Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011462.1 Corchorus capsularis cultivar CVL-1 contig11483, 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: 160505
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4166 original size:21 final size:21
Alignment explanation
Indices: 4140--4181 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4130 AATTTCTGGT
4140 GTAACCCACGCCTGGGCAAGG
1 GTAACCCACGCCTGGGCAAGG
*
4161 GTAACCCGCGCCTGGGCAAGG
1 GTAACCCACGCCTGGGCAAGG
4182 TTGCGGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.36, T:0.10
Consensus pattern (21 bp):
GTAACCCACGCCTGGGCAAGG
Found at i:5713 original size:12 final size:12
Alignment explanation
Indices: 5698--5731 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5688 GCCGGTTGGC
5698 CCATGCGTTGCT
1 CCATGCGTTGCT
* *
5710 CCATCCGATGCT
1 CCATGCGTTGCT
5722 CCATGCGTTG
1 CCATGCGTTG
5732 GCCGGTCATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.12, C:0.35, G:0.24, T:0.29
Consensus pattern (12 bp):
CCATGCGTTGCT
Found at i:11689 original size:11 final size:11
Alignment explanation
Indices: 11634--11683 Score: 75
Period size: 11 Copynumber: 4.5 Consensus size: 11
11624 TTCCTATATA
11634 AAATTAATTAAT
1 AAATTAATT-AT
11646 CAAA-TAATTAT
1 -AAATTAATTAT
11657 AAATTAATTAT
1 AAATTAATTAT
11668 AAATTAATTAT
1 AAATTAATTAT
11679 AAATT
1 AAATT
11684 TGTTATGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 3 0.08
11 25 0.69
12 5 0.14
13 3 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:16983 original size:102 final size:101
Alignment explanation
Indices: 16749--16994 Score: 329
Period size: 102 Copynumber: 2.4 Consensus size: 101
16739 CCTTTTAATT
* * *
16749 TTAATTT-GGGCTAAACTTAGTG-AATTAATTATATATTTTATTTTCAAAACGCTATAACAATAT
1 TTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTTCAAAACCCTATAACAATAT
* *
16812 TATTAGTTATGGAATTTACCCTTAAAATAAAAAAAA
66 TATTAATTATGAAATTTACCCTTAAAATAAAAAAAA
* * *
16848 TTAATTTGGGGCTAAACATAGTGAAATTTGTTTTGTATTTTA-TTTCTAAAACCCTATAACAATA
1 TTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTTC-AAAACCCTATAACAAT-
* * *
16912 AATTATTAATTTTGAAATTTACTCTTAAAATAAAAGAAA
64 -ATTATTAATTATGAAATTTACCCTTAAAATAAAAAAAA
*
16951 -TAATTTGGGGCTAAATTTAGTGAAATTAGTTTTATATTTTATTT
1 TTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTT
16995 ATATTTTATA
Statistics
Matches: 126, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
99 7 0.06
100 18 0.14
101 29 0.23
102 37 0.29
103 35 0.28
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (101 bp):
TTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTTCAAAACCCTATAACAATAT
TATTAATTATGAAATTTACCCTTAAAATAAAAAAAA
Found at i:17591 original size:16 final size:16
Alignment explanation
Indices: 17570--17600 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17560 TTTTTCTCCA
17570 TATTCTATTGTCTTTC
1 TATTCTATTGTCTTTC
*
17586 TATTCTGTTGTCTTT
1 TATTCTATTGTCTTT
17601 TTCGTACTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.16, G:0.10, T:0.65
Consensus pattern (16 bp):
TATTCTATTGTCTTTC
Found at i:21700 original size:13 final size:14
Alignment explanation
Indices: 21673--21702 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
21663 TCATGCACCC
21673 AAAATCATTTAATA
1 AAAATCATTTAATA
21687 AAAATCATTT-ATA
1 AAAATCATTTAATA
21700 AAA
1 AAA
21703 CATATCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATCATTTAATA
Found at i:23391 original size:45 final size:45
Alignment explanation
Indices: 23340--23427 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
23330 TAATAAAGTA
23340 GTGGAATTACAAAAAGATCCCTACCCCGAATTAATGATAAGCTTG
1 GTGGAATTACAAAAAGATCCCTACCCCGAATTAATGATAAGCTTG
* * *
23385 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCT
1 GTGGAATTACAAAAAGATCCCTACCCCGAATTAATGATAAGCT
23428 GGAGAAGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (45 bp):
GTGGAATTACAAAAAGATCCCTACCCCGAATTAATGATAAGCTTG
Found at i:24769 original size:217 final size:214
Alignment explanation
Indices: 24401--24815 Score: 627
Period size: 217 Copynumber: 1.9 Consensus size: 214
24391 GTTGGGGTTC
24401 TTTTTTTTGGCTTGATTCTAGCTAAGGTTTTTGAAAATCTGTGGAAAGTATTGGAAGGTAAAAGT
1 TTTTTTTTGGCTTGATTCTAGCTAAGGTTTTTGAAAATCTGTGGAAAGTATTGGAAGGTAAAAGT
*
24466 CTATATTTTCTACAGATTTAAAATTTATTATATTAAATATAATATGTATAGTACTTACCTAAATT
66 CTATATTTTCTACAGATTTAAAATTTATTATATTAAATATAATATATATAGTACTTACCTAAATT
* * *
24531 CTTAACTCTAAACTTTTAGAAGTACATGGAGTATGAATTTTCTAACATGACCTTCTTATTGGACG
131 CTTAACTCTAAACTTTTAGAAGTAAATGGAGTATGAACTTTCTAACATGACCTACTTATTGGACG
24596 ACATTCTTGTTGGTTTTTT
196 ACATTCTTGTTGGTTTTTT
* * *
24615 TTTTCTTTTGGCTTGATTCTAGTTAAGGTTTTTGAAAATCT-TTGAAAGTATTTGAAGGTAAAAG
1 TTTT-TTTTGGCTTGATTCTAGCTAAGGTTTTTGAAAATCTGTGGAAAGTATTGGAAGGTAAAA-
* * * *
24679 TGTCTATATTTTTTACAGATTTAAAGTTTATATTATATT-AATATAATATATGTAGTACTTAGCT
64 -GTCTATATTTTCTACAGATTTAAA-ATT-TATTATATTAAATATAATATATATAGTACTTACCT
* * * *
24743 AAATTTTTAACTGTAAATTTTTAGAAGTAAATGGAGTATGAACTTTCTAACATGCCCTACTTATT
126 AAATTCTTAACTCTAAACTTTTAGAAGTAAATGGAGTATGAACTTTCTAACATGACCTACTTATT
*
24808 GGGCGACA
191 GGACGACA
24816 GGAATGGAAG
Statistics
Matches: 180, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
214 24 0.13
215 35 0.19
216 23 0.13
217 89 0.49
218 9 0.05
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (214 bp):
TTTTTTTTGGCTTGATTCTAGCTAAGGTTTTTGAAAATCTGTGGAAAGTATTGGAAGGTAAAAGT
CTATATTTTCTACAGATTTAAAATTTATTATATTAAATATAATATATATAGTACTTACCTAAATT
CTTAACTCTAAACTTTTAGAAGTAAATGGAGTATGAACTTTCTAACATGACCTACTTATTGGACG
ACATTCTTGTTGGTTTTTT
Found at i:26614 original size:19 final size:19
Alignment explanation
Indices: 26590--26627 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
26580 AAATGTTGCA
26590 ATGTAGTTTTAAGCTTATT
1 ATGTAGTTTTAAGCTTATT
26609 ATGTAGTTTTAAGCTTATT
1 ATGTAGTTTTAAGCTTATT
26628 CGGTTAAATT
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:0.05, G:0.16, T:0.53
Consensus pattern (19 bp):
ATGTAGTTTTAAGCTTATT
Found at i:40443 original size:23 final size:23
Alignment explanation
Indices: 40375--40445 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 23
40365 TATGTAAACT
40375 AAATTAG-TACTAGTTATTC-CC
1 AAATTAGCTACTAGTTATTCACC
* *
40396 AAAGATAGCT-CTTTTA-TTAATCACC
1 AAA-TTAGCTAC---TAGTTATTCACC
40421 AAATTAGCTACTAGTTATTCACC
1 AAATTAGCTACTAGTTATTCACC
40444 AA
1 AA
40446 TTAAGCAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
21 3 0.08
22 6 0.16
23 11 0.29
24 10 0.26
25 8 0.21
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (23 bp):
AAATTAGCTACTAGTTATTCACC
Found at i:51810 original size:22 final size:19
Alignment explanation
Indices: 51763--51798 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
51753 TTGAAATAAT
51763 TCTTC-AATTATCTTCAAA
1 TCTTCAAATTATCTTCAAA
51781 TCTTCAAATTATCTTCAA
1 TCTTCAAATTATCTTCAA
51799 GAAATCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (19 bp):
TCTTCAAATTATCTTCAAA
Found at i:60869 original size:19 final size:18
Alignment explanation
Indices: 60836--60871 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
60826 TTGAAATAAT
60836 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
60854 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
60872 GAAATCTTCA
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:64779 original size:19 final size:18
Alignment explanation
Indices: 64755--64801 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 18
64745 TGAAGATTTC
*
64755 TTGAAGATAATTTGAAGAT
1 TTGAAGA-AAATTGAAGAT
64774 TTGAAGAAAATTGAAGAT
1 TTGAAGAAAATTGAAGAT
64792 CATTGAAGAA
1 --TTGAAGAA
64802 TTATTTCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 10 0.40
19 7 0.28
20 8 0.32
ACGTcount: A:0.47, C:0.02, G:0.21, T:0.30
Consensus pattern (18 bp):
TTGAAGAAAATTGAAGAT
Found at i:66103 original size:15 final size:16
Alignment explanation
Indices: 66083--66116 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
66073 GATTGCTCTC
*
66083 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
66098 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
66114 TTA
1 TTA
66117 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:67487 original size:26 final size:26
Alignment explanation
Indices: 67431--67490 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
67421 GTATCAAAGG
67431 AAAAA-ATAAGTATGCCTTCATGGAT
1 AAAAATATAAGTATGCCTTCATGGAT
*
67456 GAAAATATAAGTATGCCTTCATGGAT
1 AAAAATATAAGTATGCCTTCATGGAT
67482 AAAAATATA
1 AAAAATATA
67491 TCTGCTGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 4 0.12
26 28 0.88
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (26 bp):
AAAAATATAAGTATGCCTTCATGGAT
Found at i:74540 original size:19 final size:18
Alignment explanation
Indices: 74516--74551 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
74506 TGAAGATTTC
74516 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
74535 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
74552 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:75716 original size:15 final size:16
Alignment explanation
Indices: 75696--75729 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
75686 GATTGCTCTC
*
75696 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
75711 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
75727 TTA
1 TTA
75730 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:78545 original size:30 final size:30
Alignment explanation
Indices: 78511--78581 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
78501 GCATCTTTGG
*
78511 TGCGATTCCATTGGCATCTTCATGAAACCT
1 TGCGATTCCATTGGCATCTTCATAAAACCT
78541 TGCGATTCCATTGGCATCTTCATAAAACCT
1 TGCGATTCCATTGGCATCTTCATAAAACCT
78571 TGCGATTCCAT
1 TGCGATTCCAT
78582 CCTCTCCTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (30 bp):
TGCGATTCCATTGGCATCTTCATAAAACCT
Found at i:80418 original size:33 final size:34
Alignment explanation
Indices: 80381--80466 Score: 115
Period size: 33 Copynumber: 2.6 Consensus size: 34
80371 TTCTTTTCAC
*
80381 CCAAAACAGT-CCTATTTTCAATGCTATGATCAA
1 CCAAAACAGTAACTATTTTCAATGCTATGATCAA
* *
80414 CCAAAACA-TAATTATTTTGAATGCTATGATCAA
1 CCAAAACAGTAACTATTTTCAATGCTATGATCAA
*
80447 CCAAAACAG-AATTATTTTCA
1 CCAAAACAGTAACTATTTTCA
80467 TCACAATTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.02
33 46 0.98
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (34 bp):
CCAAAACAGTAACTATTTTCAATGCTATGATCAA
Found at i:80518 original size:33 final size:33
Alignment explanation
Indices: 80481--80550 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
80471 AATTAGCATC
* * *
80481 CAAAATAGATTTTGTTTCATCACAAACAACACT
1 CAAAACAGATTTAGTGTCATCACAAACAACACT
*
80514 CAAAACAGATTTAGTGTCATCGCAAACAACACT
1 CAAAACAGATTTAGTGTCATCACAAACAACACT
80547 CAAA
1 CAAA
80551 TTAGGTTCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.24
Consensus pattern (33 bp):
CAAAACAGATTTAGTGTCATCACAAACAACACT
Found at i:80572 original size:33 final size:33
Alignment explanation
Indices: 80497--80586 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 33
80487 AGATTTTGTT
* * *
80497 TCATCACAAACAACACTCAAAACAGATTTAGTG
1 TCATCGCAAACAACACTCAAAACAGATTCAGTA
** *
80530 TCATCGCAAACAACACTCAAATTAGGTTCAGTA
1 TCATCGCAAACAACACTCAAAACAGATTCAGTA
*
80563 TCATTGCAAACAACA-TCTAAAACA
1 TCATCGCAAACAACACTC-AAAACA
80587 CTCTTTGCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 2 0.04
33 45 0.96
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.22
Consensus pattern (33 bp):
TCATCGCAAACAACACTCAAAACAGATTCAGTA
Found at i:85667 original size:16 final size:16
Alignment explanation
Indices: 85646--85677 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
85636 TTTTCCTTGC
85646 ATTGCTTTGAGTGATT
1 ATTGCTTTGAGTGATT
*
85662 ATTGCTTTGATTGATT
1 ATTGCTTTGAGTGATT
85678 GTGTATTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.06, G:0.22, T:0.53
Consensus pattern (16 bp):
ATTGCTTTGAGTGATT
Found at i:90505 original size:21 final size:22
Alignment explanation
Indices: 90479--90529 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
90469 CGGACCTAAA
*
90479 GGCATCTTTAAAG-GATCAAAT
1 GGCATCTTTAAAGACATCAAAT
* *
90500 GGCATC-TTAATGACATCTAAT
1 GGCATCTTTAAAGACATCAAAT
90521 GGCATCTTT
1 GGCATCTTT
90530 GGTGCGATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 5 0.20
21 18 0.72
22 2 0.08
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (22 bp):
GGCATCTTTAAAGACATCAAAT
Found at i:96994 original size:16 final size:16
Alignment explanation
Indices: 96973--97004 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
96963 TAATTGATTA
96973 CTTAATTTACTTTGCT
1 CTTAATTTACTTTGCT
*
96989 CTTAATTTATTTTGCT
1 CTTAATTTACTTTGCT
97005 AGTTATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.59
Consensus pattern (16 bp):
CTTAATTTACTTTGCT
Found at i:98286 original size:13 final size:13
Alignment explanation
Indices: 98268--98294 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
98258 TTCCTACCCC
98268 TAAAATGAAACCA
1 TAAAATGAAACCA
98281 TAAAATGAAACCA
1 TAAAATGAAACCA
98294 T
1 T
98295 CACCAACTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.15, G:0.07, T:0.19
Consensus pattern (13 bp):
TAAAATGAAACCA
Found at i:101927 original size:30 final size:30
Alignment explanation
Indices: 101834--101931 Score: 99
Period size: 33 Copynumber: 3.2 Consensus size: 30
101824 AAAGGATCAA
* **
101834 ATGGCCGGTTGT-GCGCGGATGCCCCATGCG
1 ATGGCCGGTTGTGGC-CGGTTGCTGCATGCG
* * *
101864 ATGACCGGTTGTGGCCGGTTGTTGCCTCGTGCG
1 ATGGCCGGTTGTGGCCGGTTGCTG---CATGCG
101897 ATGGCCGGTTGTGGCCGGTTGCTGCATGCG
1 ATGGCCGGTTGTGGCCGGTTGCTGCATGCG
101927 ATGGC
1 ATGGC
101932 GCATACGATG
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
30 26 0.47
31 2 0.04
33 27 0.49
ACGTcount: A:0.08, C:0.26, G:0.41, T:0.26
Consensus pattern (30 bp):
ATGGCCGGTTGTGGCCGGTTGCTGCATGCG
Found at i:110664 original size:11 final size:11
Alignment explanation
Indices: 110648--110677 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
110638 GAAGTTCGTG
*
110648 TTTGAAGATTA
1 TTTGAAGATAA
110659 TTTGAAGATAA
1 TTTGAAGATAA
110670 TTTGAAGA
1 TTTGAAGA
110678 ATTGAAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (11 bp):
TTTGAAGATAA
Found at i:119101 original size:19 final size:18
Alignment explanation
Indices: 119077--119112 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
119067 TGAAGACTTA
119077 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
119096 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
119113 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:137272 original size:14 final size:16
Alignment explanation
Indices: 137242--137273 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
137232 TTAATTTCAT
137242 CTTCAAGAGCAGAGAC
1 CTTCAAGAGCAGAGAC
137258 CTTC-AGAGC-GAGAC
1 CTTCAAGAGCAGAGAC
137272 CT
1 CT
137274 CTTTTCTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (16 bp):
CTTCAAGAGCAGAGAC
Found at i:144661 original size:6 final size:6
Alignment explanation
Indices: 144645--144675 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
144635 CAAAGCAAAA
144645 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
144676 TAGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:149390 original size:6 final size:6
Alignment explanation
Indices: 149374--149404 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
149364 CAAAGCAAAA
149374 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
149405 TAGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:150753 original size:22 final size:21
Alignment explanation
Indices: 150723--150781 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
150713 AGTTCTTACT
* *
150723 TCTTGAAATAATTCTTCAATTG
1 TCTTCAAATAA-TCTTCAATTA
150745 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTC-AATTA
150764 TCTTCAAATAATCTTCAA
1 TCTTCAAATAATCTTCAA
150782 ACACGAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 1 0.03
21 3 0.10
22 11 0.35
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (21 bp):
TCTTCAAATAATCTTCAATTA
Found at i:150768 original size:11 final size:11
Alignment explanation
Indices: 150751--150782 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
150741 ATTGTCTTCA
150751 AATCTTCAAAT
1 AATCTTCAAAT
*
150762 TATCTTCAAAT
1 AATCTTCAAAT
150773 AATCTTCAAA
1 AATCTTCAAA
150783 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:150782 original size:22 final size:22
Alignment explanation
Indices: 150723--150782 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
150713 AGTTCTTACT
* *
150723 TCTTGAAATAATTCTTC-AATTG
1 TCTTCAAATAA-TCTTCAAATTA
150745 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTCAAATTA
150764 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
150783 CACGAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 11 0.34
20 1 0.03
21 1 0.03
22 14 0.44
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATTA
Found at i:151115 original size:33 final size:33
Alignment explanation
Indices: 151073--151136 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
151063 AGCCGCGCAA
* *
151073 CACCGGCCACGCGACTTGGAGATGCCCGGCCAT
1 CACCGGCCACGCGACATGGACATGCCCGGCCAT
*
151106 CACCGGCCACGCGACATGGCCATGCCCGGCC
1 CACCGGCCACGCGACATGGACATGCCCGGCC
151137 GCATGATCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.17, C:0.44, G:0.30, T:0.09
Consensus pattern (33 bp):
CACCGGCCACGCGACATGGACATGCCCGGCCAT
Found at i:152175 original size:11 final size:10
Alignment explanation
Indices: 152159--152197 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 10
152149 AGTTATATCG
152159 AAAAATATAAA
1 AAAAATA-AAA
152170 AAAAATAAAA
1 AAAAATAAAA
152180 AATAAATAAATA
1 AA-AAATAAA-A
152192 AAAAAT
1 AAAAAT
152198 CGACCAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.19
11 18 0.69
12 3 0.12
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:157629 original size:33 final size:32
Alignment explanation
Indices: 157593--157705 Score: 127
Period size: 33 Copynumber: 3.4 Consensus size: 32
157583 GGGAAGCCGC
157593 GCAACACCGGCCACGCGACTTGGAGATGCCCG
1 GCAACACCGGCCACGCGACTTGGAGATGCCCG
* * *
157625 CGCAACACCGGCCACGCGAATTAGAGATGTCCG
1 -GCAACACCGGCCACGCGACTTGGAGATGCCCG
* * **
157658 GCAATCACCGGCCATGCGACATGGCCATGCCCG
1 GCAA-CACCGGCCACGCGACTTGGAGATGCCCG
*
157691 GCCACAACCGGCCAC
1 GCAAC-ACCGGCCAC
157706 ATGATCCTTT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 5 0.08
33 61 0.92
ACGTcount: A:0.24, C:0.39, G:0.27, T:0.10
Consensus pattern (32 bp):
GCAACACCGGCCACGCGACTTGGAGATGCCCG
Found at i:159620 original size:17 final size:17
Alignment explanation
Indices: 159585--159617 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
159575 CTGGGCGGCC
*
159585 TGATCACTATGTTAGGG
1 TGATCACTATGTGAGGG
159602 TGATCA-TATGTGAGGG
1 TGATCACTATGTGAGGG
159618 GTGTGAGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.24, C:0.09, G:0.33, T:0.33
Consensus pattern (17 bp):
TGATCACTATGTGAGGG
Done.