Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008985.1 Hibiscus syriacus cultivar Beakdansim tig00112349_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: 1528252
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 4 of 9
Found at i:502950 original size:20 final size:20
Alignment explanation
Indices: 502925--502979 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
502915 CAAAATTTTC
502925 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
*
502945 ATGCATTGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
502965 ATGCATCGATGCACC
1 ATGCATCGATGCACC
502980 TTCAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.25
Consensus pattern (20 bp):
ATGCATCGATGCACCCCTTA
Found at i:505856 original size:9 final size:9
Alignment explanation
Indices: 505842--505866 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
505832 ACTCATTCTG
505842 CCTATTGCT
1 CCTATTGCT
505851 CCTATTGCT
1 CCTATTGCT
505860 CCTATTG
1 CCTATTG
505867 AAGTTTCCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.32, G:0.12, T:0.44
Consensus pattern (9 bp):
CCTATTGCT
Found at i:506701 original size:46 final size:46
Alignment explanation
Indices: 506649--506742 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
506639 AGTAGGACAA
*
506649 AAACTTAATTCGACATTGATTCATGTTCATATCTCTATACTAATAT
1 AAACTTAATTCGACACTGATTCATGTTCATATCTCTATACTAATAT
506695 AAACTTAATTCGACACTGATTCATGTTCATATCTCTATACTAATAT
1 AAACTTAATTCGACACTGATTCATGTTCATATCTCTATACTAATAT
506741 AA
1 AA
506743 GCTTGTCCCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (46 bp):
AAACTTAATTCGACACTGATTCATGTTCATATCTCTATACTAATAT
Found at i:512720 original size:44 final size:43
Alignment explanation
Indices: 512622--512731 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 43
512612 GCTTGAATTT
* **
512622 TGCATTGAATGAGCTCTGAAAAAGCCAACCGGTGCATTATTGT
1 TGCATTGAATGAGCTCTGAAAAAGCCAAACGGTGCATTATTAC
* *
512665 TGCATTGAATGAGCTCTGAAAAAGCTGAAATGGTGCATTATTAC
1 TGCATTGAATGAGCTCTGAAAAAGC-CAAACGGTGCATTATTAC
*
512709 TGCAATT-AATGACCTCT-AAAAAG
1 TGC-ATTGAATGAGCTCTGAAAAAG
512732 TAGCTGAAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
43 31 0.53
44 25 0.42
45 3 0.05
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (43 bp):
TGCATTGAATGAGCTCTGAAAAAGCCAAACGGTGCATTATTAC
Found at i:514485 original size:65 final size:65
Alignment explanation
Indices: 514352--514511 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
514342 TGCACTAAGA
* * *
514352 GTGCATCGATGCATCAAGTGCATTCAATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
514416 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
514479 AT
65 -G
*
514481 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
514512 CAATTTAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 28 0.33
65 54 0.64
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:514550 original size:65 final size:63
Alignment explanation
Indices: 514352--514561 Score: 205
Period size: 65 Copynumber: 3.3 Consensus size: 63
514342 TGCACTAAGA
* * * *
514352 GTGCATCGATGCATCAAGTGCATTCAATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
514415 G
63 G
*
514416 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
514481 -
63 G
* ** *
514481 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCAATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
514544 TG
62 TG
*
514546 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
514562 CTCTGAAAAT
Statistics
Matches: 124, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 47 0.38
65 65 0.52
66 5 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:516366 original size:21 final size:21
Alignment explanation
Indices: 516340--516394 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
516330 CCTAATAGCC
516340 ATTAGGAGGTTGAGGAATGAG
1 ATTAGGAGGTTGAGGAATGAG
*
516361 ATTAGGAGGTTGAGGAATGGG
1 ATTAGGAGGTTGAGGAATGAG
516382 ATTAGGAGGTTGA
1 ATTAGGAGGTTGA
516395 TTTGAACGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.25
Consensus pattern (21 bp):
ATTAGGAGGTTGAGGAATGAG
Found at i:517142 original size:23 final size:23
Alignment explanation
Indices: 517112--517192 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
517102 TGCATGGCCT
517112 TGTGCATCGATGCACATTCAAGG
1 TGTGCATCGATGCACATTCAAGG
* * * *
517135 TGTGCATCGGTGCACCTTTATGG
1 TGTGCATCGATGCACATTCAAGG
517158 TGT--ATCGATGCACATTCAAGG
1 TGTGCATCGATGCACATTCAAGG
*
517179 -ATGCATCGATGCAC
1 TGTGCATCGATGCAC
517193 TGTTAGGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 14 0.30
22 10 0.21
23 22 0.47
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.28
Consensus pattern (23 bp):
TGTGCATCGATGCACATTCAAGG
Found at i:517167 original size:44 final size:42
Alignment explanation
Indices: 517117--517211 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 42
517107 GGCCTTGTGC
* *
517117 ATCGATGCACATTCAAGGTGTGCATCGGTGCACCT-TTATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCGATGCA-CTGTTA-GGTGT
517161 ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
517203 ATCGATGCA
1 ATCGATGCA
517212 TGAATCACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
42 16 0.33
43 14 0.29
44 18 0.38
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
Found at i:517208 original size:20 final size:21
Alignment explanation
Indices: 517117--517211 Score: 86
Period size: 21 Copynumber: 4.4 Consensus size: 21
517107 GGCCTTGTGC
517117 ATCGATGCACATTCAAGGTGT
1 ATCGATGCACATTCAAGGTGT
* * * *
517138 GCATCGGTGCACCTTTATGGTGT
1 --ATCGATGCACATTCAAGGTGT
*
517161 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
517183 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
517203 ATCGATGCA
1 ATCGATGCA
517212 TGAATCACAA
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
20 11 0.19
21 18 0.31
22 13 0.22
23 17 0.29
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:522950 original size:20 final size:21
Alignment explanation
Indices: 522904--522964 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
522894 TTCCCCTGTG
522904 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
522927 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
522947 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
522965 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:526808 original size:20 final size:20
Alignment explanation
Indices: 526766--526808 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
526756 TGTTTTCATT
* *
526766 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
526786 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
526806 TTT
1 TTT
526809 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:530072 original size:23 final size:23
Alignment explanation
Indices: 530046--530122 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
530036 ACCACAGCTC
530046 ATATAATTGCACCGAAGTGCCAT
1 ATATAATTGCACCGAAGTGCCAT
* * * **
530069 ATATAATTGTACTGGAGTGCCGC
1 ATATAATTGCACCGAAGTGCCAT
* *
530092 ATAGAATTGCACCGTAGTGCCAT
1 ATATAATTGCACCGAAGTGCCAT
530115 ATAATAAT
1 AT-ATAAT
530123 GTCCATAAGG
Statistics
Matches: 41, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 37 0.90
24 4 0.10
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (23 bp):
ATATAATTGCACCGAAGTGCCAT
Found at i:530300 original size:103 final size:103
Alignment explanation
Indices: 530129--530346 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
530119 TAATGTCCAT
* *
530129 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
530194 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
530232 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
530297 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
530335 AAAGACCACATA
1 AAGGACCACATA
530347 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:531110 original size:2 final size:2
Alignment explanation
Indices: 531103--531129 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
531093 ACTGATAAAC
531103 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 A
531130 CTTCTATTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:536186 original size:64 final size:65
Alignment explanation
Indices: 536100--536250 Score: 168
Period size: 65 Copynumber: 2.3 Consensus size: 65
536090 TGCACTAAGA
* * * *
536100 GTGCATCGATGCATCAAGTGCATTCAATG-TTTC--AAAATAGCT-AGAGTGTATCGATGCATGG
1 GTGCATCGATGCATGAAATGCATTCAATGTTTTCATAAAAT-CCTCA-A-TGCATCGATGCATGG
536161 CT-G
63 -TAG
* * *
536164 GTGCATCGATGCATGAAATGCATTCGATGTTTTCATAAAATCCTCAATGCATCGGTGCATGGTAT
1 GTGCATCGATGCATGAAATGCATTCAATGTTTTCATAAAATCCTCAATGCATCGATGCATGGTAG
536229 GTGCATCGATGCATGAAATGCA
1 GTGCATCGATGCATGAAATGCA
536251 ATTGATGTTC
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
64 27 0.36
65 39 0.52
66 3 0.04
67 6 0.08
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCAATGTTTTCATAAAATCCTCAATGCATCGATGCATGGTAG
Found at i:537939 original size:15 final size:15
Alignment explanation
Indices: 537915--537964 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
537905 AAAAGATTTA
537915 ATAA-AATAAAATAG
1 ATAATAATAAAATAG
537929 ATAATAAT-AAATA-
1 ATAATAATAAAATAG
537942 A-AATAATAAAAT-G
1 ATAATAATAAAATAG
537955 ATAAATAATA
1 AT-AATAATA
537965 GAAGTAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
12 6 0.19
13 6 0.19
14 9 0.29
15 10 0.32
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (15 bp):
ATAATAATAAAATAG
Found at i:538024 original size:18 final size:18
Alignment explanation
Indices: 538003--538045 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
537993 GTTGTTTTTA
** *
538003 AAATAAAAGATCATAATT
1 AAATAAAAGAAAATAAAT
538021 AAATAAAAGAAAATAAAT
1 AAATAAAAGAAAATAAAT
538039 AAATAAA
1 AAATAAA
538046 TAAATTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAAAT
Found at i:538663 original size:19 final size:21
Alignment explanation
Indices: 538623--538666 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
538613 AAAAACAAGC
*
538623 TAAAACATCTTAAATCCTAAT
1 TAAAACATCTTAAATACTAAT
538644 TAAAACA-CTTAAA-ACTAAT
1 TAAAACATCTTAAATACTAAT
538663 TAAA
1 TAAA
538667 CTAAAATACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
20 6 0.27
21 7 0.32
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAACATCTTAAATACTAAT
Found at i:538711 original size:63 final size:63
Alignment explanation
Indices: 538633--538753 Score: 183
Period size: 63 Copynumber: 1.9 Consensus size: 63
538623 TAAAACATCT
538633 TAAATCCTAATTAAAACACTTAAAA-CTAATTAAACTAAAATACCTAAAA-ATAATATAATATTC
1 TAAATCCTAATTAAAACAC-TAAAACCTAATTAAACTAAAATACCTAAAACA-AATATAATATTC
** *
538696 TAAATCCTAATTAAAATTCTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAA
1 TAAATCCTAATTAAAACACTAAAACCTAATTAAACTAAAATACCTAAAACAAATATAA
538754 AATATAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
62 5 0.09
63 47 0.89
64 1 0.02
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (63 bp):
TAAATCCTAATTAAAACACTAAAACCTAATTAAACTAAAATACCTAAAACAAATATAATATTC
Found at i:538714 original size:19 final size:19
Alignment explanation
Indices: 538692--538729 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
538682 ATAATATAAT
*
538692 ATTCTAAATCCTAATTAAA
1 ATTCTAAAACCTAATTAAA
*
538711 ATTCTAAAACCTATTTAAA
1 ATTCTAAAACCTAATTAAA
538730 CTAAAATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTCTAAAACCTAATTAAA
Found at i:542585 original size:15 final size:14
Alignment explanation
Indices: 542559--542602 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 14
542549 TGAAAAGATT
542559 TAATAA-AATAAAA
1 TAATAATAATAAAA
542572 TAGATAATAAT-AAA
1 TA-ATAATAATAAAA
542586 TAA-AATAAT-AAA
1 TAATAATAATAAAA
542598 TAATA
1 TAATA
542603 GTAGTAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.43
13 4 0.14
14 9 0.32
15 3 0.11
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:542586 original size:19 final size:19
Alignment explanation
Indices: 542559--542602 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
542549 TGAAAAGATT
542559 TAATAAAATAAAATAGAT-AA
1 TAAT-AAATAAAATA-ATAAA
542579 TAATAAATAAAATAATAAA
1 TAATAAATAAAATAATAAA
542598 TAATA
1 TAATA
542603 GTAGTAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.09
19 17 0.74
20 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
TAATAAATAAAATAATAAA
Found at i:542665 original size:18 final size:18
Alignment explanation
Indices: 542644--542686 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
542634 GTTATTTTTA
** *
542644 AAATAAAAGATCATAATT
1 AAATAAAAGAAAATAAAT
542662 AAATAAAAGAAAATAAAT
1 AAATAAAAGAAAATAAAT
542680 AAATAAA
1 AAATAAA
542687 TAATTAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAAAT
Found at i:543348 original size:63 final size:63
Alignment explanation
Indices: 543277--543397 Score: 192
Period size: 63 Copynumber: 1.9 Consensus size: 63
543267 TAAAACATCT
*
543277 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACGTAAAA-ATAATATAATATTC
1 TAAATCCTAATTAAAACAC-TAAAACCTATTTAAACTAAAATACCTAAAATA-AATATAATATTC
*
543340 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAATATAA
1 TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAATAAATATAA
543398 AATATAAAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
62 5 0.09
63 48 0.89
64 1 0.02
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (63 bp):
TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAATAAATATAATATTC
Found at i:548240 original size:30 final size:30
Alignment explanation
Indices: 548194--548250 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
548184 TGGATTAATC
548194 ATTTCAACTAACTTGA-TTCTTTTTGTCTT
1 ATTTCAACTAACTTGATTTCTTTTTGTCTT
*
548223 ATTTCTACTAACATTGATTTCTTTTTGT
1 ATTTCAACTAAC-TTGATTTCTTTTTGT
548251 ATGGTCTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 11 0.44
30 4 0.16
31 10 0.40
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.56
Consensus pattern (30 bp):
ATTTCAACTAACTTGATTTCTTTTTGTCTT
Found at i:549806 original size:2 final size:2
Alignment explanation
Indices: 549799--549856 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
549789 ATCCTTTCGA
549799 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
549841 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
549857 CCCTTGTTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:550133 original size:10 final size:10
Alignment explanation
Indices: 550118--550205 Score: 69
Period size: 10 Copynumber: 8.9 Consensus size: 10
550108 AATATTGCAA
550118 AAAAAGAAAG
1 AAAAAGAAAG
*
550128 AAAAAGACAG
1 AAAAAGAAAG
550138 AAAAAAGAAAG
1 -AAAAAGAAAG
550149 AAAAA-AGAA-
1 AAAAAGA-AAG
* *
550158 AAATAGAGAG
1 AAAAAGAAAG
550168 AAAAAGAAA-
1 AAAAAGAAAG
*
550177 AAAATAGAGAG
1 AAAA-AGAAAG
550188 -AAAA-AAAG
1 AAAAAGAAAG
550196 AAGAAAGAAA
1 AA-AAAGAAA
550206 ATCGATCAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
8 3 0.05
9 12 0.20
10 34 0.56
11 12 0.20
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:550141 original size:20 final size:19
Alignment explanation
Indices: 550118--550205 Score: 81
Period size: 19 Copynumber: 4.5 Consensus size: 19
550108 AATATTGCAA
550118 AAAAAGAAAGAAAAAGACAG
1 AAAAAGAAAGAAAAAGA-AG
550138 AAAAAAGAAAGAAAAAAGAA-
1 -AAAAAGAAAG-AAAAAGAAG
* * *
550158 AAATAGAGAGAAAAAGAAA
1 AAAAAGAAAGAAAAAGAAG
*
550177 AAAATAGAGAGAAAAA-AAG
1 AAAA-AGAAAGAAAAAGAAG
550196 AAGAAAGAAA
1 AA-AAAGAAA
550206 ATCGATCAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.14
19 19 0.33
20 13 0.22
21 11 0.19
22 7 0.12
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAGAAAAAGAAG
Found at i:550142 original size:11 final size:11
Alignment explanation
Indices: 550117--550158 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
550107 GAATATTGCA
550117 AAAAAAGAAAG
1 AAAAAAGAAAG
*
550128 -AAAAAGACAG
1 AAAAAAGAAAG
550138 AAAAAAGAAAG
1 AAAAAAGAAAG
550149 AAAAAAGAAA
1 AAAAAAGAAA
550159 AATAGAGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:550143 original size:21 final size:19
Alignment explanation
Indices: 550117--550205 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 19
550107 GAATATTGCA
550117 AAAAAAGAAAGAAAAAGACAG
1 AAAAAAGAAAGAAAAA-A-AG
550138 AAAAAAGAAAG-AAAAAAG
1 AAAAAAGAAAGAAAAAAAG
*
550156 AAAAATAGAGAGAAAAAGAA-
1 AAAAA-AGAAAGAAAAA-AAG
*
550176 AAAAATAGAGAGAAAAAAAG
1 AAAAA-AGAAAGAAAAAAAG
*
550196 AAGAAAGAAA
1 AAAAAAGAAA
550206 ATCGATCAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.11
19 12 0.20
20 29 0.48
21 13 0.21
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.02
Consensus pattern (19 bp):
AAAAAAGAAAGAAAAAAAG
Found at i:550158 original size:28 final size:28
Alignment explanation
Indices: 550117--550180 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
550107 GAATATTGCA
550117 AAAAAAGAAAGAAAAAGACAGA-AAAAAG
1 AAAAAA-AAAGAAAAAGACAGAGAAAAAG
* *
550145 AAAGAAAAAAGAAAAATAGAGAGAAAAAG
1 AAA-AAAAAAGAAAAAGACAGAGAAAAAG
550174 AAAAAAA
1 AAAAAAA
550181 TAGAGAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 20 0.62
29 12 0.38
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (28 bp):
AAAAAAAAAGAAAAAGACAGAGAAAAAG
Found at i:550197 original size:40 final size:40
Alignment explanation
Indices: 550116--550193 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
550106 AGAATATTGC
550116 AAAAAAAGAAAGAAAAAGACAGAAAAAAGAAAGAAAAAAG
1 AAAAAAAGAAAGAAAAAGACAGAAAAAAGAAAGAAAAAAG
* * *
550156 AAAAATAGAGAGAAAAAGA-A-AAAAATAGAGAGAAAAAA
1 AAAAAAAGAAAGAAAAAGACAGAAAAA-AGAAAGAAAAAA
550194 AGAAGAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 5 0.15
39 12 0.35
40 17 0.50
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (40 bp):
AAAAAAAGAAAGAAAAAGACAGAAAAAAGAAAGAAAAAAG
Found at i:552238 original size:55 final size:58
Alignment explanation
Indices: 552141--552292 Score: 199
Period size: 52 Copynumber: 2.7 Consensus size: 58
552131 TTCAAAGCAA
* * *
552141 TTTTTAAAAGAAGGTAAGTCTAATTTTTAGGGGTTTCTTGATG-T--TTTCAAATGAG
1 TTTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATGATTTTAAATGAG
* *
552196 TTTTT-AAA-AA-CTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTTTAATGAG
1 TTTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATGATTTTAAATGAG
*
552251 TTTTTAAAAAGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGA
1 TTTTT-AAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGA
552293 CAACCAAGAA
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
52 27 0.33
53 3 0.04
54 3 0.04
55 19 0.23
57 3 0.04
58 2 0.02
59 26 0.31
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (58 bp):
TTTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATGATTTTAAATGAG
Found at i:552407 original size:42 final size:40
Alignment explanation
Indices: 552329--552442 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 40
552319 AAGGGTTTCT
* * * *
552329 TGATGAGTAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCA
1 TGATG-GTAAGTCCTTCGGGCCATCA-TAAGCCTTTCAAACA
552371 TGATGCGTAAGTCCTTCGGGCCATCTATAAGCCTTTCAAACA
1 TGATG-GTAAGTCCTTCGGGCCATC-ATAAGCCTTTCAAACA
* * *
552413 AGATGATAAGTCCTTTGGGCCATCCATAAG
1 TGATGGTAAGTCCTTCGGGCCAT-CATAAG
552443 ATCTTAGAGC
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
41 21 0.34
42 40 0.65
43 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (40 bp):
TGATGGTAAGTCCTTCGGGCCATCATAAGCCTTTCAAACA
Found at i:552552 original size:42 final size:41
Alignment explanation
Indices: 552506--552619 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 41
552496 AAGGGTTTCT
* * *
552506 TGATGAGTAAGTCCTTTGGGCCATC-AGTAAGTCTTTCGAGCG
1 TGATGA-TAAATCCTTCGGGCCATCTA-TAAGTCTTTCGAGCA
* * * *
552548 TGATGTTTAAATCCTTCAGGTCATCTATATGTCTTTCGAGCA
1 TGATG-ATAAATCCTTCGGGCCATCTATAAGTCTTTCGAGCA
* *
552590 AGATGATAAATCCTTCGGGCCATCCATAAG
1 TGATGATAAATCCTTCGGGCCATCTATAAG
552620 AACTTCGGGA
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
41 20 0.35
42 36 0.63
43 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (41 bp):
TGATGATAAATCCTTCGGGCCATCTATAAGTCTTTCGAGCA
Found at i:552595 original size:177 final size:177
Alignment explanation
Indices: 552299--552688 Score: 564
Period size: 177 Copynumber: 2.2 Consensus size: 177
552289 TTGACAACCA
*
552299 AGAAACTAGGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGAGCCATCAGTAAGTCTT
1 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGAGCCATCAGTAAGTCTT
* * * *
552364 TCGAGCATGATGCGTAAGTCCTTCGGGCCATCTATAAGCCTTTCAAACAAGATGATAAGTCCTTT
66 TCGAGCATGATGCGTAAATCCTTCAGGCCATCTATAAGCCTTTCAAACAAGATGATAAATCCTTC
* *
552429 GGGCCATCCATAAGATCTTAGAGCAAGATATTTTCAAATGAGTTTTT
131 GGGCCATCCATAAGAACTTAGAGAAAGATATTTTCAAATGAGTTTTT
* *
552476 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGGGCCATCAGTAAGTCTT
1 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGAGCCATCAGTAAGTCTT
* ** * * * * *
552541 TCGAGCGTGATGTTTAAATCCTTCAGGTCATCTATATGTCTTTCGAGCAAGATGATAAATCCTTC
66 TCGAGCATGATGCGTAAATCCTTCAGGCCATCTATAAGCCTTTCAAACAAGATGATAAATCCTTC
* * *
552606 GGGCCATCCATAAGAACTTCGGGAAAGATGTTTTCAAATGAGTTTTT
131 GGGCCATCCATAAGAACTTAGAGAAAGATATTTTCAAATGAGTTTTT
* * * *
552653 AGAAATTAAGCCTAATTTTCAGGGGTTTCTTGATGA
1 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
552689 TTATCTCCAA
Statistics
Matches: 189, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
177 189 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (177 bp):
AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGAGCCATCAGTAAGTCTT
TCGAGCATGATGCGTAAATCCTTCAGGCCATCTATAAGCCTTTCAAACAAGATGATAAATCCTTC
GGGCCATCCATAAGAACTTAGAGAAAGATATTTTCAAATGAGTTTTT
Found at i:553708 original size:91 final size:91
Alignment explanation
Indices: 553553--554370 Score: 1015
Period size: 91 Copynumber: 9.0 Consensus size: 91
553543 AGATAAACCG
* * *
553553 ATCAACATTGCCAGTGGAGAG-TCAATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAGAGGAGAGTTC-ATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCA
553617 TAATGAGAAGAACTTGTTCAACCTTGC
65 TAATGAGAAGAACTTGTTCAACCTTGC
*
553644 ATCAACATTTCCAGCAGG-GAGTTCATAATGAGAAGAACTCATCTGACGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAG-AGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCA
* *
553708 TAATGAGAAGAACTAGTTCAACCTTGG
65 TAATGAGAAGAACTTGTTCAACCTTGC
* * ** * *
553735 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATAAGATGAGGGAGAATAAGTTCAT
1 ATCAACATTTCCAGAGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCAT
* * *
553800 AATAAGAAGAGCTTGTTCAAAACTTGC
66 AATGAGAAGAACTTGTTC-AACCTTGC
* * * * * *
553827 GTCAACATTTCCAGCGGGGAGTTCATAATGAGAAGAACTCATCCGACGAGTGAGAAAAAATTCAT
1 ATCAACATTTCCAGAGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCAT
553892 AATGAGAAGAACTTGTTCAAACCTTGC
66 AATGAGAAGAACTTGTTC-AACCTTGC
* * * * ** *
553919 ATCAACATTTCCAGCGGGGAGTTCATAATGAGAAAAACTCATCCAAAAAAGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCAT
*
553984 AATGAGAAGAACTTGTTCAACATTG-
66 AATGAGAAGAACTTGTTCAACCTTGC
* * * * ** *
554009 ACTCAATATTTCCA-ATGGGGAGTTCATAATGAGAAAAACTCATCCAAAAAAGGAGAAGAAGTTC
1 A-TCAACATTTCCAGA-GGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTC
*
554073 ATAATGAGAAGAACTTGTTCAACATTG-
64 ATAATGAGAAGAACTTGTTCAACCTTGC
* * * *
554100 ACTCAATATTTCCA-ATGGAGAGTTCATAATGAGAAGAAATCATCCGACGAGAGAGAAGACGTTC
1 A-TCAACATTTCCAGA-GGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTC
*
554164 ATAATGAGAAGAACTTGTTCAACCTTAC
64 ATAATGAGAAGAACTTGTTCAACCTTGC
* *
554192 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCAT
*
554257 AATAAGAAGAACTTGTTCAACCTTGGC
66 AATGAGAAGAACTTGTTCAACCTT-GC
* * * * *
554284 -TTAATATTTCCA-ATGGAGAGTTCATAATGAGAAAAACTCATCCGATGAGGGAGAAAAAGTTCA
1 ATCAACATTTCCAGA-GGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCA
* *
554347 TAAT-AAAAGAACTTATTCAACCTT
65 TAATGAGAAGAACTTGTTCAACCTT
554371 AGATCGTTTC
Statistics
Matches: 647, Mismatches: 70, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
90 21 0.03
91 461 0.71
92 165 0.26
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (91 bp):
ATCAACATTTCCAGAGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTGC
Found at i:554700 original size:26 final size:26
Alignment explanation
Indices: 554664--554718 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
554654 ATTTTTCCGT
* *
554664 TTATTATTATTATATATATGTATATA
1 TTATTAGTATTATATATATATATATA
554690 TTATTAGTATTATATATATATATATA
1 TTATTAGTATTATATATATATATATA
554716 TTA
1 TTA
554719 CAAACTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (26 bp):
TTATTAGTATTATATATATATATATA
Found at i:558180 original size:37 final size:37
Alignment explanation
Indices: 558139--558210 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
558129 CATATGTCAG
* *
558139 AAAACTGTATAAAACATATAC-GCATCAAAATACCGCA
1 AAAACCGTATAAAACATATACGGAAT-AAAATACCGCA
*
558176 AAAACCGTATAAAACATTTACGGAATAAAATACCG
1 AAAACCGTATAAAACATATACGGAATAAAATACCG
558211 GTAATACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.51, C:0.19, G:0.10, T:0.19
Consensus pattern (37 bp):
AAAACCGTATAAAACATATACGGAATAAAATACCGCA
Found at i:558600 original size:39 final size:39
Alignment explanation
Indices: 558539--558694 Score: 215
Period size: 39 Copynumber: 4.0 Consensus size: 39
558529 CTATACACCT
* *
558539 AGTAAGGACTTACCCTGTGCACAGAGCAGAGGAGCCTGC
1 AGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTGC
* * * * **
558578 AGTAAGGTCTTATCCT-ACGCACAAAGAAGAGGAGTCTAT
1 AGTAAGGACTTACCCTGA-GCACAAAGCAGAGGAGCCTGC
558617 AGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTGC
1 AGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTGC
*
558656 AGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGC
1 AGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTGC
558695 GGAAAACGGT
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 99 0.99
40 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.16
Consensus pattern (39 bp):
AGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTGC
Found at i:564056 original size:38 final size:37
Alignment explanation
Indices: 563990--564061 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
563980 CATATGTCAA
* * *
563990 AAAATGTATAAAACATATATGTATCAAAATACCACAG
1 AAAATGTATAAAACATATACGGAACAAAATACCACAG
*
564027 AAAATCGTATAAAACATTTACGGAACAAAATACCA
1 AAAAT-GTATAAAACATATACGGAACAAAATACCA
564062 GTAATACAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 5 0.17
38 25 0.83
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.22
Consensus pattern (37 bp):
AAAATGTATAAAACATATACGGAACAAAATACCACAG
Found at i:564478 original size:39 final size:39
Alignment explanation
Indices: 564363--564480 Score: 148
Period size: 39 Copynumber: 3.0 Consensus size: 39
564353 CCTGTATACC
* * *
564363 CAGTAAGGGCTTACCCTGTGCACAAAGCAGAAGAGCCTA
1 CAGTAAGGACTTACACTGTGCACAAAGCAGAAGAGCCTG
* *
564402 CAGTAAGGACTTATTA-TGTGCACAAAGCAGAAAAGCCTG
1 CAGTAAGGACTTA-CACTGTGCACAAAGCAGAAGAGCCTG
* * *
564441 CAGTAAGGACTTACACTGAGCACAAAGCCGAGGAGCCTG
1 CAGTAAGGACTTACACTGTGCACAAAGCAGAAGAGCCTG
564480 C
1 C
564481 GGAAAGGGTA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
38 1 0.01
39 66 0.99
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (39 bp):
CAGTAAGGACTTACACTGTGCACAAAGCAGAAGAGCCTG
Found at i:566331 original size:159 final size:158
Alignment explanation
Indices: 566020--566574 Score: 612
Period size: 159 Copynumber: 3.5 Consensus size: 158
566010 GCCCCTGTTT
* * ** * ** *
566020 TCATTATTTCTTCAATTCCTTC-TTCATTTTAAGTCCATTTTTTACAAAATTTGAAATAGATG-T
1 TCATTATTTCTTCAATT-CGTCATTTATTTTAAGTCTGTTTTTTACCAAATTTGAACCACATGCT
* * *
566083 TCTTAAACCACAATAGAATACATGTGTACTTTCAATTCCA-CTTTTTGATACCAATTTTTTTTAT
65 TCATAAACCACAATAGAATACATGTGTACTTTCAATT-CATCTTTTTGATAACAA-ATTTTTTAT
* * *
566147 TTTTCAATTTAGTCATTCAATTTTTCATAATC
128 TTTTC-ATTTATTCTTTCAATTTTTCATAATA
* * *
566179 TCATTATTTCTTCAATTCGTCATTTATTTTAAGTCTGTCTTTTTACTAAATTTGAGCCACATACT
1 TCATTATTTCTTCAATTCGTCATTTATTTTAAGTCTGT-TTTTTACCAAATTTGAACCACATGCT
* *
566244 TC-TAAACCATAATAGAATACATGTGTACTTTCAATTCATCTTTTTTATAACAAATTTTTTATTT
65 TCATAAACCACAATAGAATACATGTGTACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTT
* *
566308 TTCATTTTATTCTTTCAAATTTTCATAATT
130 TTCA-TTTATTCTTTCAATTTTTCATAATA
* * **
566338 TCCTTATTTCTTCAATTTGTCATTTATTTTAAGTCTG-TTTTTACCAAATTTGAGTCACATGC-T
1 TCATTATTTCTTCAATTCGTCATTTATTTTAAGTCTGTTTTTTACCAAATTTGAACCACATGCTT
* * * *
566401 CCTAAACCATAGTAGAATACACT-TGTACTTTCAATTCCTCTTTTTGATAAC-AA-TTTTTATTT
66 CATAAACCACAATAGAATACA-TGTGTACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTT
* *
566463 TTTATTTAGTCCTTT-AATTTTTCATAATA
130 TTCATTTA-TTCTTTCAATTTTTCATAATA
* * * * * *
566492 TCTTTATTCCTTCGATTTGTGATTTATTTT-AGTCTTTTTTTTACCAAATTTGAACCACATGC-T
1 TCATTATTTCTTCAATTCGTCATTTATTTTAAGTCTGTTTTTTACCAAATTTGAACCACATGCTT
*
566555 CATATACCACAATAGAATAC
66 CATAAACCACAATAGAATAC
566575 CTATGTAACT
Statistics
Matches: 346, Mismatches: 41, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
153 5 0.01
154 82 0.24
155 17 0.05
156 4 0.01
157 66 0.19
158 5 0.01
159 101 0.29
160 63 0.18
161 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.48
Consensus pattern (158 bp):
TCATTATTTCTTCAATTCGTCATTTATTTTAAGTCTGTTTTTTACCAAATTTGAACCACATGCTT
CATAAACCACAATAGAATACATGTGTACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTT
TCATTTATTCTTTCAATTTTTCATAATA
Found at i:566786 original size:21 final size:20
Alignment explanation
Indices: 566762--566814 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
566752 TATTTAAAAT
566762 ATAATATTATGAATATATTTG
1 ATAATATTA-GAATATATTTG
* * *
566783 ATAATTTTAGATTGTATTTG
1 ATAATATTAGAATATATTTG
566803 AT-ATATTA-AATA
1 ATAATATTAGAATA
566815 ACATTATAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 2 0.08
19 5 0.19
20 11 0.42
21 8 0.31
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (20 bp):
ATAATATTAGAATATATTTG
Found at i:572871 original size:29 final size:29
Alignment explanation
Indices: 572838--572895 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
572828 TTATATTTAT
* *
572838 TTAACATAACCCAGTTAATTTTAATATCA
1 TTAACACAACACAGTTAATTTTAATATCA
* *
572867 TTAACACAAGACGGTTAATTTTAATATCA
1 TTAACACAACACAGTTAATTTTAATATCA
572896 ACAAGTTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (29 bp):
TTAACACAACACAGTTAATTTTAATATCA
Found at i:580646 original size:110 final size:111
Alignment explanation
Indices: 580440--580671 Score: 385
Period size: 110 Copynumber: 2.1 Consensus size: 111
580430 ATTGTATGCA
*
580440 AATAAATTAAAAGACTAAATTTATTTATTTATTTCAAAAATTTGAGGGCCCTATGACCCTTGAGC
1 AATAAATT-AAAGACTAAATTTATTTATTTATTTCAAAAATTTGAGGGCCCTATGACCATTGAGC
580505 CTAAATTTAAGTATGAGCCAAATGCAACTTTGAATGTGGGATTAGAT
65 CTAAATTTAAGTATGAGCCAAATGCAACTTTGAATGTGGGATTAGAT
* * *
580552 AATAAATTAAGGACTAAATTTATTTA-TTCTTTCAAAATTTTGAGGGCCCTATGACCATTGAGCC
1 AATAAATTAAAGACTAAATTTATTTATTTATTTCAAAAATTTGAGGGCCCTATGACCATTGAGCC
* * *
580616 TTAATTTAAGTATGAGCCAAATGCAACTTTGAGTGTGGGATTAGTT
66 TAAATTTAAGTATGAGCCAAATGCAACTTTGAATGTGGGATTAGAT
580662 AATAAATTAA
1 AATAAATTAA
580672 TACAACATAA
Statistics
Matches: 113, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
110 88 0.78
111 17 0.15
112 8 0.07
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (111 bp):
AATAAATTAAAGACTAAATTTATTTATTTATTTCAAAAATTTGAGGGCCCTATGACCATTGAGCC
TAAATTTAAGTATGAGCCAAATGCAACTTTGAATGTGGGATTAGAT
Found at i:586699 original size:20 final size:20
Alignment explanation
Indices: 586656--586702 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
586646 AATCCCAATC
* ** *
586656 TCGATACCAAGCCCTTGGTC
1 TCGATACCAAACCCTCAGTA
586676 TCGATACCAAACCCTCAGTA
1 TCGATACCAAACCCTCAGTA
586696 TCGATAC
1 TCGATAC
586703 TCCTAAAGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TCGATACCAAACCCTCAGTA
Found at i:588211 original size:41 final size:41
Alignment explanation
Indices: 588166--588247 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
588156 TCCCTTACGT
*
588166 TTAAAACCCAACTTAAACCACTACTTAACTTTAACTCTTGG
1 TTAAAACCCAACTAAAACCACTACTTAACTTTAACTCTTGG
588207 TTAAAACCCAACTAAAACCACTACTTAACTTTAACTCTTGG
1 TTAAAACCCAACTAAAACCACTACTTAACTTTAACTCTTGG
588248 GCTTGCCTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (41 bp):
TTAAAACCCAACTAAAACCACTACTTAACTTTAACTCTTGG
Found at i:592117 original size:26 final size:26
Alignment explanation
Indices: 592088--592149 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
592078 CCTGAAGTTT
*
592088 TAAACTTTTAGGAAGGGATGAACCTA
1 TAAAATTTTAGGAAGGGATGAACCTA
*
592114 TAAAATTTTAGGAATGGATGAACCTA
1 TAAAATTTTAGGAAGGGATGAACCTA
592140 TAAAATTTTA
1 TAAAATTTTA
592150 AGAGTCGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (26 bp):
TAAAATTTTAGGAAGGGATGAACCTA
Found at i:593002 original size:4 final size:4
Alignment explanation
Indices: 592995--594141 Score: 1849
Period size: 4 Copynumber: 296.0 Consensus size: 4
592985 GTAAGTAGTA
592995 GTAT GTAT GTAT GTA- -TAT GTAT GTAT GTAT GTAT GTAT GTAT GGTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT -GTAT
593042 GTAT GTAT GTAT GTAT GTAT GTAAT GTAT GTAT GTAT GTAT GTAT GT-T
1 GTAT GTAT GTAT GTAT GTAT GT-AT GTAT GTAT GTAT GTAT GTAT GTAT
*
593090 GTAT GTAT GTAT GTAT GTAT GTAT TTAT GTAT GTA- -TAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
593136 GTAT GTAT GTAT GTAT G-GT GTAT GTAT GTAT GTAT GTAT G--T GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
593181 GTAT GTAT GTAT G--T GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
593227 GTAT GTAT GTAT GTAT GTA- GTAT GTAT GTAT GTA- GTAT GTAT AGGTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT --GTAT
*
593275 GTAT GTAT GTAT GTA- GTAT GTAT GTAT GTAT GTAT GTAT GTAT TTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
593322 GTAT GTGT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
593370 GTAT ATAT GTAT GTAT G-AT GTAT GTAT GTAT GTAT GTAT GTAT GTA-
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
593416 -TAT GTA- GTAT G--T GTAT GTAT GTAT G--T GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
593458 GTAT GTA- -TAT GTAT GTAT TTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
593504 GTAT GTA- GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
593551 GTAT GTAT GTAT GTA- GTAT GTAT GTA- GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
593597 GTAT GTAT GTAT GTA- GTAT GTAT GTAT GTTAT GTAT G-AT G-AT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G-TAT GTAT GTAT GTAT GTAT
593643 GTAT GTAT GT-T GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
593690 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
593738 GTA- GTAT GTAT GTAT -TAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
593784 GTAT GTAT GTAT GTTT GTAT GTAT -TAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
593831 GTAT GTTGT GTAT GTAT GTAT GTAT GTAT GTAT GTA- GTAT GTA- GTAT
1 GTAT G-TAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
593878 GTAT GTAT -TAT GTAT GTAT GTAT GTAT GTAT GTAT TTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
593925 GTAT GTAT GT-T GTAT GTAT GTAT GTAT GTAT -TAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
593971 GTAT GTAT GTAT -TAT GTAT GTAT -TAT GTAT GTAT GTAT GTAT GTAG
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
594017 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G--T GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
594063 GTAT GTAT GTAT GTAT GTAT GTAT GTA- GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
594110 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
594142 TGGTTGCCAA
Statistics
Matches: 1075, Mismatches: 20, Indels: 96
0.90 0.02 0.08
Matches are distributed among these distances:
2 18 0.02
3 74 0.07
4 964 0.90
5 15 0.01
6 4 0.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:594365 original size:2 final size:2
Alignment explanation
Indices: 594358--594420 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
594348 TTATAAATAA
594358 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
594400 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
594421 GTGGGACTAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:595632 original size:2 final size:2
Alignment explanation
Indices: 595625--595665 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
595615 ACAGGCAATG
595625 AT AT AT AT 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
595666 CTGTTTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:595943 original size:2 final size:2
Alignment explanation
Indices: 595938--595964 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
595928 ATATATGTCC
595938 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 A
595965 ACTTTTATAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:596029 original size:4 final size:4
Alignment explanation
Indices: 596022--596249 Score: 435
Period size: 4 Copynumber: 57.8 Consensus size: 4
596012 TATACATATA
596022 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
596070 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
596118 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
596166 TATG TATG TAT- TATG TA-- TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
596211 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
596250 AAAAATAAAG
Statistics
Matches: 221, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.01
3 3 0.01
4 216 0.98
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:599441 original size:60 final size:59
Alignment explanation
Indices: 599309--599459 Score: 153
Period size: 60 Copynumber: 2.5 Consensus size: 59
599299 CATCATGTAT
* * * * * *
599309 CCTCAAATTATGACCCTCATTTTAAATTAGTTCTTAAACATTTAAACATTTCAATTTCAC
1 CCTCAAATTATGACTCTCA-TTCAAATTTGTCCTTAAACATTTAAACATTCCAATTTCAA
* *
599369 CCTCAAACTATGACTCTCATTCAAAGTTTGTCCTTAAA-ATTTTGAACATTCCAATTTCATA
1 CCTCAAATTATGACTCTCATTCAAA-TTTGTCCTTAAACA-TTTAAACATTCCAATTTCA-A
* * *
599430 TC-CAAATTATGATTCTCATTCTAATTTGTC
1 CCTCAAATTATGACTCTCATTCAAATTTGTC
599460 TCTAAACTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
59 12 0.16
60 63 0.83
61 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.40
Consensus pattern (59 bp):
CCTCAAATTATGACTCTCATTCAAATTTGTCCTTAAACATTTAAACATTCCAATTTCAA
Found at i:599487 original size:59 final size:60
Alignment explanation
Indices: 599312--599496 Score: 148
Period size: 60 Copynumber: 3.1 Consensus size: 60
599302 CATGTATCCT
* * * * * * *
599312 CAAATTATGACCCTCATTTTAAA-TTAGTTCTTAAACA-TTTAAACATTTCAATTTCA-CCC
1 CAAATTATGACTCTCA-TTCAAAGTTTGTCCTTAAA-ATTTTGAACATTCCAATTTCATACC
* *
599371 TCAAACTATGACTCTCATTCAAAGTTTGTCCTTAAAATTTTGAACATTCCAATTTCATATC
1 -CAAATTATGACTCTCATTCAAAGTTTGTCCTTAAAATTTTGAACATTCCAATTTCATACC
* * * * * *
599432 CAAATTATGATTCTCATTCTAA-TTTGT-CTCTAAACTTTTAGATC-TTCTAATTTCATCCC
1 CAAATTATGACTCTCATTCAAAGTTTGTCCT-TAAAATTTT-GAACATTCCAATTTCATACC
599491 CAAATT
1 CAAATT
599497 CATCCAAATA
Statistics
Matches: 103, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
58 2 0.02
59 37 0.36
60 63 0.61
61 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (60 bp):
CAAATTATGACTCTCATTCAAAGTTTGTCCTTAAAATTTTGAACATTCCAATTTCATACC
Found at i:600759 original size:20 final size:20
Alignment explanation
Indices: 600706--600760 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
600696 ATACTACCCT
600706 AAGAGTATCGATACTCTTGA
1 AAGAGTATCGATACTCTTGA
* *
600726 AAAAGCT-TTGATACTCTTGA
1 AAGAG-TATCGATACTCTTGA
*
600746 AAGAGTATCAATACT
1 AAGAGTATCGATACT
600761 TTTGCCAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (20 bp):
AAGAGTATCGATACTCTTGA
Found at i:602814 original size:22 final size:21
Alignment explanation
Indices: 602747--602824 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 21
602737 AAATAGTAAG
*
602747 TAAA-AAAATAAATAATAAAATA
1 TAAATAAAACAAATAA-AAAA-A
* *
602769 TATATAAAA-AAAGAAAAAAAA
1 TAAATAAAACAAA-TAAAAAAA
602790 TAAATAAAACAAATAAACAAAA
1 TAAATAAAACAAATAAA-AAAA
602812 T-AATAATAACAAA
1 TAAATAA-AACAAA
602825 GTATGAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
21 17 0.36
22 24 0.51
23 6 0.13
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.18
Consensus pattern (21 bp):
TAAATAAAACAAATAAAAAAA
Found at i:603347 original size:2 final size:2
Alignment explanation
Indices: 603340--603364 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
603330 CATACGCATA
603340 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
603365 AAAAATAAAT
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:603387 original size:12 final size:13
Alignment explanation
Indices: 603360--603385 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
603350 ATATATATAT
603360 ATATAAAAAATAA
1 ATATAAAAAATAA
603373 ATATAAAAAATAA
1 ATATAAAAAATAA
603386 TACAAGTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
ATATAAAAAATAA
Found at i:603497 original size:13 final size:13
Alignment explanation
Indices: 603442--603523 Score: 57
Period size: 13 Copynumber: 6.5 Consensus size: 13
603432 AATAATAATA
603442 AAAATATACATA-T
1 AAAATATA-ATAGT
*
603455 ATAATATAAATAAGT
1 AAAATAT-AAT-AGT
* *
603470 AGAATA-AA-AGG
1 AAAATATAATAGT
603481 AAAATATAATAGT
1 AAAATATAATAGT
*
603494 AAAA-ATAATAAT
1 AAAATATAATAGT
603506 -AAATATAATAGT
1 AAAATATAATAGT
*
603518 ATAATA
1 AAAATA
603524 AAAATGCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
11 10 0.19
12 16 0.30
13 20 0.37
14 2 0.04
15 6 0.11
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.28
Consensus pattern (13 bp):
AAAATATAATAGT
Found at i:604135 original size:37 final size:37
Alignment explanation
Indices: 604094--604198 Score: 140
Period size: 37 Copynumber: 2.8 Consensus size: 37
604084 GTGCTTGTGG
* *
604094 ATCCTATCTTTT-GGAGTTTAAATCATAGTAGAACTCT
1 ATCCTAT-TTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
604131 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
604168 ATCCTATTTTTATGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
604199 GACGAAAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
36 4 0.07
37 55 0.93
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:605248 original size:106 final size:106
Alignment explanation
Indices: 604926--606388 Score: 2052
Period size: 106 Copynumber: 14.0 Consensus size: 106
604916 GCATTGTTCC
* * ** *
604926 GAGTCCAATATCCTCCGAC-GTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * *
604990 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
605032 AAGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
605091 TCAGC-CTCCCTTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCC-TTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
605133 G-GTCAAATATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
605197 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
605238 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
605303 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
605344 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAG-TTGTTTGTTGACA
605409 ACCAGCGGTCCCTTCGTCG-GAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
605450 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAG-T-TTTATTGAC-A
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
605512 CCAGCGGTCCCTTCGTCGTGAAGTTTAACTTGCGTTGTCT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
605552 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAA-ATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
605616 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
605657 GAGTCC-ATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
605721 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
605762 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
605827 CCAGCGGTCCCTTCGTTGTGAAATTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
605868 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
605933 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
605974 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
606039 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
606080 GAGTCCAATATCCTTCGCTGTGAAGTTG-AATTGGCTCTGAAATTGGAAAGTTGTTTATTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * * *
606144 CCAGTGGTCCATTCATTGTGAAGTTGAACTTGAGTT-TAGATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT--CTG
* *
606186 GAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGG----G--A-----AA-TTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
606239 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
606280 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGTCAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
606344 CCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
606385 GAGT
1 GAGT
606389 GGCACGATAT
Statistics
Matches: 1228, Mismatches: 94, Indels: 71
0.88 0.07 0.05
Matches are distributed among these distances:
94 36 0.03
95 45 0.04
96 3 0.00
98 1 0.00
99 4 0.00
100 76 0.06
101 5 0.00
102 72 0.06
103 37 0.03
104 85 0.07
105 184 0.15
106 639 0.52
107 41 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:606365 original size:200 final size:200
Alignment explanation
Indices: 606012--606375 Score: 597
Period size: 200 Copynumber: 1.8 Consensus size: 200
606002 AAATTGGCTC
* *
606012 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
606077 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAATTGGCTCTGAAATTGGAAAGTTGTTTATTAAC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAATTGGCTCCGAAATTGGAAAATTGTTTATTAAC
606142 AACCAGTGGTCCATTCATTGTGAAGTTGAACTTGAGTTTAGATGGAGTCCAATATCCTTCTCTGT
131 AACCAGTGGTCCATTCATTGTGAAGTTGAACTTGAGTTTAGATGGAGTCCAATATCCTTCTCTGT
606207 GAAGT
196 GAAGT
* *
606212 TGAAATTGGGAAATTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* **
606277 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGT
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTG-AATTGGCTCCGAAATTGGAAAATTGTTTATTAA
* *
606341 CAACCAGCT-GTCCCTTCGTTGTGAAGTTGAACTTG
130 CAACCAG-TGGTCCATTCATTGTGAAGTTGAACTTG
606376 TGTTGTCTTG
Statistics
Matches: 151, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
200 127 0.84
201 24 0.16
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (200 bp):
TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAATTGGCTCCGAAATTGGAAAATTGTTTATTAAC
AACCAGTGGTCCATTCATTGTGAAGTTGAACTTGAGTTTAGATGGAGTCCAATATCCTTCTCTGT
GAAGT
Found at i:607242 original size:22 final size:22
Alignment explanation
Indices: 607216--607270 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
607206 TTGTGTTTGG
* *
607216 TCAAAGGTTTGGCATTTGATTC
1 TCAAAGGTTTGGCATTTAATGC
607238 TCAAAGGTTTGGCATTTAATGC
1 TCAAAGGTTTGGCATTTAATGC
607260 TCAAAGGTTTG
1 TCAAAGGTTTG
607271 ATGGGGTAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTAATGC
Found at i:607902 original size:25 final size:24
Alignment explanation
Indices: 607874--607947 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 24
607864 TTTTTGTCCC
607874 TTTTTCTTTTTGATTTTTGTTCTTTT
1 TTTTTCTTTTT--TTTTTGTTCTTTT
*
607900 TTTTGTTTTCTTCTTTTTTGTTTCTTTT
1 TTTT-TCTT-TT-TTTTTTG-TTCTTTT
607928 TTGTTTCTTTTTTTTTTGTT
1 TT-TTTCTTTTTTTTTTGTT
607948 TTTGCCCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
25 2 0.05
26 11 0.27
27 11 0.27
28 14 0.34
29 3 0.07
ACGTcount: A:0.01, C:0.08, G:0.08, T:0.82
Consensus pattern (24 bp):
TTTTTCTTTTTTTTTTGTTCTTTT
Found at i:607916 original size:15 final size:14
Alignment explanation
Indices: 607887--607948 Score: 62
Period size: 15 Copynumber: 4.6 Consensus size: 14
607877 TTCTTTTTGA
607887 TTTTTG-TTCTT-T
1 TTTTTGTTTCTTCT
607899 TTTTTGTTTTCTTCT
1 TTTTTG-TTTCTTCT
607914 TTTTTG--T-TTCT
1 TTTTTGTTTCTTCT
*
607925 TTTTTGTTTCTTTTT
1 TTTTTGTTTC-TTCT
607940 TTTTTGTTT
1 TTTTTGTTT
607949 TTGCCCTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
11 10 0.24
12 7 0.17
13 1 0.02
14 5 0.12
15 19 0.45
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (14 bp):
TTTTTGTTTCTTCT
Found at i:607916 original size:26 final size:24
Alignment explanation
Indices: 607887--607950 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
607877 TTCTTTTTGA
607887 TTTTTGTTCTTTTTTTTGTTTTCTTCT
1 TTTTTGTT-TTTTTTTTG-TTTCTT-T
*
607914 TTTTTGTTTCTTTTTTGTTTCTTT
1 TTTTTGTTTTTTTTTTGTTTCTTT
*
607938 TTTTT-TTGTTTTT
1 TTTTTGTTTTTTTT
607951 GCCCTTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.18
24 6 0.18
25 6 0.18
26 8 0.24
27 8 0.24
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (24 bp):
TTTTTGTTTTTTTTTTGTTTCTTT
Found at i:607926 original size:11 final size:11
Alignment explanation
Indices: 607910--607950 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
607900 TTTTGTTTTC
607910 TTCTTTTTTGT
1 TTCTTTTTTGT
607921 TTCTTTTTTGT
1 TTCTTTTTTGT
*
607932 TTCTTTTTTTT
1 TTCTTTTTTGT
*
607943 TTGTTTTT
1 TTCTTTTT
607951 GCCCTTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (11 bp):
TTCTTTTTTGT
Found at i:611221 original size:20 final size:19
Alignment explanation
Indices: 611185--611222 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
611175 TGCAGATGAT
*
611185 GGAAATAAAATAAAAGAGA
1 GGAAAAAAAATAAAAGAGA
611204 GGAAAAAAAATAAAA-AGA
1 GGAAAAAAAATAAAAGAGA
611222 G
1 G
611223 TTAGTAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (19 bp):
GGAAAAAAAATAAAAGAGA
Found at i:612392 original size:6 final size:6
Alignment explanation
Indices: 612381--612414 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
612371 AATATATATA
*
612381 AAAAAG AAAAAG AAAATG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
612415 TAAATAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:612402 original size:18 final size:18
Alignment explanation
Indices: 612381--612415 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
612371 AATATATATA
612381 AAAAAGAAAAAGAAAATG
1 AAAAAGAAAAAGAAAATG
612399 AAAAAGAAAAAGAAAAT
1 AAAAAGAAAAAGAAAAT
612416 AAATAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAATG
Found at i:612436 original size:22 final size:23
Alignment explanation
Indices: 612406--612449 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
612396 ATGAAAAAGA
612406 AAAAGAAAATAAATAA-AACAAAT
1 AAAAGAAAAT-AATAATAACAAAT
612429 AAAA-AAAATAATAATAACAAA
1 AAAAGAAAATAATAATAACAAA
612450 GTACGAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (23 bp):
AAAAGAAAATAATAATAACAAAT
Found at i:612479 original size:13 final size:13
Alignment explanation
Indices: 612456--612498 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
612446 CAAAGTACGA
*
612456 ATAATATATATAT
1 ATAAAATATATAT
*
612469 ATATAATATATAT
1 ATAAAATATATAT
612482 ATAAAAGTA-ATAT
1 ATAAAA-TATATAT
612495 ATAA
1 ATAA
612499 TTAATAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 24 0.92
14 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
ATAAAATATATAT
Found at i:612479 original size:17 final size:17
Alignment explanation
Indices: 612457--612497 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
612447 AAAGTACGAA
*
612457 TAATATATATAT-ATA-
1 TAATATATATATAAAAG
612472 TAATATATATATAAAAG
1 TAATATATATATAAAAG
612489 TAATATATA
1 TAATATATA
612498 ATTAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.52
16 2 0.09
17 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
TAATATATATATAAAAG
Found at i:612787 original size:2 final size:2
Alignment explanation
Indices: 612731--612768 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
612721 CTTGTGTAGA
612731 AT AT AT A- 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 A
612769 ATAGTAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:612964 original size:2 final size:2
Alignment explanation
Indices: 612957--613029 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
612947 GAACATACGC
612957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
612999 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 A
613030 ACAAAATAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:613066 original size:12 final size:11
Alignment explanation
Indices: 613038--613084 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
613028 TAACAAAATA
* *
613038 AATAATATAAA
1 AATAATACAAG
613049 AATAATACAAG
1 AATAATACAAG
613060 TAATAATACAAG
1 -AATAATACAAG
*
613072 AATAATAAAAG
1 AATAATACAAG
613083 AA
1 AA
613085 AGAGAAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.21
Consensus pattern (11 bp):
AATAATACAAG
Found at i:613176 original size:12 final size:13
Alignment explanation
Indices: 613154--613198 Score: 56
Period size: 12 Copynumber: 3.4 Consensus size: 13
613144 GAATAAAAGG
*
613154 AAAATATAATAGT
1 AAAATATAATAAT
613167 AAAA-ATAATAAT
1 AAAATATAATAAT
613179 AAATATAGTAATAAT
1 AAA-ATA-TAATAAT
613194 AAAAT
1 AAAAT
613199 GCAAAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 10 0.36
13 5 0.18
14 3 0.11
15 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (13 bp):
AAAATATAATAAT
Found at i:613735 original size:37 final size:37
Alignment explanation
Indices: 613694--613798 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
613684 GTACTTGCGG
* *
613694 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
** * *
613731 ATCCTATTTTTAGGAGTTTGAATCATAACAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * *
613768 ATCATATTTTTATGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
613799 GACGAAAAGG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:618766 original size:17 final size:17
Alignment explanation
Indices: 618740--618787 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
618730 AATAAATAAA
* **
618740 ATAAACAGTATATTTAT
1 ATAAAAAGTATATAGAT
618757 ATAAAAAGTATAATAGAT
1 ATAAAAAGTAT-ATAGAT
618775 ACTAAAAAGTATA
1 A-TAAAAAGTATA
618788 ATAAATACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 10 0.38
18 6 0.23
19 10 0.38
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.31
Consensus pattern (17 bp):
ATAAAAAGTATATAGAT
Found at i:618782 original size:19 final size:19
Alignment explanation
Indices: 618758--618800 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
618748 TATATTTATA
*
618758 TAAAAAGTATAATAGATAC
1 TAAAAAGTATAATAAATAC
618777 TAAAAAGTATAATAAATAC
1 TAAAAAGTATAATAAATAC
618796 -AAAAA
1 TAAAAA
618801 ACGGAAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (19 bp):
TAAAAAGTATAATAAATAC
Found at i:620669 original size:106 final size:106
Alignment explanation
Indices: 620480--621501 Score: 1719
Period size: 106 Copynumber: 9.7 Consensus size: 106
620470 GTATATAGCT
**** *
620480 CCTTCGTCGTGAAGTTGAACTTATACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * *
620545 GGCTCTGAAGTTGGGAAGTTATTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
*
620586 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
620651 GGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* *
620692 CCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* *
620757 GGCTCTGAAATTGAGAAGTTATTTGTTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* *
620798 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * *
620863 GGCTCTGAAATTGGGAA-ATGTTTATTGACAACAAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
620903 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* *
620968 GGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
621008 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * *
621073 GGCTCTGAAATTGAGAAGTTATTTGTTGACAACCAACGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
621114 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
621179 GGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
*
621219 CCTTCGTCGTGAAGTGGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* *
621284 GGCTCTGAAATTGAGAAGTTATTTGTTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
**
621325 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAACCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
621390 GGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* *
621430 CCTTCGTCGTGAAGTGGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTATGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
621495 GGCTCTG
66 GGCTCTG
621502 GGTAAAACCT
Statistics
Matches: 869, Mismatches: 45, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
105 390 0.45
106 479 0.55
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
Found at i:621104 original size:211 final size:211
Alignment explanation
Indices: 620480--621501 Score: 1733
Period size: 211 Copynumber: 4.8 Consensus size: 211
620470 GTATATAGCT
**** *
620480 CCTTCGTCGTGAAGTTGAACTTATACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * * *
620545 GGCTCTGAAGTTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
620610 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTT
130 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTT
*
620675 GTTGACAACCAGCGGTC
195 GTTGACAACAAGCGGTC
* *
620692 CCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * * *
620757 GGCTCTGAAATTGAGAAGTTATTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGC
66 GGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * * *
620822 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTT
130 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTT
*
620886 ATTGACAACAAGCGGTC
195 GTTGACAACAAGCGGTC
620903 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
620968 GGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
66 GGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
621033 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTG
131 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTG
621098 TTGACAACCAA-CGGTC
196 TTGACAA-CAAGCGGTC
621114 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
621179 GGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTGGAACTTGCG
66 GGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
621244 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTG
131 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTG
*
621309 TTGACAACCAGCGGTC
196 TTGACAACAAGCGGTC
**
621325 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAACCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
621390 GGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTGGAACTTGCG
66 GGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
*
621455 TTGTCTGGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTG
131 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
621502 GGTAAAACCT
Statistics
Matches: 774, Mismatches: 33, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
210 101 0.13
211 494 0.64
212 179 0.23
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (211 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
GGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTG
TTGACAACAAGCGGTC
Found at i:633562 original size:20 final size:20
Alignment explanation
Indices: 633532--633576 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
633522 TATATTTATA
633532 TAAAAAGGTATAATAAGATAC
1 TAAAAAGGTATAATAA-ATAC
633553 TAAAAA-GTATAATAAATAC
1 TAAAAAGGTATAATAAATAC
633572 -AAAAA
1 TAAAAA
633577 ACGGAAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 4 0.17
20 9 0.38
21 6 0.25
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.22
Consensus pattern (20 bp):
TAAAAAGGTATAATAAATAC
Found at i:639131 original size:19 final size:19
Alignment explanation
Indices: 639107--639167 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
639097 ACTTCAACAT
639107 ACTTTTATAAGTTACTATA
1 ACTTTTATAAGTTACTATA
*
639126 ACTTTTACTCCAG---C-AT-
1 ACTTTTA-T-AAGTTACTATA
639142 ACTTTTATAAGTTACTATA
1 ACTTTTATAAGTTACTATA
639161 ACTTTTA
1 ACTTTTA
639168 CTTCAGCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
14 2 0.06
15 1 0.03
16 7 0.21
17 3 0.09
18 3 0.09
19 14 0.42
20 1 0.03
21 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.05, T:0.46
Consensus pattern (19 bp):
ACTTTTATAAGTTACTATA
Found at i:639201 original size:35 final size:35
Alignment explanation
Indices: 639092--639183 Score: 157
Period size: 35 Copynumber: 2.6 Consensus size: 35
639082 GTTCAATTGA
*
639092 TTTTCACTTCAACATACTTTTATAAGTTACTATAAC
1 TTTT-ACTTCAGCATACTTTTATAAGTTACTATAAC
*
639128 TTTTACTCCAGCATACTTTTATAAGTTACTATAAC
1 TTTTACTTCAGCATACTTTTATAAGTTACTATAAC
639163 TTTTACTTCAGCATACTTTTA
1 TTTTACTTCAGCATACTTTTA
639184 CAATTTCATT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 49 0.92
36 4 0.08
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (35 bp):
TTTTACTTCAGCATACTTTTATAAGTTACTATAAC
Found at i:640944 original size:20 final size:21
Alignment explanation
Indices: 640894--640947 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
640884 AAAAAAGGGA
*
640894 AGTATTGATACTCATATAGTG
1 AGTATTGATACTCAGATAGTG
* *
640915 AGTATGGATACTCAGATATTG
1 AGTATTGATACTCAGATAGTG
640936 -GTATTGATACTC
1 AGTATTGATACTC
640948 TCTAGAGTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.37
Consensus pattern (21 bp):
AGTATTGATACTCAGATAGTG
Found at i:642063 original size:2 final size:2
Alignment explanation
Indices: 642056--642117 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
642046 AGAATAATTA
642056 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
642098 AT AT AT TT AA AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT A
642118 ATAATATTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:642120 original size:10 final size:10
Alignment explanation
Indices: 642054--642125 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 10
642044 AAAGAATAAT
642054 TAATATA-TA
1 TAATATATTA
642063 T-ATATA-TA
1 TAATATATTA
642071 TATATATATATA
1 TA-ATATAT-TA
642083 TATATATATATA
1 TA-ATATAT-TA
642095 TATATATATT-
1 TA-ATATATTA
642105 TAAATATATTA
1 T-AATATATTA
642116 TAATAATATT
1 TAAT-ATATT
642126 TCTTTTGATA
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
8 8 0.14
9 1 0.02
10 16 0.29
11 8 0.14
12 23 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TAATATATTA
Found at i:643694 original size:2 final size:2
Alignment explanation
Indices: 643687--643718 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
643677 CTTTAAATTA
643687 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
643719 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:643843 original size:3 final size:3
Alignment explanation
Indices: 643837--643877 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
643827 TAACATTAAC
643837 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
643878 TCTACATGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:645642 original size:15 final size:15
Alignment explanation
Indices: 645622--645651 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
645612 GAAGACTAAC
645622 TTTATTTTAAGTTAA
1 TTTATTTTAAGTTAA
*
645637 TTTATTTTAATTTAA
1 TTTATTTTAAGTTAA
645652 CAAAGCAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TTTATTTTAAGTTAA
Found at i:648017 original size:59 final size:59
Alignment explanation
Indices: 647921--648197 Score: 378
Period size: 59 Copynumber: 4.7 Consensus size: 59
647911 TTTATAAACC
* * ** **
647921 ATTCATACACTTAGTATGAGTTGCTTAACATTTTAGCACACGAAGTGCCCTATACAGAA
1 ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGAAGTGCCCTATATGGAA
* ** * * *
647980 ATAT-ATACACTTAATATGAATTTTTTATCATTTTAGCACACGAAGTACCTTATATGGAA
1 AT-TCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGAAGTGCCCTATATGGAA
* * *
648039 ATTCATACACTTAGTATAAATTCCTTGTCATTTTAGCACAC-ATAGTGTCCTATATGAAA
1 ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGA-AGTGCCCTATATGGAA
*
648098 ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGAAGTTCCCTATATGGAA
1 ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGAAGTGCCCTATATGGAA
648157 ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACAC
1 ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACAC
648198 TTAGTGCCAT
Statistics
Matches: 192, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
58 2 0.01
59 188 0.98
60 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (59 bp):
ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGAAGTGCCCTATATGGAA
Found at i:648675 original size:95 final size:94
Alignment explanation
Indices: 648534--648708 Score: 224
Period size: 95 Copynumber: 1.9 Consensus size: 94
648524 TTCAGTATTG
* * * * * *
648534 ATACCCTTACCATTGTATCGATACTACCCTACTATGGTATCAATACCCTATTCCAGTATCGATAC
1 ATACCCTCACCATGGTATCAATACTACCATACTATAGTATCAATACCCCATT-CAGTATCGATAC
648599 CAAAATTAGCTTCGATGTGGTTTACTATAC
65 CAAAATTAGCTTCGATGTGGTTTACTATAC
* ** * **
648629 ATACCCTCACCATGGTATCAATACTACTATACTATAGTATTGATACCCCCTTTGGTATCGATACC
1 ATACCCTCACCATGGTATCAATACTACCATACTATAGTATCAATACCCCATTCAGTATCGATACC
*
648694 AAAATTAGGTTCGAT
66 AAAATTAGCTTCGAT
648709 ATTACTTGGT
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
94 25 0.37
95 42 0.63
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (94 bp):
ATACCCTCACCATGGTATCAATACTACCATACTATAGTATCAATACCCCATTCAGTATCGATACC
AAAATTAGCTTCGATGTGGTTTACTATAC
Found at i:648735 original size:94 final size:95
Alignment explanation
Indices: 648534--648750 Score: 222
Period size: 94 Copynumber: 2.3 Consensus size: 95
648524 TTCAGTATTG
* * * *
648534 ATACCCTTACCATTGTATCGATACTACCCTACTATGGTATCAATACCCTATTCCAGTATCGATAC
1 ATACCCTTACCATAGTATCGATACTACCATACTATAGTATCAATACCCCATTCCAGTATCGATAC
* **
648599 CAAAATTAGCTTCGATGTGGTTTACTATAC
66 CAAAATTAGCTTCGATATGACTTACTATAC
* * * * ** * **
648629 ATACCCTCACCATGGTATCAATACTACTATACTATAGTATTGATACCCCCTT-TGGTATCGATAC
1 ATACCCTTACCATAGTATCGATACTACCATACTATAGTATCAATACCCCATTCCAGTATCGATAC
* * **
648693 CAAAATTAGGTTCGATATTACTTGGTAT-C
66 CAAAATTAGCTTCGATATGACTTACTATAC
*
648722 AATACCCTTACCATAGTATTGATACTACC
1 -ATACCCTTACCATAGTATCGATACTACC
648751 TCATTGGTAC
Statistics
Matches: 97, Mismatches: 24, Indels: 3
0.78 0.19 0.02
Matches are distributed among these distances:
93 1 0.01
94 54 0.56
95 42 0.43
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (95 bp):
ATACCCTTACCATAGTATCGATACTACCATACTATAGTATCAATACCCCATTCCAGTATCGATAC
CAAAATTAGCTTCGATATGACTTACTATAC
Found at i:652955 original size:24 final size:24
Alignment explanation
Indices: 652922--652969 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
652912 ATGTAGAATG
* * *
652922 TACCTGTTATGATTTTTGGATCAT
1 TACCTATTATGATCTTCGGATCAT
652946 TACCTATTATGATCTTCGGATCAT
1 TACCTATTATGATCTTCGGATCAT
652970 CCCGATCATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.46
Consensus pattern (24 bp):
TACCTATTATGATCTTCGGATCAT
Found at i:655330 original size:59 final size:59
Alignment explanation
Indices: 654869--655322 Score: 651
Period size: 59 Copynumber: 7.7 Consensus size: 59
654859 TTTATCAACC
* * ** *
654869 ATTCATACACTTAGTATGAGTTGCTTAACATTTTAGCACACGAAGTGCCCTATA--AAA
1 ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGAAGTGCCCTATATGGAA
** * *
654926 ATATCCATACACTTAACATGAATTTCTTATCATTTTAGCACACGAAGTGCCCTATATGGAA
1 AT-T-CATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGAAGTGCCCTATATGGAA
* * * *
654987 ATTCATACACTTAGTGTGAATTCCTTGTCATTTTAGCACACGATGTACCCAATATGGAA
1 ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGAAGTGCCCTATATGGAA
* * *
655046 ATTCATACATTTTGTATGAATTCCTTGTCATTTTAGCACATGAAGTGCCCTATATGGAA
1 ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGAAGTGCCCTATATGGAA
* * *
655105 ATTCATACACTTAGCATGAATTCCTTGTCATTTTAGCACACGAAGTGCCCTAAATGAAA
1 ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGAAGTGCCCTATATGGAA
*
655164 ATTCATACACTTAGTATGAATTCCTTGTAATTTTAGCACACGAAGTGCCCTATATGGAA
1 ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGAAGTGCCCTATATGGAA
* *
655223 ATTCATACACTTGGTATGAATTCCTTGTCATTTTAGCACACAAAGTGCCCTATATGGAA
1 ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGAAGTGCCCTATATGGAA
* * *
655282 ATTCATACACTTAGTATAAATTCTTTGTCGTTTTAGCACAC
1 ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACAC
655323 TTAGTGCCAT
Statistics
Matches: 355, Mismatches: 38, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
57 2 0.01
58 1 0.00
59 347 0.98
60 1 0.00
61 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (59 bp):
ATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACGAAGTGCCCTATATGGAA
Found at i:655698 original size:22 final size:20
Alignment explanation
Indices: 655652--655706 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
655642 CTGGCTCTTC
655652 AGTATCGATACCCCTACCAT
1 AGTATCGATACCCCTACCAT
* *
655672 GGTATCGATACTACCCTACTAT
1 AGTATCGATAC--CCCTACCAT
655694 AGTATCGATACCC
1 AGTATCGATACCC
655707 TCTTCCGGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (20 bp):
AGTATCGATACCCCTACCAT
Found at i:655854 original size:94 final size:95
Alignment explanation
Indices: 655653--655875 Score: 281
Period size: 94 Copynumber: 2.4 Consensus size: 95
655643 TGGCTCTTCA
* *
655653 GTATCGATACCC-CTACCATGGTATCGATACTACCCTACTATAGTATCGATACCCTCTTCCGGTA
1 GTATCGATACCCTC-ACCATGGTATCGATACTACCATACTATAGTATCGATACCCTCCTCCGGTA
* ***
655717 TCGATACCAAAATTAGCTTCGATGTGGTTTG
65 TCGATACCAAAATTAGCTTCGATATGACCTG
* *
655748 GTATCGATACCCTCACCATGGTATCGATACTACTATACTATGGTA-CTGATACCC-CCTCCGGTA
1 GTATCGATACCCTCACCATGGTATCGATACTACCATACTATAGTATC-GATACCCTCCTCCGGTA
* *
655811 TCGATACCAAAATTAGGTTCGATATTACCTG
65 TCGATACCAAAATTAGCTTCGATATGACCTG
* ** *
655842 GTATCGATACCCTTACCATATTATTGATACTACC
1 GTATCGATACCCTCACCATGGTATCGATACTACC
655876 TCATCGGTAC
Statistics
Matches: 111, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
94 63 0.57
95 47 0.42
96 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (95 bp):
GTATCGATACCCTCACCATGGTATCGATACTACCATACTATAGTATCGATACCCTCCTCCGGTAT
CGATACCAAAATTAGCTTCGATATGACCTG
Found at i:658716 original size:3 final size:3
Alignment explanation
Indices: 658708--658748 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
658698 CTATACACCA
658708 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
658749 TATGCTCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:659306 original size:20 final size:20
Alignment explanation
Indices: 659283--659332 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
659273 CTTAAACTTA
659283 AGGGGATGAACTAAAATTCC
1 AGGGGATGAACTAAAATTCC
*
659303 AGGGAGA-GAACTAAAATTCT
1 AGGG-GATGAACTAAAATTCC
*
659323 AGGGGGTGAA
1 AGGGGATGAA
659333 ATAGACTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 23 0.88
21 2 0.08
ACGTcount: A:0.40, C:0.10, G:0.32, T:0.18
Consensus pattern (20 bp):
AGGGGATGAACTAAAATTCC
Found at i:660023 original size:40 final size:39
Alignment explanation
Indices: 659979--660059 Score: 117
Period size: 40 Copynumber: 2.1 Consensus size: 39
659969 ATAACTTGAA
* *
659979 TTCTTAATTATTGAAATAGGTTTAATTATCAATTTCATTT
1 TTCTTAATTATTGAAACAGGTTTAACTATCAATTT-ATTT
* *
660019 TTCTTGATTATTGAAACAGGTTTAACTATGAATTTATTT
1 TTCTTAATTATTGAAACAGGTTTAACTATCAATTTATTT
660058 TT
1 TT
660060 GTAAAAAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 6 0.16
40 31 0.84
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (39 bp):
TTCTTAATTATTGAAACAGGTTTAACTATCAATTTATTT
Found at i:660960 original size:2 final size:2
Alignment explanation
Indices: 660953--660984 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
660943 TACATACATA
660953 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
660985 TCTGAGAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:665061 original size:21 final size:20
Alignment explanation
Indices: 665016--665064 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
665006 ATCAAAATTG
*
665016 ATAGTTTAGATACTAAATGT
1 ATAGTTTAGATACTAAATGC
* *
665036 GTAGTTTAGGTACTAAAATGC
1 ATAGTTTAGATACT-AAATGC
665057 ATAGTTTA
1 ATAGTTTA
665065 CCCTATTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (20 bp):
ATAGTTTAGATACTAAATGC
Found at i:666384 original size:25 final size:25
Alignment explanation
Indices: 666328--666384 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
666318 ATTACAGACT
*
666328 AAATAAATTTAGTAGTAACAATCGT
1 AAATAAATTTAGTAGTAACAATCGA
*
666353 AACTAAATTTAGTAGTAACAATCGA
1 AAATAAATTTAGTAGTAACAATCGA
666378 AAATAAA
1 AAATAAA
666385 ATATAACAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (25 bp):
AAATAAATTTAGTAGTAACAATCGA
Found at i:667498 original size:23 final size:23
Alignment explanation
Indices: 667472--667518 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
667462 AAAGATGCGT
*
667472 CCCATGCACTACACCTTGTGAAA
1 CCCATGCACCACACCTTGTGAAA
*
667495 CCCATGCACCGCACCTTGTGAAA
1 CCCATGCACCACACCTTGTGAAA
667518 C
1 C
667519 ATGTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.38, G:0.15, T:0.19
Consensus pattern (23 bp):
CCCATGCACCACACCTTGTGAAA
Found at i:668027 original size:8 final size:8
Alignment explanation
Indices: 668014--668045 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
668004 ATTAAAAGTT
668014 TATTTTTA
1 TATTTTTA
668022 TATTTTTA
1 TATTTTTA
668030 TATTTTTA
1 TATTTTTA
668038 TATTTTTA
1 TATTTTTA
668046 AACAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTTTTA
Found at i:668608 original size:338 final size:338
Alignment explanation
Indices: 667917--668904 Score: 1518
Period size: 338 Copynumber: 2.9 Consensus size: 338
667907 TATTAACTTC
* * * * *
667917 TAATTTTATTAAAAACGAGTAAACATTATTAATTGTTATTAAAAAAAATAATTAATGAATAATAA
1 TAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTTAAAAATAATAATTAATGAATAATAA
* * **
667982 TTTATTTGATCCTTCAATTAAAATTAAAAGTTTATTTTTATATTTTTATATTTTTATATTTTTAA
66 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTA-TTTTA-A----TAT-TTTTTATATTTTTAA
*
668047 ACAATTAATTTTAAAAGTCAATAAATATTTCAAAAATATATAAAATTTATAATTTTTTAAATTAT
124 ACAATTAATTTTAAAAGTCAATAAATATTTCAAAAATATATGAAATTTATAATTTTTTAAATTAT
668112 AAAATATTTATTATTATCATCATCATCATCATCATTTTGTAAAAGAAATAATGGTTATAAAACTT
189 AAAATATTTATTATTAT--T-ATCATCATCAT--TTTTGTAAAAGAAATAAT-GTTATAAAACTT
*
668177 TTATAAAATTATTCATATTTTAAATTACTTACCCTCAAAGTTTTACTATACTAGATTATACGTAT
248 TTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTACTATACTAGATTATACGTAT
668242 TGTGTAATTTCATGCAAAAATCAAAA
313 TGTGTAATTTCATGCAAAAATCAAAA
*
668268 TAATTTTATTAAAAATGAATAAACATTATTAACAGTTGTT-AAAATAATAATTAATGAATAATAA
1 TAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTTAAAAATAATAATTAATGAATAATAA
668332 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAATTA
66 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAATTA
*
668397 ATTTTAAAAGTCAATAAATTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATAT
131 ATTTTAAAAGTCAATAAATATTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATAT
668462 TTATTATTATTATCATCATCATTTTTGTAAAAGAAATAATGTTTATAAAACTTTTATAAAATTAT
196 TTATTATTATTATCATCATCATTTTTGTAAAAGAAATAATG-TTATAAAACTTTTATAAAATTAT
* * * * *
668527 TCATATTTTAAAATATTTATCCTCAAAGTTTTCCTATATTAGATTATATGTATTGTGTAATTTCA
260 TCATATTTTAAAATACTTACCCTCAAAGTTTTACTATACTAGATTATACGTATTGTGTAATTTCA
*
668592 TGCAAAAATTAAAA
325 TGCAAAAATCAAAA
*
668606 TAATTTTATTAAAAATGAATAAACATTATAAACTGTTGTTAAAAATAATAATTAATGAATAATAA
1 TAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTTAAAAATAATAATTAATGAATAATAA
*
668671 TTCATTTGATCCCTCAATTGTAATTATAAGTTTATTTTAATATTTTTTTATATTTTTAAACAATT
66 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATA-TTTTTTATATTTTTAAACAATT
* * *
668736 AATTTTAAAAGTCAATAAATGTTTCAAAAATATAAGAAAATTATAATTTTTTAAATTATAAAATA
130 AATTTTAAAAGTCAATAAATATTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATA
* * * *
668801 TTTATTATCATCATCATCAT--TTTTTTTAAAAGAAATACTAGTTATAAAACTTTTATAAAATTA
195 TTTATTATTATTATCATCATCATTTTTGTAAAAGAAATAAT-GTTATAAAACTTTTATAAAATTA
* *
668864 TTCATATTTTAAAACAC-TACTCTCAAAGTTTT-CTTATACTA
259 TTCATATTTTAAAATACTTACCCTCAAAGTTTTAC-TATACTA
668905 AATGAAAGAG
Statistics
Matches: 598, Mismatches: 34, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
336 1 0.00
337 20 0.03
338 205 0.34
339 66 0.11
340 113 0.19
341 1 0.00
343 95 0.16
344 3 0.01
348 1 0.00
349 5 0.01
350 53 0.09
351 35 0.06
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.44
Consensus pattern (338 bp):
TAATTTTATTAAAAATGAATAAACATTATTAACTGTTGTTAAAAATAATAATTAATGAATAATAA
TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAATTA
ATTTTAAAAGTCAATAAATATTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATAT
TTATTATTATTATCATCATCATTTTTGTAAAAGAAATAATGTTATAAAACTTTTATAAAATTATT
CATATTTTAAAATACTTACCCTCAAAGTTTTACTATACTAGATTATACGTATTGTGTAATTTCAT
GCAAAAATCAAAA
Found at i:669376 original size:17 final size:16
Alignment explanation
Indices: 669343--669382 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
669333 TTTTTTATTA
*
669343 TTTTATTAATTAATTT
1 TTTTATTAATAAATTT
669359 TTTTATTCAATAAA-TT
1 TTTTATT-AATAAATTT
669375 TTTTATTA
1 TTTTATTA
669383 TTTTTGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.73
17 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATTAATAAATTT
Found at i:669669 original size:15 final size:16
Alignment explanation
Indices: 669649--669684 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
669639 AACTGCAAAT
669649 AATAAATATA-AATTA
1 AATAAATATACAATTA
*
669664 AATAAATTTACAATTA
1 AATAAATATACAATTA
669680 AATAA
1 AATAA
669685 TAAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAATATACAATTA
Found at i:669702 original size:16 final size:16
Alignment explanation
Indices: 669683--669783 Score: 51
Period size: 16 Copynumber: 6.2 Consensus size: 16
669673 ACAATTAAAT
669683 AATAAAAAATAAAAAA
1 AATAAAAAATAAAAAA
*** *
669699 AATATTGAATATAAAA
1 AATAAAAAATAAAAAA
* * *
669715 AATAATTAAACAAAAAT
1 AATAA-AAAATAAAAAA
* **
669732 AATAAAAAAATTAATTA
1 AAT-AAAAAATAAAAAA
* **
669749 AATAAAAAAT-TAATT
1 AATAAAAAATAAAAAA
669764 AATAAAATAATAAAAAA
1 AATAAAA-AATAAAAAA
669781 AAT
1 AAT
669784 GGGGAAGGCA
Statistics
Matches: 60, Mismatches: 21, Indels: 7
0.68 0.24 0.08
Matches are distributed among these distances:
15 9 0.15
16 26 0.43
17 23 0.38
18 2 0.03
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.25
Consensus pattern (16 bp):
AATAAAAAATAAAAAA
Found at i:669729 original size:14 final size:13
Alignment explanation
Indices: 669711--669783 Score: 71
Period size: 12 Copynumber: 5.5 Consensus size: 13
669701 TATTGAATAT
669711 AAAAAATAATTAA
1 AAAAAATAATTAA
669724 ACAAAAATAA-TAA
1 A-AAAAATAATTAA
*
669737 AAAAATTAATTAAA
1 AAAAAATAATT-AA
669751 TAAAAAATTAATT-A
1 -AAAAAA-TAATTAA
*
669765 ATAAAATAA-TAA
1 AAAAAATAATTAA
669777 AAAAAAT
1 AAAAAAT
669784 GGGGAAGGCA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
11 1 0.02
12 17 0.34
13 11 0.22
14 11 0.22
15 5 0.10
16 5 0.10
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.25
Consensus pattern (13 bp):
AAAAAATAATTAA
Found at i:669753 original size:20 final size:20
Alignment explanation
Indices: 669682--669781 Score: 80
Period size: 20 Copynumber: 5.0 Consensus size: 20
669672 TACAATTAAA
*
669682 TAATAAAA-AATAAAAAAAA
1 TAATAAAATAATAAAAAAAT
* * *
669701 TATTGAATATAA-AAAATAAT
1 TAAT-AAAATAATAAAAAAAT
*
669721 TAAACAAAAATAATAAAAAAAT
1 T-AA-TAAAATAATAAAAAAAT
* *
669743 TAATTAAATAA-AAAATTAAT
1 TAATAAAATAATAAAA-AAAT
669763 TAATAAAATAATAAAAAAA
1 TAATAAAATAATAAAAAAA
669782 ATGGGGAAGG
Statistics
Matches: 61, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
19 7 0.11
20 31 0.51
21 15 0.25
22 8 0.13
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.25
Consensus pattern (20 bp):
TAATAAAATAATAAAAAAAT
Found at i:669782 original size:42 final size:41
Alignment explanation
Indices: 669675--669782 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 41
669665 ATAAATTTAC
*
669675 AATTAAATAATAAAAAAT-AAAAAAAA-T-ATTGAATATAAAA
1 AATTAATTAATAAAAAATAAAAAAAAATTAATT-AA-ATAAAA
669715 AA-TAATTAA-ACAAAAATAATAAAAAAATTAATTAAATAAAA
1 AATTAATTAATA-AAAAATAA-AAAAAAATTAATTAAATAAAA
669756 AATTAATTAATAAAATAATAAAAAAAA
1 AATTAATTAATAAAA-AATAAAAAAAA
669783 TGGGGAAGGC
Statistics
Matches: 59, Mismatches: 1, Indels: 14
0.80 0.01 0.19
Matches are distributed among these distances:
38 1 0.02
39 12 0.20
40 3 0.05
41 15 0.25
42 19 0.32
43 9 0.15
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.25
Consensus pattern (41 bp):
AATTAATTAATAAAAAATAAAAAAAAATTAATTAAATAAAA
Found at i:678030 original size:22 final size:23
Alignment explanation
Indices: 678004--678046 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
677994 TAATTCCTTT
* *
678004 ATCTTTTG-TTTATCTTGTTTTA
1 ATCTTGTGTTTTACCTTGTTTTA
678026 ATCTTGTGTTTTACCTTGTTT
1 ATCTTGTGTTTTACCTTGTTT
678047 CTAGCACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (23 bp):
ATCTTGTGTTTTACCTTGTTTTA
Found at i:687032 original size:20 final size:19
Alignment explanation
Indices: 687009--687074 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 19
686999 AGGTTGTAAA
*
687009 AACAATATCGGTACTAGATG
1 AACAATATCGATACT-GATG
*
687029 AACAGTATCGATACTGACTAAG
1 AACAATATCGATACTGA-T--G
687051 AACAATATCGATACTGGATG
1 AACAATATCGATACT-GATG
687071 AACA
1 AACA
687075 GTACCAGTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 2 0.05
20 19 0.49
22 16 0.41
23 2 0.05
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (19 bp):
AACAATATCGATACTGATG
Found at i:692204 original size:30 final size:28
Alignment explanation
Indices: 692159--692255 Score: 99
Period size: 30 Copynumber: 3.4 Consensus size: 28
692149 TAAAATAACA
* *
692159 AAATAATGGAATACATAACCAGATTAAAT
1 AAATAAT-AAATACATAACCAAATTAAAT
*
692188 AAATAAGTATAATACATAACCATATTAAAT
1 AAATAA-TA-AATACATAACCAAATTAAAT
*
692218 AAATACATAAA-A-ATAACCAAATAAAAT
1 AAATA-ATAAATACATAACCAAATTAAAT
692245 AAATAAATAAA
1 AAAT-AATAAA
692256 AATTACCTCT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
27 22 0.37
28 2 0.03
29 8 0.13
30 27 0.45
31 1 0.02
ACGTcount: A:0.63, C:0.09, G:0.04, T:0.24
Consensus pattern (28 bp):
AAATAATAAATACATAACCAAATTAAAT
Found at i:692233 original size:14 final size:14
Alignment explanation
Indices: 692214--692258 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
692204 TAACCATATT
*
692214 AAATAAATACATAA
1 AAATAAATAAATAA
**
692228 AAATAACCAAAT-A
1 AAATAAATAAATAA
692241 AAATAAATAAATAA
1 AAATAAATAAATAA
692255 AAAT
1 AAAT
692259 TACCTCTGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAATAAATAA
Done.