Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold479
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: 1265690
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 9 of 9
Found at i:1197261 original size:13 final size:13
Alignment explanation
Indices: 1197243--1197268 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1197233 TACACAAAGT
1197243 ATGTATCGATACA
1 ATGTATCGATACA
1197256 ATGTATCGATACA
1 ATGTATCGATACA
1197269 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1197266 original size:32 final size:33
Alignment explanation
Indices: 1197225--1197288 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1197215 TAGCCAAACT
**
1197225 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1197257 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1197289 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1198175 original size:81 final size:80
Alignment explanation
Indices: 1198027--1198452 Score: 383
Period size: 81 Copynumber: 5.3 Consensus size: 80
1198017 CTTTCACAAA
* * ** * ** * * *
1198027 GCGAAACCGATAAAGTCAATTGATTAGAAGGTTGGCTAAGGCGAAACCAGTAAAG-CTAATAGAT
1 GCGAAACCAATAAAGCCAACAGATTGGAAGGTTAACTAGGGCGAAACCAATAAAGTC-AACAGAT
1198091 TGGAAGGTTGGCCAGG
65 TGGAAGGTTGGCCAGG
* * * * * *
1198107 GCGAAACCAATAAAACCAAAAGATTGGAAGGGTTAAGTAGGGTGAAACCGATAAAGTCAACGGAT
1 GCGAAACCAATAAAGCCAACAGATTGGAA-GGTTAACTAGGGCGAAACCAATAAAGTCAACAGAT
*
1198172 TGGAAGGTTGGCCAGA
65 TGGAAGGTTGGCCAGG
* * * * *
1198188 GTGAATCCAATAAAGCCAACAGATTGGAAGGTTAACTAAGGCAAAACCAATAAAG-CTAATAGAT
1 GCGAAACCAATAAAGCCAACAGATTGGAAGGTTAACTAGGGCGAAACCAATAAAGTC-AACAGAT
* *
1198252 TGGAAGGTTAGCTA-G
65 TGGAAGGTTGGCCAGG
* * *
1198267 GCAAAACCAATAAAGCCAACAGATTGGAAAAGTTGACTAGGGCGAAACCAATAAAGTCAATCA-A
1 GCGAAACCAATAAAGCCAACAGATTGG-AAGGTTAACTAGGGCGAAACCAATAAAGTCAA-CAGA
** *
1198331 TTGGAAAATTAGCCAGG
64 TTGGAAGGTTGGCCAGG
* * * * * * * * *
1198348 GCGAATCTAATAAAGCCAATAGATTAGATAGTTTGACCAGGGCGAATCCAATAAAGCCAACAGAT
1 GCGAAACCAATAAAGCCAACAGATTGGA-AGGTTAACTAGGGCGAAACCAATAAAGTCAACAGAT
1198413 TGGAAGGTTGGCCAGG
65 TGGAAGGTTGGCCAGG
** * *
1198429 GTAAAATCGATAAAGCCAACAGAT
1 GCGAAACCAATAAAGCCAACAGAT
1198453 GAGAAAGTTG
Statistics
Matches: 276, Mismatches: 61, Indels: 17
0.78 0.17 0.05
Matches are distributed among these distances:
79 25 0.09
80 103 0.37
81 147 0.53
82 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.25, T:0.18
Consensus pattern (80 bp):
GCGAAACCAATAAAGCCAACAGATTGGAAGGTTAACTAGGGCGAAACCAATAAAGTCAACAGATT
GGAAGGTTGGCCAGG
Found at i:1198252 original size:121 final size:121
Alignment explanation
Indices: 1198029--1198336 Score: 293
Period size: 121 Copynumber: 2.6 Consensus size: 121
1198019 TTCACAAAGC
** * * * *
1198029 GAAACCGATAAAGTCAATTGATTAGAAGGTTGGCTAAGGCGAAACCAGTAAAGCTAATAGATTGG
1 GAAACCGATAAAGTCAACGGATTAGAAGGTTGGCCAAGGCGAAACCAATAAAGCCAACAGATTGG
** * *
1198094 AAGGTTGGCCAGGGCGAAACCAATAAAACCAAAAGATTGGAAGGGTTAAGTAGGGT
66 AAGGTTAACCAAGGCAAAACCAATAAAACCAAAAGATTGGAAGGGTTAAGTAGGGT
* * *
1198150 GAAACCGATAAAGTCAACGGATTGGAAGGTTGGCC-AGAGTGAATCCAATAAAGCCAACAGATTG
1 GAAACCGATAAAGTCAACGGATTAGAAGGTTGGCCAAG-GCGAAACCAATAAAGCCAACAGATTG
* * * * *
1198214 GAAGGTTAACTAAGGCAAAACCAATAAAGCTAATAGATTGGAA-GGTT-AGCTA-GGC
65 GAAGGTTAACCAAGGCAAAACCAATAAAACCAAAAGATTGGAAGGGTTAAG-TAGGGT
* * * * * * * * * *
1198269 AAAACCAATAAAGCCAACAGATTGGAAAAGTTGACTAGGGCGAAACCAATAAAGTCAATCA-ATT
1 GAAACCGATAAAGTCAACGGATTAG-AAGGTTGGCCAAGGCGAAACCAATAAAGCCAA-CAGATT
1198333 GGAA
64 GGAA
1198337 AATTAGCCAG
Statistics
Matches: 153, Mismatches: 29, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
119 25 0.16
120 38 0.25
121 90 0.59
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.18
Consensus pattern (121 bp):
GAAACCGATAAAGTCAACGGATTAGAAGGTTGGCCAAGGCGAAACCAATAAAGCCAACAGATTGG
AAGGTTAACCAAGGCAAAACCAATAAAACCAAAAGATTGGAAGGGTTAAGTAGGGT
Found at i:1198442 original size:40 final size:40
Alignment explanation
Indices: 1198048--1198568 Score: 313
Period size: 40 Copynumber: 12.9 Consensus size: 40
1198038 AAAGTCAATT
* * * * * * * *
1198048 GATTAGAAGGTTGGCTAAGGCGAAACCAGTAAAGCTAATA
1 GATTGGAAGGTTGGCCAGGGTGAAATCAATAAAGCCAACA
* * * *
1198088 GATTGGAAGGTTGGCCAGGGCGAAACCAATAAAACCAAAA
1 GATTGGAAGGTTGGCCAGGGTGAAATCAATAAAGCCAACA
* * * * * *
1198128 GATTGGAAGGGTTAAG-TAGGGTGAAACCGATAAAGTCAACG
1 GATTGGAA-GGTT-GGCCAGGGTGAAATCAATAAAGCCAACA
*
1198169 GATTGGAAGGTTGGCCAGAGTG-AATCCAATAAAGCCAACA
1 GATTGGAAGGTTGGCCAGGGTGAAAT-CAATAAAGCCAACA
** * * ** * * *
1198209 GATTGGAAGGTTAACTAAGGCAAAACCAATAAAGCTAATA
1 GATTGGAAGGTTGGCCAGGGTGAAATCAATAAAGCCAACA
* * ** *
1198249 GATTGGAAGGTTAGCTA-GGCAAAACCAATAAAGCCAACA
1 GATTGGAAGGTTGGCCAGGGTGAAATCAATAAAGCCAACA
* * * * * *
1198288 GATTGGAAAAGTTGACTAGGGCGAAACCAATAAAGTCAATCA
1 GATTGG-AAGGTTGGCCAGGGTGAAATCAATAAAGCCAA-CA
** * * *
1198330 -ATTGGAAAATTAGCCAGGGCG-AATCTAATAAAGCCAATA
1 GATTGGAAGGTTGGCCAGGGTGAAATC-AATAAAGCCAACA
* * * *
1198369 GATTAGATAGTTTGACCAGGGCG-AATCCAATAAAGCCAACA
1 GATTGGA-AGGTTGGCCAGGGTGAAAT-CAATAAAGCCAACA
* *
1198410 GATTGGAAGGTTGGCCAGGGTAAAATCGATAAAGCCAACA
1 GATTGGAAGGTTGGCCAGGGTGAAATCAATAAAGCCAACA
* * **
1198450 GA-TGAGAAAGTTGGCCATGGTGAAATTGATAAAGCCAACA
1 GATTG-GAAGGTTGGCCAGGGTGAAATCAATAAAGCCAACA
* * * *** *
1198490 GATTGAAAGGGTTGACCGGGGTGAAATTGGTAAAGTCAATC-
1 GATTGGAA-GGTTGGCCAGGGTGAAATCAATAAAGCCAA-CA
*
1198531 GATTGAAAGGTTGGCCAGGGTGAAA-CTAATAAAGCCAA
1 GATTGGAAGGTTGGCCAGGGTGAAATC-AATAAAGCCAA
1198569 TTGTTGACAC
Statistics
Matches: 387, Mismatches: 76, Indels: 36
0.78 0.15 0.07
Matches are distributed among these distances:
39 35 0.09
40 223 0.58
41 124 0.32
42 5 0.01
ACGTcount: A:0.40, C:0.14, G:0.27, T:0.19
Consensus pattern (40 bp):
GATTGGAAGGTTGGCCAGGGTGAAATCAATAAAGCCAACA
Found at i:1198503 original size:81 final size:80
Alignment explanation
Indices: 1198357--1198568 Score: 205
Period size: 81 Copynumber: 2.6 Consensus size: 80
1198347 GGCGAATCTA
* * * * * * *
1198357 ATAAAGCCAATAGATT-AGATAGTTTGACCAGGGCGAATCCAATAAAGCCAACAGATTGGAAGGT
1 ATAAAGCCAATCGATTGA-AAAG-TTGGCCAGGGTGAAACTAATAAAGCCAACAGATTGAAAGGT
*
1198421 TGGCCAGGGTAAAATCG
64 TGACCAGGGTAAAATCG
* * *
1198438 ATAAAGCCAA-CAGA-TGAGAAAGTTGGCCATGGTGAAATTGATAAAGCCAACAGATTGAAAGGG
1 ATAAAGCCAATC-GATTGA-AAAGTTGGCCAGGGTGAAACTAATAAAGCCAACAGATTGAAA-GG
* * *
1198501 TTGACCGGGGTGAAATTG
63 TTGACCAGGGTAAAATCG
* * *
1198519 GTAAAGTCAATCGATTGAAAGGTTGGCCAGGGTGAAACTAATAAAGCCAA
1 ATAAAGCCAATCGATTGAAAAGTTGGCCAGGGTGAAACTAATAAAGCCAA
1198569 TTGTTGACAC
Statistics
Matches: 106, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
80 31 0.29
81 71 0.67
82 4 0.04
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (80 bp):
ATAAAGCCAATCGATTGAAAAGTTGGCCAGGGTGAAACTAATAAAGCCAACAGATTGAAAGGTTG
ACCAGGGTAAAATCG
Found at i:1199004 original size:22 final size:20
Alignment explanation
Indices: 1198956--1199032 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
1198946 GCCAAGGAAA
* ** *
1198956 TGTAACGATACATTAGTAAA
1 TGTATCGATACATTTCTAAT
1198976 TGTATCGATACATGCTTAC-AAT
1 TGTATCGATACAT--TT-CTAAT
*
1198998 TGTATCGATACATTTCTCAT
1 TGTATCGATACATTTCTAAT
1199018 TGTATCGATACATTT
1 TGTATCGATACATTT
1199033 TGGGTTTCTG
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 31 0.65
22 16 0.33
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTCTAAT
Found at i:1201077 original size:13 final size:13
Alignment explanation
Indices: 1201059--1201084 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1201049 CAATTTTTTG
1201059 TGTATCGATACAT
1 TGTATCGATACAT
1201072 TGTATCGATACAT
1 TGTATCGATACAT
1201085 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1201823 original size:21 final size:21
Alignment explanation
Indices: 1201782--1201825 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1201772 CTCTCCTTTA
* *
1201782 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1201803 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1201824 TC
1 TC
1201826 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1203648 original size:13 final size:13
Alignment explanation
Indices: 1203630--1203656 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1203620 ATAATCACCC
1203630 TGTATCGATACAA
1 TGTATCGATACAA
1203643 TGTATCGATACAA
1 TGTATCGATACAA
1203656 T
1 T
1203657 ACGATACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1207589 original size:21 final size:21
Alignment explanation
Indices: 1207560--1207604 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1207550 AAGTTTTCAT
*
1207560 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1207580 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1207602 TTT
1 TTT
1207605 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1209829 original size:13 final size:13
Alignment explanation
Indices: 1209811--1209836 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1209801 CAATTTTTTG
1209811 TGTATCGATACAT
1 TGTATCGATACAT
1209824 TGTATCGATACAT
1 TGTATCGATACAT
1209837 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1212558 original size:35 final size:35
Alignment explanation
Indices: 1212518--1212603 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 35
1212508 ACTATGGATA
* *
1212518 GTGGAAAGAGTTCGACTAGGTACAGTCAAACGATG
1 GTGGAAAGAGTTCGACCAGATACAGTCAAACGATG
* *
1212553 GTGG-AAGAAGTTCTACCAGATACAGTCAAATGATG
1 GTGGAAAG-AGTTCGACCAGATACAGTCAAACGATG
*
1212588 ATGGAAAGATGTTCGA
1 GTGGAAAGA-GTTCGA
1212604 AATCTAGGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
34 3 0.07
35 31 0.74
36 8 0.19
ACGTcount: A:0.36, C:0.13, G:0.29, T:0.22
Consensus pattern (35 bp):
GTGGAAAGAGTTCGACCAGATACAGTCAAACGATG
Found at i:1213403 original size:90 final size:89
Alignment explanation
Indices: 1213173--1213437 Score: 334
Period size: 90 Copynumber: 3.0 Consensus size: 89
1213163 TATCCTTGCT
* * * * *
1213173 CCAAAGGAAATCAGGCTTTGTGATGTATCAGTACCATCTAGT-GATTGAAGAAAAAGGATATGAC
1 CCAAAGG-TATCAGGCTTTGTGATGCATCAATATCATCTAGTGGA-TGAAGGAAAAGGATATGAC
**
1213237 TAGGAAATCTATGGGCTGCACCCTTG
64 TAGGAAATGGATGGGCTGCACCCTTG
* * * * **
1213263 CCAAAGGTATCAGACTCTATGATGCATCAATATCATCTAGTGGATAAAGGAAAAGGATATGACGG
1 CCAAAGGTATCAGGCTTTGTGATGCATCAATATCATCTAGTGGATGAAGGAAAAGGATATGACTA
*
1213328 GGAAATGGATAGGCTGCACCCTTG
66 GGAAATGGATGGGCTGCACCCTTG
* * * *
1213352 CCCCAAGGTATTAGGCTTTGTGATACATCAATATCATTTAGTGGATGAAGGAAAAGGATATGACT
1 -CCAAAGGTATCAGGCTTTGTGATGCATCAATATCATCTAGTGGATGAAGGAAAAGGATATGACT
1213417 AGGAAATGGATGGGCTGCACC
65 AGGAAATGGATGGGCTGCACC
1213438 TATCTTTGAT
Statistics
Matches: 148, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
89 65 0.44
90 83 0.56
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.25
Consensus pattern (89 bp):
CCAAAGGTATCAGGCTTTGTGATGCATCAATATCATCTAGTGGATGAAGGAAAAGGATATGACTA
GGAAATGGATGGGCTGCACCCTTG
Found at i:1214118 original size:31 final size:30
Alignment explanation
Indices: 1214081--1214149 Score: 111
Period size: 31 Copynumber: 2.3 Consensus size: 30
1214071 TTTCATCCTT
*
1214081 TTTTTTTATGTTTGATTAATTTTTTGATGA
1 TTTTTTTATGTGTGATTAATTTTTTGATGA
*
1214111 TTGTTTTTATGTGTGATTGATTTTTTGATGA
1 TT-TTTTTATGTGTGATTAATTTTTTGATGA
1214142 TTTTTTTA
1 TTTTTTTA
1214150 AGCATAGTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 8 0.22
31 28 0.78
ACGTcount: A:0.17, C:0.00, G:0.16, T:0.67
Consensus pattern (30 bp):
TTTTTTTATGTGTGATTAATTTTTTGATGA
Found at i:1215499 original size:13 final size:13
Alignment explanation
Indices: 1215481--1215506 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1215471 CAATTTTTTG
1215481 TGTATCGATACAT
1 TGTATCGATACAT
1215494 TGTATCGATACAT
1 TGTATCGATACAT
1215507 ACTTTATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1215522 original size:32 final size:33
Alignment explanation
Indices: 1215461--1215524 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1215451 TACAAGCCAA
** *
1215461 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTATGTATCGATACAT
1215494 TGTATCGATAC-ATACTTTATGTATCGATACA
1 TGTATCGATACAATACTTTATGTATCGATACA
1215525 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTATGTATCGATACAT
Found at i:1217072 original size:13 final size:13
Alignment explanation
Indices: 1217054--1217079 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1217044 CAATTTTTTG
1217054 TGTATCGATACAT
1 TGTATCGATACAT
1217067 TGTATCGATACAT
1 TGTATCGATACAT
1217080 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1217094 original size:32 final size:33
Alignment explanation
Indices: 1217034--1217097 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1217024 TACAAGCCAA
** *
1217034 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1217067 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1217098 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1217786 original size:16 final size:16
Alignment explanation
Indices: 1217765--1217799 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1217755 TTGTAGCAAA
1217765 TTACGCATTCTCCCCT
1 TTACGCATTCTCCCCT
1217781 TTACGCATTCTCCCCT
1 TTACGCATTCTCCCCT
1217797 TTA
1 TTA
1217800 TCTCCCCCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.40, G:0.06, T:0.40
Consensus pattern (16 bp):
TTACGCATTCTCCCCT
Found at i:1219664 original size:13 final size:13
Alignment explanation
Indices: 1219646--1219671 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1219636 ATAATCACCC
1219646 TGTATCGATACAA
1 TGTATCGATACAA
1219659 TGTATCGATACAA
1 TGTATCGATACAA
1219672 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1223614 original size:21 final size:21
Alignment explanation
Indices: 1223585--1223629 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1223575 AAGTTTTTAT
*
1223585 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1223605 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1223627 TTT
1 TTT
1223630 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1223787 original size:15 final size:16
Alignment explanation
Indices: 1223763--1223795 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1223753 CAATCTTTTG
1223763 TTCAAGA-TTTTCAAT
1 TTCAAGATTTTTCAAT
*
1223778 TTCAATATTTTTCAAT
1 TTCAAGATTTTTCAAT
1223794 TT
1 TT
1223796 ATTATCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (16 bp):
TTCAAGATTTTTCAAT
Found at i:1225867 original size:13 final size:13
Alignment explanation
Indices: 1225849--1225874 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1225839 CAATTTTTTG
1225849 TGTATCGATACAT
1 TGTATCGATACAT
1225862 TGTATCGATACAT
1 TGTATCGATACAT
1225875 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1225889 original size:32 final size:33
Alignment explanation
Indices: 1225829--1225892 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1225819 TACAAGCCAA
** *
1225829 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1225862 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1225893 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1228603 original size:44 final size:45
Alignment explanation
Indices: 1228555--1228640 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
1228545 AAATTTCGTT
*
1228555 TTAAGACTTTCGCTTA-AAAAAATTTCTCCCCCTTGATAAAATAA
1 TTAAGACTCTCGCTTATAAAAAATTTCTCCCCCTTGATAAAATAA
* ** *
1228599 TTAAGGCTCTCTTTTATAAAAAATTTCTCCCCTTTGATAAAA
1 TTAAGACTCTCGCTTATAAAAAATTTCTCCCCCTTGATAAAA
1228641 ATTCTTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 12 0.33
45 24 0.67
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (45 bp):
TTAAGACTCTCGCTTATAAAAAATTTCTCCCCCTTGATAAAATAA
Found at i:1231956 original size:16 final size:16
Alignment explanation
Indices: 1231935--1231965 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1231925 CAACATTTCC
*
1231935 TCTATTAAAACTTTTT
1 TCTATTAAAAATTTTT
1231951 TCTATTAAAAATTTT
1 TCTATTAAAAATTTT
1231966 AAAAGCATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TCTATTAAAAATTTTT
Found at i:1235071 original size:15 final size:15
Alignment explanation
Indices: 1235053--1235087 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1235043 AGAGTCAACT
1235053 TCATCATTATCATCA
1 TCATCATTATCATCA
*
1235068 TCATCATTATCTTCA
1 TCATCATTATCATCA
1235083 TCATC
1 TCATC
1235088 TTTGATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:1236708 original size:33 final size:33
Alignment explanation
Indices: 1236666--1236731 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1236656 TTTGTGATAT
*
1236666 TGTATCGATACAATTAT-TCATGTATCGATACAA
1 TGTATCGATA-AATTATGCCATGTATCGATACAA
* *
1236699 TGTATCGATATATTGTGCCATGTATCGATACAA
1 TGTATCGATAAATTATGCCATGTATCGATACAA
1236732 ATAGTGGTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (33 bp):
TGTATCGATAAATTATGCCATGTATCGATACAA
Found at i:1242432 original size:1 final size:1
Alignment explanation
Indices: 1242426--1242534 Score: 92
Period size: 1 Copynumber: 109.0 Consensus size: 1
1242416 CATCCTCCAC
* * * * * ** *
1242426 AAAAAAAAAAAAAAAAACAAAACAAAACAAAAAAAACAAAACAAAAAAAAAGCAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
1242491 AACAAAGAAAAAAACACAAAAAAAAACAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1242535 GGGTCTGGAT
Statistics
Matches: 81, Mismatches: 27, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:1242493 original size:40 final size:39
Alignment explanation
Indices: 1242428--1242535 Score: 141
Period size: 40 Copynumber: 2.7 Consensus size: 39
1242418 TCCTCCACAA
*
1242428 AAAAAAAAAAAAAAACAAAACAAAACAAA-AAAAACAAAAC
1 AAAAAAAAACAAAAACAAAA-AAAACAAAGAAAAA-AAAAC
*
1242468 AAAAAAAAAGCAAAAACAAAAAAAACAAAGAAAAAAACAC
1 AAAAAAAAA-CAAAAACAAAAAAAACAAAGAAAAAAAAAC
1242508 AAAAAAAAACAAAAA-AAAAACAAA-AAAG
1 AAAAAAAAACAAAAACAAAAA-AAACAAAG
1242536 GGTCTGGATG
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
38 9 0.14
39 9 0.14
40 30 0.48
41 15 0.24
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (39 bp):
AAAAAAAAACAAAAACAAAAAAAACAAAGAAAAAAAAAC
Found at i:1242517 original size:50 final size:50
Alignment explanation
Indices: 1242429--1242534 Score: 146
Period size: 50 Copynumber: 2.1 Consensus size: 50
1242419 CCTCCACAAA
*
1242429 AAAAAAAAAAAAAACAAAACAAAACAAAAAAAACAAAACAAAAAAAAAGC
1 AAAAAAAAAAAAAACAAAACAAAACAAAAAAAACAAAACAAAAAAAAAAC
*
1242479 AAAAACAAAAAAAACAAAGA-AAAA-AACACAAAAA-AAAACAAAAAAAAAAC
1 AAAAAAAAAAAAAACAAA-ACAAAACAA-A-AAAAACAAAACAAAAAAAAAAC
1242529 AAAAAA
1 AAAAAA
1242535 GGGTCTGGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
49 2 0.04
50 42 0.84
51 6 0.12
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (50 bp):
AAAAAAAAAAAAAACAAAACAAAACAAAAAAAACAAAACAAAAAAAAAAC
Found at i:1242533 original size:31 final size:30
Alignment explanation
Indices: 1242427--1242534 Score: 107
Period size: 31 Copynumber: 3.7 Consensus size: 30
1242417 ATCCTCCACA
* *
1242427 AAAAAAAAAAAAA-AAACAAA-AC-AAAAC
1 AAAAAAAAAAAAACAAAAAAACACAAAAAA
* * *
1242454 AAAAAAAACAAAACAAAAAAAAAGCAAAAAC
1 AAAAAAAAAAAAACAAAAAAACA-CAAAAAA
* *
1242485 AAAAAAA-ACAAAGAAAAAAACACAAAAAA
1 AAAAAAAAAAAAACAAAAAAACACAAAAAA
1242514 AAACAAAAAAAAAACAAAAAA
1 AAA-AAAAAAAAAACAAAAAA
1242535 GGGTCTGGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
27 12 0.18
28 6 0.09
29 10 0.15
30 16 0.24
31 22 0.33
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAAAAACAAAAAAACACAAAAAA
Found at i:1244012 original size:29 final size:29
Alignment explanation
Indices: 1243973--1244207 Score: 137
Period size: 34 Copynumber: 7.0 Consensus size: 29
1243963 TTACCCTTCA
* *
1243973 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAACTCCGTGGCATCTTTTTC
1244002 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCA---TC-T-TTTTC
*
1244036 AAAGCCCACAACTCCGTGGCACCTTTTTC
1 AAAGCCCACAACTCCGTGGCATCTTTTTC
1244065 TGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCCTTTTC
1 -----AAAGCCCACAACTCCGTGGCA-TC----T----TTTTC
1244108 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTC
1 AAAGCCCACAACTCCGTGGCA-TC----T---TTTTC
* *
1244145 AAAGCCCATAACTCCGTGGCATTTTTTTC
1 AAAGCCCACAACTCCGTGGCATCTTTTTC
1244174 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
1 ----AAAGCCCACAACTCCGTGGCA-TCTTTTTC
1244208 CCTTTTAAGT
Statistics
Matches: 174, Mismatches: 8, Indels: 43
0.77 0.04 0.19
Matches are distributed among these distances:
29 29 0.17
30 1 0.01
31 1 0.01
32 3 0.02
33 21 0.12
34 54 0.31
35 1 0.01
36 1 0.01
37 28 0.16
38 29 0.17
39 1 0.01
43 5 0.03
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (29 bp):
AAAGCCCACAACTCCGTGGCATCTTTTTC
Found at i:1244038 original size:34 final size:36
Alignment explanation
Indices: 1243997--1244258 Score: 330
Period size: 34 Copynumber: 7.4 Consensus size: 36
1243987 AGTGGCATCT
*
1243997 TTTTCAAAGCCCACAACTCCGTGGCAC-CTTCTT-C
1 TTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1244031 TTTTCAAAGCCCACAACTCCGTGGCAC-CTTTTT-C
1 TTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1244065 TGTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCCCC
1 T-TTTCAAAGCCCACAACTCCGTGGCACTCTTTTT--CC
1244103 TTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTTCAAAGCCCACAACTCCGTGGCACTCTTTTT-CC
* *
1244140 TTTTCAAAGCCCATAACTCCGTGGCA-T-TTTTTTC
1 TTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1244174 TTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTTCAAAGCCCACAACTCCGTGGCACTCTTTTT-CC
* *
1244210 TTTT--AAGTCCACAACTCCGTGGCA-TCTTTCTCC
1 TTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCC
* *
1244243 CTTCCTAAAGCCCACA
1 TTTTC-AAAGCCCACA
1244259 CAAGTCGGTG
Statistics
Matches: 206, Mismatches: 10, Indels: 22
0.87 0.04 0.09
Matches are distributed among these distances:
33 24 0.12
34 68 0.33
35 38 0.18
36 14 0.07
37 31 0.15
38 31 0.15
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.33
Consensus pattern (36 bp):
TTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCC
Found at i:1244202 original size:108 final size:108
Alignment explanation
Indices: 1243997--1244258 Score: 387
Period size: 109 Copynumber: 2.5 Consensus size: 108
1243987 AGTGGCATCT
*
1243997 TTTTCAAAGCCCACAACTCCGTGGCAC-CTTCTT--CTTTTCAAAGCCCACAACTCCGTGGCACC
1 TTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACC
1244059 TTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCC
66 TTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CCC
* **
1244103 TTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCATAACTCCGTGGCATT
1 TTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACC
1244168 TTTTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
66 TTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
* * *
1244210 TTTT--AAGTCCACAACTCCGTGGCA-TCTTTCTCCC-TTCCTAAAGCCCACA
1 TTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTC-AAAGCCCACA
1244259 CAAGTCGGTG
Statistics
Matches: 144, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
103 3 0.02
104 18 0.12
105 19 0.13
106 27 0.19
107 12 0.08
108 32 0.22
109 33 0.23
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.33
Consensus pattern (108 bp):
TTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACC
TTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
Found at i:1244271 original size:143 final size:143
Alignment explanation
Indices: 1243997--1244258 Score: 388
Period size: 143 Copynumber: 1.8 Consensus size: 143
1243987 AGTGGCATCT
1243997 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTT
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTT
** * *
1244062 TTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCCTTTTCAAAGCCCACAACTCCGTGG
66 TTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTCTCCCCTTCTCAAAGCCCACAACTCCGTGG
1244127 CACTCTTTTTCCC
131 CACTCTTTTTCCC
* ** *
1244140 TTTTCAAAGCCCATAACTCCGTGGCATTTTTTTCTTTT-AAAGCCCACAACTCCGTGGCACTCTT
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCAC-CTT
* *
1244204 TTTCCCTTTTAAGTCCACAACTCCGTGGCA-TCTTTCT-CCCTTC-CTAAAGCCCACA
65 TTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTCTCCCCTTCTC-AAAGCCCACA
1244259 CAAGTCGGTG
Statistics
Matches: 107, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
140 1 0.01
141 15 0.14
142 28 0.26
143 63 0.59
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.33
Consensus pattern (143 bp):
TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTT
TTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTCTCCCCTTCTCAAAGCCCACAACTCCGTGG
CACTCTTTTTCCC
Found at i:1244286 original size:33 final size:35
Alignment explanation
Indices: 1244243--1244312 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 35
1244233 ATCTTTCTCC
1244243 CTTCCTAAAGCCCACACAAGTCGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
*
1244277 CTTCC-AAAGCCCATACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
1244311 CT
1 CT
1244313 AAGCCCAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 23 0.68
34 11 0.32
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.21
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:1244374 original size:49 final size:49
Alignment explanation
Indices: 1244312--1244605 Score: 334
Period size: 49 Copynumber: 6.0 Consensus size: 49
1244302 GCAACCCTTC
* *
1244312 TAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
1244361 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
*
1244410 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1244453 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTT
* * * *
1244505 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---TT-T-ATCTT
* * *
1244560 TAAGCCCAATATAG-TGGCCGTGAATC-GACATATTGGCATCTTTATC
1 TAAGTCCAATATAGCTGGCCTTGAATCAG-CATATTGGCACCTTTATC
1244606 ACTTTTCTCA
Statistics
Matches: 214, Mismatches: 17, Indels: 29
0.82 0.07 0.11
Matches are distributed among these distances:
43 41 0.19
44 1 0.00
48 4 0.02
49 84 0.39
50 2 0.01
52 38 0.18
53 4 0.02
54 19 0.09
55 20 0.09
56 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:1244465 original size:43 final size:43
Alignment explanation
Indices: 1244404--1244496 Score: 177
Period size: 43 Copynumber: 2.2 Consensus size: 43
1244394 TTGGCACCTT
1244404 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
*
1244447 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
1244490 CACCTTT
1 CACCTTT
1244497 TCCATCTTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (43 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
Found at i:1244474 original size:22 final size:22
Alignment explanation
Indices: 1244406--1244474 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
1244396 GGCACCTTCA
1244406 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
* * *
1244428 CCTTGAA-TCAGCACAT-TGGC--A
1 CCTTTAAGTC--CA-ATATAGCTGG
1244449 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
1244471 CCTT
1 CCTT
1244475 GAATCAGCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
CCTTTAAGTCCAATATAGCTGG
Found at i:1244485 original size:92 final size:95
Alignment explanation
Indices: 1244358--1244549 Score: 318
Period size: 92 Copynumber: 2.0 Consensus size: 95
1244348 GCACCTTTAT
1244358 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TT-CACCTTTAAGTCCAATA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTCCACCTTTAAGTCCAATA
*
1244421 TAGCTGGCCTTGAATCAGCACATTGGCA-C
66 TAGCTGGCCTTGAATCAGCACATTGACATC
* *
1244450 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTTCCACCTTTAAGTCCAAT
*
1244515 GTAGCTGGCCTTGAATCAGCACATTGACATC
65 ATAGCTGGCCTTGAATCAGCACATTGACATC
1244546 CTTT
1 CTTT
1244550 TTCTCATCTT
Statistics
Matches: 92, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
92 44 0.48
94 2 0.02
95 41 0.45
96 5 0.05
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (95 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTCCACCTTTAAGTCCAATA
TAGCTGGCCTTGAATCAGCACATTGACATC
Found at i:1244528 original size:52 final size:53
Alignment explanation
Indices: 1244450--1244602 Score: 195
Period size: 52 Copynumber: 2.9 Consensus size: 53
1244440 ACATTGGCAC
1244450 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
1244502 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * *
1244557 CTTTAAGCCCAATATAG-TGGCCGTGAATC-GACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAG-CATATTGGCACCTTT
1244603 ATCACTTTTC
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
52 41 0.48
53 4 0.05
54 24 0.28
55 17 0.20
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:1244766 original size:168 final size:169
Alignment explanation
Indices: 1244450--1245002 Score: 715
Period size: 168 Copynumber: 3.3 Consensus size: 169
1244440 ACATTGGCAC
* * * *
1244450 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TTT--ATCTTTAAGTCCAAT
* * * ** * * * *
1244515 GTAGCTGGCCTTG-A-ATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCCCAATATAG-TGG
63 ATCGCTAGCC--GCATATTGGCTCCTT--TATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGG
1244577 CCGTGAATCGACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
124 CCGTGAATCGACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
1244623 CTTTAAGTCCAATGTCGCTGG-CTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATC
*
1244687 GCTAGCCGCATATTGGCTCCTTTATCTTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAA
66 GCTAGCCGCATATTGGCTCCTTTATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAA
1244752 TCGACATATTGGCATCTTTATCAC-TTTCTCATCTTCAT
131 TCGACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
1244790 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATC
* *
1244855 GCTAGCCGCATATTGGCTCCTTTATCCTTTTTCTCATCTCTAAACCCAATATCGTTGGCCGTGAA
66 GCTAGCCGCATATTGGCTCCTTTATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAA
* * * * * *
1244920 TCAACGTATTGG--TCCTTTCATCGCTCTTCATCCTCATCAT
131 TCGACATATTGGCAT-CTTT-ATCACTTTTC-TCATCTTCAT
* * * * * *
1244960 CTTTAAGTCTAGTGTGGCAGGCCTTGAATCTGCACAGTGGCAC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1245003 ACTGCAAGAC
Statistics
Matches: 343, Mismatches: 29, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
166 1 0.00
167 69 0.20
168 154 0.45
169 31 0.09
170 45 0.13
171 3 0.01
172 21 0.06
173 19 0.06
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.36
Consensus pattern (169 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATC
GCTAGCCGCATATTGGCTCCTTTATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAA
TCGACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
Found at i:1245617 original size:13 final size:13
Alignment explanation
Indices: 1245599--1245623 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1245589 CATAAAATGT
1245599 TGTATCGATACAA
1 TGTATCGATACAA
1245612 TGTATCGATACA
1 TGTATCGATACA
1245624 TATTTTTTTT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1245705 original size:13 final size:13
Alignment explanation
Indices: 1245687--1245711 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1245677 ATTACTCAAA
1245687 TGTATCGATACAT
1 TGTATCGATACAT
1245700 TGTATCGATACA
1 TGTATCGATACA
1245712 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1245813 original size:52 final size:52
Alignment explanation
Indices: 1245720--1245843 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1245710 CACTGATCTT
*
1245720 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1245771 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1245823 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1245844 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 19 0.28
52 50 0.72
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1251909 original size:155 final size:155
Alignment explanation
Indices: 1251673--1252196 Score: 579
Period size: 156 Copynumber: 3.4 Consensus size: 155
1251663 CAAGTTTAAG
* * * * * * * * *
1251673 AAAAATTACGAAAATGCCCTTAAGG-GATACCTT-TACCTTGAATGTATTTCGGTACCCTTAAAG
1 AAAAATTACGAAAAT-ACCTTTAGGAGATACCTTCGA-CGTAAAAGTATCTCGATACCCCTAAAG
* **
1251736 GACTTAAAAAAGACTATAAAAGTGATGAACCTATCCTAAATACCCATATTCGGCATAAAAGCGGA
64 GACTTAAAAAGGACTATAAAAGTGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGA
* * *
1251801 CTCGGTAATAACCTAGGACTTGATTTCA
129 C-CAGTGATAACCTAGGACTTGATTTTA
* *
1251829 AAAAATTACAAAAATACCTTTAGGAGATACCTTCGACGTGAAAGTATCTCGATACCCC-AAAGGA
1 AAAAATTACGAAAATACCTTTAGGAGATACCTTCGACGTAAAAGTATCTCGATACCCCTAAAGGA
* * *
1251893 CTTAAAAAGGACTATAAAAG-GAATGACCCTATCCTAAATACCCACCTTCGGCATAAAAACAGAC
66 CTTAAAAAGGACTATAAAAGTG-ATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGAC
* * *
1251957 CTAGTGATAACCTAAGACTTTATTTTT
130 C-AGTGATAACCTAGGACTTGATTTTA
* * * * * * * *
1251984 AAAAATTACGAAAATACCCTTAAGAGATACTTTCGACATTAAAGTATCCCAAAACCCCTAAAGGA
1 AAAAATTACGAAAATACCTTTAGGAGATACCTTCGACGTAAAAGTATCTCGATACCCCTAAAGGA
* * * *
1252049 CTTAAAAAGGACTATAAAACTGATGAACCTACCCTAAATACCCACCTTTGGCATAAAAGTGGACC
66 CTTAAAAAGGACTATAAAAGTGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGA-C
* *
1252114 CAGTGATAACCTAGGACCTGGTTTTA
130 CAGTGATAACCTAGGACTTGATTTTA
* * * * * *
1252140 AAAAATTATGAAAATGCCTCTAGGGGATACCTTCGATGTAAAAGTATCTCGGTACCC
1 AAAAATTACGAAAATACCTTTAGGAGATACCTTCGACGTAAAAGTATCTCGATACCC
1252197 TTTGTAGACA
Statistics
Matches: 305, Mismatches: 56, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
154 2 0.01
155 137 0.45
156 162 0.53
157 4 0.01
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (155 bp):
AAAAATTACGAAAATACCTTTAGGAGATACCTTCGACGTAAAAGTATCTCGATACCCCTAAAGGA
CTTAAAAAGGACTATAAAAGTGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACC
AGTGATAACCTAGGACTTGATTTTA
Found at i:1252184 original size:156 final size:155
Alignment explanation
Indices: 1251726--1252187 Score: 559
Period size: 155 Copynumber: 3.0 Consensus size: 155
1251716 GTATTTCGGT
* * **
1251726 ACCCTTAAAGGACTTAAAAAAGACTATAAAAGTGATGAACCTATCCTAAATACCCATATTCGGCA
1 ACCCCTAAAGGACTTAAAAAGGACTATAAAA-TGATGAACCTATCCTAAATACCCACCTTCGGCA
* * * * * *
1251791 TAAAAGCGGACTCGGTAATAACCTAGGACTTGATTTCAAAAAATTACAAAAATACCTTTAGGAGA
65 TAAAAGCGGACCCAGTGATAACCTAGGACTTGATTTTAAAAAATTACGAAAATACCTCTAGGAGA
* * * *
1251856 TACCTTCGACGTGAAAGTATCTCGAT
130 TACCTTCGACGTAAAAGTATCCCAAA
* *
1251882 ACCCC-AAAGGACTTAAAAAGGACTATAAAAGGAATGACCCTATCCTAAATACCCACCTTCGGCA
1 ACCCCTAAAGGACTTAAAAAGGACTATAAAATG-ATGAACCTATCCTAAATACCCACCTTCGGCA
* * * * * * *
1251946 TAAAAACAGACCTAGTGATAACCTAAGACTTTATTTTTAAAAATTACGAAAATACC-CTTAAGAG
65 TAAAAGCGGACCCAGTGATAACCTAGGACTTGATTTTAAAAAATTACGAAAATACCTC-TAGGAG
* * *
1252010 ATACTTTCGACATTAAAGTATCCCAAA
129 ATACCTTCGACGTAAAAGTATCCCAAA
* *
1252037 ACCCCTAAAGGACTTAAAAAGGACTATAAAACTGATGAACCTACCCTAAATACCCACCTTTGGCA
1 ACCCCTAAAGGACTTAAAAAGGACTATAAAA-TGATGAACCTATCCTAAATACCCACCTTCGGCA
* * * * * *
1252102 TAAAAGTGGACCCAGTGATAACCTAGGACCTGGTTTTAAAAAATTATGAAAATGCCTCTAGGGGA
65 TAAAAGCGGACCCAGTGATAACCTAGGACTTGATTTTAAAAAATTACGAAAATACCTCTAGGAGA
*
1252167 TACCTTCGATGTAAAAGTATC
130 TACCTTCGACGTAAAAGTATC
1252188 TCGGTACCCT
Statistics
Matches: 255, Mismatches: 46, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
154 1 0.00
155 128 0.50
156 124 0.49
157 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (155 bp):
ACCCCTAAAGGACTTAAAAAGGACTATAAAATGATGAACCTATCCTAAATACCCACCTTCGGCAT
AAAAGCGGACCCAGTGATAACCTAGGACTTGATTTTAAAAAATTACGAAAATACCTCTAGGAGAT
ACCTTCGACGTAAAAGTATCCCAAA
Found at i:1252622 original size:20 final size:20
Alignment explanation
Indices: 1252592--1252667 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
1252582 GCCAAAGAGA
*
1252592 TGTATCAATACATTACTAAT
1 TGTATCGATACATTACTAAT
*
1252612 TATATCGATACATGTTTAC-AAT
1 TGTATCGATACA---TTACTAAT
* *
1252634 TGTATCGATACATTTCTCAT
1 TGTATCGATACATTACTAAT
1252654 TGTATCGATACATT
1 TGTATCGATACATT
1252668 CTGGGTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
19 3 0.06
20 26 0.55
22 14 0.30
23 4 0.09
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTACTAAT
Found at i:1256261 original size:13 final size:13
Alignment explanation
Indices: 1256243--1256268 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1256233 CAATTTTTTG
1256243 TGTATCGATACAT
1 TGTATCGATACAT
1256256 TGTATCGATACAT
1 TGTATCGATACAT
1256269 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1258828 original size:13 final size:13
Alignment explanation
Indices: 1258810--1258848 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1258800 ATAATCACCC
*
1258810 TGTATCGATACAG
1 TGTATCGATACAA
1258823 TGTATCGATACAA
1 TGTATCGATACAA
1258836 TGTATCGATACAA
1 TGTATCGATACAA
1258849 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1258859 original size:20 final size:20
Alignment explanation
Indices: 1258834--1258872 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1258824 GTATCGATAC
1258834 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1258854 AATGTATCGATACATAGAA
1 AATGTATCGATACAAAGAA
1258873 TTTCCAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.23
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1260939 original size:15 final size:15
Alignment explanation
Indices: 1260919--1260949 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1260909 ATTTCGTTTG
*
1260919 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1260934 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1260949 G
1 G
1260950 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1262780 original size:21 final size:21
Alignment explanation
Indices: 1262751--1262795 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1262741 AAGTTTTTAT
*
1262751 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1262771 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1262793 TTT
1 TTT
1262796 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1265397 original size:21 final size:22
Alignment explanation
Indices: 1265373--1265413 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1265363 ATTGGTACAA
* *
1265373 AATTTATAAAGCAT-TTATTTT
1 AATTGATAAAACATATTATTTT
1265394 AATTGATAAAACATATTATT
1 AATTGATAAAACATATTATT
1265414 GTTATTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (22 bp):
AATTGATAAAACATATTATTTT
Done.