Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold158
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: 399999
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:267655 original size:92 final size:92
Alignment explanation
Indices: 267498--267668 Score: 272
Period size: 92 Copynumber: 1.9 Consensus size: 92
267488 AGGATATTTG
*
267498 GGCATCCGAACTCGTCGAGTTGAGTCCCAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTCGAGTTGAGTCCCAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
267563 TTGAGTCAGAGTTCGAGAGATGTAACT
66 TTGAGTCAGAGTTCGAGAGATGTAACT
* * * *
267590 GGCATCCGAGCTCGTTGAGTTGAGTCCCAGTTCACTTATGGATGCGAACT-CCCGAGCTTGTTGA
1 GGCATCCGAACTCGTCGAGTTGAGTCCCAGTTCACTTATGGATGCGAA-TGCCCGAACTCGTTGA
*
267654 GTTGAGTCCGAGTTC
65 GTTGAGTCAGAGTTC
267669 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 71 0.99
93 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (92 bp):
GGCATCCGAACTCGTCGAGTTGAGTCCCAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
TTGAGTCAGAGTTCGAGAGATGTAACT
Found at i:278989 original size:35 final size:35
Alignment explanation
Indices: 278938--279012 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
278928 TCTAAAGACT
*
278938 TAAACTTTCTTGCACGCCTAACTTTCGTAAGGAAC
1 TAAAATTTCTTGCACGCCTAACTTTCGTAAGGAAC
278973 TAAAATTTCTTGCACGCCTAACTTTCGTAAGGAAC
1 TAAAATTTCTTGCACGCCTAACTTTCGTAAGGAAC
279008 TAAAA
1 TAAAA
279013 ATTTATGGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (35 bp):
TAAAATTTCTTGCACGCCTAACTTTCGTAAGGAAC
Found at i:280883 original size:18 final size:18
Alignment explanation
Indices: 280844--280883 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
280834 AATAAATTGA
*
280844 AAAATTAAATATTTGAAT
1 AAAATTAAATATTTGAAG
280862 AAAATTAAA-ATTTAGAAG
1 AAAATTAAATATTT-GAAG
280880 AAAA
1 AAAA
280884 AATTGCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (18 bp):
AAAATTAAATATTTGAAG
Found at i:283078 original size:36 final size:37
Alignment explanation
Indices: 283006--283083 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 37
282996 TTATTACGAA
* * *
283006 GTCTTACTCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
*
283043 GTCTTACCCGGACAAAATC-CCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
283079 GTCTT
1 GTCTT
283084 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 20 0.54
37 17 0.46
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
Found at i:283352 original size:47 final size:47
Alignment explanation
Indices: 283202--283627 Score: 701
Period size: 47 Copynumber: 9.1 Consensus size: 47
283192 CCCTTCGGGA
* * * * * * * *
283202 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* * *
283249 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
283295 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
283342 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
283389 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
283436 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
283483 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
283530 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
283577 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
283624 CTTA
1 CTTA
283628 CTATCATTTC
Statistics
Matches: 362, Mismatches: 16, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
46 40 0.11
47 322 0.89
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:286035 original size:30 final size:30
Alignment explanation
Indices: 285980--286036 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
285970 CTTTTCAAAA
* * *
285980 TATTTACAAAAAGAGGCATCTAATTTTTAT
1 TATTTACAAAAAGAGGAACCAAATTTTTAT
*
286010 TATTTACGAAAAGAGGAACCAAATTTT
1 TATTTACAAAAAGAGGAACCAAATTTT
286037 AAAAATAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (30 bp):
TATTTACAAAAAGAGGAACCAAATTTTTAT
Found at i:293278 original size:114 final size:114
Alignment explanation
Indices: 293073--293298 Score: 371
Period size: 114 Copynumber: 2.0 Consensus size: 114
293063 GATGGCATTC
* *
293073 GAGTTGATCCAAGTAAGATCTCTGCTATCATTGAATGCAAACCACCTAAAAATGTAACCAAGGTT
1 GAGTTGATCCAAGGAAGATCTCTACTATCATTGAATGCAAACCACCTAAAAATGTAACCAAGGTT
* * *
293138 AGAAGCTTTTTAGGCTTAGCCGGTTACTACCGAAGATTTGTTAAAGGTT
66 AGAAGATTTTTAGGCTTAGCCAGTTACTACCGAAGATTTGTGAAAGGTT
**
293187 GAGTTGATCCAAGGAAGATCTCTACTATCATTGAATGCAAACCACCTAAAAATGTAACTGAGGTT
1 GAGTTGATCCAAGGAAGATCTCTACTATCATTGAATGCAAACCACCTAAAAATGTAACCAAGGTT
* *
293252 AGAAGATTTTTGGGCTTGGCCAGTTACTACCGAAGATTTGTGAAAGG
66 AGAAGATTTTTAGGCTTAGCCAGTTACTACCGAAGATTTGTGAAAGG
293299 ATTCTCCATG
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (114 bp):
GAGTTGATCCAAGGAAGATCTCTACTATCATTGAATGCAAACCACCTAAAAATGTAACCAAGGTT
AGAAGATTTTTAGGCTTAGCCAGTTACTACCGAAGATTTGTGAAAGGTT
Found at i:303281 original size:26 final size:26
Alignment explanation
Indices: 303252--303303 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
303242 CCTTAGAAGA
*
303252 ATAAACATGCACTAATTAAGTATTGT
1 ATAAACATGCACTAATTAAATATTGT
*
303278 ATAAACATGCACTGATTAAATATTGT
1 ATAAACATGCACTAATTAAATATTGT
303304 GTTCATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (26 bp):
ATAAACATGCACTAATTAAATATTGT
Found at i:316302 original size:12 final size:13
Alignment explanation
Indices: 316281--316309 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
316271 TTTAATAAAG
316281 TAATTAAATTAAT
1 TAATTAAATTAAT
316294 TAATT-AATTAAT
1 TAATTAAATTAAT
316306 TAAT
1 TAAT
316310 ATTTTAGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:317152 original size:28 final size:28
Alignment explanation
Indices: 317090--317172 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
317080 AGGTGAATCA
*
317090 GAATATTTCCTCCATATATATATATATC
1 GAATATTTCCTCCATACATATATATATC
*
317118 GGAATATTTCCTCCCTCACATATATATAT-
1 -GAATATTTCCTCCAT-ACATATATATATC
* * *
317147 GTATATATCCTCACATATATATATAT
1 GAATATTTCCTC-CATACATATATAT
317173 TATCCAAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
28 19 0.41
29 16 0.35
30 11 0.24
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (28 bp):
GAATATTTCCTCCATACATATATATATC
Found at i:325998 original size:37 final size:37
Alignment explanation
Indices: 325945--326043 Score: 171
Period size: 37 Copynumber: 2.7 Consensus size: 37
325935 CGAATAGTCC
*
325945 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
325982 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
326019 CCACACGTAGTCATCGGATCTTACC
1 CCACACGTAGTCATCGGGTCTTACC
326044 GGAATATATT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:326273 original size:48 final size:48
Alignment explanation
Indices: 326219--326453 Score: 425
Period size: 48 Copynumber: 4.9 Consensus size: 48
326209 GCCGAATCAC
*
326219 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCGCAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
*
326267 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAC
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
*
326315 TAGCCATTCGGCTTTACCACGTATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
* *
326363 TAGCCATTCGACTTTTCCACATATACATATCTCATACATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
326411 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTT
326454 ATCTTGTACC
Statistics
Matches: 178, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 178 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (48 bp):
TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAT
Found at i:331853 original size:22 final size:22
Alignment explanation
Indices: 331827--331902 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
331817 TTCCACGTTC
331827 ATCACATTGGCCATTCTACCTT
1 ATCACATTGGCCATTCTACCTT
** *
331849 ATCACATATATCCATGT-TCACATT
1 ATCACAT-TGGCCAT-TCT-ACCTT
**
331873 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCTACCTT
331896 ATCACAT
1 ATCACAT
331903 ATTTGCATGT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 14 0.34
23 10 0.24
24 10 0.24
25 7 0.17
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCTACCTT
Found at i:331855 original size:47 final size:47
Alignment explanation
Indices: 331824--332205 Score: 674
Period size: 47 Copynumber: 8.1 Consensus size: 47
331814 CACTTCCACG
** * *
331824 TTCATCACATTGGCCATTCTACCTTATCACATATATCCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
331871 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
331918 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
* *
331965 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
*
332012 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGATCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
*
332059 TTCATCACATTGGCCATTCGGCCTTATCACATATTTTCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
332106 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
* *
332153 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
332200 TTCATC
1 TTCATC
332206 TCATAGAATC
Statistics
Matches: 321, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 321 1.00
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
Found at i:335940 original size:39 final size:40
Alignment explanation
Indices: 335895--336118 Score: 224
Period size: 40 Copynumber: 5.7 Consensus size: 40
335885 GCTCCTCGTT
* * * *
335895 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
335935 C-AATGCCTTC-GGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
335973 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
336013 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
336053 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
336094 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
336119 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
38 24 0.15
39 22 0.14
40 95 0.61
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:336127 original size:41 final size:41
Alignment explanation
Indices: 336050--336127 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
336040 CTTGTATCTC
* * *
336050 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
336091 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
336128 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:349032 original size:38 final size:37
Alignment explanation
Indices: 348950--349126 Score: 169
Period size: 40 Copynumber: 4.6 Consensus size: 37
348940 CTCATTCAAT
* *
348950 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAAT
1 GCCTTCGGGACTTAACCCGGAATTT--AACTCGCAC-AAA
*
348990 GCCTTCGGGACTTAACCCGGAATTTATCTCGCACAAA
1 GCCTTCGGGACTTAACCCGGAATTTAACTCGCACAAA
349027 GGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAA
1 -GCCTTCGGGACTTAACCCGGAATT--TAACTCGCACAAA
** * * *
349067 -CCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAA
1 GCCTTCGGGA-CTTAACCCGGA-AT-TTAAC-TCGCACAAA
*
349106 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
349127 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
37 5 0.04
38 49 0.42
39 10 0.08
40 51 0.43
41 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (37 bp):
GCCTTCGGGACTTAACCCGGAATTTAACTCGCACAAA
Found at i:357041 original size:14 final size:13
Alignment explanation
Indices: 357015--357060 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
357005 CAAACAAAAG
357015 AAAAATTAGAATTTA
1 AAAAATTA-AA-TTA
357030 AAAAATTAAATTA
1 AAAAATTAAATTA
*
357043 AAAATATTAAAATA
1 AAAA-ATTAAATTA
357057 AAAA
1 AAAA
357061 TAAAAATGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 7 0.24
14 14 0.48
15 8 0.28
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (13 bp):
AAAAATTAAATTA
Found at i:384707 original size:130 final size:130
Alignment explanation
Indices: 384459--385095 Score: 513
Period size: 130 Copynumber: 4.9 Consensus size: 130
384449 AATCAAATTA
* * * * * * * **
384459 AGAAGATTATTCAGGTTCGTAAATCAATAAACTTAGGCTATCATCA-TAAATCAACAAGCCTTAA
1 AGAAGATTGTTCATGATAGTAAATCAATGAACTTAGACTATGAT-AGTAAATCAATGAGCCTTAA
* * * *** * * *
384523 TAATATCAATTATGATATTAAATCATCGAGTTGTTCAAAATAGCTATAGAAAATCAGCTAACTCA
65 TAATATCAATTGTGATATTAAATCAGCGAGCTGTTTGGAGTAGCGATAGTAAATCAGCTAACTCA
384588 TG
130 -G
* * * * *
384590 -GAAGATTGTTCATTG-TAGTAAATCAATGAACTTA-ACCTGTGATCGTAAACCAGTGAGCCATA
1 AGAAGATTGTTCA-TGATAGTAAATCAATGAACTTAGA-CTATGATAGTAAATCAATGAGCCTTA
* * *
384652 ATAATATCAACTGTGATATGAAATCAGCGAGCTGTTTGGAGTAGCGATAGTAAATCAACTAACTC
64 ATAATATCAATTGTGATATTAAATCAGCGAGCTGTTTGGAGTAGCGATAGTAAATCAGCTAACTC
*
384717 AA
129 AG
* * * * * *
384719 AGAAGATTTTTCATGACAGTAAATCAATAAACTTAGATTATGATTAG-AAATCAACGAACCTTAA
1 AGAAGATTGTTCATGATAGTAAATCAATGAACTTAGACTATGA-TAGTAAATCAATGAGCCTTAA
* * * * * * * *
384783 TAATACCAATTATGATATTAAATCAACGAGCTATTTGGAGTAGCGTTAGCAAGT-ATGCTAACTT
65 TAATATCAATTGTGATATTAAATCAGCGAGCTGTTTGGAGTAGCGATAGTAAATCA-GCTAACTC
384847 AG
129 AG
* * *
384849 AGAAGATTGTTCATGATAGTAAAAT-AATCAACTTAGACTATGATCGTAAATCAATGAGCTTTAA
1 AGAAGATTGTTCATGATAGT-AAATCAATGAACTTAGACTATGATAGTAAATCAATGAGCCTTAA
* ** * * * * * * *
384913 TAATACCAGCTGTGATCTTAAATCAGTGAAG-TATTTGGAGTAGTGATAGTAAATCAGTTATCGC
65 TAATATCAATTGTGATATTAAATCAGCG-AGCTGTTTGGAGTAGCGATAGTAAATCAGCTAACTC
384977 AG
129 AG
* * * * * *
384979 AGAAGATTATTCATGATAGT--ATCAAATGAGCTTAGGCTGTGATAGTAAATTAGCT-AGCCTTA
1 AGAAGATTGTTCATGATAGTAAATC-AATGAACTTAGACTATGATAGTAAATCA-ATGAGCCTTA
* * * * * *
385041 ATAATATCAATTGGGATATTAAATCAGTGAACTGTTTGGTGTAGTGATTGTAAAT
64 ATAATATCAATTGTGATATTAAATCAGCGAGCTGTTTGGAGTAGCGATAGTAAAT
385096 AAAATAGGTC
Statistics
Matches: 401, Mismatches: 89, Indels: 34
0.77 0.17 0.06
Matches are distributed among these distances:
127 2 0.00
128 1 0.00
129 77 0.19
130 310 0.77
131 11 0.03
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (130 bp):
AGAAGATTGTTCATGATAGTAAATCAATGAACTTAGACTATGATAGTAAATCAATGAGCCTTAAT
AATATCAATTGTGATATTAAATCAGCGAGCTGTTTGGAGTAGCGATAGTAAATCAGCTAACTCAG
Found at i:384985 original size:260 final size:260
Alignment explanation
Indices: 384458--384999 Score: 598
Period size: 260 Copynumber: 2.1 Consensus size: 260
384448 AAATCAAATT
* * * *
384458 AAGAAGATTATTCAGGTTC-GTAAATCAATAAACTTAGGCTATCATCATAAATCAACAAGCCTTA
1 AAGAAGATTATTCATG-ACAGTAAATCAATAAACTTAGACTATCATCAGAAATCAACAAGCCTTA
* * * *
384522 ATAATATCAATTATGATATTAAATCATCGAGTTGTTCAAAATAGCTATAGAAAATCAGCTAACTC
65 ATAATACCAATTATGATATTAAATCAACGAGCTATTCAAAATAGCTATAGAAAATCAGCTAACTC
* * *
384587 ATGGAAGATTGTTCATTGTAGTAAATCAATGAACTTAACCTGTGATCGTAAACCAGTGAGCCATA
130 ATGGAAGATTGTTCATTGTAGTAAATCAATCAACTTAACCTATGATCGTAAACCAATGAGCCATA
* * *
384652 ATAATATCAACTGTGATATGAAATCAGCGAGCTGTTTGGAGTAGCGATAGTAAATCAACTAACTC
195 ATAATACCAACTGTGATATGAAATCAGCGAGCTATTTGGAGTAGCGATAGTAAATCAACTAACGC
384717 A
260 A
* * * *
384718 AAGAAGATTTTTCATGACAGTAAATCAATAAACTTAGATTATGATTAGAAATCAACGAA-CCTTA
1 AAGAAGATTATTCATGACAGTAAATCAATAAACTTAGACTATCATCAGAAATCAAC-AAGCCTTA
*** * * *
384782 ATAATACCAATTATGATATTAAATCAACGAGCTATTTGGAGTAGCGT-TAGCAAGT-ATGCTAAC
65 ATAATACCAATTATGATATTAAATCAACGAGCTATTCAAAATAGC-TATAGAAAATCA-GCTAAC
* *
384845 TTA-GAGAAGATTGTTCA-TGATAGTAAAAT-AATCAACTTAGA-CTATGATCGTAAATCAATGA
128 TCATG-GAAGATTGTTCATTG-TAGT-AAATCAATCAACTTA-ACCTATGATCGTAAACCAATGA
** * * * * * *
384906 GCTTTAATAATACCAGCTGTGATCTTAAATCAGTGAAG-TATTTGGAGTAGTGATAGTAAATCAG
189 GCCATAATAATACCAACTGTGATATGAAATCAGCG-AGCTATTTGGAGTAGCGATAGTAAATCAA
* *
384970 TTATCGCA
253 CTAACGCA
* *
384978 GAGAAGATTATTCATGATAGTA
1 AAGAAGATTATTCATGACAGTA
385000 TCAAATGAGC
Statistics
Matches: 234, Mismatches: 39, Indels: 18
0.80 0.13 0.06
Matches are distributed among these distances:
259 5 0.02
260 219 0.94
261 10 0.04
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (260 bp):
AAGAAGATTATTCATGACAGTAAATCAATAAACTTAGACTATCATCAGAAATCAACAAGCCTTAA
TAATACCAATTATGATATTAAATCAACGAGCTATTCAAAATAGCTATAGAAAATCAGCTAACTCA
TGGAAGATTGTTCATTGTAGTAAATCAATCAACTTAACCTATGATCGTAAACCAATGAGCCATAA
TAATACCAACTGTGATATGAAATCAGCGAGCTATTTGGAGTAGCGATAGTAAATCAACTAACGCA
Found at i:389115 original size:51 final size:52
Alignment explanation
Indices: 389055--389177 Score: 178
Period size: 51 Copynumber: 2.4 Consensus size: 52
389045 CATGATAAGT
* *
389055 GAAGACCATATAGTGTAAGGCCTA-ACTATTTGCTATGGTATCATATGGC-TA
1 GAAGACCATATAGTGTAAGGCCTAGAC-ATTTGCTATGGCATCATATGGCAGA
389106 GAAGACCATATAGTGTAAGGCCTAGACATTTGCTATGGCATCATATGGCAAGA
1 GAAGACCATATAGTGTAAGGCCTAGACATTTGCTATGGCATCATATGGC-AGA
* *
389159 GAAGACCACATAGAGTAAG
1 GAAGACCATATAGTGTAAG
389178 AGTTACTTGG
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
51 45 0.69
52 2 0.03
53 18 0.28
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (52 bp):
GAAGACCATATAGTGTAAGGCCTAGACATTTGCTATGGCATCATATGGCAGA
Done.