Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008693.1 Hibiscus syriacus cultivar Beakdansim tig00111721_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2243253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:1052098 original size:2 final size:2
Alignment explanation
Indices: 1052091--1052184 Score: 188
Period size: 2 Copynumber: 47.0 Consensus size: 2
1052081 TATTATGAAT
1052091 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1052133 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1052175 TA TA TA TA TA
1 TA TA TA TA TA
1052185 AATTAAAAGA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1054010 original size:89 final size:88
Alignment explanation
Indices: 1053866--1054030 Score: 294
Period size: 89 Copynumber: 1.9 Consensus size: 88
1053856 CTTTTATAGC
1053866 CAAGTTACCCTAATCATAATAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
1 CAAGTTACCCTAATCATAATAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
* *
1053931 GGAATTTAATAATCCTCTTATAT
66 GAAATTAAATAATCCTCTTATAT
*
1053954 CAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTTAATTAAT
1 CAAGTTACCCTAATCATAATAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTTAATTAAT
1054019 TGAAATTAAATA
65 TGAAATTAAATA
1054031 TTCAGGATTA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
88 23 0.32
89 50 0.68
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (88 bp):
CAAGTTACCCTAATCATAATAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
GAAATTAAATAATCCTCTTATAT
Found at i:1060771 original size:90 final size:89
Alignment explanation
Indices: 1060619--1060791 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
1060609 ACACACCCTT
*
1060619 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATTTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
1060684 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
*
1060708 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
1060773 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
1060792 TTCGGGATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 30 0.38
90 49 0.62
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:1070635 original size:626 final size:627
Alignment explanation
Indices: 1069424--1070669 Score: 1917
Period size: 626 Copynumber: 2.0 Consensus size: 627
1069414 GGCCAGATTA
* *
1069424 AATGTGAGTGAATTTCAATGGGAACCCATGGTAATCCCATCTCTTTGCAACACATTTAAATCAGG
1 AATGGGAGTGAATTTCAATGGGAACCCATGGTAATCCCACCTCTTTGCAACACATTTAAATCAGG
* * * * * *
1069489 TGGTTGTGTGTTTGAAACCACCTTACCAGATTGGGAAACTACTTTGAAAGACTTGAGTATCAACA
66 TGGCTATGTGTTTGAAACCACATCACCAGATTAGGAAACTACTTTAAAAGACTTGAGTATCAACA
* * * * *
1069554 TCATAATCACAAAGAATGCTGAAGATGCGGATAGATCCGGAATCCGCCCACTGCCACTTGGGTTT
131 CCATAATCACAAAGAATACTAAAGATGCGGATAGATCCAGAATCCGCCCACTGCCACATGGGTTT
1069619 GTGCTTAGCAACTGGTCGGCGGAAGAAATACCAATGATTTTCAAATTTCTTTCAGAGTAATATTC
196 GTGCTTAGCAACTGGTCGGCGGAAGAAATACCAATGATTTTCAAATTTCTTTCAGAGTAATATTC
1069684 AAACTATCCCTATTCGCCTATACCCGCAGCAATAGGTGATCTTTGTAAGGGTGAATAAATAGTTT
261 AAACTATCCCTATTCGCCTATACCCGCAGCAATAGGTGATCTTTGTAAGGGTGAATAAATAGTTT
* * *
1069749 TTTTAATTCAATAAAATATGCAGTTTCTTTCATGACAAACATTTTTCCTAATTCATTTCATCTTC
326 TTTTAATTCAATAAAAGATGCAGTTTCTTTCATGACAAAAATTTTTCCTAATTCATTCCATCTTC
*
1069814 TTTTGAATTTAATTTTCCTTTGTTCAGTACTTCATTTCATTTTCTTTTGAATTTAATCTTCGATC
391 TTTTGAATTTAATTTTCCTTCGTTCAGTACTTCATTTCATTTTCTTTTGAATTTAATCTTCGATC
** ** * * * *
1069879 ATTCTGTGTGGGATATTTTCCTCTCGTGCATACATATTTCCTGTCTCCTTCAGGTTCTAAGATAA
456 ATTCCATGTGGGATATTTTCCTCTCAAGCATACACATTTCCTGTCTCCTTAAGGTCCCAAGATAA
*
1069944 TGATAATGCAAGCACTGATGATCCTGACCCAAAGGTGAATTTTGAATCAGCTAATTGTCTTAGGG
521 TGATAATGCAAGCACTGATGATCCTGACCCAAAGGTGAATTTTAAATCAGCTAATTGTCTTAGGG
1070009 AAATTGATGAATGTGACAATGAAGACGAGTGCAACACATTTC
586 AAATTGATGAATGTGACAATGAAGACGAGTGCAACACATTTC
*
1070051 AATGGGAGTGAATTTCAAT-GGAACCCATGGTATTCCCACCTCTTTGCAACACATTTAAATCAGG
1 AATGGGAGTGAATTTCAATGGGAACCCATGGTAATCCCACCTCTTTGCAACACATTTAAATCAGG
* *
1070115 TGGCTATGTGTTTGAGACCACATCACGAGATTAGGAAGA-TACTTTAAAAGACTTGAGTATCAAC
66 TGGCTATGTGTTTGAAACCACATCACCAGATTAGGAA-ACTACTTTAAAAGACTTGAGTATCAAC
* * * *
1070179 ACCATAATCACAGAGAATACTAAAGATGCTGATAGATTCAGAATCCGCCCACTGGCACATGGGTT
130 ACCATAATCACAAAGAATACTAAAGATGCGGATAGATCCAGAATCCGCCCACTGCCACATGGGTT
* * **
1070244 TGTGCTTAGCAATTGGTCGGCGGAAGAACTACCTGTGATTTTCAAATTTCTTTCAGAGTAATATT
195 TGTGCTTAGCAACTGGTCGGCGGAAGAAATACCAATGATTTTCAAATTTCTTTCAGAGTAATATT
** ** *
1070309 CAAACTATCCCTATTCGCCTATACTTGGTGCTATAGGTGATCTTT-TATAGGGGTGAATAAATAG
260 CAAACTATCCCTATTCGCCTATACCCGCAGCAATAGGTGATCTTTGTA-A-GGGTGAATAAATAG
* *
1070373 -TTTTTTAATTCAATAAAAGATGTAGTTTTTTTCATGACAAAAATTTTTCCTAATTCATTCCATC
323 TTTTTTTAATTCAATAAAAGATGCAGTTTCTTTCATGACAAAAATTTTTCCTAATTCATTCCATC
* ** *
1070437 TTGTTTTGAATTTAATTTTCCTTCGTTTGGTACTTCCTTTCATTTTCTTTT-AATTTAATCTTCG
388 TTCTTTTGAATTTAATTTTCCTTCGTTCAGTACTTCATTTCATTTTCTTTTGAATTTAATCTTCG
* * *
1070501 ATCATTCCATGTGGGATGTTTTTCCTCTTAAGCATACACATTTCCTTTCTCCTTAAGGTCCCAAG
453 ATCATTCCATGTGGGAT-ATTTTCCTCTCAAGCATACACATTTCCTGTCTCCTTAAGGTCCCAAG
* ** * *
1070566 ATAATGATAATGCAGGCACTGATGATCCTGACCTGAAGGTGGATTTTAAATCATCTAATTGTCTT
517 ATAATGATAATGCAAGCACTGATGATCCTGACCCAAAGGTGAATTTTAAATCAGCTAATTGTCTT
1070631 AGGGAAATTGATGAATGTGACAATGAAGACGAGTGCAAC
582 AGGGAAATTGATGAATGTGACAATGAAGACGAGTGCAAC
1070670 TTACCTACCG
Statistics
Matches: 559, Mismatches: 56, Indels: 9
0.90 0.09 0.01
Matches are distributed among these distances:
625 30 0.05
626 496 0.89
627 33 0.06
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (627 bp):
AATGGGAGTGAATTTCAATGGGAACCCATGGTAATCCCACCTCTTTGCAACACATTTAAATCAGG
TGGCTATGTGTTTGAAACCACATCACCAGATTAGGAAACTACTTTAAAAGACTTGAGTATCAACA
CCATAATCACAAAGAATACTAAAGATGCGGATAGATCCAGAATCCGCCCACTGCCACATGGGTTT
GTGCTTAGCAACTGGTCGGCGGAAGAAATACCAATGATTTTCAAATTTCTTTCAGAGTAATATTC
AAACTATCCCTATTCGCCTATACCCGCAGCAATAGGTGATCTTTGTAAGGGTGAATAAATAGTTT
TTTTAATTCAATAAAAGATGCAGTTTCTTTCATGACAAAAATTTTTCCTAATTCATTCCATCTTC
TTTTGAATTTAATTTTCCTTCGTTCAGTACTTCATTTCATTTTCTTTTGAATTTAATCTTCGATC
ATTCCATGTGGGATATTTTCCTCTCAAGCATACACATTTCCTGTCTCCTTAAGGTCCCAAGATAA
TGATAATGCAAGCACTGATGATCCTGACCCAAAGGTGAATTTTAAATCAGCTAATTGTCTTAGGG
AAATTGATGAATGTGACAATGAAGACGAGTGCAACACATTTC
Found at i:1078419 original size:5 final size:5
Alignment explanation
Indices: 1078409--1078443 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
1078399 ACATAATACA
1078409 TATAT TATAT TATAT TATATT ATATAT TATAT TAT
1 TATAT TATAT TATAT TATA-T -TATAT TATAT TAT
1078444 TATACATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 22 0.79
6 2 0.07
7 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:1078434 original size:12 final size:12
Alignment explanation
Indices: 1078408--1078443 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1078398 TACATAATAC
1078408 ATATATTATA-T
1 ATATATTATATT
1078419 -TATATTATATT
1 ATATATTATATT
1078430 ATATATTATATT
1 ATATATTATATT
1078442 AT
1 AT
1078444 TATACATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.39
11 1 0.04
12 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATATTATATT
Found at i:1078677 original size:17 final size:17
Alignment explanation
Indices: 1078655--1078692 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1078645 TCACTGCAGC
1078655 AACCAATATAGTATCCT
1 AACCAATATAGTATCCT
1078672 AACCAATATAGTATCCT
1 AACCAATATAGTATCCT
1078689 AACC
1 AACC
1078693 CAATTAGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.26
Consensus pattern (17 bp):
AACCAATATAGTATCCT
Found at i:1082537 original size:2 final size:2
Alignment explanation
Indices: 1082532--1082589 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1082522 AATGTGTGTG
1082532 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1082574 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
1082590 AAGTTCAATT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1082651 original size:2 final size:2
Alignment explanation
Indices: 1082644--1082694 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1082634 ATCTAATTAA
1082644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1082686 AT AT AT AT A
1 AT AT AT AT A
1082695 GTAAGTTTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1082774 original size:2 final size:2
Alignment explanation
Indices: 1082767--1082791 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1082757 AGGCATCGAT
1082767 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1082792 GAAAGAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1087046 original size:10 final size:10
Alignment explanation
Indices: 1087031--1087058 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1087021 AACACGAACG
1087031 AACGAACATA
1 AACGAACATA
1087041 AACGAACATA
1 AACGAACATA
1087051 AACGAACA
1 AACGAACA
1087059 ACACAAACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.21, G:0.11, T:0.07
Consensus pattern (10 bp):
AACGAACATA
Found at i:1087048 original size:24 final size:24
Alignment explanation
Indices: 1087007--1087066 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
1086997 TTAAATAATA
** *
1087007 AACGAACATAAATTAACACGAACG
1 AACGAACATAAACGAACACAAACG
*
1087031 AACGAACATAAACGAACATAAACG
1 AACGAACATAAACGAACACAAACG
*
1087055 AAC-AACACAAAC
1 AACGAACATAAAC
1087067 ACAAAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 8 0.26
24 23 0.74
ACGTcount: A:0.58, C:0.23, G:0.10, T:0.08
Consensus pattern (24 bp):
AACGAACATAAACGAACACAAACG
Found at i:1104454 original size:12 final size:11
Alignment explanation
Indices: 1104428--1104466 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
1104418 TGAATAAGAT
1104428 AATAATAATAA
1 AATAATAATAA
*
1104439 AATAATTATGAA
1 AATAATAAT-AA
1104451 AATAATAATTAA
1 AATAATAA-TAA
1104463 AATA
1 AATA
1104467 TAAATAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.33
12 15 0.62
13 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (11 bp):
AATAATAATAA
Found at i:1104514 original size:26 final size:26
Alignment explanation
Indices: 1104430--1104516 Score: 65
Period size: 26 Copynumber: 3.3 Consensus size: 26
1104420 AATAAGATAA
* *
1104430 TAAT-AATAAAA-TAATTATGAAAA-
1 TAATAAATAAAATTAAATATAAAAAG
*
1104453 TAATAATTAAAATATAAATA-AACAATGAG
1 TAATAAATAAAAT-TAAATATAA-AA--AG
1104482 TAAAATAAATAAAATTAAATATAAAAAG
1 T--AATAAATAAAATTAAATATAAAAAG
1104510 TAATAAA
1 TAATAAA
1104517 ACTTATAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
23 4 0.08
24 6 0.12
25 1 0.02
26 13 0.26
28 4 0.08
29 1 0.02
30 8 0.16
31 13 0.26
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.28
Consensus pattern (26 bp):
TAATAAATAAAATTAAATATAAAAAG
Found at i:1105745 original size:3 final size:3
Alignment explanation
Indices: 1105739--1105810 Score: 94
Period size: 3 Copynumber: 24.0 Consensus size: 3
1105729 ATTATTTTTT
*
1105739 TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA
*
1105784 TAA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1105811 ATAAATAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.07
3 51 0.84
4 6 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1106112 original size:36 final size:37
Alignment explanation
Indices: 1106057--1106147 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 37
1106047 TTGAACAAGC
1106057 TCTTCTCA-TTGAACTTCTTC-T-TCTTCAGATAAGT
1 TCTTCTCATTTGAACTTCTTCTTATCTTCAGATAAGT
*
1106091 TCTTCTCATTGTGAACTTCTTCTTCGATCTTCAGATGAGT
1 TCTTCTCATT-TGAACTTCTTCTT--ATCTTCAGATAAGT
*
1106131 TCTGCTCATTATGAACT
1 TCTTCTCATT-TGAACT
1106148 CTACCTGGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
34 8 0.17
35 1 0.02
36 11 0.23
37 1 0.02
40 27 0.56
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (37 bp):
TCTTCTCATTTGAACTTCTTCTTATCTTCAGATAAGT
Found at i:1106132 original size:40 final size:39
Alignment explanation
Indices: 1106070--1106147 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1106060 TCTCATTGAA
* * *
1106070 CTTCTTCTTCTTCAGATAAGTTCTTCTCATTGTGAACTT
1 CTTCTTCATCTTCAGATAAGTTCTGCTCATTATGAACTT
*
1106109 CTTCTTCGATCTTCAGATGAGTTCTGCTCATTATGAACT
1 CTTCTTC-ATCTTCAGATAAGTTCTGCTCATTATGAACT
1106148 CTACCTGGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 7 0.21
40 27 0.79
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (39 bp):
CTTCTTCATCTTCAGATAAGTTCTGCTCATTATGAACTT
Found at i:1106291 original size:113 final size:113
Alignment explanation
Indices: 1106087--1106922 Score: 1113
Period size: 113 Copynumber: 7.5 Consensus size: 113
1106077 TTCTTCAGAT
* ** * *
1106087 AAGTTCTTCTCATTGTGAACTTCTTCTTCGATCTTCAGATGAGTTCTGCTCATTATGAACTCTAC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTC
* * * * * * *
1106152 -CTGGCAATGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAAC
65 TCTGGAAAAGTTGATCCATCGAATGATGAATTTAAGCAAAAAGTTGAAC
*
1106200 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
* * * *
1106265 CTGGAAAAGTTGATTCATC-AAGTGATGGATTTGAGCAAAAGGTTGAAC
66 CTGGAAAAGTTGATCCATCGAA-TGATGAATTTAAGCAAAAAGTTGAAC
* * * * *
1106313 AAATTCTTCTTATTATGAATTTCGTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTT
** * ** * * * *
1106378 TAACTGGCACTGCTGATCCA-CCAAGTGACGAATTTAAGCAAAAAGTTAAAC
63 TCTCTGGAAAAGTTGATCCATCGAA-TGATGAATTTAAGCAAAAAGTTGAAC
*
1106429 AAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
*
1106494 CTGGAAAAGTTGATCCATCGAATGATGAATTTAAGAAAAAAGTTGAAC
66 CTGGAAAAGTTGATCCATCGAATGATGAATTTAAGCAAAAAGTTGAAC
1106542 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1106607 CTGGAAAAGTTGATCCATCGAATGATGAATTTAAGCAAAAAGTTGAAC
66 CTGGAAAAGTTGATCCATCGAATGATGAATTTAAGCAAAAAGTTGAAC
*
1106655 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATTAACTTTCT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
* *
1106720 CTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAAC
66 CTGGAAAAGTTGATCCATCGAATGATGAATTTAAGCAAAAAGTTGAAC
1106768 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1106833 -T-------TTGATCCATCG-ATGATGAA-TT---C------TTGAAC
66 CTGGAAAAGTTGATCCATCGAATGATGAATTTAAGCAAAAAGTTGAAC
* * *
1106862 AAGTTCTTCTCATTATGAACTTCTTTTTTCTTCTTCAGATGAGTTCTTCTCATTAAGAACT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1106923 CGACCTGGCA
Statistics
Matches: 660, Mismatches: 56, Indels: 33
0.88 0.07 0.04
Matches are distributed among these distances:
94 64 0.10
100 1 0.00
103 1 0.00
104 8 0.01
105 11 0.02
112 5 0.01
113 473 0.72
114 3 0.00
115 1 0.00
116 93 0.14
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (113 bp):
AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
CTGGAAAAGTTGATCCATCGAATGATGAATTTAAGCAAAAAGTTGAAC
Found at i:1107439 original size:22 final size:22
Alignment explanation
Indices: 1107361--1107437 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
1107351 GATAAAGCTT
*
1107361 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
1107383 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1107405 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1107427 TCATCTTTGAA
1 TCATCTTTGAA
1107438 GAATGTAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1115421 original size:28 final size:28
Alignment explanation
Indices: 1115381--1115435 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1115371 TCAATCTGGC
1115381 AGGATCTTTGTGGAGTACTTTTGGTATT
1 AGGATCTTTGTGGAGTACTTTTGGTATT
1115409 AGGATCTTTGTGGAGTACTTTTGGTAT
1 AGGATCTTTGTGGAGTACTTTTGGTAT
1115436 CAATCTGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.07, G:0.29, T:0.45
Consensus pattern (28 bp):
AGGATCTTTGTGGAGTACTTTTGGTATT
Found at i:1115456 original size:36 final size:36
Alignment explanation
Indices: 1115409--1115480 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
1115399 TTTTGGTATT
1115409 AGGATCTTTGTGGAGTACTTTTGGTATCAATCTGGC
1 AGGATCTTTGTGGAGTACTTTTGGTATCAATCTGGC
1115445 AGGATCTTTGTGGAGTACTTTTGGTATCAATCTGGC
1 AGGATCTTTGTGGAGTACTTTTGGTATCAATCTGGC
1115481 CGCATCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.39
Consensus pattern (36 bp):
AGGATCTTTGTGGAGTACTTTTGGTATCAATCTGGC
Found at i:1116370 original size:28 final size:26
Alignment explanation
Indices: 1116326--1116383 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
1116316 AATATATAAA
*
1116326 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
1116352 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
1116380 AAAA
1 AAAA
1116384 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:1117181 original size:12 final size:11
Alignment explanation
Indices: 1117155--1117193 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
1117145 TGAATAAGAT
1117155 AATAATAATAA
1 AATAATAATAA
*
1117166 AATAATTATGAA
1 AATAATAAT-AA
1117178 AATAATAATTAA
1 AATAATAA-TAA
1117190 AATA
1 AATA
1117194 TAAATAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.33
12 15 0.62
13 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (11 bp):
AATAATAATAA
Found at i:1117241 original size:26 final size:26
Alignment explanation
Indices: 1117157--1117243 Score: 65
Period size: 26 Copynumber: 3.3 Consensus size: 26
1117147 AATAAGATAA
* *
1117157 TAAT-AATAAAA-TAATTATGAAAA-
1 TAATAAATAAAATTAAATATAAAAAG
*
1117180 TAATAATTAAAATATAAATA-AACAATGAG
1 TAATAAATAAAAT-TAAATATAA-AA--AG
1117209 TAAAATAAATAAAATTAAATATAAAAAG
1 T--AATAAATAAAATTAAATATAAAAAG
1117237 TAATAAA
1 TAATAAA
1117244 ACTTATAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
23 4 0.08
24 6 0.12
25 1 0.02
26 13 0.26
28 4 0.08
29 1 0.02
30 8 0.16
31 13 0.26
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.28
Consensus pattern (26 bp):
TAATAAATAAAATTAAATATAAAAAG
Found at i:1118427 original size:3 final size:3
Alignment explanation
Indices: 1118421--1118490 Score: 106
Period size: 3 Copynumber: 23.0 Consensus size: 3
1118411 ATTATTTTTT
*
1118421 TAA TAA TAA TAA TAA T-A TATA TAA TAA TATA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA
1118467 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
1118491 ATAAATAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
2 2 0.03
3 54 0.87
4 6 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1120599 original size:19 final size:19
Alignment explanation
Indices: 1120575--1120626 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1120565 GTTTAAAATG
1120575 AGTTGATTTAGAAAGCAAA
1 AGTTGATTTAGAAAGCAAA
1120594 AGTTGATTTAGAAAGCAAA
1 AGTTGATTTAGAAAGCAAA
1120613 AGTTGATTTAGAAA
1 AGTTGATTTAGAAA
1120627 AACAAAATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (19 bp):
AGTTGATTTAGAAAGCAAA
Found at i:1121579 original size:17 final size:19
Alignment explanation
Indices: 1121548--1121583 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1121538 ATGATAAATT
1121548 AGTACTAAAATTAAATAAA
1 AGTACTAAAATTAAATAAA
1121567 AGTA-TAAAA-TAAATAAA
1 AGTACTAAAATTAAATAAA
1121584 TAAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (19 bp):
AGTACTAAAATTAAATAAA
Found at i:1122547 original size:14 final size:15
Alignment explanation
Indices: 1122523--1122554 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1122513 GGTAGCTGCC
1122523 TTTTTCTTCTCCTAT
1 TTTTTCTTCTCCTAT
1122538 TTTTTC-TCTCCTAT
1 TTTTTCTTCTCCTAT
1122552 TTT
1 TTT
1122555 CCTTATGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTCTTCTCCTAT
Found at i:1124515 original size:18 final size:18
Alignment explanation
Indices: 1124492--1124556 Score: 112
Period size: 18 Copynumber: 3.6 Consensus size: 18
1124482 TTTATATCTA
1124492 GAATAGGCACAAGTCTTG
1 GAATAGGCACAAGTCTTG
1124510 GAATAGGCACAAGTCTTG
1 GAATAGGCACAAGTCTTG
*
1124528 GAATAGTCACAAGTCTTG
1 GAATAGGCACAAGTCTTG
*
1124546 GAATAGTCACA
1 GAATAGGCACA
1124557 CTTGTATATC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (18 bp):
GAATAGGCACAAGTCTTG
Found at i:1140889 original size:17 final size:17
Alignment explanation
Indices: 1140849--1140883 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1140839 GGAAAGTTGG
1140849 AAGGGAAGATTAGTCAT
1 AAGGGAAGATTAGTCAT
1140866 AAGGGAAGATTAGTCAT
1 AAGGGAAGATTAGTCAT
1140883 A
1 A
1140884 TAGGAATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.06, G:0.29, T:0.23
Consensus pattern (17 bp):
AAGGGAAGATTAGTCAT
Found at i:1153160 original size:22 final size:22
Alignment explanation
Indices: 1153095--1153174 Score: 94
Period size: 23 Copynumber: 3.7 Consensus size: 22
1153085 AGATCCCCAG
*
1153095 GGGGGTATCGATTCCCC-T--A
1 GGGGGAATCGATTCCCCTTCAA
* *
1153114 GGGGGAATCGGTTCCCATTCAAA
1 GGGGGAATCGATTCCCCTTC-AA
1153137 GGGGGAATCGATTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
1153159 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
1153175 TCTGCCCTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 14 0.27
20 1 0.02
22 17 0.33
23 19 0.37
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:1161729 original size:19 final size:18
Alignment explanation
Indices: 1161695--1161736 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
1161685 TTAGCATTGT
1161695 GAAAAGAAAATAATGAAA
1 GAAAAGAAAATAATGAAA
1161713 GAAAAGTAAAA-AGATGAAA
1 GAAAAG-AAAATA-ATGAAA
1161732 GAAAA
1 GAAAA
1161737 TTAGAATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (18 bp):
GAAAAGAAAATAATGAAA
Found at i:1171050 original size:25 final size:25
Alignment explanation
Indices: 1171021--1171076 Score: 96
Period size: 25 Copynumber: 2.2 Consensus size: 25
1171011 GGTTGTAATC
1171021 GGGCCTATGATTTGC-TTTGTATCTT
1 GGGCCTATGATTT-CATTTGTATCTT
1171046 GGGCCTATGATTTCATTTGTATCTT
1 GGGCCTATGATTTCATTTGTATCTT
1171071 GGGCCT
1 GGGCCT
1171077 GTGTGCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.12, C:0.18, G:0.25, T:0.45
Consensus pattern (25 bp):
GGGCCTATGATTTCATTTGTATCTT
Found at i:1176726 original size:35 final size:35
Alignment explanation
Indices: 1176680--1176753 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
1176670 AACAGTCCTT
* * *
1176680 AATTTTATTCTAAACCCCAATTTCCAAAGTAATTC
1 AATTTCATTCTAAACCCCAAATTCCAAAATAATTC
*
1176715 AATTTCATTCTAAACCCTAAATTCCAAAATAATTC
1 AATTTCATTCTAAACCCCAAATTCCAAAATAATTC
1176750 AATT
1 AATT
1176754 AAATTCAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (35 bp):
AATTTCATTCTAAACCCCAAATTCCAAAATAATTC
Found at i:1177169 original size:16 final size:16
Alignment explanation
Indices: 1177150--1177183 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1177140 CAATATACGA
1177150 ATAAACATATATTTAT
1 ATAAACATATATTTAT
**
1177166 ATAAATGTATATTTAT
1 ATAAACATATATTTAT
1177182 AT
1 AT
1177184 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAACATATATTTAT
Found at i:1177257 original size:16 final size:18
Alignment explanation
Indices: 1177225--1177258 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1177215 TATTAATGTA
1177225 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1177243 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1177259 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1177977 original size:130 final size:130
Alignment explanation
Indices: 1177719--1177966 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
1177709 AATTTTCTTC
* *
1177719 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGCGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGCGCTAACACATGTCAGAT
** *
1177784 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATAAATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATAAATAAA
* * * *
1177849 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGCGCTAACACATGTCAGAT
1177914 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
1177967 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGCGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATAAATAAA
Found at i:1178634 original size:35 final size:35
Alignment explanation
Indices: 1178588--1178661 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
1178578 AACAGTCCTT
* * *
1178588 AATTTTATTCTAAACCCCAATTTCCAAAGTAATTC
1 AATTTCATTCTAAACCCCAAATTCCAAAATAATTC
*
1178623 AATTTCATTCTAAACCCTAAATTCCAAAATAATTC
1 AATTTCATTCTAAACCCCAAATTCCAAAATAATTC
1178658 AATT
1 AATT
1178662 AAATTCAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (35 bp):
AATTTCATTCTAAACCCCAAATTCCAAAATAATTC
Found at i:1179196 original size:130 final size:130
Alignment explanation
Indices: 1179058--1179305 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
1179048 TATTTATATA
* **
1179058 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
1179123 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATTTATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATATCACCACCTAATTATTTATTTATGCT
1179188 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
1179253 TTAACACATGATCATGATATATGTTATTGGTGACACATATCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATATCACCACCTAATTA
1179306 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATATCACCACCTAATTATTTATTTATGCT
Found at i:1179336 original size:130 final size:129
Alignment explanation
Indices: 1179072--1179336 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
1179062 ATTTGGTCCT
* ** *
1179072 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * * * ** *
1179137 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATTTATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATATCACCACCTAATTAGAAAATTAAGCTATAAAATAAGT-CA
1179202 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
1179267 TGATATATGTTATTGGTGACACATATCACCACCTAATTAGAAGAAAATTAAGTTA-AAAATAAGT
66 TGACACATGTCATTGGTGACACATATCACCACCTAATT---AGAAAATTAAGCTATAAAATAAGT
1179331 -A
128 CA
1179332 AAATT
1 AAATT
1179337 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 5 0.04
133 8 0.07
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATATCACCACCTAATTAGAAAATTAAGCTATAAAATAAGTCA
Found at i:1179664 original size:28 final size:27
Alignment explanation
Indices: 1179633--1179695 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
1179623 AGTTGATACA
*
1179633 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
1179661 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
1179689 ATATTTT
1 ATATTTT
1179696 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:1179796 original size:16 final size:18
Alignment explanation
Indices: 1179775--1179808 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1179765 ATTTCTTATT
1179775 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1179791 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1179809 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1180241 original size:29 final size:29
Alignment explanation
Indices: 1180184--1180241 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1180174 CGGAATAAAT
* * *
1180184 GTTGGGGGACTATATTGCAAGTTTTAAAA
1 GTTGGGGGACTATAATGCAAGCTTCAAAA
1180213 GTTGGGGGACCTA-AATGCAAGCTTCAAAA
1 GTTGGGGGA-CTATAATGCAAGCTTCAAAA
1180242 ATGTTCAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.28
Consensus pattern (29 bp):
GTTGGGGGACTATAATGCAAGCTTCAAAA
Found at i:1180561 original size:3 final size:3
Alignment explanation
Indices: 1180553--1180588 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1180543 ATTTTTCATA
1180553 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1180589 TCTTTACCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1181440 original size:21 final size:20
Alignment explanation
Indices: 1181394--1181442 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1181384 TTGTTTTCTA
*
1181394 AATATTTTAAATAATTATTT
1 AATATTTTAAATAATTATGT
*
1181414 AATATTTTAGAATAATTCTGT
1 AATATTTTA-AATAATTATGT
*
1181435 ATTATTTT
1 AATATTTT
1181443 TTGATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (20 bp):
AATATTTTAAATAATTATGT
Found at i:1181672 original size:2 final size:2
Alignment explanation
Indices: 1181616--1181652 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1181606 GACTTTTTGA
1181616 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1181653 TAAAAAATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1185973 original size:20 final size:20
Alignment explanation
Indices: 1185948--1185992 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
1185938 TAGATTGGAG
1185948 TTTATATATTTCCTTGGTTA
1 TTTATATATTTCCTTGGTTA
1185968 TTTATATATTTCCTTGGTTA
1 TTTATATATTTCCTTGGTTA
1185988 TTTAT
1 TTTAT
1185993 TGAAGTTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (20 bp):
TTTATATATTTCCTTGGTTA
Found at i:1187954 original size:23 final size:22
Alignment explanation
Indices: 1187928--1187989 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
1187918 AATAACTCTT
1187928 TCTTTATGGCACGTTTTCTTCTA-
1 TCTTT-TGGCACGTTTTCTT-TAG
*
1187951 TCTTTTAGCTA-GTTTTCTTTAG
1 TCTTTTGGC-ACGTTTTCTTTAG
*
1187973 TCTTTTGGAACGTTTTC
1 TCTTTTGGCACGTTTTC
1187990 AATCGTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 3 0.09
22 24 0.73
23 6 0.18
ACGTcount: A:0.13, C:0.18, G:0.15, T:0.55
Consensus pattern (22 bp):
TCTTTTGGCACGTTTTCTTTAG
Found at i:1189900 original size:25 final size:24
Alignment explanation
Indices: 1189851--1189900 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
1189841 TGTTGTTGGA
1189851 TTATTATCTTCAACATTTTCATTC
1 TTATTATCTTCAACATTTTCATTC
*
1189875 TTATTATGTTCCAACATCTTTC-TTC
1 TTATTATCTT-CAACAT-TTTCATTC
1189900 T
1 T
1189901 CATAAATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 10 0.43
26 4 0.17
ACGTcount: A:0.22, C:0.22, G:0.02, T:0.54
Consensus pattern (24 bp):
TTATTATCTTCAACATTTTCATTC
Found at i:1198934 original size:30 final size:29
Alignment explanation
Indices: 1198899--1198961 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
1198889 AAACATAATA
* *
1198899 AATAATCG-AGTGATCATTTTATTAACTTTT
1 AATAATCGAAG-GATCATTTT-GTAACTTTC
*
1198929 AATAATTGAAGGATCATTTTGTAACTTTC
1 AATAATCGAAGGATCATTTTGTAACTTTC
1198958 AATA
1 AATA
1198962 TTTGTAGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 11 0.38
30 16 0.55
31 2 0.07
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.43
Consensus pattern (29 bp):
AATAATCGAAGGATCATTTTGTAACTTTC
Found at i:1201528 original size:15 final size:15
Alignment explanation
Indices: 1201497--1201545 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
1201487 TTTAAATTTT
1201497 AAATATAAAATAATAAA
1 AAATAT-AAA-AATAAA
1201514 AAATATAAAAAT-AA
1 AAATATAAAAATAAA
1201528 AAATACTAAAAATAAA
1 AAATA-TAAAAATAAA
1201544 AA
1 AA
1201546 TTAATTACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.23
15 10 0.33
16 7 0.23
17 6 0.20
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATATAAAAATAAA
Found at i:1201532 original size:21 final size:21
Alignment explanation
Indices: 1201508--1201588 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 21
1201498 AATATAAAAT
1201508 AATAAAAAATATAAAAATAAA
1 AATAAAAAATATAAAAATAAA
* *
1201529 AATACTAAAAATA-AAAATTAATT
1 AATA--AAAAATATAAAAATAA-A
* *
1201552 ACTAAAAAA-GTAAAAATAAA
1 AATAAAAAATATAAAAATAAA
* *
1201572 TATTAAAAATACTAAAA
1 AATAAAAAATA-TAAAA
1201589 GCTTAATTCA
Statistics
Matches: 44, Mismatches: 10, Indels: 11
0.68 0.15 0.17
Matches are distributed among these distances:
20 6 0.14
21 16 0.36
22 12 0.27
23 10 0.23
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.23
Consensus pattern (21 bp):
AATAAAAAATATAAAAATAAA
Found at i:1201546 original size:15 final size:14
Alignment explanation
Indices: 1201497--1201582 Score: 70
Period size: 14 Copynumber: 5.9 Consensus size: 14
1201487 TTTAAATTTT
1201497 AAATATAAAATAATAAA
1 AAATAT-AAA-AAT-AA
1201514 AAATATAAAAATAA
1 AAATATAAAAATAA
1201528 AAATACTAAAAATAA
1 AAATA-TAAAAATAA
* *
1201543 AAAT-TAATTACTAA
1 AAATATAA-AAATAA
1201557 AAA-AGTAAAAATAA
1 AAATA-TAAAAATAA
*
1201571 ATAT-TAAAAATA
1 AAATATAAAAATA
1201583 CTAAAAGCTT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
13 11 0.19
14 20 0.34
15 19 0.32
16 3 0.05
17 6 0.10
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.24
Consensus pattern (14 bp):
AAATATAAAAATAA
Found at i:1201560 original size:22 final size:23
Alignment explanation
Indices: 1201497--1201571 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 23
1201487 TTTAAATTTT
*
1201497 AAATATAAAATAATAAAAAATATAA
1 AAATA-AAAATACTAAAAAA-ATAA
1201522 AAATAAAAATACT--AAAAATAA
1 AAATAAAAATACTAAAAAAATAA
* * *
1201543 AAAT-TAATTACTAAAAAAGTAA
1 AAATAAAAATACTAAAAAAATAA
1201565 AAATAAA
1 AAATAAA
1201572 TATTAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 6 0.14
21 8 0.19
22 15 0.36
23 1 0.02
24 7 0.17
25 5 0.12
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.23
Consensus pattern (23 bp):
AAATAAAAATACTAAAAAAATAA
Found at i:1202043 original size:23 final size:21
Alignment explanation
Indices: 1202015--1202060 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1202005 GAATATTTTT
1202015 ATATTTTAAATTTTAAATTAAAA
1 ATATTTT-AATTTT-AATTAAAA
* *
1202038 ATATTTTTATTTTTATTAAAA
1 ATATTTTAATTTTAATTAAAA
1202059 AT
1 AT
1202061 CAAATAAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 5 0.24
23 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATTTTAATTTTAATTAAAA
Found at i:1205338 original size:30 final size:30
Alignment explanation
Indices: 1205302--1205432 Score: 190
Period size: 30 Copynumber: 4.4 Consensus size: 30
1205292 CTCAAAAGTG
1205302 AATAAAGTGAATGGTACATGCTATGAAATA
1 AATAAAGTGAATGGTACATGCTATGAAATA
**
1205332 AATAAAGTGAATATTACATGCTATGAAATA
1 AATAAAGTGAATGGTACATGCTATGAAATA
* * *
1205362 AATGAATTGAATGTTACATGCTATGAAATA
1 AATAAAGTGAATGGTACATGCTATGAAATA
* * *
1205392 AATAAAATGAATGGTACATGTTATGAAATG
1 AATAAAGTGAATGGTACATGCTATGAAATA
1205422 AATAAAGTGAA
1 AATAAAGTGAA
1205433 AAGCATGGGT
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 90 1.00
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (30 bp):
AATAAAGTGAATGGTACATGCTATGAAATA
Found at i:1207194 original size:24 final size:20
Alignment explanation
Indices: 1207167--1207224 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
1207157 GCATGGGTAG
1207167 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
1207191 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
1207211 TGTATCGATGCACT
1 TGCATCGATGCACT
1207225 TCAAGGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:1208306 original size:31 final size:31
Alignment explanation
Indices: 1208235--1208324 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 31
1208225 AGTCGAGGGT
*
1208235 TTACCTATGTTCTATGGAACATATGGACAGAA
1 TTACCTATG-TCTATCGAACATATGGACAGAA
* *
1208267 TTACCTATGTCTTTCGAGACATATGGACAGTA
1 TTACCTATGTCTATCGA-ACATATGGACAGAA
**
1208299 -TACCTATGTTCTAAGGAACATATGGA
1 TTACCTATG-TCTATCGAACATATGGA
1208325 TAGTTTACCT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
31 23 0.46
32 27 0.54
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (31 bp):
TTACCTATGTCTATCGAACATATGGACAGAA
Found at i:1208334 original size:31 final size:31
Alignment explanation
Indices: 1208233--1208341 Score: 130
Period size: 31 Copynumber: 3.5 Consensus size: 31
1208223 AGAGTCGAGG
1208233 GTTTACCTATGTTCTATGGAACATATGGACA
1 GTTTACCTATGTTCTATGGAACATATGGACA
* * *
1208264 GAATTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTATGGA-ACATATGGACA
* * *
1208296 GTATACCTATGTTCTAAGGAACATATGGATA
1 GTTTACCTATGTTCTATGGAACATATGGACA
*
1208327 GTTTACCTAGGTTCT
1 GTTTACCTATGTTCT
1208342 TCGGGACCTA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
31 38 0.59
32 26 0.41
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTATGGAACATATGGACA
Found at i:1212416 original size:15 final size:16
Alignment explanation
Indices: 1212389--1212418 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1212379 CTGTTGTAAC
1212389 CTATTTCCCATTTCTA
1 CTATTTCCCATTTCTA
1212405 CTATTT-CCATTTCT
1 CTATTTCCCATTTCT
1212419 CAGTAGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.30, G:0.00, T:0.53
Consensus pattern (16 bp):
CTATTTCCCATTTCTA
Found at i:1214259 original size:23 final size:23
Alignment explanation
Indices: 1214216--1214259 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1214206 TAAAACCTTT
*
1214216 TATTAGATACCAAATTCCAAAAA
1 TATTAGATACCAAATTACAAAAA
*
1214239 TATTAGATGCCCAAA-TACAAA
1 TATTAGAT-ACCAAATTACAAA
1214260 CAGTCTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.50, C:0.18, G:0.07, T:0.25
Consensus pattern (23 bp):
TATTAGATACCAAATTACAAAAA
Found at i:1215571 original size:15 final size:15
Alignment explanation
Indices: 1215540--1215577 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
1215530 TGATCTGGGA
1215540 AATTTCTAACTTACT
1 AATTTCTAACTTACT
1215555 AATTTACTAACTT-CT
1 AATTT-CTAACTTACT
1215570 AATTTCTA
1 AATTTCTA
1215578 TAATATATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 12 0.55
16 7 0.32
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTCTAACTTACT
Found at i:1223084 original size:130 final size:129
Alignment explanation
Indices: 1222846--1223198 Score: 431
Period size: 130 Copynumber: 2.7 Consensus size: 129
1222836 AGCGATTCTT
* * * * *
1222846 GAAGATAAAATCTG-AAAAGGGATATGCTTCACTGCTCTTCAGGTATATCAGATCTGGAAACATT
1 GAAGATCAAATCTGAAAAAGGGGTATGCTCCACTGCTCTTCAGGTAGATTAGATCTGGAAACATT
* * * * * * *
1222910 GATTCACTCCATTTCTTTTCAGAGAAGACTGAATCGAGGCAGATTTGTTCTATTGCTCCTCAGG
66 GATTCATTCCACTACTTTTCAGGGAAGACTGAATCAAGGCAGATTTGTTCCACTGCTCCTCAGG
1222974 GAAGATCAAATCTGAAAAAGGGGTATGCTCCACTGCTCTTCGAGGTAGATTAGATCTGGAAACAT
1 GAAGATCAAATCTGAAAAAGGGGTATGCTCCACTGCTCTTC-AGGTAGATTAGATCTGGAAACAT
* * * * * * *
1223039 TGATTCATTCCGCTACTTTTCAGGGAATATTGATTCAAGGTAGATTTGTTCCACTGCTCTTTAGG
65 TGATTCATTCCACTACTTTTCAGGGAAGACTGAATCAAGGCAGATTTGTTCCACTGCTCCTCAGG
* * * * *
1223104 GAAGATCAAATATAAAAAAGAGGGATATGCTCCACT-TTTTTCAGGGGAGATTAGATCTGGAAAC
1 GAAGATCAAATCTGAAAAAG-GGG-TATGCTCCACTGCTCTTCA-GGTAGATTAGATCTGGAAAC
*
1223168 ATTGATTCATTCCACTACTCTTCAGGGAAGA
63 ATTGATTCATTCCACTACTTTTCAGGGAAGA
1223199 TCAAATATGA
Statistics
Matches: 193, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
128 13 0.07
129 24 0.12
130 91 0.47
131 54 0.28
132 11 0.06
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (129 bp):
GAAGATCAAATCTGAAAAAGGGGTATGCTCCACTGCTCTTCAGGTAGATTAGATCTGGAAACATT
GATTCATTCCACTACTTTTCAGGGAAGACTGAATCAAGGCAGATTTGTTCCACTGCTCCTCAGG
Found at i:1223204 original size:90 final size:91
Alignment explanation
Indices: 1223087--1223277 Score: 260
Period size: 91 Copynumber: 2.1 Consensus size: 91
1223077 GGTAGATTTG
* * * *
1223087 TTCCACTGCTCTTTAGGGAAGATCAAATAT-AAAAAAGAGGGATATGCTCCACT-TTTTTCAGGG
1 TTCCACTACTCTTCAGGGAAGATCAAATATGAAAAAAG-GGGATATGCTCCACTGCTCTTCAGGG
1223150 GAGATTAGATCTGGAAACATTGATTCA
65 GAGATTAGATCTGGAAACATTGATTCA
* * * * *
1223177 TTCCACTACTCTTCAGGGAAGATCAAATATGAAACAAGGGTATCTGCTCCGCTGCTCTTCAGGGT
1 TTCCACTACTCTTCAGGGAAGATCAAATATGAAAAAAGGGGATATGCTCCACTGCTCTTCAGGGG
*
1223242 AGATTAGATCTGGAAACGTTGATTCA
66 AGATTAGATCTGGAAACATTGATTCA
*
1223268 CTCCACTACT
1 TTCCACTACT
1223278 ATTTAGGGTA
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
90 40 0.45
91 48 0.55
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (91 bp):
TTCCACTACTCTTCAGGGAAGATCAAATATGAAAAAAGGGGATATGCTCCACTGCTCTTCAGGGG
AGATTAGATCTGGAAACATTGATTCA
Found at i:1224574 original size:7 final size:7
Alignment explanation
Indices: 1224559--1224654 Score: 53
Period size: 7 Copynumber: 14.4 Consensus size: 7
1224549 TTTTATTTAT
*
1224559 TTTTTTC
1 TTTTCTC
1224566 TTTTCTC
1 TTTTCTC
*
1224573 TTTTTTTC
1 -TTTTCTC
*
1224581 TTTTTTC
1 TTTTCTC
1224588 TTTTCTC
1 TTTTCTC
*
1224595 TTTTCTA
1 TTTTCTC
*
1224602 TTAT-T-
1 TTTTCTC
*
1224607 TTTTCTA
1 TTTTCTC
*
1224614 TTTTTTC
1 TTTTCTC
*
1224621 -ATTCAT-
1 TTTTC-TC
1224627 TTTTC-C
1 TTTTCTC
1224633 TTTTC-C
1 TTTTCTC
1224639 TTTT-TC
1 TTTTCTC
1224645 TTTTCTC
1 TTTTCTC
1224652 TTT
1 TTT
1224655 CTTTATGCGA
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
5 3 0.04
6 19 0.27
7 42 0.60
8 6 0.09
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCTC
Found at i:1224578 original size:15 final size:15
Alignment explanation
Indices: 1224558--1224600 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1224548 TTTTTATTTA
1224558 TTTTTTTCTTTTCTC
1 TTTTTTTCTTTTCTC
*
1224573 TTTTTTTCTTTTTTC
1 TTTTTTTCTTTTCTC
*
1224588 -TTTTCTCTTTTCT
1 TTTTTTTCTTTTCT
1224601 ATTATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTCTTTTCTC
Found at i:1224587 original size:22 final size:24
Alignment explanation
Indices: 1224545--1224612 Score: 88
Period size: 22 Copynumber: 2.9 Consensus size: 24
1224535 ATCTTGAACC
1224545 CTCTTTT-TATTTATTTTTTTCTTTT
1 CTCTTTTCTA-TTA-TTTTTTCTTTT
*
1224570 CTCTTTT-T-TTCTTTTTTCTTTT
1 CTCTTTTCTATTATTTTTTCTTTT
1224592 CTCTTTTCTATTATTTTTTCT
1 CTCTTTTCTATTATTTTTTCT
1224613 ATTTTTTCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
22 18 0.46
23 3 0.08
24 10 0.26
25 8 0.21
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (24 bp):
CTCTTTTCTATTATTTTTTCTTTT
Found at i:1230884 original size:20 final size:21
Alignment explanation
Indices: 1230859--1230902 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1230849 TGTGGTCGTG
1230859 TCTAGTCG-TTGGGGATGATT
1 TCTAGTCGTTTGGGGATGATT
*
1230879 TCTAGTCGTTTGGGGATGTTT
1 TCTAGTCGTTTGGGGATGATT
1230900 TCT
1 TCT
1230903 CTACAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.11, C:0.11, G:0.32, T:0.45
Consensus pattern (21 bp):
TCTAGTCGTTTGGGGATGATT
Found at i:1238653 original size:20 final size:20
Alignment explanation
Indices: 1238625--1238662 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1238615 AGCTGAGTTG
*
1238625 AGCTGTTGACTTTGACCATT
1 AGCTATTGACTTTGACCATT
1238645 AGCTATTGACTTTGACCA
1 AGCTATTGACTTTGACCA
1238663 ACATTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (20 bp):
AGCTATTGACTTTGACCATT
Found at i:1243047 original size:35 final size:35
Alignment explanation
Indices: 1243001--1243076 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
1242991 AAAACAGTCA
* *
1243001 TCAATTTCATTCTAAA-CCTCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCT-AAATTCCAAAATAAT
1243036 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1243071 TCAATT
1 TCAATT
1243077 AAATTCAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 35 0.92
36 3 0.08
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
Found at i:1243624 original size:130 final size:130
Alignment explanation
Indices: 1243471--1243718 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
1243461 TATTTATATA
* **
1243471 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
1243536 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCGCCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
1243601 ATCAATTTGGTTCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
1243666 TTAACGCATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
1243719 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1244078 original size:28 final size:27
Alignment explanation
Indices: 1244047--1244109 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
1244037 AGTTGATACA
*
1244047 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
1244075 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
1244103 ATATTTT
1 ATATTTT
1244110 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:1244200 original size:16 final size:18
Alignment explanation
Indices: 1244179--1244212 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1244169 ATTTCTTATT
1244179 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1244195 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1244213 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1249049 original size:18 final size:18
Alignment explanation
Indices: 1249028--1249086 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1249018 TTTTTTTATG
1249028 TCTAGGGATTTACTTTGT
1 TCTAGGGATTTACTTTGT
** *
1249046 TCTACTG--TTATTTTGT
1 TCTAGGGATTTACTTTGT
*
1249062 TCTAGGTATTT-CTTCTGT
1 TCTAGGGATTTACTT-TGT
1249080 TCTAGGG
1 TCTAGGG
1249087 TTTGAGTACA
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
16 12 0.40
17 2 0.07
18 16 0.53
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.53
Consensus pattern (18 bp):
TCTAGGGATTTACTTTGT
Found at i:1250092 original size:15 final size:15
Alignment explanation
Indices: 1250069--1250104 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1250059 GAAACGTCAA
1250069 AGTCAAGTACTAATG
1 AGTCAAGTACTAATG
*
1250084 AGTCGAGTACTAATG
1 AGTCAAGTACTAATG
1250099 AGTCAA
1 AGTCAA
1250105 CTTTTATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (15 bp):
AGTCAAGTACTAATG
Found at i:1250203 original size:24 final size:24
Alignment explanation
Indices: 1250153--1250204 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1250143 ATGAGTATTA
* **
1250153 TGATGTAAATGTTGGGTTAGGTTG
1 TGATGTAAATGTTAGGTTAGGCAG
* *
1250177 TGATGTTAATGTTAGGTTGGGCAG
1 TGATGTAAATGTTAGGTTAGGCAG
1250201 TGAT
1 TGAT
1250205 CAAATGAGGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.02, G:0.37, T:0.40
Consensus pattern (24 bp):
TGATGTAAATGTTAGGTTAGGCAG
Found at i:1252969 original size:34 final size:34
Alignment explanation
Indices: 1252920--1252989 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
1252910 CTTGTCTATT
* *
1252920 TTGTTTACTTTATACATTCGACCAAGTGTTGTGA
1 TTGTGTACTTCATACATTCGACCAAGTGTTGTGA
*
1252954 TTGTGTACTTCATACATTTGACCAAGTGTTGTGA
1 TTGTGTACTTCATACATTCGACCAAGTGTTGTGA
1252988 TT
1 TT
1252990 ATGAACATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (34 bp):
TTGTGTACTTCATACATTCGACCAAGTGTTGTGA
Found at i:1255808 original size:17 final size:17
Alignment explanation
Indices: 1255758--1255819 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
1255748 GCATGTTAAA
*
1255758 TCATTGAAAGCATGTACT
1 TCATT-AAAGCATGTAGT
* * *
1255776 TAATT-TAGCATTTAGT
1 TCATTAAAGCATGTAGT
1255792 TCATTAAAGCATGTAGT
1 TCATTAAAGCATGTAGT
*
1255809 TCATTTAAGCA
1 TCATTAAAGCA
1255820 AGCTACTTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
16 12 0.34
17 19 0.54
18 4 0.11
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.39
Consensus pattern (17 bp):
TCATTAAAGCATGTAGT
Found at i:1258477 original size:12 final size:12
Alignment explanation
Indices: 1258452--1258521 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
1258442 ACGAAGATAT
* *
1258452 CAGAAATCAAAA
1 CAGAATTCAGAA
1258464 CAGAATTCAGAA
1 CAGAATTCAGAA
1258476 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1258488 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1258500 CAGAAATCAGAA
1 CAGAATTCAGAA
1258512 CAGAATTCAG
1 CAGAATTCAG
1258522 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1258521 original size:48 final size:47
Alignment explanation
Indices: 1258450--1258558 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
1258440 AAACGAAGAT
*
1258450 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
1258497 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
1258545 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
1258559 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:1258556 original size:24 final size:25
Alignment explanation
Indices: 1258450--1258558 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
1258440 AAACGAAGAT
*
1258450 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
1258474 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
1258498 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
1258522 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
1258547 -TCGGAAATCAGA
1 ATCAGAAATCAGA
1258559 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:1259706 original size:18 final size:18
Alignment explanation
Indices: 1259685--1259720 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1259675 CTTCCATCCG
*
1259685 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1259703 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1259721 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1261008 original size:10 final size:9
Alignment explanation
Indices: 1260995--1261049 Score: 50
Period size: 10 Copynumber: 6.6 Consensus size: 9
1260985 GTCAAAGTTT
1260995 TGGTCAACAG
1 TGGTCAAC-G
1261005 TGGTCAACG
1 TGGTCAACG
1261014 TGGGTCAAC-
1 T-GGTCAACG
1261023 -GGTCAACG
1 TGGTCAACG
1261031 -GGTCAAC-
1 TGGTCAACG
1261038 -GGTCAACG
1 TGGTCAACG
1261046 -GGTC
1 TGGTC
1261050 GGGTCAACGG
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
7 14 0.33
8 11 0.26
9 2 0.05
10 15 0.36
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.18
Consensus pattern (9 bp):
TGGTCAACG
Found at i:1261028 original size:7 final size:7
Alignment explanation
Indices: 1261016--1261046 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
1261006 GGTCAACGTG
1261016 GGTCAAC
1 GGTCAAC
1261023 GGTCAAC
1 GGTCAAC
1261030 GGGTCAAC
1 -GGTCAAC
1261038 GGTCAAC
1 GGTCAAC
1261045 GG
1 GG
1261047 GTCGGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:1261036 original size:8 final size:8
Alignment explanation
Indices: 1260996--1261075 Score: 68
Period size: 8 Copynumber: 10.5 Consensus size: 8
1260986 TCAAAGTTTT
1260996 GGTCAACAG
1 GGTCAAC-G
1261005 TGGTCAACGTG
1 -GGTCAAC--G
1261016 GGTCAAC-
1 GGTCAACG
1261023 GGTCAACG
1 GGTCAACG
1261031 GGTCAAC-
1 GGTCAACG
1261038 GGTCAACG
1 GGTCAACG
1261046 GGT---CG
1 GGTCAACG
1261051 GGTCAACG
1 GGTCAACG
1261059 GGT---CG
1 GGTCAACG
1261064 GGTCAACG
1 GGTCAACG
1261072 GGTC
1 GGTC
1261076 GGGTCAACTG
Statistics
Matches: 60, Mismatches: 1, Indels: 20
0.74 0.01 0.25
Matches are distributed among these distances:
5 10 0.17
7 14 0.23
8 21 0.35
10 14 0.23
11 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.39, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:1261056 original size:13 final size:13
Alignment explanation
Indices: 1261023--1261119 Score: 131
Period size: 13 Copynumber: 7.3 Consensus size: 13
1261013 GTGGGTCAAC
*
1261023 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1261038 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1261051 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1261064 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1261077 GGTCAACTGGTCG
1 GGTCAACGGGTCG
* *
1261090 GGTAAATGGGTCG
1 GGTCAACGGGTCG
*
1261103 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1261116 GGTC
1 GGTC
1261120 GGGTCGGGTT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
13 63 0.84
15 12 0.16
ACGTcount: A:0.19, C:0.21, G:0.43, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1263231 original size:12 final size:12
Alignment explanation
Indices: 1263206--1263275 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
1263196 ACGAAGATAT
* *
1263206 CAGAAATCAAAA
1 CAGAATTCAGAA
1263218 CAGAATTCAGAA
1 CAGAATTCAGAA
1263230 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1263242 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1263254 CAGAAATCAGAA
1 CAGAATTCAGAA
1263266 CAGAATTCAG
1 CAGAATTCAG
1263276 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1263275 original size:48 final size:47
Alignment explanation
Indices: 1263204--1263312 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
1263194 AAACGAAGAT
*
1263204 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
1263251 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
1263299 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
1263313 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:1263310 original size:24 final size:25
Alignment explanation
Indices: 1263204--1263312 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
1263194 AAACGAAGAT
*
1263204 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
1263228 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
1263252 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
1263276 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
1263301 -TCGGAAATCAGA
1 ATCAGAAATCAGA
1263313 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:1264458 original size:18 final size:18
Alignment explanation
Indices: 1264437--1264472 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1264427 CTTCCATCCG
*
1264437 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1264455 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1264473 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1265776 original size:7 final size:7
Alignment explanation
Indices: 1265764--1265794 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
1265754 TGGTCAACGG
1265764 GGTCAAC
1 GGTCAAC
1265771 GGTCAAC
1 GGTCAAC
1265778 GGGTCAAC
1 -GGTCAAC
1265786 GGTCAAC
1 GGTCAAC
1265793 GG
1 GG
1265795 GTCGGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:1265783 original size:15 final size:13
Alignment explanation
Indices: 1265755--1265867 Score: 100
Period size: 13 Copynumber: 8.3 Consensus size: 13
1265745 GGTCAACAGT
1265755 GGTCAACGGGGTCAAC
1 GGTCAAC-GGGTC--C
1265771 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--C
*
1265786 GGTCAACGGGTCG
1 GGTCAACGGGTCC
*
1265799 GGTCAACGGGTCG
1 GGTCAACGGGTCC
*
1265812 GGTCAACGGGTCG
1 GGTCAACGGGTCC
* *
1265825 GGTCAACTGGTCG
1 GGTCAACGGGTCC
* *
1265838 GGTAAACGGGTCG
1 GGTCAACGGGTCC
* *
1265851 GGTAAACGGGTCG
1 GGTCAACGGGTCC
1265864 GGTC
1 GGTC
1265868 GGGTCGGGTT
Statistics
Matches: 92, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
13 65 0.71
15 20 0.22
16 7 0.08
ACGTcount: A:0.19, C:0.22, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCC
Found at i:1265784 original size:8 final size:8
Alignment explanation
Indices: 1265745--1265823 Score: 75
Period size: 8 Copynumber: 10.5 Consensus size: 8
1265735 TCAAAGTTTT
1265745 GGTCAACAG
1 GGTCAAC-G
1265754 TGGTCAACGG
1 -GGTCAAC-G
1265764 GGTCAAC-
1 GGTCAACG
1265771 GGTCAACG
1 GGTCAACG
1265779 GGTCAAC-
1 GGTCAACG
1265786 GGTCAACG
1 GGTCAACG
1265794 GGT---CG
1 GGTCAACG
1265799 GGTCAACG
1 GGTCAACG
1265807 GGT---CG
1 GGTCAACG
1265812 GGTCAACG
1 GGTCAACG
1265820 GGTC
1 GGTC
1265824 GGGTCAACTG
Statistics
Matches: 60, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
5 10 0.17
7 14 0.23
8 21 0.35
9 7 0.12
10 8 0.13
ACGTcount: A:0.22, C:0.24, G:0.39, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1265804 original size:13 final size:13
Alignment explanation
Indices: 1265771--1265867 Score: 140
Period size: 13 Copynumber: 7.3 Consensus size: 13
1265761 CGGGGTCAAC
*
1265771 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1265786 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1265799 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1265812 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1265825 GGTCAACTGGTCG
1 GGTCAACGGGTCG
*
1265838 GGTAAACGGGTCG
1 GGTCAACGGGTCG
*
1265851 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1265864 GGTC
1 GGTC
1265868 GGGTCGGGTT
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
13 65 0.84
15 12 0.16
ACGTcount: A:0.19, C:0.22, G:0.43, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1269494 original size:25 final size:25
Alignment explanation
Indices: 1269466--1269530 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
1269456 TGATTATTAA
*
1269466 ATATATATGTTATATATGTAAGTAT
1 ATATATATATTATATATGTAAGTAT
*
1269491 ATATATATATTATATGTGTAAGTAT
1 ATATATATATTATATATGTAAGTAT
* *
1269516 ATATATTTAATATAT
1 ATATATATATTATAT
1269531 GTGTTGTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (25 bp):
ATATATATATTATATATGTAAGTAT
Found at i:1279019 original size:3 final size:3
Alignment explanation
Indices: 1279011--1279050 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1279001 CTTTCATTCT
1279011 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1279051 CATTCTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1284339 original size:44 final size:43
Alignment explanation
Indices: 1284192--1284339 Score: 122
Period size: 44 Copynumber: 3.4 Consensus size: 43
1284182 TTTTCTGAAA
*
1284192 AGTAGTGAAATAAATCAAGATTTCA-AGATCTGGTCTTCCTAAAG
1 AGTAGTGAAATAAATCAAGATTT-ATAGATCTAG-CTTCCTAAAG
** * * * * * *
1284236 AGTAGTGAAGCAGATC-A-ATTTCTCAGATTTGATCTTCTTGAAG
1 AGTAGTGAAATAAATCAAGATTTAT-AGATCT-AGCTTCCTAAAG
* *
1284279 AGTAGTGAAATGAATCAAGATTTATAAATCTAAGCTTCCTAAAG
1 AGTAGTGAAATAAATCAAGATTTATAGATCT-AGCTTCCTAAAG
*
1284323 AGTAGTGAAGTAAATCA
1 AGTAGTGAAATAAATCA
1284340 CTCTCCCAGA
Statistics
Matches: 77, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
42 4 0.05
43 26 0.34
44 42 0.55
45 5 0.06
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (43 bp):
AGTAGTGAAATAAATCAAGATTTATAGATCTAGCTTCCTAAAG
Found at i:1284355 original size:87 final size:87
Alignment explanation
Indices: 1284187--1284358 Score: 222
Period size: 87 Copynumber: 2.0 Consensus size: 87
1284177 TCAATTTTTC
* * *
1284187 TGAAAAGTAGTGAAATAAATCAAGATTTCAAGATCTGGTCTTCCTAAAGAGTAGTGAAGCAGATC
1 TGAAAAGTAGTGAAATAAATCAAGATTTCAAAATCTAGTCTTCCTAAAGAGTAGTGAAGCAAATC
* * *
1284252 AATTTCTCAGATTTGATCTTCT
66 AATCTCCCAGAGTTGATCTTCT
* * *
1284274 TGAAGAGTAGTGAAATGAATCAAGATTT-ATAAATCTAAG-CTTCCTAAAGAGTAGTGAAGTAAA
1 TGAAAAGTAGTGAAATAAATCAAGATTTCA-AAATCT-AGTCTTCCTAAAGAGTAGTGAAGCAAA
*
1284337 TCACTCTCCCAGAGTTGATCTT
64 TCAATCTCCCAGAGTTGATCTT
1284359 GCCAAAAAGA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 1 0.01
87 71 0.97
88 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (87 bp):
TGAAAAGTAGTGAAATAAATCAAGATTTCAAAATCTAGTCTTCCTAAAGAGTAGTGAAGCAAATC
AATCTCCCAGAGTTGATCTTCT
Found at i:1287152 original size:17 final size:17
Alignment explanation
Indices: 1287112--1287174 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
1287102 TATTAACTCA
* *
1287112 ATTTAA-CATTTAGGTC
1 ATTTAAGCATGTAGTTC
*
1287128 ATTAAAGCATGTAGTTC
1 ATTTAAGCATGTAGTTC
* *
1287145 ATTTAAGCAAGCTACTTC
1 ATTTAAGCATG-TAGTTC
*
1287163 ATTTAAGTATGT
1 ATTTAAGCATGT
1287175 TGGACCATTC
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
16 5 0.14
17 18 0.49
18 14 0.38
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (17 bp):
ATTTAAGCATGTAGTTC
Found at i:1287225 original size:18 final size:18
Alignment explanation
Indices: 1287179--1287226 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
1287169 GTATGTTGGA
*
1287179 CCATTCAATAAAACTAGT
1 CCATTCAATTAAACTAGT
1287197 CCATT-AATTAAACTAGT
1 CCATTCAATTAAACTAGT
*
1287214 CCATTCATTTAAA
1 CCATTCAATTAAA
1287227 TTGGTTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (18 bp):
CCATTCAATTAAACTAGT
Found at i:1288780 original size:18 final size:17
Alignment explanation
Indices: 1288739--1288812 Score: 60
Period size: 18 Copynumber: 4.2 Consensus size: 17
1288729 TTTAAAGGAT
* *
1288739 CTAGTTTAATTAGTGAA
1 CTAGTTTAATGAATGAA
1288756 C-ATGTTTAAATGAATGAA
1 CTA-GTTT-AATGAATGAA
* *
1288774 CTAGTTTAATTAATGGA
1 CTAGTTTAATGAATGAA
* *
1288791 CTAGTTTTATTGAATGAT
1 CTAG-TTTAATGAATGAA
1288809 CTAG
1 CTAG
1288813 CATAATTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
16 1 0.02
17 17 0.38
18 26 0.58
19 1 0.02
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.41
Consensus pattern (17 bp):
CTAGTTTAATGAATGAA
Found at i:1288793 original size:17 final size:17
Alignment explanation
Indices: 1288739--1288812 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 17
1288729 TTTAAAGGAT
*
1288739 CTAGTTTAATTAGTGAA
1 CTAGTTTAATTAATGAA
*
1288756 C-ATGTTTAAATGAATGAA
1 CTA-GTTT-AATTAATGAA
*
1288774 CTAGTTTAATTAATGGA
1 CTAGTTTAATTAATGAA
* *
1288791 CTAGTTTTATTGAATGAT
1 CTAGTTTAATT-AATGAA
1288809 CTAG
1 CTAG
1288813 CATAATTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
16 1 0.02
17 23 0.50
18 21 0.46
19 1 0.02
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.41
Consensus pattern (17 bp):
CTAGTTTAATTAATGAA
Found at i:1293428 original size:18 final size:17
Alignment explanation
Indices: 1293364--1293429 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
1293354 AAAGGAGCTT
* *
1293364 GTTTTATTAATGAACCA
1 GTTTAATTAATGAACTA
*
1293381 GTTTAAATAAATGAACTA
1 GTTT-AATTAATGAACTA
*
1293399 GTTTAATTAATGGACTA
1 GTTTAATTAATGAACTA
*
1293416 GTTTTATTGAATGA
1 GTTTAATT-AATGA
1293430 TCCAACATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
17 22 0.55
18 18 0.45
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (17 bp):
GTTTAATTAATGAACTA
Found at i:1294544 original size:29 final size:29
Alignment explanation
Indices: 1294512--1294589 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
1294502 TAAATGACAC
1294512 AAATTAAAGGACTGAAATT-AAAGTGATG
1 AAATTAAAGGACTGAAATTGAAAGTGATG
* * *
1294540 AAAATTAAAGGGCGGAAATTGAAAGTGCTG
1 -AAATTAAAGGACTGAAATTGAAAGTGATG
* *
1294570 GAATTTAAGGTACTGAAATT
1 AAATTAAAGG-ACTGAAATT
1294590 TAAATAACAG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (29 bp):
AAATTAAAGGACTGAAATTGAAAGTGATG
Found at i:1294546 original size:15 final size:14
Alignment explanation
Indices: 1294512--1294589 Score: 61
Period size: 15 Copynumber: 5.4 Consensus size: 14
1294502 TAAATGACAC
1294512 AAATTAAAGGACTG
1 AAATTAAAGGACTG
1294526 AAATTAAAGTGA-TG
1 AAATTAAAG-GACTG
* *
1294540 AAAATTAAAGGGCGG
1 -AAATTAAAGGACTG
1294555 AAATTGAAAGTG-CTG
1 AAATT-AAAG-GACTG
* *
1294570 GAATTTAAGGTACTG
1 AAATTAAAGG-ACTG
1294585 AAATT
1 AAATT
1294590 TAAATAACAG
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
13 1 0.02
14 20 0.39
15 29 0.57
16 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (14 bp):
AAATTAAAGGACTG
Found at i:1303287 original size:21 final size:20
Alignment explanation
Indices: 1303261--1303314 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
1303251 GGCGTTATTC
*
1303261 TTAATTTTTATAATTTTCATT
1 TTAATTTTTATAA-TTTAATT
* *
1303282 TTAATTTGTTTTTATTTAATT
1 TTAATTT-TTATAATTTAATT
1303303 TTCAATTTTTAT
1 TT-AATTTTTAT
1303315 TTAATTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.69
Consensus pattern (20 bp):
TTAATTTTTATAATTTAATT
Found at i:1303317 original size:22 final size:21
Alignment explanation
Indices: 1303279--1303329 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
1303269 TATAATTTTC
*
1303279 ATTTTAATTTGTTTTTATTTA
1 ATTTTAATTTGTTTTTAATTA
*
1303300 ATTTTCAATTT-TTATTTAATTC
1 ATTTT-AATTTGTT-TTTAATTA
1303322 ATTTTAAT
1 ATTTTAAT
1303330 CAAGTATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTAATTTGTTTTTAATTA
Found at i:1303385 original size:2 final size:2
Alignment explanation
Indices: 1303378--1303409 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1303368 TTCGTAAAAC
1303378 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
1303410 TTAATTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1307050 original size:81 final size:80
Alignment explanation
Indices: 1306953--1307327 Score: 403
Period size: 81 Copynumber: 4.6 Consensus size: 80
1306943 TCCAAAGGTA
* * * * *
1306953 TTTAACCTTTCATCTAACTTGCATGATTGGCACTTGTCTGTCAAATGCACAACTAGGCCATTTAT
1 TTTAACCGTTCATCTAACTAGCATAATTGACACTT-TCTGCCAAATGCACAACTAGGCCATTTAT
* * *
1307018 CATTTACTCAATGATT
65 CTTTTACTCAATGGTC
*
1307034 TTTAACCGTTCATCTAACTAGCATAATTGGCACCTTTCTGCCAAATGCACAACTAGGCCATTTAT
1 TTTAACCGTTCATCTAACTAGCATAATTGACA-CTTTCTGCCAAATGCACAACTAGGCCATTTAT
1307099 CTTTTACTCAACT-GTC
65 CTTTTACTCAA-TGGTC
* * * * * * *
1307115 TCTAACCGTTCATCTAACTAGCATATTTGCCACATTTTTGCCAAATTCATAGCTAGGCCATTTAT
1 TTTAACCGTTCATCTAACTAGCATAATTGACAC-TTTCTGCCAAATGCACAACTAGGCCATTTAT
** *
1307180 CTTTTACTTTACGGTC
65 CTTTTACTCAATGGTC
* * * * *
1307196 TTTAACCGTTCATCTAACT-GTCATAATTGACACTTTTCTACCAAACGCATAGCTAGGTCATTTA
1 TTTAACCGTTCATCTAACTAG-CATAATTGACAC-TTTCTGCCAAATGCACAACTAGGCCATTTA
*
1307260 TCTTTTACTTAATGGTC
64 TCTTTTACTCAATGGTC
* * * * *
1307277 ATTAATCTTTCATCTAACTGGCATAATTGACACTTTTATGCCAAATGCACA
1 TTTAACCGTTCATCTAACTAGCATAATTGACAC-TTTCTGCCAAATGCACA
1307328 GTTAGGCCTC
Statistics
Matches: 253, Mismatches: 35, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
80 2 0.01
81 246 0.97
82 5 0.02
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (80 bp):
TTTAACCGTTCATCTAACTAGCATAATTGACACTTTCTGCCAAATGCACAACTAGGCCATTTATC
TTTTACTCAATGGTC
Found at i:1307392 original size:68 final size:68
Alignment explanation
Indices: 1307283--1307536 Score: 366
Period size: 68 Copynumber: 3.7 Consensus size: 68
1307273 GGTCATTAAT
* *
1307283 CTTTCATCTAACTGGCATAATTGACA-CTTTTATGCCAAATGCACAGTTAGGCCTCAAAGGAACT
1 CTTTCATCTAACTGGCATAATTGACAGC-TTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1307347 TAGC
65 TAGC
* * ** *
1307351 CTTTCATTTAACTAGCATAATTGACAGCTTTCCGTCAAATGCATAGTTAGGCCTCAAAGGCACTT
1 CTTTCATCTAACTGGCATAATTGACAGCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACTT
1307416 AGC
66 AGC
* * * *
1307419 CTTTCATCTAACTGGCATAATTGAAATCTTTCTGTCAACTGCACAGTTAGGCCTCAAAGGCACTT
1 CTTTCATCTAACTGGCATAATTGACAGCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACTT
*
1307484 AGA
66 AGC
* *
1307487 CTTTCATCTAACTGGTATAATTGACAGCTTTATGTCAAATGCACAATTAG
1 CTTTCATCTAACTGGCATAATTGACAGCTTTATGTCAAATGCACAGTTAG
1307537 ACCTATTAAT
Statistics
Matches: 164, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
68 163 0.99
69 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31
Consensus pattern (68 bp):
CTTTCATCTAACTGGCATAATTGACAGCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACTT
AGC
Found at i:1308149 original size:55 final size:55
Alignment explanation
Indices: 1308047--1308234 Score: 299
Period size: 55 Copynumber: 3.4 Consensus size: 55
1308037 CAAGCAACCC
* *
1308047 CTTAGTAT-AGATTTCTTAG-TTTACACACATAGTGCCCATACGAAAATTCATACA
1 CTTAGTATGA-ATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCATACA
1308101 CTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCATACA
1 CTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCATACA
* *
1308156 CTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCTCATACTGAAATTCATACA
1 CTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCATACA
*
1308211 CTTAATATGAATTTCTTAAGTTTT
1 CTTAGTATGAATTTCTT-AGTTTT
1308235 TTCACACTTA
Statistics
Matches: 126, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
54 17 0.13
55 103 0.82
56 6 0.05
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (55 bp):
CTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCATACA
Found at i:1311251 original size:17 final size:16
Alignment explanation
Indices: 1311225--1311260 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1311215 TTTTCAAAAT
1311225 TTTTTATATTTTTGCTA
1 TTTTTATATTTTT-CTA
*
1311242 TTTTTCTATTTTTCTA
1 TTTTTATATTTTTCTA
1311258 TTT
1 TTT
1311261 GGTTTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTTATATTTTTCTA
Found at i:1311253 original size:7 final size:8
Alignment explanation
Indices: 1311225--1311260 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
1311215 TTTTCAAAAT
*
1311225 TTTTTATA
1 TTTTTCTA
1311233 TTTTTGCTA
1 TTTTT-CTA
1311242 TTTTTCTA
1 TTTTTCTA
1311250 TTTTTCTA
1 TTTTTCTA
1311258 TTT
1 TTT
1311261 GGTTTTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (8 bp):
TTTTTCTA
Found at i:1313229 original size:117 final size:118
Alignment explanation
Indices: 1312947--1313246 Score: 334
Period size: 118 Copynumber: 2.6 Consensus size: 118
1312937 AATATAGACG
* * ** * * * *
1312947 ATAACATAACCGGTTAATTACTGGAAACATTATCAAGCACAATAACATATTAGGTAACGCTTATA
1 ATAACATAATCGATTAATTACTAAAAATATTATCAAGCATAATAACATATTATGTAACGCTTAAA
* *
1313012 TAACGTAATAAATAATGTCTTTTTAAAGCTGATGGGGCTTTGAAAATCCGACA
66 TAACGTAATAAATAATGTCTTTTTAAAGCTGATAGGACTTTGAAAATCCGACA
* * *
1313065 ATAATATAATCGATTAATTTCTAAAAATATTATCAAGCATAATAACATATTATGTAGCGCTTAAA
1 ATAACATAATCGATTAATTACTAAAAATATTATCAAGCATAATAACATATTATGTAACGCTTAAA
** * * * *
1313130 TAACGTAATAGGTAGTGTCTTTTT-AAGCTGATATGACTTTGGAAATCCGACG
66 TAACGTAATAAATAATGTCTTTTTAAAGCTGATAGGACTTTGAAAATCCGACA
* * * * * * * *
1313182 ATAACATAATCGGTTAATTACTTATATTGTTATTAA-TATTATCAACATATTATGTAACGCTTAA
1 ATAACATAATCGATTAATTACTAAAAATATTATCAAGCATAAT-AACATATTATGTAACGCTTAA
1313246 A
65 A
1313247 ATGTTACCAA
Statistics
Matches: 151, Mismatches: 30, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
116 4 0.03
117 72 0.48
118 75 0.50
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (118 bp):
ATAACATAATCGATTAATTACTAAAAATATTATCAAGCATAATAACATATTATGTAACGCTTAAA
TAACGTAATAAATAATGTCTTTTTAAAGCTGATAGGACTTTGAAAATCCGACA
Found at i:1313475 original size:226 final size:225
Alignment explanation
Indices: 1313054--1313592 Score: 735
Period size: 226 Copynumber: 2.4 Consensus size: 225
1313044 TGGGGCTTTG
* * * * * ** * *
1313054 AAAATCCGACAATAATATAATCGATTAATTTCTAAAAATATTATCAAGCATAATAACATATTATG
1 AAAATCCAACGATAACATAAACGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
** *
1313119 TAGCGCTTAAATAACGTAATAGGTAGTGTCTTTTTAAGCTGATATGACTTTGGAAATCCGACGAT
66 TAGCGCTTATGTAACGTAATAGGCAGTGTCTTTTTAAGCTGATATGACTTTGGAAATCCGACGAT
* * * *
1313184 AACATAATCGGTTAATTACTTATATTGTTATTAATATTATCAACATATTATGTAACGCTTAAAAT
131 AACAAAATAGGTTAATTACTTATATTGTTATTAATATTATCAACATATTAGGTAACGCCTAAAAT
1313249 GTTACCAAAGTTTAAGCTGATAGAGCCCTA
196 GTTACCAAAGTTTAAGCTGATAGAGCCCTA
* * *
1313279 GAAATGCAACGATAACATAAACTATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
1 AAAATCCAACGATAACATAAACGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
* *
1313344 TAGCGCTTATGTAACGTAATAGGCA-TCGTCTTTTTAAAGC-G-TTTGGGACTTTGGAAATCTGA
66 TAGCGCTTATGTAACGTAATAGGCAGT-GTCTTTTT-AAGCTGATAT--GACTTTGGAAATCCGA
**
1313406 CGATAACAAAATAGGTTAATTACTTA-ATTTGTTATTTGTATTATCAACATATTAGGTAACGCCT
127 CGATAACAAAATAGGTTAATTACTTATA-TTGTTATTAATATTATCAACATATTAGGTAACGCCT
* *
1313470 AAAATGTTACCACAGTTTAAGCTGATAGAGCCTTA
191 AAAATGTTACCAAAGTTTAAGCTGATAGAGCCCTA
* * * *
1313505 AAAATCCGACGATAACATAATCGGTTAATTACTGGAAACATTACCAAGCATAATAACATATTAGG
1 AAAATCCAACGATAACATAAACGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
*
1313570 TAGAGCTTATGTAACGTAATAGG
66 TAGCGCTTATGTAACGTAATAGG
1313593 TTGGCATTAT
Statistics
Matches: 276, Mismatches: 33, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
224 3 0.01
225 85 0.31
226 188 0.68
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (225 bp):
AAAATCCAACGATAACATAAACGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
TAGCGCTTATGTAACGTAATAGGCAGTGTCTTTTTAAGCTGATATGACTTTGGAAATCCGACGAT
AACAAAATAGGTTAATTACTTATATTGTTATTAATATTATCAACATATTAGGTAACGCCTAAAAT
GTTACCAAAGTTTAAGCTGATAGAGCCCTA
Found at i:1313879 original size:2 final size:2
Alignment explanation
Indices: 1313874--1313911 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1313864 ATAGAATATA
* *
1313874 TG TG TG TG TG TG TG TG TG AG TG AG TG -G TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1313912 TGATACATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.05, C:0.00, G:0.50, T:0.45
Consensus pattern (2 bp):
TG
Found at i:1317214 original size:54 final size:54
Alignment explanation
Indices: 1317132--1317235 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
1317122 TATTGCATCA
1317132 GACAATGTTAAACCAACCGAGGAATGCAATGAAGTACATATTGTTGATGAATCT
1 GACAATGTTAAACCAACCGAGGAATGCAATGAAGTACATATTGTTGATGAATCT
* *
1317186 GACAATGTTAAGCCAACTGAGGAATGCAATGAAGTACATATTGTTGATGA
1 GACAATGTTAAACCAACCGAGGAATGCAATGAAGTACATATTGTTGATGA
1317236 TTCTAATAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.26
Consensus pattern (54 bp):
GACAATGTTAAACCAACCGAGGAATGCAATGAAGTACATATTGTTGATGAATCT
Found at i:1320854 original size:66 final size:66
Alignment explanation
Indices: 1320784--1320908 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
1320774 CCATTATCCC
* *
1320784 CTTAAGTTCACCCCTCAATTCCACAACTTTTTTCATCACCCCATCAAATTTTCCACCCATCACCA
1 CTTAAGTTCACCCCTCAATTCCACAACTTCTTTCACCACCCCATCAAATTTTCCACCCATCACCA
1320849 T
66 T
* * * * * *
1320850 CTTAAGTTCACCTCTCAATTCCTCTACTTCTTTCACCACTCCATCTATTTTTCCACCCA
1 CTTAAGTTCACCCCTCAATTCCACAACTTCTTTCACCACCCCATCAAATTTTCCACCCA
1320909 CTTCCCCCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.24, C:0.39, G:0.02, T:0.35
Consensus pattern (66 bp):
CTTAAGTTCACCCCTCAATTCCACAACTTCTTTCACCACCCCATCAAATTTTCCACCCATCACCA
T
Found at i:1320920 original size:66 final size:65
Alignment explanation
Indices: 1320781--1320921 Score: 167
Period size: 66 Copynumber: 2.1 Consensus size: 65
1320771 CTCCCATTAT
* *
1320781 CCCCTTAAGTTCACCCCTCAATTCCACAACTTTTTTCATCACCCCATCAAATTTTCCACCCATCA
1 CCCCTTAAGTTCACCCCTCAATTCCACAACTTCTTTCACCACCCCATCAAATTTTCCACCCATCA
* * * * * * *
1320846 CCATCTTAAGTTCACCTCTCAATTCCTCTACTTCTTTCACCACTCCATCTATTTTTCCACCCACT
1 CC-CCTTAAGTTCACCCCTCAATTCCACAACTTCTTTCACCACCCCATCAAATTTTCCACCCA--
1320911 TC-
63 TCA
1320913 CCCCTTAAG
1 CCCCTTAAG
1320922 CCTCTGAATT
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
65 2 0.03
66 57 0.90
67 2 0.03
68 2 0.03
ACGTcount: A:0.23, C:0.41, G:0.02, T:0.34
Consensus pattern (65 bp):
CCCCTTAAGTTCACCCCTCAATTCCACAACTTCTTTCACCACCCCATCAAATTTTCCACCCATCA
Found at i:1322500 original size:162 final size:163
Alignment explanation
Indices: 1322177--1322513 Score: 536
Period size: 162 Copynumber: 2.1 Consensus size: 163
1322167 ATGAAACTAG
**
1322177 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATATTTATAAATTATCGATACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATATTTATAAAGCATCGATACTT
* * * *
1322242 TATAGGTGCTAGTATTGCTTTTCTTTTTAATTCCAAAAGTATTGATACTTATTTGAATTGTATGG
66 TATAGGTGCTAGTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCG
1322307 ATACCTTCAACATATCCGGTAGCTATTTACCGA
131 ATACCTTCAACATATCCGGTAGCTATTTACCGA
* *
1322340 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATTGATACATGTTTATAAAGCATCGATACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATATTTATAAAGCATCGATACTT
* * *
1322405 T-TAGGCT-CTATTATTTCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTTAATGGTATC
66 TATAGG-TGCTAGTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATC
1322468 GATACCTTCAACATATCCGGTAGC-ACTTTACCGA
130 GATACCTTCAACATATCCGGTAGCTA-TTTACCGA
1322502 TTTTGTCATATT
1 TTTTGTCATATT
1322514 AAACCCGGTT
Statistics
Matches: 161, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
161 1 0.01
162 97 0.60
163 63 0.39
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (163 bp):
TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATATTTATAAAGCATCGATACTT
TATAGGTGCTAGTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCG
ATACCTTCAACATATCCGGTAGCTATTTACCGA
Done.