Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 316 of 316
Found at i:103909015 original size:21 final size:22
Alignment explanation
Indices: 103908989--103909035 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
103908979 CTCTGCTCAA
*
103908989 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
103909010 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
103909032 ACTC
1 ACTC
103909036 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:103912789 original size:22 final size:22
Alignment explanation
Indices: 103912764--103912807 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
103912754 GGAACGGAAC
103912764 AATACTTCTGTGCGATGGGGAT
1 AATACTTCTGTGCGATGGGGAT
**
103912786 AATACTTCTGTTTGATGGGGAT
1 AATACTTCTGTGCGATGGGGAT
103912808 CAAAGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.36
Consensus pattern (22 bp):
AATACTTCTGTGCGATGGGGAT
Found at i:103918941 original size:19 final size:20
Alignment explanation
Indices: 103918904--103918947 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
103918894 TTAACAAAAA
103918904 TTATAGAAAAATTCAAAATAT
1 TTATAGAAAAATTCAAAAT-T
*
103918925 TTATA-AAAATTTC-AAATT
1 TTATAGAAAAATTCAAAATT
103918943 TTATA
1 TTATA
103918948 TTTTTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 4 0.18
20 7 0.32
21 5 0.23
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (20 bp):
TTATAGAAAAATTCAAAATT
Found at i:103921860 original size:7 final size:7
Alignment explanation
Indices: 103921849--103921893 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
103921839 CTACAGCTGT
*
103921849 CACCACT
1 CACCACA
103921856 CACCACA
1 CACCACA
103921863 CACCACA
1 CACCACA
103921870 CACCACA
1 CACCACA
103921877 CACCACA
1 CACCACA
103921884 CACCACA
1 CACCACA
103921891 CAC
1 CAC
103921894 GTAACCTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.40, C:0.58, G:0.00, T:0.02
Consensus pattern (7 bp):
CACCACA
Found at i:103931225 original size:46 final size:46
Alignment explanation
Indices: 103931158--103931254 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
103931148 GTGCACAAGG
103931158 ATTCTGGAAACCATGCTTTTACTTCCTTGCTTTCATTTTCTGCTGC
1 ATTCTGGAAACCATGCTTTTACTTCCTTGCTTTCATTTTCTGCTGC
*
103931204 ATTCTGGAAACCATTCTTTTACTTCCTTGCTTTCATTTTCTGCTGC
1 ATTCTGGAAACCATGCTTTTACTTCCTTGCTTTCATTTTCTGCTGC
103931250 ATTCT
1 ATTCT
103931255 AGTTGTGTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.15, C:0.26, G:0.11, T:0.47
Consensus pattern (46 bp):
ATTCTGGAAACCATGCTTTTACTTCCTTGCTTTCATTTTCTGCTGC
Found at i:103937230 original size:46 final size:46
Alignment explanation
Indices: 103937139--103937232 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 46
103937129 CTAACTCGAA
*
103937139 TTTAATTGTTTTATTTTTTATTTTGAAGCAAATGGAATTACTTTTT
1 TTTAATTGTTTTATTTTTTATTTTGAAGCAAATAGAATTACTTTTT
*
103937185 TTTAATTGTTTTA-TTTTTATTTTGAAGCAAATA-AGATTATTTTTT
1 TTTAATTGTTTTATTTTTTATTTTGAAGCAAATAGA-ATTACTTTTT
103937230 TTT
1 TTT
103937233 GAGTTTAGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 1 0.02
45 31 0.69
46 13 0.29
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.61
Consensus pattern (46 bp):
TTTAATTGTTTTATTTTTTATTTTGAAGCAAATAGAATTACTTTTT
Found at i:103942882 original size:118 final size:118
Alignment explanation
Indices: 103942674--103942911 Score: 476
Period size: 118 Copynumber: 2.0 Consensus size: 118
103942664 AACCTGGCAC
103942674 GGTGCTTCTTTCCCAGGTGTATTTTTATACTTGTCACTTCTAATATTAATACTATACTTCTACTG
1 GGTGCTTCTTTCCCAGGTGTATTTTTATACTTGTCACTTCTAATATTAATACTATACTTCTACTG
103942739 CTTAATTCAAAAGTATCATGCTTGAATTTGATGCATATCTAATCGACATCTCA
66 CTTAATTCAAAAGTATCATGCTTGAATTTGATGCATATCTAATCGACATCTCA
103942792 GGTGCTTCTTTCCCAGGTGTATTTTTATACTTGTCACTTCTAATATTAATACTATACTTCTACTG
1 GGTGCTTCTTTCCCAGGTGTATTTTTATACTTGTCACTTCTAATATTAATACTATACTTCTACTG
103942857 CTTAATTCAAAAGTATCATGCTTGAATTTGATGCATATCTAATCGACATCTCA
66 CTTAATTCAAAAGTATCATGCTTGAATTTGATGCATATCTAATCGACATCTCA
103942910 GG
1 GG
103942912 AGTTGATCCG
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 120 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (118 bp):
GGTGCTTCTTTCCCAGGTGTATTTTTATACTTGTCACTTCTAATATTAATACTATACTTCTACTG
CTTAATTCAAAAGTATCATGCTTGAATTTGATGCATATCTAATCGACATCTCA
Found at i:103952998 original size:10 final size:10
Alignment explanation
Indices: 103952985--103953028 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
103952975 AGTTTAATTA
103952985 TAATTAAACT
1 TAATTAAACT
103952995 TAATT-AA-T
1 TAATTAAACT
103953003 TAACTTAAACT
1 TAA-TTAAACT
103953014 TAATTAAACCT
1 TAATTAAA-CT
103953025 TAAT
1 TAAT
103953029 AACCAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 4 0.13
9 4 0.13
10 12 0.40
11 10 0.33
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (10 bp):
TAATTAAACT
Found at i:103953012 original size:19 final size:20
Alignment explanation
Indices: 103952978--103953020 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
103952968 TATAGTTAGT
103952978 TTAATTATAATTAAACTTAA
1 TTAATTATAATTAAACTTAA
*
103952998 TTAATTA-ACTTAAACTTAA
1 TTAATTATAATTAAACTTAA
103953017 TTAA
1 TTAA
103953021 ACCTTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTATAATTAAACTTAA
Found at i:103955757 original size:21 final size:21
Alignment explanation
Indices: 103955731--103955771 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
103955721 ATTACATTTT
*
103955731 CAAGTTTTCAATTTCAATTAA
1 CAAGTTTCCAATTTCAATTAA
103955752 CAAGTTTCCAATTTCAATTA
1 CAAGTTTCCAATTTCAATTA
103955772 TAGTGTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (21 bp):
CAAGTTTCCAATTTCAATTAA
Found at i:103965601 original size:25 final size:25
Alignment explanation
Indices: 103965573--103965650 Score: 61
Period size: 25 Copynumber: 3.1 Consensus size: 25
103965563 TTAGCTTAAA
103965573 GTTTATTTTTCTGCATTTACTTCTT
1 GTTTATTTTTCTGCATTTACTTCTT
* * * * ***
103965598 GTTT-TTATTATTC-TTAAAGCTTAAA
1 GTTTATTTTTCTGCATT-TA-CTTCTT
103965623 GTTTATTTTTCTGCATTTACTTCTT
1 GTTTATTTTTCTGCATTTACTTCTT
103965648 GTT
1 GTT
103965651 CTTATTGTTC
Statistics
Matches: 35, Mismatches: 14, Indels: 8
0.61 0.25 0.14
Matches are distributed among these distances:
23 2 0.06
24 7 0.20
25 17 0.49
26 7 0.20
27 2 0.06
ACGTcount: A:0.18, C:0.13, G:0.09, T:0.60
Consensus pattern (25 bp):
GTTTATTTTTCTGCATTTACTTCTT
Found at i:103965626 original size:50 final size:50
Alignment explanation
Indices: 103965565--103965693 Score: 181
Period size: 50 Copynumber: 2.6 Consensus size: 50
103965555 ATTCTACCTT
*
103965565 AGCTTAAAGTTTATTTTTCTGCATTTACTTCTTGTTTTTATTATTCTTAA
1 AGCTTAAAGTTTATTTTTCTGCATTTACTTCTTGTTCTTATTATTCTTAA
* *
103965615 AGCTTAAAGTTTATTTTTCTGCATTTACTTCTTGTTCTTATTGTTCTTAG
1 AGCTTAAAGTTTATTTTTCTGCATTTACTTCTTGTTCTTATTATTCTTAA
* * * *
103965665 TG-TT-AGGCTTATTTTTCTACATTTACTTC
1 AGCTTAAAGTTTATTTTTCTGCATTTACTTC
103965694 ACTGTAGCTT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
48 22 0.31
49 2 0.03
50 48 0.67
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (50 bp):
AGCTTAAAGTTTATTTTTCTGCATTTACTTCTTGTTCTTATTATTCTTAA
Found at i:103972111 original size:87 final size:87
Alignment explanation
Indices: 103971948--103972112 Score: 258
Period size: 87 Copynumber: 1.9 Consensus size: 87
103971938 GCAGAGTTTT
* * *
103971948 AAACAACCTCCTCAAGGACTCCTGGAGAAGCAACAAAGTTTTAAACAATCTGAAAAACAGCAGAG
1 AAACAACCACCTCAACGACTCCTGGAGAAGCAACAAAGTTTTAAACAATCTGAAAAACAACAGAG
* *
103972013 TTTTCGCGGTGTTATGACAGAA
66 TGTCCGCGGTGTTATGACAGAA
* *
103972035 AAACAACCACCTCAACGTCTCCTGGAGAAGCAACAAAGTTTTAAACAATCTGAAAAGCAACAGAG
1 AAACAACCACCTCAACGACTCCTGGAGAAGCAACAAAGTTTTAAACAATCTGAAAAACAACAGAG
*
103972100 TGTCCGTGGTGTT
66 TGTCCGCGGTGTT
103972113 TCAAGTGAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (87 bp):
AAACAACCACCTCAACGACTCCTGGAGAAGCAACAAAGTTTTAAACAATCTGAAAAACAACAGAG
TGTCCGCGGTGTTATGACAGAA
Found at i:103986179 original size:40 final size:40
Alignment explanation
Indices: 103986132--103986210 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
103986122 ATAATTATGT
* * * *
103986132 ATAATTATGTCTGTTTTATTGATATTATTATTTAGAAAAG
1 ATAATTATATCTCTTTTATGGATATTATTATTCAGAAAAG
*
103986172 ATAATTATATTTCTTTTATGGATATTATTATTCAGAAAA
1 ATAATTATATCTCTTTTATGGATATTATTATTCAGAAAA
103986211 ATATATATGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (40 bp):
ATAATTATATCTCTTTTATGGATATTATTATTCAGAAAAG
Found at i:103988769 original size:20 final size:20
Alignment explanation
Indices: 103988744--103988781 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
103988734 GCCACCTACA
103988744 ATGGTATCGCGATACCAATG
1 ATGGTATCGCGATACCAATG
*
103988764 ATGGTATCGCGGTACCAA
1 ATGGTATCGCGATACCAA
103988782 ACCCACAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (20 bp):
ATGGTATCGCGATACCAATG
Found at i:103989883 original size:16 final size:16
Alignment explanation
Indices: 103989862--103989900 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
103989852 ATGAAATAGC
103989862 ATAAAT-AAACAATTAA
1 ATAAATCAAA-AATTAA
103989878 ATAAATCAAAAATTAA
1 ATAAATCAAAAATTAA
103989894 ATTAAAT
1 A-TAAAT
103989901 TGAGAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAATCAAAAATTAA
Found at i:103991003 original size:11 final size:11
Alignment explanation
Indices: 103990981--103991020 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
103990971 GAAAAAATGG
*
103990981 TAAATTGAAAA
1 TAAAGTGAAAA
*
103990992 TAAAGTGTAAA
1 TAAAGTGAAAA
*
103991003 TTAAGTGAAAA
1 TAAAGTGAAAA
103991014 TAAAGTG
1 TAAAGTG
103991021 GTCATCTTCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (11 bp):
TAAAGTGAAAA
Found at i:104004127 original size:31 final size:31
Alignment explanation
Indices: 104004092--104004157 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
104004082 CTTAACAACC
* *
104004092 TAATGACTT-AAATAAAAACTTTTGAATAGTT
1 TAATGA-TTAAAATAAAAACTCTCGAATAGTT
*
104004123 TAATGATTAAAATGAAAACTCTCGAATAGTT
1 TAATGATTAAAATAAAAACTCTCGAATAGTT
104004154 TAAT
1 TAAT
104004158 CACTATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (31 bp):
TAATGATTAAAATAAAAACTCTCGAATAGTT
Found at i:104004755 original size:19 final size:19
Alignment explanation
Indices: 104004731--104004768 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
104004721 TTATATCAAG
104004731 GCACCAAGTTTGAGCCTAT
1 GCACCAAGTTTGAGCCTAT
104004750 GCACCAAGTTTGAGCCTAT
1 GCACCAAGTTTGAGCCTAT
104004769 AAAAACATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (19 bp):
GCACCAAGTTTGAGCCTAT
Found at i:104005061 original size:34 final size:34
Alignment explanation
Indices: 104005014--104005089 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
104005004 AGGGAGATTT
104005014 TTAGCTTGCTAATAGGAGTAGGAAGCTAAGTTTG
1 TTAGCTTGCTAATAGGAGTAGGAAGCTAAGTTTG
* * *
104005048 TTAGCTTGGTAATAGGAGTAGGAAGTTGAGTTTG
1 TTAGCTTGCTAATAGGAGTAGGAAGCTAAGTTTG
104005082 TTAGCTTG
1 TTAGCTTG
104005090 AGTCATGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.26, C:0.07, G:0.32, T:0.36
Consensus pattern (34 bp):
TTAGCTTGCTAATAGGAGTAGGAAGCTAAGTTTG
Found at i:104010167 original size:32 final size:33
Alignment explanation
Indices: 104010131--104010194 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
104010121 TCAATACTTG
* *
104010131 ATTTCATTTTTCAATTCACATTTCAT-TTCATC
1 ATTTCATATTTCAATTCACATATCATGTTCATC
* *
104010163 ATTTCATATTTCATTTCTCATATCATGTTCAT
1 ATTTCATATTTCAATTCACATATCATGTTCAT
104010195 TTCTCATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.25, C:0.20, G:0.02, T:0.53
Consensus pattern (33 bp):
ATTTCATATTTCAATTCACATATCATGTTCATC
Found at i:104010195 original size:18 final size:19
Alignment explanation
Indices: 104010152--104010201 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
104010142 CAATTCACAT
* *
104010152 TTCATTTCATCATTTCATAT
1 TTCATTTC-TCATATCATAG
104010172 TTCATTTCTCATATCAT-G
1 TTCATTTCTCATATCATAG
104010190 TTCATTTCTCAT
1 TTCATTTCTCAT
104010202 TTTTGCCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.43
19 8 0.29
20 8 0.29
ACGTcount: A:0.22, C:0.22, G:0.02, T:0.54
Consensus pattern (19 bp):
TTCATTTCTCATATCATAG
Found at i:104016978 original size:6 final size:6
Alignment explanation
Indices: 104016967--104016993 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
104016957 CAGCCAAAAC
104016967 ATCCAG ATCCAG ATCCAG ATCCAG ATC
1 ATCCAG ATCCAG ATCCAG ATCCAG ATC
104016994 ATCATCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.19
Consensus pattern (6 bp):
ATCCAG
Found at i:104021211 original size:21 final size:21
Alignment explanation
Indices: 104021187--104021233 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
104021177 GGTTCATTAT
104021187 TTTTAGTGC-CCGGTTCAGCTG
1 TTTTAG-GCACCGGTTCAGCTG
*
104021208 TTTT-GGCATCCGGTTCAGCTT
1 TTTTAGGCA-CCGGTTCAGCTG
104021229 TTTTA
1 TTTTA
104021234 AGTGTTTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 1 0.05
21 19 0.86
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (21 bp):
TTTTAGGCACCGGTTCAGCTG
Found at i:104023037 original size:24 final size:24
Alignment explanation
Indices: 104023005--104023056 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
104022995 GTATTGGAGC
104023005 TAAGCACATCATGATAGTAATATT
1 TAAGCACATCATGATAGTAATATT
104023029 TAAGCACATCATGATAGTAATATT
1 TAAGCACATCATGATAGTAATATT
104023053 TAAG
1 TAAG
104023057 AAATGATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (24 bp):
TAAGCACATCATGATAGTAATATT
Found at i:104031848 original size:39 final size:39
Alignment explanation
Indices: 104031794--104031877 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
104031784 CCTACGGCCA
** *
104031794 CCACCATTGTCGTTCACGAGTCAGGCAGTCACCAACGGT
1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCAACGGT
* *
104031833 CCACCATCATCGTTCACCAGTCAGGTAGTCACCATCGGT
1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCAACGGT
104031872 CCACCA
1 CCACCA
104031878 GTCAATCGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.20
Consensus pattern (39 bp):
CCACCATCATCGTTCACCAGTCAGGCAGTCACCAACGGT
Found at i:104035984 original size:21 final size:21
Alignment explanation
Indices: 104035960--104036020 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
104035950 CAAATTCCGT
104035960 TCCGGTTCAGAATTTTTTGTG
1 TCCGGTTCAGAATTTTTTGTG
*
104035981 TCCGGTTC-G-GTTGTTTTGGTG
1 TCCGGTTCAGAATT-TTTT-GTG
* *
104036002 TTCGGTTCAGATTTTTTTG
1 TCCGGTTCAGAATTTTTTG
104036021 CGTATAGACC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 19 0.58
22 5 0.15
23 2 0.06
ACGTcount: A:0.08, C:0.13, G:0.28, T:0.51
Consensus pattern (21 bp):
TCCGGTTCAGAATTTTTTGTG
Found at i:104036083 original size:31 final size:31
Alignment explanation
Indices: 104036048--104036146 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
104036038 TTGTCGCACT
*
104036048 TATCCCGG-GTGGGGATATCCCATTCCAGGGA
1 TATCCCGGCGTGGGCATATCCCATTCC-GGGA
*
104036079 TATCCCGGCTTGGGCATATCCCAAGTT--GGGA
1 TATCCCGGCGTGGGCATATCCC-A-TTCCGGGA
* * *
104036110 TATTCCGGCGTGAGTATATCCCATTCCGGGGA
1 TATCCCGGCGTGGGCATATCCCATTCC-GGGA
104036142 TATCC
1 TATCC
104036147 TGGCATTGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
29 2 0.04
30 1 0.02
31 30 0.55
32 19 0.35
33 1 0.02
34 2 0.04
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (31 bp):
TATCCCGGCGTGGGCATATCCCATTCCGGGA
Found at i:104038252 original size:28 final size:29
Alignment explanation
Indices: 104038217--104038274 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
104038207 TCAACATTTT
104038217 ATAATTTTAATA-ATTTTTAATTTTAAAA
1 ATAATTTTAATAGATTTTTAATTTTAAAA
* *
104038245 ATAATTTTTATAGTTTTTTTAATTTTAAAA
1 ATAATTTTAATAG-ATTTTTAATTTTAAAA
104038275 TTTATGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 11 0.42
30 15 0.58
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (29 bp):
ATAATTTTAATAGATTTTTAATTTTAAAA
Found at i:104041601 original size:229 final size:228
Alignment explanation
Indices: 104041118--104041641 Score: 714
Period size: 229 Copynumber: 2.3 Consensus size: 228
104041108 TAGCAGAATA
*
104041118 ATTTTTGTAATATCCGCTGAGCAGAATACTTTTCCTCTCTGTTTTTAGTTGATATATTCTTCTTT
1 ATTTTTGTAAT-TTCGCTGAGCAGAATACTTTTCCTCTCTGTTTTTAGTTGATATATTCTTCTTT
* **
104041183 TCTTGTTTTTGCTTAGCAGAGTAATTTTGGGGTTTGGTGTTTTTGAGCCTGAATCACGATTAGAT
65 TCTTGTTTTTGCTTAGCAGAATAATTTTGGGGTTTGGTGTTTTTGAGCCCAAATCACGATTAGAT
* *
104041248 TTTGGCTTTCATTTATATTTTTGTCATTATAGTTACTTTTCCAATTAACATGACACTAGTTCTAT
130 TTCGGCTTTCATTTATATTTTTGTCATTATAGTTACTTTTCCAAATAACATGACACTAGTTCTAT
*
104041313 TGCTCCCAACACTGAAGAAAATATCTATATTAAC
195 TGCTCCCAACACTCAAGAAAATATCTATATTAAC
* * *
104041347 ATTTTTTTAATATTCGCTGAGCAGAATAATTTTCCTCTCTGTTTTTAGTTAATATATTCTTCTTT
1 ATTTTTGTAAT-TTCGCTGAGCAGAATACTTTTCCTCTCTGTTTTTAGTTGATATATTCTTCTTT
* * * * *
104041412 TCTTGTTTTTGCTTAGTAGAATAATTTTGTGGTTTGGTTTTTTTGGGCCCAAATCACGCTTAGAT
65 TCTTGTTTTTGCTTAGCAGAATAATTTTGGGGTTTGGTGTTTTTGAGCCCAAATCACGATTAGAT
* *
104041477 TTCGGCTTATCATTTATATTTTTGTCATTATAGTT-CATTTTCCAAATAACTTTACACTAGTTCC
130 TTCGGCTT-TCATTTATATTTTTGTCATTATAGTTAC-TTTTCCAAATAACATGACACTAGTT-C
* * * * * *
104041541 T-TTGCTCTCAGA-ACTCAGGATAGTATCTTTA-TAAT
192 TATTGCTCCCA-ACACTCAAGAAAATATCTATATTAAC
* * * *
104041576 ATTTTTGTAATTTCTGCTTAGCAGAATACTATTCCTCTCTGTTTTTAGTTGACATATGCTTCTTT
1 ATTTTTGTAATTTC-GCTGAGCAGAATACTTTTCCTCTCTGTTTTTAGTTGATATATTCTTCTTT
104041641 T
65 T
104041642 TGCTAATATG
Statistics
Matches: 260, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
228 3 0.01
229 184 0.71
230 70 0.27
231 3 0.01
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.48
Consensus pattern (228 bp):
ATTTTTGTAATTTCGCTGAGCAGAATACTTTTCCTCTCTGTTTTTAGTTGATATATTCTTCTTTT
CTTGTTTTTGCTTAGCAGAATAATTTTGGGGTTTGGTGTTTTTGAGCCCAAATCACGATTAGATT
TCGGCTTTCATTTATATTTTTGTCATTATAGTTACTTTTCCAAATAACATGACACTAGTTCTATT
GCTCCCAACACTCAAGAAAATATCTATATTAAC
Found at i:104044077 original size:40 final size:40
Alignment explanation
Indices: 104044022--104044105 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
104044012 TTACTGCATC
*
104044022 TGTGTTGGCTTGATTTTGGTTCTAGGAACCTGGTGGGAGT
1 TGTGTTGGCTTGATTTTGGTTCTAGGAACCCGGTGGGAGT
*
104044062 TGTGTTGGCTTGATTTTGGTTCTAGGCACCCGGTGGGAGT
1 TGTGTTGGCTTGATTTTGGTTCTAGGAACCCGGTGGGAGT
104044102 TGTG
1 TGTG
104044106 ACGCACGTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.11, C:0.12, G:0.38, T:0.39
Consensus pattern (40 bp):
TGTGTTGGCTTGATTTTGGTTCTAGGAACCCGGTGGGAGT
Found at i:104044212 original size:12 final size:12
Alignment explanation
Indices: 104044195--104044219 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
104044185 GTTTCTTAGT
104044195 TTTCTCAAAAAG
1 TTTCTCAAAAAG
104044207 TTTCTCAAAAAG
1 TTTCTCAAAAAG
104044219 T
1 T
104044220 CTATACTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TTTCTCAAAAAG
Found at i:104047078 original size:14 final size:14
Alignment explanation
Indices: 104047061--104047094 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
104047051 ATAGCAATTA
**
104047061 TAATATTATTTAAT
1 TAATATTATACAAT
104047075 TAATATTATACAAT
1 TAATATTATACAAT
104047089 TAATAT
1 TAATAT
104047095 AAAATGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATTATACAAT
Found at i:104049687 original size:1 final size:1
Alignment explanation
Indices: 104049681--104049705 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
104049671 TAGAAGATCA
104049681 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
104049706 GTTTCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:104049751 original size:1 final size:1
Alignment explanation
Indices: 104049745--104049769 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
104049735 TTTATTTGAG
104049745 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
104049770 ATTTCTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.