Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008423.1 Hibiscus syriacus cultivar Beakdansim tig00111206_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: 1633377
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1058253 original size:60 final size:61
Alignment explanation
Indices: 1058086--1058253 Score: 187
Period size: 60 Copynumber: 2.8 Consensus size: 61
1058076 CGTATAGTTT
* * *
1058086 GGGATGAAATTGAAATATTAAAAAATTTTAAGTACCAATTTAGAAT-AAAAGTCATATTTTA
1 GGGATGAAATTGAAATATTTAAAAA-TTTAAGGACCAATTTAGAATGAAAAGTCATACTTTA
* * * * * *
1058147 GGGATGAAAATAAAATATTTAAAAATTTGAGGACTAATCTAGAATGATAA-TCATACTTTA
1 GGGATGAAATTGAAATATTTAAAAATTTAAGGACCAATTTAGAATGAAAAGTCATACTTTA
* * * * *
1058207 GGGATGAACTTGAAACATTTAAAAGTTTAAGGACCATTTTAAAATGA
1 GGGATGAAATTGAAATATTTAAAAATTTAAGGACCAATTTAGAATGA
1058254 GGGTCATACA
Statistics
Matches: 87, Mismatches: 19, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
60 62 0.71
61 25 0.29
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (61 bp):
GGGATGAAATTGAAATATTTAAAAATTTAAGGACCAATTTAGAATGAAAAGTCATACTTTA
Found at i:1059625 original size:47 final size:47
Alignment explanation
Indices: 1059573--1059681 Score: 218
Period size: 47 Copynumber: 2.3 Consensus size: 47
1059563 TAAAATTTAT
1059573 TAGTCTAAATATTTAACAGAAATATATAAGAGTCTGTCTAATATTAC
1 TAGTCTAAATATTTAACAGAAATATATAAGAGTCTGTCTAATATTAC
1059620 TAGTCTAAATATTTAACAGAAATATATAAGAGTCTGTCTAATATTAC
1 TAGTCTAAATATTTAACAGAAATATATAAGAGTCTGTCTAATATTAC
1059667 TAGTCTAAATATTTA
1 TAGTCTAAATATTTA
1059682 CAATTTATAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 62 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (47 bp):
TAGTCTAAATATTTAACAGAAATATATAAGAGTCTGTCTAATATTAC
Found at i:1060491 original size:29 final size:29
Alignment explanation
Indices: 1060433--1060627 Score: 177
Period size: 29 Copynumber: 6.6 Consensus size: 29
1060423 CTAACTTTAA
*
1060433 AAAATATATTTTATTTTTTATTCAACTTAT
1 AAAATATATTTTA-TTCTTATTCAACTTAT
* *
1060463 TAAATACATTTTATTCTTATTCAACTTAT
1 AAAATATATTTTATTCTTATTCAACTTAT
* * *
1060492 TAAATATATTTTATTTTTATTTTAACTTA-
1 AAAATATATTTTATTCTTA-TTCAACTTAT
* *
1060521 AAAATGTATTTTATTCTTATGCTAACTT-T
1 AAAATATATTTTATTCTTATTC-AACTTAT
1060550 AAAAATATATTTTATTCTTTATT-AACTTA-
1 -AAAATATATTTTATTC-TTATTCAACTTAT
* *
1060579 AAAATATATTTTGTTATTAACTT-AACTTCA-
1 AAAATATATTTTATTCTT-A-TTCAACTT-AT
1060609 AATAATATATTTTATTCTT
1 AA-AATATATTTTATTCTT
1060628 TTATAAACTT
Statistics
Matches: 138, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
27 2 0.01
28 16 0.12
29 65 0.47
30 37 0.27
31 18 0.13
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (29 bp):
AAAATATATTTTATTCTTATTCAACTTAT
Found at i:1060498 original size:59 final size:58
Alignment explanation
Indices: 1060414--1060639 Score: 224
Period size: 59 Copynumber: 3.8 Consensus size: 58
1060404 CTTAACTTAA
* * *
1060414 ATTCATATCCTAACTTTAAAAAATATATTTTATTTTTTATTCAACTTATTAAATACATTTT
1 ATTCTTATGCTAACTTT-AAAAATATATTTTATTTTTTATT-AACTTA-AAAATACATTTT
* * * **
1060475 ATTCTTATTC-AAC-TTATTAAATATATTTTATTTTTATTTTAACTTAAAAATGTATTTT
1 ATTCTTATGCTAACTTTA-AAAATATATTTTATTTTT-TATTAACTTAAAAATACATTTT
* *
1060533 ATTCTTATGCTAACTTTAAAAATATATTTTATTCTTTATTAACTTAAAAATATATTTT
1 ATTCTTATGCTAACTTTAAAAATATATTTTATTTTTTATTAACTTAAAAATACATTTT
* * * * *
1060591 GTTATTA-ACTTAACTTCAAATAATATATTTTATTCTTTTATAAACTTAA
1 ATTCTTATGC-TAACTTTAAA-AATATATTTTATT-TTTTATTAACTTAA
1060640 GATAATAATA
Statistics
Matches: 140, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
57 1 0.01
58 53 0.38
59 57 0.41
60 21 0.15
61 8 0.06
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.52
Consensus pattern (58 bp):
ATTCTTATGCTAACTTTAAAAATATATTTTATTTTTTATTAACTTAAAAATACATTTT
Found at i:1060730 original size:57 final size:56
Alignment explanation
Indices: 1060638--1060804 Score: 194
Period size: 57 Copynumber: 2.9 Consensus size: 56
1060628 TTATAAACTT
*
1060638 AAGATAATAATAAAATGCATTTTTAAGTCAATAAAAGAATAAAATATATATTTG-AAGTA
1 AAGATAATAATAAAAT--ATTTTTAAGT-TATAAAAGAATAAAATATAT-TTTGAAAGTA
*
1060697 AAGATAATAA-AAAATATTTTTTAAGTTGATAAAAGAATAAAATATATTTTGAAAGTT
1 AAGATAATAATAAAATA-TTTTTAAGTT-ATAAAAGAATAAAATATATTTTGAAAGTA
* * *
1060754 AAGATAAGAATTAAACATATTTTTAAGTTAAAATAAAAATAAAATATATTT
1 AAGATAATAA-TAAA-ATATTTTTAAGTTATAA-AAGAATAAAATATATTT
1060805 AATAAGTTTA
Statistics
Matches: 96, Mismatches: 5, Indels: 14
0.83 0.04 0.12
Matches are distributed among these distances:
56 5 0.05
57 41 0.43
58 8 0.08
59 39 0.41
60 3 0.03
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (56 bp):
AAGATAATAATAAAATATTTTTAAGTTATAAAAGAATAAAATATATTTTGAAAGTA
Found at i:1060738 original size:30 final size:29
Alignment explanation
Indices: 1060657--1060804 Score: 115
Period size: 30 Copynumber: 5.1 Consensus size: 29
1060647 ATAAAATGCA
*
1060657 TTTTTAAGTCAATAAAAGAATAAAATATAT
1 TTTTTAAGT-TATAAAAGAATAAAATATAT
* * * * *
1060687 ATTTGAAG-TA-AAGATAATAAAAAATAT
1 TTTTTAAGTTATAAAAGAATAAAATATAT
1060714 TTTTTAAGTTGATAAAAGAATAAAATATAT
1 TTTTTAAGTT-ATAAAAGAATAAAATATAT
** * *
1060744 TTTGAAAGTTA-AGATAAGAATTAAACATA-
1 TTTTTAAGTTATA-A-AAGAATAAAATATAT
* *
1060773 TTTTTAAGTTAAAATAAAAATAAAATATAT
1 TTTTTAAGTTATAA-AAGAATAAAATATAT
1060803 TT
1 TT
1060805 AATAAGTTTA
Statistics
Matches: 91, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
27 20 0.22
28 3 0.03
29 25 0.27
30 43 0.47
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.36
Consensus pattern (29 bp):
TTTTTAAGTTATAAAAGAATAAAATATAT
Found at i:1060812 original size:59 final size:54
Alignment explanation
Indices: 1060627--1060812 Score: 151
Period size: 59 Copynumber: 3.2 Consensus size: 54
1060617 ATTTTATTCT
* * *
1060627 TTTATAAACTTAAGATAATAATAAAATGCATTTTTAAGTCAATAAAAGAATAAAATATA
1 TTTAT-AAGTTAAGATAAGAA-AAAAT--ATTTTTAAGTTAA-AAAAGAATAAAATATA
* * *
1060686 TATT-TGAAGTAAAGATAATAAAAAATATTTTTTAAGTTGATAAAAGAATAAAATATA
1 T-TTAT-AAGTTAAGATAAGAAAAAATA-TTTTTAAGTT-AAAAAAGAATAAAATATA
*
1060743 TTT-TGAAAGTTAAGATAAGAATTAAACATATTTTTAAGTTAAAATAAAAATAAAATATA
1 TTTAT--AAGTTAAGATAAGAA--AAA-ATATTTTTAAGTTAAAA-AAGAATAAAATATA
1060802 TTTAATAAGTT
1 TTT-ATAAGTT
1060813 TAATAAAAAA
Statistics
Matches: 107, Mismatches: 10, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
56 4 0.04
57 39 0.36
58 9 0.08
59 49 0.46
60 5 0.05
61 1 0.01
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (54 bp):
TTTATAAGTTAAGATAAGAAAAAATATTTTTAAGTTAAAAAAGAATAAAATATA
Found at i:1060817 original size:29 final size:28
Alignment explanation
Indices: 1060675--1060821 Score: 88
Period size: 29 Copynumber: 5.1 Consensus size: 28
1060665 TCAATAAAAG
* *
1060675 AATAAAATATATATT-TGAAGTAAAGATAAT
1 AATAAAATATAT-TTAT-AAGTTAA-ATAAA
* *
1060705 AA-AAAATAT-TTTTTAAGTTGATAA-AAG
1 AATAAAATATATTTATAAGTT-A-AATAAA
*
1060732 AATAAAATATATTT-TGAAAGTTAAGATAAG
1 AATAAAATATATTTAT--AAGTTAA-ATAAA
* * *
1060762 AATTAAACATATTTTTAAGTTAAAATAAA
1 AATAAAATATATTTATAAGTT-AAATAAA
*
1060791 AATAAAATATATTTAATAAGTTTAATAAA
1 AATAAAATATATTT-ATAAGTTAAATAAA
1060820 AA
1 AA
1060822 AATTAAAATT
Statistics
Matches: 96, Mismatches: 9, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
27 10 0.10
28 13 0.14
29 42 0.44
30 30 0.31
31 1 0.01
ACGTcount: A:0.56, C:0.01, G:0.08, T:0.35
Consensus pattern (28 bp):
AATAAAATATATTTATAAGTTAAATAAA
Found at i:1060822 original size:30 final size:28
Alignment explanation
Indices: 1060646--1060822 Score: 92
Period size: 30 Copynumber: 6.1 Consensus size: 28
1060636 TTAAGATAAT
** * *
1060646 AATAAAATGCATTTTTAAGTCAATAAAA
1 AATAAAATATATTTATAAGTTAATAAAA
* *
1060674 GAATAAAATATATATT-TGAAG-TAA-AGAT
1 -AATAAAATATAT-TTAT-AAGTTAATAAAA
* * *
1060702 AATAAAAAATATTTTTTAAGTTGATAAAA
1 AATAAAATATA-TTTATAAGTTAATAAAA
* *
1060731 GAATAAAATATATTT-TGAAAGTTAAGATAAG
1 -AATAAAATATATTTAT--AAGTTAATA-AAA
* * * *
1060762 AATTAAACATATTTTTAAGTTAAAATAAA
1 AATAAAATATATTTATAAGTTAATA-AAA
1060791 AATAAAATATATTTAATAAGTTTAATAAAA
1 AATAAAATATATTT-ATAAG-TTAATAAAA
1060821 AA
1 AA
1060823 ATTAAAATTA
Statistics
Matches: 114, Mismatches: 21, Indels: 25
0.71 0.13 0.16
Matches are distributed among these distances:
27 15 0.13
28 7 0.06
29 41 0.36
30 43 0.38
31 8 0.07
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.34
Consensus pattern (28 bp):
AATAAAATATATTTATAAGTTAATAAAA
Found at i:1063885 original size:30 final size:32
Alignment explanation
Indices: 1063849--1063908 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1063839 TTAATTTAAA
*
1063849 TTATTAG-TAATA-ATTTATTTATT-TAATTTT
1 TTATTAGTTAATATATTAATTT-TTGTAATTTT
1063879 TTATTAGTTAATATATTAATTTTTGTAATT
1 TTATTAGTTAATATATTAATTTTTGTAATT
1063909 ATTAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 7 0.27
31 7 0.27
32 12 0.46
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (32 bp):
TTATTAGTTAATATATTAATTTTTGTAATTTT
Found at i:1063897 original size:23 final size:24
Alignment explanation
Indices: 1063871--1063915 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
1063861 ATTTATTTAT
1063871 TTAATTTTT-T-ATTAGTTAATATA
1 TTAATTTTTGTAATTA-TTAATATA
1063894 TTAATTTTTGTAATTATTAATA
1 TTAATTTTTGTAATTATTAATA
1063916 ATTTTAGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 7 0.35
25 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TTAATTTTTGTAATTATTAATATA
Found at i:1063902 original size:24 final size:23
Alignment explanation
Indices: 1063871--1063915 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1063861 ATTTATTTAT
*
1063871 TTAATTTT-TTATTAGTTAATATA
1 TTAATTTTGTAATTA-TTAATATA
1063894 TTAATTTTTGTAATTATTAATA
1 TTAA-TTTTGTAATTATTAATA
1063916 ATTTTAGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 10 0.53
25 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTAATTTTGTAATTATTAATATA
Found at i:1064110 original size:24 final size:25
Alignment explanation
Indices: 1064065--1064112 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
1064055 ATTTATTTAT
1064065 TTAATTTTTTATTATTAGTTAATATA
1 TTAATTTTTTA-TATTAGTTAATATA
1064091 TTAATTTTTGTA-ATTA-TTAATA
1 TTAATTTTT-TATATTAGTTAATA
1064113 ATTTTAGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.29
25 4 0.19
26 9 0.43
27 2 0.10
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (25 bp):
TTAATTTTTTATATTAGTTAATATA
Found at i:1071184 original size:28 final size:29
Alignment explanation
Indices: 1071132--1071189 Score: 68
Period size: 28 Copynumber: 2.0 Consensus size: 29
1071122 AATTTTTTAT
1071132 TTATTTTAATTTTAGCACATAATTT-TCA
1 TTATTTTAATTTTAGCACATAATTTGTCA
*
1071160 TTATTTTCAA-TTTAGC-CACTGATTTGTCA
1 TTATTTT-AATTTTAGCACA-TAATTTGTCA
1071189 T
1 T
1071190 ATTCCTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 2 0.08
28 18 0.69
29 6 0.23
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (29 bp):
TTATTTTAATTTTAGCACATAATTTGTCA
Found at i:1071550 original size:109 final size:110
Alignment explanation
Indices: 1071292--1071566 Score: 306
Period size: 109 Copynumber: 2.5 Consensus size: 110
1071282 TAATTTTATG
* * * * *
1071292 ACTTTGCGATTACCCAACCTGGGGTATGATCCACATTATCTACGGTCCGAGTAAAATTCGAACAC
1 ACTTTGCGGTGACCCAACCCGGGGTATGATCCACATTATTTACGGTCTGAGTAAAATTCGAACAC
* *
1071357 TAACCCACTAACTCTTTTATTTTTATTGTTCGAACTAATTTTACA
66 TAACCCACTAACTCTCTTATTTTTATTGTTCGAACTAATTCTACA
* ** * *
1071402 ACTTTGCGGTGA-CCAACCCAGGGTATGATCTGCAATATTTACGGTCTGAGTAAAATTCTAACAC
1 ACTTTGCGGTGACCCAACCCGGGGTATGATCCACATTATTTACGGTCTGAGTAAAATTCGAACAC
* * * **
1071466 TAATCCGCTAA-T-TCTTATTTTCTTTTGTTCGAA-TCAATTCTAGG
66 TAACCCACTAACTCTCTTATTTT-TATTGTTCGAACT-AATTCTACA
* * * * *
1071510 ACTTTGTGGTGACCCACCCCGGGGTATGATCCACATTATTTATGGCCTGGGTAAAAT
1 ACTTTGCGGTGACCCAACCCGGGGTATGATCCACATTATTTACGGTCTGAGTAAAAT
1071567 ATTAAAAATA
Statistics
Matches: 136, Mismatches: 26, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
107 9 0.07
108 28 0.21
109 89 0.65
110 10 0.07
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (110 bp):
ACTTTGCGGTGACCCAACCCGGGGTATGATCCACATTATTTACGGTCTGAGTAAAATTCGAACAC
TAACCCACTAACTCTCTTATTTTTATTGTTCGAACTAATTCTACA
Found at i:1071716 original size:14 final size:14
Alignment explanation
Indices: 1071697--1071733 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1071687 TTTGGTCCTT
*
1071697 TTAATTTTCAGCAC
1 TTAATTTTCAACAC
1071711 TTAATTTTCAACAC
1 TTAATTTTCAACAC
1071725 TTAATTTTC
1 TTAATTTTC
1071734 TGTAGTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.19, G:0.03, T:0.49
Consensus pattern (14 bp):
TTAATTTTCAACAC
Found at i:1074723 original size:65 final size:65
Alignment explanation
Indices: 1074590--1074749 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
1074580 TGCACTAAGA
* *
1074590 GTGCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * * *
1074654 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
1074717 AT
65 -G
* *
1074719 GTGCATTGATGCATGAAATGCATTTGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
1074750 CAATTTAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 28 0.34
65 52 0.63
66 3 0.04
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:1074788 original size:65 final size:63
Alignment explanation
Indices: 1074590--1074799 Score: 187
Period size: 65 Copynumber: 3.3 Consensus size: 63
1074580 TGCACTAAGA
* * * * *
1074590 GTGCATCGATGCATGAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCT
1 GTGCATTGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
1074653 G
63 G
* *
1074654 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATTGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
1074719 -
63 G
* * **
1074719 GTGCATTGATGCATGAAATGCATTTGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATTGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
1074782 TG
62 TG
*
1074784 GTGCATTGGTGCATCA
1 GTGCATTGATGCATCA
1074800 CTTTGATAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 48 0.39
65 63 0.51
66 5 0.04
67 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (63 bp):
GTGCATTGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:1077466 original size:23 final size:22
Alignment explanation
Indices: 1077436--1077515 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
1077426 GCATGACCCT
*
1077436 GTGCATCGATGTACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
1077458 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
1077480 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
1077502 ATGCATCGATGCAC
1 GTGCATCGATGCAC
1077516 TGTTAGCTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 15 0.33
22 16 0.35
23 15 0.33
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1077492 original size:21 final size:22
Alignment explanation
Indices: 1077437--1077515 Score: 88
Period size: 21 Copynumber: 3.6 Consensus size: 22
1077427 CATGACCCTG
* *
1077437 TGCATCGATGTACATTCAAGGCG
1 TGCATCGATGCACATTCAAGG-A
* * *
1077460 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
*
1077481 TGTATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
1077503 TGCATCGATGCAC
1 TGCATCGATGCAC
1077516 TGTTAGCTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 17 0.37
22 12 0.26
23 17 0.37
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:1077534 original size:42 final size:44
Alignment explanation
Indices: 1077440--1077534 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
1077430 GACCCTGTGC
* * * *
1077440 ATCGATGTACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGCATGCATCGATGCACCTTCATGCTGT
*
1077484 ATCGATGCACATTCAAGG-ATGCATCGATGCA-CTGTTA-GCTGT
1 ATCGATGCACATTCAAGGCATGCATCGATGCACCT-TCATGCTGT
1077526 ATCGATGCA
1 ATCGATGCA
1077535 TGAAGCACAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
42 15 0.33
43 13 0.29
44 17 0.38
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCATGCATCGATGCACCTTCATGCTGT
Found at i:1081314 original size:22 final size:21
Alignment explanation
Indices: 1081272--1081314 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1081262 GAGTTTATTT
*
1081272 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1081293 TCATTTTT-ATATTTTAAGAACA
1 TCATTTTTCA-ATTTTAA-AACA
1081315 ATTTCTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 14 0.74
22 4 0.21
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1083411 original size:64 final size:63
Alignment explanation
Indices: 1083233--1083411 Score: 177
Period size: 64 Copynumber: 2.8 Consensus size: 63
1083223 TTGAACCCTT
* * * *
1083233 AGTGCATCGGTGCACTAAGA-GTGCATCGATGCATCATGTTCATTCAATG-TTTCAAAATAGCAA
1 AGTGCATCGGTGCA-TGATATGTGCATCGATGCATAATG--CATTCGATGTTTTCAAAATAGCAA
*
1083296 G
63 C
* * * *
1083297 AGTGCATCGATGCATG-TCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCC
1 AGTGCATCGGTGCATGATAT-GTGCATCGATGCAT--AATGCATTCGATGTTTTCA-AAATAGCA
1083360 AC
62 AC
1083362 AGTGCATCGGTGCATGATATGTGCATCGATGCATGAATGCATTCGATGTT
1 AGTGCATCGGTGCATGATATGTGCATCGATGCAT-AATGCATTCGATGTT
1083412 CAATTTAATT
Statistics
Matches: 96, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
63 1 0.01
64 50 0.52
65 37 0.39
66 8 0.08
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (63 bp):
AGTGCATCGGTGCATGATATGTGCATCGATGCATAATGCATTCGATGTTTTCAAAATAGCAAC
Found at i:1091303 original size:26 final size:26
Alignment explanation
Indices: 1091274--1091350 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
1091264 CGAAGTACAT
*
1091274 TACACATAAGGTCGTTCCCACCATAG
1 TACACATAAGGTCGTTCCCACCATAA
*
1091300 TACACATAAGGTCATTCCCACCATAA
1 TACACATAAGGTCGTTCCCACCATAA
* *
1091326 TACACATAAGGTAGTGCCCACCATA
1 TACACATAAGGTCGTTCCCACCATA
1091351 TGCACCTAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (26 bp):
TACACATAAGGTCGTTCCCACCATAA
Found at i:1093395 original size:22 final size:22
Alignment explanation
Indices: 1093367--1093409 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1093357 TATTCTTGAG
1093367 ATAAACTATTTATTTATGAGGT
1 ATAAACTATTTATTTATGAGGT
1093389 ATAAACTATTTATTTATGAGG
1 ATAAACTATTTATTTATGAGG
1093410 CCCAAAATAT
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:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (22 bp):
ATAAACTATTTATTTATGAGGT
Found at i:1098922 original size:26 final size:26
Alignment explanation
Indices: 1098887--1098967 Score: 135
Period size: 26 Copynumber: 3.1 Consensus size: 26
1098877 GAAGTACATT
1098887 ACACATAAGGTCGTGCCCGCCATAGC
1 ACACATAAGGTCGTGCCCGCCATAGC
*
1098913 ACACATAAGGTCGTGCCCGCCATAGT
1 ACACATAAGGTCGTGCCCGCCATAGC
*
1098939 ACACATAAGGTCGTGCCCACCATATGC
1 ACACATAAGGTCGTGCCCGCCATA-GC
1098966 AC
1 AC
1098968 CTATTGTCCT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 48 0.94
27 3 0.06
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.17
Consensus pattern (26 bp):
ACACATAAGGTCGTGCCCGCCATAGC
Found at i:1099898 original size:30 final size:31
Alignment explanation
Indices: 1099840--1099908 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1099830 AACCATTCAC
*
1099840 AACTTTTCAAAAATTACCAAATTGGTCCCCT
1 AACTTTTCAAAAATTACCAAATTGGTCCCCA
*
1099871 AACTTTTCAAAAATTA-TAGAA-TGGTCCCCA
1 AACTTTTCAAAAATTACCA-AATTGGTCCCCA
*
1099901 AATTTTTC
1 AACTTTTC
1099909 TAAGGCTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (31 bp):
AACTTTTCAAAAATTACCAAATTGGTCCCCA
Found at i:1104639 original size:13 final size:13
Alignment explanation
Indices: 1104621--1104661 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
1104611 TTGAAATCGA
1104621 TACATTTTGCATT
1 TACATTTTGCATT
*
1104634 TACATTATGCATT
1 TACATTTTGCATT
1104647 TAACATTTTGCATT
1 T-ACATTTTGCATT
1104661 T
1 T
1104662 TGCACTTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (13 bp):
TACATTTTGCATT
Found at i:1104671 original size:27 final size:28
Alignment explanation
Indices: 1104622--1104677 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
1104612 TGAAATCGAT
*
1104622 ACATTTTGCATTTACATTATGCAT-TTA
1 ACATTTTGCATTTACACTATGCATATTA
*
1104649 ACATTTTGCATTTTGCACT-TGCATATTA
1 ACATTTTGCA-TTTACACTATGCATATTA
1104677 A
1 A
1104678 TTTTTGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (28 bp):
ACATTTTGCATTTACACTATGCATATTA
Found at i:1115815 original size:29 final size:30
Alignment explanation
Indices: 1115777--1115833 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
1115767 TTGACTAATC
*
1115777 ATTTCAACTAACTTGA-TTCTTTTTGTCTT
1 ATTTCAACTAACTTGATTTCCTTTTGTCTT
*
1115806 ATTTCTACTAACTTGATTTCCTTTTGTC
1 ATTTCAACTAACTTGATTTCCTTTTGTC
1115834 CGGTCTTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.54
Consensus pattern (30 bp):
ATTTCAACTAACTTGATTTCCTTTTGTCTT
Found at i:1117715 original size:5 final size:5
Alignment explanation
Indices: 1117705--1117787 Score: 73
Period size: 5 Copynumber: 16.2 Consensus size: 5
1117695 AAGAAGAGAG
* * *
1117705 AGAAA AGAAA A-TAA AGAAT AGAAA A-AAG AGAAA AGAAA AGAAA AGAATA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAA-A
1117754 AGAAAA AGAAGA AGAAA TA-AAA AGAAAA AGAAA A
1 AG-AAA AGAA-A AGAAA -AGAAA AG-AAA AGAAA A
1117788 CAGAAAGAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
4 7 0.11
5 38 0.59
6 17 0.27
7 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (5 bp):
AGAAA
Found at i:1117727 original size:28 final size:29
Alignment explanation
Indices: 1117703--1117801 Score: 91
Period size: 29 Copynumber: 3.4 Consensus size: 29
1117693 GGAAGAAGAG
*
1117703 AGAGAAAAGAAAA-TAAAGAATAGAAAAA
1 AGAGAAAAGAAAAGAAAAGAATAGAAAAA
1117731 AGAGAAAAGAAAAGAAAAGAATA-AGAAAA
1 AGAGAAAAGAAAAGAAAAGAATAGA-AAAA
* * *
1117760 AGA-AGAAGAAATA-AAAAGAAAAAGAAAAC
1 AGAGAAAAGAAA-AGAAAAG-AATAGAAAAA
1117789 AGA-AAGAAGAAAA
1 AGAGAA-AAGAAAA
1117802 CAGATCAAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
28 26 0.43
29 27 0.45
30 7 0.12
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (29 bp):
AGAGAAAAGAAAAGAAAAGAATAGAAAAA
Found at i:1117762 original size:6 final size:6
Alignment explanation
Indices: 1117727--1117801 Score: 68
Period size: 6 Copynumber: 12.7 Consensus size: 6
1117717 AAAGAATAGA
* * *
1117727 AAAAAG AGAAAAG -AAAAG -AAAAG AATAAG AAAAAG AAGAAG --AAAT
1 AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1117772 AAAAAG AAAAAG AAAACAG AAAGAAG AAAA
1 AAAAAG AAAAAG AAAA-AG AAA-AAG AAAA
1117802 CAGATCAAAC
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
4 2 0.04
5 10 0.18
6 29 0.51
7 15 0.26
8 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:1117770 original size:33 final size:33
Alignment explanation
Indices: 1117705--1117799 Score: 96
Period size: 33 Copynumber: 3.0 Consensus size: 33
1117695 AAGAAGAGAG
*
1117705 AGAAAAGAAAA-TAAAGAAT-AG-AAAA-AAG-
1 AGAAAAGAAAAGAAAAGAATAAGAAAAAGAAGA
1117733 AGAAAAGAAAAGAAAAGAATAAGAAAAAGAAGA
1 AGAAAAGAAAAGAAAAGAATAAGAAAAAGAAGA
* *
1117766 AGAAATA-AAAAGAAAAAGAA-AACAGAAAGAAGA
1 AGAAA-AGAAAAG-AAAAGAATAAGAAAAAGAAGA
1117799 A
1 A
1117800 AACAGATCAA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
28 11 0.19
29 7 0.12
30 2 0.04
31 4 0.07
32 3 0.05
33 22 0.39
34 8 0.14
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (33 bp):
AGAAAAGAAAAGAAAAGAATAAGAAAAAGAAGA
Found at i:1117784 original size:16 final size:16
Alignment explanation
Indices: 1117756--1117786 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1117746 AAAGAATAAG
*
1117756 AAAAAGAAGAAGAAAT
1 AAAAAGAAAAAGAAAT
1117772 AAAAAGAAAAAGAAA
1 AAAAAGAAAAAGAAA
1117787 ACAGAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAT
Found at i:1117801 original size:19 final size:18
Alignment explanation
Indices: 1117717--1117801 Score: 67
Period size: 17 Copynumber: 4.8 Consensus size: 18
1117707 AAAAGAAAAT
1117717 AAAGAATAGAA-AAAAGAGA
1 AAAGAA-AGAAGAAAAGA-A
1117736 AAAG-AA-AAGAAAAGAA
1 AAAGAAAGAAGAAAAGAA
*
1117752 TAAGAAA-AAGAAGAAGAA
1 AAAGAAAGAAGAA-AAGAA
1117770 ATAA-AAAG-A-AAAAGAA
1 A-AAGAAAGAAGAAAAGAA
1117786 AACAGAAAGAAGAAAA
1 AA-AGAAAGAAGAAAA
1117802 CAGATCAAAC
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
15 1 0.02
16 13 0.24
17 20 0.36
18 11 0.20
19 10 0.18
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (18 bp):
AAAGAAAGAAGAAAAGAA
Found at i:1122408 original size:32 final size:32
Alignment explanation
Indices: 1122359--1122447 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
1122349 AGGAATAATG
* *
1122359 GGGGCATCTTTGAAGATTCAACATCAAATATT
1 GGGGCATTTTTGGAGATTCAACATCAAATATT
**
1122391 GGGGCATTTTTGGAGATTCAACATTGAATATT
1 GGGGCATTTTTGGAGATTCAACATCAAATATT
* *
1122423 AGGGTATTTTTTGG-GATTCAACATC
1 GGGGCA-TTTTTGGAGATTCAACATC
1122448 TTGATGCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
32 42 0.86
33 7 0.14
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.36
Consensus pattern (32 bp):
GGGGCATTTTTGGAGATTCAACATCAAATATT
Found at i:1123143 original size:85 final size:85
Alignment explanation
Indices: 1122993--1123148 Score: 204
Period size: 85 Copynumber: 1.8 Consensus size: 85
1122983 TTAGAGGAAA
* * *
1122993 TTTACAGCATAGCTCAAGGCGAGAAAGGCTATCTTTCAACAAAAACCTTCGAGTTCAATTACATT
1 TTTACAACATAGCTCAAGACGAGAAAGGCTATCTGTCAACAAAAACCTTCGAGTTCAATTACATT
1123058 CAGCTCAAGGGCATGTCAAG
66 CAGCTCAAGGGCATGTCAAG
* * * * ** * * *
1123078 TTTACAACATAGTTTAAGACGAGAAGGGCTATCTGTCAACAAGAATTTTTGAGTTCGATTTCATT
1 TTTACAACATAGCTCAAGACGAGAAAGGCTATCTGTCAACAAAAACCTTCGAGTTCAATTACATT
1123143 CAGCTC
66 CAGCTC
1123149 GAAGATATAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
85 59 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (85 bp):
TTTACAACATAGCTCAAGACGAGAAAGGCTATCTGTCAACAAAAACCTTCGAGTTCAATTACATT
CAGCTCAAGGGCATGTCAAG
Found at i:1123453 original size:201 final size:201
Alignment explanation
Indices: 1123098--1123467 Score: 575
Period size: 201 Copynumber: 1.8 Consensus size: 201
1123088 AGTTTAAGAC
*
1123098 GAGAAGGGCTATCTGTCAACAAGAATTTTTGAGTTCGATTTCATTCAGCTCGAAGATATATCAAC
1 GAGAAGGGCTATCTGTCAACAAGAATTTTCGAGTTCGATTTCATTCAGCTCGAAGATATATCAAC
* * *
1123163 TGCATGGTAGCAATGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGTCTTTAAGTCAAGAAA
66 TGCATGGTAGCAACGAGGAACTACTTTCCGGTCGAATTTCAAACCGAGGTCTTTAAGTCAAGAAA
* * * *
1123228 AAGACTTGGGTTGGCTGTGATTTAGCCACAAGGAACTATATCCCACTTAAATTTATAGCATAGGT
131 AAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTATATCCCACTTAAATTTATAGCATAGGT
1123293 TAAGGT
196 TAAGGT
*
1123299 GAGAAGGGCTATCTGTTAACAAGAATTTTCGAGTTCG-TTCTCATTCAGCTCGAAGATATATCAA
1 GAGAAGGGCTATCTGTCAACAAGAATTTTCGAGTTCGATT-TCATTCAGCTCGAAGATATATCAA
* *
1123363 CTGCATGGTAAG-AACGAGGAATTACCTTT-CGGTCGAATTTCAAACCTAGGTCTTTAAGTCAAG
65 CTGCATGGT-AGCAACGAGGAACTA-CTTTCCGGTCGAATTTCAAACCGAGGTCTTTAAGTCAAG
* *
1123426 AAGAAGACCTAGGTTGGTTGCGATTTAGCAACAAGGAACTAT
128 AAAAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTAT
1123468 CTCTCAGTCA
Statistics
Matches: 153, Mismatches: 13, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
200 2 0.01
201 145 0.95
202 6 0.04
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.29
Consensus pattern (201 bp):
GAGAAGGGCTATCTGTCAACAAGAATTTTCGAGTTCGATTTCATTCAGCTCGAAGATATATCAAC
TGCATGGTAGCAACGAGGAACTACTTTCCGGTCGAATTTCAAACCGAGGTCTTTAAGTCAAGAAA
AAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTATATCCCACTTAAATTTATAGCATAGGT
TAAGGT
Found at i:1123515 original size:201 final size:201
Alignment explanation
Indices: 1123073--1123518 Score: 558
Period size: 201 Copynumber: 2.2 Consensus size: 201
1123063 CAAGGGCATG
* * * * *
1123073 TCAAGTTTACAACATAGTTTAA-GACGAGAAGGGCTATCTGTCAACAAGAATTTTTGAGTTCGAT
1 TCAAATTTACAACATAGCTCAAGGA-AAGAAGGGCTATCTGTCAACAAGAATTTTCGAGTTCGAT
* *
1123137 TTCATTCAGCTCGAAGATATATCAACTGCATGGTAGCAATGAGGAACTACTTTCCGGTTGAATTT
65 TTCATTCAGCTCGAAGATATATCAACTGCATGGTAGCAACGAGGAACTACTTTCCGGTCGAATTT
* * * * *
1123202 TAAACCGAGGTCTTTAAGTCAAGAAAAAGACTTGGGTTGGCTGTGATTTAGCCACAAGGAACTAT
130 CAAACCGAGGTCTTTAAGTCAAGAAAAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTAT
1123267 ATCCCAC
195 ATCCCAC
* * * * * ** *
1123274 TTAAATTTATAGCATAGGTTAAGGTGAGAAGGGCTATCTGTTAACAAGAATTTTCGAGTTCG-TT
1 TCAAATTTACAACATAGCTCAAGGAAAGAAGGGCTATCTGTCAACAAGAATTTTCGAGTTCGATT
*
1123338 CTCATTCAGCTCGAAGATATATCAACTGCATGGTAAG-AACGAGGAATTACCTTT-CGGTCGAAT
66 -TCATTCAGCTCGAAGATATATCAACTGCATGGT-AGCAACGAGGAACTA-CTTTCCGGTCGAAT
* * *
1123401 TTCAAACCTAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGTTGCGATTTAGCAACAAGGAACT
128 TTCAAACCGAGGTCTTTAAGTCAAGAAAAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACT
* * *
1123466 ATCTCTCAG
193 ATATCCCAC
* * *
1123475 TCAAATTTACAATATAGCTCAAGGAAATAAGGGTTATCTGTCAA
1 TCAAATTTACAACATAGCTCAAGGAAAGAAGGGCTATCTGTCAA
1123519 TAAAAACCTT
Statistics
Matches: 208, Mismatches: 33, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
200 2 0.01
201 199 0.96
202 7 0.03
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (201 bp):
TCAAATTTACAACATAGCTCAAGGAAAGAAGGGCTATCTGTCAACAAGAATTTTCGAGTTCGATT
TCATTCAGCTCGAAGATATATCAACTGCATGGTAGCAACGAGGAACTACTTTCCGGTCGAATTTC
AAACCGAGGTCTTTAAGTCAAGAAAAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTATA
TCCCAC
Found at i:1123573 original size:201 final size:201
Alignment explanation
Indices: 1123073--1123573 Score: 479
Period size: 201 Copynumber: 2.5 Consensus size: 201
1123063 CAAGGGCATG
* * * * * ** ** *
1123073 TCAAGTTTACAACATAGTTTAA-GACGAGAAGGGCTATCTGTCAACAAGAATTTTTGAGTTCGAT
1 TCAAATTTACAACATAGCTCAAGGA-AAGAAGGGCTATCTGTCAACAAAAACCTTCAAGTTCAAT
* * * * * *
1123137 TTCATTCAGCTCGAAGATATATCAACTGCATGGT-AGCAATGAGGAACTACTTTCCGGTTGAATT
65 CTCATTCAACTCGAAGACATATCAACTACATGGTAAG-AACGAGGAACTACTTTCCGGTCGAATT
* * * * *
1123201 TTAAACCGAGGTCTTTAAGTCAAGAAAAAGACTTGGGTTGGCTGTGATTTAGCCACAAGGAACTA
129 TCAAACCGAGGTCTTTAAGTCAAGAAAAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTA
1123266 TATCCCAC
194 TATCCCAC
* * * * * ** * * ** * **
1123274 TTAAATTTATAGCATAGGTTAAGGTGAGAAGGGCTATCTGTTAACAAGAATTTTCGAGTTCGTTC
1 TCAAATTTACAACATAGCTCAAGGAAAGAAGGGCTATCTGTCAACAAAAACCTTCAAGTTCAATC
* * * *
1123339 TCATTCAGCTCGAAGATATATCAACTGCATGGTAAGAACGAGGAATTACCTTT-CGGTCGAATTT
66 TCATTCAACTCGAAGACATATCAACTACATGGTAAGAACGAGGAACTA-CTTTCCGGTCGAATTT
* * *
1123403 CAAACCTAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGTTGCGATTTAGCAACAAGGAACTAT
130 CAAACCGAGGTCTTTAAGTCAAGAAAAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTAT
* * *
1123468 CTCTCAG
195 ATCCCAC
* * * *
1123475 TCAAATTTACAATATAGCTCAAGGAAATAAGGGTTATCTGTCAATAAAAACCTTCAAGTTCAATC
1 TCAAATTTACAACATAGCTCAAGGAAAGAAGGGCTATCTGTCAACAAAAACCTTCAAGTTCAATC
* *
1123540 TCATTCAACTCGAGGGCATATCAAAC-ACATGGTA
66 TCATTCAACTCGAAGACATATC-AACTACATGGTA
1123574 GCCACACATG
Statistics
Matches: 249, Mismatches: 47, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
201 239 0.96
202 10 0.04
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (201 bp):
TCAAATTTACAACATAGCTCAAGGAAAGAAGGGCTATCTGTCAACAAAAACCTTCAAGTTCAATC
TCATTCAACTCGAAGACATATCAACTACATGGTAAGAACGAGGAACTACTTTCCGGTCGAATTTC
AAACCGAGGTCTTTAAGTCAAGAAAAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTATA
TCCCAC
Found at i:1132689 original size:22 final size:21
Alignment explanation
Indices: 1132665--1132704 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1132655 GAGAAATTAT
1132665 TTTTAAAATAT-AAAAATGATG
1 TTTTAAAAT-TGAAAAATGATG
1132686 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
1132705 AAACAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATG
Found at i:1136541 original size:20 final size:20
Alignment explanation
Indices: 1136516--1136577 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 20
1136506 TTTTGGTGCA
1136516 GAGGGAATCC-ATCCCCCCTT
1 GAGGGAA-CCGATCCCCCCTT
*
1136536 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCCCTT
1136557 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGA-TCCCCCC
1136578 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 2 0.06
20 8 0.22
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.37, G:0.24, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:1136553 original size:21 final size:23
Alignment explanation
Indices: 1136527--1136577 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1136517 AGGGAATCCA
1136527 TCCCCCCTTG-A-GGGAACCGAT
1 TCCCCCCTTGAAGGGGAACCGAT
*
1136548 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCTTGAAGGGGAACCGAT
1136571 TCCCCCC
1 TCCCCCC
1136578 ACAGGGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 1 0.04
23 16 0.62
ACGTcount: A:0.18, C:0.41, G:0.22, T:0.20
Consensus pattern (23 bp):
TCCCCCCTTGAAGGGGAACCGAT
Found at i:1136603 original size:20 final size:21
Alignment explanation
Indices: 1136559--1136598 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1136549 CCCCCTTTGA
*
1136559 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1136580 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1136599 TAGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1139184 original size:22 final size:23
Alignment explanation
Indices: 1139159--1139202 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1139149 AATTAAGTTT
1139159 TAATATTA-AAACAATTTCAAAA
1 TAATATTACAAACAATTTCAAAA
* **
1139181 TAATTTTACAAAGTATTTCAAA
1 TAATATTACAAACAATTTCAAA
1139203 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATATTACAAACAATTTCAAAA
Found at i:1139648 original size:18 final size:18
Alignment explanation
Indices: 1139627--1139663 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1139617 TTTCAAGCCT
*
1139627 ATTTTTCATTCAATATTC
1 ATTTTGCATTCAATATTC
1139645 ATTTTGCATTCAATATTC
1 ATTTTGCATTCAATATTC
1139663 A
1 A
1139664 ATGCTCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTTGCATTCAATATTC
Found at i:1148053 original size:31 final size:30
Alignment explanation
Indices: 1148007--1148109 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 30
1147997 TTAAACTTTT
*
1148007 AAATTTATAAAAATGATCATTAAATTTTATCA
1 AAATTT-TACAAATGATCATTAAA-TTTATCA
*
1148039 AAATTTTACAAATGACCATTAAACTTTATC-
1 AAATTTTACAAATGATCATTAAA-TTTATCA
* * *
1148069 GAATTATTATC-AATGGTCATTAAATATATCA
1 AAATT-TTA-CAAATGATCATTAAATTTATCA
*
1148100 AATTTTTACA
1 AAATTTTACA
1148110 CTTATTATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
29 1 0.02
30 12 0.21
31 38 0.66
32 7 0.12
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.40
Consensus pattern (30 bp):
AAATTTTACAAATGATCATTAAATTTATCA
Found at i:1150096 original size:15 final size:16
Alignment explanation
Indices: 1150066--1150099 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1150056 TTCAGGGACT
1150066 AAATATCAAAGATCTA
1 AAATATCAAAGATCTA
*
1150082 AAATATC-AAGTTCTA
1 AAATATCAAAGATCTA
1150097 AAA
1 AAA
1150100 GATTTAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (16 bp):
AAATATCAAAGATCTA
Found at i:1150462 original size:28 final size:31
Alignment explanation
Indices: 1150431--1150488 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1150421 ACAAATAATA
1150431 ATAAA-AA-ATAAA-AACAACA-AAAAATAAC
1 ATAAATAACATAAATAACAA-ATAAAAATAAC
1150459 ATAAATAACATAAATAACAAATAAAAATAA
1 ATAAATAACATAAATAACAAATAAAAATAA
1150489 AAAAAGTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 5 0.19
29 2 0.08
30 6 0.23
31 13 0.50
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.16
Consensus pattern (31 bp):
ATAAATAACATAAATAACAAATAAAAATAAC
Found at i:1150464 original size:9 final size:9
Alignment explanation
Indices: 1150452--1150477 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1150442 AAACAACAAA
1150452 AAATAACAT
1 AAATAACAT
1150461 AAATAACAT
1 AAATAACAT
1150470 AAATAACA
1 AAATAACA
1150478 AATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAACAT
Found at i:1150486 original size:13 final size:13
Alignment explanation
Indices: 1150420--1150488 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
1150410 AAATTAAAGG
*
1150420 AACAAATAATAAT
1 AACAAATAAAAAT
* *
1150433 AAAAAATAAAAAC
1 AACAAATAAAAAT
*
1150446 AACAAAAAATAACAT
1 AACAAATAA-AA-AT
* *
1150461 AA-ATAACATAAAT
1 AACA-AATAAAAAT
1150474 AACAAATAAAAAT
1 AACAAATAAAAAT
1150487 AA
1 AA
1150489 AAAAAGTACA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
13 30 0.71
14 6 0.14
15 6 0.14
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (13 bp):
AACAAATAAAAAT
Found at i:1150900 original size:2 final size:2
Alignment explanation
Indices: 1150893--1150928 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1150883 TGATTCTTCA
1150893 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
1150929 CTTTTTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1159897 original size:3 final size:3
Alignment explanation
Indices: 1159889--1159964 Score: 138
Period size: 3 Copynumber: 26.0 Consensus size: 3
1159879 GATATCATTC
1159889 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1159936 TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1159965 AAATAATTAC
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.06
3 67 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1160013 original size:21 final size:21
Alignment explanation
Indices: 1159988--1160033 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1159978 TAAATACATG
1159988 CCCAATTTATAAAGAACCCGA
1 CCCAATTTATAAAGAACCCGA
1160009 CCCAATTTATAAAGAACCCGA
1 CCCAATTTATAAAGAACCCGA
1160030 CCCA
1 CCCA
1160034 GTTACACGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.41, C:0.33, G:0.09, T:0.17
Consensus pattern (21 bp):
CCCAATTTATAAAGAACCCGA
Found at i:1169772 original size:55 final size:55
Alignment explanation
Indices: 1169684--1169792 Score: 155
Period size: 55 Copynumber: 2.0 Consensus size: 55
1169674 TCAATGATTG
* **
1169684 AGAAATCTGAGCAGAAGTCACAGGAAATTATGAATGTGTTATAAAATGTTTTACT
1 AGAAATCTGAGCAGAAGCCACAGGAAAGAATGAATGTGTTATAAAATGTTTTACT
* * * *
1169739 AGAAATCTGGGCAGAAGCCACATGAAAGAATGAATGTGTTGTCAAATGTTTTAC
1 AGAAATCTGAGCAGAAGCCACAGGAAAGAATGAATGTGTTATAAAATGTTTTAC
1169793 GAACCAGTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (55 bp):
AGAAATCTGAGCAGAAGCCACAGGAAAGAATGAATGTGTTATAAAATGTTTTACT
Found at i:1175461 original size:34 final size:32
Alignment explanation
Indices: 1175397--1175466 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1175387 CCTTACAAAC
* *
1175397 TCCCTAGTTTTTCCGGGATAAACTATAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
* *
1175429 TCCCTAGCTTTTACACGGGATTAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
1175463 TCCC
1 TCCC
1175467 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:1175977 original size:24 final size:23
Alignment explanation
Indices: 1175936--1175980 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1175926 GATACCCCCT
*
1175936 GGGGGGAATCTGTTCCCCTGGGG
1 GGGGGGAATCTGTCCCCCTGGGG
1175959 GGGGGGAATCTGTACCCCCTGG
1 GGGGGGAATCTGT-CCCCCTGG
1175981 ACAATCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.11, C:0.24, G:0.44, T:0.20
Consensus pattern (23 bp):
GGGGGGAATCTGTCCCCCTGGGG
Found at i:1179011 original size:34 final size:32
Alignment explanation
Indices: 1178951--1179020 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1178941 CCTTACAAAC
*
1178951 TCCCTAGTTTTTCCGGGATAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
* *
1178983 TCCCTAGATTTTACACGGGATTAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
1179017 TCCC
1 TCCC
1179021 CTTTAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:1179330 original size:21 final size:21
Alignment explanation
Indices: 1179304--1179345 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1179294 CGGAATGGGG
*
1179304 GGAATCGGTACCCCTTCATAA
1 GGAATCGATACCCCTTCATAA
*
1179325 GGAATCGATACCCCTTTATAA
1 GGAATCGATACCCCTTCATAA
1179346 TATTCAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (21 bp):
GGAATCGATACCCCTTCATAA
Found at i:1180558 original size:23 final size:23
Alignment explanation
Indices: 1180526--1180611 Score: 102
Period size: 23 Copynumber: 3.8 Consensus size: 23
1180516 TTAGTGCAGA
*
1180526 GGGAATCGATACCCCCCTTGAAG
1 GGGAACCGATACCCCCCTTGAAG
* *
1180549 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCCCTTGAAG
* *
1180572 GGGAACCGAT-TCCCCCTTGTAG
1 GGGAACCGATACCCCCCTTGAAG
* *
1180594 GGGAATCGATATCCCCCT
1 GGGAACCGATACCCCCCT
1180612 GGGGTACTGG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
22 18 0.33
23 37 0.67
ACGTcount: A:0.22, C:0.31, G:0.26, T:0.21
Consensus pattern (23 bp):
GGGAACCGATACCCCCCTTGAAG
Found at i:1180563 original size:22 final size:22
Alignment explanation
Indices: 1180538--1180611 Score: 112
Period size: 23 Copynumber: 3.3 Consensus size: 22
1180528 GAATCGATAC
1180538 CCCCCTTGAAGGGGAACCGATT
1 CCCCCTTGAAGGGGAACCGATT
1180560 CCCCCTTTGAAGGGGAACCGATT
1 CCCCC-TTGAAGGGGAACCGATT
* *
1180583 CCCCCTTGTAGGGGAATCGATAT
1 CCCCCTTGAAGGGGAACCGAT-T
1180606 CCCCCT
1 CCCCCT
1180612 GGGGTACTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
22 19 0.40
23 29 0.60
ACGTcount: A:0.20, C:0.34, G:0.24, T:0.22
Consensus pattern (22 bp):
CCCCCTTGAAGGGGAACCGATT
Found at i:1184272 original size:22 final size:20
Alignment explanation
Indices: 1184222--1184276 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 20
1184212 ATATCTACAT
*
1184222 TCTTCAATGATGATAGATTC
1 TCTTCAAAGATGATAGATTC
1184242 TCTTCAAAGATGATAGATTC
1 TCTTCAAAGATGATAGATTC
1184262 TCTTTTCAAAGATGA
1 TC--TTCAAAGATGA
1184277 ACGCTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 21 0.66
22 11 0.34
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
TCTTCAAAGATGATAGATTC
Found at i:1184980 original size:45 final size:47
Alignment explanation
Indices: 1184916--1185092 Score: 254
Period size: 45 Copynumber: 3.9 Consensus size: 47
1184906 CCCACATCTG
1184916 TAAGACCTACAGTGCATGATGTTTTC-AAAA-CCTTCGGGTCATCCA
1 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGTCATCCA
* **
1184961 TAAGACCTATAGTGCATGATGTTTTCAAAAAGCCTTCGGGTCATCTG
1 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGTCATCCA
* * *
1185008 TAAGCCCTTCAGTGCATGATGCTTTC-AAAA-CCTTCGGGTCATCCA
1 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGTCATCCA
* *
1185053 TAAGACCTACAGTGTAGGATGTTTTCAAAAAGCCTTCGGG
1 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGG
1185093 AGCTTTTTGA
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
45 59 0.52
46 12 0.11
47 43 0.38
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (47 bp):
TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGTCATCCA
Found at i:1185074 original size:92 final size:92
Alignment explanation
Indices: 1184910--1185092 Score: 312
Period size: 92 Copynumber: 2.0 Consensus size: 92
1184900 CTATTTCCCA
* *
1184910 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTATAGTG
1 CATCTGTAAGACCTACAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
*
1184975 CATGATGTTTTCAAAAAGCCTTCGGGT
66 CAGGATGTTTTCAAAAAGCCTTCGGGT
* *
1185002 CATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
1 CATCTGTAAGACCTACAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
*
1185067 TAGGATGTTTTCAAAAAGCCTTCGGG
66 CAGGATGTTTTCAAAAAGCCTTCGGG
1185093 AGCTTTTTGA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 85 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (92 bp):
CATCTGTAAGACCTACAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
CAGGATGTTTTCAAAAAGCCTTCGGGT
Found at i:1185149 original size:45 final size:45
Alignment explanation
Indices: 1185100--1185258 Score: 201
Period size: 45 Copynumber: 3.5 Consensus size: 45
1185090 GGGAGCTTTT
*
1185100 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAATGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAATGCA
* * *
1185145 TGATGTTTTCAAAACCTTCAGGTCAGCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAATGCA
* * ** * *
1185190 TGATGCTTTCAAAACTTTCGGGTCATCCATAAGACCTACAATGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAATGCA
*
1185235 GGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
1185259 AGCTTTTTGG
Statistics
Matches: 96, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
45 85 0.89
46 4 0.04
47 7 0.07
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAATGCA
Found at i:1185203 original size:121 final size:122
Alignment explanation
Indices: 1184977--1185203 Score: 339
Period size: 121 Copynumber: 1.9 Consensus size: 122
1184967 CTATAGTGCA
*
1184977 TGATGTTTTCAAAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTT
1 TGATGTTTTC-AAAAGCCTTCGGGTCATCTGTAAGCCCTTCAATGCATGATGCTTTCAAAACCTT
* * * *
1185042 CGGGTCATCCATAAGACCTACAGTGTAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
65 CAGGTCAGCCATAAGACCTACAGTGCAGGATGCTTTCAAAAAGCCTTCGGGAGCTTTT
*
1185100 TGATGTTTTC-AAAGCCTTCGGGTCATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAACCTTC
1 TGATGTTTTCAAAAGCCTTCGGGTCATCTGTAAGCCCTTCAATGCATGATGCTTTCAAAACCTTC
** * * *
1185164 AGGTCAGCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAA
66 AGGTCAGCCATAAGACCTACAGTGCAGGATGCTTTCAAAA
1185204 CTTTCGGGTC
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
121 83 0.89
123 10 0.11
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.32
Consensus pattern (122 bp):
TGATGTTTTCAAAAGCCTTCGGGTCATCTGTAAGCCCTTCAATGCATGATGCTTTCAAAACCTTC
AGGTCAGCCATAAGACCTACAGTGCAGGATGCTTTCAAAAAGCCTTCGGGAGCTTTT
Found at i:1185215 original size:166 final size:166
Alignment explanation
Indices: 1184932--1185435 Score: 776
Period size: 166 Copynumber: 3.0 Consensus size: 166
1184922 CTACAGTGCA
* ** *
1184932 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTAT-AGTGCATGATGTTTTCAAAAAGCCT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCT-TCAGTGCATGATGTTTTC-AAAA-CCT
*
1184996 TCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCT
63 TCAGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCT
*
1185061 ACAGTGTAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
128 ACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
*
1185100 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAACCTTCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCA
* *
1185165 GGTCAGCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACTTTCGGGTCATCCATAAGACCTACA
66 GGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTACA
*
1185230 ATGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
131 GTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
* * ** * *
1185266 TGGTATTTTCAAAGCCTTCGTTTCATCTGTAAGCCCTTCAGTGCATAATGTTTTTAAAACCTTCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCA
** * * *
1185331 GGTCATCTGTAAGATCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCGATAAGACCTACA
66 GGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTACA
*
1185396 GTGCAGGATGTTTTCAAAAAGCCTTTGGGAGCTTTT
131 GTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
1185432 TGAT
1 TGAT
1185436 ATTTAAAACG
Statistics
Matches: 308, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
166 255 0.83
167 5 0.02
168 48 0.16
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (166 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCA
GGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTACA
GTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
Found at i:1185275 original size:121 final size:119
Alignment explanation
Indices: 1185150--1185377 Score: 305
Period size: 121 Copynumber: 1.9 Consensus size: 119
1185140 ATGCATGATG
* * *
1185150 TTTTCAAAACCTTCAG-GTCAGCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACTTTCGGGTC
1 TTTTCAAAACCTTC-GTGTCAGCTGTAAGCCCTTCAGTGCATAATGCTTTCAAAACCTTCAGGTC
1185214 ATCCATAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGGTA
65 ATCCATAAGACCTACAATGCAGGATGTTTTC-AAAA-CCTTCGGGAGCTTTTTGGTA
* * * * *
1185271 TTTTCAAAGCCTTCGTTTCATCTGTAAGCCCTTCAGTGCATAATGTTTTTAAAACCTTCAGGTCA
1 TTTTCAAAACCTTCGTGTCAGCTGTAAGCCCTTCAGTGCATAATGCTTTCAAAACCTTCAGGTCA
** * * *
1185336 TCTGTAAGATCTACAGTGCATGATGTTTTCAAAACCTTCGGG
66 TCCATAAGACCTACAATGCAGGATGTTTTCAAAACCTTCGGG
1185378 TCATCGATAA
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
119 8 0.09
120 5 0.05
121 80 0.86
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (119 bp):
TTTTCAAAACCTTCGTGTCAGCTGTAAGCCCTTCAGTGCATAATGCTTTCAAAACCTTCAGGTCA
TCCATAAGACCTACAATGCAGGATGTTTTCAAAACCTTCGGGAGCTTTTTGGTA
Found at i:1185329 original size:45 final size:44
Alignment explanation
Indices: 1185271--1185414 Score: 164
Period size: 45 Copynumber: 3.2 Consensus size: 44
1185261 CTTTTTGGTA
* * * *
1185271 TTTTCAAAGCCTTCGTTTCATCTGTAAGCCCTTCAGTGCATAATG
1 TTTTCAAAACCTTCG-GTCATCTGTAAGACCTACAGTGCATAATG
* * *
1185316 TTTTTAAAACCTTCAGGTCATCTGTAAGATCTACAGTGCATGATG
1 TTTTCAAAACCTTC-GGTCATCTGTAAGACCTACAGTGCATAATG
**
1185361 TTTTCAAAACCTTCGGGTCATC-GATAAGACCTACAGTGCAGGATG
1 TTTTCAAAACCTTC-GGTCATCTG-TAAGACCTACAGTGCATAATG
1185406 TTTTCAAAA
1 TTTTCAAAA
1185415 AGCCTTTGGG
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
44 1 0.01
45 84 0.98
46 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (44 bp):
TTTTCAAAACCTTCGGTCATCTGTAAGACCTACAGTGCATAATG
Found at i:1185656 original size:3 final size:3
Alignment explanation
Indices: 1185648--1185699 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
1185638 TTTTTCATTC
1185648 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1185694 TAT TAT
1 TAT TAT
1185700 AAATAATTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 43 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1185678 original size:23 final size:23
Alignment explanation
Indices: 1185648--1185699 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1185638 TTTTTCATTC
1185648 TATTATTATTATTATTATTATAT
1 TATTATTATTATTATTATTATAT
*
1185671 TATTATTATTATTATTATTATTT
1 TATTATTATTATTATTATTATAT
1185694 TATTAT
1 TATTAT
1185700 AAATAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTATTATTATTATTATTATAT
Found at i:1190063 original size:7 final size:7
Alignment explanation
Indices: 1190051--1190114 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
1190041 TCTATTATTC
1190051 TTTTTAT
1 TTTTTAT
1190058 TTTTTAT
1 TTTTTAT
1190065 TTTTTAT
1 TTTTTAT
**
1190072 TTTTTCC
1 TTTTTAT
*
1190079 TTTTAAT
1 TTTTTAT
*
1190086 TTATTTAA
1 TT-TTTAT
*
1190094 TATTTAT
1 TTTTTAT
*
1190101 TTATTAT
1 TTTTTAT
*
1190108 TTCTTAT
1 TTTTTAT
1190115 ATAACATTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
7 40 0.91
8 4 0.09
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTAT
Found at i:1193173 original size:15 final size:15
Alignment explanation
Indices: 1193139--1193181 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1193129 AAAAGAGAAA
1193139 AGAATAAAAAA-AAA-
1 AGAA-AAAAAACAAAG
*
1193153 AGAAAAAAATCAAAG
1 AGAAAAAAAACAAAG
1193168 AGAAAAAAAACAAA
1 AGAAAAAAAACAAA
1193182 AACAAAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 13 0.52
ACGTcount: A:0.81, C:0.05, G:0.09, T:0.05
Consensus pattern (15 bp):
AGAAAAAAAACAAAG
Found at i:1193173 original size:34 final size:34
Alignment explanation
Indices: 1193130--1193194 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
1193120 ATCAGAACAA
1193130 AAAGAGAAAAGAATAA-AAAAA-AAAGAAAAAAATC
1 AAAGAGAAAA-AA-AACAAAAACAAAGAAAAAAATC
*
1193164 AAAGAGAAAAAAAACAAAAACAAAGGAAAAA
1 AAAGAGAAAAAAAACAAAAACAAAGAAAAAA
1193195 GTGAAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 2 0.07
33 7 0.25
34 19 0.68
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.03
Consensus pattern (34 bp):
AAAGAGAAAAAAAACAAAAACAAAGAAAAAAATC
Found at i:1194829 original size:44 final size:44
Alignment explanation
Indices: 1194780--1194882 Score: 197
Period size: 44 Copynumber: 2.3 Consensus size: 44
1194770 ACTTTCCTAT
*
1194780 TAAGGGGAGTCATCCAAAGATCATCTCACTTGGCTTAAACCCAC
1 TAAGGGGAGCCATCCAAAGATCATCTCACTTGGCTTAAACCCAC
1194824 TAAGGGGAGCCATCCAAAGATCATCTCACTTGGCTTAAACCCAC
1 TAAGGGGAGCCATCCAAAGATCATCTCACTTGGCTTAAACCCAC
1194868 TAAGGGGAGCCATCC
1 TAAGGGGAGCCATCC
1194883 TTCACTTAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (44 bp):
TAAGGGGAGCCATCCAAAGATCATCTCACTTGGCTTAAACCCAC
Found at i:1194829 original size:77 final size:77
Alignment explanation
Indices: 1194684--1194831 Score: 201
Period size: 77 Copynumber: 1.9 Consensus size: 77
1194674 CTGAAGAACA
* * * * *
1194684 TCTCACGTGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGATCCGTGA
1 TCTCACATGACTTTCCCATGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAAACCCCTGA
1194749 AGGGGAACCACC
66 AGGGGAACCACC
* *
1194761 TCTCACATGACTTTCCTATTAAGGGGAGTCATCCAAAGATCATCTCACTTGGCTT-AAACCCACT
1 TCTCACATGACTTTCCCATGAAGGGGAGTCATCCAAAGATCATCTCACTTGG-TTCAAACCC-CT
1194825 -AAGGGGA
64 GAAGGGGA
1194832 GCCATCCAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
77 59 0.95
78 3 0.05
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (77 bp):
TCTCACATGACTTTCCCATGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAAACCCCTGA
AGGGGAACCACC
Found at i:1195249 original size:201 final size:201
Alignment explanation
Indices: 1194904--1195343 Score: 585
Period size: 201 Copynumber: 2.2 Consensus size: 201
1194894 GAACTATGCG
* * ** *
1194904 CAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAATGAGAACTTTCAAGTTCGATTTCATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATTTGTCAACAAGAACTTTCAAGTTCGATTTCATTCAAC
* * *
1194969 TCGAAGACATATCAACCACATGGTAGTAGTGAGGAACTACTTCCCAATTGAATTTTAAATCGAGG
66 TCAAAGACATATCAACCACATGGTAGTAGCGAGGAACTACTTCCCAATTGAATTTTAAACCGAGG
* ** *
1195034 TCTTTAAGTCAAGAAGAAGACCTGGGTTGGATGTGATTTAGCAACAAGGAACTATATCCCAGTCA
131 TCTTTAAGTCAAGAAGAAGACCTAGGTTGGATACGATTTAGCAACAAGGAACAATATCCCAGTCA
1195099 AATTTA
196 AATTTA
* * * * *
1195105 CAGCATAACTTAAGGCGATAAGGGCTATTTGTCAACAAGAATTTTCGAGTTCGATTTCATTCAAC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATTTGTCAACAAGAACTTTCAAGTTCGATTTCATTCAAC
** ** * **
1195170 TCAAAGATGTATCAACTGCATTGTAGTAGCGAGGAACTACCTT-CCGGTTGAATTTTAAACCGAG
66 TCAAAGACATATCAACCACATGGTAGTAGCGAGGAACTA-CTTCCCAATTGAATTTTAAACCGAG
* * * *
1195234 GTCTTTAAGTCAAGAAGAAGACCTAGGTTGGTTACGATTTAGTAACAAGGAACAATCTCTCAGTC
130 GTCTTTAAGTCAAGAAGAAGACCTAGGTTGGATACGATTTAGCAACAAGGAACAATATCCCAGTC
1195299 AAATTTA
195 AAATTTA
* * *
1195306 CAGAATAGCTCAAGGCGAGAAGGGTTATTTATCAACAA
1 CAGCATAGCTCAAGGCGAGAAGGGCTATTTGTCAACAA
1195344 AATCCTTTGA
Statistics
Matches: 204, Mismatches: 34, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
201 201 0.99
202 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (201 bp):
CAGCATAGCTCAAGGCGAGAAGGGCTATTTGTCAACAAGAACTTTCAAGTTCGATTTCATTCAAC
TCAAAGACATATCAACCACATGGTAGTAGCGAGGAACTACTTCCCAATTGAATTTTAAACCGAGG
TCTTTAAGTCAAGAAGAAGACCTAGGTTGGATACGATTTAGCAACAAGGAACAATATCCCAGTCA
AATTTA
Found at i:1195939 original size:66 final size:65
Alignment explanation
Indices: 1195769--1195946 Score: 270
Period size: 65 Copynumber: 2.7 Consensus size: 65
1195759 CGTAACTTAC
*
1195769 ACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTCGGTGAAATTTAT
1 ACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTCGGTGAAATATAT
* *
1195834 ACAAGATTGGATTTCAACTTCGCAATGAAGGATATCCAACTCAAAGCCAAATT-GGTGAAGCA-A
1 ACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCC-AATTCGGTGAA--ATA
1195897 TAT
63 TAT
* *
1195900 TCAAGATTGGATTTCAACTTCACAACGAAGGATAACCAACTCAAAGC
1 ACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGC
1195947 TCAACTTTAC
Statistics
Matches: 103, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
65 52 0.50
66 50 0.49
67 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (65 bp):
ACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTCGGTGAAATATAT
Found at i:1197255 original size:18 final size:18
Alignment explanation
Indices: 1197232--1197272 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1197222 TTTATTCAGA
1197232 TTTTTTAAATTTTTTTAT
1 TTTTTTAAATTTTTTTAT
**
1197250 TTTTTTATTTTTTTTTAT
1 TTTTTTAAATTTTTTTAT
1197268 TTTTT
1 TTTTT
1197273 CCATTTAATT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTAAATTTTTTTAT
Found at i:1197267 original size:10 final size:10
Alignment explanation
Indices: 1197241--1197272 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1197231 ATTTTTTAAA
1197241 TTTTTTTA--
1 TTTTTTTATT
1197249 TTTTTTTATT
1 TTTTTTTATT
1197259 TTTTTTTATT
1 TTTTTTTATT
1197269 TTTT
1 TTTT
1197273 CCATTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:1202596 original size:18 final size:17
Alignment explanation
Indices: 1202565--1202600 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1202555 GTTCTTATTA
*
1202565 TTATTTTTATTAATTTT
1 TTATTTTTAATAATTTT
1202582 TTATATTTTAATAATTTT
1 TTAT-TTTTAATAATTTT
1202600 T
1 T
1202601 CCAAATGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTAATAATTTT
Found at i:1203567 original size:20 final size:20
Alignment explanation
Indices: 1203484--1203568 Score: 57
Period size: 20 Copynumber: 4.0 Consensus size: 20
1203474 TACGTTACTA
*
1203484 AAATATATATTTAGAGTTAATT
1 AAATATAGATTTA-A-TTAATT
*
1203506 AAATATATGTTTTAA-TAATCT
1 AAATATA-GATTTAATTAAT-T
*
1203527 CGAATATTTA-ATTTCAATTAATT
1 --AA-ATATAGATTT-AATTAATT
1203550 AAATATAGATTTAATTAAT
1 AAATATAGATTTAATTAAT
1203569 ATTAAATAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
20 15 0.30
21 7 0.14
22 11 0.22
23 9 0.18
24 8 0.16
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (20 bp):
AAATATAGATTTAATTAATT
Found at i:1203651 original size:90 final size:89
Alignment explanation
Indices: 1203531--1203703 Score: 278
Period size: 90 Copynumber: 1.9 Consensus size: 89
1203521 TAATCTCGAA
* *
1203531 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATATT-AAATAATAAAATACC-TAATATG
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAAT-TTGAAATAAT-AAA-ACCATAATATG
1203594 ATTAGGGTAACTTGGATATAAGAGGAT
63 ATTAGGGTAACTTGGATATAAGAGGAT
1203621 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCATAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCATAATATGATT
*
1203686 AGGGTAACTTGGCTATAA
66 AGGGTAACTTGGATATAA
1203704 AAGAGTGTGT
Statistics
Matches: 78, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
88 3 0.04
89 32 0.41
90 43 0.55
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCATAATATGATT
AGGGTAACTTGGATATAAGAGGAT
Found at i:1214486 original size:118 final size:118
Alignment explanation
Indices: 1214332--1214568 Score: 456
Period size: 118 Copynumber: 2.0 Consensus size: 118
1214322 ACAGCAGATA
*
1214332 AAGGTCTTCATCCTAAATGGTTAATAGAAATGATATTTCTACCAACCTCTGGACCTTTATCTCTC
1 AAGGTCTTCATCCTAAATGGTTAATAGAAATAATATTTCTACCAACCTCTGGACCTTTATCTCTC
*
1214397 ATAAACCCCACTTTTGCAATCTGGATTCAATACTTGAAACAGTACATACCGAC
66 ATAAACCCCACTTTTGCAATCTGGATTAAATACTTGAAACAGTACATACCGAC
1214450 AAGGTCTTCATCCTAAATGGTTAATAGAAATAATATTTCTACCAACCTCTGGACCTTTATCTCTC
1 AAGGTCTTCATCCTAAATGGTTAATAGAAATAATATTTCTACCAACCTCTGGACCTTTATCTCTC
1214515 ATAAACCCCACTTTTGCAATCTGGATTAAATACTTGAAACAGTACATACCGAC
66 ATAAACCCCACTTTTGCAATCTGGATTAAATACTTGAAACAGTACATACCGAC
1214568 A
1 A
1214569 TCATATCCCC
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 117 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.31
Consensus pattern (118 bp):
AAGGTCTTCATCCTAAATGGTTAATAGAAATAATATTTCTACCAACCTCTGGACCTTTATCTCTC
ATAAACCCCACTTTTGCAATCTGGATTAAATACTTGAAACAGTACATACCGAC
Found at i:1219114 original size:45 final size:45
Alignment explanation
Indices: 1218976--1219117 Score: 239
Period size: 45 Copynumber: 3.2 Consensus size: 45
1218966 TATTAATTAT
*
1218976 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * *
1219021 TTTTATTTATGGCATCTTTTCATGCCTTTAATGCACCGTTATGTA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
*
1219066 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
1219111 TTTCATT
1 TTTCATT
1219118 AATGAAATAA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 89 1.00
ACGTcount: A:0.20, C:0.22, G:0.11, T:0.46
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:1227349 original size:45 final size:45
Alignment explanation
Indices: 1227295--1227486 Score: 278
Period size: 45 Copynumber: 4.3 Consensus size: 45
1227285 ATTATTAATT
*
1227295 ATTTCCATTTATGGCATCATTTCATGCCTTTAATGCACCGTTATAC
1 ATTT-CATTTATGGCATCATTTCATGCCTTTAATGCACCATTATAC
* * * *
1227341 ATTTCATTTATGTCATCCTTTCATGCCTTTAAAGCA-CATTATGC
1 ATTTCATTTATGGCATCATTTCATGCCTTTAATGCACCATTATAC
* * *
1227385 ATTTCATTTATGGAATCCTTTCATGCCTTTAATGCACCGTTATAC
1 ATTTCATTTATGGCATCATTTCATGCCTTTAATGCACCATTATAC
* *
1227430 ATTTCATTTATGACATCATTTCATGCCTTTAATGCACCATTATGC
1 ATTTCATTTATGGCATCATTTCATGCCTTTAATGCACCATTATAC
1227475 ATTTCATTTATG
1 ATTTCATTTATG
1227487 AAATAAAAAC
Statistics
Matches: 130, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
44 39 0.30
45 87 0.67
46 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (45 bp):
ATTTCATTTATGGCATCATTTCATGCCTTTAATGCACCATTATAC
Found at i:1227407 original size:89 final size:90
Alignment explanation
Indices: 1227295--1227486 Score: 323
Period size: 89 Copynumber: 2.1 Consensus size: 90
1227285 ATTATTAATT
* * *
1227295 ATTTCCATTTATGGCATCATTTCATGCCTTTAATGCACCGTTATACATTTCATTTATGTCATCCT
1 ATTT-CATTTATGGAATCATTTCATGCCTTTAATGCACCGTTATACATTTCATTTATGACATCAT
1227360 TTCATGCCTTTAAAGCA-CATTATGC
65 TTCATGCCTTTAAAGCACCATTATGC
*
1227385 ATTTCATTTATGGAATCCTTTCATGCCTTTAATGCACCGTTATACATTTCATTTATGACATCATT
1 ATTTCATTTATGGAATCATTTCATGCCTTTAATGCACCGTTATACATTTCATTTATGACATCATT
*
1227450 TCATGCCTTTAATGCACCATTATGC
66 TCATGCCTTTAAAGCACCATTATGC
1227475 ATTTCATTTATG
1 ATTTCATTTATG
1227487 AAATAAAAAC
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
89 72 0.75
90 24 0.25
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (90 bp):
ATTTCATTTATGGAATCATTTCATGCCTTTAATGCACCGTTATACATTTCATTTATGACATCATT
TCATGCCTTTAAAGCACCATTATGC
Found at i:1227470 original size:21 final size:21
Alignment explanation
Indices: 1227403--1227470 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
1227393 TATGGAATCC
*
1227403 TTTCATGCCTTTAATGCACCG
1 TTTCATGCCTTTAATGCACCA
* * *
1227424 TTATACATTTCATTT-ATGACATCA
1 TT-T-CA-TGCCTTTAATG-CACCA
1227448 TTTCATGCCTTTAATGCACCA
1 TTTCATGCCTTTAATGCACCA
1227469 TT
1 TT
1227471 ATGCATTTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
21 13 0.37
22 6 0.17
23 6 0.17
24 10 0.29
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.43
Consensus pattern (21 bp):
TTTCATGCCTTTAATGCACCA
Found at i:1227484 original size:24 final size:23
Alignment explanation
Indices: 1227412--1227484 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 23
1227402 CTTTCATGCC
*
1227412 TTTAATGCACCGTTATACATTTCA
1 TTTAATGCACCATTAT-CATTTCA
* * *
1227436 TTT-ATGACATCATT-TCA-TGCC
1 TTTAATG-CACCATTATCATTTCA
1227457 TTTAATGCACCATTATGCATTTCA
1 TTTAATGCACCATTAT-CATTTCA
1227481 TTTA
1 TTTA
1227485 TGAAATAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
21 11 0.30
22 6 0.16
23 6 0.16
24 14 0.38
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (23 bp):
TTTAATGCACCATTATCATTTCA
Found at i:1234421 original size:6 final size:6
Alignment explanation
Indices: 1234410--1234443 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1234400 TTAGCATGTT
1234410 TAAAAA TAAAAA T-AAAA T-AAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
1234444 ATTGAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:1234433 original size:16 final size:16
Alignment explanation
Indices: 1234412--1234442 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1234402 AGCATGTTTA
1234412 AAAATAAAAATAAAAT
1 AAAATAAAAATAAAAT
1234428 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
1234443 AATTGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAATAAAAATAAAAT
Found at i:1243189 original size:6 final size:6
Alignment explanation
Indices: 1243174--1243210 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
1243164 AAACCTAGAG
*
1243174 ATAAAC ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
1243211 ATCCTAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:1245561 original size:11 final size:11
Alignment explanation
Indices: 1245545--1245576 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1245535 AAAGTTTGCT
1245545 AAAAATAAAAC
1 AAAAATAAAAC
1245556 AAAAATAAAAC
1 AAAAATAAAAC
1245567 AAAAATAAAA
1 AAAAATAAAA
1245577 TGAAATGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.09
Consensus pattern (11 bp):
AAAAATAAAAC
Found at i:1248794 original size:21 final size:21
Alignment explanation
Indices: 1248768--1248851 Score: 109
Period size: 21 Copynumber: 4.0 Consensus size: 21
1248758 TTTCAGATTT
1248768 GCAACGCGATAATACATAATC
1 GCAACGCGATAATACATAATC
1248789 GCAACGCGATAATACATAATC
1 GCAACGCGATAATACATAATC
* **
1248810 ACAACGCGATTCTGAC-T-ATC
1 GCAACGCGATAAT-ACATAATC
*
1248830 GCAACGCGATAATACAAAATC
1 GCAACGCGATAATACATAATC
1248851 G
1 G
1248852 TAATGTGATT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.04
20 13 0.25
21 36 0.68
22 2 0.04
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.19
Consensus pattern (21 bp):
GCAACGCGATAATACATAATC
Found at i:1249035 original size:22 final size:22
Alignment explanation
Indices: 1249005--1249052 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1248995 CTACAGCAAC
* *
1249005 ATCCGTCCCCATCTCTGACGAA
1 ATCCATCCCCATCTCCGACGAA
1249027 ATCCATCCCCATCTCCGACGAA
1 ATCCATCCCCATCTCCGACGAA
1249049 ATCC
1 ATCC
1249053 GTCTATCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.44, G:0.10, T:0.21
Consensus pattern (22 bp):
ATCCATCCCCATCTCCGACGAA
Found at i:1249454 original size:20 final size:20
Alignment explanation
Indices: 1249429--1249502 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
1249419 AAAATCGCAA
*
1249429 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAATTTCGCGTTG
* * *
1249449 CGATAGTCATTTTTGTGTTG
1 CGATAGTCAATTTCGCGTTG
**
1249469 CGATTTTC-ATTTCGCGTTG
1 CGATAGTCAATTTCGCGTTG
*
1249488 CGATAGTCATTTTCG
1 CGATAGTCAATTTCG
1249503 TGTAGAGATT
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
19 14 0.34
20 27 0.66
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.42
Consensus pattern (20 bp):
CGATAGTCAATTTCGCGTTG
Found at i:1249494 original size:39 final size:40
Alignment explanation
Indices: 1249440--1249531 Score: 141
Period size: 39 Copynumber: 2.3 Consensus size: 40
1249430 GATAGTCAAA
* * *
1249440 TTCGCGTTGCGATAGTCATTTTTGTGTTGCGATTTTCA-T
1 TTCGCGTTGCGATAGTCATTTTCGTGTAGAGATTTTCATT
1249479 TTCGCGTTGCGATAGTCATTTTCGTGTAGAGATTTTCATT
1 TTCGCGTTGCGATAGTCATTTTCGTGTAGAGATTTTCATT
*
1249519 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
1249532 TTTCAGAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
39 35 0.73
40 13 0.27
ACGTcount: A:0.14, C:0.15, G:0.24, T:0.47
Consensus pattern (40 bp):
TTCGCGTTGCGATAGTCATTTTCGTGTAGAGATTTTCATT
Found at i:1249517 original size:20 final size:20
Alignment explanation
Indices: 1249494--1249536 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1249484 GTTGCGATAG
1249494 TCATTTTCGTGTAGAGATTT
1 TCATTTTCGTGTAGAGATTT
* *
1249514 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTAGAGATTT
1249534 TCA
1 TCA
1249537 GAAACATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (20 bp):
TCATTTTCGTGTAGAGATTT
Found at i:1251090 original size:12 final size:12
Alignment explanation
Indices: 1251073--1251103 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1251063 TGTCAGATAC
1251073 GTCATGCACAAA
1 GTCATGCACAAA
*
1251085 GTCATGAACAAA
1 GTCATGCACAAA
1251097 GTCATGC
1 GTCATGC
1251104 CCACTAATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (12 bp):
GTCATGCACAAA
Found at i:1254855 original size:19 final size:22
Alignment explanation
Indices: 1254814--1254855 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1254804 TTCTCATGTA
*
1254814 TTTTTCTTCTTTCTTTTTGTTG
1 TTTTTCTTCTTTCATTTTGTTG
1254836 TTTTTCTT-TTT-ATTTT-TTG
1 TTTTTCTTCTTTCATTTTGTTG
1254855 T
1 T
1254856 CCAAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.21
20 4 0.21
21 3 0.16
22 8 0.42
ACGTcount: A:0.02, C:0.10, G:0.07, T:0.81
Consensus pattern (22 bp):
TTTTTCTTCTTTCATTTTGTTG
Found at i:1265423 original size:15 final size:14
Alignment explanation
Indices: 1265394--1265428 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1265384 CATCAGATAG
*
1265394 AATAAATAGAATGA
1 AATAAATAAAATGA
1265408 AATAAATTAAAATGA
1 AATAAA-TAAAATGA
1265423 AATAAA
1 AATAAA
1265429 GTCTGCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (14 bp):
AATAAATAAAATGA
Found at i:1270220 original size:34 final size:33
Alignment explanation
Indices: 1270138--1270233 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 33
1270128 TGACAAGTTG
*
1270138 GAAAATTCATCTTGGTTGGTGTCCAACTTATTT
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATTT
*
1270171 GAAATTTCATCTTGGTTGGTGGCCAACTTA-TT
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATTT
*
1270203 GAAAAATTCATCTTTGGTAGGTGGCCAACTT
1 G-AAAATTCATC-TTGGTTGGTGGCCAACTT
1270234 TGCACATGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 3 0.05
33 37 0.65
34 17 0.30
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.39
Consensus pattern (33 bp):
GAAAATTCATCTTGGTTGGTGGCCAACTTATTT
Found at i:1272290 original size:25 final size:25
Alignment explanation
Indices: 1272261--1272312 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1272251 ATTTCTAGCT
*
1272261 TTGATTTCCAGCCTCCAA-ATTTGAC
1 TTGATTTACAGCC-CCAACATTTGAC
*
1272286 TTGATTTACAGCCCCAACTTTTGAC
1 TTGATTTACAGCCCCAACATTTGAC
1272311 TT
1 TT
1272313 CCAAAAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (25 bp):
TTGATTTACAGCCCCAACATTTGAC
Found at i:1276357 original size:16 final size:17
Alignment explanation
Indices: 1276331--1276363 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1276321 TATCGCCGAC
1276331 AAAATTTCACTATTCAT
1 AAAATTTCACTATTCAT
1276348 AAAA-TTCACTATTCAT
1 AAAATTTCACTATTCAT
1276364 GTGAATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATTTCACTATTCAT
Found at i:1279615 original size:16 final size:17
Alignment explanation
Indices: 1279589--1279625 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1279579 AGGATATTAT
*
1279589 TAATAAAACAATAATAA
1 TAATAAAACAACAATAA
1279606 TAAT-AAACAACAATAA
1 TAATAAAACAACAATAA
1279622 TAAT
1 TAAT
1279626 TAATAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (17 bp):
TAATAAAACAACAATAA
Found at i:1286031 original size:17 final size:17
Alignment explanation
Indices: 1286009--1286041 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1285999 GTCGGCTAAA
*
1286009 AGAAATGGTTATGGTAT
1 AGAAATGGATATGGTAT
1286026 AGAAATGGATATGGTA
1 AGAAATGGATATGGTA
1286042 AAGGTAAGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (17 bp):
AGAAATGGATATGGTAT
Found at i:1288096 original size:22 final size:22
Alignment explanation
Indices: 1288066--1288116 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1288056 CATGGGCCTA
*
1288066 ATGGGCCTAGTTGTAAGACCTT
1 ATGGACCTAGTTGTAAGACCTT
*
1288088 ATGGACCTATTTGTAAGACCTT
1 ATGGACCTAGTTGTAAGACCTT
1288110 ATGGACC
1 ATGGACC
1288117 CTAAGGTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (22 bp):
ATGGACCTAGTTGTAAGACCTT
Found at i:1290852 original size:14 final size:15
Alignment explanation
Indices: 1290831--1290922 Score: 68
Period size: 14 Copynumber: 6.3 Consensus size: 15
1290821 ATGATAATTA
1290831 ATATACTTTATATTT
1 ATATACTTTATATTT
1290846 A-ATAC-TTATATTT
1 ATATACTTTATATTT
*
1290859 ATATACTTTAATACTT
1 ATATACTTT-ATATTT
*** *
1290875 ATAT-CCAAACACTTT
1 ATATACTTTATA-TTT
*
1290890 AT-TACTTTACATTT
1 ATATACTTTATATTT
*
1290904 -TATACTTTATATAT
1 ATATACTTTATATTT
1290918 ATATA
1 ATATA
1290923 TAGATTATAT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
13 10 0.17
14 24 0.41
15 16 0.27
16 9 0.15
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATACTTTATATTT
Found at i:1290888 original size:22 final size:22
Alignment explanation
Indices: 1290843--1290896 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1290833 ATACTTTATA
** * *
1290843 TTTAATACTTATATTTATATAC
1 TTTAATACTTATATCCAAACAC
1290865 TTTAATACTTATATCCAAACAC
1 TTTAATACTTATATCCAAACAC
*
1290887 TTTATTACTT
1 TTTAATACTT
1290897 TACATTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAATACTTATATCCAAACAC
Found at i:1291056 original size:25 final size:24
Alignment explanation
Indices: 1291008--1291053 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1290998 TGATGAGGGA
1291008 TGAAATTGAATTAATTATAAAATG
1 TGAAATTGAATTAATTATAAAATG
*
1291032 TGAAGTTGATATTAA-TATAAAA
1 TGAAATTGA-ATTAATTATAAAA
1291054 ATGGACGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (24 bp):
TGAAATTGAATTAATTATAAAATG
Found at i:1292201 original size:570 final size:559
Alignment explanation
Indices: 1290940--1292536 Score: 2275
Period size: 570 Copynumber: 2.9 Consensus size: 559
1290930 TATATGTATA
* *
1290940 CAAATTGAACAAACATGAAATTGAAAATAAAAAATTGAATAAATTAAACAACACACATTGATGAG
1 CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
* * *
1291005 GGATGAAATTGAATTAATTATAAAATGTGAAGTTGATATTAATATAAAAATGGACGAAATTGCAT
66 GGATGAAATTGAATTAATTATAAAATGTGAAGCTAATATTAATATAAAAATGGACTAAATTGCAT
*
1291070 ACATTTAAAAAGTTGGTGAACATAATTTGAAAATAAATTTATTATGTGATTTACATTTTATA-GG
131 ACATTTAAAAAGTTGGTGAACATAATTTGAAAACAAATTTATTATGTGATTTACATTTTATAGGG
*
1291134 ---GTTTTAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTCAGATACAAATATACTTT
196 TTTGTTTTAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTCAGATACAAATATAATTT
*
1291196 GAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATACAATAAACAACATAAAA
261 GAAGGAATAAATTGAACAAATATGAAATTACAAATT-AAATTTAAATA-AATAAACAACATAAAA
*
1291261 GGATCAAATAAAAAAAAGTGTAAAATGTGAGGAAAATTGTAAAAAGAACTGAATTGCATTAATTT
324 GGATCAAAT--AAAAAA-TGTAAAATGTGAGGAAAATTGTAAAATGAACTGAATTGCATTAATTT
* *
1291326 TAAAAGTTGGAGAAAAA-T--A-AA--A-AA-AT-TATA-ATATATA-TTTATGTTTAATGAATG
386 CAAAAGTTGGA-AAAAATTAAACAATTATAATATATATATATATATATTTTATGTATAATGAATG
* * *
1291380 TTATGATAATATGATGCTTGTATATCTAATGTACATTATACTTTATATATATAGATATACACATA
450 TTATGATAATATGATGCATGTACATATAATGTACATTATACTTTATATATATA-ATATACACATA
*
1291445 TGCATATATACTTATACTTTATAGTTCATATATGTATATAAAGTAC
514 TACATATATACTTATACTTTATAGTTCATATATGTATATAAAGTAC
*
1291491 CAAATTGAGCAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
1 CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
1291556 GGATGAAATTGAATTAATTATAAAATGTGAAGC-AGATATTAATATAAAAATGGACTAAATTGCA
66 GGATGAAATTGAATTAATTATAAAATGTGAAGCTA-ATATTAATATAAAAATGGACTAAATTGCA
* * * *
1291620 TACACTTAAAAAGTCGATGAACATAATTTGAAAAGAAATTTATTATGTGATTTACATTTTATAGG
130 TACATTTAAAAAGTTGGTGAACATAATTTGAAAACAAATTTATTATGTGATTTACATTTTATAGG
*
1291685 GTTTGTTTTAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTCGGATACAAATATAATT
195 GTTTGTTTTAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTCAGATACAAATATAATT
* *
1291750 TGAAGGAATAAATTGAACAAATATGAAATTA-AAAATAAACTTTTAAATAAATTAAACAACACAA
260 TGAAGGAATAAATTGAACAAATATGAAATTACAAATTAAA--TTTAAATAAA-TAAACAACATAA
* * * * * *
1291814 ATGGATTAAATCGAAATAATTGTAAAATGTGAAGAAAATGTGTAAAATTAACTAAATTGCATTAA
322 AAGGATCAAAT--AAA-AAATGTAAAATGTGAGGAAAAT-TGTAAAATGAACTGAATTGCATTAA
*
1291879 TTTCAAAAGTTAAGAAAAAATTGAAACAATTATAATATATATATATATATATGTATAATATGTAT
383 TTTCAAAAGTT-GGAAAAAATT-AAACAATTATAATATATATATATATATAT-T-T--TATGTAT
*
1291944 AATGAATGTTATGATAATATGATGCATGTACATATAATGTACATTATACTTTATGTATAT-ATAT
442 AATGAATGTTATGATAATATGATGCATGTACATATAATGTACATTATACTTTATATATATAATAT
* *
1292008 ATACATATACATATATACTTATACTTTATAGTTTATATATGTATATAAAGTAC
507 ACACATATACATATATACTTATACTTTATAGTTCATATATGTATATAAAGTAC
*
1292061 CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACGCATTGATGAG
1 CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
* *
1292126 GGATGAAATTGAATTAATTATAAAATGTGAAACTAATATTAATATAAAAATGGAATAAATT-CGA
66 GGATGAAATTGAATTAATTATAAAATGTGAAGCTAATATTAATATAAAAATGGACTAAATTGC-A
*
1292190 TACATTTAAAAAGTTGGTGAACATAATTTGAAAACAAATTTATTATGTGATTTATATTTTATAGG
130 TACATTTAAAAAGTTGGTGAACATAATTTGAAAACAAATTTATTATGTGATTTACATTTTATAGG
* **
1292255 GTTTGTTTTAAGTAAATTA-ATAAAATATAAATAAGGATGGGTCAATTTCAGATATGAATATAAT
195 GTTTGTTTTAAGTAAATTACA-AAAATATAAATAAGTATGGGTCAATTTCAGATACAAATATAAT
* *
1292319 TTGAA-GAACTAAATTGAACAAATCTGAAATTACAAATTTAAATTTAAATAAAATAAATAACATA
259 TTGAAGGAA-TAAATTGAACAAATATGAAATTACAAA-TTAAATTTAAAT-AAATAAACAACATA
* * *
1292383 AAAGGATCAAA-AAAAAATGTAAAATGTGAGGAAAAATTATAAAATGGATTGAATTGCATTAATT
321 AAAGGATCAAATAAAAAATGTAAAATGTGAGG-AAAATTGTAAAATGAACTGAATTGCATTAATT
* **
1292447 TCAAAAATTGGTGAAAATTAAAACAA-T-T-ATA-ATATATATATATA---TA--TATAATGAAT
385 TCAAAAGTTGGAAAAAATT-AAACAATTATAATATATATATATATATATTTTATGTATAATGAAT
* *
1292503 GTTATAATAATATGATGCATGTATATATAATGTA
449 GTTATGATAATATGATGCATGTACATATAATGTA
1292537 AAATATAAGT
Statistics
Matches: 944, Mismatches: 67, Indels: 69
0.87 0.06 0.06
Matches are distributed among these distances:
551 181 0.19
552 44 0.05
553 3 0.00
554 8 0.01
555 138 0.15
556 39 0.04
557 3 0.00
560 1 0.00
561 15 0.02
562 3 0.00
563 2 0.00
564 3 0.00
565 15 0.02
566 49 0.05
567 15 0.02
569 6 0.01
570 346 0.37
571 7 0.01
572 66 0.07
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (559 bp):
CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
GGATGAAATTGAATTAATTATAAAATGTGAAGCTAATATTAATATAAAAATGGACTAAATTGCAT
ACATTTAAAAAGTTGGTGAACATAATTTGAAAACAAATTTATTATGTGATTTACATTTTATAGGG
TTTGTTTTAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTCAGATACAAATATAATTT
GAAGGAATAAATTGAACAAATATGAAATTACAAATTAAATTTAAATAAATAAACAACATAAAAGG
ATCAAATAAAAAATGTAAAATGTGAGGAAAATTGTAAAATGAACTGAATTGCATTAATTTCAAAA
GTTGGAAAAAATTAAACAATTATAATATATATATATATATATTTTATGTATAATGAATGTTATGA
TAATATGATGCATGTACATATAATGTACATTATACTTTATATATATAATATACACATATACATAT
ATACTTATACTTTATAGTTCATATATGTATATAAAGTAC
Found at i:1292515 original size:20 final size:20
Alignment explanation
Indices: 1292483--1292533 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1292473 TTATAATATA
1292483 TATATATATATATAATGAATG
1 TATATATA-ATATAATGAATG
* *
1292504 T-TATAATAATATGATGCATG
1 TATAT-ATAATATAATGAATG
1292524 TATATATAAT
1 TATATATAAT
1292534 GTAAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (20 bp):
TATATATAATATAATGAATG
Found at i:1292562 original size:26 final size:25
Alignment explanation
Indices: 1292524--1292656 Score: 107
Period size: 26 Copynumber: 5.4 Consensus size: 25
1292514 ATGATGCATG
1292524 TATATATAATGTAAAATAT-AAGTA
1 TATATATAATGTAAAATATAAAGTA
*
1292548 TATATATAAAGTGTAAACTATAAAGTA
1 TATATAT-AA-TGTAAAATATAAAGTA
* *
1292575 TATATACT--T-TAAAGTATAAAGTG
1 TATATA-TAATGTAAAATATAAAGTA
* *
1292598 TATATATATATATAAACTATAAAGTA
1 TATATATA-ATGTAAAATATAAAGTA
* * *
1292624 TAAAGTATAA-GTATATTAT-AAGTA
1 TATA-TATAATGTAAAATATAAAGTA
1292648 TATATATAA
1 TATATATAA
1292657 ATTATAAAGT
Statistics
Matches: 90, Mismatches: 10, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
22 1 0.01
23 23 0.26
24 16 0.18
25 9 0.10
26 25 0.28
27 15 0.17
28 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (25 bp):
TATATATAATGTAAAATATAAAGTA
Found at i:1292594 original size:7 final size:7
Alignment explanation
Indices: 1292543--1292669 Score: 72
Period size: 7 Copynumber: 19.0 Consensus size: 7
1292533 TGTAAAATAT
1292543 AAGTATA
1 AAGTATA
*
1292550 TA-TATA
1 AAGTATA
*
1292556 AAGTGTA
1 AAGTATA
*
1292563 AACTATA
1 AAGTATA
1292570 AAGTATA
1 AAGTATA
* *
1292577 TATACTTTA
1 -A-AGTATA
1292586 AAGTATA
1 AAGTATA
*
1292593 AAGTGTA
1 AAGTATA
*
1292600 TA-TATA
1 AAGTATA
*
1292606 TA-TATA
1 AAGTATA
*
1292612 AACTATA
1 AAGTATA
1292619 AAGTATA
1 AAGTATA
1292626 AAGTAT-
1 AAGTATA
1292632 AAGTAT-
1 AAGTATA
*
1292638 -ATTAT-
1 AAGTATA
1292643 AAGTATA
1 AAGTATA
*
1292650 TA-TATA
1 AAGTATA
*
1292656 AATTATA
1 AAGTATA
1292663 AAGTATA
1 AAGTATA
1292670 TATACTTTCT
Statistics
Matches: 93, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
5 4 0.04
6 30 0.32
7 53 0.57
8 2 0.02
9 4 0.04
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37
Consensus pattern (7 bp):
AAGTATA
Found at i:1292618 original size:13 final size:13
Alignment explanation
Indices: 1292589--1292662 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 13
1292579 TACTTTAAAG
*
1292589 TATAAAGTGTATA
1 TATAAAGTATATA
* *
1292602 TATATA-TATAAA
1 TATAAAGTATATA
*
1292614 CTATAAAGTATAAA
1 -TATAAAGTATATA
1292628 GTAT-AAGTATAT-
1 -TATAAAGTATATA
1292640 TAT-AAGTATATA
1 TATAAAGTATATA
*
1292652 TATAAATTATA
1 TATAAAGTATA
1292663 AAGTATATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
11 11 0.22
12 7 0.14
13 23 0.46
14 9 0.18
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.39
Consensus pattern (13 bp):
TATAAAGTATATA
Found at i:1292621 original size:33 final size:34
Alignment explanation
Indices: 1292573--1292673 Score: 116
Period size: 33 Copynumber: 2.9 Consensus size: 34
1292563 AACTATAAAG
* *
1292573 TATATATACTTTAAAGTATAAAGTGTATATA-TA
1 TATATATACTATAAAGTATAAAGTATATATATTA
*
1292606 TATATAAACTATAAAGTATAAAGTATAAGTATATTA
1 TATATATACTATAAAGTATAAAGTAT-A-TATATTA
*
1292642 TAAGTATATA-TATAAATTATAAAGTATATATA
1 T-A-TATATACTATAAAGTATAAAGTATATATA
1292674 CTTTCTACTA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
33 23 0.40
34 1 0.02
35 8 0.14
36 4 0.07
37 17 0.29
38 5 0.09
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (34 bp):
TATATATACTATAAAGTATAAAGTATATATATTA
Found at i:1292645 original size:11 final size:12
Alignment explanation
Indices: 1292597--1292673 Score: 60
Period size: 11 Copynumber: 6.8 Consensus size: 12
1292587 AGTATAAAGT
1292597 GTATATATAT-A
1 GTATATATATAA
*
1292608 -TATAAACTATAAA
1 GTATATA-TAT-AA
*
1292621 GTATAAAGTATAA
1 GTATATA-TATAA
1292634 GTATAT-TATAA
1 GTATATATATAA
1292645 GTATATATATAA
1 GTATATATATAA
1292657 --AT-TATA-AA
1 GTATATATATAA
1292665 GTATATATA
1 GTATATATA
1292674 CTTTCTACTA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
8 2 0.04
9 4 0.07
10 9 0.16
11 18 0.33
12 5 0.09
13 8 0.15
14 9 0.16
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (12 bp):
GTATATATATAA
Found at i:1292712 original size:15 final size:14
Alignment explanation
Indices: 1292692--1292779 Score: 53
Period size: 13 Copynumber: 6.4 Consensus size: 14
1292682 TAAAACTTTA
*
1292692 TATATATTATAAAC
1 TATATATTATAAAG
1292706 T-TATATATATAAAG
1 TATATAT-TATAAAG
1292720 TATA-ATTATAAAG
1 TATATATTATAAAG
* **
1292733 -ACA-AAAATATAAG
1 TATATATTATA-AAG
1292746 TATA-A-TATAAAG
1 TATATATTATAAAG
*
1292758 TATATAAGTATATAAG
1 TATAT-ATTATA-AAG
1292774 TATATA
1 TATATA
1292780 AGAATATAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
12 13 0.22
13 18 0.30
14 14 0.23
15 7 0.12
16 8 0.13
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (14 bp):
TATATATTATAAAG
Found at i:1292768 original size:8 final size:8
Alignment explanation
Indices: 1292746--1292852 Score: 69
Period size: 8 Copynumber: 14.5 Consensus size: 8
1292736 AAAATATAAG
1292746 TATAA-TA
1 TATAAGTA
1292753 TA-AAGTA
1 TATAAGTA
1292760 TATAAGTA
1 TATAAGTA
1292768 TATAAGTA
1 TATAAGTA
*
1292776 TATAAGAA
1 TATAAGTA
1292784 TATAAAGTA
1 TAT-AAGTA
1292793 -A-AAGTA
1 TATAAGTA
*
1292799 TATATA-TC
1 TATA-AGTA
1292807 TATAA--A
1 TATAAGTA
1292813 GTATAAGTA
1 -TATAAGTA
1292822 TAT-A-TA
1 TATAAGTA
1292828 TAT-A-TA
1 TATAAGTA
1292834 TATAA--A
1 TATAAGTA
1292840 CTATAAGTA
1 -TATAAGTA
1292849 TATA
1 TATA
1292853 TATATAAAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 25
0.74 0.04 0.22
Matches are distributed among these distances:
6 19 0.23
7 20 0.24
8 37 0.45
9 7 0.08
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.36
Consensus pattern (8 bp):
TATAAGTA
Done.