Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008372.1 Hibiscus syriacus cultivar Beakdansim tig00111128_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1214897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1065002 original size:14 final size:14
Alignment explanation
Indices: 1064983--1065016 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1064973 AACGGAAAAT
1064983 AGGACAAAGATAAA
1 AGGACAAAGATAAA
1064997 AGGACAAAGATAAA
1 AGGACAAAGATAAA
1065011 AGGACA
1 AGGACA
1065017 CAATTTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.62, C:0.09, G:0.24, T:0.06
Consensus pattern (14 bp):
AGGACAAAGATAAA
Found at i:1065908 original size:84 final size:84
Alignment explanation
Indices: 1065526--1066999 Score: 1822
Period size: 84 Copynumber: 17.5 Consensus size: 84
1065516 GAATTTGACT
* * * * * * * * *
1065526 TGCCCTTGAGCTGAATGTAATCGAACTCGAATGT-ATTTATTGACATATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
** * *
1065590 AGCTATTTTGTAAATTTGATA
66 AGCTATGCTGCAAA--TGATG
* * * * *
1065611 TGCTTTTGAGCTGAGTGTAATCGAACTCGAAGGT-ATTTGTTGACAGATAACCATTCTTGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
* *
1065675 AGCTATGTTGTAAATTTGATG
66 AGCTATGCTGCAAA--TGATG
* * * * *
1065696 TTCCTTTTAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCGTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
* * *
1065761 AGTTATGTTGTAAATTGGATG
66 AGCTATGCTGCAAA-T-GATG
* * * *
1065782 TGCCTTTGAGCTGAGTGTAATCGAACTAGAAGGTCTTTTGTTGGAAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
** *
1065847 AGCTATGCTAAAAATAATG
66 AGCTATGCTGCAAATGATG
** * * *
1065866 TGCCTTTGAGCTGAGTGTAATCAAACTTAAATGTCTTTTGTTGGCATATAGCCCTTCTTGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
*
1065931 AGCTATGTTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* * ** * *
1065950 TGCCTTTGAGCTGAGTGTAATCGAACCCGAAGGTCTTTTGTCAGCAGATATCCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
*
1066015 AGCTATGCTGCAAATAATG
66 AGCTATGCTGCAAATGATG
* * * *
1066034 TGCCTTTGAGCTGAGTATAATCAAACTCGAAGGTATTTTTTTGGCAGATAACCCTTCTTACCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
* * *
1066099 AGTTATGCTGCAAATAACG
66 AGCTATGCTGCAAATGATG
* * *
1066118 TGCCTTTGAGCTGAGTGTAATCAAACTTGAAGGTCTTTTTTTGGCAGATAACCCTTATTGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
* *
1066183 AGTTATGATGCAAATGATG
66 AGCTATGCTGCAAATGATG
* * * * *
1066202 TGTCTTTGAGTTGAGTATAATCAAGCTCTAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
1066267 AGCTATGCTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* * *
1066286 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTATTGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
* *
1066351 AGTTATGCTGTAAATGATG
66 AGCTATGCTGCAAATGATG
* * ** * *
1066370 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCATATATTCGTTCTTTCCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
*
1066435 AGCTATGTTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* * *
1066454 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAAGCCTTATTGACTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
**
1066519 AGCTATATTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* * * *
1066538 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATATCCCTTATTGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
*
1066603 AGCTATGCCGCAAATGATG
66 AGCTATGCTGCAAATGATG
* *
1066622 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTATCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
* * *
1066686 AGCTATACTGTAGATGATG
66 AGCTATGCTGCAAATGATG
* *
1066705 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
1066770 AGCTATGCTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* * * * * * *
1066789 TGCTTTTGAGCTAAGTGTAATCGAACTCGAAGGTCGTTTGTTGGCAGATAGCTCTTATTGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
* *
1066854 AGTTATACTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* * * * * *
1066873 TGCCCTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGATGGCAGATATA-CCATCTTTCCTT
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATA-ACCCTTCTTGCCTT
*
1066937 GAGCTATGCTGTAAATGATG
65 GAGCTATGCTGCAAATGATG
* ** * *
1066957 TGTCTTTGAGCTGAGTGTAATTGAACTCAAAGGTTTTTTGTTG
1 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTG
1067000 AAGGTGCTTT
Statistics
Matches: 1221, Mismatches: 164, Indels: 9
0.88 0.12 0.01
Matches are distributed among these distances:
83 76 0.06
84 926 0.76
85 108 0.09
86 111 0.09
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.36
Consensus pattern (84 bp):
TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG
AGCTATGCTGCAAATGATG
Found at i:1072467 original size:410 final size:410
Alignment explanation
Indices: 1071707--1072524 Score: 1573
Period size: 410 Copynumber: 2.0 Consensus size: 410
1071697 CGAGTCGATA
1071707 CATGAGTGCTGGGATCGATACAAGGCATTGCTTCGCAAGTGCTCAAACCATGGTTTTCAAGATTG
1 CATGAGTGCTGGGATCGATACAAGGCATTGCTTCGCAAGTGCTCAAACCATGGTTTTCAAGATTG
* * *
1071772 GACACAAGTGGTGATGTTTTACAATGGAGTAAACGCTCCCACGAGGATGATGCTAGATGCCTCGA
66 GACACAAGTGGTGATGTTTTACAATGGAGTAAACGCTCCCACAAGAATGATGCTAGATGCCCCGA
1071837 CAAATGGGACGTTACTGGATAAATCACCAGCAGAGGCATTTGACATCTTGGATAGGATTGCTACC
131 CAAATGGGACGTTACTGGATAAATCACCAGCAGAGGCATTTGACATCTTGGATAGGATTGCTACC
*
1071902 AATGATTATCAGTTTCCCTCTACTATGCATGGATTCGGATGCAAATCACATGGAGCTCTCGAGCT
196 AATGATTATCAGTTTCCCTCTACTATGCATGGATTCGGATGCAAATCACATGGAACTCTCGAGCT
1071967 AGATTCTAAGGATGTCGTGTCAACCCAACTTGCTGCTATCACCAATATGTTGAAGAATTTGCAAA
261 AGATTCTAAGGATGTCGTGTCAACCCAACTTGCTGCTATCACCAATATGTTGAAGAATTTGCAAA
1072032 GGCCAAGTGAGGTGAGAGAAGTGAAGGCAGCCCATTCAGCATGTTTATTATGCCAAGGCAATCAC
326 GGCCAAGTGAGGTGAGAGAAGTGAAGGCAGCCCATTCAGCATGTTTATTATGCCAAGGCAATCAC
1072097 AATGAGAGTGATTGCCCATG
391 AATGAGAGTGATTGCCCATG
1072117 CATGAGTGCTGGGATCGATACAAGGCATTGCTTCGCAAGTGCTCAAACCATGGTTTTCAAGATTG
1 CATGAGTGCTGGGATCGATACAAGGCATTGCTTCGCAAGTGCTCAAACCATGGTTTTCAAGATTG
1072182 GACACAAGTGGTGATGTTTTACAATGGAGTAAACGCTCCCACAAGAATGATGCTAGATGCCCCGA
66 GACACAAGTGGTGATGTTTTACAATGGAGTAAACGCTCCCACAAGAATGATGCTAGATGCCCCGA
1072247 CAAATGGGACGTTACTGGATAAATCACCAGCAGAGGCATTTGACATCTTGGATAGGATTGCTACC
131 CAAATGGGACGTTACTGGATAAATCACCAGCAGAGGCATTTGACATCTTGGATAGGATTGCTACC
* *
1072312 AATGATTATCAGTTTCCCTCTACTATGTATGGATTCGGATGCAAATCACATGGAACTCTCGATCT
196 AATGATTATCAGTTTCCCTCTACTATGCATGGATTCGGATGCAAATCACATGGAACTCTCGAGCT
*
1072377 AGATTCTAAGGATGTCGTGTCAGCCCAACTTGCTGCTATCACCAATATGTTGAAGAATTTGCAAA
261 AGATTCTAAGGATGTCGTGTCAACCCAACTTGCTGCTATCACCAATATGTTGAAGAATTTGCAAA
1072442 GGCCAAGTGAGGTGAGAGAAGTGAAGGCAGCCCATTCAGCATGTTTATTATGCCAAGGCAATCAC
326 GGCCAAGTGAGGTGAGAGAAGTGAAGGCAGCCCATTCAGCATGTTTATTATGCCAAGGCAATCAC
1072507 AATGAGAGTGATTGCCCA
391 AATGAGAGTGATTGCCCA
1072525 ACCAATCAAG
Statistics
Matches: 401, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
410 401 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (410 bp):
CATGAGTGCTGGGATCGATACAAGGCATTGCTTCGCAAGTGCTCAAACCATGGTTTTCAAGATTG
GACACAAGTGGTGATGTTTTACAATGGAGTAAACGCTCCCACAAGAATGATGCTAGATGCCCCGA
CAAATGGGACGTTACTGGATAAATCACCAGCAGAGGCATTTGACATCTTGGATAGGATTGCTACC
AATGATTATCAGTTTCCCTCTACTATGCATGGATTCGGATGCAAATCACATGGAACTCTCGAGCT
AGATTCTAAGGATGTCGTGTCAACCCAACTTGCTGCTATCACCAATATGTTGAAGAATTTGCAAA
GGCCAAGTGAGGTGAGAGAAGTGAAGGCAGCCCATTCAGCATGTTTATTATGCCAAGGCAATCAC
AATGAGAGTGATTGCCCATG
Found at i:1077109 original size:15 final size:15
Alignment explanation
Indices: 1077098--1077133 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1077088 TTTATTTTCA
1077098 TATTTCTCATTTTAAT
1 TATTT-TCATTTTAAT
1077114 TATTTTCATTTTAAT
1 TATTTTCATTTTAAT
1077129 T-TTTT
1 TATTTT
1077134 GCAAGGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 11 0.55
16 5 0.25
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTCATTTTAAT
Found at i:1085971 original size:27 final size:28
Alignment explanation
Indices: 1085926--1085986 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1085916 GCTAAGGATA
*
1085926 GAAAAAGAAGAAGAAATAA-AGCAAAGG
1 GAAAAAGAAGAAGAAATAAGAACAAAGG
*
1085953 GAAAAAG-TGAAGAAGATAAGAACAAAGG
1 GAAAAAGAAGAAGAA-ATAAGAACAAAGG
*
1085981 AAAAAA
1 GAAAAA
1085987 ATTGGGGGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 6 0.21
27 11 0.38
28 12 0.41
ACGTcount: A:0.67, C:0.03, G:0.25, T:0.05
Consensus pattern (28 bp):
GAAAAAGAAGAAGAAATAAGAACAAAGG
Found at i:1086089 original size:7 final size:8
Alignment explanation
Indices: 1086064--1086100 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
1086054 CCTTGAAGCT
1086064 AAAGT-AA
1 AAAGTGAA
1086071 AAAGGTGAA
1 AAA-GTGAA
1086080 AAAGTGAA
1 AAAGTGAA
1086088 AAAGTGAA
1 AAAGTGAA
1086096 AAAGT
1 AAAGT
1086101 TTTCCCTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 3 0.11
8 20 0.71
9 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (8 bp):
AAAGTGAA
Found at i:1087533 original size:22 final size:22
Alignment explanation
Indices: 1087508--1087551 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1087498 AACTTAACAT
*
1087508 TATACTGAAA-CCTCTTCTTACC
1 TATACT-AAAGCCTCTTATTACC
1087530 TATACTAAAGCCTCTTATTACC
1 TATACTAAAGCCTCTTATTACC
1087552 CTGGCTGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.36
Consensus pattern (22 bp):
TATACTAAAGCCTCTTATTACC
Found at i:1091350 original size:36 final size:36
Alignment explanation
Indices: 1091307--1091409 Score: 188
Period size: 36 Copynumber: 2.9 Consensus size: 36
1091297 AGTTGAGTAT
1091307 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
1091343 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCC
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
1091379 TATCAGCTTCGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
1091410 CCAGCACCAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.41
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:1095773 original size:17 final size:16
Alignment explanation
Indices: 1095742--1095775 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1095732 CACGTGAGGA
1095742 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1095758 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1095775 T
1 T
1095776 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1102113 original size:19 final size:21
Alignment explanation
Indices: 1102076--1102118 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1102066 TAACTTTTTC
1102076 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
1102096 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
1102116 TTT
1 TTT
1102119 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:1102124 original size:19 final size:20
Alignment explanation
Indices: 1102075--1102124 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1102065 TTAACTTTTT
*
1102075 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
1102095 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
1102114 CTTTTACCTTT
1 CTTTTACCTTT
1102125 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:1105301 original size:17 final size:16
Alignment explanation
Indices: 1105270--1105303 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1105260 CACGTGAGGA
1105270 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1105286 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1105303 T
1 T
1105304 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1108051 original size:20 final size:20
Alignment explanation
Indices: 1108028--1108070 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1108018 ATTCCACCAC
*
1108028 ATGCATATAAATGCTCCTAA
1 ATGCATATAAATGATCCTAA
* *
1108048 ATGCATCTATATGATCCTAA
1 ATGCATATAAATGATCCTAA
1108068 ATG
1 ATG
1108071 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCATATAAATGATCCTAA
Found at i:1110928 original size:21 final size:20
Alignment explanation
Indices: 1110891--1110943 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
1110881 GAAAAAACAT
1110891 AAGGAAAAAAT--AAATCAA
1 AAGGAAAAAATAAAAATCAA
1110909 AAGGAAAAAATTAAAAATCAA
1 AAGGAAAAAA-TAAAAATCAA
*
1110930 AAGG-GAAAATAAAA
1 AAGGAAAAAATAAAA
1110944 TGAAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 10 0.32
19 6 0.19
20 4 0.13
21 11 0.35
ACGTcount: A:0.72, C:0.04, G:0.13, T:0.11
Consensus pattern (20 bp):
AAGGAAAAAATAAAAATCAA
Found at i:1111013 original size:14 final size:15
Alignment explanation
Indices: 1110996--1111032 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1110986 ATGTAAAAAT
1110996 AAAAATAAAA-ATAA
1 AAAAATAAAACATAA
1111010 AAAAATAAAACATAA
1 AAAAATAAAACATAA
*
1111025 TAAAATAA
1 AAAAATAA
1111033 TGAATCAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAATAAAACATAA
Found at i:1113810 original size:17 final size:17
Alignment explanation
Indices: 1113769--1113836 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
1113759 ATTCATGCAT
1113769 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
1113786 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
1113804 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
1113821 CTAGTCCATTTATTAA
1 CTAGTTCATTAATTAA
1113837 CCTAACTCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
17 29 0.69
18 13 0.31
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:1122301 original size:2 final size:2
Alignment explanation
Indices: 1122290--1122326 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1122280 TACAACTATC
1122290 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1122327 TTAATTACTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1123374 original size:41 final size:41
Alignment explanation
Indices: 1123312--1123401 Score: 96
Period size: 41 Copynumber: 2.2 Consensus size: 41
1123302 AAAACAAGAA
*
1123312 ATTTTTAATTAAATACTAAATTA-TTAAATTATATAA-AAATT
1 ATTTTTAATTAAATACCAAATTACTT-AATTATA-AATAAATT
* *
1123353 ATTTTTCATTATAA-ACCAAATTACTTAGTTATAAATTAAATT
1 ATTTTTAATTA-AATACCAAATTACTTAATTATAAA-TAAATT
1123395 ATTTTTA
1 ATTTTTA
1123402 CTTTATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
40 2 0.05
41 24 0.59
42 15 0.37
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.48
Consensus pattern (41 bp):
ATTTTTAATTAAATACCAAATTACTTAATTATAAATAAATT
Found at i:1123581 original size:28 final size:28
Alignment explanation
Indices: 1123513--1123582 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
1123503 AAATGTAAAT
*
1123513 TAAATAAATATTAAAATTTATTTTTATCA
1 TAAAT-AATATTAAAATTTATATTTATCA
*
1123542 TAAATAAT-TTAAAAGTTTATATTTAT-T
1 TAAATAATATTAAAA-TTTATATTTATCA
*
1123569 TAATTAATATTAAA
1 TAAATAATATTAAA
1123583 TTAATTGAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 13 0.36
28 18 0.50
29 5 0.14
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
TAAATAATATTAAAATTTATATTTATCA
Found at i:1128626 original size:26 final size:26
Alignment explanation
Indices: 1128578--1128630 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1128568 AATAAAAGAG
1128578 AAAAAATACTCTGAAAAAGAAATCCC
1 AAAAAATACTCTGAAAAAGAAATCCC
1128604 AAAAAATACTCTGAAAAAGAAATCCC
1 AAAAAATACTCTGAAAAAGAAATCCC
1128630 A
1 A
1128631 GACACCTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.58, C:0.19, G:0.08, T:0.15
Consensus pattern (26 bp):
AAAAAATACTCTGAAAAAGAAATCCC
Found at i:1132617 original size:36 final size:36
Alignment explanation
Indices: 1132570--1132651 Score: 155
Period size: 36 Copynumber: 2.3 Consensus size: 36
1132560 TTTATGCTAT
1132570 GAACACAAGGAATCCTTCATATTATAAGATCAAAAG
1 GAACACAAGGAATCCTTCATATTATAAGATCAAAAG
*
1132606 GAACACAAGGAATCCTTCTTATTATAAGATCAAAAG
1 GAACACAAGGAATCCTTCATATTATAAGATCAAAAG
1132642 GAACACAAGG
1 GAACACAAGG
1132652 CGTGGAGATA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.21
Consensus pattern (36 bp):
GAACACAAGGAATCCTTCATATTATAAGATCAAAAG
Found at i:1134229 original size:39 final size:39
Alignment explanation
Indices: 1134164--1134269 Score: 101
Period size: 39 Copynumber: 2.7 Consensus size: 39
1134154 TCAGGTGTTC
* * *
1134164 CATG-CGTCTTCAAGTTAAAT-ATGAAGACTCTACAACTA
1 CATGACGTCTTC-AGCTAAATGAAGAAGACTCCACAACTA
* *
1134202 CATGACGTCTTCAGAC-AAATGAAGAAGACTCCACGACTG
1 CATGACGTCTTCAG-CTAAATGAAGAAGACTCCACAACTA
* * *
1134241 CATGGCGTCTTTAGCTAAATGGAGAAGAC
1 CATGACGTCTTCAGCTAAATGAAGAAGAC
1134270 CCCAAGAGTG
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
38 11 0.20
39 45 0.80
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (39 bp):
CATGACGTCTTCAGCTAAATGAAGAAGACTCCACAACTA
Found at i:1134848 original size:17 final size:16
Alignment explanation
Indices: 1134819--1134854 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1134809 TCTATCTCAT
*
1134819 AATAAATATATATATA
1 AATAAATAAATATATA
1134835 AATATAATAAATATATA
1 AATA-AATAAATATATA
1134852 AAT
1 AAT
1134855 TATTACATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATAAATAAATATATA
Found at i:1135492 original size:20 final size:22
Alignment explanation
Indices: 1135455--1135496 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
1135445 TATTAAATGA
1135455 ACTAATAAAATTAAATAAAAAT
1 ACTAATAAAATTAAATAAAAAT
*
1135477 ACTAA-AAAA-TACATAAAAAT
1 ACTAATAAAATTAAATAAAAAT
1135497 GAGTATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 4 0.21
22 5 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
ACTAATAAAATTAAATAAAAAT
Found at i:1136118 original size:18 final size:19
Alignment explanation
Indices: 1136083--1136119 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1136073 CACTGAATGT
1136083 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1136103 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1136120 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1136856 original size:21 final size:22
Alignment explanation
Indices: 1136805--1136857 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
1136795 TCATTTATGA
1136805 GTTTCATTTTACACAGGCAACT
1 GTTTCATTTTACACAGGCAACT
* * * *
1136827 CTTGC-TTTTACACAGG-TATT
1 GTTTCATTTTACACAGGCAACT
1136847 GTTTCATTTTA
1 GTTTCATTTTA
1136858 GTTATTTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
20 5 0.21
21 16 0.67
22 3 0.12
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (22 bp):
GTTTCATTTTACACAGGCAACT
Found at i:1139269 original size:38 final size:38
Alignment explanation
Indices: 1139217--1139312 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
1139207 CTCGTATAAA
* * *
1139217 TGTCCCGAATGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATCTG
*
1139255 TGTCCCGAAGGACCTGTCATCCCAAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATCTG
*
1139293 TGTCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
1139313 ATGTCTTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATCTG
Found at i:1139518 original size:46 final size:46
Alignment explanation
Indices: 1139461--1139565 Score: 158
Period size: 46 Copynumber: 2.3 Consensus size: 46
1139451 ATGTGTAACC
*
1139461 ATGT-ATTTCATATCATATCACATGTATCAGGCATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGCATTACATATTCAT
* * *
1139506 ATGTCATTTCATATCATATCATATGTATCACGTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGCATTACATATTCAT
*
1139552 ATATCATTTCATAT
1 ATGTCATTTCATAT
1139566 AGTCACATAG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 4 0.07
46 50 0.93
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.43
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACGCATTACATATTCAT
Found at i:1146118 original size:17 final size:17
Alignment explanation
Indices: 1146096--1146139 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
1146086 CGTATAAATG
1146096 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
*
1146113 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTATCA
1146130 TCCCGAAGGA
1 TCCCGAAGGA
1146140 TGTAATATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.27, C:0.34, G:0.23, T:0.16
Consensus pattern (17 bp):
TCCCGAAGGACCTATCA
Found at i:1146356 original size:23 final size:22
Alignment explanation
Indices: 1146329--1146403 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
1146319 GTATTTTATA
*
1146329 TCATATCACATGTATCACGTAT
1 TCATATCAAATGTATCACGTAT
* ** *
1146351 TACATATTCATATGTCATTTCATA-
1 T-CATA-TCAAATGT-ATCACGTAT
1146375 TCATATCAAATGTATCACGTATT
1 TCATATCAAATGTATCACGTA-T
1146398 TCATAT
1 TCATAT
1146404 TCATATATCA
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 5 0.12
22 8 0.20
23 14 0.35
24 8 0.20
25 5 0.12
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (22 bp):
TCATATCAAATGTATCACGTAT
Found at i:1146379 original size:46 final size:46
Alignment explanation
Indices: 1146321--1146421 Score: 166
Period size: 46 Copynumber: 2.2 Consensus size: 46
1146311 GTAACCAAGT
* * *
1146321 ATTTTATATCATATCACATGTATCACGTATTACATATTCATATGTC
1 ATTTCATATCATATCAAATGTATCACGTATTACATATTCATATATC
*
1146367 ATTTCATATCATATCAAATGTATCACGTATTTCATATTCATATATC
1 ATTTCATATCATATCAAATGTATCACGTATTACATATTCATATATC
1146413 ATTTCATAT
1 ATTTCATAT
1146422 AGTCACATAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.45
Consensus pattern (46 bp):
ATTTCATATCATATCAAATGTATCACGTATTACATATTCATATATC
Found at i:1154855 original size:62 final size:63
Alignment explanation
Indices: 1154779--1154902 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 63
1154769 AACCCACCCC
1154779 TGGACTTTCATCTACAAAATTACTTTTATATTTATGTTGGATC-TTTGTTTCAAGTTTTTTCT
1 TGGACTTTCATCTACAAAATTACTTTTATATTTATGTTGGATCTTTTGTTTCAAGTTTTTTCT
* *
1154841 TGGACTTTCATCTACAAAATTACTTTTATTTTTATGTTGGATCTTTTTTTTCAAGTTTTTTC
1 TGGACTTTCATCTACAAAATTACTTTTATATTTATGTTGGATCTTTTGTTTCAAGTTTTTTC
1154903 GGCCGAAAGG
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
62 42 0.71
63 17 0.29
ACGTcount: A:0.22, C:0.13, G:0.10, T:0.55
Consensus pattern (63 bp):
TGGACTTTCATCTACAAAATTACTTTTATATTTATGTTGGATCTTTTGTTTCAAGTTTTTTCT
Found at i:1155525 original size:17 final size:17
Alignment explanation
Indices: 1155482--1155533 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1155472 ATTACAGTAG
*
1155482 AAACTCTTTAAATTAAT
1 AAACTCTATAAATTAAT
*
1155499 --ACTCGATAAATTAAT
1 AAACTCTATAAATTAAT
* *
1155514 AAACTCTCTAAAATAAT
1 AAACTCTATAAATTAAT
1155531 AAA
1 AAA
1155534 TTTGTCCGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (17 bp):
AAACTCTATAAATTAAT
Found at i:1159895 original size:21 final size:21
Alignment explanation
Indices: 1159844--1159896 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1159834 ATTATGACTA
1159844 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1159865 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1159886 TCGCAATGCGA
1 TCGCAATGCGA
1159897 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1159929 original size:21 final size:21
Alignment explanation
Indices: 1159886--1160000 Score: 187
Period size: 21 Copynumber: 5.5 Consensus size: 21
1159876 TTTTCCCAAT
** *
1159886 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
1159906 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
1159927 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
1159948 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
1159969 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
1159990 TCGCAACGCGA
1 TCGCAATGCGA
1160001 TACTGACTAT
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
20 12 0.13
21 78 0.87
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:1160014 original size:20 final size:20
Alignment explanation
Indices: 1159989--1160103 Score: 133
Period size: 20 Copynumber: 5.7 Consensus size: 20
1159979 AATTTGGAAA
1159989 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1160009 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
1160030 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1160050 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1160070 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1160090 TTCGCAACGAGATA
1 ATCGCAACGCGATA
1160104 ATACATAATC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.78
21 14 0.17
22 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1160031 original size:41 final size:41
Alignment explanation
Indices: 1159986--1160117 Score: 178
Period size: 41 Copynumber: 3.2 Consensus size: 41
1159976 GCGAATTTGG
* *
1159986 AAAATCGCAACGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
1160027 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTTAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA-ATAC
** *
1160069 --TTTCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
1160108 ATAATCGCAA
1 AAAATCGCAA
1160118 TGTGATTTTC
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
39 3 0.04
40 32 0.41
41 41 0.52
42 3 0.04
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:1160645 original size:20 final size:20
Alignment explanation
Indices: 1160596--1160654 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1160586 TTTATTCTCT
* **
1160596 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
1160616 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
*
1160636 TGTTGCGATT-TCCATTTTC
1 CGTTGCGATTGT-CATTTTC
1160655 AGAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:1161419 original size:14 final size:14
Alignment explanation
Indices: 1161385--1161423 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1161375 TTGATTGTTT
1161385 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1161399 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1161413 TGTTGATTTGT
1 AATTGATTTGT
1161424 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1161615 original size:19 final size:19
Alignment explanation
Indices: 1161563--1161608 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1161553 GCAACGAGAG
*
1161563 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATAAA
1161582 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATAAA
1161601 AATCGCAA
1 AATCGCAA
1161609 CGAGAAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATAAA
Found at i:1161920 original size:20 final size:20
Alignment explanation
Indices: 1161895--1161986 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
1161885 TTGAAGATGA
1161895 TTGCGATTTTCAGAAT-GTCG
1 TTGCGATTTTCAGAATCG-CG
***
1161915 TTGCGAAAGTCAGAATCGCG
1 TTGCGATTTTCAGAATCGCG
* **
1161935 TTGCGATTTTGTATTATCGCG
1 TTGCGATTTT-CAGAATCGCG
** * *
1161956 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCGCG
1161976 TTGCGATTTTC
1 TTGCGATTTTC
1161987 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 38 0.70
21 16 0.30
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCGCG
Found at i:1166175 original size:30 final size:30
Alignment explanation
Indices: 1166132--1166188 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1166122 TTAAAGATAA
1166132 TTTTAAATAATTTGATATT-AAATATTTATAT
1 TTTTAAATAATTTGA-ATTCAAA-ATTTATAT
*
1166163 TTTTTAAT-ATTTGAATTCAAAATTTA
1 TTTTAAATAATTTGAATTCAAAATTTA
1166189 AAAGACTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 8 0.33
30 9 0.38
31 7 0.29
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (30 bp):
TTTTAAATAATTTGAATTCAAAATTTATAT
Found at i:1174529 original size:21 final size:19
Alignment explanation
Indices: 1174496--1174534 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1174486 TACTGTAAAT
*
1174496 ACAACAAACATCATATTAA
1 ACAACAAACATCAAATTAA
1174515 ACAACCAAACAATCAAATTA
1 ACAA-CAAAC-ATCAAATTA
1174535 TACTTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
21 8 0.47
ACGTcount: A:0.59, C:0.23, G:0.00, T:0.18
Consensus pattern (19 bp):
ACAACAAACATCAAATTAA
Found at i:1177111 original size:20 final size:20
Alignment explanation
Indices: 1177086--1177124 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1177076 TAAATTAAAT
* *
1177086 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAATTTTA
1177106 ATTAGATAGAATCAATTTT
1 ATTAGATAGAATCAATTTT
1177125 TATTCTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAATTTTA
Found at i:1181773 original size:20 final size:20
Alignment explanation
Indices: 1181748--1181786 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1181738 TAAATTAAAT
* *
1181748 ATTAGATTGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
1181768 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
1181787 TATTCTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:1181825 original size:20 final size:20
Alignment explanation
Indices: 1181800--1181838 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1181790 TCTATTAGTT
1181800 ATTAGATA-AGATCATTTTTA
1 ATTAGATAGA-ATCATTTTTA
1181820 ATTAGATAGAATCATTTTT
1 ATTAGATAGAATCATTTTT
1181839 TTATTCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:1181866 original size:53 final size:52
Alignment explanation
Indices: 1181741--1181872 Score: 194
Period size: 52 Copynumber: 2.5 Consensus size: 52
1181731 GAATATCTAA
* *
1181741 ATTAAATATTAGAT-TGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCT
1 ATTAATTATTAGATAT-GATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
* * *
1181793 ATTAGTTATTAGATAAGATCATTTTTAATTAGATAGAATCATTTTTTTATTCT
1 ATTAATTATTAGATATGATCATTTTTAATTAGATAGAATCA-GTTTTTATTCT
1181846 ATTAATTATTAGATATGATCATTTTTA
1 ATTAATTATTAGATATGATCATTTTTA
1181873 TTCTGTTGCT
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
52 36 0.51
53 35 0.49
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (52 bp):
ATTAATTATTAGATATGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
Found at i:1188413 original size:34 final size:36
Alignment explanation
Indices: 1188373--1188452 Score: 119
Period size: 34 Copynumber: 2.3 Consensus size: 36
1188363 AACACAATCA
* *
1188373 TCAATTACATTTTAAACC-CAAATTCC-AAAATACT
1 TCAATTACATTCTAAACCTCAAATTCCAAAAAAACT
*
1188407 TCAATTACATTCTAAACCTCAGATTCCAAAAAAACT
1 TCAATTACATTCTAAACCTCAAATTCCAAAAAAACT
1188443 TCAATTACAT
1 TCAATTACAT
1188453 GCCCAACCCC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
34 17 0.41
35 7 0.17
36 17 0.41
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.31
Consensus pattern (36 bp):
TCAATTACATTCTAAACCTCAAATTCCAAAAAAACT
Found at i:1189219 original size:139 final size:142
Alignment explanation
Indices: 1188950--1189227 Score: 393
Period size: 139 Copynumber: 1.9 Consensus size: 142
1188940 AAACTATTTA
* ** *
1188950 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACATAAAGTCAAA
1 AATTAGAATCAAATAATATTATAATACGATAAATATCTATAATTAAATTT----ATAAAG-CAAA
* *
1189015 AATTCAATTCAATTCGACTTGATTTAATTTTATATACTCAAATCGAAAAAATTTCGAGTCAACTA
61 AATTCAATTCAATTCGACTTGATTTAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAACTA
1189080 TTTTATAAAAGGATATG
126 TTTTATAAAAGGATATG
1189097 AATTAGAATCAAATAATATTATAATACGATAAATATCTATAATTAAA-TT-TAAA-CAAAAATTC
1 AATTAGAATCAAATAATATTATAATACGATAAATATCTATAATTAAATTTATAAAGCAAAAATTC
* * *
1189159 AATTCAATTCGATTTGATTTAAATTTTATAAACTTAAATCTAAAAAATTT-GAGTAAACTATTTT
66 AATTCAATTCGACTTGATTT-AATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAACTATTTT
1189223 ATAAA
130 ATAAA
1189228 CTGAATTGAG
Statistics
Matches: 121, Mismatches: 9, Indels: 10
0.86 0.06 0.07
Matches are distributed among these distances:
139 46 0.38
140 26 0.21
141 4 0.03
146 2 0.02
147 43 0.36
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (142 bp):
AATTAGAATCAAATAATATTATAATACGATAAATATCTATAATTAAATTTATAAAGCAAAAATTC
AATTCAATTCGACTTGATTTAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAACTATTTTA
TAAAAGGATATG
Found at i:1189442 original size:35 final size:35
Alignment explanation
Indices: 1189403--1189480 Score: 122
Period size: 35 Copynumber: 2.2 Consensus size: 35
1189393 GGGGTTGAAC
1189403 ATGTAATTGAAGT-ATTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAA-TCATTTTGGAATTTGAGGTTTAGA
* *
1189438 ATGTAATTGAATCATTTTGGATTTTGGGGTTTAGA
1 ATGTAATTGAATCATTTTGGAATTTGAGGTTTAGA
1189473 ATGTAATT
1 ATGTAATT
1189481 AATGACTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
34 1 0.03
35 39 0.98
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.45
Consensus pattern (35 bp):
ATGTAATTGAATCATTTTGGAATTTGAGGTTTAGA
Found at i:1189841 original size:10 final size:10
Alignment explanation
Indices: 1189776--1189822 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
1189766 AAAATATATT
*
1189776 TTCATTTATG
1 TTCATTTACG
*
1189786 TTCGTTTACG
1 TTCATTTACG
1189796 TTCATTTAC-
1 TTCATTTACG
*
1189805 TTCCATTTATG
1 TT-CATTTACG
1189816 TTCATTT
1 TTCATTT
1189823 TTTGTGTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.87
11 2 0.06
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (10 bp):
TTCATTTACG
Found at i:1189860 original size:10 final size:10
Alignment explanation
Indices: 1189847--1189880 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1189837 CGTTCGTTCA
1189847 TTTATATTCG
1 TTTATATTCG
**
1189857 TTTACGTTCG
1 TTTATATTCG
1189867 TTTATATTCG
1 TTTATATTCG
1189877 TTTA
1 TTTA
1189881 CATCCTTTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.59
Consensus pattern (10 bp):
TTTATATTCG
Found at i:1189864 original size:24 final size:24
Alignment explanation
Indices: 1189833--1189902 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 24
1189823 TTTGTGTTCA
1189833 TTTACGTTCGTTCATTTATATTCG
1 TTTACGTTCGTTCATTTATATTCG
1189857 TTTACGTTCG----TTTATATTCG
1 TTTACGTTCGTTCATTTATATTCG
* * * *
1189877 TTTACATCCTTTCATTTATGTTCG
1 TTTACGTTCGTTCATTTATATTCG
1189901 TT
1 TT
1189903 CATTTGTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 17 0.45
24 21 0.55
ACGTcount: A:0.16, C:0.17, G:0.11, T:0.56
Consensus pattern (24 bp):
TTTACGTTCGTTCATTTATATTCG
Found at i:1189870 original size:20 final size:20
Alignment explanation
Indices: 1189841--1189881 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1189831 CATTTACGTT
1189841 CGTTCATTTATATTCGTTTA
1 CGTTCATTTATATTCGTTTA
*
1189861 CGTTCGTTTATATTCGTTTA
1 CGTTCATTTATATTCGTTTA
1189881 C
1 C
1189882 ATCCTTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.54
Consensus pattern (20 bp):
CGTTCATTTATATTCGTTTA
Found at i:1189943 original size:13 final size:14
Alignment explanation
Indices: 1189925--1189954 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1189915 TTTATCATTT
1189925 AAATGAACGG-CAC
1 AAATGAACGGACAC
1189938 AAATGAACGGACAC
1 AAATGAACGGACAC
1189952 AAA
1 AAA
1189955 CAAGCTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.53, C:0.20, G:0.20, T:0.07
Consensus pattern (14 bp):
AAATGAACGGACAC
Found at i:1209742 original size:3 final size:3
Alignment explanation
Indices: 1209734--1209777 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
1209724 CTCGGGTTAA
*
1209734 AAT AAT AAT AAT ATAT AA- ATT AAT AAAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT A-AT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
1209778 TATATTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 1 0.03
3 29 0.81
4 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1210726 original size:23 final size:20
Alignment explanation
Indices: 1210685--1210730 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 20
1210675 AAAAAATATT
1210685 TTCATTTATGTTCGTTTACG
1 TTCATTTATGTTCGTTTACG
1210705 TTCATTTATTGTGCTCGTTTACG
1 TTCATTTA-TGT--TCGTTTACG
1210728 TTC
1 TTC
1210731 GTTCATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.35
21 3 0.13
23 12 0.52
ACGTcount: A:0.13, C:0.17, G:0.15, T:0.54
Consensus pattern (20 bp):
TTCATTTATGTTCGTTTACG
Found at i:1210783 original size:37 final size:36
Alignment explanation
Indices: 1210689--1210787 Score: 98
Period size: 37 Copynumber: 2.8 Consensus size: 36
1210679 AATATTTTCA
*
1210689 TTTATGTTCGTTT-A--CGTTCATTTATTGTGCTCG
1 TTTATGTTCGTTTCATTCGTTCGTTTATTGTGCTCG
* * * *
1210722 TTTACGTTCG-TTCATTTGTATTCGTTTATTGTGTTTG
1 TTTATGTTCGTTTCATTCG--TTCGTTTATTGTGCTCG
1210759 TTTATGTTCGTTTACATTCGTTCGTTTAT
1 TTTATGTTCGTTT-CATTCGTTCGTTTAT
1210788 GTCCGTTCAT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
32 2 0.04
33 10 0.19
35 1 0.02
37 32 0.62
38 2 0.04
39 5 0.10
ACGTcount: A:0.12, C:0.13, G:0.17, T:0.58
Consensus pattern (36 bp):
TTTATGTTCGTTTCATTCGTTCGTTTATTGTGCTCG
Found at i:1210794 original size:14 final size:14
Alignment explanation
Indices: 1210775--1210822 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
1210765 TTCGTTTACA
*
1210775 TTCGTTCGTTTATG
1 TTCGTTCATTTATG
* *
1210789 TCCGTTCATTTGTG
1 TTCGTTCATTTATG
1210803 TTCGTTCATTTATG
1 TTCGTTCATTTATG
1210817 TTCGTT
1 TTCGTT
1210823 TATCATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.08, C:0.17, G:0.19, T:0.56
Consensus pattern (14 bp):
TTCGTTCATTTATG
Found at i:1211395 original size:14 final size:14
Alignment explanation
Indices: 1211376--1211418 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1211366 ATCAGAAATA
1211376 TAACTATATATATT
1 TAACTATATATATT
* *
1211390 TAACTATTTATATA
1 TAACTATATATATT
*
1211404 TAAATAATATATATT
1 TAACT-ATATATATT
1211419 ATATATTATC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (14 bp):
TAACTATATATATT
Done.