Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015897.1 Corchorus olitorius cultivar O-4 contig15930, 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: 62900
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:46 original size:18 final size:18
Alignment explanation
Indices: 19--66 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
9 TAAAAAACCG
* *
19 AAAATAATTTTTTTGAAAA
1 AAAAT-ATTTTTCTCAAAA
38 AAAATA-TTTTCTCAAAA
1 AAAATATTTTTCTCAAAA
55 AAACATATTTTT
1 AAA-ATATTTTT
67 AAAATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 12 0.48
18 4 0.16
19 9 0.36
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (18 bp):
AAAATATTTTTCTCAAAA
Found at i:1759 original size:558 final size:555
Alignment explanation
Indices: 708--1821 Score: 1870
Period size: 558 Copynumber: 2.0 Consensus size: 555
698 CTAATATATA
*
708 TACTAAATAGTAGTTGAAAGACCCAGGAAATTTACCAAAGGCCCCTTTTGAGGATCGATGAGGAG
1 TACTAAATAGTAGTTGAAAGACCCAGGAAATTTACCAAAGGCCCCTTTTCAGGATCGATGAGGAG
* * *
773 GTTCCATTTGAACTTTTTTTATCCTTTTCTGTCTTTTCTCACTTGCCAAATTACTAAGAATACCC
66 GCTCCATTTGAACTTTTTTTATCATTTTCTGTCTTTTCTCACTTGCCAAATTACTAAGAAGACCC
* *
838 TAGGTTAGTTTCTAGCCAGTTTTTGCCCTTGAGCCCTTTTTTTAATTATCCTTTCCTTTCACATA
131 TAGGTTAGTTTCTAGCCAGTTCTTGCCCTTGAGCCCTTTTTTTAATTATCATTTCCTTTCACATA
* * * * * *
903 GATGTTATAATAAATCTTATCCCCCTTAATTATCTATAATTGTAACTTCTCTCCAGGCCTTTCAT
196 AATATTACAATAAATCCTATCCCCCTTAATTATCTAGAATTGTAACATCTCTCCAGGCCTTTCAT
*
968 GTCCATATGAAGAAAAGAGTAAACTTAGTTTTTGTTTAAATGCTACACACTTTAGAGGAGGAAAT
261 GTCCATATGAAGAAAAGAGTAAACTTAGTTTTTGTTTAAATGCTACACACTTTAGAGGAGGAAAC
*
1033 AAAATTGAAGCTATTGCACCTGTCCATGTACAAACTAATATTTACTATTTAATGCTAACTTTAGG
326 AAAATTGAAGCTATTGCACCTATCCATGTACAAACTAATATTTACTATTTAATGCTAACTTTAGG
*
1098 GCATATGCTCAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTCAAATCATAGTACTTT
391 GCATATGCTCAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAGTACTTT
*
1163 CGAAATTTCCTACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAAAGAAATAGATTGCTA
456 CAAAATTTCCTACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAAAGAAATAGATTGCTA
* * *
1228 AATGCCCGACGCGCCAGCGCGGGCCGATCTACTTG
521 AACGCCCGACGCGCCAGCGCGGACCGATATACTTG
* *
1263 TACTAAATAGTATTTGAAAGACCCAGGGAATTTACCAAAGGCCCCTTTTCAGGATCGATGAGGAG
1 TACTAAATAGTAGTTGAAAGACCCAGGAAATTTACCAAAGGCCCCTTTTCAGGATCGATGAGGAG
*
1328 GCTCCATTTGAACTTTTTTTTGTCATTTTCTGTCTTTTCTCACTTGCCAAATTACTAAGAAGACC
66 GCTCCATTTGAAC-TTTTTTTATCATTTTCTGTCTTTTCTCACTTGCCAAATTACTAAGAAGACC
*
1393 CTAGGTTAGTTTCTAGTCAGTTCTTGCCCTTGAGCCCTTTTTTGTAATTATCATTTCCCTTTCAC
130 CTAGGTTAGTTTCTAGCCAGTTCTTGCCCTTGAGCCCTTTTTT-TAATTATCATTT-CCTTTCAC
* **
1458 ATAAATATTACAATAAATCCTATCCCTCTTAATTATCTAGAATTGTAACATCTCTTTAGGCCTTT
193 ATAAATATTACAATAAATCCTATCCCCCTTAATTATCTAGAATTGTAACATCTCTCCAGGCCTTT
*
1523 CATGTCCATATGAAGAAGAA-AGTAAACTTAGTTTTTGTTTAAGTGCTACACACTTTAGAGGAGG
258 CATGTCCATATGAAGAA-AAGAGTAAACTTAGTTTTTGTTTAAATGCTACACACTTTAGAGGAGG
* *
1587 AAACAAAATTGAAGCTATTGCACCTATCCATGTACAGACTAATATTTACTATTTATTGCTAACTT
322 AAACAAAATTGAAGCTATTGCACCTATCCATGTACAAACTAATATTTACTATTTAATGCTAACTT
*
1652 TAGGGCATATGCTTAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAGTA
387 TAGGGCATATGCTCAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAGTA
* *
1717 CTTTCAAAATTTCCTACGTATCAAAGAATTTAATTCGAATAGAAAATTGTTCAAAGAAGTAGATT
452 CTTTCAAAATTTCCTACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAAAGAAATAGATT
* * *
1782 GTTGAACGTCCGACGCGCCAGCGCGGACCGATATACTTG
517 GCTAAACGCCCGACGCGCCAGCGCGGACCGATATACTTG
1821 T
1 T
1822 TATTATTATT
Statistics
Matches: 520, Mismatches: 35, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
555 74 0.14
556 89 0.17
557 11 0.02
558 344 0.66
559 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (555 bp):
TACTAAATAGTAGTTGAAAGACCCAGGAAATTTACCAAAGGCCCCTTTTCAGGATCGATGAGGAG
GCTCCATTTGAACTTTTTTTATCATTTTCTGTCTTTTCTCACTTGCCAAATTACTAAGAAGACCC
TAGGTTAGTTTCTAGCCAGTTCTTGCCCTTGAGCCCTTTTTTTAATTATCATTTCCTTTCACATA
AATATTACAATAAATCCTATCCCCCTTAATTATCTAGAATTGTAACATCTCTCCAGGCCTTTCAT
GTCCATATGAAGAAAAGAGTAAACTTAGTTTTTGTTTAAATGCTACACACTTTAGAGGAGGAAAC
AAAATTGAAGCTATTGCACCTATCCATGTACAAACTAATATTTACTATTTAATGCTAACTTTAGG
GCATATGCTCAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAGTACTTT
CAAAATTTCCTACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAAAGAAATAGATTGCTA
AACGCCCGACGCGCCAGCGCGGACCGATATACTTG
Found at i:3718 original size:25 final size:25
Alignment explanation
Indices: 3690--3741 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
3680 AATGAGTTTT
* *
3690 TTTTTCTTTAATTAATTTAATGGTA
1 TTTTTCTTCAATGAATTTAATGGTA
3715 TTTTTCTTCAATGAATTTAATGGTA
1 TTTTTCTTCAATGAATTTAATGGTA
3740 TT
1 TT
3742 ATGATGGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.58
Consensus pattern (25 bp):
TTTTTCTTCAATGAATTTAATGGTA
Found at i:4780 original size:2 final size:2
Alignment explanation
Indices: 4773--4807 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4763 AGTATAAATT
4773 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4808 GCGTCTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9995 original size:25 final size:27
Alignment explanation
Indices: 9958--10010 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
9948 ATTTATTTTT
*
9958 TTTAAAAAAATT-ATTTA-AATAAAAA
1 TTTAAAAAAATTAATTTAGAAAAAAAA
* *
9983 TTTATAAACATTAATTTAGAAAAAAAA
1 TTTAAAAAAATTAATTTAGAAAAAAAA
10010 T
1 T
10011 ATACTTAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 10 0.43
26 5 0.22
27 8 0.35
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
TTTAAAAAAATTAATTTAGAAAAAAAA
Found at i:12022 original size:21 final size:20
Alignment explanation
Indices: 11985--12023 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
11975 TATTTTCTTT
* *
11985 TTTAAGTTTAAATAATTAAA
1 TTTAAATTTAAAAAATTAAA
12005 TTTAAATTATAAAAAATTA
1 TTTAAATT-TAAAAAATTA
12024 TCATTAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
TTTAAATTTAAAAAATTAAA
Found at i:12850 original size:26 final size:26
Alignment explanation
Indices: 12795--12851 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
12785 GTCTACCCAT
12795 ATTT-AATTTTTTAAAAAAAAGAATA
1 ATTTAAATTTTTTAAAAAAAAGAATA
*
12820 A-TTAAATTTTTTAATAAAAAATAA-A
1 ATTTAAATTTTTTAA-AAAAAAGAATA
12845 ATTTAAA
1 ATTTAAA
12852 CATTAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 2 0.07
25 13 0.46
26 13 0.46
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
ATTTAAATTTTTTAAAAAAAAGAATA
Found at i:13021 original size:16 final size:18
Alignment explanation
Indices: 12991--13026 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
12981 TATAAATATA
12991 ATTATTTTATTATATAAT
1 ATTATTTTATTATATAAT
13009 ATTA-TTTA-TATATAAT
1 ATTATTTTATTATATAAT
13025 AT
1 AT
13027 GGTCCGGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 4 0.22
18 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTATTTTATTATATAAT
Found at i:14867 original size:48 final size:49
Alignment explanation
Indices: 14792--14911 Score: 145
Period size: 48 Copynumber: 2.4 Consensus size: 49
14782 AAATCACACA
* *
14792 GCCACATAGTGGTCGTGAGATTTGACCACATGGAGGTCGTGAGA-AACG
1 GCCACATGGTGGTCGTGAGATTTGACCACATGGAGGTCATGAGATAACG
* **
14840 GCCACATGGTGGTCGTGAG-TTTCGACCACATGGTGGTCATGAGATTCGGTCG
1 GCCACATGGTGGTCGTGAGATTT-GACCACATGGAGGTCATGAGA-T--AACG
14892 GCCACATGGTGGTCGTGAGA
1 GCCACATGGTGGTCGTGAGA
14912 AAAGACCAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
47 3 0.05
48 37 0.61
52 21 0.34
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.23
Consensus pattern (49 bp):
GCCACATGGTGGTCGTGAGATTTGACCACATGGAGGTCATGAGATAACG
Found at i:14897 original size:28 final size:25
Alignment explanation
Indices: 14792--14911 Score: 129
Period size: 24 Copynumber: 4.8 Consensus size: 25
14782 AAATCACACA
*
14792 GCCACATAGTGGTCGTGAGATTT-G
1 GCCACATGGTGGTCGTGAGATTTCG
* * **
14816 ACCACATGGAGGTCGTGAGA-AACG
1 GCCACATGGTGGTCGTGAGATTTCG
14840 GCCACATGGTGGTCGTGAG-TTTCG
1 GCCACATGGTGGTCGTGAGATTTCG
* *
14864 ACCACATGGTGGTCATGAGATTCGGTCG
1 GCCACATGGTGGTCGTGAGATT---TCG
14892 GCCACATGGTGGTCGTGAGA
1 GCCACATGGTGGTCGTGAGA
14912 AAAGACCAAT
Statistics
Matches: 77, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
24 54 0.70
25 2 0.03
28 21 0.27
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.23
Consensus pattern (25 bp):
GCCACATGGTGGTCGTGAGATTTCG
Found at i:19151 original size:48 final size:48
Alignment explanation
Indices: 19051--19197 Score: 168
Period size: 48 Copynumber: 3.1 Consensus size: 48
19041 AATCACACGG
* * ** *
19051 CCACATAGTGGTCGTGAAATTTGACCACATGGAGGTCATGAGAAACGG
1 CCACATAGTGGTCGTGAGATTTGACCACATGGTGGTTGTGAGAAACGA
* ***
19099 CCACATAGTGGTCGTGAGATTTGACCACAAGGTGGTTGTGAGTTTCGA
1 CCACATAGTGGTCGTGAGATTTGACCACATGGTGGTTGTGAGAAACGA
* * * * *
19147 CCACATGGTGGTCATGAGATTCGGCCACATGGTGGTTGTGAGAAAAGA
1 CCACATAGTGGTCGTGAGATTTGACCACATGGTGGTTGTGAGAAACGA
19195 CCA
1 CCA
19198 ATGCTACACC
Statistics
Matches: 81, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 81 1.00
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (48 bp):
CCACATAGTGGTCGTGAGATTTGACCACATGGTGGTTGTGAGAAACGA
Found at i:19188 original size:24 final size:24
Alignment explanation
Indices: 19051--19189 Score: 134
Period size: 24 Copynumber: 5.8 Consensus size: 24
19041 AATCACACGG
* * *
19051 CCACATAGTGGTCGTGAAATTTGA
1 CCACATGGTGGTCGTGAGATTCGA
* * ** *
19075 CCACATGGAGGTCATGAGAAACGG
1 CCACATGGTGGTCGTGAGATTCGA
* *
19099 CCACATAGTGGTCGTGAGATTTGA
1 CCACATGGTGGTCGTGAGATTCGA
* * *
19123 CCACAAGGTGGTTGTGAGTTTCGA
1 CCACATGGTGGTCGTGAGATTCGA
* *
19147 CCACATGGTGGTCATGAGATTCGG
1 CCACATGGTGGTCGTGAGATTCGA
*
19171 CCACATGGTGGTTGTGAGA
1 CCACATGGTGGTCGTGAGA
19190 AAAGACCAAT
Statistics
Matches: 88, Mismatches: 27, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 88 1.00
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (24 bp):
CCACATGGTGGTCGTGAGATTCGA
Found at i:22162 original size:16 final size:17
Alignment explanation
Indices: 22141--22172 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22131 ACTAGAGAAA
22141 CAAAAA-TTTTGAAAAG
1 CAAAAATTTTTGAAAAG
22157 CAAAAATTTTTGAAAA
1 CAAAAATTTTTGAAAA
22173 ATTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.28
Consensus pattern (17 bp):
CAAAAATTTTTGAAAAG
Found at i:26956 original size:22 final size:22
Alignment explanation
Indices: 26931--27055 Score: 105
Period size: 22 Copynumber: 5.7 Consensus size: 22
26921 TTAAGAAAGT
* *
26931 TTATTAAAATTTCATAGTTAGG
1 TTATCAAAATTTCATAGTTAGA
* * * *
26953 TTATCAAAGTTTCTTA-TGGAGT
1 TTATCAAAATTTCATAGT-TAGA
* *
26975 TTATCACAATTTTATAGTTA-A
1 TTATCAAAATTTCATAGTTAGA
*
26996 TTATCAAAATTTCATACGGT-GA
1 TTATCAAAATTTCATA-GTTAGA
*
27018 TTATCAAAATTTGATAGGTTAG-
1 TTATCAAAATTTCATA-GTTAGA
27040 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
27056 AAAATATTCA
Statistics
Matches: 80, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
21 15 0.19
22 63 0.79
23 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTTAGA
Found at i:26986 original size:44 final size:43
Alignment explanation
Indices: 26928--27055 Score: 148
Period size: 44 Copynumber: 2.9 Consensus size: 43
26918 TTCTTAAGAA
* * * *
26928 AGTTTATTAAAATTTCATAGTTAGGTTATCAAAGTTTCTTATGG
1 AGTTTATCAAAATTTCATAGTTA-GTTATCAAAATTTCATACGG
* * *
26972 AGTTTATCACAATTTTATAGTTAATTATCAAAATTTCATACGG
1 AGTTTATCAAAATTTCATAGTTAGTTATCAAAATTTCATACGG
* * *
27015 TGATTATCAAAATTTGATAGGTTAGTTATCAAAATTTCATA
1 AGTTTATCAAAATTTCATA-GTTAGTTATCAAAATTTCATA
27056 AAAATATTCA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 31 0.44
44 40 0.56
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (43 bp):
AGTTTATCAAAATTTCATAGTTAGTTATCAAAATTTCATACGG
Found at i:27121 original size:2 final size:2
Alignment explanation
Indices: 27114--27145 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
27104 CTAAAACTAG
27114 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27146 TAGGATATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:27134 original size:15 final size:15
Alignment explanation
Indices: 27114--27143 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27104 CTAAAACTAG
27114 TATATATATATATAT
1 TATATATATATATAT
27129 TATATATATATATAT
1 TATATATATATATAT
27144 ATTAGGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:27136 original size:17 final size:17
Alignment explanation
Indices: 27114--27147 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27104 CTAAAACTAG
27114 TATATATATATATATTA
1 TATATATATATATATTA
27131 TATATATATATATATTA
1 TATATATATATATATTA
27148 GGATATCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATTA
Found at i:38906 original size:23 final size:23
Alignment explanation
Indices: 38880--38925 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
38870 ATTGCTTAAT
* *
38880 CTCAATAATGGTAGAGGCATGAC
1 CTCAACAATAGTAGAGGCATGAC
38903 CTCAACAATAGTAGAGGCATGAC
1 CTCAACAATAGTAGAGGCATGAC
38926 AACTTTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (23 bp):
CTCAACAATAGTAGAGGCATGAC
Found at i:51137 original size:21 final size:21
Alignment explanation
Indices: 51111--51173 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
51101 GGGGCTACAG
*
51111 AAGAGACAGATACAGAAATGA
1 AAGAGAAAGATACAGAAATGA
* * *
51132 AAGAGATAGATTCAAAAATGA
1 AAGAGAAAGATACAGAAATGA
*
51153 CAGAGAAAGATACAGAAATGA
1 AAGAGAAAGATACAGAAATGA
51174 TGATTACAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.57, C:0.08, G:0.22, T:0.13
Consensus pattern (21 bp):
AAGAGAAAGATACAGAAATGA
Found at i:52768 original size:19 final size:18
Alignment explanation
Indices: 52735--52770 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
52725 TTGAGATAAT
52735 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
52753 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
52771 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:58541 original size:27 final size:28
Alignment explanation
Indices: 58494--58548 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
58484 GGAAGAAAAT
58494 GAAGAAGATAAGAAATCTGAGG-AAGAA
1 GAAGAAGATAAGAAATCTGAGGCAAGAA
*
58521 GAAGTAGATGAAGAAAT-TGAGGCAAGAA
1 GAAGAAGAT-AAGAAATCTGAGGCAAGAA
58549 CAGATGGCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.53, C:0.04, G:0.31, T:0.13
Consensus pattern (28 bp):
GAAGAAGATAAGAAATCTGAGGCAAGAA
Found at i:59846 original size:3 final size:3
Alignment explanation
Indices: 59838--59902 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
59828 AATTTTTATA
59838 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
59886 AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT
59903 GCTTTAAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:60128 original size:34 final size:28
Alignment explanation
Indices: 60058--60112 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
60048 CACGAATAGG
60058 CATGAACATGAATATTTCTACGAAATTA
1 CATGAACATGAATATTTCTACGAAATTA
*
60086 CATTAACATGAATATTTCTACGAAATT
1 CATGAACATGAATATTTCTACGAAATT
60113 GCTAAGGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.35
Consensus pattern (28 bp):
CATGAACATGAATATTTCTACGAAATTA
Found at i:62867 original size:2 final size:2
Alignment explanation
Indices: 62860--62900 Score: 64
Period size: 2 Copynumber: 19.5 Consensus size: 2
62850 TTTATTCTAC
62860 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT A
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 33 0.89
3 4 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Done.