Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397268.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_81.0, 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: 6219335
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 77647 characters in sequence are not A, C, G, or T
File 3 of 13
Found at i:1592709 original size:3 final size:3
Alignment explanation
Indices: 1592701--1592730 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1592691 AGAATCCATA
1592701 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1592731 CAAATTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1595030 original size:158 final size:158
Alignment explanation
Indices: 1594863--1595180 Score: 546
Period size: 158 Copynumber: 2.0 Consensus size: 158
1594853 TTATGTTTTA
* * * *
1594863 TATAATTTATTTATTAACGTAGTGACGATGTTTGATGAACTAATAGTGTAATTAATACTAAAAAT
1 TATAATTTATTTATCAACGTAGTGACAATGTTTGATGAAATAATAGTGTAATTAATACTAAAAAA
* * *
1594928 GTACTTGAAATTAACTTTATGATTGGAAAATGAAAGATTAAGAGGAGCAATCATACCTTTTTGTA
66 GTACTTGAAATTAACATTATGATTAGAAAATGAAAGATTAAGAGGAGCAATCATACCTTTTTGGA
*
1594993 CACTTGAAGTAACATGTTGTATCCCGTG
131 CACTTGAAGTAACATGTTATATCCCGTG
*
1595021 TATAATTTATTTATCAACGTAGTGACAATGTTTGATGAAATAATGGTGTAATTAATACTAAAAAA
1 TATAATTTATTTATCAACGTAGTGACAATGTTTGATGAAATAATAGTGTAATTAATACTAAAAAA
*
1595086 GTACTTGAAATTAACATTATGATTAGAAAATGAAAGATTAAGAGGGGCAATCATACCTTTTTGGA
66 GTACTTGAAATTAACATTATGATTAGAAAATGAAAGATTAAGAGGAGCAATCATACCTTTTTGGA
1595151 CACTTGAAGTAACATGTTATATCCCGTG
131 CACTTGAAGTAACATGTTATATCCCGTG
1595179 TA
1 TA
1595181 ATCCGATCAA
Statistics
Matches: 150, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
158 150 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (158 bp):
TATAATTTATTTATCAACGTAGTGACAATGTTTGATGAAATAATAGTGTAATTAATACTAAAAAA
GTACTTGAAATTAACATTATGATTAGAAAATGAAAGATTAAGAGGAGCAATCATACCTTTTTGGA
CACTTGAAGTAACATGTTATATCCCGTG
Found at i:1599180 original size:2 final size:2
Alignment explanation
Indices: 1599173--1599202 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1599163 GCAATGATTA
1599173 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
1599203 CACTAGCTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1605725 original size:18 final size:18
Alignment explanation
Indices: 1605715--1605749 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1605705 TAAGAAATAT
1605715 TAAAAAGTTAAAAAATTG
1 TAAAAAGTTAAAAAATTG
1605733 TAAAAAG-TAAAATAATT
1 TAAAAAGTTAAAA-AATT
1605750 TCAAATAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.29
Consensus pattern (18 bp):
TAAAAAGTTAAAAAATTG
Found at i:1619792 original size:18 final size:19
Alignment explanation
Indices: 1619753--1619802 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
1619743 TAGTACAGTG
*
1619753 GATAGTGATGTAATATACT
1 GATAGTGATATAATATACT
1619772 GATA-TGATATAATTATA-T
1 GATAGTGATATAA-TATACT
1619790 GATCATGTGATAT
1 GAT-A-GTGATAT
1619803 TTTTTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 11 0.42
19 9 0.35
21 6 0.23
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (19 bp):
GATAGTGATATAATATACT
Found at i:1626751 original size:9 final size:9
Alignment explanation
Indices: 1626737--1626763 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1626727 ACCGTACCCT
1626737 CCACCGCCA
1 CCACCGCCA
1626746 CCACCGCCA
1 CCACCGCCA
1626755 CCACCGCCA
1 CCACCGCCA
1626764 TATCCCCTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.67, G:0.11, T:0.00
Consensus pattern (9 bp):
CCACCGCCA
Found at i:1643814 original size:26 final size:26
Alignment explanation
Indices: 1643779--1643832 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
1643769 TCCTCTAAGC
*
1643779 TTTATCATCTAAAAATCAATAAGCTT
1 TTTATCATCTAAAAATAAATAAGCTT
* * *
1643805 TTTATGATCTAGAAGTAAATAAGCTT
1 TTTATCATCTAAAAATAAATAAGCTT
1643831 TT
1 TT
1643833 ATTCCTCAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (26 bp):
TTTATCATCTAAAAATAAATAAGCTT
Found at i:1643942 original size:22 final size:22
Alignment explanation
Indices: 1643917--1643968 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1643907 ATGAGTTTAT
1643917 TGACCAAGTTAAATCATGATGG
1 TGACCAAGTTAAATCATGATGG
1643939 TGACCAAGTTAAATCATGATGG
1 TGACCAAGTTAAATCATGATGG
*
1643961 TGAACAAG
1 TGACCAAG
1643969 CTCAATCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Consensus pattern (22 bp):
TGACCAAGTTAAATCATGATGG
Found at i:1643975 original size:22 final size:22
Alignment explanation
Indices: 1643921--1643975 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1643911 GTTTATTGAC
* *
1643921 CAAGTTAAATCATGATGGTGAC
1 CAAGCTAAATCATGATGGTGAA
*
1643943 CAAGTTAAATCATGATGGTGAA
1 CAAGCTAAATCATGATGGTGAA
*
1643965 CAAGCTCAATC
1 CAAGCTAAATC
1643976 TAATTTTGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (22 bp):
CAAGCTAAATCATGATGGTGAA
Found at i:1647136 original size:7 final size:7
Alignment explanation
Indices: 1647126--1647175 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
1647116 CTCAAACTTC
*
1647126 TTTGGTT
1 TTTGGCT
1647133 TTTGGCT
1 TTTGGCT
1647140 TTTGGCT
1 TTTGGCT
*
1647147 TTCGGCT
1 TTTGGCT
*
1647154 TCTGGCT
1 TTTGGCT
*
1647161 TCTGGCT
1 TTTGGCT
*
1647168 TCTGGCT
1 TTTGGCT
1647175 T
1 T
1647176 CGGCTTTACG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.00, C:0.20, G:0.28, T:0.52
Consensus pattern (7 bp):
TTTGGCT
Found at i:1647176 original size:7 final size:7
Alignment explanation
Indices: 1647135--1647181 Score: 62
Period size: 7 Copynumber: 6.9 Consensus size: 7
1647125 CTTTGGTTTT
*
1647135 TGGCTTT
1 TGGCTTC
1647142 TGGCTT-
1 TGGCTTC
1647148 TCGGCTTC
1 T-GGCTTC
1647156 TGGCTTC
1 TGGCTTC
1647163 TGGCTTC
1 TGGCTTC
1647170 TGGCTTC
1 TGGCTTC
1647177 -GGCTT
1 TGGCTT
1647182 TACGGTGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.16
7 31 0.82
8 1 0.03
ACGTcount: A:0.00, C:0.26, G:0.30, T:0.45
Consensus pattern (7 bp):
TGGCTTC
Found at i:1648442 original size:5 final size:5
Alignment explanation
Indices: 1648432--1648460 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1648422 ATATTATAGT
1648432 AATAA AATAA AATAA AATAA AATAA AATA
1 AATAA AATAA AATAA AATAA AATAA AATA
1648461 TTTTTACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:1659245 original size:1 final size:1
Alignment explanation
Indices: 1659239--1659264 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1659229 GTATTGGGTT
1659239 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
1659265 AGTTATTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1663848 original size:29 final size:31
Alignment explanation
Indices: 1663803--1663863 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 31
1663793 ATCGTGATAA
* *
1663803 TAAATTTATTTTTTAATTTA-TAAA-ATTTT
1 TAAATTTATTTTATAATATATTAAATATTTT
1663832 TAAATTT-TTTTGATAATATATTAAATATTTT
1 TAAATTTATTTT-ATAATATATTAAATATTTT
1663863 T
1 T
1663864 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.15
29 13 0.48
30 4 0.15
31 6 0.22
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (31 bp):
TAAATTTATTTTATAATATATTAAATATTTT
Found at i:1664407 original size:21 final size:21
Alignment explanation
Indices: 1664377--1664435 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1664367 TTATGAGTTC
1664377 TTATTT-TTAATTT-AAAAAA
1 TTATTTATTAATTTAAAAAAA
*
1664396 TATATTTATTAATTGAAAAAAA
1 T-TATTTATTAATTTAAAAAAA
*
1664418 TTATTTATAAATTTAAAA
1 TTATTTATTAATTTAAAA
1664436 TTTATCTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.03
20 5 0.15
21 21 0.62
22 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TTATTTATTAATTTAAAAAAA
Found at i:1672994 original size:2 final size:2
Alignment explanation
Indices: 1672987--1673033 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1672977 AGATAATTGA
* *
1672987 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AT AC AT AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1673029 AC AC A
1 AC AC A
1673034 TATATATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.45, G:0.00, T:0.04
Consensus pattern (2 bp):
AC
Found at i:1676567 original size:15 final size:17
Alignment explanation
Indices: 1676535--1676568 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1676525 GTTTTGCCTA
1676535 TTTGTCACTTACTTTCT
1 TTTGTCACTTACTTTCT
1676552 TTTG-CACTTA-TTTCT
1 TTTGTCACTTACTTTCT
1676567 TT
1 TT
1676569 AATTGTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 6 0.35
17 4 0.24
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTGTCACTTACTTTCT
Found at i:1689134 original size:2 final size:2
Alignment explanation
Indices: 1689127--1689160 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1689117 GAATCAGAGA
*
1689127 AT AT AT AT AT CT 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
1689161 TAAGAGAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1689476 original size:23 final size:23
Alignment explanation
Indices: 1689419--1689484 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
1689409 TCGATAATTA
*
1689419 TAAGTATCTAATATTTTAATAA-
1 TAAGTATCTAATATTTCAATAAT
*
1689441 T-A-T-TTTGAA-ATTTCAATAAT
1 TAAGTATCT-AATATTTCAATAAT
1689461 TAAGTATCTAATATTTCAATAAT
1 TAAGTATCTAATATTTCAATAAT
1689484 T
1 T
1689485 CTAAATTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
19 11 0.31
20 4 0.11
21 2 0.06
22 4 0.11
23 14 0.40
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (23 bp):
TAAGTATCTAATATTTCAATAAT
Found at i:1699115 original size:29 final size:28
Alignment explanation
Indices: 1699073--1699129 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 28
1699063 GAATTTAATC
1699073 TATGTATAATAATTTATAAACAAAAAATT
1 TATGTATAATAATTTATAAA-AAAAAATT
1699102 TATGTATAATAATTTATAAAAAAAAATT
1 TATGTATAATAATTTATAAAAAAAAATT
1699130 AGTTGCTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (28 bp):
TATGTATAATAATTTATAAAAAAAAATT
Found at i:1701384 original size:2 final size:2
Alignment explanation
Indices: 1701367--1701408 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1701357 ATCATTACCC
* *
1701367 AT AT AC AT AC 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
1701409 CAAACGTGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1709258 original size:31 final size:31
Alignment explanation
Indices: 1709215--1709286 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
1709205 ACGAAAATGG
* *
1709215 AATTATTTCCCCCAGTTCGGAGTTAAAAGAC
1 AATTATTCCCCCCAGTTCAGAGTTAAAAGAC
*
1709246 AATTATTCCCCCCAGTTCAGAGTTATAAGAC
1 AATTATTCCCCCCAGTTCAGAGTTAAAAGAC
1709277 AATTATTCCC
1 AATTATTCCC
1709287 TCCTTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (31 bp):
AATTATTCCCCCCAGTTCAGAGTTAAAAGAC
Found at i:1729360 original size:2 final size:2
Alignment explanation
Indices: 1729348--1729388 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1729338 AAGTTCATTA
*
1729348 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1729389 AAAGATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1736581 original size:2 final size:2
Alignment explanation
Indices: 1736574--1736599 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1736564 TTCGATGATA
1736574 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
1736600 TGATGTACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1737931 original size:2 final size:2
Alignment explanation
Indices: 1737924--1737948 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1737914 CAAATAAAGA
1737924 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1737949 ACATTAATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1751383 original size:18 final size:19
Alignment explanation
Indices: 1751360--1751408 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
1751350 TAAAATTATT
1751360 TTAATTTAATTTTTTAA-A
1 TTAATTTAATTTTTTAACA
* *
1751378 TTAATTAAATTTATTAACA
1 TTAATTTAATTTTTTAACA
1751397 -TAATTTAATTTT
1 TTAATTTAATTTT
1751409 AGATCTATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAATTTAATTTTTTAACA
Found at i:1759884 original size:28 final size:29
Alignment explanation
Indices: 1759828--1759892 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
1759818 TGATAAATGA
*
1759828 TATTTTAAT-TAATAAAAAAATAAAGATT
1 TATTTAAATATAATAAAAAAATAAAGATT
1759856 TGA-TTAAATATAATAAAAAAATAAA-ATT
1 T-ATTTAAATATAATAAAAAAATAAAGATT
1759884 TATTTAAAT
1 TATTTAAAT
1759893 TTTTTAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.03
28 16 0.48
29 16 0.48
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
TATTTAAATATAATAAAAAAATAAAGATT
Found at i:1759928 original size:2 final size:2
Alignment explanation
Indices: 1759919--1759948 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1759909 AATTTTTTAA
1759919 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1759949 AATTTGGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1762492 original size:53 final size:54
Alignment explanation
Indices: 1762428--1762536 Score: 150
Period size: 53 Copynumber: 2.0 Consensus size: 54
1762418 TTTCACAGAA
* * * *
1762428 TTTTCTTTGCTTTTTTTTATGCTCATTCT-AAGATGAGA-TTTTATGATCAAATT
1 TTTTCTTTGCTTTCTTCTATGCTCATT-TGAAGATGACATTTTTATAATCAAATT
*
1762481 TTTTCTTTGCTTTCTTCTATTCTCATTTGAAGATGACATTTTTATAATCAAATT
1 TTTTCTTTGCTTTCTTCTATGCTCATTTGAAGATGACATTTTTATAATCAAATT
1762535 TT
1 TT
1762537 AAAAAATACA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
52 1 0.02
53 32 0.65
54 16 0.33
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (54 bp):
TTTTCTTTGCTTTCTTCTATGCTCATTTGAAGATGACATTTTTATAATCAAATT
Found at i:1769903 original size:25 final size:25
Alignment explanation
Indices: 1769875--1769935 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
1769865 TAAGAGCTTT
1769875 TTTGATTTAAAATAAAAATATAA-AA
1 TTTGATTTAAAATAAAAA-ATAATAA
1769900 TTTGA-TTAAACATAAAAAATAATAA
1 TTTGATTTAAA-ATAAAAAATAATAA
*
1769925 TTT-TTTTAAAA
1 TTTGATTTAAAA
1769936 AATTTCATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 10 0.31
25 22 0.69
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (25 bp):
TTTGATTTAAAATAAAAAATAATAA
Found at i:1770723 original size:2 final size:2
Alignment explanation
Indices: 1770716--1770744 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1770706 AAAATTATTT
1770716 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1770745 GCACGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1776304 original size:177 final size:177
Alignment explanation
Indices: 1775996--1776329 Score: 542
Period size: 177 Copynumber: 1.9 Consensus size: 177
1775986 GTGTGCCTTA
*
1775996 TCAAGTCTAAACATCACAAAATATAGCTACATGACCTATAGCACAACTACTAGGCCCCTCAACAC
1 TCAAGTCTAAACATCACAAAATATAGCCACATGACCTATAGCACAACTACTAGGCCCCTCAACAC
* * * * *
1776061 ACAAATATAACCATTCACACATCATATATATTCATATGGCATGTAACATAGGTTATGTGACCCTT
66 ACAAATATAACAATTCACACATCATATATATTCATATGACATGTAACATAAGTGATATGACCCTT
1776126 AGTAAATCTCAAATCACCAATTCACATTGATAATCATTGATCATATT
131 AGTAAATCTCAAATCACCAATTCACATTGATAATCATTGATCATATT
* * * * * *
1776173 TCAAGTTTAAACATCTCAAAATATAGCCACATGACCTATAGCTCAACTATTAGGGCCCTCAGCAC
1 TCAAGTCTAAACATCACAAAATATAGCCACATGACCTATAGCACAACTACTAGGCCCCTCAACAC
*
1776238 ACAAATATAACAATTCACACATCATATATATTCATATGACATGTAACATAAGTGATATGGCCCTT
66 ACAAATATAACAATTCACACATCATATATATTCATATGACATGTAACATAAGTGATATGACCCTT
*
1776303 AGTAAATCTCAAATTACCAATTCACAT
131 AGTAAATCTCAAATCACCAATTCACAT
1776330 CAATAAGCAT
Statistics
Matches: 143, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
177 143 1.00
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.28
Consensus pattern (177 bp):
TCAAGTCTAAACATCACAAAATATAGCCACATGACCTATAGCACAACTACTAGGCCCCTCAACAC
ACAAATATAACAATTCACACATCATATATATTCATATGACATGTAACATAAGTGATATGACCCTT
AGTAAATCTCAAATCACCAATTCACATTGATAATCATTGATCATATT
Found at i:1787115 original size:17 final size:17
Alignment explanation
Indices: 1787078--1787114 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1787068 ATGCCTCGTT
*
1787078 AAAACCTTACGAGGAAA
1 AAAACCTTACGAGAAAA
1787095 AAAACCTTAC-AGAAAA
1 AAAACCTTACGAGAAAA
1787111 AAAA
1 AAAA
1787115 ATCTGAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.62, C:0.16, G:0.11, T:0.11
Consensus pattern (17 bp):
AAAACCTTACGAGAAAA
Found at i:1795736 original size:11 final size:11
Alignment explanation
Indices: 1795716--1795748 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1795706 CCACTTTCCC
1795716 TCTCTTTCTTT
1 TCTCTTTCTTT
*
1795727 TCTCTGTCTTT
1 TCTCTTTCTTT
1795738 TC-CTTTCTTT
1 TCTCTTTCTTT
1795748 T
1 T
1795749 TTACAACAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (11 bp):
TCTCTTTCTTT
Found at i:1813591 original size:22 final size:22
Alignment explanation
Indices: 1813566--1813620 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
1813556 TTAAGATTAA
*
1813566 TTTTT-TTGTAAGTTAATAATT
1 TTTTTATTTTAAGTTAATAATT
* *
1813587 TTTTTATTTTATGTTAATTATT
1 TTTTTATTTTAAGTTAATAATT
* *
1813609 TATATATTTTAA
1 TTTTTATTTTAA
1813621 TAGATAAGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (22 bp):
TTTTTATTTTAAGTTAATAATT
Found at i:1813952 original size:13 final size:13
Alignment explanation
Indices: 1813926--1813971 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 13
1813916 AAAATTTTCA
*
1813926 TTTTTA-AATAAT
1 TTTTTATAATTAT
1813938 TTTTTATAATTA-
1 TTTTTATAATTAT
*
1813950 TTTTTAAAATTAT
1 TTTTTATAATTAT
*
1813963 ATTTTATAA
1 TTTTTATAA
1813972 CAGAAAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTTTATAATTAT
Found at i:1813967 original size:25 final size:24
Alignment explanation
Indices: 1813925--1813971 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1813915 TAAAATTTTC
*
1813925 ATTTTTAAATAATTTTTTATAATT
1 ATTTTTAAATAATATTTTATAATT
*
1813949 ATTTTTAAAATTATATTTTATAA
1 ATTTTT-AAATAATATTTTATAA
1813972 CAGAAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTTTAAATAATATTTTATAATT
Found at i:1814867 original size:21 final size:22
Alignment explanation
Indices: 1814843--1814889 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1814833 CATATTAACA
*
1814843 AATTATT-TAATTTTTTAAAAT
1 AATTATTAAAATTTTTTAAAAT
1814864 AATT-TTAAAATTTTTTAAAAT
1 AATTATTAAAATTTTTTAAAAT
1814885 -ATTAT
1 AATTAT
1814890 GTTATCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATTATTAAAATTTTTTAAAAT
Found at i:1814881 original size:10 final size:10
Alignment explanation
Indices: 1814851--1814884 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1814841 CAAATTATTT
1814851 AATTTTTTAA
1 AATTTTTTAA
*
1814861 AATAATTTTAA
1 AAT-TTTTTAA
1814872 AATTTTTTAA
1 AATTTTTTAA
1814882 AAT
1 AAT
1814885 ATTATGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:1825968 original size:120 final size:121
Alignment explanation
Indices: 1825758--1825980 Score: 297
Period size: 120 Copynumber: 1.9 Consensus size: 121
1825748 TTTACTTGCA
* * * *
1825758 CTATTTTCGAATTCATTCCATTCAAAATATTATATTTTTAAACTCTTTTATCTTTTATTATTTTA
1 CTATTTTCGAATTCATACCACTCAAAATATTATATTATCAAACTCTTTTATCTTTTATTATTTTA
* * * *
1825823 TAAAAACTTACCATGACTAATATAAATTTTGAAGTAAAATTTATATTTTATTCATT
66 AAAAAACTTACCATCAATAATATAAATTTTGAAATAAAATTTATATTTTATTCATT
* * * *
1825879 CTATTTTCGAATTCATACTACTCAAACTATTATATTATCGAATTC-TTTATCTTTTAGTT-TTTT
1 CTATTTTCGAATTCATACCACTCAAAATATTATATTATCAAACTCTTTTATCTTTTA-TTATTTT
**
1825942 AAAAAAACTTACTGTCAATAATATAAATTTTGAAATAAA
65 AAAAAAACTTACCATCAATAATATAAATTTTGAAATAAA
1825981 GTTTTTTCGA
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
120 48 0.55
121 39 0.45
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (121 bp):
CTATTTTCGAATTCATACCACTCAAAATATTATATTATCAAACTCTTTTATCTTTTATTATTTTA
AAAAAACTTACCATCAATAATATAAATTTTGAAATAAAATTTATATTTTATTCATT
Found at i:1836394 original size:27 final size:27
Alignment explanation
Indices: 1836349--1836423 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
1836339 TTAAAATAAA
*
1836349 TAAA-TAAATAAATTATTAT-TTTTAT
1 TAAATTAAATAAATTTTTATATTTTAT
* * *
1836374 TATATTTAATTAAATTTTTATATTTTTT
1 TA-AATTAAATAAATTTTTATATTTTAT
1836402 TAAATTAAATAAATTTTTATAT
1 TAAATTAAATAAATTTTTATAT
1836424 AATAATTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 2 0.05
26 1 0.02
27 31 0.76
28 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TAAATTAAATAAATTTTTATATTTTAT
Found at i:1837138 original size:16 final size:16
Alignment explanation
Indices: 1837117--1837151 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1837107 AGACATATGC
*
1837117 TTTAATATTATATATT
1 TTTAATACTATATATT
*
1837133 TTTAATACTATTTATT
1 TTTAATACTATATATT
1837149 TTT
1 TTT
1837152 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTAATACTATATATT
Found at i:1853838 original size:30 final size:30
Alignment explanation
Indices: 1853804--1853868 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1853794 TCATAAAACG
*
1853804 TATTTGA-TGTAAATTAAAAATATAAAAATT
1 TATTTGACT-TAAAATAAAAATATAAAAATT
* **
1853834 TATTTGACTTAAAATAAAAGTATAAAGGTT
1 TATTTGACTTAAAATAAAAATATAAAAATT
1853864 TATTT
1 TATTT
1853869 TAATAATAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.42
Consensus pattern (30 bp):
TATTTGACTTAAAATAAAAATATAAAAATT
Found at i:1854302 original size:8 final size:8
Alignment explanation
Indices: 1854289--1854320 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
1854279 AGCATTATGC
1854289 TCTTCTTT
1 TCTTCTTT
1854297 TCTTCTTT
1 TCTTCTTT
1854305 TCTTCTTT
1 TCTTCTTT
1854313 TCTT-TTT
1 TCTTCTTT
1854320 T
1 T
1854321 ATCTATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (8 bp):
TCTTCTTT
Found at i:1866978 original size:9 final size:9
Alignment explanation
Indices: 1866964--1867004 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
1866954 CTCTAGTTAT
1866964 TATATAATA
1 TATATAATA
*
1866973 TATATAACA
1 TATATAATA
1866982 TATAT-ATA
1 TATATAATA
*
1866990 TGTATAATA
1 TATATAATA
1866999 TATATA
1 TATATA
1867005 TGTATTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 6 0.22
9 21 0.78
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (9 bp):
TATATAATA
Found at i:1867006 original size:15 final size:15
Alignment explanation
Indices: 1866981--1867009 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1866971 TATATATAAC
1866981 ATATATATATGTATA
1 ATATATATATGTATA
1866996 ATATATATATGTAT
1 ATATATATATGTAT
1867010 TAAATTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
ATATATATATGTATA
Found at i:1867456 original size:19 final size:19
Alignment explanation
Indices: 1867434--1867473 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1867424 TCGACCTTAA
**
1867434 TTATTATTTTAATATTATT
1 TTATTATTAAAATATTATT
1867453 TTATTATTAAAATATTATT
1 TTATTATTAAAATATTATT
1867472 TT
1 TT
1867474 TATTTCACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTATTAAAATATTATT
Found at i:1869277 original size:103 final size:103
Alignment explanation
Indices: 1869096--1869287 Score: 303
Period size: 103 Copynumber: 1.9 Consensus size: 103
1869086 TCAAACAAGA
* * * * *
1869096 AATTTAGCTTGGTGAGCAATCTTGCCTTATGGATCAACGTAAGGGTATCTTCTTAGAAAACAAAA
1 AATTTAGCCTAGTGAGCAATCTTGCCTTATGGATCAACGTAAAGGTATCTTCCTACAAAACAAAA
1869161 TATTGAACCTGATCAAAGCCAAGATCGAAGTAGGTAGG
66 TATTGAACCTGATCAAAGCCAAGATCGAAGTAGGTAGG
* *
1869199 AATTTAGCCTAGTGAGCAATCTTGTCTTATGGATCAACGTAAAGGTATTTTCCTACAAAACAAAA
1 AATTTAGCCTAGTGAGCAATCTTGCCTTATGGATCAACGTAAAGGTATCTTCCTACAAAACAAAA
* *
1869264 TATTGAACTTGATCTAAGCCAAGA
66 TATTGAACCTGATCAAAGCCAAGA
1869288 AGTAGGCAGG
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 80 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (103 bp):
AATTTAGCCTAGTGAGCAATCTTGCCTTATGGATCAACGTAAAGGTATCTTCCTACAAAACAAAA
TATTGAACCTGATCAAAGCCAAGATCGAAGTAGGTAGG
Found at i:1869468 original size:15 final size:17
Alignment explanation
Indices: 1869448--1869482 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1869438 TATTTTTTTA
1869448 AAAAAAT-AA-AAAAAT
1 AAAAAATAAAGAAAAAT
1869463 AAAAAATAAAGAAAAAT
1 AAAAAATAAAGAAAAAT
1869480 AAA
1 AAA
1869483 GAAAGGAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 2 0.11
17 9 0.50
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (17 bp):
AAAAAATAAAGAAAAAT
Found at i:1869821 original size:3 final size:3
Alignment explanation
Indices: 1869813--1869847 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1869803 ATTTATTTAG
1869813 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1869848 TATATTGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1869853 original size:12 final size:13
Alignment explanation
Indices: 1869805--1869850 Score: 69
Period size: 12 Copynumber: 3.6 Consensus size: 13
1869795 TTTTATTTAT
1869805 TTATTTAGTTATTA
1 TTATTTA-TTATTA
1869819 TTA-TTATTATTA
1 TTATTTATTATTA
1869831 TTA-TTATTATTA
1 TTATTTATTATTA
1869843 TTATTTAT
1 TTATTTAT
1869851 ATTGATGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 21 0.68
13 7 0.23
14 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:1870249 original size:41 final size:40
Alignment explanation
Indices: 1870202--1870292 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 40
1870192 AATATAGGTA
*
1870202 AAAGAAATTAAAATAAAATATATAATATAAAAAATTATATT
1 AAAGAAATGAAAATAAAATATATAATATAAAAAA-TATATT
* *
1870243 AAAGAAATGAAAATAAAATATATGATATTAAAAATATATT
1 AAAGAAATGAAAATAAAATATATAATATAAAAAATATATT
* *
1870283 TAAGAGATGA
1 AAAGAAATGA
1870293 TATTATATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 14 0.31
41 31 0.69
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.30
Consensus pattern (40 bp):
AAAGAAATGAAAATAAAATATATAATATAAAAAATATATT
Found at i:1870519 original size:15 final size:15
Alignment explanation
Indices: 1870481--1870522 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1870471 TTATTTTCCC
* *
1870481 TGCAATCACATTATT
1 TGCAATCATATTACT
1870496 TGCAATCATATTACT
1 TGCAATCATATTACT
*
1870511 TGTAATCATATT
1 TGCAATCATATT
1870523 GTATTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (15 bp):
TGCAATCATATTACT
Found at i:1877420 original size:78 final size:78
Alignment explanation
Indices: 1877322--1877465 Score: 270
Period size: 78 Copynumber: 1.8 Consensus size: 78
1877312 CTTAAACACG
* *
1877322 TTAAACCAGATTGAAAGCTTAGAATGTGAAAGGCTTTGGTGTGTGTTGAGAGTGAAGGTGTGAGG
1 TTAAACCAGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTGTGTGTTGAGAGTAAAGGTGTGAGG
1877387 CCAGATTGAAAGC
66 CCAGATTGAAAGC
1877400 TTAAACCAGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTGTGTGTTGAGAGTAAAGGTGTGAGG
1 TTAAACCAGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTGTGTGTTGAGAGTAAAGGTGTGAGG
1877465 C
66 C
1877466 TATATTTATA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.31, C:0.08, G:0.34, T:0.27
Consensus pattern (78 bp):
TTAAACCAGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTGTGTGTTGAGAGTAAAGGTGTGAGG
CCAGATTGAAAGC
Found at i:1877621 original size:260 final size:260
Alignment explanation
Indices: 1877160--1877636 Score: 819
Period size: 260 Copynumber: 1.8 Consensus size: 260
1877150 TTTGGTCCTC
* * *
1877160 AGAAGGTGAAAGGCTTTAGTGTGTGTTGAGAGTGAAGGTGTGAGGCTATATTTATAGGCACGTTG
1 AGAAGGTGAAAGGCTTTAGTGTGTGTTGAGAGTAAAGGTGTGAGGCTATATTTATAAGCACATTG
* * * *
1877225 AACCAGATTAGGGTGAGGCTGTATTTATAGGCATAGAATGAGGTGAGCATTGCACCAAATAAGGT
66 AACCAAATTAGGGTGAGGCTGTATTTATAGACATAGAATGAGGTGAACATTACACCAAATAAGGT
*
1877290 GAACGTTGAACCAGATTGAAAGCTTAAACACGTTAAACCAGATTGAAAGCTTAGAATGTGAAAGG
131 GAACGTTGAACCAGATTGAAAGCTTAAACACGTTAAACCAGATTGAAAGCTTAGAAGGTGAAAGG
*
1877355 CTTTGGTGTGTGTTGAGAGTGAAGGTGTGAGGCCAGATTGAAAGCTTAAACCAGATTGAAAGCTT
196 CTTTGGTATGTGTTGAGAGTGAAGGTGTGAGGCCAGATTGAAAGCTTAAACCAGATTGAAAGCTT
* *
1877420 AGAAGGTGAAAGGCTTTGGTGTGTGTTGAGAGTAAAGGTGTGAGGCTATATTTATAAGCACATTT
1 AGAAGGTGAAAGGCTTTAGTGTGTGTTGAGAGTAAAGGTGTGAGGCTATATTTATAAGCACATTG
* * *
1877485 AACCAAATTAGGGTGAGGTTGTATTTATAGACATAGAGTGAGGTGAACCTTACACCAAATAAGGT
66 AACCAAATTAGGGTGAGGCTGTATTTATAGACATAGAATGAGGTGAACATTACACCAAATAAGGT
*
1877550 GAACGTTGAACTAGATTGAAAGCTTAAACACGTTAAACCAGATTGAAAGCTTAGAAGGTGAAAGG
131 GAACGTTGAACCAGATTGAAAGCTTAAACACGTTAAACCAGATTGAAAGCTTAGAAGGTGAAAGG
1877615 CTTTGGTATGTGTTGAGAGTGA
196 CTTTGGTATGTGTTGAGAGTGA
1877637 GATTGAAAGC
Statistics
Matches: 202, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
260 202 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.27
Consensus pattern (260 bp):
AGAAGGTGAAAGGCTTTAGTGTGTGTTGAGAGTAAAGGTGTGAGGCTATATTTATAAGCACATTG
AACCAAATTAGGGTGAGGCTGTATTTATAGACATAGAATGAGGTGAACATTACACCAAATAAGGT
GAACGTTGAACCAGATTGAAAGCTTAAACACGTTAAACCAGATTGAAAGCTTAGAAGGTGAAAGG
CTTTGGTATGTGTTGAGAGTGAAGGTGTGAGGCCAGATTGAAAGCTTAAACCAGATTGAAAGCTT
Found at i:1877658 original size:47 final size:47
Alignment explanation
Indices: 1877589--1877683 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
1877579 ACGTTAAACC
1877589 AGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTATGTGTTGAGAGTG
1 AGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTATGTGTTGAGAGTG
1877636 AGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTATGTGTTGAGAGTG
1 AGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTATGTGTTGAGAGTG
1877683 A
1 A
1877684 AGTGTGAGGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.31, C:0.04, G:0.36, T:0.29
Consensus pattern (47 bp):
AGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTATGTGTTGAGAGTG
Found at i:1877735 original size:83 final size:84
Alignment explanation
Indices: 1877634--1877793 Score: 295
Period size: 83 Copynumber: 1.9 Consensus size: 84
1877624 GTGTTGAGAG
1877634 TGAGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTATGTGTTGAGAGTGAA-GTGTGAGGCTATA
1 TGAGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTATGTGTTGAGAGTGAAGGTGTGAGGCTATA
*
1877698 TTTATAGGCACGATTAGGA
66 TTTATAAGCACGATTAGGA
*
1877717 TGAGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTGTGTGTTGAGAGTGAAGGTGTGAGGCTATA
1 TGAGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTATGTGTTGAGAGTGAAGGTGTGAGGCTATA
1877782 TTTATAAGCACG
66 TTTATAAGCACG
1877794 TTTAACCAGA
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
83 50 0.68
84 24 0.32
ACGTcount: A:0.29, C:0.06, G:0.34, T:0.30
Consensus pattern (84 bp):
TGAGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTATGTGTTGAGAGTGAAGGTGTGAGGCTATA
TTTATAAGCACGATTAGGA
Found at i:1877935 original size:155 final size:155
Alignment explanation
Indices: 1877719--1878020 Score: 487
Period size: 155 Copynumber: 1.9 Consensus size: 155
1877709 GATTAGGATG
* **
1877719 AGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTGTGTGTTGAGAGTGAAGGTGTGAGGCTATATT
1 AGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTATGTGTTGAGAGTGAAGGCATGAGGCTATATT
* * * * * **
1877784 TATAAGCACGTTTAACCAGATTAGGGTGAGGTTGTATTTATAGACATAGAGTGAGGTGAACCTTA
66 TATAAGCACGTTGAACCAAATTAGGATGAGATTGTATTTATAGACATAGAGTAAGACGAACCTTA
*
1877849 CATCAAATAAGGTGAACGTTGAACC
131 CACCAAATAAGGTGAACGTTGAACC
*
1877874 AGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTATGTGTTGAGAGTGAAGGCATGTGGCTATATT
1 AGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTATGTGTTGAGAGTGAAGGCATGAGGCTATATT
*
1877939 TATAGGCACGTTGAACCAAATTAGGATGAGATTGTATTTATAGACATAGAGTAAGACGAACCTTA
66 TATAAGCACGTTGAACCAAATTAGGATGAGATTGTATTTATAGACATAGAGTAAGACGAACCTTA
1878004 CACCAAATAAGGTGAAC
131 CACCAAATAAGGTGAAC
1878021 ACACTCCGTT
Statistics
Matches: 134, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
155 134 1.00
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.28
Consensus pattern (155 bp):
AGATTGAAAGCTTAGAAGGTGAAAGGCTTTGGTATGTGTTGAGAGTGAAGGCATGAGGCTATATT
TATAAGCACGTTGAACCAAATTAGGATGAGATTGTATTTATAGACATAGAGTAAGACGAACCTTA
CACCAAATAAGGTGAACGTTGAACC
Found at i:1883279 original size:23 final size:25
Alignment explanation
Indices: 1883253--1883332 Score: 101
Period size: 27 Copynumber: 3.1 Consensus size: 25
1883243 ATATATAATA
1883253 TAATTATTT-T-TATAATTACTTTT
1 TAATTATTTATATATAATTACTTTT
1883276 TAATTACCTTTATAATATAATTACTTTT
1 TAATTA--TTTAT-ATATAATTACTTTT
1883304 ATAATTATTATATATATAATTACTTTT
1 -TAATTATT-TATATATAATTACTTTT
1883331 TA
1 TA
1883333 TAATAAGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
23 6 0.12
25 3 0.06
26 3 0.06
27 16 0.32
28 16 0.32
29 6 0.12
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (25 bp):
TAATTATTTATATATAATTACTTTT
Found at i:1883281 original size:11 final size:12
Alignment explanation
Indices: 1883251--1883336 Score: 66
Period size: 12 Copynumber: 6.5 Consensus size: 12
1883241 AGATATATAA
*
1883251 TATAATTATTTT
1 TATAATTACTTT
1883263 TATAATTACTTT
1 TATAATTACTTT
1883275 T-TAATTACCTTTAT
1 TATAATTA-C-TT-T
1883289 AATATAATTACTTT
1 --TATAATTACTTT
*
1883303 TATAATTATTATAT
1 TATAATTACT-T-T
1883317 ATATAATTACTTTT
1 -TATAATTAC-TTT
1883331 TATAAT
1 TATAAT
1883337 AAGAGAAAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
11 6 0.10
12 22 0.36
13 9 0.15
14 4 0.07
15 11 0.18
16 3 0.05
17 6 0.10
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (12 bp):
TATAATTACTTT
Found at i:1883298 original size:17 final size:17
Alignment explanation
Indices: 1883276--1883308 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1883266 AATTACTTTT
1883276 TAATTACCTTTATAATA
1 TAATTACCTTTATAATA
*
1883293 TAATTACTTTTATAAT
1 TAATTACCTTTATAAT
1883309 TATTATATAT
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:0.09, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATTACCTTTATAATA
Found at i:1885136 original size:22 final size:22
Alignment explanation
Indices: 1885087--1885136 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1885077 ATCAGATAAA
*
1885087 TTTTAAGTTTATAAATAAAATT
1 TTTTAAATTTATAAATAAAATT
* *
1885109 TATTAAATTTAATAAAT-ATATT
1 TTTTAAATTT-ATAAATAAAATT
1885131 TTTTAA
1 TTTTAA
1885137 GTTAAAAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTAAATTTATAAATAAAATT
Found at i:1886006 original size:117 final size:117
Alignment explanation
Indices: 1885798--1886026 Score: 386
Period size: 117 Copynumber: 2.0 Consensus size: 117
1885788 TTTAAAAGCC
* * * *
1885798 CATTGGATTTTAAAAATCAAAGTTTCAAGCCCATTTTCTGGTCCTTGAGTCTCATATTAATTTGC
1 CATTGCATTTTAAAAATCAAAGTTTCAAGCCCATTTTCTAGTCCTTGAGTCTAAGATTAATTTGC
1885863 ATAAAATAGTTATTTTAGGGGAAAGATTATATAAAAGTAATTCTTTTAGGGT
66 ATAAAATAGTTATTTTAGGGGAAAGATTATATAAAAGTAATTCTTTTAGGGT
*
1885915 CATTGCATTTTAAAAATCAAAGTTTCGAGCCCATTTTCTAGTCCTTGAGTCTAAGATTAATTTGC
1 CATTGCATTTTAAAAATCAAAGTTTCAAGCCCATTTTCTAGTCCTTGAGTCTAAGATTAATTTGC
* * *
1885980 ATAAAATAGTTTTTTTAGGGGGAAGATTATATAAAAGTAATTTTTTT
66 ATAAAATAGTTATTTTAGGGGAAAGATTATATAAAAGTAATTCTTTT
1886027 CAAGAGATAA
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 104 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (117 bp):
CATTGCATTTTAAAAATCAAAGTTTCAAGCCCATTTTCTAGTCCTTGAGTCTAAGATTAATTTGC
ATAAAATAGTTATTTTAGGGGAAAGATTATATAAAAGTAATTCTTTTAGGGT
Found at i:1898096 original size:20 final size:20
Alignment explanation
Indices: 1898073--1898110 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1898063 ATTTATTGTA
1898073 TAAATAAATTTTTTAATTAG
1 TAAATAAATTTTTTAATTAG
*
1898093 TAAATATATTTTTTAATT
1 TAAATAAATTTTTTAATT
1898111 TAAAATATTA
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:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TAAATAAATTTTTTAATTAG
Found at i:1898124 original size:21 final size:20
Alignment explanation
Indices: 1898074--1898124 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
1898064 TTTATTGTAT
1898074 AAATA-AATTTTTTAATTAG
1 AAATATAATTTTTTAATTAG
1898093 TAAATAT-ATTTTTTAATTTA-
1 -AAATATAATTTTTTAA-TTAG
1898113 AAATATTAATTT
1 AAATA-TAATTT
1898125 ATGATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.19
20 15 0.56
21 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
AAATATAATTTTTTAATTAG
Found at i:1915899 original size:16 final size:16
Alignment explanation
Indices: 1915880--1915914 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1915870 TAAAATTATA
*
1915880 AAATTATATATATATT
1 AAATTATATATATAAT
1915896 AAATTATATATATAAT
1 AAATTATATATATAAT
1915912 AAA
1 AAA
1915915 AAATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTATATATATAAT
Found at i:1941318 original size:18 final size:18
Alignment explanation
Indices: 1941288--1941322 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1941278 TATCTTTAAA
1941288 ATAATAAATAATAATATG
1 ATAATAAATAATAATATG
1941306 ATAA-AAATAAATAATAT
1 ATAATAAAT-AATAATAT
1941323 TTTAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
ATAATAAATAATAATATG
Found at i:1941700 original size:26 final size:25
Alignment explanation
Indices: 1941640--1941700 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
1941630 TTCTATCATC
* *
1941640 TTTTGTGCTAATATCGTAATTCGTA
1 TTTTGTGTTAATATCATAATTCGTA
* *
1941665 TTTCTATGTTAATATCATAATTTGTA
1 TTT-TGTGTTAATATCATAATTCGTA
1941691 TTGTTGTGTT
1 TT-TTGTGTT
1941701 TTAATTGGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 3 0.10
26 25 0.86
27 1 0.03
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (25 bp):
TTTTGTGTTAATATCATAATTCGTA
Found at i:1942965 original size:15 final size:15
Alignment explanation
Indices: 1942945--1942973 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1942935 TGAAAGAGAA
1942945 AAAATATTCAAATTT
1 AAAATATTCAAATTT
1942960 AAAATATTCAAATT
1 AAAATATTCAAATT
1942974 ATTTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATTCAAATTT
Found at i:1944305 original size:25 final size:26
Alignment explanation
Indices: 1944277--1944333 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
1944267 GAATTTAAAA
1944277 TTAAAAGAAAAAAATTAAAG-TTAAT
1 TTAAAAGAAAAAAATTAAAGTTTAAT
* * *
1944302 TTAAAATAAAAAAGTTTAAGTTTTAAT
1 TTAAAAGAAAAAAATTAAAG-TTTAAT
1944329 TTAAA
1 TTAAA
1944334 TTATAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 17 0.63
27 10 0.37
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (26 bp):
TTAAAAGAAAAAAATTAAAGTTTAAT
Found at i:1947038 original size:2 final size:2
Alignment explanation
Indices: 1947027--1947065 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1947017 TTAATAAATT
1947027 TA TA -A 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
1947066 GTCTTAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1969583 original size:21 final size:19
Alignment explanation
Indices: 1969554--1969615 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
1969544 ACCATTATCA
*
1969554 GCTTTATTACCCATTGTAGGT
1 GCTTCATTACCC--TGTAGGT
1969575 GCTTCATTA-CCTGTAGGT
1 GCTTCATTACCCTGTAGGT
* *
1969593 GCTTCATTA-CTTGCAGGT
1 GCTTCATTACCCTGTAGGT
1969611 GCTTC
1 GCTTC
1969616 TTCAATTGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 28 0.74
20 2 0.05
21 8 0.21
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (19 bp):
GCTTCATTACCCTGTAGGT
Found at i:1969591 original size:18 final size:18
Alignment explanation
Indices: 1969568--1969615 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1969558 TATTACCCAT
1969568 TGTAGGTGCTTCATTACC
1 TGTAGGTGCTTCATTACC
*
1969586 TGTAGGTGCTTCATTACT
1 TGTAGGTGCTTCATTACC
*
1969604 TGCAGGTGCTTC
1 TGTAGGTGCTTC
1969616 TTCAATTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (18 bp):
TGTAGGTGCTTCATTACC
Found at i:1969624 original size:18 final size:17
Alignment explanation
Indices: 1969566--1969651 Score: 64
Period size: 18 Copynumber: 4.8 Consensus size: 17
1969556 TTTATTACCC
*
1969566 ATTGTAGGTGCTTCATTA
1 ATTGCAGGTGCTTC-TTA
** *
1969584 CCTGTAGGTGCTTCATTA
1 ATTGCAGGTGCTTC-TTA
*
1969602 CTTGCAGGTGCTTCTTCA
1 ATTGCAGGTGCTTCTT-A
*
1969620 ATTGCTGGTGCTTCTTTA
1 ATTGCAGGTGCTTC-TTA
* *
1969638 ACTGCAGGCGCTTC
1 ATTGCAGGTGCTTC
1969652 ATTACTTTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
17 2 0.04
18 53 0.93
19 2 0.04
ACGTcount: A:0.15, C:0.22, G:0.23, T:0.40
Consensus pattern (17 bp):
ATTGCAGGTGCTTCTTA
Found at i:1971343 original size:15 final size:15
Alignment explanation
Indices: 1971312--1971353 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1971302 CCCCTTCTTA
*
1971312 TTCTTATTGTTCT-TC
1 TTCTTATTCTT-TGTC
*
1971327 TTCTTTTTCTTTGTC
1 TTCTTATTCTTTGTC
1971342 TTCTTATTCTTT
1 TTCTTATTCTTT
1971354 CCCTTCTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.05, C:0.19, G:0.05, T:0.71
Consensus pattern (15 bp):
TTCTTATTCTTTGTC
Found at i:1971648 original size:12 final size:13
Alignment explanation
Indices: 1971623--1971651 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1971613 TTGCCAACAG
1971623 TTCTGCTCTAAGC
1 TTCTGCTCTAAGC
1971636 TTCTGCT-TAAGC
1 TTCTGCTCTAAGC
1971648 TTCT
1 TTCT
1971652 TGTTTGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (13 bp):
TTCTGCTCTAAGC
Found at i:1979198 original size:18 final size:17
Alignment explanation
Indices: 1979170--1979204 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1979160 CTTAGGAAGA
1979170 AGAAAAAGAAGAAGAAC
1 AGAAAAAGAAGAAGAAC
*
1979187 AGAAACAAGAAGCAGAAC
1 AGAAA-AAGAAGAAGAAC
1979205 CAACCCAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.66, C:0.11, G:0.23, T:0.00
Consensus pattern (17 bp):
AGAAAAAGAAGAAGAAC
Found at i:1981385 original size:17 final size:18
Alignment explanation
Indices: 1981363--1981397 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1981353 CTTTTGCCTA
1981363 TTTTTTTACTGT-AAAAT
1 TTTTTTTACTGTCAAAAT
*
1981380 TTTTTTTGCTGTCAAAAT
1 TTTTTTTACTGTCAAAAT
1981398 CTCTTGTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (18 bp):
TTTTTTTACTGTCAAAAT
Found at i:1982527 original size:52 final size:52
Alignment explanation
Indices: 1982465--1982568 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
1982455 CAAGTTTTTT
* * **
1982465 TAAATTACCTTTAACATGATCAAATTAATTTTAACCCTTGTTATTTGAACAG
1 TAAATGACCTTTAACATGATCAAATCAATTCCAACCCTTGTTATTTGAACAG
* * * *
1982517 TAAATGACCTTTGACATGGTTAAATCAATTCCAACTCTTGTTATTTGAACAG
1 TAAATGACCTTTAACATGATCAAATCAATTCCAACCCTTGTTATTTGAACAG
1982569 GAATTTGGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (52 bp):
TAAATGACCTTTAACATGATCAAATCAATTCCAACCCTTGTTATTTGAACAG
Found at i:1983688 original size:142 final size:142
Alignment explanation
Indices: 1983432--1983691 Score: 502
Period size: 142 Copynumber: 1.8 Consensus size: 142
1983422 ATACGTGTGA
1983432 ATTGCACCTGGAAAACGCCATGCTCGATTTCAGACGAGGCCCTCGTCATAACTGCACCGATAGAC
1 ATTGCACCTGGAAAACGCCATGCTCGATTTCAGACGAGGCCCTCGTCATAACTGCACCGATAGAC
1983497 CTGTTCTTAAATCAATGCTTCAAAGCATACAAAGTGTTAAATCACTAACACTACGAAAACGCCAT
66 CTGTTCTTAAATCAATGCTTCAAAGCATACAAAGTGTTAAATCACTAACACTACGAAAACGCCAT
1983562 GCTCGATTTCAG
131 GCTCGATTTCAG
* *
1983574 ATTGCACCTGGAAAACGCCATGCTCGATTTCAGACGAGGCCGTCGTCATAACTGCATCGATAGAC
1 ATTGCACCTGGAAAACGCCATGCTCGATTTCAGACGAGGCCCTCGTCATAACTGCACCGATAGAC
1983639 CTGTTCTTAAATCAATGCTTCAAAGCATACAAAGTGTTAAATCACTAACACTA
66 CTGTTCTTAAATCAATGCTTCAAAGCATACAAAGTGTTAAATCACTAACACTA
1983692 TGTAGATGGA
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 116 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.25
Consensus pattern (142 bp):
ATTGCACCTGGAAAACGCCATGCTCGATTTCAGACGAGGCCCTCGTCATAACTGCACCGATAGAC
CTGTTCTTAAATCAATGCTTCAAAGCATACAAAGTGTTAAATCACTAACACTACGAAAACGCCAT
GCTCGATTTCAG
Found at i:2000953 original size:21 final size:20
Alignment explanation
Indices: 2000916--2000954 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2000906 CTATCATATA
*
2000916 TTATAACATTAATATATAAG
1 TTATAACATTAAAATATAAG
*
2000936 TTATATCATTTAAAATATA
1 TTATAACA-TTAAAATATA
2000955 TACCTTGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (20 bp):
TTATAACATTAAAATATAAG
Found at i:2001122 original size:16 final size:16
Alignment explanation
Indices: 2001100--2001140 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2001090 AATTTTCTTA
2001100 ATATATATAAAAATAT
1 ATATATATAAAAATAT
* * *
2001116 TTATATATTAATATAT
1 ATATATATAAAAATAT
2001132 ATATATATA
1 ATATATATA
2001141 TAATGTTTAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATATATAAAAATAT
Found at i:2001137 original size:14 final size:14
Alignment explanation
Indices: 2001097--2001137 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2001087 GTTAATTTTC
2001097 TTAATATATATA-A
1 TTAATATATATATA
* *
2001110 -AAATATTTATATA
1 TTAATATATATATA
2001123 TTAATATATATATA
1 TTAATATATATATA
2001137 T
1 T
2001138 ATATAATGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
12 9 0.41
13 1 0.05
14 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAATATATATATA
Found at i:2007924 original size:45 final size:45
Alignment explanation
Indices: 2007874--2007960 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
2007864 GTCCCTTTAT
* * *
2007874 AACCGTTAGGTTCGAATTATTCTTTTACAGCATGAACCCCTTTGC
1 AACCGTTAGGATCAAAGTATTCTTTTACAGCATGAACCCCTTTGC
* *
2007919 AACCGTTAGGATCAAAGTATTTTTTTACAGCATGAGCCCCTT
1 AACCGTTAGGATCAAAGTATTCTTTTACAGCATGAACCCCTT
2007961 CCAGGTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (45 bp):
AACCGTTAGGATCAAAGTATTCTTTTACAGCATGAACCCCTTTGC
Found at i:2014332 original size:14 final size:14
Alignment explanation
Indices: 2014313--2014342 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2014303 ATGATAAATT
*
2014313 TAGAAAATAGGAAC
1 TAGAAAATAGAAAC
2014327 TAGAAAATAGAAAC
1 TAGAAAATAGAAAC
2014341 TA
1 TA
2014343 AGGATTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.17, T:0.17
Consensus pattern (14 bp):
TAGAAAATAGAAAC
Found at i:2021749 original size:34 final size:35
Alignment explanation
Indices: 2021687--2021769 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 35
2021677 ATAATAATAA
* *
2021687 ATCCTAATTGTATTTATTTTTTTGAATAGCAATAT
1 ATCCTAATTGTATTTATTTTTTTAAATAGCAACAT
* *
2021722 ATGCTAATTGTATTT-TTTTTTTAAATAGCACCAT
1 ATCCTAATTGTATTTATTTTTTTAAATAGCAACAT
2021756 ATCCTAATTGTATT
1 ATCCTAATTGTATT
2021770 AAAATAAGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 29 0.67
35 14 0.33
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (35 bp):
ATCCTAATTGTATTTATTTTTTTAAATAGCAACAT
Found at i:2024447 original size:2 final size:2
Alignment explanation
Indices: 2024440--2024481 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2024430 CCTTAAAGCA
*
2024440 AT AT AT AT AT AT AT AT AT AT AT AT AC 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
2024482 TCTCATTCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2041814 original size:11 final size:11
Alignment explanation
Indices: 2041798--2041827 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2041788 CCAGCAGTGA
2041798 TTTTTCTTTTT
1 TTTTTCTTTTT
2041809 TTTTTCTTTTT
1 TTTTTCTTTTT
2041820 TCTTTTCT
1 T-TTTTCT
2041828 CTTTCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:2041818 original size:10 final size:10
Alignment explanation
Indices: 2041798--2041886 Score: 56
Period size: 10 Copynumber: 8.9 Consensus size: 10
2041788 CCAGCAGTGA
2041798 TTTTTC-TTT
1 TTTTTCTTTT
*
2041807 TTTTT-TTCT
1 TTTTTCTTTT
2041816 TTTTTCTTTT
1 TTTTTCTTTT
*
2041826 CTCTTTCCTTTT
1 -T-TTTTCTTTT
** *
2041838 TTCCTCTTTA
1 TTTTTCTTTT
* *
2041848 ATTTTCTTCT
1 TTTTTCTTTT
* *
2041858 GTGTTCTTTT
1 TTTTTCTTTT
2041868 TTTTTCTTTT
1 TTTTTCTTTT
*
2041878 TCTTTCTTT
1 TTTTTCTTT
2041887 GACTTGGATT
Statistics
Matches: 58, Mismatches: 18, Indels: 7
0.70 0.22 0.08
Matches are distributed among these distances:
9 12 0.21
10 36 0.62
11 2 0.03
12 8 0.14
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:2044045 original size:20 final size:21
Alignment explanation
Indices: 2044008--2044047 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2043998 AATTAATGTT
2044008 AGAAAATTTAGAAGAAGAAGG
1 AGAAAATTTAGAAGAAGAAGG
*
2044029 AGAATATTTAG-AGAAGAAG
1 AGAAAATTTAGAAGAAGAAG
2044048 AAAGAGTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (21 bp):
AGAAAATTTAGAAGAAGAAGG
Found at i:2069045 original size:18 final size:18
Alignment explanation
Indices: 2069022--2069058 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2069012 AGGCGGCTCA
*
2069022 ATCTCTTCCGCCTCCTCC
1 ATCTCTTCCGCCGCCTCC
*
2069040 ATCTCTTCCTCCGCCTCC
1 ATCTCTTCCGCCGCCTCC
2069058 A
1 A
2069059 CCTGCGCCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.54, G:0.05, T:0.32
Consensus pattern (18 bp):
ATCTCTTCCGCCGCCTCC
Found at i:2069266 original size:16 final size:16
Alignment explanation
Indices: 2069245--2069280 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2069235 AACCCTAAAA
2069245 CTCTCTCTCTCTTTCT
1 CTCTCTCTCTCTTTCT
*
2069261 CTCTCTCTCTCTTTTT
1 CTCTCTCTCTCTTTCT
2069277 CTCT
1 CTCT
2069281 AAATTTAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (16 bp):
CTCTCTCTCTCTTTCT
Found at i:2069763 original size:4 final size:4
Alignment explanation
Indices: 2069756--2069780 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2069746 CTGTTTGTTT
2069756 GTTG GTTG GTTG GTTG GTTG GTTG G
1 GTTG GTTG GTTG GTTG GTTG GTTG G
2069781 ATCATCTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (4 bp):
GTTG
Found at i:2072869 original size:13 final size:13
Alignment explanation
Indices: 2072834--2072876 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
2072824 TACACTTTCC
*
2072834 TTTTTAGCTTCTT
1 TTTTTAGCTTTTT
* *
2072847 CTTTT-CCTTTTT
1 TTTTTAGCTTTTT
2072859 TTTTTAGCTTTTT
1 TTTTTAGCTTTTT
2072872 TTTTT
1 TTTTT
2072877 TTTTGCTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTTTAGCTTTTT
Found at i:2082892 original size:42 final size:43
Alignment explanation
Indices: 2082833--2082916 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
2082823 GTTAGGATAA
2082833 GATTATTGTATTTGG-CCCTATAAAAGGATCCTGTAATCTCTC
1 GATTATTGTATTTGGCCCCTATAAAAGGATCCTGTAATCTCTC
2082875 GATTATTGTATTTGGCCCCTATAAAAGGATCCTGTAATCTCT
1 GATTATTGTATTTGGCCCCTATAAAAGGATCCTGTAATCTCT
2082917 TAATCACCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 15 0.37
43 26 0.63
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (43 bp):
GATTATTGTATTTGGCCCCTATAAAAGGATCCTGTAATCTCTC
Found at i:2096623 original size:14 final size:14
Alignment explanation
Indices: 2096604--2096631 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2096594 CAGAGGCATG
2096604 TGTCACGGGCCACA
1 TGTCACGGGCCACA
2096618 TGTCACGGGCCACA
1 TGTCACGGGCCACA
2096632 GCCCAGACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.29, T:0.14
Consensus pattern (14 bp):
TGTCACGGGCCACA
Found at i:2096689 original size:27 final size:27
Alignment explanation
Indices: 2096657--2096714 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
2096647 GAGGCCCAAG
*
2096657 AGGGTGCCAGCCCACCAAGATCCATGT
1 AGGGTGCCAGCCCACCAAGACCCATGT
2096684 AGGGTGCCAGCCCACCAAGACCCATGT
1 AGGGTGCCAGCCCACCAAGACCCATGT
2096711 AGGG
1 AGGG
2096715 ATTTCCCTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.33, G:0.29, T:0.12
Consensus pattern (27 bp):
AGGGTGCCAGCCCACCAAGACCCATGT
Found at i:2096785 original size:15 final size:15
Alignment explanation
Indices: 2096765--2096822 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
2096755 TCCCAAATGG
2096765 TTTTGGAGGGAAATC
1 TTTTGGAGGGAAATC
2096780 TTTTGGAGGGAAATC
1 TTTTGGAGGGAAATC
* *
2096795 CTTTGGAGGGAAA-A
1 TTTTGGAGGGAAATC
2096809 TTTTGGAGGGAAAT
1 TTTTGGAGGGAAAT
2096823 GGGTGGGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
14 12 0.31
15 27 0.69
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.31
Consensus pattern (15 bp):
TTTTGGAGGGAAATC
Found at i:2096820 original size:29 final size:30
Alignment explanation
Indices: 2096766--2096822 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
2096756 CCCAAATGGT
*
2096766 TTTGGAGGGAAATCTTTTGGAGGGAAATCC
1 TTTGGAGGGAAATATTTTGGAGGGAAATCC
2096796 TTTGGAGGGAAA-ATTTTGGAGGGAAAT
1 TTTGGAGGGAAATATTTTGGAGGGAAAT
2096823 GGGTGGGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (30 bp):
TTTGGAGGGAAATATTTTGGAGGGAAATCC
Found at i:2111132 original size:10 final size:9
Alignment explanation
Indices: 2111114--2111153 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
2111104 TATAGAAATT
2111114 AAAAAATAA
1 AAAAAATAA
2111123 AAATAAATAA
1 AAA-AAATAA
2111133 CAAAAAATAA
1 -AAAAAATAA
*
2111143 GAAAAATAA
1 AAAAAATAA
2111152 AA
1 AA
2111154 GTACCAACGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 12 0.44
10 12 0.44
11 3 0.11
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:2111543 original size:57 final size:57
Alignment explanation
Indices: 2111476--2111584 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 57
2111466 CTTCTTCTAC
* * *
2111476 ATTTCCATTATTTATCTTATTTATTATCATTATTTACCTCTTTCTATTCAAACTGTCA
1 ATTTCCATTATTTATATTATTTATTATCATTA-TCACCTCTTTCAATTCAAACTGTCA
*
2111534 ATTT-CATTATTTATATTATTTATTATCGTTATCACCTCTTTCAATTCAAAC
1 ATTTCCATTATTTATATTATTTATTATCATTATCACCTCTTTCAATTCAAAC
2111585 AGTAATTGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
56 18 0.38
57 25 0.53
58 4 0.09
ACGTcount: A:0.28, C:0.18, G:0.02, T:0.52
Consensus pattern (57 bp):
ATTTCCATTATTTATATTATTTATTATCATTATCACCTCTTTCAATTCAAACTGTCA
Found at i:2125141 original size:200 final size:201
Alignment explanation
Indices: 2124798--2125199 Score: 727
Period size: 200 Copynumber: 2.0 Consensus size: 201
2124788 CTAGTTAAAG
*
2124798 AGTATGGATTTAAATCCCCTTACCTCAATTGTGTATATATAAAAAAGAAAGTAAGCCTTCCGCAC
1 AGTATGGATTTAAATCCCCTTACCTCAATTGTGTATATATAAAAAAGAAAGTAAGCCTTCCACAC
*
2124863 TAACCCATTAAATCCCTTTCAAAACGCACCGTTTGGTGCTTCAACCCTCTCTAAGTGAAGTGATT
66 TAACCCATTAAATCCCTTTCAAAACGCACCGTTTGGTGCTTCAACCCTCTCCAAGTGAAGTGATT
* *
2124928 TGAGCCTAAATTTACTCTTCCCTCACCACTCTAAAACGTCGTCA-TTAGGGATCATTAAACCTTG
131 TGAGACTAAATTTACTCTTCCCTCACCACTCTAAAACGTCATCATTTAGGGATCATTAAACCTTG
2124992 GTATAA
196 GTATAA
* *
2124998 AGTATGGATTTGAATCCCCTTCCCTCAATTGTGTATATA-AATAAAAGAAAGTAAGCCTTCCACA
1 AGTATGGATTTAAATCCCCTTACCTCAATTGTGTATATATAA-AAAAGAAAGTAAGCCTTCCACA
2125062 CTAACCCATTAAATCCCTTTCAAAACGCACCGTTTGGTGCTTCAACCCTCTCCAAGTGAAGTGAT
65 CTAACCCATTAAATCCCTTTCAAAACGCACCGTTTGGTGCTTCAACCCTCTCCAAGTGAAGTGAT
2125127 TTGAGACTAAATTTACTCTTCCCTCACCACTCTAAAACGTCATCATTTAGGGATCATTAAACCTT
130 TTGAGACTAAATTTACTCTTCCCTCACCACTCTAAAACGTCATCATTTAGGGATCATTAAACCTT
2125192 GGTATAA
195 GGTATAA
2125199 A
1 A
2125200 CCCTTTTTTC
Statistics
Matches: 194, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
199 2 0.01
200 165 0.85
201 27 0.14
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (201 bp):
AGTATGGATTTAAATCCCCTTACCTCAATTGTGTATATATAAAAAAGAAAGTAAGCCTTCCACAC
TAACCCATTAAATCCCTTTCAAAACGCACCGTTTGGTGCTTCAACCCTCTCCAAGTGAAGTGATT
TGAGACTAAATTTACTCTTCCCTCACCACTCTAAAACGTCATCATTTAGGGATCATTAAACCTTG
GTATAA
Found at i:2129839 original size:2 final size:2
Alignment explanation
Indices: 2129832--2129858 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2129822 TGTATGTATG
2129832 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2129859 TGAATATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2141018 original size:14 final size:14
Alignment explanation
Indices: 2140999--2141029 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2140989 TTAACCTGTT
2140999 ATTATTGAATTATA
1 ATTATTGAATTATA
*
2141013 ATTATTTAATTATA
1 ATTATTGAATTATA
2141027 ATT
1 ATT
2141030 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
ATTATTGAATTATA
Found at i:2141037 original size:14 final size:14
Alignment explanation
Indices: 2140999--2141040 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2140989 TTAACCTGTT
*
2140999 ATTATTGAATTATA
1 ATTATTAAATTATA
*
2141013 ATTATTTAATTATA
1 ATTATTAAATTATA
2141027 ATT-TTAAAATTATA
1 ATTATT-AAATTATA
2141041 TTAATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 2 0.08
14 23 0.92
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
ATTATTAAATTATA
Found at i:2142134 original size:22 final size:22
Alignment explanation
Indices: 2142108--2142156 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2142098 TTTCATTTAT
*
2142108 AAATATTATATATATAATAATA
1 AAATATTATAAATATAATAATA
**
2142130 AAATATTATAAATATCCTAATA
1 AAATATTATAAATATAATAATA
2142152 AAATA
1 AAATA
2142157 ATTAAACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATATTATAAATATAATAATA
Found at i:2145063 original size:31 final size:31
Alignment explanation
Indices: 2144964--2145063 Score: 82
Period size: 31 Copynumber: 3.2 Consensus size: 31
2144954 GCCCAATTTA
* *
2144964 GTTGGCATTCAAGGTGTATAAGTCCAGTTAC
1 GTTGGCATCCAAGATGTATAAGTCCAGTTAC
* * * *
2144995 GTTGGCA-CGAAAGGA-GTGTAAGCCCAATTTAAC
1 GTTGGCATC-CAA-GATGTATAAGTCC-AGTT-AC
2145028 --TGGCATCCAAGATGTATAAGTCCAGTTAC
1 GTTGGCATCCAAGATGTATAAGTCCAGTTAC
2145057 GTTGGCA
1 GTTGGCA
2145064 CGAAAGGAGT
Statistics
Matches: 51, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
29 2 0.04
30 5 0.10
31 37 0.73
32 5 0.10
33 2 0.04
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (31 bp):
GTTGGCATCCAAGATGTATAAGTCCAGTTAC
Found at i:2145185 original size:61 final size:60
Alignment explanation
Indices: 2144947--2146380 Score: 864
Period size: 61 Copynumber: 23.5 Consensus size: 60
2144937 AACATGAGAG
* ** * * * * *
2144947 GATTTTAGCCCAATTTAGTTGGCATTCAAGGTGTATAAGTCCAGTTACGTTGGCACGAAAG
1 GATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCAC-AAAA
* * * *
2145008 GAGTGTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCCAGTTACGTTGGCACGAAAG
1 GA-TTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCAC-AAAA
* * * * * * ** ** *
2145070 GAGTTT-ACCCCTAATTTAGCTAGCATCCAAGATTTTTAAGCCTAACTATGTTGGCATAAAGA
1 GA-TTTAAGCCC-AATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCACAAA-A
*
2145132 GATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAATTACATTGGCACAAAA
1 GATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCACAAAA
* * * ** * *
2145192 GGAGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTTTAAGTCTACCTACGTTAGCACGAAAA
1 -GA-TTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCAC-AAAA
* * * * * **
2145255 GATTTAAGCCCAATTAAATTGACGTCCAAGATATATAAGTCTAGTTATGTTGGCACAAAAA
1 GATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCAC-AAAA
* * * * *
2145316 GATATTTAAGCCCAATTTAGCTAGTATCCAAGATGTATAAGTCCAGTTACATTGCCACAAAA
1 G--ATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCACAAAA
* * * ** * * *
2145378 GGAGTTTAAGCCCAATTTATCTAGCATCCAAGATGTTTAAGTCTAACTACGTTGGTATGAAAA
1 -GA-TTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCA-CAAAA
* * * *
2145441 GATTTAAGCCCAATTTAACTGTCATCCAAGATATGTAAGTCCAGTTACATTGGCACAAAA
1 GATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCACAAAA
* * * * * * **
2145501 GGAGTTTAAGCCCAATTTAGCTAGCATTCAAGATGTTTAAGCCTAATTATGTTGGCACAAAAA
1 -GA-TTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCAC-AAAA
* ** * * * * * * *
2145564 GATTTAAGCCCAATTTAGCCAGCATCTACGATGTACAAGTCCAATTACGTTGGCTCAAAAA
1 GATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCAC-AAAA
* * ** * * * * *
2145625 AATTTTCAAACCCAATTTAGTTGGCA-CCTAAGATATTTAAGTCCAATTACATTAGCACAAAA
1 GA-TTT-AAGCCCAATTTAACTGGCATCC-AAGATGTATAAGTCTAGTTACATTGGCACAAAA
* * * * * * * * *
2145687 GGAGTTTAAGCTCAATTTAGCTAGCATCGAAGATGTTTAAGTCTAGCTACGTTGACATGAAAA
1 -GA-TTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCA-CAAAA
* * * *
2145750 AATTTAAGCCCAATTTAACTGGCATCCAAGATATATAAGT-TCAATTACATTAGCACAAAAA
1 GATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCT-AGTTACATTGGCAC-AAAA
* * * * * * *
2145811 GAGTTTAAGTCCAATTAAACTAGCATTCAAGATGTATAAGTCCAATTACATTGGCA-TAAA
1 GA-TTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCACAAAA
*
2145871 GATCTTTAAGCCCAATTT-ACTAGGCA-CTCAAGATGTATAAGTCTAGTTA-AGTTGGCATGAAT
1 GA--TTTAAGCCCAATTTAACT-GGCATC-CAAGATGTATAAGTCTAGTTACA-TTGGCA-CAA-
2145933 AA
59 AA
* * * * * *
2145935 G-TTTAAGCCCAATTAAAATAGCATCCAAGATGT-TATGT-T-G--GCA-T-G-A-ATAA
1 GATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCACAAAA
* * * * * *
2145985 G-TTTAAGTCCAATTAAAATAGCATCCAAGATGTATAAATCCAGTTACATTGGCACAAAAA
1 GATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCAC-AAAA
* * * * * *
2146045 GAGTTTAAACCCAATTAAACCGACATCCAAAATGTATAAGTCTAGTTACATTGACAC-AAA
1 GA-TTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCACAAAA
* * **
2146105 GATGTTTAAGCCCAATTT-ACTTGGGATCCAAGATAG-ATAAGCCTAGTTGTATTGGCACGAATA
1 GA--TTTAAGCCCAATTTAAC-TGGCATCCAAGAT-GTATAAGTCTAGTTACATTGGCAC-AA-A
2146168 A
60 A
* ** * * * *** * *
2146169 G-TTTAAGCACAATCAAACTGACATCCAAGATGTATAAATCTAATTGTGTTGGCACGAAT
1 GATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCACAAAA
* * * * * * * * *
2146228 GAGTTTAAGCTCAATTAAACTGGCATCCAAGATGTGTAAGTCCAATTATATTGGTACGAAT
1 GA-TTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCACAAAA
* * * * * * * * *
2146289 GAGCTTAAACCCAATTAAACTGACATCTAAGATGTTTAAGTCCAGTTATATTGACAC-AAA
1 GA-TTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCACAAAA
* *
2146349 GATGTTTAAGCCTAA-TTATACTAGCATCCAAG
1 GA--TTTAAGCCCAATTTA-ACTGGCATCCAAG
2146381 TTATTTAAAC
Statistics
Matches: 1084, Mismatches: 230, Indels: 118
0.76 0.16 0.08
Matches are distributed among these distances:
50 34 0.03
51 4 0.00
53 2 0.00
54 1 0.00
55 3 0.00
56 1 0.00
57 2 0.00
58 2 0.00
59 3 0.00
60 38 0.04
61 501 0.46
62 383 0.35
63 104 0.10
64 6 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (60 bp):
GATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCACAAAA
Found at i:2145185 original size:123 final size:122
Alignment explanation
Indices: 2144953--2146275 Score: 924
Period size: 123 Copynumber: 10.8 Consensus size: 122
2144943 AGAGGATTTT
* * * * * * * *
2144953 AGCCCAATTTAGTTGGCATTCAAGGTGTATAAGTCCAGTTACGTTGGCACGAAAGGAGTGTAAGC
1 AGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAATTACGTTGGCA-TAAAAGA-TTTAAGC
* * * *
2145018 CCAATTTAACTGGCATCCAAGATGTATAAGTCCAGTTACGTTGGCACGAAAGGAGTTT-
64 CCAATTTAACTGGCATCCAAGATGTATAAGTCTAATTACGTTGGCACAAAAAGAGTTTA
* * * * *
2145076 ACCCCTAATTTAGCTAGCATCCAAGATTTTTAAG-CCTAACTATGTTGGCATAAAGAGATTTAAG
1 AGCCC-AATTTAGCTAGCATCCAAGATGTATAAGTCC-AATTACGTTGGCATAAA-AGATTTAAG
* *
2145140 CCCAATTTAACTGGCATCCAAGATGTATAAGTCTAATTACATTGGCACAAAAGGAGTTTA
63 CCCAATTTAACTGGCATCCAAGATGTATAAGTCTAATTACGTTGGCACAAAAAGAGTTTA
* * ** * *
2145200 AGCCCAATTTAGCTAGCATCCAAGATGTTTAAGTCTACCTACGTTAGCACGAAAAGATTTAAGCC
1 AGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAATTACGTTGGCA-TAAAAGATTTAAGCC
* * * * * * * *
2145265 CAATTAAATTGACGTCCAAGATATATAAGTCTAGTTATGTTGGCACAAAAAGATATTTA
65 CAATTTAACTGGCATCCAAGATGTATAAGTCTAATTACGTTGGCACAAAAAGA-GTTTA
* * * * *
2145324 AGCCCAATTTAGCTAGTATCCAAGATGTATAAGTCCAGTTACATTGCCACAAAAGGAGTTTAAGC
1 AGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAATTACGTTGGCATAAAA-GA-TTTAAGC
* * * * * **
2145389 CCAATTTATCTAGCATCCAAGATGTTTAAGTCTAACTACGTTGGTATGAAAAGA-TTTA
64 CCAATTTAACTGGCATCCAAGATGTATAAGTCTAATTACGTTGGCACAAAAAGAGTTTA
* * * * * *
2145447 AGCCCAATTTAACT-GTCATCCAAGATATGTAAGTCCAGTTACATTGGCACAAAAGGAGTTTAAG
1 AGCCCAATTTAGCTAG-CATCCAAGATGTATAAGTCCAATTACGTTGGCATAAAA-GA-TTTAAG
* * * * * *
2145511 CCCAATTTAGCTAGCATTCAAGATGTTTAAGCCTAATTATGTTGGCACAAAAAGA-TTTA
63 CCCAATTTAACTGGCATCCAAGATGTATAAGTCTAATTACGTTGGCACAAAAAGAGTTTA
* * * * *
2145570 AGCCCAATTTAGCCAGCATCTACGATGTACAAGTCCAATTACGTTGGC-TCAAAAAAATTTTCAA
1 AGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAATTACGTTGGCAT--AAAAGA-TTT-AA
* ** * * * * * *
2145634 ACCCAATTTAGTTGGCA-CCTAAGATATTTAAGTCCAATTACATTAGCACAAAAGGAGTTTA
62 GCCCAATTTAACTGGCATCC-AAGATGTATAAGTCTAATTACGTTGGCACAAAAAGAGTTTA
* * * * ** * *
2145695 AGCTCAATTTAGCTAGCATCGAAGATGTTTAAGTCTAGCTACGTTGACATGAAAAAATTTAAGCC
1 AGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAATTACGTTGGCAT-AAAAGATTTAAGCC
* * *
2145760 CAATTTAACTGGCATCCAAGATATATAAGT-TCAATTACATTAGCACAAAAAGAGTTTA
65 CAATTTAACTGGCATCCAAGATGTATAAGTCT-AATTACGTTGGCACAAAAAGAGTTTA
* * * * *
2145818 AGTCCAATTAAACTAGCATTCAAGATGTATAAGTCCAATTACATTGGCAT-AAAGATCTTTAAGC
1 AGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAATTACGTTGGCATAAAAGA--TTTAAGC
* * ** *
2145882 CCAATTT-ACTAGGCA-CTCAAGATGTATAAGTCTAGTTAAGTTGGCATGAATA-AGTTTA
64 CCAATTTAACT-GGCATC-CAAGATGTATAAGTCTAATTACGTTGGCACAAAAAGAGTTTA
* ** *
2145940 AGCCCAATTAAAATAGCATCCAAGATG--T---T---A-T--GTTGGCATGAATAAG-TTTAAGT
1 AGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAATTACGTTGGCAT-AA-AAGATTTAAGC
* * * * * * *
2145993 CCAATTAAAATAGCATCCAAGATGTATAAATCCAGTTACATTGGCACAAAAAGAGTTTA
64 CCAATTTAACTGGCATCCAAGATGTATAAGTCTAATTACGTTGGCACAAAAAGAGTTTA
* * * * * * * * * *
2146052 AACCCAATTAAAC-CGACATCCAAAATGTATAAGTCTAGTTACATTGACA-CAAAGATGTTTAAG
1 AGCCCAATTTAGCTAG-CATCCAAGATGTATAAGTCCAATTACGTTGGCATAAAAGA--TTTAAG
* * * *** * *
2146115 CCCAATTT-ACTTGGGATCCAAGATAG-ATAAGCCTAGTTGTATTGGCACGAATA-AGTTTA
63 CCCAATTTAAC-TGGCATCCAAGAT-GTATAAGTCTAATTACGTTGGCACAAAAAGAGTTTA
* ** * * * ** ** *
2146174 AGCACAATCAAACT-GACATCCAAGATGTATAAATCTAATTGTGTTGGCACGAATGAGTTTAAGC
1 AGCCCAATTTAGCTAG-CATCCAAGATGTATAAGTCCAATTACGTTGGCATAAAAGA-TTTAAGC
* * * *
2146238 TCAATTAAACTGGCATCCAAGATGTGTAAGTCCAATTA
64 CCAATTTAACTGGCATCCAAGATGTATAAGTCTAATTA
2146276 TATTGGTACG
Statistics
Matches: 963, Mismatches: 186, Indels: 103
0.77 0.15 0.08
Matches are distributed among these distances:
111 51 0.05
112 30 0.03
113 2 0.00
114 5 0.01
117 2 0.00
120 4 0.00
121 7 0.01
122 113 0.12
123 507 0.53
124 146 0.15
125 95 0.10
126 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (122 bp):
AGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAATTACGTTGGCATAAAAGATTTAAGCCC
AATTTAACTGGCATCCAAGATGTATAAGTCTAATTACGTTGGCACAAAAAGAGTTTA
Found at i:2145572 original size:309 final size:305
Alignment explanation
Indices: 2144973--2145967 Score: 1131
Period size: 309 Copynumber: 3.2 Consensus size: 305
2144963 AGTTGGCATT
* * * * * *
2144973 CAAGGTGTATAAGTCCAGTTACGTTGGCACGAAAGGAGTGTAAGCCCAATTTAACTGGCATCCAA
1 CAAGATGTATAAGTCCAGTTACGTTGGCACAAAAAGATTTTAAGCCCAATTTAGCTGGCATCCAA
* * *
2145038 GATGTATAAGTCCAGTTACGTTGGCACGAAAGGAGTTT-ACCCCTAATTTAGCTAGCATCCAAGA
66 GATGTATAAGTCCAGTTACATT-GCACAAAAGGAGTTTAAGCCC-AATTTAGCTAGCATCCAAGA
* * * *
2145102 TTTTTAAGCCTAACTATGTTGGCAT-AAAGAGATTTAAGCCCAATTTAACTGGCATCCAAGATGT
129 TGTTTAAGTCTAACTACGTTGGCATGAAA-AGATTTAAGCCCAATTTAACTGGCATCCAAGATAT
* *
2145166 ATAAGTCTAATTACATTGGCACAAAAGGAGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTTTA
193 ATAAGTCCAATTACATTGGCACAAAAGGAGTTTAAGCCCAATTTAGCTAGCATTCAAGATGTTTA
* ** * * *
2145231 AGTCTACCTACGTTAGCACGAAAAGATTTAAGCCCAATTAAATTGACGTC
258 AGCCTAATTACGTTGGCACAAAAAGATTTAAGCCCAATT-AATCGAC-TC
* * * * *
2145281 CAAGATATATAAGTCTAGTTATGTTGGCACAAAAAGATATTTAAGCCCAATTTAGCTAGTATCCA
1 CAAGATGTATAAGTCCAGTTACGTTGGCACAAAAAGAT-TTTAAGCCCAATTTAGCTGGCATCCA
*
2145346 AGATGTATAAGTCCAGTTACATTGCCACAAAAGGAGTTTAAGCCCAATTTATCTAGCATCCAAGA
65 AGATGTATAAGTCCAGTTACATTG-CACAAAAGGAGTTTAAGCCCAATTTAGCTAGCATCCAAGA
* * *
2145411 TGTTTAAGTCTAACTACGTTGGTATGAAAAGATTTAAGCCCAATTTAACTGTCATCCAAGATATG
129 TGTTTAAGTCTAACTACGTTGGCATGAAAAGATTTAAGCCCAATTTAACTGGCATCCAAGATATA
*
2145476 TAAGTCCAGTTACATTGGCACAAAAGGAGTTTAAGCCCAATTTAGCTAGCATTCAAGATGTTTAA
194 TAAGTCCAATTACATTGGCACAAAAGGAGTTTAAGCCCAATTTAGCTAGCATTCAAGATGTTTAA
* * * *
2145541 GCCTAATTATGTTGGCACAAAAAGATTTAAGCCCAATTTAGCCAGCATC
259 GCCTAATTACGTTGGCACAAAAAGATTTAAGCCCAATTAATCGA-C-TC
* * * * * * * *
2145590 TACGATGTACAAGTCCAATTACGTTGGCTCAAAAAAATTTTCAAACCCAATTTAGTTGGCA-CCT
1 CAAGATGTATAAGTCCAGTTACGTTGGCACAAAAAGATTTT-AAGCCCAATTTAGCTGGCATCC-
* * * * *
2145654 AAGATATTTAAGTCCAATTACATTAGCACAAAAGGAGTTTAAGCTCAATTTAGCTAGCATCGAAG
64 AAGATGTATAAGTCCAGTTACATT-GCACAAAAGGAGTTTAAGCCCAATTTAGCTAGCATCCAAG
* * *
2145719 ATGTTTAAGTCTAGCTACGTTGACATGAAAAAATTTAAGCCCAATTTAACTGGCATCCAAGATAT
128 ATGTTTAAGTCTAACTACGTTGGCATGAAAAGATTTAAGCCCAATTTAACTGGCATCCAAGATAT
* * * * * * *
2145784 ATAAGTTCAATTACATTAGCACAAAAAGAGTTTAAGTCCAATTAAACTAGCATTCAAGATGTATA
193 ATAAGTCCAATTACATTGGCACAAAAGGAGTTTAAGCCCAATTTAGCTAGCATTCAAGATGTTTA
* * * ** * *
2145849 AGTCC-AATTACATTGGCATAAAGATCTTTAAGCCCAATTTACTAGGCACT-
258 AG-CCTAATTACGTTGGCACAAAAAGATTTAAGCCCAA-TTAAT-CG-ACTC
* * * * * ** *
2145899 CAAGATGTATAAGTCTAGTTAAGTTGGCATGAATAAG--TTTAAGCCCAATTAAAATAGCATCCA
1 CAAGATGTATAAGTCCAGTTACGTTGGCA-CAAAAAGATTTTAAGCCCAATTTAGCTGGCATCCA
2145962 AGATGT
65 AGATGT
2145968 TATGTTGGCA
Statistics
Matches: 577, Mismatches: 96, Indels: 29
0.82 0.14 0.04
Matches are distributed among these distances:
307 20 0.03
308 44 0.08
309 494 0.86
310 17 0.03
311 1 0.00
312 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (305 bp):
CAAGATGTATAAGTCCAGTTACGTTGGCACAAAAAGATTTTAAGCCCAATTTAGCTGGCATCCAA
GATGTATAAGTCCAGTTACATTGCACAAAAGGAGTTTAAGCCCAATTTAGCTAGCATCCAAGATG
TTTAAGTCTAACTACGTTGGCATGAAAAGATTTAAGCCCAATTTAACTGGCATCCAAGATATATA
AGTCCAATTACATTGGCACAAAAGGAGTTTAAGCCCAATTTAGCTAGCATTCAAGATGTTTAAGC
CTAATTACGTTGGCACAAAAAGATTTAAGCCCAATTAATCGACTC
Found at i:2145851 original size:31 final size:31
Alignment explanation
Indices: 2145754--2145913 Score: 92
Period size: 31 Copynumber: 5.2 Consensus size: 31
2145744 TGAAAAAATT
* * * * *
2145754 TAAGCCCAATTTAACTGGCATCCAAGATATA
1 TAAGTCCAATTAAACTAGCATTCAAGATGTA
* * * *** *
2145785 TAAGTTCAATTACATTAGCACAAAAAGA-GTT
1 TAAGTCCAATTAAACTAGCA-TTCAAGATGTA
2145816 TAAGTCCAATTAAACTAGCATTCAAGATGTA
1 TAAGTCCAATTAAACTAGCATTCAAGATGTA
* * * * * *
2145847 TAAGTCCAATTACATTGGCA-TAAAGATCTT
1 TAAGTCCAATTAAACTAGCATTCAAGATGTA
* * *
2145877 TAAGCCCAATT-TACTAGGCACTCAAGATGTA
1 TAAGTCCAATTAAACTA-GCATTCAAGATGTA
2145908 TAAGTC
1 TAAGTC
2145914 TAGTTAAGTT
Statistics
Matches: 93, Mismatches: 32, Indels: 8
0.70 0.24 0.06
Matches are distributed among these distances:
29 2 0.02
30 24 0.26
31 63 0.68
32 4 0.04
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (31 bp):
TAAGTCCAATTAAACTAGCATTCAAGATGTA
Found at i:2145997 original size:50 final size:50
Alignment explanation
Indices: 2145916--2146017 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
2145906 TATAAGTCTA
2145916 GTTAAGTTGGCATGAATAAGTTTAAGCCCAATTAAAATAGCATCCAAGAT
1 GTTAAGTTGGCATGAATAAGTTTAAGCCCAATTAAAATAGCATCCAAGAT
* *
2145966 GTTATGTTGGCATGAATAAGTTTAAGTCCAATTAAAATAGCATCCAAGAT
1 GTTAAGTTGGCATGAATAAGTTTAAGCCCAATTAAAATAGCATCCAAGAT
2146016 GT
1 GT
2146018 ATAAATCCAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (50 bp):
GTTAAGTTGGCATGAATAAGTTTAAGCCCAATTAAAATAGCATCCAAGAT
Found at i:2146115 original size:234 final size:237
Alignment explanation
Indices: 2145737--2146380 Score: 689
Period size: 234 Copynumber: 2.7 Consensus size: 237
2145727 GTCTAGCTAC
* * * * * * *
2145737 GTTGACATGAAAAAATTTAAGCCCAATTTAACTGGCATCCAAGATATATAAGTTCAATTACATTA
1 GTTGGCATGAATAAGTTTAAG-CCAATTAAACTGGCATCCAAGATGTATAAGTCCAATTACATTG
** * * * *
2145802 GCACAAAAAGAGTTTAAGTCCAATTAAA-CTAGCATTCAAGATGTATAAGTCCAATTACATTGGC
65 GCACAAAAAGAGTTTAAACCCAATTAAACCGA-CATCCAAGATGTATAAGTCCAGTTACATTGAC
* * *
2145866 ATAAAGATCTTTAAGCCCAATTTACTAGGCA-CTCAAGAT-GTATAAGTCTAGTT-AAGTTGGCA
129 ACAAAGATGTTTAAGCCCAATTTACTAGGCATC-CAAGATAG-ATAAGCCTAGTTGAA-TTGGCA
* * *
2145928 TGAATAAGTTTAAGCCCAATTAAAAT-AGCATCCAAGATG-T-T-A-T
191 CGAATAAGTTTAAGCACAATCAAAATGA-CATCCAAGATGATCTAATT
* * * *
2145971 GTTGGCATGAATAAGTTTAAGTCCAATTAAAATAGCATCCAAGATGTATAAATCCAGTTACATTG
1 GTTGGCATGAATAAGTTTAAG-CCAATTAAACTGGCATCCAAGATGTATAAGTCCAATTACATTG
* *
2146036 GCACAAAAAGAGTTTAAACCCAATTAAACCGACATCCAAAATGTATAAGTCTAGTTACATTGACA
65 GCACAAAAAGAGTTTAAACCCAATTAAACCGACATCCAAGATGTATAAGTCCAGTTACATTGACA
* * *
2146101 CAAAGATGTTTAAGCCCAATTTACTTGGGATCCAAGATAGATAAGCCTAGTTGTATTGGCACGAA
130 CAAAGATGTTTAAGCCCAATTTACTAGGCATCCAAGATAGATAAGCCTAGTTGAATTGGCACGAA
*
2146166 TAAGTTTAAGCACAATCAAACTGACATCCAAGATGTATAAATCTAATTGT
195 TAAGTTTAAGCACAATCAAAATGACATCCAAGATG-----ATCTAA-T-T
* * * *
2146216 GTTGGCACGAATGAGTTTAAGCTCAATTAAACTGGCATCCAAGATGTGTAAGTCCAATTATATTG
1 GTTGGCATGAATAAGTTTAAGC-CAATTAAACTGGCATCCAAGATGTATAAGTCCAATTACATTG
* * * * * * * *
2146281 GTAC-GAATGAGCTTAAACCCAATTAAACTGACATCTAAGATGTTTAAGTCCAGTTATATTGACA
65 GCACAAAAAGAGTTTAAACCCAATTAAACCGACATCCAAGATGTATAAGTCCAGTTACATTGACA
*
2146345 CAAAGATGTTTAAGCCTAATTATACTA-GCATCCAAG
130 CAAAGATGTTTAAGCCCAATT-TACTAGGCATCCAAG
2146381 TTATTTAAAC
Statistics
Matches: 341, Mismatches: 51, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
234 189 0.55
235 6 0.02
240 1 0.00
241 1 0.00
242 1 0.00
244 80 0.23
245 63 0.18
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (237 bp):
GTTGGCATGAATAAGTTTAAGCCAATTAAACTGGCATCCAAGATGTATAAGTCCAATTACATTGG
CACAAAAAGAGTTTAAACCCAATTAAACCGACATCCAAGATGTATAAGTCCAGTTACATTGACAC
AAAGATGTTTAAGCCCAATTTACTAGGCATCCAAGATAGATAAGCCTAGTTGAATTGGCACGAAT
AAGTTTAAGCACAATCAAAATGACATCCAAGATGATCTAATT
Found at i:2154160 original size:12 final size:12
Alignment explanation
Indices: 2154137--2154167 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2154127 GAATTGCCAG
2154137 AATATA-TTGAA
1 AATATATTTGAA
2154148 AATATATTTGAA
1 AATATATTTGAA
2154160 AATATATT
1 AATATATT
2154168 ATCTTCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (12 bp):
AATATATTTGAA
Found at i:2156226 original size:9 final size:9
Alignment explanation
Indices: 2156209--2156254 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
2156199 AATATCCATC
2156209 TATAAATAT
1 TATAAATAT
2156218 TAT--ATA-
1 TATAAATAT
*
2156224 TATAAATAA
1 TATAAATAT
2156233 TA-AAATAT
1 TATAAATAT
2156241 TATAAATAT
1 TATAAATAT
2156250 TATAA
1 TATAA
2156255 TTAAATAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
6 3 0.09
7 3 0.09
8 10 0.31
9 16 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TATAAATAT
Found at i:2156248 original size:32 final size:30
Alignment explanation
Indices: 2156209--2156278 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 30
2156199 AATATCCATC
2156209 TATAAATATTATATATATAAATAA-TAAAATAT
1 TATAAATATTATA-AT-TAAATAATTAAAA-AT
2156241 TATAAATATTATAATTAAATAATTAAAAAT
1 TATAAATATTATAATTAAATAATTAAAAAT
2156271 TGATAAAT
1 T-ATAAAT
2156279 TAAAAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
30 10 0.28
31 13 0.36
32 13 0.36
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (30 bp):
TATAAATATTATAATTAAATAATTAAAAAT
Found at i:2156259 original size:23 final size:23
Alignment explanation
Indices: 2156212--2156283 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 23
2156202 ATCCATCTAT
* *
2156212 AAATATTATATATATAAATAA-TA
1 AAATATTATAAATAT-TATAATTA
2156235 AAATATTATAAATATTATAATT-
1 AAATATTATAAATATTATAATTA
2156257 AAATAATTA-AAA-ATTGATAAATTA
1 AAAT-ATTATAAATATT-AT-AATTA
2156281 AAA
1 AAA
2156284 AAATAAGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 3 0.07
22 13 0.31
23 23 0.55
24 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (23 bp):
AAATATTATAAATATTATAATTA
Found at i:2156276 original size:22 final size:22
Alignment explanation
Indices: 2156229--2156306 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
2156219 ATATATATAA
*
2156229 ATAATAAAAT-ATTATAAATATT-
1 ATAATTAAATAATTA-AAA-ATTG
2156251 ATAATTAAATAATTAAAAATTG
1 ATAATTAAATAATTAAAAATTG
* * *
2156273 ATAAATTAAAAAAATAAGAATTG
1 AT-AATTAAATAATTAAAAATTG
*
2156296 AAAATTAAATA
1 ATAATTAAATA
2156307 TAAAGGGTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.06
22 22 0.47
23 22 0.47
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
ATAATTAAATAATTAAAAATTG
Found at i:2156294 original size:23 final size:22
Alignment explanation
Indices: 2156253--2156304 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
2156243 TAAATATTAT
* *
2156253 AATTAAATAATTAAAAATTGATA
1 AATTAAAAAAATAAAAATTGA-A
*
2156276 AATTAAAAAAATAAGAATTGAA
1 AATTAAAAAAATAAAAATTGAA
2156298 AATTAAA
1 AATTAAA
2156305 TATAAAGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
AATTAAAAAAATAAAAATTGAA
Found at i:2170936 original size:18 final size:19
Alignment explanation
Indices: 2170913--2170959 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
2170903 ATATAACCTG
*
2170913 AAATATTAAACA-AAATAA
1 AAATATTAAAAATAAATAA
2170931 AAATATTAAAAATAAATAA
1 AAATATTAAAAATAAATAA
2170950 AAA-ATTAAAA
1 AAATATTAAAA
2170960 GAATGGAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (19 bp):
AAATATTAAAAATAAATAA
Done.