Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 178 of 310
Found at i:57939923 original size:31 final size:31
Alignment explanation
Indices: 57939874--57939949 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
57939864 CCATGTGATC
* * *
57939874 CACACGAGTGTGTAGGCCCACAC-GGTCAGGG
1 CACACGGGCGTGTGGGCCCACACGGGT-AGGG
57939905 CACACGGGCGTGTGGGCCCACACGGGTAGGG
1 CACACGGGCGTGTGGGCCCACACGGGTAGGG
57939936 CACACGGGCGTGTG
1 CACACGGGCGTGTG
57939950 AACCCAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 38 0.93
32 3 0.07
ACGTcount: A:0.18, C:0.29, G:0.41, T:0.12
Consensus pattern (31 bp):
CACACGGGCGTGTGGGCCCACACGGGTAGGG
Found at i:57940720 original size:43 final size:43
Alignment explanation
Indices: 57940672--57940855 Score: 183
Period size: 43 Copynumber: 4.3 Consensus size: 43
57940662 TTTTAGAAAT
* * *
57940672 AAACGCCGCTATAGATCAGGATCTTTAGCGGCGCTTTTCTAAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCTAAC
*** * *
57940715 AAACGCCGCTATA-ACTTGGGATCTTTAGCGGCGCTTTTCTAAC
1 AAACGCCGCTATAGA-TCAAGACCTTTAGCGACGCTTTTCTAAC
* * *
57940758 AAACGCCACTATAGCTCAAGACCTTTAGCGACGCTTTTAC-CAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTT-CTAAC
* * ** *
57940801 AAACGCCACTATATATCAAAGACCTTTAGCGACGCTTTGATTAC
1 AAACGCCGCTATAGATC-AAGACCTTTAGCGACGCTTTTCTAAC
57940845 AAACGCCGCTA
1 AAACGCCGCTA
57940856 AAAACACCAT
Statistics
Matches: 120, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
42 1 0.01
43 86 0.72
44 33 0.28
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCTAAC
Found at i:57940948 original size:16 final size:16
Alignment explanation
Indices: 57940927--57940960 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57940917 AAATATTAAA
*
57940927 TATTAAAATAAAACAT
1 TATTAAAATAAAAAAT
*
57940943 TATTAATATAAAAAAT
1 TATTAAAATAAAAAAT
57940959 TA
1 TA
57940961 ATTAGTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATAAAAAAT
Found at i:57941214 original size:15 final size:15
Alignment explanation
Indices: 57941194--57941223 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
57941184 TGGATCATCT
57941194 TCATCTTCATCTTCA
1 TCATCTTCATCTTCA
*
57941209 TCATCTTCTTCTTCA
1 TCATCTTCATCTTCA
57941224 CTTTCAACTC
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:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (15 bp):
TCATCTTCATCTTCA
Found at i:57942408 original size:14 final size:14
Alignment explanation
Indices: 57942389--57942418 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
57942379 CAGATTAGGT
57942389 GTGGGAAAAGGTTA
1 GTGGGAAAAGGTTA
57942403 GTGGGAAAAGGTTA
1 GTGGGAAAAGGTTA
57942417 GT
1 GT
57942419 TGCTTTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.23
Consensus pattern (14 bp):
GTGGGAAAAGGTTA
Found at i:57945587 original size:47 final size:46
Alignment explanation
Indices: 57945533--57945633 Score: 157
Period size: 47 Copynumber: 2.2 Consensus size: 46
57945523 ATACATAGGT
* * *
57945533 TTTTTTAAGTTATATTTATAAAAATTAGATAAATTTAAAAATTTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATT-AAAAGTTTAG
57945580 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAGTTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAGTTTAG
57945626 TGTTTTTA
1 T-TTTTTA
57945634 TTTCATTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
46 10 0.20
47 40 0.80
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (46 bp):
TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAGTTTAG
Found at i:57946153 original size:14 final size:15
Alignment explanation
Indices: 57946130--57946167 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
57946120 GTCCCTTAAT
57946130 TAAA-CCATAATACC
1 TAAATCCATAATACC
*
57946144 T-AATCCATAATCCC
1 TAAATCCATAATACC
57946158 TAAATCCATA
1 TAAATCCATA
57946168 TATATAGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 8 0.38
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATACC
Found at i:57946427 original size:22 final size:21
Alignment explanation
Indices: 57946402--57946444 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
57946392 TAGCTAACAT
57946402 CTAACTCCTAAACCCCTAACCC
1 CTAACTCCTAAACCCC-AACCC
* * *
57946424 CTAAGTCTTAAATCCCAACCC
1 CTAACTCCTAAACCCCAACCC
57946445 TTAATTAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21
Consensus pattern (21 bp):
CTAACTCCTAAACCCCAACCC
Found at i:57946474 original size:17 final size:17
Alignment explanation
Indices: 57946448--57946491 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
57946438 CCAACCCTTA
*
57946448 ATTAAACCATAATCCCT
1 ATTAATCCATAATCCCT
57946465 ATTAATCCATAATCCCT
1 ATTAATCCATAATCCCT
57946482 A--AATCCATAA
1 ATTAATCCATAA
57946492 ATACTCCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 9 0.35
17 17 0.65
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (17 bp):
ATTAATCCATAATCCCT
Found at i:57946512 original size:323 final size:312
Alignment explanation
Indices: 57945959--57946549 Score: 717
Period size: 323 Copynumber: 1.8 Consensus size: 312
57945949 TAAATTATAC
* * *
57945959 ATCTTTTACAATTACATAATAACATATTTAAAATATAAATAAAAATCTAAACCCAAAACCCTAAC
1 ATCTTTTACAACTACATAATAACATATTTAAAATATAAATAAAAACCAAAACCCAAAACCCTAAC
* * *
57946024 CCGACCCCTAAAACTCTAAACCCTAAATCCCTAACTCTTAACCACTAACGTCTAACCCCTAAACT
66 CCGACCCATAAAACTCTAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCCTAAACC
*
57946089 CTTAACCCCTAAACCTTAAATCTCGACCAACGTCCCTTAATTAAACCATAATACCTAATCCATAA
131 CCTAACCCCTAAACCTTAAA-CTC-ACCAAC--CCCTTAATTAAACCATAATACCTAATCCATAA
* * ** * *
57946154 TCCCTAAATCCATATATATAGTAGTCCCTAAACCTTTAAATATGAACCCCTAAACCGGCCTTAAA
192 TCCCTAAATCCATATATATACTACTAACTAAACCTTAAAATATGAACCCCTAAACCGACCTTAAA
57946219 TATTAAATTTATCATATACTCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
257 TATTAAATTTATCATATACTCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
*
57946275 ATCTTTTACAACTACATAATAACATATTTTAAATATAATAATAATCTAAACCCAAAACCCAAAAC
1 ATCTTTTACAACTACATAATAACATATTTAAAATAT-A-AATAA---AAA-CCAAAACCCAAAAC
* * *
57946340 CCTAACCTGACCCATGAAAC-CTTAAGCCCCTAAATCCCTAACTCTTAACCCTTAGCTAACATCT
60 CCTAACCCGACCCATAAAACTC-TAA-ACCCTAAATCCCTAACTCTTAA-CC--A-CTAACATCT
* ** *
57946404 AACTCCTAAACCCCTAACCCCTAAGTCTTAAA-TC-CCAA-CCCTTAATTAAACCATAATCCCTA
119 AACCCCTAAACCCCTAACCCCTAAACCTTAAACTCACCAACCCCTTAATTAAACCATAATACC--
* * * *
57946466 TTAATCCATAATCCCTAAATCCATA-A-ATACTCCCTAACTAAAACCTTAAAATATGATCTCTTA
182 -TAATCCATAATCCCTAAATCCATATATATACT-ACTAACT-AAACCTTAAAATATGAACCCCTA
*
57946529 AACCGACCTTAAATCTTAAAT
244 AACCGACCTTAAATATTAAAT
57946550 AAAATTATAT
Statistics
Matches: 232, Mismatches: 26, Indels: 27
0.81 0.09 0.09
Matches are distributed among these distances:
316 34 0.15
317 1 0.00
318 5 0.02
320 21 0.09
321 8 0.03
322 36 0.16
323 87 0.38
324 2 0.01
325 2 0.01
326 1 0.00
327 35 0.15
ACGTcount: A:0.41, C:0.28, G:0.03, T:0.28
Consensus pattern (312 bp):
ATCTTTTACAACTACATAATAACATATTTAAAATATAAATAAAAACCAAAACCCAAAACCCTAAC
CCGACCCATAAAACTCTAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCCTAAACC
CCTAACCCCTAAACCTTAAACTCACCAACCCCTTAATTAAACCATAATACCTAATCCATAATCCC
TAAATCCATATATATACTACTAACTAAACCTTAAAATATGAACCCCTAAACCGACCTTAAATATT
AAATTTATCATATACTCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
Found at i:57946969 original size:73 final size:73
Alignment explanation
Indices: 57946845--57947003 Score: 237
Period size: 73 Copynumber: 2.2 Consensus size: 73
57946835 TAAATCAATT
* * *
57946845 AAACACCGCTAAATCCCCGAAAGCGCAAAAAAAGGTGTAGTTTTGGCTTAGGTTTTTTGCGGCGC
1 AAACGCCGCTAAATCCCCGAAAGCGCAAAAAAAGGCGTAGTTTTGGATTAGGTTTTTTGCGGCGC
*
57946910 TTTCTAAA
66 TTTCCAAA
* * * *
57946918 AAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGATTAGGTTTTTTGCGGCGC
1 AAACGCCGCTAAATCCCCGAAAGCGCAAAAAAAGGCGTAGTTTTGGATTAGGTTTTTTGCGGCGC
*
57946983 TTTCCCAA
66 TTTCCAAA
57946991 AAACGCCGCTAAA
1 AAACGCCGCTAAA
57947004 GCCCTGAGCA
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (73 bp):
AAACGCCGCTAAATCCCCGAAAGCGCAAAAAAAGGCGTAGTTTTGGATTAGGTTTTTTGCGGCGC
TTTCCAAA
Found at i:57947171 original size:114 final size:113
Alignment explanation
Indices: 57946903--57947229 Score: 503
Period size: 115 Copynumber: 2.9 Consensus size: 113
57946893 TAGGTTTTTT
* *
57946903 GCGGCGCTTTCTAAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGATTA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACTGCGTCGTTTTGGATTA
**
57946968 GGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTA
66 GGTTTTTTGCGGCGC-TTCTTAAAAACGCCGCTAAAGCCCTGAGCATTA
**
57947017 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAAACTGCGTCGTTTTACATT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAC-AAAACTGCGTCGTTTTGGATT
*
57947082 AGGTTTTTTGCGGCGCTATCTTAAAAACGCCGCTAAAGCCGTGAGCATTA
65 AGGTTTTTTGCGGCGCT-TCTTAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * *
57947132 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCAC-AAAGCTCACAAAACTGCATTGTTTTGGATTA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACTGCGTCGTTTTGGATTA
*
57947196 GGTTTTTTGCGGCGCTTTTTAAAAAACGCCGCTA
66 GGTTTTTTGCGGCGCTTCTT-AAAAACGCCGCTA
57947230 TTGCTTATTG
Statistics
Matches: 196, Mismatches: 14, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
112 3 0.02
113 47 0.24
114 52 0.27
115 94 0.48
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (113 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACTGCGTCGTTTTGGATTA
GGTTTTTTGCGGCGCTTCTTAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:57951738 original size:11 final size:11
Alignment explanation
Indices: 57951724--57951772 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
57951714 AATAAAAGAG
57951724 AAATAAAATTA
1 AAATAAAATTA
*
57951735 AAATAAAATAA
1 AAATAAAATTA
57951746 AGAAT-AAA--A
1 A-AATAAAATTA
*
57951755 AAATAAAAGTA
1 AAATAAAATTA
57951766 AAATAAA
1 AAATAAA
57951773 TCAAAGAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
8 3 0.09
9 5 0.15
11 22 0.67
12 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (11 bp):
AAATAAAATTA
Found at i:57951759 original size:15 final size:15
Alignment explanation
Indices: 57951739--57951780 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
57951729 AAATTAAAAT
57951739 AAAATAAAGAATAAA
1 AAAATAAAGAATAAA
*
57951754 AAAATAAA-AGTAAA
1 AAAATAAAGAATAAA
57951768 ATAAATCAAAGAA
1 A-AAAT-AAAGAA
57951781 AAGAAAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.27
15 12 0.55
16 3 0.14
17 1 0.05
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAATAAAGAATAAA
Found at i:57951767 original size:6 final size:5
Alignment explanation
Indices: 57951714--57951772 Score: 50
Period size: 5 Copynumber: 11.2 Consensus size: 5
57951704 ATAAATGATG
*
57951714 AATAA AAGAGA AATAA AATTAA AATAA AATAA AGA-ATA AA-AA AATAA
1 AATAA AATA-A AATAA AA-TAA AATAA AATAA A-ATA-A AATAA AATAA
57951761 AAGTAA AATAA A
1 AA-TAA AATAA A
57951773 TCAAAGAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
4 3 0.07
5 26 0.57
6 17 0.37
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:57958356 original size:18 final size:19
Alignment explanation
Indices: 57958335--57958370 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
57958325 ACCTACCAGA
57958335 AGTAAATAAAA-AAAATTT
1 AGTAAATAAAATAAAATTT
*
57958353 AGTAATTAAAATAAAATT
1 AGTAAATAAAATAAAATT
57958371 AAATTGCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (19 bp):
AGTAAATAAAATAAAATTT
Found at i:57964906 original size:40 final size:40
Alignment explanation
Indices: 57964845--57964920 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
57964835 CCGTACCTTA
*
57964845 TGGTGTGTAGGGCTGGATGGGTTGATTAAATCCCCATACT
1 TGGTGTGTAGGGCTGGATGGGTCGATTAAATCCCCATACT
* * **
57964885 TGGTGTGTAGGGTTGGGTGGGTCGATTCTATCCCCA
1 TGGTGTGTAGGGCTGGATGGGTCGATTAAATCCCCA
57964921 CATGGTGTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.36, T:0.33
Consensus pattern (40 bp):
TGGTGTGTAGGGCTGGATGGGTCGATTAAATCCCCATACT
Found at i:57965769 original size:35 final size:35
Alignment explanation
Indices: 57965703--57965778 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
57965693 AATAAAATTT
*
57965703 AAATATTTTTAAACTATATTCATAATAAAAT-ATCA
1 AAATATTTTAAAACTATATTCATAATAAAATAAT-A
* * *
57965738 AAATATTTTAAAAATTATATTTA-AATCAAATAATA
1 AAATATTTT-AAAACTATATTCATAATAAAATAATA
57965773 AAATAT
1 AAATAT
57965779 AAATTAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (35 bp):
AAATATTTTAAAACTATATTCATAATAAAATAATA
Found at i:57968527 original size:21 final size:22
Alignment explanation
Indices: 57968503--57968550 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
57968493 TAAGTTGATA
57968503 TGTTGAAAGGTATA-TTGGTTG
1 TGTTGAAAGGTATACTTGGTTG
* *
57968524 TGTTTGGAGGGTATACTTGGTTG
1 TG-TTGAAAGGTATACTTGGTTG
57968547 TGTT
1 TGTT
57968551 TGAAGGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 12 0.52
23 9 0.39
ACGTcount: A:0.17, C:0.02, G:0.35, T:0.46
Consensus pattern (22 bp):
TGTTGAAAGGTATACTTGGTTG
Found at i:57968545 original size:23 final size:22
Alignment explanation
Indices: 57968511--57968646 Score: 119
Period size: 23 Copynumber: 5.9 Consensus size: 22
57968501 TATGTTGAAA
57968511 GGTATATTGGTTGTGTTTGGAG
1 GGTATATTGGTTGTGTTTGGAG
*
57968533 GGTATACTTGGTTGTGTTTGAAG
1 GGTATA-TTGGTTGTGTTTGGAG
*
57968556 GTTATATATATGGTTGTGTTTGGAG
1 G--GTATAT-TGGTTGTGTTTGGAG
* *
57968581 GGTAAATTTGGTTGTGTTCGGAG
1 GGTATA-TTGGTTGTGTTTGGAG
* * *
57968604 GGTACATATGGTTGTCTTTAGAG
1 GGTATAT-TGGTTGTGTTTGGAG
* * * *
57968627 GGAAAAATGATTGTGTTTGG
1 GGTATATTGGTTGTGTTTGG
57968647 TAGGTGATAG
Statistics
Matches: 92, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
22 17 0.18
23 54 0.59
24 2 0.02
25 19 0.21
ACGTcount: A:0.20, C:0.03, G:0.35, T:0.42
Consensus pattern (22 bp):
GGTATATTGGTTGTGTTTGGAG
Found at i:57973228 original size:13 final size:13
Alignment explanation
Indices: 57973210--57973238 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
57973200 TACAAGATTG
57973210 ATATGTTATATTA
1 ATATGTTATATTA
57973223 ATATGTTATATTA
1 ATATGTTATATTA
57973236 ATA
1 ATA
57973239 AAACCTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (13 bp):
ATATGTTATATTA
Found at i:57974323 original size:61 final size:61
Alignment explanation
Indices: 57974228--57974350 Score: 212
Period size: 61 Copynumber: 2.0 Consensus size: 61
57974218 CTATGTACAT
57974228 TTCATGTTGATATACAAGGACCAATTTTTAATAGTAAAAGT-GAATGAAATTTTTAATAGTA
1 TTCATGTTGATATACAAGGACCAATTTTTAATAGTAAAAGTAG-ATGAAATTTTTAATAGTA
* *
57974289 TTCATGTTGATATATAAGGACCATTTTTTAATAGTAAAAGTAGATGAAATTTTTAATAGTA
1 TTCATGTTGATATACAAGGACCAATTTTTAATAGTAAAAGTAGATGAAATTTTTAATAGTA
57974350 T
1 T
57974351 GACTAACTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 58 0.98
62 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (61 bp):
TTCATGTTGATATACAAGGACCAATTTTTAATAGTAAAAGTAGATGAAATTTTTAATAGTA
Found at i:57974766 original size:12 final size:12
Alignment explanation
Indices: 57974749--57974774 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
57974739 ACAAATATTT
57974749 AAAATATTTATA
1 AAAATATTTATA
57974761 AAAATATTTATA
1 AAAATATTTATA
57974773 AA
1 AA
57974775 TATTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATATTTATA
Found at i:57974767 original size:21 final size:23
Alignment explanation
Indices: 57974741--57974792 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
57974731 ATTTTTTAAC
*
57974741 AAATATTTA-AAATATT-TATAA
1 AAATATTTATAAATATTAAATAA
57974762 AAATATTTATAAATATTAAATAA
1 AAATATTTATAAATATTAAATAA
57974785 ATAATATT
1 A-AATATT
57974793 AAATCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 9 0.33
22 7 0.26
23 5 0.19
24 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATATTTATAAATATTAAATAA
Found at i:57974777 original size:10 final size:10
Alignment explanation
Indices: 57974741--57974778 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 10
57974731 ATTTTTTAAC
57974741 AAATATTTA-
1 AAATATTTAT
57974750 AAATATTTAT
1 AAATATTTAT
57974760 AAAAATATTTAT
1 --AAATATTTAT
57974772 AAATATT
1 AAATATT
57974779 AAATAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.35
10 7 0.27
12 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AAATATTTAT
Found at i:57974818 original size:17 final size:19
Alignment explanation
Indices: 57974788--57974836 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
57974778 TAAATAAATA
* *
57974788 ATATTAAATCATTTTTA-T
1 ATATAAAATCATTTATAGT
57974806 ATATAAAAT-ATTTATAGTT
1 ATATAAAATCATTTATAG-T
57974825 ATATAAAA-CATT
1 ATATAAAATCATT
57974837 CATAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.23
18 8 0.31
19 12 0.46
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (19 bp):
ATATAAAATCATTTATAGT
Found at i:57978271 original size:50 final size:48
Alignment explanation
Indices: 57978177--57978274 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 48
57978167 TCATTAAGGA
* * *
57978177 TTACCGATCCTCAGCCGTATGAACTTACCGATTGCAGCTCGTGAGAGC
1 TTACCAATCCTCAGCCATATGAACTTACCGATTACAGCTCGTGAGAGC
* * *
57978225 TTACCAATTCTCAGCACATATGAGCTTACTGATTTACAGCTCGTGAGAGC
1 TTACCAATCCTCAGC-CATATGAACTTACCGA-TTACAGCTCGTGAGAGC
57978275 ACACCGATTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 13 0.31
49 13 0.31
50 16 0.38
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (48 bp):
TTACCAATCCTCAGCCATATGAACTTACCGATTACAGCTCGTGAGAGC
Found at i:57978274 original size:25 final size:25
Alignment explanation
Indices: 57978211--57978274 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
57978201 TTACCGATTG
57978211 CAGCTCGTGAGAGCTTACCAATTCT
1 CAGCTCGTGAGAGCTTACCAATTCT
* * **
57978236 CAGCACAT-ATGAGCTTACTGATT-T
1 CAGCTCGTGA-GAGCTTACCAATTCT
57978260 ACAGCTCGTGAGAGC
1 -CAGCTCGTGAGAGC
57978275 ACACCGATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
24 2 0.07
25 27 0.90
26 1 0.03
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (25 bp):
CAGCTCGTGAGAGCTTACCAATTCT
Found at i:57978456 original size:30 final size:30
Alignment explanation
Indices: 57978417--57978478 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
57978407 TACATGAGAT
57978417 ACATGGAAAT-GAT-ATTACATGATATATTGAA
1 ACATGGAAATGGATGA-TACATG-TATA-TGAA
57978448 ACAT-GAAATGGATGATACATGTATATGAA
1 ACATGGAAATGGATGATACATGTATATGAA
57978477 AC
1 AC
57978479 TTGCTTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 6 0.21
30 9 0.31
31 13 0.45
32 1 0.03
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (30 bp):
ACATGGAAATGGATGATACATGTATATGAA
Found at i:57979903 original size:24 final size:24
Alignment explanation
Indices: 57979871--57979921 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
57979861 ATCTTTGGTA
57979871 ATGCTCCGTAACCCTATTCTAGCG
1 ATGCTCCGTAACCCTATTCTAGCG
* *
57979895 ATGCTCCGTAACCCTGTTCTGGCG
1 ATGCTCCGTAACCCTATTCTAGCG
57979919 ATG
1 ATG
57979922 AATACAGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.31, G:0.22, T:0.29
Consensus pattern (24 bp):
ATGCTCCGTAACCCTATTCTAGCG
Found at i:57984392 original size:17 final size:17
Alignment explanation
Indices: 57984352--57984394 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
57984342 TTAATTATGT
*
57984352 TTAAAAAATTTTAAAAA
1 TTAAAAATTTTTAAAAA
57984369 TTCAAAAATTTATTAAAAA
1 TT-AAAAATTT-TTAAAAA
57984388 -TAAAAAT
1 TTAAAAAT
57984395 ATCAAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 8 0.35
19 7 0.30
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAATTTTTAAAAA
Found at i:57986006 original size:43 final size:43
Alignment explanation
Indices: 57985941--57986042 Score: 150
Period size: 43 Copynumber: 2.4 Consensus size: 43
57985931 AGCTACAAGG
* *
57985941 GACACACGACCGTGTCACCTGGCCGTGTGTCACAAATGGCTGA
1 GACACACGCCCGTGTCACCTGGCCGTGTGTCACAAACGGCTGA
** *
57985984 GACACACGCCCGTGTCGTCTGGCCGTGTGTCACACACGGCTGA
1 GACACACGCCCGTGTCACCTGGCCGTGTGTCACAAACGGCTGA
*
57986027 GACACCCGCCCGTGTC
1 GACACACGCCCGTGTC
57986043 TCTAACCATG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.19, C:0.35, G:0.28, T:0.18
Consensus pattern (43 bp):
GACACACGCCCGTGTCACCTGGCCGTGTGTCACAAACGGCTGA
Found at i:57986952 original size:39 final size:39
Alignment explanation
Indices: 57986887--57987006 Score: 154
Period size: 39 Copynumber: 3.1 Consensus size: 39
57986877 ATTTTCAATA
* *
57986887 CACCGGCACATAGCCTGCTAGGCACATAGCCCGAATAAT
1 CACCGACACACAGCCTGCTAGGCACATAGCCCGAATAAT
* *
57986926 CACCAGTACA-A-AGCCTGCAAGACACATAGCCCGAATAAT
1 CACC-G-ACACACAGCCTGCTAGGCACATAGCCCGAATAAT
* *
57986965 TACCGACACACAACCTGCTAGGCACATAGCCCGAATAAT
1 CACCGACACACAGCCTGCTAGGCACATAGCCCGAATAAT
57987004 CAC
1 CAC
57987007 TGTATTTCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
37 3 0.04
38 2 0.03
39 60 0.87
40 2 0.03
41 2 0.03
ACGTcount: A:0.36, C:0.33, G:0.17, T:0.14
Consensus pattern (39 bp):
CACCGACACACAGCCTGCTAGGCACATAGCCCGAATAAT
Found at i:57988594 original size:46 final size:46
Alignment explanation
Indices: 57988527--57988615 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
57988517 CCTTAAGAGA
* * * *
57988527 ATTCACTATTTTAGTACCTCATACCACAAGTGTATTCAAGCTCAAT
1 ATTCACTATCTTAATACCTCATACAACAAGTGTATCCAAGCTCAAT
* *
57988573 ATTCATTATCTTAATACCTCATACAACAAGTGTGTCCAAGCTC
1 ATTCACTATCTTAATACCTCATACAACAAGTGTATCCAAGCTC
57988616 TAGCACTCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.34
Consensus pattern (46 bp):
ATTCACTATCTTAATACCTCATACAACAAGTGTATCCAAGCTCAAT
Found at i:57991256 original size:6 final size:6
Alignment explanation
Indices: 57991245--57991335 Score: 182
Period size: 6 Copynumber: 15.2 Consensus size: 6
57991235 ATAAAATGTA
57991245 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
57991293 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT G
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT G
57991336 GAGATGTTCT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (6 bp):
GTATAT
Found at i:57995247 original size:35 final size:35
Alignment explanation
Indices: 57994979--57995245 Score: 347
Period size: 35 Copynumber: 7.6 Consensus size: 35
57994969 CACGGCAAAG
*
57994979 TGTGAAACGTAGGTATGGTATTAACTATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
*
57995014 TGTGAAACGTAAGTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
* *
57995049 TGTGAAACGTAAGTATGGTATTAACCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
* * * **
57995084 TCTGAAACGTAGGTATGGTATCATCCATACCAAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
* *
57995119 TGTAAAACGTAGGTATGGTATTAACTATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
*
57995154 TGTGAAACGTAGGTATGGTATTATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
** * * * *
57995189 TAAGCAACGTAGGTATGGCATT-TCTCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTAAC-CATACTGAGT
*
57995224 TGTGAAATGTAGGTATGGTATT
1 TGTGAAACGTAGGTATGGTATT
57995246 TCAATGAGGA
Statistics
Matches: 203, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
34 2 0.01
35 201 0.99
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.32
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
Found at i:57999010 original size:23 final size:23
Alignment explanation
Indices: 57998979--57999032 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
57998969 ATAAAGACAT
*
57998979 GTGGCAAATAATTATCGTGCCAA
1 GTGGGAAATAATTATCGTGCCAA
* *
57999002 GTGGGAAATATTTATTGTGCCAA
1 GTGGGAAATAATTATCGTGCCAA
*
57999025 AT-GGAAAT
1 GTGGGAAAT
57999033 TTCTTAACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (23 bp):
GTGGGAAATAATTATCGTGCCAA
Found at i:58000172 original size:18 final size:18
Alignment explanation
Indices: 58000149--58000186 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
58000139 AGCAACTACG
58000149 ATCAACTACATTCAATTT
1 ATCAACTACATTCAATTT
58000167 ATCAACTACATTCAATTT
1 ATCAACTACATTCAATTT
58000185 AT
1 AT
58000187 ACTATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (18 bp):
ATCAACTACATTCAATTT
Found at i:58016441 original size:13 final size:12
Alignment explanation
Indices: 58016403--58016452 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
58016393 AGCAATTTTT
58016403 TTCTTTTTCTT-
1 TTCTTTTTCTTC
58016414 TTAACTTTTTCTTC
1 TT--CTTTTTCTTC
58016428 TTCTTTTTCATTC
1 TTCTTTTTC-TTC
*
58016441 -TCTTCTTCTTC
1 TTCTTTTTCTTC
58016452 T
1 T
58016453 CCCTCTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
11 5 0.15
12 14 0.42
13 12 0.36
14 2 0.06
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:58017264 original size:19 final size:16
Alignment explanation
Indices: 58017242--58017284 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 16
58017232 AAATAATATA
58017242 TTTTTTATCAAATTATAGT
1 TTTTTTATCAAA-TA-A-T
*
58017261 TTTTTTTTCAAATAAT
1 TTTTTTATCAAATAAT
58017277 TTTTTTAT
1 TTTTTTAT
58017285 TTTTAGATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 8 0.36
17 1 0.05
18 2 0.09
19 11 0.50
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTTTTATCAAATAAT
Found at i:58017560 original size:23 final size:23
Alignment explanation
Indices: 58017516--58017561 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
58017506 AAATGAATAA
*
58017516 TTTAAAAAATAAAGAGATTAAAT
1 TTTAAAAAATAAAGAGACTAAAT
*
58017539 TTTAACAAATAAA-ATGACTAAAT
1 TTTAAAAAATAAAGA-GACTAAAT
58017562 CCAAAATCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (23 bp):
TTTAAAAAATAAAGAGACTAAAT
Found at i:58025171 original size:5 final size:5
Alignment explanation
Indices: 58025161--58025192 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
58025151 TGCTCTTCGT
58025161 TTTTA TTTTA TTTTA TTTTA -TTT- TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
58025193 TGGTAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.24
5 19 0.76
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTA
Found at i:58026810 original size:15 final size:15
Alignment explanation
Indices: 58026790--58026819 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
58026780 AAAACCATTG
58026790 AATTATCTTCAATAT
1 AATTATCTTCAATAT
58026805 AATTATCTTCAATAT
1 AATTATCTTCAATAT
58026820 TGTAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTATCTTCAATAT
Found at i:58028295 original size:70 final size:70
Alignment explanation
Indices: 58028182--58028322 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
58028172 AAAAAAAAAC
*
58028182 ATTGTGTCGTTGAATCTTATATTCATAGCGATTATGATTCAAGAAATATGATTATCATTTTTGTA
1 ATTGTGTCGTTGAATCTTATATTCATAGCGATTATGATTCAAGAAATATGATTACCATTTTTGTA
58028247 TTTTA
66 TTTTA
*
58028252 ATTGTGTTGTTGAATCTTATATTCATAGCGATTATGATTCAAGAAATATGATTACCATTTTTGTA
1 ATTGTGTCGTTGAATCTTATATTCATAGCGATTATGATTCAAGAAATATGATTACCATTTTTGTA
58028317 TTTTA
66 TTTTA
58028322 A
1 A
58028323 ACATGTGAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (70 bp):
ATTGTGTCGTTGAATCTTATATTCATAGCGATTATGATTCAAGAAATATGATTACCATTTTTGTA
TTTTA
Found at i:58030636 original size:31 final size:28
Alignment explanation
Indices: 58030582--58030648 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
58030572 ACTTTTTTTT
*
58030582 AATAAAAACTTAATAGTCTAATGATTTA
1 AATAAAAACTTAATAGTCTAATGACTTA
58030610 AATAAAAACTTTTGAATAGT-TAAATGACTTA
1 AATAAAAAC--TT-AATAGTCT-AATGACTTA
*
58030641 AATGAAAA
1 AATAAAAA
58030649 GTGTCAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 9 0.27
30 3 0.09
31 21 0.64
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (28 bp):
AATAAAAACTTAATAGTCTAATGACTTA
Found at i:58032617 original size:21 final size:21
Alignment explanation
Indices: 58032559--58032617 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 21
58032549 TATCTGTCGA
* *
58032559 ATTTCTCTCAA-TTTTCTCTT
1 ATTTCTCTCAACTTTTTTTTT
* **
58032579 AATT-TCTC-ACTTAATTTTT
1 ATTTCTCTCAACTTTTTTTTT
58032598 ATTTCTCTCAACTTTTTTTT
1 ATTTCTCTCAACTTTTTTTT
58032618 ATATATTAAG
Statistics
Matches: 28, Mismatches: 8, Indels: 5
0.68 0.20 0.12
Matches are distributed among these distances:
18 1 0.04
19 12 0.43
20 7 0.25
21 8 0.29
ACGTcount: A:0.19, C:0.20, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTCTCTCAACTTTTTTTTT
Found at i:58033393 original size:21 final size:21
Alignment explanation
Indices: 58033368--58033437 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 21
58033358 AAAATTAAAG
*
58033368 AAATATATAAATATATTTTAA
1 AAATATATAAAAATATTTTAA
* *
58033389 AAATATATATAAAAAATTTTGA
1 AAATATATA-AAAATATTTTAA
58033411 AAATATAATAACAAATATTTTTAA
1 AAATAT-ATAA-AAATA-TTTTAA
58033435 AAA
1 AAA
58033438 AGTATTTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 9 0.22
22 16 0.40
23 7 0.17
24 8 0.20
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (21 bp):
AAATATATAAAAATATTTTAA
Found at i:58033413 original size:23 final size:22
Alignment explanation
Indices: 58033355--58033437 Score: 75
Period size: 22 Copynumber: 3.7 Consensus size: 22
58033345 ATACTAATTT
58033355 TAAAAAA--TTAAAGAA-ATATA
1 TAAAAAATTTTAAA-AATATATA
*
58033375 TAAATATATTTTAAAAATATATA
1 TAAA-AAATTTTAAAAATATATA
*
58033398 TAAAAAATTTTGAAAATATA-A
1 TAAAAAATTTTAAAAATATATA
58033419 TAACAAATATTTTTAAAAA
1 TAA-AAA-A-TTTTAAAAA
58033438 AGTATTTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.08
21 6 0.12
22 19 0.37
23 15 0.29
24 8 0.15
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAAAAATTTTAAAAATATATA
Found at i:58034352 original size:10 final size:10
Alignment explanation
Indices: 58034295--58034359 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
58034285 GTTTCTTGAC
*
58034295 ATTTTTATAC
1 ATTTTTATAT
*
58034305 ATTTTT-TAA
1 ATTTTTATAT
58034314 ATTTATTATTAT
1 ATTT-TTA-TAT
* *
58034326 ATTTTAAAAT
1 ATTTTTATAT
* *
58034336 ATATTTATGT
1 ATTTTTATAT
58034346 ATTTTTATAT
1 ATTTTTATAT
58034356 ATTT
1 ATTT
58034360 CAAATTAAGA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
9 6 0.14
10 28 0.67
11 2 0.05
12 6 0.14
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:58036091 original size:3 final size:3
Alignment explanation
Indices: 58036083--58036108 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
58036073 ACATCAGAAT
58036083 CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CA
58036109 GCAGCAGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:58038824 original size:36 final size:37
Alignment explanation
Indices: 58038777--58038849 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 37
58038767 CACAAAATAT
58038777 TCCCACTCAACAGAGTGGGGAAAC-AAACCTAATCAA
1 TCCCACTCAACAGAGTGGGGAAACAAAACCTAATCAA
*
58038813 TCCCACTCAACAGAGTTGGGAAACAAAACCTAATCAA
1 TCCCACTCAACAGAGTGGGGAAACAAAACCTAATCAA
58038850 AGACAANCCC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 23 0.66
37 12 0.34
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.15
Consensus pattern (37 bp):
TCCCACTCAACAGAGTGGGGAAACAAAACCTAATCAA
Found at i:58042755 original size:21 final size:20
Alignment explanation
Indices: 58042714--58042755 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
58042704 ATGAATGTAA
* *
58042714 TTTTATTTATTTAAAATTAT
1 TTTTATTTAATAAAAATTAT
58042734 TTTTATTTAATAAAATATTAT
1 TTTTATTTAATAAAA-ATTAT
58042755 T
1 T
58042756 AAAATGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTATTTAATAAAAATTAT
Found at i:58045055 original size:15 final size:15
Alignment explanation
Indices: 58045042--58045072 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
58045032 CCAATTTCTT
58045042 CGCTCTCCATTTCTCC
1 CGCT-TCCATTTCTCC
58045058 CGCTTCCATTTCTCC
1 CGCTTCCATTTCTCC
58045073 TTTTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.06, C:0.48, G:0.06, T:0.39
Consensus pattern (15 bp):
CGCTTCCATTTCTCC
Found at i:58058200 original size:93 final size:93
Alignment explanation
Indices: 58058088--58058259 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
58058078 CGCCCATAAG
* *
58058088 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
58058153 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
58058181 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
58058246 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
58058260 TCAATCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:58058256 original size:46 final size:46
Alignment explanation
Indices: 58058081--58058256 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
58058071 TGTAACCCGC
* * *
58058081 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
58058127 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
58058177 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
58058220 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
58058257 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:58060861 original size:55 final size:55
Alignment explanation
Indices: 58060745--58060866 Score: 124
Period size: 55 Copynumber: 2.2 Consensus size: 55
58060735 CGTGTGCAAT
* * * **
58060745 ACTGACTTTAAAACACGGCCATGACACACGCCCGTGTGGCCTGTCCATGTATAAC
1 ACTGACTTTAAAACACGACCATGACACACGCCCATATGGCCTACCCATGTATAAC
* * * *
58060800 AATGACTTTAGAAA-ACGACCATGACATACGCCTATATGGCCTACCCGTGTACTAA-
1 ACTGACTTTA-AAACACGACCATGACACACGCCCATATGGCCTACCCATGTA-TAAC
58060855 ACTGAC-TTAAAA
1 ACTGACTTTAAAA
58060867 TTTTAAGTGC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
53 3 0.05
54 3 0.05
55 43 0.78
56 6 0.11
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (55 bp):
ACTGACTTTAAAACACGACCATGACACACGCCCATATGGCCTACCCATGTATAAC
Found at i:58061839 original size:49 final size:48
Alignment explanation
Indices: 58061623--58061892 Score: 204
Period size: 49 Copynumber: 5.7 Consensus size: 48
58061613 GATAAGTTGT
* *
58061623 CGATGCCATGTCCCAGACATGGTCTCACACAGGCTATCATCATCGAGGC
1 CGATG-CATGTCCCAGACATGGTCTTACACTGGCTATCATCATCGAGGC
* ** * * **
58061672 CGATGCCATGTCCCAGACATGGTCTTATACTATCTCTCGT-ATATATGTGC
1 CGATG-CATGTCCCAGACATGGTCTTACACTGGCTATCATCATCGA-G-GC
* * *
58061722 TGATGCATGTCCC-GAACAT-GTCTTACACTAGC-A-CGA-C-TCTTA-GC
1 CGATGCATGTCCCAG-ACATGGTCTTACACTGGCTATC-ATCATC-GAGGC
* ** *
58061766 CGATGCGTGTTTCAGACA-CGTCTTACACTGGCTATCATCATCGAGGC
1 CGATGCATGTCCCAGACATGGTCTTACACTGGCTATCATCATCGAGGC
* * *
58061813 TGATGCCATGTCCCAGACATGGTCTTACACTGGC-ACTCATAAT-GTGGC
1 CGATG-CATGTCCCAGACATGGTCTTACACTGGCTA-TCATCATCGAGGC
58061861 CGATGCATGTCCCAGACAT-GTCTTACACTGGC
1 CGATGCATGTCCCAGACATGGTCTTACACTGGC
58061893 ACACAAGAAA
Statistics
Matches: 176, Mismatches: 29, Indels: 35
0.73 0.12 0.15
Matches are distributed among these distances:
44 26 0.15
45 3 0.02
46 18 0.10
47 24 0.14
48 34 0.19
49 65 0.37
50 6 0.03
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (48 bp):
CGATGCATGTCCCAGACATGGTCTTACACTGGCTATCATCATCGAGGC
Found at i:58067911 original size:55 final size:55
Alignment explanation
Indices: 58067851--58067972 Score: 185
Period size: 55 Copynumber: 2.2 Consensus size: 55
58067841 CGTATGCAAC
* *
58067851 ACTGACTTTAAAACACGACCATGACACACGCCCGTGTGGCCTGCCCGTGTAC-AA
1 ACTGACTTTAAAACACGACCATGACACACACCCGTGTGGCCTACCCGTGTACTAA
* *
58067905 TACTGACTTCAAAACACGACCATGACACACACCTGTGTGGCCTACCCGTGTACTAA
1 -ACTGACTTTAAAACACGACCATGACACACACCCGTGTGGCCTACCCGTGTACTAA
58067961 ACTGAC-TTAAAA
1 ACTGACTTTAAAA
58067973 TTTTAAGTGC
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
54 5 0.08
55 54 0.89
56 2 0.03
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.20
Consensus pattern (55 bp):
ACTGACTTTAAAACACGACCATGACACACACCCGTGTGGCCTACCCGTGTACTAA
Found at i:58069022 original size:89 final size:91
Alignment explanation
Indices: 58068779--58069047 Score: 266
Period size: 89 Copynumber: 3.0 Consensus size: 91
58068769 TCATTATCGA
* * * * * *
58068779 AGCCGATGCCATGTCTCAGACATGGTCTTATACTAGCTCTCGTATATACGT-GCTGATGCATGTC
1 AGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTC--ATA-ATGTGGCTGATGAATGTC
* *
58068843 TCGGACATGTCTTACATTAGCACGACTCTT
63 CCAGACATGTCTTACATTAGCAC-ACTCTT
** *
58068873 AGCCGATG-CATGTCCCAGACA-CATCTTACACTGGCTA-TCATCATCGTGGCTGAT-ACATGTC
1 AGCCGATGCCATGTCCCAGACATGGTCTTACACTGGC-ACTCATAAT-GTGGCTGATGA-ATGTC
*
58068934 CCAGACATGTCTTACATT-GCA-TCTC-T
63 CCAGACATGTCTTACATTAGCACACTCTT
*
58068960 ACGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAATGTGGCCGATGAATGTCCC
1 A-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAATGTGGCTGATGAATGTCCC
* * *
58069025 AGACATGTTTTACACTGGCACAC
65 AGACATGTCTTACATTAGCACAC
58069048 AAGAAATCCG
Statistics
Matches: 145, Mismatches: 19, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
87 2 0.01
88 10 0.07
89 44 0.30
90 29 0.20
91 28 0.19
92 12 0.08
93 12 0.08
94 8 0.06
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (91 bp):
AGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAATGTGGCTGATGAATGTCCCA
GACATGTCTTACATTAGCACACTCTT
Found at i:58069025 original size:47 final size:45
Alignment explanation
Indices: 58068874--58069045 Score: 151
Period size: 47 Copynumber: 3.8 Consensus size: 45
58068864 ACGACTCTTA
* **
58068874 GCCGATGCATGTCCCAGACACATCTTACACTGGCTA-TCATCATCGTG
1 GCCGATGAATGTCCCAGACATGTCTTACACTGGC-ACTCAT-AT-GTG
* * *
58068921 GCTGAT-ACATGTCCCAGACATGTCTTACA-TTGCATCTC-TA---C
1 GCCGATGA-ATGTCCCAGACATGTCTTACACTGGCA-CTCATATGTG
*
58068962 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAATGTG
1 GCCGATG-AATGTCCCAGACAT-GTCTTACACTGGCACTCAT-ATGTG
*
58069010 GCCGATGAATGTCCCAGACATGTTTTACACTGGCAC
1 GCCGATGAATGTCCCAGACATGTCTTACACTGGCAC
58069046 ACAAGAAATC
Statistics
Matches: 101, Mismatches: 12, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
41 5 0.05
42 13 0.13
43 11 0.11
44 5 0.05
45 3 0.03
46 18 0.18
47 39 0.39
48 7 0.07
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.27
Consensus pattern (45 bp):
GCCGATGAATGTCCCAGACATGTCTTACACTGGCACTCATATGTG
Found at i:58087412 original size:13 final size:13
Alignment explanation
Indices: 58087386--58087466 Score: 81
Period size: 13 Copynumber: 6.2 Consensus size: 13
58087376 ACCATTACAA
* *
58087386 AAATGGTAAAATG
1 AAATGGTTATATG
* *
58087399 AAATGTTTAGATG
1 AAATGGTTATATG
*
58087412 AAATGGTTATATA
1 AAATGGTTATATG
* *
58087425 AAATGATTACATG
1 AAATGGTTATATG
*
58087438 AAATGGTTAAATG
1 AAATGGTTATATG
*
58087451 AATTGGTTATATG
1 AAATGGTTATATG
58087464 AAA
1 AAA
58087467 ATAGATGTAT
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 54 1.00
ACGTcount: A:0.46, C:0.01, G:0.20, T:0.33
Consensus pattern (13 bp):
AAATGGTTATATG
Found at i:58087464 original size:26 final size:26
Alignment explanation
Indices: 58087386--58087466 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 26
58087376 ACCATTACAA
* * *
58087386 AAATGGTAAAATGAAATGTTTAGATG
1 AAATGGTTAAATGAAATGATTACATG
* *
58087412 AAATGGTTATATAAAATGATTACATG
1 AAATGGTTAAATGAAATGATTACATG
* * *
58087438 AAATGGTTAAATGAATTGGTTATATG
1 AAATGGTTAAATGAAATGATTACATG
58087464 AAA
1 AAA
58087467 ATAGATGTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.46, C:0.01, G:0.20, T:0.33
Consensus pattern (26 bp):
AAATGGTTAAATGAAATGATTACATG
Found at i:58093083 original size:21 final size:22
Alignment explanation
Indices: 58093053--58093093 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
58093043 CTTGTAGTTT
58093053 TTAATTAGCTCAATTAAGCTCA
1 TTAATTAGCTCAATTAAGCTCA
58093075 TTAA-TAGCTCAATTAAGCT
1 TTAATTAGCTCAATTAAGCT
58093094 GAGTGTGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
TTAATTAGCTCAATTAAGCTCA
Found at i:58095018 original size:35 final size:34
Alignment explanation
Indices: 58094937--58095020 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 34
58094927 GTGTTACCTG
* *
58094937 GTGTGCTAGATAGTACTGGCTCTTATGAGCATAT
1 GTGTGCTGGATGGTACTGGCTCTTATGAGCATAT
* *
58094971 GATGTG-TCGGATGGTACTGGCTGTTATGAGCATCT
1 G-TGTGCT-GGATGGTACTGGCTCTTATGAGCATAT
58095006 AGTGTGCTGGATGGT
1 -GTGTGCTGGATGGT
58095021 TAACCGTGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
34 2 0.05
35 38 0.90
36 2 0.05
ACGTcount: A:0.19, C:0.13, G:0.33, T:0.35
Consensus pattern (34 bp):
GTGTGCTGGATGGTACTGGCTCTTATGAGCATAT
Found at i:58095946 original size:45 final size:45
Alignment explanation
Indices: 58095846--58095972 Score: 147
Period size: 45 Copynumber: 2.9 Consensus size: 45
58095836 TTTTCTCAAA
* *
58095846 TCACCGGCATT-TCGCCTGTTAGGCTCG-AGGCCCG-ATATCAGT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
58095888 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-A-T
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TCAGT
** * *
58095932 CTCACCGGCATTATAGTTTGCTAAGCTCAAAGGCCCGAATA
1 -TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
58095973 ATCAAGTCAA
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
42 11 0.15
43 14 0.19
44 8 0.11
45 40 0.54
46 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
Found at i:58096350 original size:43 final size:43
Alignment explanation
Indices: 58096303--58096413 Score: 177
Period size: 43 Copynumber: 2.6 Consensus size: 43
58096293 CGGCATTACG
**
58096303 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAA
1 CCTGCTAGGCACGAAGGCCCGAATACACATCACAAGCACGAAA
* *
58096346 CCTGCTAGGCACGAAGGCCCGAATACACATCATAAGCACGAAG
1 CCTGCTAGGCACGAAGGCCCGAATACACATCACAAGCACGAAA
*
58096389 CCTGCGAGGCACGAAGGCCCGAATA
1 CCTGCTAGGCACGAAGGCCCGAATA
58096414 TAATACCAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.32, C:0.32, G:0.25, T:0.10
Consensus pattern (43 bp):
CCTGCTAGGCACGAAGGCCCGAATACACATCACAAGCACGAAA
Found at i:58096541 original size:40 final size:38
Alignment explanation
Indices: 58096406--58096600 Score: 219
Period size: 38 Copynumber: 5.1 Consensus size: 38
58096396 GGCACGAAGG
* * * * * *
58096406 CCCGAATATAATACCAGTACTAGGCCTGCAGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
58096444 CCTGGATATAATACTAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
** ** * *
58096482 CCTAGATATTTTACCAGCACGAAGCCTGTGGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGG-ATTTAA
*
58096521 GCCCGGATATAATGCCAGCACGAAGCCTGCGGGATTTAA
1 -CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
58096560 CCCGGATATAATACCAGCACAAAGCCTGCAGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
58096598 CCC
1 CCC
58096601 TAATATACAT
Statistics
Matches: 131, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
38 95 0.73
39 10 0.08
40 26 0.20
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:58098753 original size:14 final size:13
Alignment explanation
Indices: 58098727--58098751 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58098717 GGAAAATTGC
58098727 ATGAAAATTTTTA
1 ATGAAAATTTTTA
58098740 ATGAAAATTTTT
1 ATGAAAATTTTT
58098752 TATCGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
ATGAAAATTTTTA
Found at i:58098848 original size:17 final size:18
Alignment explanation
Indices: 58098807--58098849 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
58098797 TGTCAAAGTT
*
58098807 GGATTCTAATAGCTATAA
1 GGATTCAAATAGCTATAA
*
58098825 GGA-TCAAATAGCTAT-G
1 GGATTCAAATAGCTATAA
58098841 GGATTCAAA
1 GGATTCAAA
58098850 ATGTGAGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 3 0.14
17 16 0.73
18 3 0.14
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.28
Consensus pattern (18 bp):
GGATTCAAATAGCTATAA
Found at i:58099928 original size:33 final size:33
Alignment explanation
Indices: 58099882--58100061 Score: 179
Period size: 33 Copynumber: 5.6 Consensus size: 33
58099872 TACCTAAATG
58099882 GTAC-ATTTGAAAAGGTTATGTACACTTTGTGT
1 GTACAATTTGAAAAGGTTATGTACACTTTGTGT
*
58099914 GTACAATTTGAAAAGGTTATGTACACTTTGTGC
1 GTACAATTTGAAAAGGTTATGTACACTTTGTGT
*
58099947 GTACAATTTGAAAAGGCTATG---ACTTTGTGT
1 GTACAATTTGAAAAGGTTATGTACACTTTGTGT
* * * * *
58099977 GTAGAACTTGAAAAGGATACGTACACTTTGAGT
1 GTACAATTTGAAAAGGTTATGTACACTTTGTGT
* * ** * * * *
58100010 GTACCACTTGAAAAGGGAATATACACCTCGAGT
1 GTACAATTTGAAAAGGTTATGTACACTTTGTGT
* *
58100043 GTACGATTGGAAAAGGTTA
1 GTACAATTTGAAAAGGTTA
58100062 CGTCCTTCGA
Statistics
Matches: 123, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
30 25 0.20
32 4 0.03
33 94 0.76
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (33 bp):
GTACAATTTGAAAAGGTTATGTACACTTTGTGT
Found at i:58099975 original size:63 final size:63
Alignment explanation
Indices: 58099882--58100025 Score: 173
Period size: 63 Copynumber: 2.2 Consensus size: 63
58099872 TACCTAAATG
* * * * *
58099882 GTACATTTGAAAAGGTTATGTACACTTTGTGTGTACAATTTGAAAAGGTTATGTACACTTTGTGC
1 GTACATTTGAAAAGGCTATG-A-ACTTTGTGTGTACAACTTGAAAAGGATACGTACACTTTGAGC
* *
58099947 GTACAATTTGAAAAGGCTATG-ACTTTGTGTGTAGAACTTGAAAAGGATACGTACACTTTGAGT
1 GTAC-ATTTGAAAAGGCTATGAACTTTGTGTGTACAACTTGAAAAGGATACGTACACTTTGAGC
*
58100010 GTACCACTTGAAAAGG
1 GTA-CATTTGAAAAGG
58100026 GAATATACAC
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 49 0.71
64 1 0.01
65 4 0.06
66 15 0.22
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (63 bp):
GTACATTTGAAAAGGCTATGAACTTTGTGTGTACAACTTGAAAAGGATACGTACACTTTGAGC
Found at i:58105602 original size:26 final size:23
Alignment explanation
Indices: 58105557--58105603 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 23
58105547 CATATAATAT
*
58105557 TTATCATATAATACCATACTATA
1 TTATCATAAAATACCATACTATA
58105580 TTATCATCAAAATACACATTACTA
1 TTATCAT-AAAATAC-CA-TACTA
58105604 GTCATTCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 2 0.10
26 5 0.25
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (23 bp):
TTATCATAAAATACCATACTATA
Found at i:58106095 original size:33 final size:33
Alignment explanation
Indices: 58106055--58106244 Score: 258
Period size: 33 Copynumber: 5.8 Consensus size: 33
58106045 TACACTTGAG
** * *
58106055 GTGTACATTCCCTTTTTAAGTGGTACACACAAA
1 GTGTACATAACCTTTTCAAGTTGTACACACAAA
* * * *
58106088 GTTTACATATCCTTTTCAAATTGTACACTCAAA
1 GTGTACATAACCTTTTCAAGTTGTACACACAAA
58106121 GTGTACATAACCTTTTCAAGTTGTACACACAAA
1 GTGTACATAACCTTTTCAAGTTGTACACACAAA
*
58106154 GTGTACATAACCTTTTCAAGTTGTACATACAAA
1 GTGTACATAACCTTTTCAAGTTGTACACACAAA
* *
58106187 GTGTACATAGCCCTTTTCAAATTGTACACACAAA
1 GTGTACATA-ACCTTTTCAAGTTGTACACACAAA
58106221 GTGTACATAACC-TTTCAAG-TGTAC
1 GTGTACATAACCTTTTCAAGTTGTAC
58106245 CATTTAGGTA
Statistics
Matches: 139, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
31 5 0.04
32 6 0.04
33 98 0.71
34 30 0.22
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (33 bp):
GTGTACATAACCTTTTCAAGTTGTACACACAAA
Found at i:58106237 original size:66 final size:66
Alignment explanation
Indices: 58106029--58106244 Score: 276
Period size: 66 Copynumber: 3.3 Consensus size: 66
58106019 CCATTGGACG
* * ** * * * * *
58106029 TAACCTTTTCTAGTCGTACACTTGAGGTGTACATTCCCTTTTTAAGTGGTACACACAAAGTTTAC
1 TAACCTTTTCAAGTTGTACACTCAAAGTGTACATACCCTTTTCAAGTTGTACACACAAAGTGTAC
58106094 A
66 A
* * *
58106095 TATCCTTTTCAAATTGTACACTCAAAGTGTACATAACCTTTTCAAGTTGTACACACAAAGTGTAC
1 TAACCTTTTCAAGTTGTACACTCAAAGTGTACATACCCTTTTCAAGTTGTACACACAAAGTGTAC
58106160 A
66 A
*
58106161 TAACCTTTTCAAGTTGTACA-TACAAAGTGTACATAGCCCTTTTCAAATTGTACACACAAAGTGT
1 TAACCTTTTCAAGTTGTACACT-CAAAGTGTACATA-CCCTTTTCAAGTTGTACACACAAAGTGT
58106225 ACA
64 ACA
58106228 TAACC-TTTCAAG-TGTAC
1 TAACCTTTTCAAGTTGTAC
58106245 CATTTAGGTA
Statistics
Matches: 132, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
65 6 0.05
66 92 0.70
67 34 0.26
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.34
Consensus pattern (66 bp):
TAACCTTTTCAAGTTGTACACTCAAAGTGTACATACCCTTTTCAAGTTGTACACACAAAGTGTAC
A
Found at i:58112182 original size:37 final size:37
Alignment explanation
Indices: 58112130--58112203 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
58112120 ATGAAATGGT
*
58112130 GTTACTTCAATCAATAAAGCAATATTGGAGAAAAGCA
1 GTTACTTCAACCAATAAAGCAATATTGGAGAAAAGCA
*
58112167 GTTACTTCAACCAATAAAGCGATATTGGAGAAAAGCA
1 GTTACTTCAACCAATAAAGCAATATTGGAGAAAAGCA
58112204 ACAACCAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.23
Consensus pattern (37 bp):
GTTACTTCAACCAATAAAGCAATATTGGAGAAAAGCA
Found at i:58119673 original size:19 final size:20
Alignment explanation
Indices: 58119636--58119675 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
58119626 ACATCATCAC
58119636 TAATGCATACATTTCGAAAA
1 TAATGCATACATTTCGAAAA
* *
58119656 TAATG-ATATATTTTGAAAA
1 TAATGCATACATTTCGAAAA
58119675 T
1 T
58119676 CGAAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (20 bp):
TAATGCATACATTTCGAAAA
Found at i:58124243 original size:98 final size:98
Alignment explanation
Indices: 58124110--58124290 Score: 242
Period size: 98 Copynumber: 1.8 Consensus size: 98
58124100 ACCCATCTCC
58124110 TCCCTCAAAATTTTCTAAATATTTTCCCCCCAAAATTTACT-CATTTATTTACTTTCCCCCT-AA
1 TCCCTCAAAATTTTCTAAATATTTTCCCCCCAAAATTTACTCCA-TTATTTACTTTCCCCCTAAA
*
58124173 ACTTTTTATTCCTCTCCTATTCCAACCCTTTATCT
65 AC-TTTTACTCCTCTCCTATTCCAACCCTTTATCT
* * * * * * *
58124208 TCCC-CAAAATTTTATTGAATATTTTCTCTCTAAAATTTACTCCATTATTTACTTTTCCCTTAAA
1 TCCCTCAAAATTTT-CTAAATATTTTCCCCCCAAAATTTACTCCATTATTTACTTTCCCCCTAAA
58124272 ACTTTTACTCCTCTCCTAT
65 ACTTTTACTCCTCTCCTAT
58124291 CCTAACTCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
97 9 0.12
98 57 0.79
99 6 0.08
ACGTcount: A:0.25, C:0.29, G:0.01, T:0.45
Consensus pattern (98 bp):
TCCCTCAAAATTTTCTAAATATTTTCCCCCCAAAATTTACTCCATTATTTACTTTCCCCCTAAAA
CTTTTACTCCTCTCCTATTCCAACCCTTTATCT
Found at i:58124311 original size:98 final size:98
Alignment explanation
Indices: 58124127--58124313 Score: 238
Period size: 98 Copynumber: 1.9 Consensus size: 98
58124117 AAATTTTCTA
*
58124127 AATATTTTCCCCCCAAAATTTACTCATTTATTTACTTTCCCCCTAAACTTTTTATTCCTCTCCTA
1 AATATTTTCCCCCCAAAATTTACTCATTTATTTACTTTCCCCCTAAACTTTTTACTCCTCTCCTA
* *
58124192 TTCCAACCCTTTATCTTCCCCAAAATTTTATTG
66 TTCCAACCCTCTATCTACCCCAAAATTTTATTG
* * * * *
58124225 AATATTTTCTCTCTAAAATTTACTCCA-TTATTTACTTTTCCCTTAAAAC-TTTTACTCCTCTCC
1 AATATTTTCCCCCCAAAATTTACT-CATTTATTTACTTTCCCCCT-AAACTTTTTACTCCTCTCC
58124288 TA-TCCTAACTCCTCT-TCTACCCCAAA
64 TATTCC-AAC-CCTCTATCTACCCCAAA
58124314 CCAATTTTCT
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
97 3 0.04
98 64 0.83
99 10 0.13
ACGTcount: A:0.25, C:0.31, G:0.01, T:0.43
Consensus pattern (98 bp):
AATATTTTCCCCCCAAAATTTACTCATTTATTTACTTTCCCCCTAAACTTTTTACTCCTCTCCTA
TTCCAACCCTCTATCTACCCCAAAATTTTATTG
Found at i:58124393 original size:115 final size:116
Alignment explanation
Indices: 58124210--58124524 Score: 311
Period size: 115 Copynumber: 2.7 Consensus size: 116
58124200 CTTTATCTTC
* * * *
58124210 CCCAAAATTTTATTGAATATTTTC-TCTCTAAAATTTACTCCAT-TATTTACTTTTCCCTTAAAA
1 CCCAAATTTTTTTTGAATATTTTCTTC-CCAAAATTTACTCC-TCTATTTACTTTTCCC-CAAAA
* * *
58124273 CTTTTACTCCTCTCCTATCCT-AA-CTCCTCTTCTACCC-CAAACCAATTTTCT
63 TTTTTACTCCTCTCCTATCCTAAATCTACTCATCTACCCTCAAACCAATTTTCT
*
58124324 CCCAAATTCTTTTTTGAATATTTTCTTCCCAAAATTTACTCCTCTATTTACTTTTCCTCCAATAT
1 CCCAAATT-TTTTTTGAATATTTTCTTCCCAAAATTTACTCCTCTATTTACTTTTCC-CCAAAAT
* * * *
58124389 TTTTACTCCCTATCACTTTCCTCACAAATTGTTTACTCATCTACCCTCAAACCCATTTTCT
64 TTTTACT-CCTCTC-CTATCCT---AAA---TCTACTCATCTACCCTCAAACCAATTTTCT
* * * * *
58124450 CCCCAATTTTTTTTGAATCTTTT-TCCCCAAAAGTTACTCCCCTATTTACTTTTCCCCAAAATTT
1 CCCAAATTTTTTTTGAATATTTTCTTCCCAAAATTTACTCCTCTATTTACTTTTCCCCAAAATTT
58124514 TTACTCC-CTCC
66 TTACTCCTCTCC
58124525 CACTTTTCCC
Statistics
Matches: 167, Mismatches: 19, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
114 8 0.05
115 51 0.31
116 8 0.05
117 6 0.04
120 1 0.01
121 4 0.02
122 2 0.01
123 13 0.08
124 29 0.17
125 25 0.15
126 20 0.12
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.43
Consensus pattern (116 bp):
CCCAAATTTTTTTTGAATATTTTCTTCCCAAAATTTACTCCTCTATTTACTTTTCCCCAAAATTT
TTACTCCTCTCCTATCCTAAATCTACTCATCTACCCTCAAACCAATTTTCT
Found at i:58124424 original size:30 final size:32
Alignment explanation
Indices: 58124358--58124431 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 32
58124348 CTTCCCAAAA
*
58124358 TTTACTCCTCTATTTACTTTTCCTCCAATATT
1 TTTACTCCTCTATTCACTTTTCCTCCAATATT
58124390 TTTACTCC-CTA-TCAC-TTTCCTCACAA-ATT
1 TTTACTCCTCTATTCACTTTTCCTC-CAATATT
*
58124419 GTTTACTCATCTA
1 -TTTACTCCTCTA
58124432 CCCTCAAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
29 10 0.27
30 13 0.35
31 6 0.16
32 8 0.22
ACGTcount: A:0.22, C:0.30, G:0.01, T:0.47
Consensus pattern (32 bp):
TTTACTCCTCTATTCACTTTTCCTCCAATATT
Found at i:58124529 original size:29 final size:31
Alignment explanation
Indices: 58124497--58124557 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
58124487 TCCCCTATTT
*
58124497 ACTTTTCCC-CAAAATTTTTACTCC-CTCCC
1 ACTTTTCCCTCAAAACTTTTACTCCTCTCCC
* *
58124526 ACTTTTCCCTTAACACTTTTACTCCTCTCCC
1 ACTTTTCCCTCAAAACTTTTACTCCTCTCCC
58124557 A
1 A
58124558 TCCTAACCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 9 0.33
30 12 0.44
31 6 0.22
ACGTcount: A:0.20, C:0.41, G:0.00, T:0.39
Consensus pattern (31 bp):
ACTTTTCCCTCAAAACTTTTACTCCTCTCCC
Found at i:58124533 original size:124 final size:125
Alignment explanation
Indices: 58124303--58124530 Score: 345
Period size: 124 Copynumber: 1.8 Consensus size: 125
58124293 TAACTCCTCT
* * *
58124303 TCTACCCCAAACCAATTTTCTCCCAAATTCTTTTTTGAATATTTTCTTCCCAAAATTTACTCCTC
1 TCTACCCCAAACCAATTTTCTCCCAAATTCTTTTTTGAATATTTTCTCCCCAAAAGTTACTCCCC
* *
58124368 TATTTACTTTTCCTCCAATATTTTTACTCCCTATCACTTTCCTCACAAATTGTTTACTCA
66 TATTTACTTTTCCTCCAAAATTTTTACTCCCTACCACTTTCCTCACAAATTGTTTACTCA
* * *
58124428 TCTACCCTCAAACCCATTTTCTCCCCAATT-TTTTTTGAATCTTTT-TCCCCAAAAGTTACTCCC
1 TCTACCC-CAAACCAATTTTCTCCCAAATTCTTTTTTGAATATTTTCTCCCCAAAAGTTACTCCC
*
58124491 CTATTTACTTTTCC-CCAAAATTTTTACTCCCTCCCACTTT
65 CTATTTACTTTTCCTCCAAAATTTTTACTCCCTACCACTTT
58124531 TCCCTTAACA
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
123 23 0.25
124 29 0.31
125 21 0.23
126 20 0.22
ACGTcount: A:0.23, C:0.32, G:0.02, T:0.43
Consensus pattern (125 bp):
TCTACCCCAAACCAATTTTCTCCCAAATTCTTTTTTGAATATTTTCTCCCCAAAAGTTACTCCCC
TATTTACTTTTCCTCCAAAATTTTTACTCCCTACCACTTTCCTCACAAATTGTTTACTCA
Found at i:58127021 original size:21 final size:21
Alignment explanation
Indices: 58126997--58127036 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
58126987 GTGGTTTTTT
58126997 AAATAACTAAAAAATTATATA
1 AAATAACTAAAAAATTATATA
* * *
58127018 AAATTATTTAAAAATTATA
1 AAATAACTAAAAAATTATA
58127037 AATATATTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATAACTAAAAAATTATATA
Found at i:58127038 original size:19 final size:18
Alignment explanation
Indices: 58127006--58127050 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
58126996 TAAATAACTA
*
58127006 AAAAATTATATAAAATTATTT
1 AAAAATTATA-AATA-TA-TT
58127027 AAAAATTATAAATATATT
1 AAAAATTATAAATATATT
58127045 AAAAAT
1 AAAAAT
58127051 AATTTAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 3 0.13
21 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATTATAAATATATT
Found at i:58127416 original size:19 final size:19
Alignment explanation
Indices: 58127394--58127442 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
58127384 TCCAAAAAGG
58127394 ATTATTAAA-AATAAAAAAA
1 ATTATTAAATAAT-AAAAAA
* *
58127413 ATTATCAAATAATATAAAA
1 ATTATTAAATAATAAAAAA
58127432 ATTATTAAATA
1 ATTATTAAATA
58127443 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 23 0.88
20 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTATTAAATAATAAAAAA
Found at i:58127602 original size:21 final size:21
Alignment explanation
Indices: 58127562--58127611 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
58127552 AAACATATTT
*
58127562 AAAACAT-TTAAAATTTTATA
1 AAAACATATTAAAATTCTATA
*
58127582 AAAACATATTAAGATTCTATA
1 AAAACATATTAAAATTCTATA
58127603 AAAATCATA
1 AAAA-CATA
58127612 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 7 0.27
21 15 0.58
22 4 0.15
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAACATATTAAAATTCTATA
Found at i:58131050 original size:19 final size:17
Alignment explanation
Indices: 58131017--58131068 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
58131007 TAAGAATTCT
58131017 AATAATTTTTTAATTTA
1 AATAATTTTTTAATTTA
58131034 AATAAGTTTTATTAATTT-
1 AATAA-TTTT-TTAATTTA
*
58131052 TATAATTTTTTATATTT
1 AATAATTTTTTA-ATTT
58131069 TATCTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 3 0.10
17 13 0.42
18 8 0.26
19 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
AATAATTTTTTAATTTA
Found at i:58131054 original size:9 final size:9
Alignment explanation
Indices: 58131019--58131081 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 9
58131009 AGAATTCTAA
58131019 TAATTTT-T
1 TAATTTTAT
* *
58131027 TAATTTAAA
1 TAATTTTAT
58131036 TAAGTTTTAT
1 TAA-TTTTAT
58131046 TAATTTTA-
1 TAATTTTAT
58131054 TAATTTT-T
1 TAATTTTAT
58131062 TATATTTTAT
1 TA-ATTTTAT
*
58131072 CTATTTTTAT
1 -TAATTTTAT
58131082 AATATTTACA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
8 15 0.34
9 13 0.30
10 14 0.32
11 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TAATTTTAT
Found at i:58131064 original size:10 final size:10
Alignment explanation
Indices: 58131049--58131194 Score: 50
Period size: 10 Copynumber: 14.3 Consensus size: 10
58131039 GTTTTATTAA
58131049 TTTTATAATT
1 TTTTATAATT
58131059 TTTTAT-ATT
1 TTTTATAATT
* *
58131068 TTATCT-A-T
1 TTTTATAATT
58131076 TTTTATAA-T
1 TTTTATAATT
* * *
58131085 ATTTACAAGT
1 TTTTATAATT
*
58131095 TTTTATATTT
1 TTTTATAATT
*
58131105 TTATTATAGTT
1 TT-TTATAATT
58131116 ATTATTATAA-T
1 -TT-TTATAATT
* *
58131127 TTTAATAAGT
1 TTTTATAATT
** *
58131137 TGATATCATT
1 TTTTATAATT
58131147 TTTAATATTTAATAT
1 TTT--TA--TAAT-T
*
58131162 TTTTGTAATT
1 TTTTATAATT
* *
58131172 TTTTCTTATT
1 TTTTATAATT
58131182 TTTTATAATT
1 TTTTATAATT
58131192 TTT
1 TTT
58131195 AAGAGTTTTT
Statistics
Matches: 100, Mismatches: 26, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
8 5 0.05
9 21 0.21
10 44 0.44
11 12 0.12
12 10 0.10
13 1 0.01
14 3 0.03
15 4 0.04
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:58131462 original size:19 final size:19
Alignment explanation
Indices: 58131440--58131479 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
58131430 TAAGAATTTA
*
58131440 TAAATAATTATTAAA-TTAT
1 TAAATAA-TAATAAAGTTAT
58131459 TAAATAATAATAAAGTTAT
1 TAAATAATAATAAAGTTAT
58131478 TA
1 TA
58131480 TGAAAGGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAATAATAATAAAGTTAT
Found at i:58142090 original size:30 final size:30
Alignment explanation
Indices: 58142055--58142114 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
58142045 TGGTTTTAAG
58142055 AATTAGAAGGTATTTTCTTTTTTATTTTCT
1 AATTAGAAGGTATTTTCTTTTTTATTTTCT
58142085 AATTAGAAGGTATTTTCTTTTTTATTTTCT
1 AATTAGAAGGTATTTTCTTTTTTATTTTCT
58142115 TAGAAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.07, G:0.10, T:0.60
Consensus pattern (30 bp):
AATTAGAAGGTATTTTCTTTTTTATTTTCT
Found at i:58142679 original size:27 final size:27
Alignment explanation
Indices: 58142659--58142726 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
58142649 GCCTTTCTTT
* *
58142659 GAGGTGCAAATGGTTTTGCCTATCTCA
1 GAGGCGCAAATGGTTGTGCCTATCTCA
*
58142686 GAGGCGCAAATGGTTGTGCCTATCCCA
1 GAGGCGCAAATGGTTGTGCCTATCTCA
58142713 GAGGCGCAAATGGT
1 GAGGCGCAAATGGT
58142727 GGGGCCCACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.25
Consensus pattern (27 bp):
GAGGCGCAAATGGTTGTGCCTATCTCA
Found at i:58145659 original size:18 final size:18
Alignment explanation
Indices: 58145633--58145667 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58145623 ATTTTTTTAT
* *
58145633 TGTTTATATTATTTGTAA
1 TGTTAATATTAATTGTAA
58145651 TGTTAATATTAATTGTA
1 TGTTAATATTAATTGTA
58145668 TTATTTGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
TGTTAATATTAATTGTAA
Found at i:58149256 original size:33 final size:33
Alignment explanation
Indices: 58149218--58149315 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 33
58149208 ATGAACTTGA
* *
58149218 GCCGGGAGGAGTGGAGTACGATGATTGATACGG
1 GCCGGGAGGAGTGGAGTACGACGATGGATACGG
*
58149251 GCCGGGAGGAGTGGAGTACGGCGATGGATACGG
1 GCCGGGAGGAGTGGAGTACGACGATGGATACGG
* * * *
58149284 GCCAGAAGGAGCGGAGTACTGA-GGTGGATACG
1 GCCGGGAGGAGTGGAGTAC-GACGATGGATACG
58149316 AGCCAGGATA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 55 0.98
34 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.47, T:0.14
Consensus pattern (33 bp):
GCCGGGAGGAGTGGAGTACGACGATGGATACGG
Found at i:58152609 original size:14 final size:13
Alignment explanation
Indices: 58152586--58152645 Score: 52
Period size: 14 Copynumber: 4.6 Consensus size: 13
58152576 ACCTTTTTTT
58152586 TTCTTTCTTCTGC
1 TTCTTTCTTCTGC
*
58152599 TTCTCTTCTTCTTC
1 TTCT-TTCTTCTGC
*
58152613 TTCTTT-TTCTTC
1 TTCTTTCTTCTGC
* *
58152625 TCCTTTCTCTCT-T
1 TTCTTTCT-TCTGC
58152638 TTCTTTCT
1 TTCTTTCT
58152646 CTCTTCCGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 11 0.28
13 14 0.35
14 15 0.38
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.67
Consensus pattern (13 bp):
TTCTTTCTTCTGC
Found at i:58153110 original size:23 final size:24
Alignment explanation
Indices: 58153062--58153112 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
58153052 GCGTGAATGA
* *
58153062 AAAAAATACCCCATTTTCGTATAT
1 AAAAAATACCCAATTTTCGTAAAT
58153086 AAAAAATA-CCAATTTT-GATAAAT
1 AAAAAATACCCAATTTTCG-TAAAT
58153109 AAAA
1 AAAA
58153113 TTTTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 15 0.62
24 8 0.33
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.29
Consensus pattern (24 bp):
AAAAAATACCCAATTTTCGTAAAT
Found at i:58154150 original size:50 final size:48
Alignment explanation
Indices: 58154062--58154157 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 48
58154052 CTTAAAACAT
*
58154062 AAAAACATAAAAATTCAAAACCTTAAATACCAAAAACCCTAACAAATAAA
1 AAAAACATAAAAATTCAAAACCTAAAATACC-AAAACCCTAA-AAATAAA
*
58154112 AAAAACAT-AAAATCTCAAAACCTAAAAATATCC-TAACCCTAAAAAT
1 AAAAACATAAAAAT-TCAAAACCT-AAAATA-CCAAAACCCTAAAAAT
58154158 CCTAATCCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
49 9 0.22
50 25 0.61
51 5 0.12
52 2 0.05
ACGTcount: A:0.61, C:0.21, G:0.00, T:0.18
Consensus pattern (48 bp):
AAAAACATAAAAATTCAAAACCTAAAATACCAAAACCCTAAAAATAAA
Found at i:58154154 original size:17 final size:16
Alignment explanation
Indices: 58154132--58154169 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
58154122 AATCTCAAAA
58154132 CCTAAAAATATCCTAAC
1 CCTAAAAA-ATCCTAAC
*
58154149 CCT-AAAAATCCTAAT
1 CCTAAAAAATCCTAAC
58154164 CCTAAA
1 CCTAAA
58154170 TAACTTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 10 0.53
16 6 0.32
17 3 0.16
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (16 bp):
CCTAAAAAATCCTAAC
Found at i:58154161 original size:15 final size:16
Alignment explanation
Indices: 58154136--58154169 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
58154126 TCAAAACCTA
58154136 AAAATATCCTAACCCT
1 AAAATATCCTAACCCT
*
58154152 AAAA-ATCCTAATCCT
1 AAAATATCCTAACCCT
58154167 AAA
1 AAA
58154170 TAACTTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATATCCTAACCCT
Found at i:58155740 original size:17 final size:18
Alignment explanation
Indices: 58155710--58155743 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
58155700 AATTTGTATT
58155710 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
58155728 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
58155744 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:58156175 original size:14 final size:15
Alignment explanation
Indices: 58156151--58156181 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
58156141 GAATGGCTTC
58156151 TGCTATTCTTTCTTT
1 TGCTATTCTTTCTTT
58156166 TGCT-TTCTTTCTTT
1 TGCTATTCTTTCTTT
58156180 TG
1 TG
58156182 TATCTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.03, C:0.19, G:0.10, T:0.68
Consensus pattern (15 bp):
TGCTATTCTTTCTTT
Found at i:58157338 original size:39 final size:41
Alignment explanation
Indices: 58157279--58157371 Score: 113
Period size: 39 Copynumber: 2.3 Consensus size: 41
58157269 AAAAATTATA
* *
58157279 TTTAATAT-AATAAAATATTTATTATATTTAT-TT-GTATTT
1 TTTAATATAAAT-AAACATTTATTATACTTATGTTAGTATTT
*
58157318 TTTAA-ATACAATAAACATTTATTATACTTATGTTAGTGTTT
1 TTTAATATA-AATAAACATTTATTATACTTATGTTAGTATTT
58157359 TTTAATATAAATA
1 TTTAATATAAATA
58157372 TTTTTTAATG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
38 2 0.04
39 22 0.48
40 5 0.11
41 14 0.30
42 3 0.07
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (41 bp):
TTTAATATAAATAAACATTTATTATACTTATGTTAGTATTT
Found at i:58157448 original size:16 final size:17
Alignment explanation
Indices: 58157429--58157461 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
58157419 TTTAATATAT
58157429 TATATTTTTAAA-AAAA
1 TATATTTTTAAATAAAA
58157445 TATATTTTTAAATAAAA
1 TATATTTTTAAATAAAA
58157462 ACTAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATATTTTTAAATAAAA
Found at i:58158653 original size:22 final size:23
Alignment explanation
Indices: 58158606--58158654 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
58158596 CATTCAAGAT
** *
58158606 AAAA-TAATATATAAAACTCTTT
1 AAAATTAATATATAAAACAATTC
58158628 AAAATTAATATAT-AAACAATTC
1 AAAATTAATATATAAAACAATTC
58158650 AAAAT
1 AAAAT
58158655 ATATAATGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATTAATATATAAAACAATTC
Found at i:58158721 original size:26 final size:26
Alignment explanation
Indices: 58158651--58158721 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 26
58158641 AAACAATTCA
* *
58158651 AAATATATAATGTGTAAAAAAGTTTG
1 AAATAAATAATGTATAAAAAAGTTTG
* *
58158677 AAATACATAATATAT-AAAAA-TATT-
1 AAATAAATAATGTATAAAAAAGT-TTG
58158701 AAAGTAAATAATGTATAAAAA
1 AAA-TAAATAATGTATAAAAA
58158722 TTTGAATTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
24 4 0.11
25 17 0.46
26 16 0.43
ACGTcount: A:0.59, C:0.01, G:0.08, T:0.31
Consensus pattern (26 bp):
AAATAAATAATGTATAAAAAAGTTTG
Found at i:58158867 original size:35 final size:34
Alignment explanation
Indices: 58158827--58158908 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 34
58158817 ATATATAAGA
*
58158827 AAAATAATAATGAAAATAATATTAG-TATATAAATAG
1 AAAATAATAAT-AAAATAA-A-TAGAAATATAAATAG
* *
58158863 -AAATAAAAATATAATAAATAGAAATATAAATAG
1 AAAATAATAATAAAATAAATAGAAATATAAATAG
58158896 ATAAATAATAATA
1 A-AAATAATAATA
58158909 GTATTACAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
32 3 0.08
33 11 0.28
34 6 0.15
35 19 0.49
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (34 bp):
AAAATAATAATAAAATAAATAGAAATATAAATAG
Found at i:58158881 original size:21 final size:20
Alignment explanation
Indices: 58158855--58158902 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
58158845 ATATTAGTAT
58158855 ATAAATAGAAATAAAAATATA
1 ATAAATAGAAATAAAAATA-A
* *
58158876 ATAAATAGAAATATAAATAG
1 ATAAATAGAAATAAAAATAA
58158896 ATAAATA
1 ATAAATA
58158903 ATAATAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (20 bp):
ATAAATAGAAATAAAAATAA
Found at i:58158887 original size:15 final size:15
Alignment explanation
Indices: 58158863--58158905 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
58158853 ATATAAATAG
58158863 AAATAAAAATATAAT
1 AAATAAAAATATAAT
*
58158878 AAATAGAAATATAAAT
1 AAATAAAAATAT-AAT
*
58158894 AGATAAATAATA
1 AAATAAA-AATA
58158906 ATAGTATTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 11 0.48
16 8 0.35
17 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (15 bp):
AAATAAAAATATAAT
Found at i:58167183 original size:14 final size:14
Alignment explanation
Indices: 58167160--58167193 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
58167150 TACCTTTTCG
*
58167160 CTATTATATTGTTA
1 CTATTTTATTGTTA
58167174 CTATTTTATTGTTA
1 CTATTTTATTGTTA
*
58167188 TTATTT
1 CTATTT
58167194 GGATATCGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (14 bp):
CTATTTTATTGTTA
Found at i:58177457 original size:43 final size:43
Alignment explanation
Indices: 58177410--58177515 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
58177400 TCCCAGATAT
* * *
58177410 GGTCTTACATGTTATCACATATCGATGCCACTGTCCCAAACAG
1 GGTCTTACATGTAATCACATAACGATGCCAATGTCCCAAACAG
* * * * *
58177453 GGTCTTACATGAAATCGA-TTAACGATGCCAATGTCCTAGACAT
1 GGTCTTACATGTAATC-ACATAACGATGCCAATGTCCCAAACAG
58177496 GGTCTTACATGTAATCACAT
1 GGTCTTACATGTAATCACAT
58177516 CTCGGTAACC
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
42 1 0.02
43 49 0.96
44 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (43 bp):
GGTCTTACATGTAATCACATAACGATGCCAATGTCCCAAACAG
Found at i:58180136 original size:31 final size:31
Alignment explanation
Indices: 58180098--58180176 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
58180088 GGACCTCAAA
*
58180098 AAGTTTAAGTACCAACTTAAGAAAAAGTGAC
1 AAGTTTAAGTACCAAATTAAGAAAAAGTGAC
* **
58180129 AAGTTTAAGTACCAAATTAATAAAAAGTGTT
1 AAGTTTAAGTACCAAATTAAGAAAAAGTGAC
* *
58180160 AAGTTCAAATACCAAAT
1 AAGTTTAAGTACCAAAT
58180177 GTTATATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAGAAAAAGTGAC
Found at i:58184551 original size:15 final size:15
Alignment explanation
Indices: 58184514--58184551 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
58184504 CTCACTATTA
58184514 TTATTATTATTTTAT
1 TTATTATTATTTTAT
*
58184529 TTTTTATTA-TTTAT
1 TTATTATTATTTTAT
58184543 TTATGTATT
1 TTAT-TATT
58184552 TTATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTATTATTATTTTAT
Found at i:58184558 original size:12 final size:11
Alignment explanation
Indices: 58184509--58184558 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
58184499 TTTTTCTCAC
58184509 TATTATTATTAT
1 TATTATTATT-T
58184521 TATT-TTATTT
1 TATTATTATTT
58184531 T-TTATTA-TT
1 TATTATTATTT
58184540 TATTTATGTATTT
1 TA-TTAT-TATTT
58184553 TATTAT
1 TATTAT
58184559 AAATTGCACC
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
9 5 0.15
10 5 0.15
11 9 0.27
12 10 0.30
13 4 0.12
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (11 bp):
TATTATTATTT
Found at i:58184744 original size:15 final size:12
Alignment explanation
Indices: 58184715--58184763 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
58184705 ATTTTGTCAC
58184715 TATTA-TTATTGT
1 TATTATTTATT-T
*
58184727 TATTA-TCATTGT
1 TATTATTTATT-T
58184739 TATTATTTATTT
1 TATTATTTATTT
58184751 TATTATTTATTT
1 TATTATTTATTT
58184763 T
1 T
58184764 TTTCTTTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
12 30 0.88
13 4 0.12
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (12 bp):
TATTATTTATTT
Found at i:58184763 original size:12 final size:12
Alignment explanation
Indices: 58184715--58184757 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
58184705 ATTTTGTCAC
58184715 TATTATTATTGT
1 TATTATTATTGT
*
58184727 TATTATCATTGT
1 TATTATTATTGT
58184739 TATTATTTATT-T
1 TATTA-TTATTGT
58184751 TATTATT
1 TATTATT
58184758 TATTTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 2 0.07
12 22 0.79
13 4 0.14
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (12 bp):
TATTATTATTGT
Found at i:58187757 original size:21 final size:20
Alignment explanation
Indices: 58187733--58187872 Score: 103
Period size: 18 Copynumber: 7.7 Consensus size: 20
58187723 CATGTTGAAG
58187733 GAGAAGGAGGAGGAGAAGATA
1 GAGAAGGAGGAGGAGAAGA-A
58187754 GAGAAGGA-GA--AGAAG-A
1 GAGAAGGAGGAGGAGAAGAA
* *
58187770 -AGAAGGAAGAGGAG--GAG
1 GAGAAGGAGGAGGAGAAGAA
* *
58187787 GAGAAGGAGAAGAAGAAGAA
1 GAGAAGGAGGAGGAGAAGAA
*
58187807 -AG-AGGAGGAGGAGGAGAA
1 GAGAAGGAGGAGGAGAAGAA
58187825 G-G-AGGAGGAGGAG-A-AA
1 GAGAAGGAGGAGGAGAAGAA
* *
58187841 GAGGAGGAGGAGGGGAAG--
1 GAGAAGGAGGAGGAGAAGAA
58187859 GAGAAGGAGGAGGA
1 GAGAAGGAGGAGGA
58187873 AGGAAAGGAG
Statistics
Matches: 96, Mismatches: 11, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
15 7 0.07
16 7 0.07
17 2 0.02
18 65 0.68
19 3 0.03
20 4 0.04
21 8 0.08
ACGTcount: A:0.47, C:0.00, G:0.52, T:0.01
Consensus pattern (20 bp):
GAGAAGGAGGAGGAGAAGAA
Found at i:58187791 original size:33 final size:33
Alignment explanation
Indices: 58187754--58187890 Score: 159
Period size: 33 Copynumber: 4.2 Consensus size: 33
58187744 GGAGAAGATA
*
58187754 GAGAAGGAGAAGAAGAAGAAGGAAGAGGAGGAG
1 GAGAAGGAGAAGAAGAAGAAAGAAGAGGAGGAG
*
58187787 GAGAAGGAGAAGAAGAAGAAAGAGGAGGAGGAG
1 GAGAAGGAGAAGAAGAAGAAAGAAGAGGAGGAG
* * * *
58187820 GAGAAGGAGGAGGAGGAGAAAGAGGAGGAGGAG
1 GAGAAGGAGAAGAAGAAGAAAGAAGAGGAGGAG
* * * *
58187853 GGGAAGGAGAAGGAGGAGGAAGGAA-AGGAGGAG
1 GAGAAGGAGAA-GAAGAAGAAAGAAGAGGAGGAG
*
58187886 AAGAA
1 GAGAA
58187891 AGAGGAGGAA
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
33 81 0.92
34 7 0.08
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (33 bp):
GAGAAGGAGAAGAAGAAGAAAGAAGAGGAGGAG
Found at i:58187814 original size:3 final size:3
Alignment explanation
Indices: 58187773--58187914 Score: 90
Period size: 3 Copynumber: 47.3 Consensus size: 3
58187763 AAGAAGAAGA
* * * * * * *
58187773 AGG AAG AGG AGG AGG AGA AGG AGA AGA AGA AGA AAG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
* * * *
58187821 AGA AGG AGG AGG AGG AGA AAG AGG AGG AGG AGG -GG AAGG AGA AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG -AGG AGG AGG
* * * * ** *
58187866 AGG AGG AAGG A-A AGG AGG AGA AGA AAG AGG AGG AAA AGG AGG AGA
1 AGG AGG -AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
58187911 AGG A
1 AGG A
58187915 AAAGGAGGGA
Statistics
Matches: 107, Mismatches: 28, Indels: 8
0.75 0.20 0.06
Matches are distributed among these distances:
2 3 0.03
3 99 0.93
4 5 0.05
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:58187829 original size:15 final size:15
Alignment explanation
Indices: 58187731--58187922 Score: 133
Period size: 15 Copynumber: 12.8 Consensus size: 15
58187721 ACCATGTTGA
58187731 AGGAGAAGGAGGAGG
1 AGGAGAAGGAGGAGG
* *
58187746 AGAAGATA-GAGAAGG
1 AGGAGA-AGGAGGAGG
* * *
58187761 AGAAGAAGAAGAAGG
1 AGGAGAAGGAGGAGG
* * *
58187776 AAGAGGAGGAGGAGA
1 AGGAGAAGGAGGAGG
* *
58187791 AGGAGAA-GAAGAAG
1 AGGAGAAGGAGGAGG
*
58187805 A-AAG-AGGAGGAGG
1 AGGAGAAGGAGGAGG
58187818 AGGAGAAGGAGGAGG
1 AGGAGAAGGAGGAGG
58187833 AGGAGAAAGAGGAGGAGG
1 AGGAG--A-AGGAGGAGG
* *
58187851 AGGGGAAGGAGAAGG
1 AGGAGAAGGAGGAGG
*
58187866 AGGAGGAAGGA-AAGG
1 AGGA-GAAGGAGGAGG
* *
58187881 AGGAGAAGAAAGAGG
1 AGGAGAAGGAGGAGG
* *
58187896 AGGAAAAGGAGGAGA
1 AGGAGAAGGAGGAGG
*
58187911 AGGAAAAGGAGG
1 AGGAGAAGGAGG
58187923 GAGTTGAAGA
Statistics
Matches: 140, Mismatches: 27, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
12 1 0.01
13 8 0.06
14 13 0.09
15 96 0.69
16 8 0.06
17 1 0.01
18 13 0.09
ACGTcount: A:0.48, C:0.00, G:0.51, T:0.01
Consensus pattern (15 bp):
AGGAGAAGGAGGAGG
Found at i:58187914 original size:6 final size:6
Alignment explanation
Indices: 58187729--58187906 Score: 82
Period size: 6 Copynumber: 29.2 Consensus size: 6
58187719 CCACCATGTT
*
58187729 GAAGGA GAAGGA GGAGGA GAAGATAGA GAAGGA GAAGAAGAA GAAGGA
1 GAAGGA GAAGGA GAAGGA GAAG---GA GAAGGA GAAG--G-A GAAGGA
* * * *
58187777 -AGAGGA GGAGGA GAAGGA GAAGAA GAA-GA -AA-GA GGAGGA GGAGGA
1 GA-AGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA
* * * * *
58187822 GAAGGA GGAGGAGGA GAAAGA GGAGGA GGAGGG GAAGGA GAAGGA GGA-G-
1 GAAGGA -GA--AGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA
* * * * *
58187871 GAAGGA -AAGGA GGAGAA GAAAGA GGAGGA AAAGGA G
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA G
58187907 GAGAAGGAAA
Statistics
Matches: 130, Mismatches: 26, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
4 6 0.05
5 10 0.08
6 93 0.72
7 3 0.02
8 3 0.02
9 15 0.12
ACGTcount: A:0.48, C:0.00, G:0.51, T:0.01
Consensus pattern (6 bp):
GAAGGA
Done.