Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014870.1 Corchorus capsularis cultivar CVL-1 contig14891, 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: 85372
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1783 original size:29 final size:31
Alignment explanation
Indices: 1751--1816 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1741 AGTTTATGGA
1751 GCAAAACGTCCAAAA-T-TA-AAGTGTAGGGG
1 GCAAAACGT-CAAAATTGTACAAGTGTAGGGG
*
1780 GCAAAACGTCAAAATTGTACAAGTTTAGGGG
1 GCAAAACGTCAAAATTGTACAAGTGTAGGGG
1811 GCAAAA
1 GCAAAA
1817 AGGGCATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 5 0.15
29 10 0.30
30 2 0.06
31 16 0.48
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.18
Consensus pattern (31 bp):
GCAAAACGTCAAAATTGTACAAGTGTAGGGG
Found at i:1812 original size:31 final size:30
Alignment explanation
Indices: 1733--1816 Score: 100
Period size: 29 Copynumber: 2.8 Consensus size: 30
1723 AAATGGTTTC
* * *
1733 AAATTGCAAGTTTATGGAGCAAAACGTCCA
1 AAATTACAAGTTTAGGGGGCAAAACGTCCA
*
1763 AAATTA-AAGTGTAGGGGGCAAAACGT-CA
1 AAATTACAAGTTTAGGGGGCAAAACGTCCA
1791 AAATTGTACAAGTTTAGGGGGCAAAA
1 AAA-T-TACAAGTTTAGGGGGCAAAA
1817 AGGGCATTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.11
29 18 0.39
30 7 0.15
31 16 0.35
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (30 bp):
AAATTACAAGTTTAGGGGGCAAAACGTCCA
Found at i:8109 original size:31 final size:31
Alignment explanation
Indices: 8049--8143 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 31
8039 TCGTGCCATA
* * *
8049 TGTACAAAAAAGTGACACAT-ATCACGCCACG
1 TGTACCAAAAAGTGACACGTGA-CATGCCACG
* *
8080 TGTACCAAAAAGTGACACGTGGCATGCCACA
1 TGTACCAAAAAGTGACACGTGACATGCCACG
* ** * *
8111 CGTTTCAAAAAATGGCACGTGACATGCCACG
1 TGTACCAAAAAGTGACACGTGACATGCCACG
8142 TG
1 TG
8144 CACAAAAGGA
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (31 bp):
TGTACCAAAAAGTGACACGTGACATGCCACG
Found at i:22361 original size:10 final size:10
Alignment explanation
Indices: 22348--22381 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
22338 ACGTTTTTTC
22348 TTTTTTTCCTT
1 TTTTTTTCC-T
22359 TTTTTTTCCT
1 TTTTTTTCCT
*
22369 TTTTTTTTCT
1 TTTTTTTCCT
22379 TTT
1 TTT
22382 CAAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTCCT
Found at i:22365 original size:12 final size:11
Alignment explanation
Indices: 22348--22381 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
22338 ACGTTTTTTC
22348 TTTTTTTCCTT
1 TTTTTTTCCTT
22359 TTTTTTTCCTT
1 TTTTTTTCCTT
22370 TTTTTTT-CTT
1 TTTTTTTCCTT
22380 TT
1 TT
22382 CAAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTCCTT
Found at i:33887 original size:169 final size:169
Alignment explanation
Indices: 33608--33942 Score: 643
Period size: 169 Copynumber: 2.0 Consensus size: 169
33598 AGGTCACATC
*
33608 AAGATTCAAACTTAGCTTTCATGATCAAAGCAACCATGTCTCCTTCTCAAACTGATCATGGCTTC
1 AAGATTCAAACTTAGCTTTCATGATCAAAGCAACCATGTCTCCTTCTCAAACTGATCATGCCTTC
* *
33673 TTCTTCTGCATCTCCTTTCTACCTCTCTATGGATACTTTCTTATAGAAAAGTTAAGTTTTTTCAC
66 TTCTTCCGCATCTCCTTTCTACCTCTCTATAGATACTTTCTTATAGAAAAGTTAAGTTTTTTCAC
33738 CATTTGAAGTATTCAATTTGCAATCAAAAGTAGCAAAAG
131 CATTTGAAGTATTCAATTTGCAATCAAAAGTAGCAAAAG
33777 AAGATTCAAACTTAGCTTTCATGATCAAAGCAACCATGTCTCCTTCTCAAACTGATCATGCCTTC
1 AAGATTCAAACTTAGCTTTCATGATCAAAGCAACCATGTCTCCTTCTCAAACTGATCATGCCTTC
33842 TTCTTCCGCATCTCCTTTCTACCTCTCTATAGATACTTTCTTATAGAAAAGTTAAGTTTTTTCAC
66 TTCTTCCGCATCTCCTTTCTACCTCTCTATAGATACTTTCTTATAGAAAAGTTAAGTTTTTTCAC
33907 CATTTGAAGTATTCAATTTGCAATCAAAAGTAGCAA
131 CATTTGAAGTATTCAATTTGCAATCAAAAGTAGCAA
33943 GAAAACAGAG
Statistics
Matches: 163, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
169 163 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (169 bp):
AAGATTCAAACTTAGCTTTCATGATCAAAGCAACCATGTCTCCTTCTCAAACTGATCATGCCTTC
TTCTTCCGCATCTCCTTTCTACCTCTCTATAGATACTTTCTTATAGAAAAGTTAAGTTTTTTCAC
CATTTGAAGTATTCAATTTGCAATCAAAAGTAGCAAAAG
Found at i:34147 original size:2 final size:2
Alignment explanation
Indices: 34142--34176 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
34132 AAAGTACACT
34142 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
34177 TGTCGGTCAG
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:35679 original size:18 final size:18
Alignment explanation
Indices: 35656--35693 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
35646 TATTATATAC
35656 AATTTATA-ATGAAGAAAA
1 AATTTATATATGAA-AAAA
35674 AATTTATATATGAAAAAA
1 AATTTATATATGAAAAAA
35692 AA
1 AA
35694 AAGATGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (18 bp):
AATTTATATATGAAAAAA
Found at i:35692 original size:19 final size:18
Alignment explanation
Indices: 35656--35694 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
35646 TATTATATAC
*
35656 AATTTATAATGAAGAAAA
1 AATTTATAATGAAAAAAA
35674 AATTTATATATGAAAAAAA
1 AATTTATA-ATGAAAAAAA
35693 AA
1 AA
35695 AGATGCTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (18 bp):
AATTTATAATGAAAAAAA
Found at i:40822 original size:108 final size:110
Alignment explanation
Indices: 40690--40906 Score: 332
Period size: 109 Copynumber: 2.0 Consensus size: 110
40680 TATTATAATT
* *
40690 TAAGCAATGTTATTCAATAAAATCTAGCTTTATACA-CAAATATAATCCTATCGTACGCATAAT-
1 TAAGCAATGTTATTCAATAAAATCTAGCTTTATACATAAAATATAATCCTATCGTACACATAATC
* * *
40753 CTATGCACCAAACACGCCC-TTATTGTTATTAGATATGATGGTATC
66 CT-TGCACCAAACACACCCTTTATTGTTATCAGATATAATGGTATC
* *
40798 TAAGCGATGTTATTCAATAAAATCTAGCTTTATACATAAAATATAATCCTATTGTACACATAATC
1 TAAGCAATGTTATTCAATAAAATCTAGCTTTATACATAAAATATAATCCTATCGTACACATAATC
*
40863 CTTGCACCAAACATACCCTTTATTGTTATCAGATATAATGGTAT
66 CTTGCACCAAACACACCCTTTATTGTTATCAGATATAATGGTAT
40907 ACAAATGGCA
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
108 35 0.36
109 38 0.39
110 25 0.26
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (110 bp):
TAAGCAATGTTATTCAATAAAATCTAGCTTTATACATAAAATATAATCCTATCGTACACATAATC
CTTGCACCAAACACACCCTTTATTGTTATCAGATATAATGGTATC
Found at i:44678 original size:21 final size:21
Alignment explanation
Indices: 44612--44678 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
44602 ATAGTGGTGT
44612 TTAGATACTGTACAGATGAGA
1 TTAGATACTGTACAGATGAGA
* * * * *
44633 TTATGCTAGTGTAAAGATCAAA
1 TTA-GATACTGTACAGATGAGA
*
44655 TTAGGTACTGTACAGATGAGA
1 TTAGATACTGTACAGATGAGA
44676 TTA
1 TTA
44679 TTAGAACAGC
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.31
Consensus pattern (21 bp):
TTAGATACTGTACAGATGAGA
Found at i:46475 original size:16 final size:15
Alignment explanation
Indices: 46452--46488 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
46442 TCCTTCCATA
46452 CTTTTCTTTACTTTT
1 CTTTTCTTTACTTTT
*
46467 CTGTTTCTTTTCTTTT
1 CT-TTTCTTTACTTTT
46483 CTTTTC
1 CTTTTC
46489 ATTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.73
Consensus pattern (15 bp):
CTTTTCTTTACTTTT
Found at i:46493 original size:6 final size:5
Alignment explanation
Indices: 46452--46497 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
46442 TCCTTCCATA
*
46452 CTTTT CTTTA CTTTT CTGTTT CTTTT CTTTT CTTTT CATTTT -TTTT
1 CTTTT CTTTT CTTTT CT-TTT CTTTT CTTTT CTTTT C-TTTT CTTTT
46498 TTATCATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.11
5 24 0.65
6 9 0.24
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.76
Consensus pattern (5 bp):
CTTTT
Found at i:59603 original size:28 final size:26
Alignment explanation
Indices: 59512--59591 Score: 106
Period size: 26 Copynumber: 3.0 Consensus size: 26
59502 TTTTTTGGGT
* *
59512 ACAAAAAAATACTACTCTGTTTCATGTA
1 ACAAAAAAA-ACT-CTGTTTTTCATGTA
* *
59540 ACAAAAAACACTCTGTTTTCCATGTA
1 ACAAAAAAAACTCTGTTTTTCATGTA
59566 ACAAAAAAAACTCTGTTTTTCATGTA
1 ACAAAAAAAACTCTGTTTTTCATGTA
59592 TAAAAATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 35 0.76
27 3 0.07
28 8 0.17
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (26 bp):
ACAAAAAAAACTCTGTTTTTCATGTA
Found at i:68074 original size:102 final size:102
Alignment explanation
Indices: 67904--68164 Score: 405
Period size: 102 Copynumber: 2.6 Consensus size: 102
67894 GCTCATAAAC
* *
67904 TGGTGGTTTCTTTGGAGGTTCATAGACTGGTGGCTTGGGTTTTGGCTCCTCTTTCTTTGGAGGTG
1 TGGTGGTTTCTTTGGAGGTTCATAGACTGGTGGTTTGGGTTTTGGCTCCTCTTTCTTTGGAGGAG
67969 TATAAACTGGTGGCTTGGGTGGCTTAGGTTCATAAGT
66 TATAAACTGGTGGCTTGGGTGGCTTAGGTTCATAAGT
* *
68006 TGGTGGTTTCTTTGGAGGTTCATAGACAGGTGGTTTGGGTTTTGGCTCTTCTTTCTTTGGAGGAG
1 TGGTGGTTTCTTTGGAGGTTCATAGACTGGTGGTTTGGGTTTTGGCTCCTCTTTCTTTGGAGGAG
* * *
68071 TATAAACTGGTGGCTTTGGTGGCTTAGGTTCGTATGT
66 TATAAACTGGTGGCTTGGGTGGCTTAGGTTCATAAGT
* * * * * *
68108 TGGTGGTTTCTTTGGTGTTTCATAAACTGGTGGTTTGGGCTTTGGCTTCTCCTTCTT
1 TGGTGGTTTCTTTGGAGGTTCATAGACTGGTGGTTTGGGTTTTGGCTCCTCTTTCTT
68165 CGGGGGCTCG
Statistics
Matches: 144, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 144 1.00
ACGTcount: A:0.11, C:0.13, G:0.33, T:0.43
Consensus pattern (102 bp):
TGGTGGTTTCTTTGGAGGTTCATAGACTGGTGGTTTGGGTTTTGGCTCCTCTTTCTTTGGAGGAG
TATAAACTGGTGGCTTGGGTGGCTTAGGTTCATAAGT
Found at i:68536 original size:45 final size:45
Alignment explanation
Indices: 68115--68533 Score: 511
Period size: 45 Copynumber: 9.3 Consensus size: 45
68105 TGTTGGTGGT
* * * * *
68115 TTCTTTGGTGTTTCATAAACTGGTGGTTTGGGCTT-TGGCTTCTCC
1 TTCTTTGGGGGTTCGTAAACTGGTGGCTTGGG-TTCAGGCTTCTCC
* * * **
68160 TTCTTCGGGGGCTCGTAAACTGGTGGTTTGTCCTTC-GGCTTCTCC
1 TTCTTTGGGGGTTCGTAAACTGGTGGCTTG-GGTTCAGGCTTCTCC
* *
68205 TTCTTTGGTGGTTCGTAAACTGGTGGCTTGGGTTCAGGCTTTTCC
1 TTCTTTGGGGGTTCGTAAACTGGTGGCTTGGGTTCAGGCTTCTCC
* * **
68250 TTCTTTGGAGGTTCGTAAACTGGTGGTTTGTCCTTC-GGCTTCTCC
1 TTCTTTGGGGGTTCGTAAACTGGTGGCTTG-GGTTCAGGCTTCTCC
* *
68295 TTCTTTGGTGGTTCGTAAACTGGTGGCTTAGGTTCAGGCTTCTCC
1 TTCTTTGGGGGTTCGTAAACTGGTGGCTTGGGTTCAGGCTTCTCC
* ** *
68340 TTCTTTGGTGGTTCGTAAACTGGTGGCTTAAGTTCAGGCTTTTCC
1 TTCTTTGGGGGTTCGTAAACTGGTGGCTTGGGTTCAGGCTTCTCC
*
68385 TTCTTTGGGGGTTCGTAAACTGGTGGCTTGGGTTCGGGCTTCTCC
1 TTCTTTGGGGGTTCGTAAACTGGTGGCTTGGGTTCAGGCTTCTCC
* *
68430 TTCTTTGGGGGTTCGTAAACTGGTGGCTTGGGTTCGGGTTTCTCC
1 TTCTTTGGGGGTTCGTAAACTGGTGGCTTGGGTTCAGGCTTCTCC
* * * * * *
68475 TTCTTTGGGGGTTCATAAACGGGTGGTTTAGGCTCAGGCTTTTCC
1 TTCTTTGGGGGTTCGTAAACTGGTGGCTTGGGTTCAGGCTTCTCC
68520 TTCTTTGGGGGTTC
1 TTCTTTGGGGGTTC
68534 ATAGACAGGG
Statistics
Matches: 329, Mismatches: 40, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
44 6 0.02
45 320 0.97
46 3 0.01
ACGTcount: A:0.09, C:0.20, G:0.30, T:0.41
Consensus pattern (45 bp):
TTCTTTGGGGGTTCGTAAACTGGTGGCTTGGGTTCAGGCTTCTCC
Found at i:70369 original size:32 final size:32
Alignment explanation
Indices: 70323--70397 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
70313 GATGACGTGA
* *
70323 CATTGCCACATCGAACCAAACCGATAATGTGG
1 CATTACCACGTCGAACCAAACCGATAATGTGG
* *
70355 CATTACCACGTCGAACCAAACTGATGATGTGG
1 CATTACCACGTCGAACCAAACCGATAATGTGG
*
70387 CAATACCACGT
1 CATTACCACGT
70398 GGAAATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (32 bp):
CATTACCACGTCGAACCAAACCGATAATGTGG
Found at i:70535 original size:29 final size:29
Alignment explanation
Indices: 70474--70544 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
70464 GAGAGGGGCC
* *
70474 AAAATGTCCAAAATTATGAATTCAGGGGGT
1 AAAATGTCCAAAATTA-GAATTCAGGAGAT
70504 AAAATGTCCAAAATT-GAAATTCAGGAGAT
1 AAAATGTCCAAAATTAG-AATTCAGGAGAT
*
70533 AAAACGTCCAAA
1 AAAATGTCCAAA
70545 CGTTACAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.03
29 21 0.57
30 15 0.41
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (29 bp):
AAAATGTCCAAAATTAGAATTCAGGAGAT
Found at i:73852 original size:51 final size:51
Alignment explanation
Indices: 73773--74068 Score: 427
Period size: 51 Copynumber: 5.9 Consensus size: 51
73763 TGGCCCGTGG
* ** *
73773 GGTGGTCCATGTGGA-G-GG-CCATAAGGTGGCTCGTACGGTGGCTCGTAT
1 GGTGGTTCATGTGGAGGAGGCCCATGGGGTGGCTCGTACGGTGGCTGGTAT
*
73821 GGTGGTTCATGTGCAGGAGGCCCATGGGGTGGCTCGTACGGTGGCTGGTAT
1 GGTGGTTCATGTGGAGGAGGCCCATGGGGTGGCTCGTACGGTGGCTGGTAT
* * *
73872 GGTGGTTCATGTGGAGGAGGCCCATGGGGTGGCTCATAAGGTGGCTGGTGT
1 GGTGGTTCATGTGGAGGAGGCCCATGGGGTGGCTCGTACGGTGGCTGGTAT
*
73923 GGTGGTCCATGTGGAGGAGGCCCATGGGGTGGCTCGTACGGTGGCTGGTAT
1 GGTGGTTCATGTGGAGGAGGCCCATGGGGTGGCTCGTACGGTGGCTGGTAT
* * * *
73974 GGTGGTTCATGTGGAGGAGGCCCATGGGGTGGCTCATAAGGTGGCTCGTAC
1 GGTGGTTCATGTGGAGGAGGCCCATGGGGTGGCTCGTACGGTGGCTGGTAT
* * *
74025 AGTGGTTCATGTGGAGGAGGCCCATGGGGTGGCTGGTAGGGTGG
1 GGTGGTTCATGTGGAGGAGGCCCATGGGGTGGCTCGTACGGTGG
74069 TTCATGTGGA
Statistics
Matches: 223, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
48 13 0.06
49 1 0.00
50 2 0.01
51 207 0.93
ACGTcount: A:0.14, C:0.16, G:0.46, T:0.24
Consensus pattern (51 bp):
GGTGGTTCATGTGGAGGAGGCCCATGGGGTGGCTCGTACGGTGGCTGGTAT
Found at i:73954 original size:39 final size:41
Alignment explanation
Indices: 73911--74119 Score: 133
Period size: 51 Copynumber: 4.8 Consensus size: 41
73901 TGGCTCATAA
*
73911 GGTGGCTGGT-G-TGGTGGTCCATGTGGAGGAGGCCCATGG
1 GGTGGCTGGTGGATGGTGGTTCATGTGGAGGAGGCCCATGG
73950 GGTGGCTCGTACGGTGGCTGGTATGGTGGTTCATGTGGAGGAGGCCCATGG
1 GGT-G---G--C--TGG-TGG-ATGGTGGTTCATGTGGAGGAGGCCCATGG
*
74001 GGTGGCTCATAAGGTGGCTCGTACAGTGGTTCATGTGGAGGAGGCCCATGG
1 GGTGG--C-T--GGTGGAT-G----GTGGTTCATGTGGAGGAGGCCCATGG
* *
74052 GGTGGCTGGT--AGGGTGGTTCATGTGGAGGAGGCCCATAG
1 GGTGGCTGGTGGATGGTGGTTCATGTGGAGGAGGCCCATGG
** *
74091 GGTGGCTCAT--AAGGTGGTTCATGTGGAGG
1 GGTGGCTGGTGGATGGTGGTTCATGTGGAGG
74120 CATTGGTTGT
Statistics
Matches: 140, Mismatches: 11, Indels: 38
0.74 0.06 0.20
Matches are distributed among these distances:
39 54 0.39
40 1 0.01
43 2 0.01
45 1 0.01
46 5 0.04
47 9 0.06
48 4 0.03
49 2 0.01
50 1 0.01
51 61 0.44
ACGTcount: A:0.14, C:0.15, G:0.46, T:0.24
Consensus pattern (41 bp):
GGTGGCTGGTGGATGGTGGTTCATGTGGAGGAGGCCCATGG
Found at i:81952 original size:36 final size:33
Alignment explanation
Indices: 81912--82061 Score: 174
Period size: 36 Copynumber: 4.2 Consensus size: 33
81902 CGACTTCTTT
*
81912 GGAGGTTGGTAATAATTTGGTGGTGACTTGTATTCA
1 GGAGGTTTGTAATAA---GGTGGTGACTTGTATTCA
81948 GGAGGTGATTTGTAATAAGGTGGTGACTTGTATTCA
1 GGA-G-G-TTTGTAATAAGGTGGTGACTTGTATTCA
*
81984 GGAGGTGACTTGTAATAAGGTGGTGATTTGTATTCA
1 GGAGGT---TTGTAATAAGGTGGTGACTTGTATTCA
82020 GGAGGTGATTTGTAATAAGGTGGTGACTTGTATTCA
1 GGA-G-G-TTTGTAATAAGGTGGTGACTTGTATTCA
82056 GGAGGT
1 GGAGGT
82062 GATTTGTATT
Statistics
Matches: 102, Mismatches: 3, Indels: 21
0.81 0.02 0.17
Matches are distributed among these distances:
33 2 0.02
34 2 0.02
35 2 0.02
36 82 0.80
37 2 0.02
38 2 0.02
39 10 0.10
ACGTcount: A:0.24, C:0.05, G:0.35, T:0.36
Consensus pattern (33 bp):
GGAGGTTTGTAATAAGGTGGTGACTTGTATTCA
Found at i:82124 original size:15 final size:15
Alignment explanation
Indices: 82058--82191 Score: 70
Period size: 15 Copynumber: 8.3 Consensus size: 15
82048 TGTATTCAGG
* * *
82058 AGGTGATTTGTATTC
1 AGGTGACTTGTAATA
82073 AGGTGACTTGTAATA
1 AGGTGACTTGTAATA
* * *
82088 CGGTGGTGACTTGTATTC
1 ---AGGTGACTTGTAATA
82106 AGGTGACTTGTAATA
1 AGGTGACTTGTAATA
*
82121 AGGTGGTGACTTGTAAGA
1 A---GGTGACTTGTAATA
*
82139 AGGTGATTTGTAATA
1 AGGTGACTTGTAATA
* * *
82154 GGGTGGTGACTTGTATTC
1 ---AGGTGACTTGTAATA
*
82172 AGGTGATTTGTAATA
1 AGGTGACTTGTAATA
*
82187 GGGTG
1 AGGTG
82192 GTGACTTGTA
Statistics
Matches: 89, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
15 52 0.58
18 37 0.42
ACGTcount: A:0.24, C:0.07, G:0.33, T:0.37
Consensus pattern (15 bp):
AGGTGACTTGTAATA
Found at i:82143 original size:66 final size:66
Alignment explanation
Indices: 82041--82306 Score: 228
Period size: 66 Copynumber: 3.9 Consensus size: 66
82031 GTAATAAGGT
* * * * *** *
82041 GGTGACTTGTATTCAGGAGGTGATTTGTATTCAGGTGACTTGTAATACGGTGGTGACTTGTATTC
1 GGTGACTTGTAATAAGGTGGTGACTTGTAAGAAGGTGACTTGTAATAAGGTGGTGACTTGTATTC
82106 A
66 A
* *
82107 GGTGACTTGTAATAAGGTGGTGACTTGTAAGAAGGTGATTTGTAATAGGGTGGTGACTTGTATTC
1 GGTGACTTGTAATAAGGTGGTGACTTGTAAGAAGGTGACTTGTAATAAGGTGGTGACTTGTATTC
82172 A
66 A
* * ** * *
82173 GGTGATTTGTAATAGGGTGGTGACTTGTATTCAGGTGGTGACTTATGATAAGGTGGTGACTTGTA
1 GGTGACTTGTAATAAGGTGGTGACTTGTA---AGAAGGTGACTTGTAATAAGGTGGTGACTTGTA
* *
82238 ATAA
63 TTCA
* * ** ** * *
82242 GGTGGTGA-TTGGTAAGAAGGTGGTGATTTGTAAGGTGGTGACTCATAGTAAGGTGGTGATTTGT
1 ---GGTGACTT-GTAATAAGGTGGTGACTTGTAAGAAGGTGACTTGTAATAAGGTGGTGACTTGT
82306 A
62 A
82307 ATAAGGTGGC
Statistics
Matches: 167, Mismatches: 26, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
66 84 0.50
69 58 0.35
71 2 0.01
72 23 0.14
ACGTcount: A:0.24, C:0.06, G:0.34, T:0.36
Consensus pattern (66 bp):
GGTGACTTGTAATAAGGTGGTGACTTGTAAGAAGGTGACTTGTAATAAGGTGGTGACTTGTATTC
A
Found at i:82226 original size:18 final size:18
Alignment explanation
Indices: 81930--82387 Score: 330
Period size: 18 Copynumber: 26.4 Consensus size: 18
81920 GTAATAATTT
* *
81930 GGTGGTGACTTGTATTCA
1 GGTGGTGACTTGTAATAA
* *
81948 GGAGGTGATTTGTAATAA
1 GGTGGTGACTTGTAATAA
* *
81966 GGTGGTGACTTGTATTCA
1 GGTGGTGACTTGTAATAA
*
81984 GGAGGTGACTTGTAATAA
1 GGTGGTGACTTGTAATAA
* * *
82002 GGTGGTGATTTGTATTCA
1 GGTGGTGACTTGTAATAA
* *
82020 GGAGGTGATTTGTAATAA
1 GGTGGTGACTTGTAATAA
* *
82038 GGTGGTGACTTGTATTCA
1 GGTGGTGACTTGTAATAA
* * * *
82056 GGAGGTGATTTGTATTCA
1 GGTGGTGACTTGTAATAA
*
82074 ---GGTGACTTGTAATAC
1 GGTGGTGACTTGTAATAA
* *
82089 GGTGGTGACTTGTATTCA
1 GGTGGTGACTTGTAATAA
82107 ---GGTGACTTGTAATAA
1 GGTGGTGACTTGTAATAA
*
82122 GGTGGTGACTTGTAAGAA
1 GGTGGTGACTTGTAATAA
* *
82140 ---GGTGATTTGTAATAG
1 GGTGGTGACTTGTAATAA
* *
82155 GGTGGTGACTTGTATTCA
1 GGTGGTGACTTGTAATAA
* *
82173 ---GGTGATTTGTAATAG
1 GGTGGTGACTTGTAATAA
* *
82188 GGTGGTGACTTGTATTCA
1 GGTGGTGACTTGTAATAA
* *
82206 GGTGGTGACTTATGATAA
1 GGTGGTGACTTGTAATAA
82224 GGTGGTGACTTGTAATAA
1 GGTGGTGACTTGTAATAA
*
82242 GGTGGTGA-TTGGTAAGAA
1 GGTGGTGACTT-GTAATAA
*
82260 GGTGGTGA-TT-T-GTAA
1 GGTGGTGACTTGTAATAA
** *
82275 GGTGGTGACTCATAGTAA
1 GGTGGTGACTTGTAATAA
*
82293 GGTGGTGATTTGTAATAA
1 GGTGGTGACTTGTAATAA
* *
82311 GGTGGCGA-TTGGTAATAG
1 GGTGGTGACTT-GTAATAA
* *
82329 GGTGGTGA-TTG--GTAG
1 GGTGGTGACTTGTAATAA
* *
82344 GGTGGCGA-TTGGTAATAG
1 GGTGGTGACTT-GTAATAA
82362 GGTGGTGA-TTGGTAATAA
1 GGTGGTGACTT-GTAATAA
82380 GGTGGTGA
1 GGTGGTGA
82388 TTTCCCATAG
Statistics
Matches: 349, Mismatches: 71, Indels: 40
0.76 0.15 0.09
Matches are distributed among these distances:
15 69 0.20
16 3 0.01
17 6 0.02
18 271 0.78
ACGTcount: A:0.24, C:0.05, G:0.36, T:0.35
Consensus pattern (18 bp):
GGTGGTGACTTGTAATAA
Found at i:82281 original size:33 final size:33
Alignment explanation
Indices: 82239--82376 Score: 125
Period size: 33 Copynumber: 4.1 Consensus size: 33
82229 TGACTTGTAA
* *
82239 TAAGGTGGTGATTGGTAAGAAGGTGGTGATTTG
1 TAAGGTGGCGATTGGTAAGAAGGTGGTGATTGG
* * ** *
82272 TAAGGTGGTGACTCAT-AGTAAGGTGGTGATTTGTAA
1 TAAGGTGGCGATTGGTAAG-AAGGTGGTGA-TTG--G
* *
82308 TAAGGTGGCGATTGGTAATAGGGTGGTGATTGG
1 TAAGGTGGCGATTGGTAAGAAGGTGGTGATTGG
* * *
82341 TAGGGTGGCGATTGGTAATAGGGTGGTGATTGG
1 TAAGGTGGCGATTGGTAAGAAGGTGGTGATTGG
82374 TAA
1 TAA
82377 TAAGGTGGTG
Statistics
Matches: 86, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
32 2 0.02
33 57 0.66
34 2 0.02
35 3 0.03
36 21 0.24
37 1 0.01
ACGTcount: A:0.24, C:0.03, G:0.41, T:0.32
Consensus pattern (33 bp):
TAAGGTGGCGATTGGTAAGAAGGTGGTGATTGG
Found at i:82377 original size:51 final size:50
Alignment explanation
Indices: 82239--82389 Score: 171
Period size: 51 Copynumber: 3.0 Consensus size: 50
82229 TGACTTGTAA
* *
82239 TAAGGTGGTGATTGGTAAGAAGGTGGTGATTTGT-A-AGGTGGTGACTCATAG
1 TAAGGTGGTGATTGGTAATAAGGTGGTGATTGGTAATAGGTGGTGA-T--TAG
* * *
82290 TAAGGTGGTGATTTGTAATAAGGTGGCGATTGGTAATAGGGTGGTGATTGG
1 TAAGGTGGTGATTGGTAATAAGGTGGTGATTGGTAATA-GGTGGTGATTAG
* * *
82341 TAGGGTGGCGATTGGTAATAGGGTGGTGATTGGTAATAAGGTGGTGATT
1 TAAGGTGGTGATTGGTAATAAGGTGGTGATTGGTAAT-AGGTGGTGATT
82390 TCCCATAGGG
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
51 74 0.86
52 2 0.02
53 2 0.02
54 8 0.09
ACGTcount: A:0.24, C:0.03, G:0.41, T:0.32
Consensus pattern (50 bp):
TAAGGTGGTGATTGGTAATAAGGTGGTGATTGGTAATAGGTGGTGATTAG
Found at i:84610 original size:11 final size:11
Alignment explanation
Indices: 84596--84633 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
84586 ATTCATAACA
84596 AATTTATAATT
1 AATTTATAATT
84607 AATTTATAATT
1 AATTTATAATT
84618 -ATTTGATAATT
1 AATTT-ATAATT
*
84629 TATTT
1 AATTT
84634 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Done.