGGAACAG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAACAG
* ** * **
31054632 ATTGAAGCCACAATGGCGAATCTTACTTCCCCAACA
65 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * ** * *
31054668 TTGCAACTCAAAAGATTGAAGCCACAATGGCGAATCTTAC-TTCCCAGGCAGTATAGCA---GAA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GC-GT-T-GCAGTGGAA
* ** ** * * ** *
31054729 TAGATTGAAGCTACAATGGCAAATCTCATTTTTTCTGATA
62 CAGATTGAAGCTACAACAGCGGATCTTA-CTTCCCTGACA
* * * * * * * *
31054769 TTGCAATT-GAAAGATTGAGGCCACGACGGTGAATCTTACTTTCCTAGCGTTGCAGTGGAATAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
*
31054833 TTGAAGCTACAACAGTGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
31054868 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
**
31054933 TTGAAGCTACAACAGCGGATCTTGTTTCCC---C-
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * * * *
31054964 -GGCAGTTAAAAAGATTGAAGCTACAACAGTGGATCTTACTTTCCTAGTGTTGCAGCGGAACAAA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
* * **
31055028 TTGAAGCTACAACAGTGGATTTTGTTTCCC---C-
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * *
31055059 -GGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
31055123 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
*
31055158 TTGCAATTAAAAAGATTGAAGCTACAACAGCAGATCTTAC
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTAC
31055198 CCCCCTGACA
Statistics
Matches: 1101, Mismatches: 113, Indels: 32
0.88 0.09 0.03
Matches are distributed among these distances:
95 174 0.16
97 4 0.00
98 2 0.00
99 23 0.02
100 877 0.80
101 17 0.02
102 1 0.00
103 3 0.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (100 bp):
TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
Found at i:31055936 original size:18 final size:18
Alignment explanation
Indices: 31055913--31055950 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31055903 GATCTATTCC
31055913 TCTTTTATTTATTTATTT
1 TCTTTTATTTATTTATTT
* *
31055931 TCTTTTCTTTCTTTATTT
1 TCTTTTATTTATTTATTT
31055949 TC
1 TC
31055951 CTTCCTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (18 bp):
TCTTTTATTTATTTATTT
Found at i:31055958 original size:18 final size:18
Alignment explanation
Indices: 31055924--31055958 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31055914 CTTTTATTTA
* *
31055924 TTTATTTTCTTTTCTTTC
1 TTTATTTTCCTTCCTTTC
31055942 TTTATTTTCCTTCCTTT
1 TTTATTTTCCTTCCTTT
31055959 TGAAACTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTCCTTCCTTTC
Found at i:31056676 original size:3 final size:3
Alignment explanation
Indices: 31056670--31056783 Score: 76
Period size: 3 Copynumber: 38.7 Consensus size: 3
31056660 TTAGTAGCAA
* * * * *
31056670 TAT TAT T-T ATAT TAT TAA TAG TAT TAT TAT TAT TAT TAA TGT CAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
31056715 CAT TAC TA- TAG TAT TAT TACC T-T TAT TAC T-T TAT TACT T-T TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA-T TAT TAT
31056758 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
31056784 CTACTACTAT
Statistics
Matches: 88, Mismatches: 15, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
2 7 0.08
3 77 0.88
4 4 0.05
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:31056682 original size:24 final size:24
Alignment explanation
Indices: 31056648--31056700 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
31056638 TATGTTATCG
* *
31056648 TTATTTTTATTATTAGTAGCAATA
1 TTATTTATATTATTAATAGCAATA
* *
31056672 TTATTTATATTATTAATAGTATTA
1 TTATTTATATTATTAATAGCAATA
31056696 TTATT
1 TTATT
31056701 ATTATTAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
TTATTTATATTATTAATAGCAATA
Found at i:31056706 original size:24 final size:23
Alignment explanation
Indices: 31056652--31056709 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
31056642 TTATCGTTAT
*
31056652 TTTTATTATTAGTAGCAATATTA
1 TTTTATTATTAATAGCAATATTA
31056675 TTTATATTATTAATAG---TATTA
1 TTT-TATTATTAATAGCAATATTA
31056696 TTATTATTATTAAT
1 TT-TTATTATTAAT
31056710 GTCATCATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 17 0.53
22 1 0.03
23 3 0.09
24 11 0.34
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTTATTATTAATAGCAATATTA
Found at i:31057130 original size:2 final size:2
Alignment explanation
Indices: 31057123--31057156 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31057113 TTTTACGCAC
31057123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31057157 TTTATAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31060533 original size:30 final size:30
Alignment explanation
Indices: 31060497--31060560 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
31060487 TATGAGGACG
31060497 TTCAGGAACTTAAGAAGAC-CAAATATCTCA
1 TTCAGGAACTTAAGAAGACTC-AATATCTCA
* ** *
31060527 TTCAGGAGCTTGGGAGGACTCAATATCTCA
1 TTCAGGAACTTAAGAAGACTCAATATCTCA
31060557 TTCA
1 TTCA
31060561 AGATCTTAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (30 bp):
TTCAGGAACTTAAGAAGACTCAATATCTCA
Found at i:31060673 original size:36 final size:35
Alignment explanation
Indices: 31060509--31060671 Score: 93
Period size: 30 Copynumber: 4.9 Consensus size: 35
31060499 CAGGAACTTA
* *
31060509 AGAAGACCAAATATCTCATTCAGGAGCTTGG---G
1 AGAAGACCTAATATCTCATTCAGGATCTTGGATTG
*
31060541 AG--GA-CTCAATATCTCATTCAAGATCTTAGGATTG
1 AGAAGACCT-AATATCTCATTCAGGATCTT-GGATTG
* * *
31060575 AGAAGACATGATATCTCATTTAGGA-----GATTCG
1 AGAAGACCTAATATCTCATTCAGGATCTTGGATT-G
* * *
31060606 A-AAGA-CTCGATATCGCATTCAAGAGT-TTGGGATTG
1 AGAAGACCT-AATATCTCATTCAGGA-TCTT-GGATTG
31060641 AGAAGACCTAATATCTCATTCAGGATCTTGG
1 AGAAGACCTAATATCTCATTCAGGATCTTGG
31060672 GAAGATACGA
Statistics
Matches: 98, Mismatches: 14, Indels: 35
0.67 0.10 0.24
Matches are distributed among these distances:
29 2 0.02
30 41 0.42
31 4 0.04
32 2 0.02
34 3 0.03
35 5 0.05
36 38 0.39
37 3 0.03
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (35 bp):
AGAAGACCTAATATCTCATTCAGGATCTTGGATTG
Found at i:31060683 original size:66 final size:66
Alignment explanation
Indices: 31060509--31060684 Score: 212
Period size: 66 Copynumber: 2.7 Consensus size: 66
31060499 CAGGAACTTA
* * * *
31060509 AGAAGACCAAATATCTCATTCAGGAGCTTGGGAGGACTCAATATCTCATTCAAGATCTTAGGATT
1 AGAAGACCTAATATCTCATTCAGGAGCTTGGGAAGACTCGATATCGCATTCAAGATCTTAGGATT
31060574 G
66 G
* * * * * * *
31060575 AGAAGACATGATATCTCATTTAGGAGATTCGAAAGACTCGATATCGCATTCAAGAGT-TTGGGAT
1 AGAAGACCTAATATCTCATTCAGGAGCTTGGGAAGACTCGATATCGCATTCAAGA-TCTTAGGAT
31060639 TG
65 TG
*
31060641 AGAAGACCTAATATCTCATTCAGGATCTTGGGAAGA-TACGATAT
1 AGAAGACCTAATATCTCATTCAGGAGCTTGGGAAGACT-CGATAT
31060685 TTATTCTTTT
Statistics
Matches: 90, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
65 1 0.01
66 88 0.98
67 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (66 bp):
AGAAGACCTAATATCTCATTCAGGAGCTTGGGAAGACTCGATATCGCATTCAAGATCTTAGGATT
G
Found at i:31089737 original size:27 final size:27
Alignment explanation
Indices: 31089697--31089793 Score: 158
Period size: 27 Copynumber: 3.6 Consensus size: 27
31089687 AGGTCAATAT
*
31089697 ATGATTGAAATACCCCTATAGGGTAAA
1 ATGATCGAAATACCCCTATAGGGTAAA
* *
31089724 ATGATCGAAGTACCCCTGTAGGGTAAA
1 ATGATCGAAATACCCCTATAGGGTAAA
31089751 ATGATCGAAATACCCCTATAGGGTAAA
1 ATGATCGAAATACCCCTATAGGGTAAA
*
31089778 ATGACCGAAATACCCC
1 ATGATCGAAATACCCC
31089794 CATATACCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (27 bp):
ATGATCGAAATACCCCTATAGGGTAAA
Found at i:31089779 original size:54 final size:55
Alignment explanation
Indices: 31089697--31090034 Score: 355
Period size: 54 Copynumber: 6.1 Consensus size: 55
31089687 AGGTCAATAT
* * * * *
31089697 ATGATTGAAATACCCCTATAGGGTAAAATGATCGAAGTACCCCT-GTAGGGTAAA
1 ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTCATAGGGTAAA
*
31089751 ATGATCGAAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATATACCCTCATAGGGTAAA
1 ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATA----C-----CCCTCATAGGGTAAA
* * * **
31089815 ATGACCAAAATACCCCCCATAGGATAAAATGATTGAAATA-CCCTCATAGGGTAAA
1 ATGATCGAAATA-CCCCCATAGGGTAAAATGACCGAAATACCCCTCATAGGGTAAA
* * **
31089870 ATGATCGAAATA-CCACAGAGGGTAAAATGACTAAAATA-CCCTCATAGGGTAAA
1 ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTCATAGGGTAAA
31089923 ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCC-CATAGGGTAAA
1 ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTCATAGGGTAAA
* * ** * *
31089977 ATTATCGAAATACCCCCATAGAGTAGTATGACCAAAATACCAC-CATAGGGTAAA
1 ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTCATAGGGTAAA
31090031 ATGA
1 ATGA
31090035 CTGTTATACC
Statistics
Matches: 243, Mismatches: 28, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
53 48 0.20
54 120 0.49
55 28 0.12
58 1 0.00
63 4 0.02
64 19 0.08
65 23 0.09
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (55 bp):
ATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTCATAGGGTAAA
Found at i:31089827 original size:27 final size:27
Alignment explanation
Indices: 31089797--31090035 Score: 282
Period size: 27 Copynumber: 8.9 Consensus size: 27
31089787 ATACCCCCAT
* *
31089797 ATACCCTCATAGGGTAAAATGACCAAA
1 ATACCCCCATAGGGTAAAATGACCGAA
* **
31089824 ATACCCCCCATAGGATAAAATGATTGAA
1 ATA-CCCCCATAGGGTAAAATGACCGAA
* *
31089852 ATACCCTCATAGGGTAAAATGATCGAA
1 ATACCCCCATAGGGTAAAATGACCGAA
* * **
31089879 ATA-CCACAGAGGGTAAAATGACTAAA
1 ATACCCCCATAGGGTAAAATGACCGAA
* *
31089905 ATACCCTCATAGGGTAAAATGATCGAA
1 ATACCCCCATAGGGTAAAATGACCGAA
31089932 ATACCCCCATAGGGTAAAATGACCGAA
1 ATACCCCCATAGGGTAAAATGACCGAA
* *
31089959 ATACCCCCATAGGGTAAAATTATCGAA
1 ATACCCCCATAGGGTAAAATGACCGAA
* ** *
31089986 ATACCCCCATAGAGTAGTATGACCAAA
1 ATACCCCCATAGGGTAAAATGACCGAA
*
31090013 ATACCACCATAGGGTAAAATGAC
1 ATACCCCCATAGGGTAAAATGAC
31090036 TGTTATACCC
Statistics
Matches: 178, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 21 0.12
27 135 0.76
28 22 0.12
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (27 bp):
ATACCCCCATAGGGTAAAATGACCGAA
Found at i:31091008 original size:28 final size:28
Alignment explanation
Indices: 31090968--31091022 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
31090958 GTATCGGTAT
31090968 AGTGTGGGCCTTAGCCC-ATTACAGTAAC
1 AGTGTGGGCCTTAGCCCAATT-CAGTAAC
31090996 AGTGTGGGCCTTAGCCCAATTCAGTAA
1 AGTGTGGGCCTTAGCCCAATTCAGTAA
31091023 TACAATCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAATTCAGTAAC
Found at i:31091148 original size:26 final size:26
Alignment explanation
Indices: 31091119--31091189 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
31091109 CCAATATTGT
**
31091119 AGCAAAGCTGCCAGTAATAATGACAC
1 AGCAAAGCTGCCAGTAATAACAACAC
* * **
31091145 AGCAAAGCTGCCAGTAACAGCAACGT
1 AGCAAAGCTGCCAGTAATAACAACAC
31091171 AGCAAAGCTGCCAGTAATA
1 AGCAAAGCTGCCAGTAATA
31091190 GTATATGTGG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.14
Consensus pattern (26 bp):
AGCAAAGCTGCCAGTAATAACAACAC
Found at i:31091388 original size:27 final size:25
Alignment explanation
Indices: 31091358--31091617 Score: 117
Period size: 27 Copynumber: 9.7 Consensus size: 25
31091348 TCAACTCCTA
31091358 GGGGTATAATAGTCATTTTACCCTATG
1 GGGGTAT-ATAGTCATTTTACCC-ATG
* *
31091385 GGGGTATTTTGGTCATTTTACCCATCG
1 GGGGTA-TATAGTCATTTTACCCAT-G
* *
31091412 GGGGTATGTCAGTTATTTTACCCAATG
1 GGGGTATAT-AGTCATTTTACCC-ATG
* * *
31091439 GGGGTATTTCGATAATTTTACCCATCG
1 GGGGTATATAG-TCATTTTACCCAT-G
* * * *
31091466 AGGGTATTTTGGTCATTTTACCCATCA
1 GGGGTA-TATAGTCATTTTACCCAT-G
** * *
31091493 AAGGTATTTCAGTCATTTTACCCATC
1 GGGGTATAT-AGTCATTTTACCCATG
* * *
31091519 AGGGTATTTCGATCATTTTACCCATCG
1 GGGGTATATAG-TCATTTTACCCAT-G
** * *
31091546 ATGATATTTCAGTCATTTTACCCA-G
1 GGGGTATAT-AGTCATTTTACCCATG
* *
31091571 CGAGGGTATTTCGATCATTTTACCCATTG
1 -G-GGGTATATAG-TCATTTTACCCA-TG
*
31091600 GGGGTATGTCAGTCATTT
1 GGGGTATAT-AGTCATTT
31091618 GCCTATGAAT
Statistics
Matches: 189, Mismatches: 27, Indels: 34
0.76 0.11 0.14
Matches are distributed among these distances:
25 2 0.01
26 32 0.17
27 144 0.76
28 10 0.05
29 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.38
Consensus pattern (25 bp):
GGGGTATATAGTCATTTTACCCATG
Found at i:31091484 original size:54 final size:53
Alignment explanation
Indices: 31091369--31091617 Score: 268
Period size: 54 Copynumber: 4.6 Consensus size: 53
31091359 GGGTATAATA
** * * *
31091369 GTCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCATCGGGGGTATGTCA
1 GTCATTTTACCC-ATGGGGGTATTTCAGTCATTTTACCCATCGAGGGTATTTCG
* * *
31091423 GTTATTTTACCCAATGGGGGTATTTC-GATAATTTTACCCATCGAGGGTATTTTG
1 GTCATTTTACCC-ATGGGGGTATTTCAG-TCATTTTACCCATCGAGGGTATTTCG
***
31091477 GTCATTTTACCCATCAAAGGTATTTCAGTCATTTTACCCATC-AGGGTATTTCG
1 GTCATTTTACCCAT-GGGGGTATTTCAGTCATTTTACCCATCGAGGGTATTTCG
* ** * *
31091530 ATCATTTTACCCATCGATGATATTTCAGTCATTTTACCCAGCGAGGGTATTTCG
1 GTCATTTTACCCAT-GGGGGTATTTCAGTCATTTTACCCATCGAGGGTATTTCG
* *
31091584 ATCATTTTACCCATTGGGGGTATGTCAGTCATTT
1 GTCATTTTACCCA-TGGGGGTATTTCAGTCATTT
31091618 GCCTATGAAT
Statistics
Matches: 167, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
53 50 0.30
54 115 0.69
55 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (53 bp):
GTCATTTTACCCATGGGGGTATTTCAGTCATTTTACCCATCGAGGGTATTTCG
Found at i:31091543 original size:53 final size:54
Alignment explanation
Indices: 31091453--31091597 Score: 229
Period size: 53 Copynumber: 2.7 Consensus size: 54
31091443 TATTTCGATA
* * *
31091453 ATTTTACCCATCGAGGGTATTTTGGTCATTTTACCCATCAAAGGTATTTCAGTC
1 ATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCAAAGATATTTCAGTC
* *
31091507 ATTTTACCCATC-AGGGTATTTCGATCATTTTACCCATCGATGATATTTCAGTC
1 ATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCAAAGATATTTCAGTC
*
31091560 ATTTTACCCAGCGAGGGTATTTCGATCATTTTACCCAT
1 ATTTTACCCATCGAGGGTATTTCGATCATTTTACCCAT
31091598 TGGGGGTATG
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 47 0.56
54 37 0.44
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (54 bp):
ATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCAAAGATATTTCAGTC
Found at i:31091579 original size:80 final size:80
Alignment explanation
Indices: 31091396--31091597 Score: 262
Period size: 80 Copynumber: 2.5 Consensus size: 80
31091386 GGGTATTTTG
* * * **
31091396 GTCATTTTACCCATCGGGGGTATGTCAGTTATTTTACCCAATGGGGGTATTTCGATAATTTTACC
1 GTCATTTTACCCATCGAGGGTATTTCAGTCATTTTACCC-ATCAGGGTATTTCGATAATTTTACC
* **
31091461 CATCGAGGGTATTTTG
65 CATCGAGGATATTTCA
* * *
31091477 GTCATTTTACCCATCAAAGGTATTTCAGTCATTTTACCCATCAGGGTATTTCGATCATTTTACCC
1 GTCATTTTACCCATCGAGGGTATTTCAGTCATTTTACCCATCAGGGTATTTCGATAATTTTACCC
*
31091542 ATCGATGATATTTCA
66 ATCGAGGATATTTCA
*
31091557 GTCATTTTACCCAGCGAGGGTATTTC-GATCATTTTACCCAT
1 GTCATTTTACCCATCGAGGGTATTTCAG-TCATTTTACCCAT
31091598 TGGGGGTATG
Statistics
Matches: 105, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
79 1 0.01
80 70 0.67
81 34 0.32
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (80 bp):
GTCATTTTACCCATCGAGGGTATTTCAGTCATTTTACCCATCAGGGTATTTCGATAATTTTACCC
ATCGAGGATATTTCA
Found at i:31093642 original size:43 final size:43
Alignment explanation
Indices: 31093584--31093670 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
31093574 AGAAACCAAC
31093584 TCTGGCCCCAGAACTCGCCGCTCGCCCAACTCAGTCCAACAGG
1 TCTGGCCCCAGAACTCGCCGCTCGCCCAACTCAGTCCAACAGG
* *
31093627 TCTGGCCCCATAACTCGCCGCTCGCCCAACTCAGTGCAACAGG
1 TCTGGCCCCAGAACTCGCCGCTCGCCCAACTCAGTCCAACAGG
31093670 T
1 T
31093671 GGGAGTACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.21, C:0.43, G:0.21, T:0.16
Consensus pattern (43 bp):
TCTGGCCCCAGAACTCGCCGCTCGCCCAACTCAGTCCAACAGG
Found at i:31097836 original size:28 final size:28
Alignment explanation
Indices: 31097795--31097850 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
31097785 GTATCGGTAC
*
31097795 AGTGTGGGCTTTAGCCCATTACAGTAAT
1 AGTGTGGGCTTTAGCCCAATACAGTAAT
31097823 AGTGTGGG-TCTTAGCCCAATACAGTAAT
1 AGTGTGGGCT-TTAGCCCAATACAGTAAT
31097851 TAATGCAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (28 bp):
AGTGTGGGCTTTAGCCCAATACAGTAAT
Found at i:31098036 original size:26 final size:26
Alignment explanation
Indices: 31097966--31098036 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
31097956 ATATTACAGG
* * *
31097966 AAAGCTTCCAGTAATAATGACGCAGC
1 AAAGCTGCCAGTAATAGTAACGCAGC
* * *
31097992 AAAGCTGTCAGTAACAGTAACGTAGC
1 AAAGCTGCCAGTAATAGTAACGCAGC
*
31098018 AAAGCTGCCATTAATAGTA
1 AAAGCTGCCAGTAATAGTA
31098037 TATGTGGCAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (26 bp):
AAAGCTGCCAGTAATAGTAACGCAGC
Found at i:31098258 original size:27 final size:27
Alignment explanation
Indices: 31098213--31098548 Score: 340
Period size: 27 Copynumber: 12.5 Consensus size: 27
31098203 GGGTATAACA
* *
31098213 GTCATTTTACCTTAT-GGGGGTACTTT-G
1 GTCATTTTACC-CATCGAGGGTA-TTTCG
* *
31098240 GTCATTTTACCCATCGGGGGTGTTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
31098267 ATTATTTTACCCATC-AGTGGTATTTCG
1 GTCATTTTACCCATCGAG-GGTATTTCG
* * *
31098294 GTCATTTTACCCATCAAGAGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
*
31098321 GTCATTTTACCCATCGAGGGTATTTCT
1 GTCATTTTACCCATCGAGGGTATTTCG
* * **
31098348 ATCATTTTACCCATCAAGGGTATTTTT
1 GTCATTTTACCCATCGAGGGTATTTCG
* * * *
31098375 GTTATTTTACCCATCAATGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
31098402 GTTATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
31098429 ATCATTTTATCCATCGAAGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
31098456 ATCATTTTACCCATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
31098483 ATCATTTTACCCATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
31098510 ATCATTTTACCCAT-TAGGGGTATTTCA
1 GTCATTTTACCCATCGA-GGGTATTTCG
31098537 GTCA-TTTACCCA
1 GTCATTTTACCCA
31098549 CGAAATCCAG
Statistics
Matches: 272, Mismatches: 32, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
26 15 0.06
27 255 0.94
28 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCATCGAGGGTATTTCG
Found at i:31098355 original size:81 final size:79
Alignment explanation
Indices: 31098240--31098548 Score: 386
Period size: 81 Copynumber: 3.8 Consensus size: 79
31098230 GGGTACTTTG
* * *
31098240 GTCATTTTACCCATCGGGGGTGTTTCGATTATTTTACCCATCAGTGGTATTTCGGTCATTTTACC
1 GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCAG-GGTATTTCGGTCATTTTACC
31098305 CATCAAGAGTATTTCA
65 CATCAAG-GTATTTCA
* ** *
31098321 GTCATTTTACCCATCGAGGGTATTTCTATCATTTTACCCATCAAGGGTATTTTTGTTATTTTACC
1 GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATC-AGGGTATTTCGGTCATTTTACC
**
31098386 CATCAATGGTATTTTG
65 CATCAA-GGTATTTCA
* * * *
31098402 GTTATTTTACCCATCGAGGGTATTTCGATCATTTTATCCATCGAAGGTATTTCGATCATTTTACC
1 GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATC-AGGGTATTTCGGTCATTTTACC
*
31098467 CATCGAGGGTATTTCA
65 CATC-AAGGTATTTCA
* * * *
31098483 ATCATTTTACCCATCGAGGGTATTTCAATCATTTTACCCATTAGGGGTATTTCAGTCA-TTTACC
1 GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCA-GGGTATTTCGGTCATTTTACC
31098547 CA
65 CA
31098549 CGAAATCCAG
Statistics
Matches: 195, Mismatches: 29, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
80 9 0.05
81 182 0.93
82 4 0.02
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.40
Consensus pattern (79 bp):
GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCAGGGTATTTCGGTCATTTTACCC
ATCAAGGTATTTCA
Found at i:31111783 original size:20 final size:19
Alignment explanation
Indices: 31111744--31111786 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
31111734 CAACACAATG
*
31111744 AAAATAAAATAAAATAAAC
1 AAAATAAAATAAAAGAAAC
*
31111763 AAAATAACAATAAAAGCAAC
1 AAAATAA-AATAAAAGAAAC
31111783 AAAA
1 AAAA
31111787 CTTAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.12
Consensus pattern (19 bp):
AAAATAAAATAAAAGAAAC
Found at i:31120185 original size:25 final size:27
Alignment explanation
Indices: 31120121--31120197 Score: 88
Period size: 25 Copynumber: 2.9 Consensus size: 27
31120111 CATCCCGACC
**
31120121 CACAGCTCGTGTGAGCAGACCCA-ATTT
1 CACAGCTCGTGTGAGCA-ACTTATATTT
*
31120148 CACAGCTCATGTGAGCAA-TTATATTT
1 CACAGCTCGTGTGAGCAACTTATATTT
*
31120174 -ACAGCTCGTGTGAGCAATTTATAT
1 CACAGCTCGTGTGAGCAACTTATAT
31120198 CTGGTGTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
25 17 0.39
26 11 0.25
27 16 0.36
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (27 bp):
CACAGCTCGTGTGAGCAACTTATATTT
Found at i:31123294 original size:22 final size:22
Alignment explanation
Indices: 31123266--31123308 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
31123256 AAAAAAGATG
31123266 AAAGTTAGGATTTTTAATCTAA
1 AAAGTTAGGATTTTTAATCTAA
31123288 AAAGTTAGGATTTTTAATCTA
1 AAAGTTAGGATTTTTAATCTA
31123309 GGAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (22 bp):
AAAGTTAGGATTTTTAATCTAA
Found at i:31139063 original size:39 final size:39
Alignment explanation
Indices: 31138934--31139066 Score: 167
Period size: 39 Copynumber: 3.4 Consensus size: 39
31138924 TAGTAGATAA
* *
31138934 CTGTTGTACTTCGGTACCCGTGTTTGCACATACGTGCCC
1 CTGTTGTTCTTCGGTACCCCTGTTTGCACATACGTGCCC
* * * * * *
31138973 CTATTGTTCTTAGATACCCTTGTTTGTACATATGTGCCC
1 CTGTTGTTCTTCGGTACCCCTGTTTGCACATACGTGCCC
* *
31139012 CTGTTGTTCTTCGGTACCCCTATTCGCACATACGTGCCC
1 CTGTTGTTCTTCGGTACCCCTGTTTGCACATACGTGCCC
*
31139051 CTGTTGTGCTTCGGTA
1 CTGTTGTTCTTCGGTA
31139067 ACATTTATTA
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.14, C:0.29, G:0.20, T:0.38
Consensus pattern (39 bp):
CTGTTGTTCTTCGGTACCCCTGTTTGCACATACGTGCCC
Found at i:31144456 original size:54 final size:54
Alignment explanation
Indices: 31144369--31144485 Score: 171
Period size: 54 Copynumber: 2.2 Consensus size: 54
31144359 TATGACATGG
* * * *
31144369 CCGTGTGACCCAATTCAGTGAGTTACATAGGCAGAGACACGGGCTGGGACACGA
1 CCGTGTGTCTCAAGTCAGTGAGTTACATAGGCAGAGACACGGGATGGGACACGA
** *
31144423 TTGTGTGTCTCAAGTCAGTGAGTTACATGGGCAGAGACACGGGATGGGACACGA
1 CCGTGTGTCTCAAGTCAGTGAGTTACATAGGCAGAGACACGGGATGGGACACGA
31144477 CCGTGTGTC
1 CCGTGTGTC
31144486 CCCTATTCTA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (54 bp):
CCGTGTGTCTCAAGTCAGTGAGTTACATAGGCAGAGACACGGGATGGGACACGA
Found at i:31150040 original size:45 final size:44
Alignment explanation
Indices: 31149990--31150082 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
31149980 GGTTCGCTAT
**
31149990 AATGGAATAGAGGTGTAAAAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAAAGT-ATTC-ATGTGTTTGGTTGAATGG
* *
31150035 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAAAGTATTCATGTGTTTGGTTGAATGG
31150079 AATG
1 AATG
31150083 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.53
45 19 0.44
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAACTGTAAAAGTATTCATGTGTTTGGTTGAATGG
Found at i:31157347 original size:41 final size:41
Alignment explanation
Indices: 31157298--31157390 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
31157288 TGTTTTTCTT
* * *
31157298 ATAAACGCCACAAAAGGTAAAGTAATAGCGGCGTTTCTCCC
1 ATAAACGCCACAAAAGATAAAGCAATAGAGGCGTTTCTCCC
*
31157339 ATAAACGCCACAAAAGATAAAGCAATAGAGGCGTTTTTCCC
1 ATAAACGCCACAAAAGATAAAGCAATAGAGGCGTTTCTCCC
*
31157380 ATAAACACCAC
1 ATAAACGCCAC
31157391 GAATTTTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (41 bp):
ATAAACGCCACAAAAGATAAAGCAATAGAGGCGTTTCTCCC
Found at i:31162492 original size:8 final size:8
Alignment explanation
Indices: 31162479--31162527 Score: 54
Period size: 7 Copynumber: 6.8 Consensus size: 8
31162469 TTCTATGAAC
31162479 TTTTTATA
1 TTTTTATA
31162487 -TTTT-TA
1 TTTTTATA
31162493 TTTTTAT-
1 TTTTTATA
31162500 TTTTTA-A
1 TTTTTATA
31162507 TTTTTA-A
1 TTTTTATA
31162514 TTTTTATA
1 TTTTTATA
*
31162522 ATTTTA
1 TTTTTA
31162528 AAATTTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
6 2 0.06
7 27 0.75
8 7 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTATA
Found at i:31162498 original size:14 final size:14
Alignment explanation
Indices: 31162479--31162520 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
31162469 TTCTATGAAC
31162479 TTTTTATATTTTTA
1 TTTTTATATTTTTA
31162493 TTTTTAT-TTTTTAA
1 TTTTTATATTTTT-A
31162507 TTTTTA-ATTTTTA
1 TTTTTATATTTTTA
31162520 T
1 T
31162521 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.27
14 19 0.73
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATATTTTTA
Found at i:31162503 original size:21 final size:21
Alignment explanation
Indices: 31162479--31162520 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
31162469 TTCTATGAAC
31162479 TTTTTATATTTTT-ATTTTTAT
1 TTTTTA-ATTTTTAATTTTTAT
31162500 TTTTTAATTTTTAATTTTTAT
1 TTTTTAATTTTTAATTTTTAT
31162521 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTAATTTTTAATTTTTAT
Found at i:31163050 original size:13 final size:13
Alignment explanation
Indices: 31163032--31163071 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
31163022 GTTGACAATC
31163032 TATTTGTAACTAA
1 TATTTGTAACTAA
31163045 TATTTGTAACTAA
1 TATTTGTAACTAA
*
31163058 CT-TTTGTAATTAA
1 -TATTTGTAACTAA
31163071 T
1 T
31163072 TAGGCCGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (13 bp):
TATTTGTAACTAA
Found at i:31166291 original size:220 final size:220
Alignment explanation
Indices: 31165875--31166969 Score: 2056
Period size: 220 Copynumber: 5.0 Consensus size: 220
31165865 TGAACTATCC
* *
31165875 AATATAATGAAAGTTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
1 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
*
31165940 AGCCGTCTTGACTTTATGCAACTTAGAGAAGATC-TTTCACCTTCGTTCTTCACTATTATGTTGC
66 AGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
31166004 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
131 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
31166069 CTTATAGAGAGGTGCTAATTTATTT
196 CTTATAGAGAGGTGCTAATTTATTT
31166094 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
1 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
31166159 AGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
66 AGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
31166224 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
131 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
31166289 CTTATAGAGAGGTGCTAATTTATTT
196 CTTATAGAGAGGTGCTAATTTATTT
31166314 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
1 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
* *
31166379 AGTCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTTACCTTCGTTCTTCACTATTATGTTGC
66 AGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
31166444 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
131 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
31166509 CTTATAGAGAGGTGCTAATTTATTT
196 CTTATAGAGAGGTGCTAATTTATTT
*
31166534 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGATAAAGTACAAGATCA
1 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
*
31166599 AGTCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
66 AGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
31166664 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
131 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
*
31166729 CTTATAGAGAGGTCCT-A---ATTT
196 CTTATAGAGAGGTGCTAATTTATTT
31166750 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
1 AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
*
31166815 AGCTGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
66 AGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
* *
31166880 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTAGACCAGTTTTCTATCGGTGGCTGTAT
131 ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
31166945 CTTATAGAGAGGTGCTAATTTATTT
196 CTTATAGAGAGGTGCTAATTTATTT
31166970 GCCAAGTTAT
Statistics
Matches: 857, Mismatches: 14, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
216 209 0.24
217 1 0.00
219 97 0.11
220 550 0.64
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (220 bp):
AATATAATGAATGCTATTTGTGGCAAAGTTTTGATTGTTGAAGAACTTGAGAAAGTACAAGATCA
AGCCGTCTTGACTTTATGCAACTTGGAGAAGATCTTTTCACCTTCGTTCTTCACTATTATGTTGC
ACTTACTAATCCATCTCCCTCATGAAGCAAAACTTGGTGGACCAGTTTTCTATCGGTGGATGTAT
CTTATAGAGAGGTGCTAATTTATTT
Found at i:31185480 original size:28 final size:28
Alignment explanation
Indices: 31185396--31185492 Score: 115
Period size: 28 Copynumber: 3.4 Consensus size: 28
31185386 TATACAGTAT
* *
31185396 CAGT-ACAGTGTAGGCCTTAGCCCATTA
1 CAGTAACAGTGGAGGCCTTAGCCCAATA
* *
31185423 CAGTAACAGTGTGTGAGCCTTAGCCTAATA
1 CAGTAACAGTG-GAG-GCCTTAGCCCAATA
31185453 CAGTAACAGTGGAGGCCTTAGCCCAATA
1 CAGTAACAGTGGAGGCCTTAGCCCAATA
*
31185481 TAGTAATCAGTG
1 CAGTAA-CAGTG
31185493 CAATGCAGTA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
27 4 0.07
28 24 0.41
29 8 0.14
30 23 0.39
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (28 bp):
CAGTAACAGTGGAGGCCTTAGCCCAATA
Found at i:31185657 original size:26 final size:26
Alignment explanation
Indices: 31185597--31185673 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 26
31185587 ACACCAATAT
* *
31185597 CGCAGCAAAGCTGCTAGTAATAGTGA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
* *
31185623 CACATCAAAGCTGCCAGTAATAGTAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
* * *
31185649 TGCAGCAAAGCTACCAGTAACAGTA
1 CGCAGCAAAGCTGCCAGTAATAGTA
31185674 TATGTGGTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAATAGTAA
Found at i:31185868 original size:27 final size:26
Alignment explanation
Indices: 31185848--31186293 Score: 235
Period size: 27 Copynumber: 16.7 Consensus size: 26
31185838 GGGTATAACA
*
31185848 GTCATTTTACCCTATGGGGGTATTTC
1 GTCATTTTACCCTATGAGGGTATTTC
31185874 GATCATTTTACCCTATGAGGGTATTTC
1 G-TCATTTTACCCTATGAGGGTATTTC
* *
31185901 GGTCATTTTACCCT-TCAGGGGTATTTTG
1 -GTCATTTTACCCTATGA-GGGTA-TTTC
* *
31185929 GTTATTTTACCCGTCA--AGGGCA-TTC
1 GTCATTTTACCC-T-ATGAGGGTATTTC
31185954 GATCATTTTACCCT-TCGAGGGTATTTC
1 G-TCATTTTACCCTAT-GAGGGTATTTC
* * * *
31185981 GATCATTTTACCAT-TCAAAGGTATTCC
1 G-TCATTTTACCCTAT-GAGGGTATTTC
*
31186008 AGTCATTTTACCCT-TCAAGGGTATTTC
1 -GTCATTTTACCCTAT-GAGGGTATTTC
* *
31186035 GATCATTTTA-CCTTTCGAGGGTATTTTG
1 G-TCATTTTACCCTAT-GAGGGTA-TTTC
*
31186063 GTCATTTTACCCT-TCGGGGGTATTTC
1 GTCATTTTACCCTAT-GAGGGTATTTC
* * * *
31186089 GATCATTTTACCCTTTAAGGTTATTTTA
1 G-TCATTTTACCCTATGAGGGTA-TTTC
* *
31186117 GTCATTTTACCCT-TCAGGGGTATTTTA
1 GTCATTTTACCCTATGA-GGGTA-TTTC
31186144 GTTC-TTTTACCCT-TCGAGGGTATTTC
1 G-TCATTTTACCCTAT-GAGGGTATTTC
* * * *
31186170 GATTATTTTACCCTTTAAGGGTATTTTG
1 G-TCATTTTACCCTATGAGGGTA-TTTC
* *
31186198 GTCATTTTACCCT-TCAGGGGTACTTC
1 GTCATTTTACCCTATGA-GGGTATTTC
31186224 GATCATTTTACCCCTCA--AGGGTATTTC
1 G-TCATTTTA-CCCT-ATGAGGGTATTTC
* * *
31186251 AGTCATTTTATCCT-TCAAGGCTATTTC
1 -GTCATTTTACCCTAT-GAGGGTATTTC
31186278 GGTCA-TTTACCC-ATGA
1 -GTCATTTTACCCTATGA
31186294 ATTGCAAGTT
Statistics
Matches: 343, Mismatches: 41, Indels: 73
0.75 0.09 0.16
Matches are distributed among these distances:
25 5 0.01
26 48 0.14
27 257 0.75
28 33 0.10
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (26 bp):
GTCATTTTACCCTATGAGGGTATTTC
Found at i:31185922 original size:54 final size:54
Alignment explanation
Indices: 31185848--31186289 Score: 457
Period size: 54 Copynumber: 8.2 Consensus size: 54
31185838 GGGTATAACA
* *
31185848 GTCATTTTACCCTAT-GGGGGTATTTCGATCATTTTACCCTAT-GAGGGTATTTCG
1 GTCATTTTACCCT-TCAGGGGTATTTCGATCATTTTACCCT-TCAAGGGTATTTCG
* * * * *
31185902 GTCATTTTACCCTTCAGGGGTATTTTGGTTATTTTACCCGTCAAGGGCA-TTCG
1 GTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
* * * * *
31185955 ATCATTTTACCCTTC-GAGGGTATTTCGATCATTTTACCATTCAAAGGTATTCCA
1 GTCATTTTACCCTTCAG-GGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
* * * *
31186009 GTCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCTTTCGAGGGTATTTTG
1 GTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
* * * **
31186063 GTCATTTTACCCTTCGGGGGTATTTCGATCATTTTACCCTTTAAGGTTATTTTA
1 GTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
* * *
31186117 GTCATTTTACCCTTCAGGGGTATTTTAGTTC-TTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCAGGGGTA-TTTCGATCATTTTACCCTTCAAGGGTATTTCG
* * * * * * * *
31186171 ATTATTTTACCCTTTAAGGGTATTTTGGTCATTTTACCCTTCAGGGGTACTTCG
1 GTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
* * * * *
31186225 ATCATTTTACCCCTCAAGGGTATTTC-AGTCATTTTATCCTTCAAGGCTATTTCG
1 GTCATTTTACCCTTCAGGGGTATTTCGA-TCATTTTACCCTTCAAGGGTATTTCG
31186279 GTCA-TTTACCC
1 GTCATTTTACCC
31186290 ATGAATTGCA
Statistics
Matches: 321, Mismatches: 59, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
52 1 0.00
53 58 0.18
54 256 0.80
55 6 0.02
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.42
Consensus pattern (54 bp):
GTCATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
Found at i:31186068 original size:81 final size:81
Alignment explanation
Indices: 31185836--31186289 Score: 460
Period size: 81 Copynumber: 5.6 Consensus size: 81
31185826 TTCAACTCCT
** **
31185836 AAGGGTATAACAGTCATTTTACCCTAT-GGGGGTATTTCGATCATTTTACCCTAT-GAGGGTATT
1 AAGGGTATTTCAGTCATTTTACCCT-TCAAGGGTATTTCGATCATTTTACCCT-TCGAGGGTATT
*
31185899 TCGGTCATTTTACCCTTC
64 TCGATCATTTTACCCTTC
* ** * * *
31185917 AGGGGTATTTTGGTTATTTTACCCGTCAAGGGCA-TTCGATCATTTTACCCTTCGAGGGTATTTC
1 AAGGGTATTTCAGTCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTC
*
31185981 GATCATTTTACCATTC
66 GATCATTTTACCCTTC
* * * *
31185997 AAAGGTATTCCAGTCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCTTTCGAGGGTATTTT
1 AAGGGTATTTCAGTCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTC
*
31186062 GGTCATTTTACCCTTC
66 GATCATTTTACCCTTC
** * * *
31186078 GGGGGTATTTC-GATCATTTTACCCTTTAAGGTTATTT-TAGTCATTTTACCCTTC-AGGGGTAT
1 AAGGGTATTTCAG-TCATTTTACCCTTCAAGGGTATTTCGA-TCATTTTACCCTTCGA-GGGTA-
* *
31186140 TTTAGTTC-TTTTACCCTTC
62 TTTCGATCATTTTACCCTTC
* * * * * *
31186159 GAGGGTATTTC-GATTATTTTACCCTTTAAGGGTATTTTGGTCATTTTACCCTTC-AGGGGTACT
1 AAGGGTATTTCAG-TCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCCTTCGA-GGGTATT
*
31186222 TCGATCATTTTACCCCTC
64 TCGATCATTTTACCCTTC
* * *
31186240 AAGGGTATTTCAGTCATTTTATCCTTCAAGGCTATTTCGGTCA-TTTACCC
1 AAGGGTATTTCAGTCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCC
31186290 ATGAATTGCA
Statistics
Matches: 314, Mismatches: 49, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
79 1 0.00
80 84 0.27
81 222 0.71
82 7 0.02
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (81 bp):
AAGGGTATTTCAGTCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTC
GATCATTTTACCCTTC
Found at i:31189630 original size:14 final size:13
Alignment explanation
Indices: 31189597--31189639 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
31189587 TCAAGTCCTT
31189597 TACAGATACAGATA
1 TACAGA-ACAGATA
31189611 -ACAGAACCAGATA
1 TACAGAA-CAGATA
31189624 TACAGAACAGAT-
1 TACAGAACAGATA
31189636 TACA
1 TACA
31189640 AAATCCCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 5 0.19
13 16 0.59
14 6 0.22
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (13 bp):
TACAGAACAGATA
Found at i:31190186 original size:18 final size:17
Alignment explanation
Indices: 31190163--31190197 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
31190153 CGTGTGCAAT
31190163 GCCCGTATGGGCCCACAC
1 GCCCGTAT-GGCCCACAC
*
31190181 GCCCGTGTGGCCCACAC
1 GCCCGTATGGCCCACAC
31190198 TACCAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.14, C:0.46, G:0.29, T:0.11
Consensus pattern (17 bp):
GCCCGTATGGCCCACAC
Found at i:31192613 original size:18 final size:18
Alignment explanation
Indices: 31192590--31192630 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
31192580 CTTTTCCCCC
*
31192590 TTCTTTCATTTGTTTATT
1 TTCTTTCATTTATTTATT
*
31192608 TTCTTTCGTTTATTTATT
1 TTCTTTCATTTATTTATT
31192626 TTCTT
1 TTCTT
31192631 ACTTTTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.73
Consensus pattern (18 bp):
TTCTTTCATTTATTTATT
Found at i:31193899 original size:28 final size:28
Alignment explanation
Indices: 31193864--31193926 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
31193854 TTTATATGTA
*
31193864 TTAATTATTTTACCACTAATATGTATAC
1 TTAATTATTTTACCACTAACATGTATAC
*
31193892 TTAATTATTTTACCATTAACATGTATAC
1 TTAATTATTTTACCACTAACATGTATAC
31193920 TT-ATTAT
1 TTAATTAT
31193927 ATTATCTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 5 0.15
28 28 0.85
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.49
Consensus pattern (28 bp):
TTAATTATTTTACCACTAACATGTATAC
Found at i:31202063 original size:17 final size:18
Alignment explanation
Indices: 31202036--31202069 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
31202026 TAATTATTTT
31202036 ATTAATAATATTAATGAA
1 ATTAATAATATTAATGAA
31202054 ATTAAT-ATATTAATGA
1 ATTAATAATATTAATGA
31202070 TTACTTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (18 bp):
ATTAATAATATTAATGAA
Found at i:31206115 original size:13 final size:13
Alignment explanation
Indices: 31206097--31206169 Score: 85
Period size: 13 Copynumber: 5.7 Consensus size: 13
31206087 TCTTCATTGT
31206097 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
31206110 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
* *
31206123 TGTGGAAAAGTGC
1 TTTTGAAAAGTGC
* *
31206136 TTTTCAGAAGTGC
1 TTTTGAAAAGTGC
* *
31206149 TTTTCAGAAGTGC
1 TTTTGAAAAGTGC
31206162 TTTT-AAAA
1 TTTTGAAAA
31206170 ATTTGGAGTG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
12 3 0.06
13 50 0.94
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:31209507 original size:25 final size:26
Alignment explanation
Indices: 31209453--31209510 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
31209443 AGATATTTAA
*
31209453 TTTAAT-TTAATATTAAGATAATCAC
1 TTTAATATTAATATTAAGAAAATCAC
*
31209478 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAATATTAATATTAAGAAAATCAC
31209502 TATTAATAT
1 T-TTAATAT
31209511 ACGTATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 3 0.10
25 22 0.76
26 4 0.14
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (26 bp):
TTTAATATTAATATTAAGAAAATCAC
Found at i:31211814 original size:18 final size:16
Alignment explanation
Indices: 31211772--31211814 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
31211762 TAGCATATTT
31211772 TTTTTATTCACAATGC
1 TTTTTATTCACAATGC
* *
31211788 CTTTAATTCTAACAATGC
1 TTTTTATTC--ACAATGC
31211806 TTTTTATTC
1 TTTTTATTC
31211815 GTTCGCTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 7 0.33
18 14 0.67
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.51
Consensus pattern (16 bp):
TTTTTATTCACAATGC
Found at i:31214540 original size:14 final size:14
Alignment explanation
Indices: 31214501--31214551 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
31214491 TAATAAATTT
*
31214501 ATTATTTAACATAA
1 ATTATTTAATATAA
31214515 ATATAAATTTAATATAA
1 AT-T--ATTTAATATAA
*
31214532 ATTATTTAATATGA
1 ATTATTTAATATAA
31214546 ATTATT
1 ATTATT
31214552 ATTAATAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 18 0.56
15 1 0.03
16 1 0.03
17 12 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (14 bp):
ATTATTTAATATAA
Found at i:31214552 original size:17 final size:16
Alignment explanation
Indices: 31214480--31214558 Score: 60
Period size: 16 Copynumber: 5.0 Consensus size: 16
31214470 AATCAAAATT
31214480 TAATTATT-TATTAATA
1 TAATTATTAT-TTAATA
*
31214496 -AATTTATTATTTAACA
1 TAA-TTATTATTTAATA
* *
31214512 TAAATATAAATTTAATA
1 TAATTAT-TATTTAATA
31214529 TAA--ATTATTTAATA
1 TAATTATTATTTAATA
31214543 TGAATTATTA-TTAATA
1 T-AATTATTATTTAATA
31214559 ATCAATTTGC
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 9 0.18
15 6 0.12
16 19 0.37
17 17 0.33
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (16 bp):
TAATTATTATTTAATA
Found at i:31215176 original size:22 final size:20
Alignment explanation
Indices: 31215138--31215182 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 20
31215128 TATATTTTTA
31215138 TTTCTATAAAATTTTGAAAT
1 TTTCTATAAAATTTTGAAAT
31215158 TTTCTAATAAATATTTTGAAAT
1 TTTCT-ATAAA-ATTTTGAAAT
31215180 TTT
1 TTT
31215183 GAAGATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 5 0.22
21 5 0.22
22 13 0.57
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTCTATAAAATTTTGAAAT
Found at i:31216808 original size:60 final size:60
Alignment explanation
Indices: 31216683--31216811 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
31216673 TTAAGTTCTG
* * * * * * * *
31216683 TTATTTTCAAAATCTGATGCGCCAAACATATTATCATATGTGTAATGCCCTTTTAGCCTA
1 TTATTTCCAAAACCGGATGCGCCAAACATATTATCATATATGTAATGCCATATCAACCTA
* * *
31216743 CTATTTCCAAAACCGGATGCGCCAAACATATTATCATATATGTAATGTCATATCAACTTA
1 TTATTTCCAAAACCGGATGCGCCAAACATATTATCATATATGTAATGCCATATCAACCTA
31216803 TTATTTCCA
1 TTATTTCCA
31216812 CATATTACTT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (60 bp):
TTATTTCCAAAACCGGATGCGCCAAACATATTATCATATATGTAATGCCATATCAACCTA
Found at i:31222288 original size:15 final size:16
Alignment explanation
Indices: 31222256--31222288 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
31222246 CTTCATCTGT
*
31222256 TTAATTTATTCTTCCA
1 TTAATTTATTCTTACA
31222272 TTAATTT-TTCTTACA
1 TTAATTTATTCTTACA
31222287 TT
1 TT
31222289 TATAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATTTATTCTTACA
Found at i:31224095 original size:59 final size:62
Alignment explanation
Indices: 31224014--31224130 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 62
31224004 ATCACTTTAA
* * * *
31224014 TATTAAATTAATATAATATTTATC-A-AA-ATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATCAATAAGATAAACATTAAATTAAATTTAATATTAAATCT
* * *
31224073 TATTAAAATGATAGAATGTTTATCAATAAGATAAACATTAAATTTAATTTAATATTAA
1 TATTAAAATAATAGAATATTTATCAATAAGATAAACATTAAATTAAATTTAATATTAA
31224131 GATAATCACT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 20 0.42
60 1 0.02
61 2 0.04
62 25 0.52
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (62 bp):
TATTAAAATAATAGAATATTTATCAATAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:31225642 original size:51 final size:51
Alignment explanation
Indices: 31225514--31225698 Score: 169
Period size: 51 Copynumber: 3.6 Consensus size: 51
31225504 AACGTGATTG
* * ** * *
31225514 TCACGTGTGTAGTACTATGTGCAGGCTACTAGGTGTACCGGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCATACCGGATAGTAAT-GA
* * *
31225564 TCGCATGTGTAGTACAATGTGCAGGCTACTATGCATACCGGATAGT-TTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCATACCGGATAGTAAT-GA
** * ** * * *
31225615 TCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCATACCGGATAGTAATGA
*
31225666 TCACATGTATAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
31225699 TGAACCGAAC
Statistics
Matches: 108, Mismatches: 24, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
50 36 0.33
51 70 0.65
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCATACCGGATAGTAATGA
Found at i:31225753 original size:45 final size:45
Alignment explanation
Indices: 31225702--31225796 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
31225692 TACTATGTGA
* ** *
31225702 ACCGAACATCATTAATTAGTAAGGTGGTTGTTATGTGCTGATTCC
1 ACCGAACATCATTAATTAATAAGGTGGTTACTATGTGCTGAATCC
*
31225747 ACCGAACATCATTGATTAATAAGGTGGTTACTATGTGCTGAATCC
1 ACCGAACATCATTAATTAATAAGGTGGTTACTATGTGCTGAATCC
31225792 ACCGA
1 ACCGA
31225797 GTATCTGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (45 bp):
ACCGAACATCATTAATTAATAAGGTGGTTACTATGTGCTGAATCC
Found at i:31226926 original size:13 final size:13
Alignment explanation
Indices: 31226910--31226943 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
31226900 TATTTGGCAA
31226910 GCATGCTTGGTGT
1 GCATGCTTGGTGT
31226923 GCATGCTTGGTGT
1 GCATGCTTGGTGT
*
31226936 GTATGCTT
1 GCATGCTT
31226944 AGGCTTTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.09, C:0.15, G:0.35, T:0.41
Consensus pattern (13 bp):
GCATGCTTGGTGT
Found at i:31229410 original size:7 final size:7
Alignment explanation
Indices: 31229400--31229445 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
31229390 TTTTTAAATT
31229400 TTTAAAA
1 TTTAAAA
31229407 TTTAAAA
1 TTTAAAA
31229414 TTTAAAAA
1 TTT-AAAA
31229422 TTTAAAA
1 TTTAAAA
31229429 CTCGTTAAAA
1 -T--TTAAAA
31229439 TTTAAAA
1 TTTAAAA
31229446 ATAAAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 20 0.57
8 8 0.23
9 1 0.03
10 6 0.17
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (7 bp):
TTTAAAA
Found at i:31229412 original size:15 final size:15
Alignment explanation
Indices: 31229392--31229428 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
31229382 ACATTAAATT
* *
31229392 TTTAAATTTTTAAAA
1 TTTAAAATTTAAAAA
31229407 TTTAAAATTTAAAAA
1 TTTAAAATTTAAAAA
31229422 TTTAAAA
1 TTTAAAA
31229429 CTCGTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAAAATTTAAAAA
Found at i:31229468 original size:31 final size:32
Alignment explanation
Indices: 31229400--31229470 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
31229390 TTTTTAAATT
* *
31229400 TTTAAAATTTAAAATTTAAAAATTTAAAACTC
1 TTTAAAATTTAAAATATAAAAATATAAAACTC
* * **
31229432 GTTAAAATTTAAAA-ATAAAAATATATATTTC
1 TTTAAAATTTAAAATATAAAAATATAAAACTC
31229463 TTTAAAAT
1 TTTAAAAT
31229471 ATATTTAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
31 19 0.59
32 13 0.41
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (32 bp):
TTTAAAATTTAAAATATAAAAATATAAAACTC
Found at i:31231000 original size:60 final size:60
Alignment explanation
Indices: 31230901--31231014 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
31230891 AAATGAGGTG
** * ** *
31230901 TTATTCAGGCTTAGTGTTTAGTAGGCTTAGTGCTGGTGTTGTTCAGGCTTAGTGCAAGTA
1 TTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCAGTGTTATTCAGGCTTAGTGCAAGTA
*
31230961 TTATTTAGGCTTAGTGCCTAGCAGGCTTAGTGCCAGTGTTATTCAGGCTTAGTG
1 TTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCAGTGTTATTCAGGCTTAGTG
31231015 TGTAACACCC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.18, C:0.14, G:0.29, T:0.39
Consensus pattern (60 bp):
TTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCAGTGTTATTCAGGCTTAGTGCAAGTA
Found at i:31231007 original size:22 final size:22
Alignment explanation
Indices: 31230923--31231014 Score: 79
Period size: 22 Copynumber: 4.5 Consensus size: 22
31230913 AGTGTTTAGT
** *
31230923 AGGCTTAGTGCTGGTGTTGTTC
1 AGGCTTAGTGCCAGTGTTATTC
* * *
31230945 AGGCTTAGTGCAAGTATTATTT
1 AGGCTTAGTGCCAGTGTTATTC
*
31230967 AGGCTTAGTGCC-----TA-GC
1 AGGCTTAGTGCCAGTGTTATTC
31230983 AGGCTTAGTGCCAGTGTTATTC
1 AGGCTTAGTGCCAGTGTTATTC
31231005 AGGCTTAGTG
1 AGGCTTAGTG
31231015 TGTAACACCC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
16 12 0.22
17 2 0.04
21 2 0.04
22 39 0.71
ACGTcount: A:0.18, C:0.15, G:0.30, T:0.36
Consensus pattern (22 bp):
AGGCTTAGTGCCAGTGTTATTC
Found at i:31232893 original size:20 final size:20
Alignment explanation
Indices: 31232851--31232891 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
31232841 TATAACACAA
*
31232851 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
31232871 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
31232890 TT
1 TT
31232892 TCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:31233365 original size:21 final size:21
Alignment explanation
Indices: 31233305--31233365 Score: 50
Period size: 26 Copynumber: 2.7 Consensus size: 21
31233295 GTTTTCTTTC
**
31233305 TTCTTTCTCTTTTTATTTTCT
1 TTCTTTCTCTTTTTAGCTTCT
*
31233326 TTCCTTTCTGTTTCATTTTAGCTTCT
1 TT-CTTTC----TCTTTTTAGCTTCT
31233352 TTCTTTCTCTTTTT
1 TTCTTTCTCTTTTT
31233366 CTTATTTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
21 8 0.26
22 5 0.16
25 5 0.16
26 13 0.42
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.70
Consensus pattern (21 bp):
TTCTTTCTCTTTTTAGCTTCT
Found at i:31233447 original size:32 final size:34
Alignment explanation
Indices: 31233388--31233462 Score: 79
Period size: 37 Copynumber: 2.3 Consensus size: 34
31233378 TATTATAATT
*
31233388 TTATAATATATATATACTTAATTCTTAAGGTTTTATA
1 TTATAATATATATATA-TTAA-TCTTAA-ATTTTATA
31233425 TTATAATATATAT-T-TTAA-CTTAAATTTTATA
1 TTATAATATATATATATTAATCTTAAATTTTATA
31233456 --ATAATAT
1 TTATAATAT
31233463 TACACCTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
29 7 0.19
31 7 0.19
32 5 0.14
34 4 0.11
36 1 0.03
37 13 0.35
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (34 bp):
TTATAATATATATATATTAATCTTAAATTTTATA
Found at i:31237073 original size:21 final size:20
Alignment explanation
Indices: 31237049--31237094 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
31237039 AGGTACCACA
* *
31237049 ATTATATCATCATTTCATATC
1 ATTATAACATCA-TTCAAATC
*
31237070 ATTAAAACATCATTCAAATC
1 ATTATAACATCATTCAAATC
31237090 ATTAT
1 ATTAT
31237095 TTTAAATCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTATAACATCATTCAAATC
Found at i:31238280 original size:20 final size:19
Alignment explanation
Indices: 31238257--31238297 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
31238247 TATAACACAA
*
31238257 TTCAATTTCATATTTAATAT
1 TTCAATTT-ATACTTAATAT
*
31238277 TTCAATTTTTACTTAATAT
1 TTCAATTTATACTTAATAT
31238296 TT
1 TT
31238298 TCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (19 bp):
TTCAATTTATACTTAATAT
Found at i:31238750 original size:17 final size:19
Alignment explanation
Indices: 31238701--31238750 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
31238691 AAGCCGTGGC
31238701 TTTCTTT-CTTCTTTCTCTT
1 TTTCTTTCCTT-TTTCTCTT
*
31238720 TTTCTTTCCCTTTTC-C-T
1 TTTCTTTCCTTTTTCTCTT
31238737 TTTCTTTCCTTTTT
1 TTTCTTTCCTTTTT
31238751 TGTTTCGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 14 0.50
18 1 0.04
19 11 0.39
20 2 0.07
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTCTTTCCTTTTTCTCTT
Found at i:31240872 original size:27 final size:26
Alignment explanation
Indices: 31240842--31240903 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
31240832 CAAATTGAAC
*
31240842 AAAAAAAGTAGATACTAAATTGGACAA
1 AAAAAAAGTAGAT-CTAAATTAGACAA
** *
31240869 AAAAAAAGTTTATGTAAATTAGACAA
1 AAAAAAAGTAGATCTAAATTAGACAA
31240895 AAAAAAAGT
1 AAAAAAAGT
31240904 TTATGTACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (26 bp):
AAAAAAAGTAGATCTAAATTAGACAA
Found at i:31240886 original size:26 final size:26
Alignment explanation
Indices: 31240857--31240910 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
31240847 AAGTAGATAC
*
31240857 TAAATTGGACAAAAAAAAAGTTTATG
1 TAAATTAGACAAAAAAAAAGTTTATG
31240883 TAAATTAGACAAAAAAAAAGTTTATG
1 TAAATTAGACAAAAAAAAAGTTTATG
31240909 TA
1 TA
31240911 CCAAAACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.13, T:0.28
Consensus pattern (26 bp):
TAAATTAGACAAAAAAAAAGTTTATG
Found at i:31242149 original size:8 final size:9
Alignment explanation
Indices: 31242053--31242157 Score: 58
Period size: 8 Copynumber: 11.7 Consensus size: 9
31242043 AAATAAAAAT
*
31242053 AATTTTTAA
1 AATTTTAAA
*
31242062 AA-TTCAAA
1 AATTTTAAA
31242070 ACATTTATAAA
1 A-ATTT-TAAA
*
31242081 AA-TTTCAA
1 AATTTTAAA
31242089 AA-TTT-AA
1 AATTTTAAA
31242096 AATTTTAAAA
1 AATTTT-AAA
*
31242106 AATTCTAAA
1 AATTTTAAA
* *
31242115 TATTCTAAAA
1 AATT-TTAAA
*
31242125 AATATATAAA
1 AAT-TTTAAA
*
31242135 AAATTT-AA
1 AATTTTAAA
31242143 AATTTTAAA
1 AATTTTAAA
31242152 AATTTT
1 AATTTT
31242158 CCAAAATAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
7 4 0.05
8 23 0.32
9 21 0.29
10 20 0.27
11 5 0.07
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (9 bp):
AATTTTAAA
Found at i:31248654 original size:19 final size:20
Alignment explanation
Indices: 31248626--31248663 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31248616 GATTTAATTT
31248626 ATTTTAAAC-AATAAAATAG
1 ATTTTAAACAAATAAAATAG
*
31248645 ATTTTCAACAAATAAAATA
1 ATTTTAAACAAATAAAATA
31248664 TTCCAACCAA
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:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (20 bp):
ATTTTAAACAAATAAAATAG
Found at i:31249302 original size:2 final size:2
Alignment explanation
Indices: 31249292--31249340 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
31249282 TTTAAAAAAC
*
31249292 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31249334 TA TA TA T
1 TA TA TA T
31249341 NNNNNNNNNN
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:31252234 original size:41 final size:40
Alignment explanation
Indices: 31252179--31252290 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 40
31252169 GTTTGGACAA
*
31252179 AAAAACGCCACTAAAAAATCAAGCATTAGCGGCGCTTCTAT-
1 AAAAACGCCGCT-AAAAATCAAGCATTAGCGGCGCTT-TATG
** * * * *
31252220 AAAAACGCCGCTAAAGGTCGAGAATTAGCGTCGCTTTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTATG
*
31252260 GAAAACGCCGCTAAAAAT-AAGCATTAGCGGC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGC
31252291 ATTTTTTTAA
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
39 12 0.21
40 34 0.60
41 11 0.19
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTATG
Found at i:31252412 original size:41 final size:41
Alignment explanation
Indices: 31252350--31252509 Score: 230
Period size: 41 Copynumber: 3.9 Consensus size: 41
31252340 TGAGTTTTTG
* * *
31252350 GGGCATTTAGCAACGTTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGACGTTTTTGAAAAAGCGCCACTAATGCTC
* *
31252391 GGTCCTTTAGCGACATTTTTGAAAAAGCGCCACTAATGCTC
1 GGGCCTTTAGCGACGTTTTTGAAAAAGCGCCACTAATGCTC
* *
31252432 GGGCCTTTAGCGGCTTTTTTGAAAAAGCGCCACTAATGCTC
1 GGGCCTTTAGCGACGTTTTTGAAAAAGCGCCACTAATGCTC
* * *
31252473 GGGCCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAAT
1 GGGCCTTTAGCGACGTTTTTGAAAAAGCGCCACTAAT
31252510 AATAATAATA
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 108 1.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGACGTTTTTGAAAAAGCGCCACTAATGCTC
Found at i:31254618 original size:133 final size:134
Alignment explanation
Indices: 31254459--31254724 Score: 414
Period size: 133 Copynumber: 2.0 Consensus size: 134
31254449 GATTTTTAGC
* * * *
31254459 ATAGTAAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTGCGGCGTTTTTCATAAAAGGTA
1 ATAGCAAAACAGTGTCGTTTTATTCCAAATAAAATAATTTTTTGCGGCGTTTTT-ACAAAAGATA
31254524 AGCAATAGCGGCGTTTTT-TAAAAAACGCCACAAAA-AATAATTTTA-TTTT-AAAAATAGCGCC
65 AGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAA-AA-TTTACTTTTAAAAAATAGCGCC
31254585 ATTTTAT
128 ATTTTAT
*
31254592 ATAGCAAAACAGTGTCGTTTTATTCCAAATAAAATAATTTTTTGCGGCGTTTTTACAATAGATAA
1 ATAGCAAAACAGTGTCGTTTTATTCCAAATAAAATAATTTTTTGCGGCGTTTTTACAAAAGATAA
*
31254657 GCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAAAATTTACTTTTAAAAAAATAGTGCCAT
66 GCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAAAATTTACTTTT-AAAAAATAGCGCCAT
31254722 TTT
130 TTT
31254725 TTAAAATTCC
Statistics
Matches: 122, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
132 29 0.24
133 75 0.61
134 2 0.02
135 16 0.13
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (134 bp):
ATAGCAAAACAGTGTCGTTTTATTCCAAATAAAATAATTTTTTGCGGCGTTTTTACAAAAGATAA
GCAATAGCGGCGTTTTTATAAAAAACGCCACAAAATAAAATTTACTTTTAAAAAATAGCGCCATT
TTAT
Found at i:31254764 original size:22 final size:22
Alignment explanation
Indices: 31254736--31254782 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
31254726 TAAAATTCCC
*
31254736 TCCCCCCCCAAATCCCCAACTT
1 TCCCCCCCAAAATCCCCAACTT
* * *
31254758 TCCCCCCTAAAATCCCTAATTT
1 TCCCCCCCAAAATCCCCAACTT
31254780 TCC
1 TCC
31254783 ACATCCAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.51, G:0.00, T:0.26
Consensus pattern (22 bp):
TCCCCCCCAAAATCCCCAACTT
Found at i:31257598 original size:43 final size:43
Alignment explanation
Indices: 31257458--31257749 Score: 281
Period size: 43 Copynumber: 6.8 Consensus size: 43
31257448 AGGTTATATT
* * *
31257458 TTTAGCGGCGTTTTTGTG-AGAAGCGCCGCTAAAGGT--TTGTCC
1 TTTAGCGGCGTTTGTG-GAAAAAGCGCCGCTAAAGGTCATGGT-C
* *
31257500 TTTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAGCTTCATGATC
1 TTTAGCGGCGTTTGTGGA-AAAAGCGCCGCTAAAG-GTCATGGTC
* **
31257544 TTTAGCAGCGTTTGTGGAAAAAGCATCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTC
*
31257587 TTTAGCGGCGTTT-TCGGAAAAAGCGCCGCTAAAGGTTATGGTC
1 TTTAGCGGCGTTTGT-GGAAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
31257630 TATAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTC
* ** * * * **
31257673 TTTAGCGGCGTTTTTGGGTAAAGCGTCGCTAAA-GACTAAGACC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTC-ATGGTC
**
31257716 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAG
31257750 TTAGCGACGT
Statistics
Matches: 212, Mismatches: 28, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.00
42 32 0.15
43 145 0.68
44 30 0.14
45 4 0.02
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:31257696 original size:129 final size:127
Alignment explanation
Indices: 31257458--31257749 Score: 320
Period size: 129 Copynumber: 2.3 Consensus size: 127
31257448 AGGTTATATT
* * *
31257458 TTTAGCGGCGTTTTTGTGAGAAGCGCCGCTAAAGGTTTGTCCTTTAGCGGCGTTTGTGATAAAAG
1 TTTAGCGGCG-TTTTG-GAAAAGCGCCGCTAAAGGTTTGTCCTATAGCGGCGTTTGTGAGAAAAG
* * * **
31257523 CGCCGCTAAAGCTTCATGATCTTTAGCAGCGTTTGTGGAAAAAGCATCGCTAAAG-GTCATGGTC
64 CGCCGCTAAAGCGTCATGATCTTTAGCAGCGTTTGTGGAAAAAGCATCGCTAAAGACT-AAGACC
* *
31257587 TTTAGCGGCGTTTTCGGAAAAAGCGCCGCTAAAGGTTATGGT-CTATAGCGGCGTTTTTGGGAAA
1 TTTAGCGGCGTTTT-GG-AAAAGCGCCGCTAAAGGTT-T-GTCCTATAGCGGCGTTTGTGAGAAA
* * * * ** *
31257651 AGCGCCGCTAAAG-GTCTTGGTCTTTAGCGGCGTTTTTGGGTAAAGCGTCGCTAAAGACTAAGAC
62 AGCGCCGCTAAAGCGTCATGATCTTTAGCAGCGTTTGTGGAAAAAGCATCGCTAAAGACTAAGAC
31257715 C
127 C
*
31257716 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTT-T-GGAAAAGCGCCGCTAAAG
31257750 TTAGCGACGT
Statistics
Matches: 138, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
128 5 0.04
129 95 0.69
130 36 0.26
131 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (127 bp):
TTTAGCGGCGTTTTGGAAAAGCGCCGCTAAAGGTTTGTCCTATAGCGGCGTTTGTGAGAAAAGCG
CCGCTAAAGCGTCATGATCTTTAGCAGCGTTTGTGGAAAAAGCATCGCTAAAGACTAAGACC
Found at i:31262140 original size:43 final size:42
Alignment explanation
Indices: 31261979--31262308 Score: 529
Period size: 42 Copynumber: 7.8 Consensus size: 42
31261969 CAAACAAAAA
31261979 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
*
31262021 CGCCACTAAAGAACATGTTCTTTAGCGGCG-TTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
31262062 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
** * *
31262104 AACCTCTAAAGAACATTTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
*
31262146 CGCCGCTAAAGAACAT-TGTCTTTAGCGGCGTTTTTTTCTGAG
1 CGCCGCTAAAGAACATGT-TCTTTAGCGGCGTTTTTTTCTAAG
* *
31262188 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCTATG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTTCTAAG
*
31262231 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTCTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGT-TTTTTTCTAAG
*
31262274 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
31262309 GTACAAAAAT
Statistics
Matches: 267, Mismatches: 16, Indels: 10
0.91 0.05 0.03
Matches are distributed among these distances:
41 41 0.15
42 147 0.55
43 79 0.30
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:31262653 original size:21 final size:21
Alignment explanation
Indices: 31262627--31262678 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
31262617 TTTTGCTCTG
31262627 CTCTGCTT-CTCTCGCGGCAGC
1 CTCTGCTTCCT-TCGCGGCAGC
*
31262648 CTCTGCTTCCTTCGCTGCAGC
1 CTCTGCTTCCTTCGCGGCAGC
*
31262669 CGCTGCTTCC
1 CTCTGCTTCC
31262679 CTCACTTCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.04, C:0.44, G:0.21, T:0.31
Consensus pattern (21 bp):
CTCTGCTTCCTTCGCGGCAGC
Found at i:31266920 original size:9 final size:9
Alignment explanation
Indices: 31266897--31267121 Score: 186
Period size: 9 Copynumber: 26.0 Consensus size: 9
31266887 AGTATAAATG
31266897 AGTTATGT-
1 AGTTATGTA
31266905 A-TTATGTA
1 AGTTATGTA
*
31266913 ACTTATGTA
1 AGTTATGTA
31266922 AGTTATGT-
1 AGTTATGTA
31266930 A-TTATGTA
1 AGTTATGTA
*
31266938 ACTTATGTA
1 AGTTATGTA
*
31266947 AGTTGTGT-
1 AGTTATGTA
31266955 A-TTATGTA
1 AGTTATGTA
*
31266963 ACTTATGTA
1 AGTTATGTA
**
31266972 AGTTATCAA
1 AGTTATGTA
*
31266981 AGTAATGTA
1 AGTTATGTA
*
31266990 TGTTATGTA
1 AGTTATGTA
31266999 AG-T-TGTA
1 AGTTATGTA
31267006 AGTTAT-TA
1 AGTTATGTA
* *
31267014 TGTATTATATA
1 AG--TTATGTA
* *
31267025 ACTTCTGTA
1 AGTTATGTA
31267034 AGTTATGTA
1 AGTTATGTA
31267043 AGTTATGTA
1 AGTTATGTA
31267052 AGTTATGTA
1 AGTTATGTA
*
31267061 AGTTGTGTA
1 AGTTATGTA
* * *
31267070 AGCTATTTT
1 AGTTATGTA
31267079 AGTTATGTA
1 AGTTATGTA
31267088 AGCTT-TGT-
1 AG-TTATGTA
31267096 A-TTATGTA
1 AGTTATGTA
31267104 AGTTATGTA
1 AGTTATGTA
*
31267113 GGTTATGTA
1 AGTTATGTA
31267122 TGATGTAAGT
Statistics
Matches: 173, Mismatches: 29, Indels: 29
0.75 0.13 0.13
Matches are distributed among these distances:
6 2 0.01
7 26 0.15
8 13 0.08
9 124 0.72
10 6 0.03
11 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.47
Consensus pattern (9 bp):
AGTTATGTA
Found at i:31266920 original size:16 final size:17
Alignment explanation
Indices: 31266899--31266971 Score: 73
Period size: 16 Copynumber: 4.4 Consensus size: 17
31266889 TATAAATGAG
31266899 TTATGTA-TTATGTAAC
1 TTATGTACTTATGTAAC
*
31266915 TTATGTAAGTTATGT-A-
1 TTATGT-ACTTATGTAAC
*
31266931 TTATGTAACTTATGTAAG
1 TTATGT-ACTTATGTAAC
*
31266949 TTGTGTA-TTATGTAAC
1 TTATGTACTTATGTAAC
31266965 TTATGTA
1 TTATGTA
31266972 AGTTATCAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
16 34 0.69
17 4 0.08
18 11 0.22
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.49
Consensus pattern (17 bp):
TTATGTACTTATGTAAC
Found at i:31267122 original size:25 final size:26
Alignment explanation
Indices: 31266897--31267121 Score: 164
Period size: 25 Copynumber: 8.7 Consensus size: 26
31266887 AGTATAAATG
31266897 AGTTATGTA-TTATGTAACTTATGTA
1 AGTTATGTAGTTATGTAACTTATGTA
31266922 AGTTATGTA-TTATGTAACTTATGTA
1 AGTTATGTAGTTATGTAACTTATGTA
*
31266947 AGTTGTGTA-TTATGTAACTTATGTA
1 AGTTATGTAGTTATGTAACTTATGTA
** * **
31266972 AGTTATCAAAGTAATGTATGTTATGTA
1 AGTTAT-GTAGTTATGTAACTTATGTA
* *
31266999 AGTTGTAAGTTA-TTATGT-A-TTATATA
1 AG-T-TATG-TAGTTATGTAACTTATGTA
* * *
31267025 ACTTCTGTAAGTTATGTAAGTTATGTA
1 AGTTATGT-AGTTATGTAACTTATGTA
* * *
31267052 AGTTATGTAAGTTGTGTAAGC-TATTTT
1 AGTTATGT-AGTTATGTAA-CTTATGTA
31267079 AGTTATGTAAGCTT-TGT-A-TTATGTA
1 AGTTATGT-AG-TTATGTAACTTATGTA
31267104 AGTTATGTAGGTTATGTA
1 AGTTATGTA-GTTATGTA
31267122 TGATGTAAGT
Statistics
Matches: 160, Mismatches: 25, Indels: 29
0.75 0.12 0.14
Matches are distributed among these distances:
23 1 0.01
24 6 0.04
25 77 0.48
26 10 0.06
27 55 0.34
28 8 0.05
29 3 0.02
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.47
Consensus pattern (26 bp):
AGTTATGTAGTTATGTAACTTATGTA
Found at i:31267299 original size:53 final size:53
Alignment explanation
Indices: 31267230--31267365 Score: 220
Period size: 53 Copynumber: 2.6 Consensus size: 53
31267220 TTTATAGCGG
*
31267230 GTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
1 GTAATGTATTTAAGTAATATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
* *
31267283 GTAATGT-TTCTGAGTAATATATTTAAGTAAAAAATTTAACGAAATTTTAGTAA
1 GTAATGTATT-TAAGTAATATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
*
31267336 GTAATGTATTTAAGTAATTTATTTAAGTAA
1 GTAATGTATTTAAGTAATATATTTAAGTAA
31267366 TATATTCAAG
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
52 2 0.03
53 72 0.95
54 2 0.03
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (53 bp):
GTAATGTATTTAAGTAATATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
Found at i:31267311 original size:13 final size:13
Alignment explanation
Indices: 31267295--31267384 Score: 85
Period size: 13 Copynumber: 6.8 Consensus size: 13
31267285 AATGTTTCTG
31267295 AGTAATATATTTA
1 AGTAATATATTTA
* *
31267308 AGTAAAAAATTTA
1 AGTAATATATTTA
*
31267321 ACG-AA-ATTTTAGTA
1 A-GTAATATATT--TA
*
31267335 AGTAATGTATTTA
1 AGTAATATATTTA
*
31267348 AGTAATTTATTTA
1 AGTAATATATTTA
*
31267361 AGTAATATATTCA
1 AGTAATATATTTA
31267374 AGTAATATATT
1 AGTAATATATT
31267385 AAGAGTAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
12 3 0.05
13 51 0.81
14 6 0.10
15 3 0.05
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (13 bp):
AGTAATATATTTA
Found at i:31267714 original size:13 final size:13
Alignment explanation
Indices: 31267692--31267846 Score: 91
Period size: 13 Copynumber: 11.8 Consensus size: 13
31267682 TTCATAGCGG
*
31267692 GTAATGTATTTAA
1 GTAATATATTTAA
*
31267705 GTAACATATTTAA
1 GTAATATATTTAA
* *
31267718 GTAAAAAATTTAA
1 GTAATATATTTAA
** *
31267731 CCAA-ATTTTTGTAA
1 GTAATA-TATT-TAA
* * *
31267745 GTAATGTATCTGA
1 GTAATATATTTAA
*
31267758 GTAACATATTTAA
1 GTAATATATTTAA
* *
31267771 GTAAAAAATTTAA
1 GTAATATATTTAA
*
31267784 CG-AA-ATTTTAGTAA
1 -GTAATATATT--TAA
*
31267798 GTAATGTATTTAA
1 GTAATATATTTAA
*
31267811 GTAATTTATTTAA
1 GTAATATATTTAA
*
31267824 GTAATATATTCAA
1 GTAATATATTTAA
31267837 GTAATATATT
1 GTAATATATT
31267847 AAGAGTAAAA
Statistics
Matches: 107, Mismatches: 27, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
12 4 0.04
13 87 0.81
14 13 0.12
15 3 0.03
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.41
Consensus pattern (13 bp):
GTAATATATTTAA
Found at i:31267761 original size:53 final size:53
Alignment explanation
Indices: 31267692--31267827 Score: 218
Period size: 53 Copynumber: 2.6 Consensus size: 53
31267682 TTCATAGCGG
*
31267692 GTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTTGTAA
1 GTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
* * *
31267745 GTAATGTATCTGAGTAACATATTTAAGTAAAAAATTTAACGAAATTTTAGTAA
1 GTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
**
31267798 GTAATGTATTTAAGTAATTTATTTAAGTAA
1 GTAATGTATTTAAGTAACATATTTAAGTAA
31267828 TATATTCAAG
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 75 1.00
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (53 bp):
GTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
Found at i:31267969 original size:462 final size:462
Alignment explanation
Indices: 31267105--31268019 Score: 1724
Period size: 462 Copynumber: 2.0 Consensus size: 462
31267095 TATTATGTAA
* * * *
31267105 GTTATGTAGGTTATGTATGATGTAAGTATATCACTATTACGTATCTGATTTATAACCGATTTAAA
1 GTTATGTAAGATATGTATGATGTAAGTATACCACTATTACATATCTGATTTATAACCGATTTAAA
*
31267170 ACTATAATATATTTTAACAAGTTCTGTAAGTAATGTAATATATACTTAAATTTATAGCGGGTAAT
66 ACTATAATATATTTTAACAAGTTCTGTAAGTAATGTAATATATACTTAAATTCATAGCGGGTAAT
*
31267235 GTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAAGTAATGTTTCTGAGTAA
131 GTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAAGTAATGTATCTGAGTAA
*
31267300 TATATTTAAGTAAAAAATTTAACGAAATTTTAGTAAGTAATGTATTTAAGTAATTTATTTAAGTA
196 CATATTTAAGTAAAAAATTTAACGAAATTTTAGTAAGTAATGTATTTAAGTAATTTATTTAAGTA
31267365 ATATATTCAAGTAATATATTAAGAGTAAAATTTAGTAAAAAATATGTTTTATTTATTAATGTAAG
261 ATATATTCAAGTAATATATTAAGAGTAAAATTTAGTAAAAAATATGTTTTATTTATTAATGTAAG
*
31267430 ACATCTAAAATATACTTAAAAATATTTATTTAAGTAATGTAAGATATAAATTTTAAAAAATTATA
326 ACATCTAAAATATACTTAAAAATATTTATTTAAGTAACGTAAGATATAAATTTTAAAAAATTATA
31267495 TTCGAACAATATATATATTAGTAATAAGTTAAATTAAATTGTAAAAATATTAACATATATATACA
391 TTCGAACAATATATATATTAGTAATAAGTTAAATTAAATTGTAAAAATATTAACATATATATACA
31267560 AATTTTG
456 AATTTTG
31267567 GTTATGTAAGATATGTATGATGTAAGTCAT-CCACTATTACATATCTGATTTATAACCGATTTAA
1 GTTATGTAAGATATGTATGATGTAAGT-ATACCACTATTACATATCTGATTTATAACCGATTTAA
31267631 AACTATAATATATTTTAACAAGTTCTGTAAGTAATGTAATATATACTTAAATTCATAGCGGGTAA
65 AACTATAATATATTTTAACAAGTTCTGTAAGTAATGTAATATATACTTAAATTCATAGCGGGTAA
*
31267696 TGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTTGTAAGTAATGTATCTGAGTA
130 TGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAAGTAATGTATCTGAGTA
31267761 ACATATTTAAGTAAAAAATTTAACGAAATTTTAGTAAGTAATGTATTTAAGTAATTTATTTAAGT
195 ACATATTTAAGTAAAAAATTTAACGAAATTTTAGTAAGTAATGTATTTAAGTAATTTATTTAAGT
31267826 AATATATTCAAGTAATATATTAAGAGTAAAATTTAGTAAAAAATATGTTTTATTTATTAATGTAA
260 AATATATTCAAGTAATATATTAAGAGTAAAATTTAGTAAAAAATATGTTTTATTTATTAATGTAA
*
31267891 GACATCTAAAATATACTTAAAAATATTTATTTAAGTAACGTAAGGTATAAATTTTAAAAAATTAT
325 GACATCTAAAATATACTTAAAAATATTTATTTAAGTAACGTAAGATATAAATTTTAAAAAATTAT
31267956 ATTCGAACAATATATATATTAGTAATAAGTTAAATTAAATTGTAAAAATATTAACATATATATA
390 ATTCGAACAATATATATATTAGTAATAAGTTAAATTAAATTGTAAAAATATTAACATATATATA
31268020 TTTTTAATAT
Statistics
Matches: 442, Mismatches: 10, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
462 440 1.00
463 2 0.00
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (462 bp):
GTTATGTAAGATATGTATGATGTAAGTATACCACTATTACATATCTGATTTATAACCGATTTAAA
ACTATAATATATTTTAACAAGTTCTGTAAGTAATGTAATATATACTTAAATTCATAGCGGGTAAT
GTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAAGTAATGTATCTGAGTAA
CATATTTAAGTAAAAAATTTAACGAAATTTTAGTAAGTAATGTATTTAAGTAATTTATTTAAGTA
ATATATTCAAGTAATATATTAAGAGTAAAATTTAGTAAAAAATATGTTTTATTTATTAATGTAAG
ACATCTAAAATATACTTAAAAATATTTATTTAAGTAACGTAAGATATAAATTTTAAAAAATTATA
TTCGAACAATATATATATTAGTAATAAGTTAAATTAAATTGTAAAAATATTAACATATATATACA
AATTTTG
Found at i:31268048 original size:44 final size:44
Alignment explanation
Indices: 31268000--31268083 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
31267990 TTAAATTGTA
31268000 AAAATAT-TAACATATATA-TATTTTTAATATTAATAAGTTATGAT
1 AAAATATATAA-ATATATACT-TTTTTAATATTAATAAGTTATGAT
*
31268044 AAAATATATGAATATATACTTTTTTAATATTAATAAGTTA
1 AAAATATATAAATATATACTTTTTTAATATTAATAAGTTA
31268084 AATAAAAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
44 34 0.92
45 3 0.08
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (44 bp):
AAAATATATAAATATATACTTTTTTAATATTAATAAGTTATGAT
Found at i:31268441 original size:7 final size:7
Alignment explanation
Indices: 31268421--31268476 Score: 69
Period size: 7 Copynumber: 7.9 Consensus size: 7
31268411 TTCATTCAAT
*
31268421 AGAAAAT
1 AGAAAAC
31268428 AGCAAAAC
1 AG-AAAAC
31268436 AGAAAAC
1 AGAAAAC
*
31268443 A-AAACAT
1 AGAAA-AC
31268450 AGAAAAC
1 AGAAAAC
31268457 AGAAAAC
1 AGAAAAC
31268464 AGAAAAC
1 AGAAAAC
31268471 AGAAAA
1 AGAAAA
31268477 TAAAGAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
6 3 0.07
7 31 0.72
8 9 0.21
ACGTcount: A:0.71, C:0.12, G:0.12, T:0.04
Consensus pattern (7 bp):
AGAAAAC
Found at i:31268474 original size:21 final size:21
Alignment explanation
Indices: 31268421--31268476 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 21
31268411 TTCATTCAAT
31268421 AGAAAATAGCAAAACAGAAAAC
1 AGAAAATAG-AAAACAGAAAAC
31268443 A-AAACATAGAAAACAGAAAAC
1 AGAAA-ATAGAAAACAGAAAAC
*
31268464 AGAAAACAGAAAA
1 AGAAAATAGAAAA
31268477 TAAAGAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.71, C:0.12, G:0.12, T:0.04
Consensus pattern (21 bp):
AGAAAATAGAAAACAGAAAAC
Found at i:31269312 original size:303 final size:305
Alignment explanation
Indices: 31268760--31269360 Score: 956
Period size: 303 Copynumber: 2.0 Consensus size: 305
31268750 TAAACTAGAT
*
31268760 ATTAAAACTATATATATTATATATTAAAAATGTATATAAATTTTAAGTATATTATAAAAGAAAAA
1 ATTAAAACTATATATATTATATATTAAAAATGTATATAAATTTTAAATATATTATAAAAGAAAAA
* *
31268825 AATGAAAAAAAGAAGAAGATTGAATCTCATATTTCAACCAAAAATATAACTTTGCTCTTTAGAAG
66 AAT---AAAAAGAAGAAGATTGAATCTCAGATTTCAACCAAAAATATAACTTTGCTCTTTAGAAA
*
31268890 TTTGAACTTACAAGTTTTGAACAATGCTGTAGTGTTCAGTTCCTTGAGACTATTGGATTTTTTCT
128 TTTGAACTTACAAGTTTTGAACAATGCTGTAGTGTTCAGTTCCTTGACACTATTGGATTTTTTCT
*
31268955 AATAGTAGTATAGTAGCCCTACCATAGCAAATATTAATAGATATCATTCAATAGGTTTAGAACAG
193 AATAGTAGTATAGTAGCCCTACCATAGCAAATATTAATAGATATCATTCAATAGGTTTAGAACAA
*
31269020 TTTTGCAATTTTCAACAGAACAGCAGTAAATGATTCAACATGGTAGCA
258 TTTTGCAATTTTCAACAGAACAACAGTAAATGATTCAACATGGTAGCA
31269068 ATTAAAACTATATATATTATATATTAAAAATGTATATAAATTTTAAATATATTATAAAAGAAACA
1 ATTAAAACTATATATATTATATATTAAAAATGTATATAAATTTTAAATATATTATAAAAGAAA-A
*** * *
31269133 AAAT-AAAA-AA-AAGATTGAATCTCAGATTTCGTGCTAAAATATTACTTTGCTCTTTAGAAATT
65 AAATAAAAAGAAGAAGATTGAATCTCAGATTTCAACCAAAAATATAACTTTGCTCTTTAGAAATT
* * * * *
31269195 TGAACTTACAAGTTTTGAACAGTGGTGTAGTGTTCAGTTCCTTGCCAGTATTGGATTTTTTCTGA
130 TGAACTTACAAGTTTTGAACAATGCTGTAGTGTTCAGTTCCTTGACACTATTGGATTTTTTCTAA
* * * *
31269260 TAGTAGTATAGTAGCCTTGCCATAGCGAATATTAATAGATATCATTCAATAGGTTTTGAACAATT
195 TAGTAGTATAGTAGCCCTACCATAGCAAATATTAATAGATATCATTCAATAGGTTTAGAACAATT
*
31269325 TTGCAATTTTCGACAGAACAACAGTAAATGATTCAA
260 TTGCAATTTTCAACAGAACAACAGTAAATGATTCAA
31269361 TTTGAAATGA
Statistics
Matches: 271, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
303 198 0.73
304 2 0.01
305 4 0.01
308 62 0.23
309 5 0.02
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (305 bp):
ATTAAAACTATATATATTATATATTAAAAATGTATATAAATTTTAAATATATTATAAAAGAAAAA
AATAAAAAGAAGAAGATTGAATCTCAGATTTCAACCAAAAATATAACTTTGCTCTTTAGAAATTT
GAACTTACAAGTTTTGAACAATGCTGTAGTGTTCAGTTCCTTGACACTATTGGATTTTTTCTAAT
AGTAGTATAGTAGCCCTACCATAGCAAATATTAATAGATATCATTCAATAGGTTTAGAACAATTT
TGCAATTTTCAACAGAACAACAGTAAATGATTCAACATGGTAGCA
Found at i:31270382 original size:47 final size:47
Alignment explanation
Indices: 31270294--31270385 Score: 121
Period size: 47 Copynumber: 2.0 Consensus size: 47
31270284 NNNNGTTTCG
* **
31270294 GTAATATTTAAAAAAATTAGATAAAATTATCAATCTCAGTTTTTTAA
1 GTAATATTTAAAAAAATTAGATAAAAATAAAAATCTCAGTTTTTTAA
* * * *
31270341 GTAATATTTATAAAAATTAGGTAAAAATAAAAATTTTAGTTTTTT
1 GTAATATTTAAAAAAATTAGATAAAAATAAAAATCTCAGTTTTTT
31270386 TATTTATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (47 bp):
GTAATATTTAAAAAAATTAGATAAAAATAAAAATCTCAGTTTTTTAA
Found at i:31270414 original size:13 final size:12
Alignment explanation
Indices: 31270374--31270415 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
31270364 AAAATAAAAA
31270374 TTTTAGTTTT-TT
1 TTTTA-TTTTATT
31270386 TATTTATTTTATT
1 T-TTTATTTTATT
31270399 TTTTATTTTCATT
1 TTTTATTTT-ATT
31270412 TTTT
1 TTTT
31270416 TTGTAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 13 0.48
13 14 0.52
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:31270717 original size:7 final size:7
Alignment explanation
Indices: 31270705--31270773 Score: 68
Period size: 7 Copynumber: 9.9 Consensus size: 7
31270695 ATAGCCCAAT
31270705 CCCTAAC
1 CCCTAAC
31270712 CCCTAAC
1 CCCTAAC
*
31270719 CCTTAAC
1 CCCTAAC
*
31270726 CCATAA-
1 CCCTAAC
31270732 CCCTAAAC
1 CCCT-AAC
*
31270740 CCTTAAC
1 CCCTAAC
* *
31270747 CCATGAC
1 CCCTAAC
*
31270754 CTCTAAC
1 CCCTAAC
31270761 CCCTAAC
1 CCCTAAC
31270768 CCCTAA
1 CCCTAA
31270774 ATCTTATTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
6 3 0.06
7 44 0.88
8 3 0.06
ACGTcount: A:0.32, C:0.48, G:0.01, T:0.19
Consensus pattern (7 bp):
CCCTAAC
Found at i:31270734 original size:21 final size:21
Alignment explanation
Indices: 31270708--31270769 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
31270698 GCCCAATCCC
31270708 TAACCCCTAACCCTTAACCCA
1 TAACCCCTAACCCTTAACCCA
31270729 TAA-CCCTAAACCCTTAACCCA
1 TAACCCCT-AACCCTTAACCCA
* * *
31270750 TGACCTCTAACCCCTAACCC
1 TAACCCCTAACCCTTAACCC
31270770 CTAAATCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 4 0.11
21 29 0.81
22 3 0.08
ACGTcount: A:0.32, C:0.47, G:0.02, T:0.19
Consensus pattern (21 bp):
TAACCCCTAACCCTTAACCCA
Found at i:31270883 original size:7 final size:7
Alignment explanation
Indices: 31270873--31270905 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
31270863 CTCTTAACAT
31270873 CTAACCC
1 CTAACCC
31270880 CTAA--C
1 CTAACCC
31270885 CTAACCC
1 CTAACCC
31270892 CTAACCC
1 CTAACCC
31270899 CTAACCC
1 CTAACCC
31270906 ATAAACATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.21
7 19 0.79
ACGTcount: A:0.30, C:0.55, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAACCC
Found at i:31270890 original size:12 final size:12
Alignment explanation
Indices: 31270873--31270897 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31270863 CTCTTAACAT
31270873 CTAACCCCTAAC
1 CTAACCCCTAAC
31270885 CTAACCCCTAAC
1 CTAACCCCTAAC
31270897 C
1 C
31270898 CCTAACCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (12 bp):
CTAACCCCTAAC
Done.