Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015880.1 Corchorus capsularis cultivar CVL-1 contig15901, 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: 37884
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:2180 original size:303 final size:303
Alignment explanation
Indices: 1628--2234 Score: 885
Period size: 303 Copynumber: 2.0 Consensus size: 303
1618 TGCTTCTCAA
* * *
1628 GCAGAAGAAGATGGTGAAATGTCGATGACTGAGACACATGTGTTCCACGTATTTGTACTCTTCTT
1 GCAGAAGAAGATGGAGAAATGTCGATCACTGAGACACATGTGTTCCACGTATTTATACTCTTCTT
* * * * *
1693 TGCAATTGCTGACTCACTCAAATTTTTATATATAGGGTCTTCAAGAGTCTTCTTTACAAATGCAT
66 CGCAATTGCTGACTCACTCAAATCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
** * * *
1758 CGTGACAAACTTTACCCAATACCTTGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGATTTTG
131 CGTGACAAACTTTACCCAATACAATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGAGTATA
* * ** * *
1823 AATATACTTGTGAAAACTTCCCTGACACAGGGCAGTTCCATTTTTGTTTTGCAATTTTTTTCCTT
196 AATATACTTGTCAAAACTTCCCTGACACAGCGCAGACCCATTTTTGTCTTGCAATTATTTTCCTT
* *
1888 AATAATCAAGTCGGGGTTTTCTGCAGGTGAAATGACTCCGCTT
261 AATAATCAAGTCGGGGTTTTCTGCAGCTGAAACGACTCCGCTT
* * * *
1931 GCAGAAGAGGATGGAGAAATGTCGATCACTGAGGCACATGTGTTCCATGTTTTTATACTCTTCTT
1 GCAGAAGAAGATGGAGAAATGTCGATCACTGAGACACATGTGTTCCACGTATTTATACTCTTCTT
* * * *
1996 CGCAATTGTTGACTCGCTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
66 CGCAATTGCTGACTCACTCAAATCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
* *
2061 CGTGACAAACTTTACCCAATATAATGAGTTCACCGCAACACTTTTTAGTGACAGCTCCG-GTATA
131 CGTGACAAACTTTACCCAATACAATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGAGTATA
2125 AATTATACTTGTCAAAACTTCCCTGGA-ACAGCGCAGACCCATTTTTGTCTTGCAATTATTTTCC
196 AA-TATACTTGTCAAAACTTCCCT-GACACAGCGCAGACCCATTTTTGTCTTGCAATTATTTTCC
* *
2189 TTAATAATCAAGTCTGGTTTTTCTGCAGCTGAAACGACTCCGCTT
259 TTAATAATCAAGTCGGGGTTTTCTGCAGCTGAAACGACTCCGCTT
2234 G
1 G
2235 TTAAAACAAG
Statistics
Matches: 269, Mismatches: 33, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
302 4 0.01
303 263 0.98
304 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (303 bp):
GCAGAAGAAGATGGAGAAATGTCGATCACTGAGACACATGTGTTCCACGTATTTATACTCTTCTT
CGCAATTGCTGACTCACTCAAATCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
CGTGACAAACTTTACCCAATACAATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGAGTATA
AATATACTTGTCAAAACTTCCCTGACACAGCGCAGACCCATTTTTGTCTTGCAATTATTTTCCTT
AATAATCAAGTCGGGGTTTTCTGCAGCTGAAACGACTCCGCTT
Found at i:5586 original size:303 final size:302
Alignment explanation
Indices: 5035--5640 Score: 908
Period size: 303 Copynumber: 2.0 Consensus size: 302
5025 TGCTTCTCAA
* * *
5035 GCAGAAGAAGATGGTGAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTTTGTACTCTTGTT
1 GCAGAAGAAGATGGTGAAATGTCGATGACTGAGGCACATGTGTTCCACGTTATTATACTCTTCTT
* * * *
5100 TGCAATTGTTGACTCACTCAAATTTTATATATAGGGTCTGCAAGAGTCTTCTTTACAAATGCATC
66 CGCAATTGTTGACTCACTCAAATTTTATATAAAGGATCTGCAAGAGTCTTCTTAACAAATGCATC
* * * **
5165 GTGACAAACTTTACCCAATACCTTGAGTTCACCGCAACACTTCTTAGTGATAGCTCCGGTTTTGA
131 GTGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAAA
* * ** * * *
5230 ATATACTTGTGAAAACTTCCCTGGCACAGGGCAGTTCAATTTTTGTTTTGCAATTGTTTTCCTTA
196 ATATACTTGTGAAAACTTCCCTGGAACAGGGAAGACCAATTTTTGTCTTGCAATTATTGTCCTTA
* *
5295 ATAATCAAGTCGGGGTTTTCTGCAGGTGAAATGACTTCGCTT
261 ATAATCAAGTCGGGGTTTTCTGCAGGTGAAACGACTCCGCTT
* * *
5337 GCAGAAGAGGATGGTGAAATGTCGATGACTGAGGCACATGTTTTCCATGTTATTATACTCTTCTT
1 GCAGAAGAAGATGGTGAAATGTCGATGACTGAGGCACATGTGTTCCACGTTATTATACTCTTCTT
* * *
5402 CGCAATTGTTGACTCGCTTAAGTCTTTATATAAAGGATCAT-CAAGAGTCTTCTTAACAAATGCA
66 CGCAATTGTTGACTCACTCAAAT-TTTATATAAAGGATC-TGCAAGAGTCTTCTTAACAAATGCA
5466 TCGTGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATA
129 TCGTGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATA
* *
5531 AAATATACTTGTGAAAACTTCCTTGGAACAGGGAAGACCCATTTTTGTCTTGCAATTATTGTCCT
194 AAATATACTTGTGAAAACTTCCCTGGAACAGGGAAGACCAATTTTTGTCTTGCAATTATTGTCCT
* *
5596 TAATAATCAAGTCTGGGTTTTCTGCAGTTGAAACGACTCCGCTT
259 TAATAATCAAGTCGGGGTTTTCTGCAGGTGAAACGACTCCGCTT
5640 G
1 G
5641 TTAAAACAAG
Statistics
Matches: 271, Mismatches: 31, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
302 78 0.29
303 192 0.71
304 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (302 bp):
GCAGAAGAAGATGGTGAAATGTCGATGACTGAGGCACATGTGTTCCACGTTATTATACTCTTCTT
CGCAATTGTTGACTCACTCAAATTTTATATAAAGGATCTGCAAGAGTCTTCTTAACAAATGCATC
GTGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAAA
ATATACTTGTGAAAACTTCCCTGGAACAGGGAAGACCAATTTTTGTCTTGCAATTATTGTCCTTA
ATAATCAAGTCGGGGTTTTCTGCAGGTGAAACGACTCCGCTT
Found at i:9889 original size:113 final size:113
Alignment explanation
Indices: 9688--9914 Score: 427
Period size: 113 Copynumber: 2.0 Consensus size: 113
9678 AATGTGATTA
*
9688 TTACAATATTTCAGGTTCCATAGAATTAATTATACTGGTTTATAAGACAAACATTTAATAGTATA
1 TTACAATATTTCAGGTTCCATAGAATTAATTATACTGGTTTATAACACAAACATTTAATAGTATA
9753 CGTTTGTTCTCCTTTGTTGTCATTAATGGCATTCATTAAACCACAATG
66 CGTTTGTTCTCCTTTGTTGTCATTAATGGCATTCATTAAACCACAATG
*
9801 TTACAATATTTCAGGTTCCATAGAATTAATTATACTGGTTTATAACCCAAACATTTAATAGTATA
1 TTACAATATTTCAGGTTCCATAGAATTAATTATACTGGTTTATAACACAAACATTTAATAGTATA
*
9866 CGTTTGTTCTCCTTTGTTTTCATTAATGGCATTCATTAAACCACAATG
66 CGTTTGTTCTCCTTTGTTGTCATTAATGGCATTCATTAAACCACAATG
9914 T
1 T
9915 AAAGGTTAAG
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (113 bp):
TTACAATATTTCAGGTTCCATAGAATTAATTATACTGGTTTATAACACAAACATTTAATAGTATA
CGTTTGTTCTCCTTTGTTGTCATTAATGGCATTCATTAAACCACAATG
Found at i:11866 original size:28 final size:27
Alignment explanation
Indices: 11813--11866 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
11803 CTCTGTGTGC
* * **
11813 TTTCTTTTTCCTTCTTTATGTTTTTTT
1 TTTCTTTTCCCTTCTTCATGCCTTTTT
11840 TTTCTTTTCCTCTTCTTCATGCCTTTT
1 TTTCTTTTCC-CTTCTTCATGCCTTTT
11867 CTCCTTCCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.70
Consensus pattern (27 bp):
TTTCTTTTCCCTTCTTCATGCCTTTTT
Found at i:12968 original size:2 final size:2
Alignment explanation
Indices: 12961--13014 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
12951 GTTTGATACC
12961 CT CT CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
13002 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
13015 GCTTTTTATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:16849 original size:15 final size:15
Alignment explanation
Indices: 16807--16852 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
16797 AGGGGAAAAG
16807 CCTCTCTCTTTCC-T-
1 CCTCTCT-TTTCCTTC
16821 CCTCTCCTTCTTCCTTC
1 CCTCT-CTT-TTCCTTC
16838 CCTCTCTTTTCCTTC
1 CCTCTCTTTTCCTTC
16853 TCCATCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 6 0.21
15 13 0.46
16 4 0.14
17 5 0.18
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (15 bp):
CCTCTCTTTTCCTTC
Found at i:17337 original size:20 final size:20
Alignment explanation
Indices: 17294--17338 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
17284 TTTGCTTTGA
*
17294 ATTTGGGGTTCACAAGAGAT
1 ATTTGGGGTTCACAAGAGAG
*
17314 ATTTGGGGTTTAC-AGTAGAG
1 ATTTGGGGTTCACAAG-AGAG
17334 ATTTG
1 ATTTG
17339 AGATTTCAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.27, C:0.07, G:0.31, T:0.36
Consensus pattern (20 bp):
ATTTGGGGTTCACAAGAGAG
Found at i:17584 original size:20 final size:21
Alignment explanation
Indices: 17545--17584 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
17535 TTCAATACCC
17545 TTGATCCTTAATTTAACTTTA
1 TTGATCCTTAATTTAACTTTA
* *
17566 TTGATTCTT-ATTTAGCTTT
1 TTGATCCTTAATTTAACTTT
17585 TCTTTATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.57
Consensus pattern (21 bp):
TTGATCCTTAATTTAACTTTA
Found at i:21741 original size:22 final size:22
Alignment explanation
Indices: 21716--21757 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
21706 TTTTTGTTTG
21716 GTCTGCCACTTAGATATTATTA
1 GTCTGCCACTTAGATATTATTA
*
21738 GTCTGTCACTTAGATATTAT
1 GTCTGCCACTTAGATATTAT
21758 ATGTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (22 bp):
GTCTGCCACTTAGATATTATTA
Found at i:23822 original size:18 final size:18
Alignment explanation
Indices: 23787--23822 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
23777 TTTATTAATG
*
23787 TTTTATTAAATTGATTTT
1 TTTTATTAAATTAATTTT
23805 TTTTATTAAA-TAATTTT
1 TTTTATTAAATTAATTTT
23822 T
1 T
23823 GGTGCATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTATTAAATTAATTTT
Found at i:27775 original size:2 final size:2
Alignment explanation
Indices: 27770--27802 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
27760 GTGTGTGTGG
*
27770 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27803 ACGATCACGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:30563 original size:49 final size:48
Alignment explanation
Indices: 30411--30577 Score: 246
Period size: 48 Copynumber: 3.5 Consensus size: 48
30401 AGAAAACCTG
*
30411 CACCTTCCGACCGGGAAGGGCATTTTGGGAATAGAGATGAAAAACCTT
1 CACCTTCCGACCGGGAAGGGCATTTTGGGAATAGAGATGAAAAAACTT
* * * *
30459 CACCTACCGACCGGGAAGGGTATTTTGGGGATAAAGAT-AAAAAACTT
1 CACCTTCCGACCGGGAAGGGCATTTTGGGAATAGAGATGAAAAAACTT
*
30506 ACACCTTCCGACCGGGAAGGGCATTTTTGGAATAGAGATGAAAAAAACTT
1 -CACCTTCCGACCGGGAAGGGCATTTTGGGAATAGAGATG-AAAAAACTT
*
30556 CAACTTCCGACCGGGAAGGGCA
1 CACCTTCCGACCGGGAAGGGCA
30578 AAACTGGAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
47 8 0.08
48 67 0.64
49 21 0.20
50 9 0.09
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (48 bp):
CACCTTCCGACCGGGAAGGGCATTTTGGGAATAGAGATGAAAAAACTT
Found at i:30622 original size:48 final size:48
Alignment explanation
Indices: 30549--31253 Score: 789
Period size: 48 Copynumber: 14.7 Consensus size: 48
30539 AGAGATGAAA
* * * *
30549 AAAACTTCAACTTCCGACCGGGAAGGGCAAAACTGGAAAAAAACACCG
1 AAAACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
* * *
30597 AAAACTGCACCTTCCGACCGAGAAGGGCAAAACTAGAAATAGACACTG
1 AAAACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
* * * * *
30645 AAAA-TAGCGCCTTCCGACTGGGAAGGGCAAAA-TAGCAAATAACCACCG
1 AAAACT-GCACCTTCCGACCGGGAAGGGCAAAACT-GGAAATAAACACTG
* * *
30693 AAGACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAGACATTG
1 AAAACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
* ** * * * *
30741 AAAA-TAGCGCCTTCTAACCGGGAAGGGCAAAACAGCAAATAACCACCG
1 AAAACT-GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
** * *
30789 AGGACTGCACCTTCCGACCGGGAAGGGCAAAATTGGAAATAGACACTG
1 AAAACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
30837 AAAA-TAGCACCTTCC-ACCGGGAAGGGCAAAA-TAGGAAATAAACACTG
1 AAAACT-GCACCTTCCGACCGGGAAGGGCAAAACT-GGAAATAAACACTG
* * * *
30884 AAAATTAGCACCTTCCGACCAGGAAGGGCAAAA-TGGAAAGAAACATTG
1 AAAACT-GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
* * * * **
30932 AAGACAGCACCTTCCGACCAGGAAGGGCAAAATTGGAAATTGACACTG
1 AAAACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
* * * **
30980 AAGACTGCACCTTCCGACCGGGAAAGGCAAAACTAGAAATTGACACTG
1 AAAACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
* * *
31028 AAGA-TAGCACCTTCCGACCGGGAAGGGCAAAATTGGAAATAAACACCG
1 AAAACT-GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
*
31076 AAGAA-TGCACCTTCCGACCGGGAAGGACAAAACTGGAAATAAACACTG
1 AA-AACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
* * *
31124 AAAATTAGCACCTTCCGACCGGGAAGGGCAAAACAGGAAAGAAACACTG
1 AAAACT-GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
* * * *
31173 AAGACAGCACCTTCCGACCGGGAAGGGCAAAACTGGAAGTAGACACTG
1 AAAACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
*
31221 AAAACCGCACCTTCCGACCGGGAAGGGCAAAAC
1 AAAACTGCACCTTCCGACCGGGAAGGGCAAAAC
31254 AGGGAATCGA
Statistics
Matches: 558, Mismatches: 84, Indels: 30
0.83 0.12 0.04
Matches are distributed among these distances:
46 1 0.00
47 66 0.12
48 428 0.77
49 63 0.11
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (48 bp):
AAAACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
Found at i:30676 original size:96 final size:96
Alignment explanation
Indices: 30559--31253 Score: 912
Period size: 96 Copynumber: 7.2 Consensus size: 96
30549 AAAACTTCAA
* * *
30559 CTTCCGACCGGGAAGGGCAAAACTGGAAAAAAACACCGAAAACTGCACCTTCCGACCGAGAAGGG
1 CTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACTGCACCTTCCGACCGGGAAGGG
* *
30624 CAAAACTAGAAATAGACACTGAAAATAGCGC
66 CAAAACTGGAAATAGACACTGAAAATAGCAC
* * *
30655 CTTCCGACTGGGAAGGGCAAAA-TAGCAAATAACCACCGAAGACTGCACCTTCCGACCGGGAAGG
1 CTTCCGACCGGGAAGGGCAAAACT-GGAAATAAACACCGAAGACTGCACCTTCCGACCGGGAAGG
* *
30719 GCAAAACTGGAAATAGACATTGAAAATAGCGC
65 GCAAAACTGGAAATAGACACTGAAAATAGCAC
** * * * *
30751 CTTCTAACCGGGAAGGGCAAAACAGCAAATAACCACCGAGGACTGCACCTTCCGACCGGGAAGGG
1 CTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACTGCACCTTCCGACCGGGAAGGG
*
30816 CAAAATTGGAAATAGACACTGAAAATAGCAC
66 CAAAACTGGAAATAGACACTGAAAATAGCAC
* * * *
30847 CTTCC-ACCGGGAAGGGCAAAA-TAGGAAATAAACACTGAAAATTAGCACCTTCCGACCAGGAAG
1 CTTCCGACCGGGAAGGGCAAAACT-GGAAATAAACACCGAAGACT-GCACCTTCCGACCGGGAAG
* * * * *
30910 GGCAAAA-TGGAAAGAAACATTGAAGACAGCAC
64 GGCAAAACTGGAAATAGACACTGAAAATAGCAC
* * ** * *
30942 CTTCCGACCAGGAAGGGCAAAATTGGAAATTGACACTGAAGACTGCACCTTCCGACCGGGAAAGG
1 CTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACTGCACCTTCCGACCGGGAAGGG
* * *
31007 CAAAACTAGAAATTGACACTGAAGATAGCAC
66 CAAAACTGGAAATAGACACTGAAAATAGCAC
* * *
31038 CTTCCGACCGGGAAGGGCAAAATTGGAAATAAACACCGAAGAATGCACCTTCCGACCGGGAAGGA
1 CTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACTGCACCTTCCGACCGGGAAGGG
*
31103 CAAAACTGGAAATAAACACTGAAAATTAGCAC
66 CAAAACTGGAAATAGACACTGAAAA-TAGCAC
* * * *
31135 CTTCCGACCGGGAAGGGCAAAACAGGAAAGAAACACTGAAGACAGCACCTTCCGACCGGGAAGGG
1 CTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACTGCACCTTCCGACCGGGAAGGG
* **
31200 CAAAACTGGAAGTAGACACTGAAAACCGCAC
66 CAAAACTGGAAATAGACACTGAAAATAGCAC
31231 CTTCCGACCGGGAAGGGCAAAAC
1 CTTCCGACCGGGAAGGGCAAAAC
31254 AGGGAATCGA
Statistics
Matches: 526, Mismatches: 65, Indels: 16
0.87 0.11 0.03
Matches are distributed among these distances:
95 80 0.15
96 358 0.68
97 88 0.17
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.12
Consensus pattern (96 bp):
CTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCGAAGACTGCACCTTCCGACCGGGAAGGG
CAAAACTGGAAATAGACACTGAAAATAGCAC
Found at i:31858 original size:34 final size:34
Alignment explanation
Indices: 31815--31882 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
31805 AGCATTAATC
*
31815 AAAATTCAATCTTTTAATTCAAAGATTTCATTTT
1 AAAATTCAATCTTTTAATCCAAAGATTTCATTTT
* * *
31849 AAAATTCAATTTTTTAGTCCAAAGGTTTCATTTT
1 AAAATTCAATCTTTTAATCCAAAGATTTCATTTT
31883 TATCACAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (34 bp):
AAAATTCAATCTTTTAATCCAAAGATTTCATTTT
Found at i:31914 original size:50 final size:50
Alignment explanation
Indices: 31849--32118 Score: 209
Period size: 50 Copynumber: 5.3 Consensus size: 50
31839 ATTTCATTTT
* * * *
31849 AAAATTCAATTTTTTAGTCCAAAGGTTTCATTTTTATCACAAATTAATCA
1 AAAATTTAATCTTTTAGTCCAAAGATCTCATTTTTATCACAAATTAATCA
* * * *
31899 AAAATTTAATCTTTTAATCCAAAGATCTCATTTCTATTCACAAATTACTTA
1 AAAATTTAATCTTTTAGTCCAAAGATCTCATTTTTA-TCACAAATTAATCA
* ** * ** * * *
31950 CAAGGTTAATCTTTTATTTAAAAAATCTCACTTTTATTTACAAATTAATCA
1 AAAATTTAATCTTTTAGTCCAAAGATCTCATTTTTA-TCACAAATTAATCA
* * * * * ** * *
32001 AAAGGTTCAATCTCTTACTTCACTGATCTCATTTTTATCATAAATCAATCA
1 AAA-ATTTAATCTTTTAGTCCAAAGATCTCATTTTTATCACAAATTAATCA
* * * * *
32052 AAAATTTCATCTTTTAG-CTTAAAGATCTCATTTTTATCATAAATCAATCG
1 AAAATTTAATCTTTTAGTC-CAAAGATCTCATTTTTATCACAAATTAATCA
*
32102 AAAATTTCATCTTTTAG
1 AAAATTTAATCTTTTAG
32119 CTTAAAATTT
Statistics
Matches: 174, Mismatches: 43, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
50 83 0.48
51 67 0.39
52 24 0.14
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (50 bp):
AAAATTTAATCTTTTAGTCCAAAGATCTCATTTTTATCACAAATTAATCA
Found at i:31961 original size:51 final size:50
Alignment explanation
Indices: 31860--32117 Score: 155
Period size: 51 Copynumber: 5.1 Consensus size: 50
31850 AAATTCAATT
* * * *
31860 TTTTAGTCCAAAGGTTTCATTTT-TATCACAAATTAATCAAAAATTTAATC
1 TTTTAATCCAAAGATCTCATTTTAT-TCACAAATTAATCAAAAAGTTAATC
* * * *
31910 TTTTAATCCAAAGATCTCATTTCTATTCACAAATTACTTACAAGGTTAATC
1 TTTTAATCCAAAGATCTCATTT-TATTCACAAATTAATCAAAAAGTTAATC
* ** * * *
31961 TTTTATTTAAAAAATCTCACTTTTATTTACAAATTAATCAAAAGGTTCAATC
1 TTTTAATCCAAAGATCTCA-TTTTATTCACAAATTAATCAAAAAGTT-AATC
* * * ** * * * *
32013 TCTTACTTCACTGATCTCATTTT-TATCATAAATCAATCAAAAATTTCATC
1 TTTTAATCCAAAGATCTCATTTTAT-TCACAAATTAATCAAAAAGTTAATC
* * * * * * *
32063 TTTT-AGCTTAAAGATCTCATTTT-TATCATAAATCAATCGAAAATTTCATC
1 TTTTAATC-CAAAGATCTCATTTTAT-TCACAAATTAATCAAAAAGTTAATC
32113 TTTTA
1 TTTTA
32118 GCTTAAAATT
Statistics
Matches: 165, Mismatches: 36, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
50 68 0.41
51 76 0.46
52 21 0.13
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (50 bp):
TTTTAATCCAAAGATCTCATTTTATTCACAAATTAATCAAAAAGTTAATC
Found at i:32138 original size:50 final size:50
Alignment explanation
Indices: 32025--32135 Score: 197
Period size: 50 Copynumber: 2.2 Consensus size: 50
32015 TTACTTCACT
32025 GATCTCATTTTTATCATAAATCAATCAAAAATTTCATCTTTTAGCTTAAA
1 GATCTCATTTTTATCATAAATCAATCAAAAATTTCATCTTTTAGCTTAAA
*
32075 GATCTCATTTTTATCATAAATCAATCGAAAATTTCATCTTTTAGCTTAAA
1 GATCTCATTTTTATCATAAATCAATCAAAAATTTCATCTTTTAGCTTAAA
*
32125 -ATTTCATTTTT
1 GATCTCATTTTT
32136 TATTGCTAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
49 10 0.17
50 49 0.83
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (50 bp):
GATCTCATTTTTATCATAAATCAATCAAAAATTTCATCTTTTAGCTTAAA
Found at i:35632 original size:36 final size:35
Alignment explanation
Indices: 35549--35633 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 35
35539 GGCCCAAGCT
*
35549 TGGGTGCTGGGCCATGGCTGGCCCGCGCGGCAGGCC
1 TGGGCGCTGGGCCATGGCTGGCCCGCGC-GCAGGCC
* * *
35585 TGGGCGCTGGGCCATGCGCTGGCTCGCGC-CTGGGC
1 TGGGCGCTGGGCCATG-GCTGGCCCGCGCGCAGGCC
35620 TGGGCGCTTGGGCC
1 TGGGCGC-TGGGCC
35634 GCGCCAGGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 11 0.26
36 21 0.49
37 11 0.26
ACGTcount: A:0.04, C:0.33, G:0.47, T:0.16
Consensus pattern (35 bp):
TGGGCGCTGGGCCATGGCTGGCCCGCGCGCAGGCC
Done.