Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024421.1 Corchorus olitorius cultivar O-4 contig24454, 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: 55938
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TA 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 TA T
38 TCCCACTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2219 original size:28 final size:29
Alignment explanation
Indices: 2188--2244 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2178 TATATTTTGC
* *
2188 TTTT-GGGACAAAATAATTCCTTATGTTT
1 TTTTCGGGACAAAATAATCCCTTACGTTT
*
2216 TTTTCGGGACAAATTAATCCCTTACGTTT
1 TTTTCGGGACAAAATAATCCCTTACGTTT
2245 CAAAAATGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (29 bp):
TTTTCGGGACAAAATAATCCCTTACGTTT
Found at i:2423 original size:31 final size:31
Alignment explanation
Indices: 2388--2452 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
2378 AAGGGACTAA
* *
2388 TTTGTCCCAAAAGAAAAATATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAAGGATTTT
2419 TTTGTCCCAAAAGAAAAACATAAAGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAAGGATTTT
2450 TTT
1 TTT
2453 AGTATTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAAGGATTTT
Found at i:3230 original size:126 final size:125
Alignment explanation
Indices: 3062--3300 Score: 336
Period size: 126 Copynumber: 1.9 Consensus size: 125
3052 CTTATTTTTC
* * **
3062 AAATATATTTCTTAAGTGTCATTTTTAAACTTTTACAATTTTACTCAATTAAAAACTCTATTTTT
1 AAATATATTTCTTAAATGACATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
* *
3127 ATTTAATCAAA-TCTAATATATTTATAACTATTTTATTTTTACTATTTTACTATTTTAATT
66 ATTTAATCAAATTC-AATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
* * ** *
3187 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAGTTTTATTTTACCAAAAATTCTATTTT
1 AAATATATTTCTTAAATGACATT-TTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTT
* *
3252 TATTTAATTAAATTCAATATTTTTATAACTATTTTATCTTTACCATTTT
65 TATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTT
3301 TTAGGGAATT
Statistics
Matches: 99, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
125 21 0.21
126 76 0.77
127 2 0.02
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (125 bp):
AAATATATTTCTTAAATGACATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
ATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
Found at i:3507 original size:29 final size:31
Alignment explanation
Indices: 3452--3514 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
3442 ACTAAATACT
* * *
3452 AAAAAAGTCCTTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGAAC
3483 AAAAAAATCCCTTATG-TTTT-TTTTGGAAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGAAC
3512 AAA
1 AAA
3515 TTAGTCCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.38
30 4 0.14
31 14 0.48
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGAAC
Found at i:3522 original size:29 final size:31
Alignment explanation
Indices: 3452--3524 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
3442 ACTAAATACT
* *
3452 AAAAAAGTCCTTTATGTTTTTCTTTTGGGAC
1 AAAAAAGTCCCTTATGTTTTTCTTTTGGAAC
*
3483 AAAAAAATCCCTTATG-TTTT-TTTTGGAAC
1 AAAAAAGTCCCTTATGTTTTTCTTTTGGAAC
**
3512 AAATTAGTCCCTT
1 AAAAAAGTCCCTT
3525 GCTGAGGTGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 18 0.50
30 4 0.11
31 14 0.39
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (31 bp):
AAAAAAGTCCCTTATGTTTTTCTTTTGGAAC
Found at i:3706 original size:29 final size:30
Alignment explanation
Indices: 3658--3737 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
3648 CTCATTTTTG
* *
3658 AAACGTAAGGGATTAATTTGTCCCAAAA-A
1 AAACATAAGGGATTATTTTGTCCCAAAACA
**
3687 AATTATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA-CA
*
3718 AAACATAAGGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
3738 GGTATTTAGC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 24 0.57
31 18 0.43
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.31
Consensus pattern (30 bp):
AAACATAAGGGATTATTTTGTCCCAAAACA
Found at i:4348 original size:103 final size:104
Alignment explanation
Indices: 4202--4460 Score: 389
Period size: 103 Copynumber: 2.5 Consensus size: 104
4192 AGTTTAGCCT
*
4202 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
*
4267 AATAAT-TTATTTATAGGGTTTTAGAAATAAAATACAAAAC
65 AATAATATT-GTTATAGGGTTTTAGAAATAAAATACAAAAC
*
4307 TAATTTCACTAAGTTTAG-CCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTA
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
* *
4371 ATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 ATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* ** *
4410 TAA-TTCACTAAATTTAGCCCAAATTAAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATT-AAAATTTTATTTTTATTTTAAGGGT
4461 TAGAAAAATT
Statistics
Matches: 142, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
102 13 0.09
103 87 0.61
104 24 0.17
105 18 0.13
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (104 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:4646 original size:29 final size:31
Alignment explanation
Indices: 4591--4653 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
4581 CAAAGTCCCT
* * *
4591 AAAAAAGTCCTTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGAAC
4622 AAAAAAATCCCTTATG-TTTT-TTTTGGAAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGAAC
4651 AAA
1 AAA
4654 TTAGTCCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.38
30 4 0.14
31 14 0.48
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGAAC
Found at i:4661 original size:29 final size:31
Alignment explanation
Indices: 4591--4663 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
4581 CAAAGTCCCT
* *
4591 AAAAAAGTCCTTTATGTTTTTCTTTTGGGAC
1 AAAAAAGTCCCTTATGTTTTTCTTTTGGAAC
*
4622 AAAAAAATCCCTTATG-TTTT-TTTTGGAAC
1 AAAAAAGTCCCTTATGTTTTTCTTTTGGAAC
**
4651 AAATTAGTCCCTT
1 AAAAAAGTCCCTT
4664 GCTGAGGTGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 18 0.50
30 4 0.11
31 14 0.39
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (31 bp):
AAAAAAGTCCCTTATGTTTTTCTTTTGGAAC
Found at i:4853 original size:28 final size:30
Alignment explanation
Indices: 4797--4876 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
4787 CTCATTTTTG
* * *
4797 AAACGTAAAGGATTAATTTGTCCCGAAAA-
1 AAACATAAGGGATTATTTTGTCCCGAAAAC
4826 AAACATAAGGGATTATTTTGTCCC-AAAAGC
1 AAACATAAGGGATTATTTTGTCCCGAAAA-C
* *
4856 AGAACTTAAGGGATTTTTTTG
1 A-AACATAAGGGATTATTTTG
4877 GATATTTAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 4 0.09
29 21 0.49
30 1 0.02
31 17 0.40
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (30 bp):
AAACATAAGGGATTATTTTGTCCCGAAAAC
Found at i:5899 original size:12 final size:12
Alignment explanation
Indices: 5882--5920 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5872 AAAAACCCTT
*
5882 TCTCTTTCTTTC
1 TCTCTTTCTCTC
5894 TCTCTTTCTCTC
1 TCTCTTTCTCTC
* *
5906 TTTGTTTCTCTC
1 TCTCTTTCTCTC
5918 TCT
1 TCT
5921 GGGTTAAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (12 bp):
TCTCTTTCTCTC
Found at i:7162 original size:20 final size:20
Alignment explanation
Indices: 7137--7181 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
7127 GGCTCACCTA
7137 TTTATGTACTCTATATGATT
1 TTTATGTACTCTATATGATT
7157 TTTATGTACTCTATATGATT
1 TTTATGTACTCTATATGATT
7177 TTTAT
1 TTTAT
7182 TTTGTTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (20 bp):
TTTATGTACTCTATATGATT
Found at i:11625 original size:21 final size:21
Alignment explanation
Indices: 11599--11725 Score: 159
Period size: 21 Copynumber: 6.0 Consensus size: 21
11589 GAGTCACGAC
11599 AGCGAATGCCTAATTCAAGGG
1 AGCGAATGCCTAATTCAAGGG
*
11620 AGCGAATGCCTGATTCAAGGG
1 AGCGAATGCCTAATTCAAGGG
* *
11641 AGCGAATGCCTGATTCGAGGG
1 AGCGAATGCCTAATTCAAGGG
* **
11662 AGCGAATGCCTGACCCAAGGG
1 AGCGAATGCCTAATTCAAGGG
*
11683 AGCGAATGCCTGAA-CCAAGGG
1 AGCGAATGCCT-AATTCAAGGG
11704 AGCGAATGCCTGAA-TCAAGGG
1 AGCGAATGCCT-AATTCAAGGG
11725 A
1 A
11726 AGCCAGCATG
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
21 97 0.99
22 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (21 bp):
AGCGAATGCCTAATTCAAGGG
Found at i:11662 original size:42 final size:42
Alignment explanation
Indices: 11599--11725 Score: 191
Period size: 42 Copynumber: 3.0 Consensus size: 42
11589 GAGTCACGAC
* *
11599 AGCGAATGCCTAATTCAAGGGAGCGAATGCCTGATTCAAGGG
1 AGCGAATGCCTGATTCAAGGGAGCGAATGCCTGAATCAAGGG
* **
11641 AGCGAATGCCTGATTCGAGGGAGCGAATGCCTGACCCAAGGG
1 AGCGAATGCCTGATTCAAGGGAGCGAATGCCTGAATCAAGGG
**
11683 AGCGAATGCCTGAACCAAGGGAGCGAATGCCTGAATCAAGGG
1 AGCGAATGCCTGATTCAAGGGAGCGAATGCCTGAATCAAGGG
11725 A
1 A
11726 AGCCAGCATG
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (42 bp):
AGCGAATGCCTGATTCAAGGGAGCGAATGCCTGAATCAAGGG
Found at i:11702 original size:63 final size:63
Alignment explanation
Indices: 11599--11725 Score: 191
Period size: 63 Copynumber: 2.0 Consensus size: 63
11589 GAGTCACGAC
** ** * *
11599 AGCGAATGCCTAATTCAAGGGAGCGAATGCCTGATTCAAGGGAGCGAATGCCTGATTCGAGGG
1 AGCGAATGCCTAACCCAAGGGAGCGAATGCCTGAACCAAGGGAGCGAATGCCTGAATCAAGGG
*
11662 AGCGAATGCCTGACCCAAGGGAGCGAATGCCTGAACCAAGGGAGCGAATGCCTGAATCAAGGG
1 AGCGAATGCCTAACCCAAGGGAGCGAATGCCTGAACCAAGGGAGCGAATGCCTGAATCAAGGG
11725 A
1 A
11726 AGCCAGCATG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (63 bp):
AGCGAATGCCTAACCCAAGGGAGCGAATGCCTGAACCAAGGGAGCGAATGCCTGAATCAAGGG
Found at i:22759 original size:14 final size:14
Alignment explanation
Indices: 22740--22766 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22730 CTTTTAATTT
22740 TTGTTAATCTTTGA
1 TTGTTAATCTTTGA
22754 TTGTTAATCTTTG
1 TTGTTAATCTTTG
22767 TAGAAGGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (14 bp):
TTGTTAATCTTTGA
Found at i:24683 original size:18 final size:18
Alignment explanation
Indices: 24660--24700 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
24650 AGCCCAAAGC
*
24660 ATGGCATCGTGTGCTCTT
1 ATGGCATCGTGCGCTCTT
24678 ATGGCATCGTGCGCTCTT
1 ATGGCATCGTGCGCTCTT
24696 ATGGC
1 ATGGC
24701 GTTATGTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.24, G:0.29, T:0.34
Consensus pattern (18 bp):
ATGGCATCGTGCGCTCTT
Found at i:24711 original size:18 final size:18
Alignment explanation
Indices: 24660--24712 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
24650 AGCCCAAAGC
*
24660 ATGGCATCGTGTGCTCTT
1 ATGGCATCATGTGCTCTT
* *
24678 ATGGCATCGTGCGCTCTT
1 ATGGCATCATGTGCTCTT
* *
24696 ATGGCGTTATGTGCTCT
1 ATGGCATCATGTGCTCT
24713 CCGCTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.11, C:0.23, G:0.28, T:0.38
Consensus pattern (18 bp):
ATGGCATCATGTGCTCTT
Found at i:25268 original size:59 final size:59
Alignment explanation
Indices: 25196--25307 Score: 215
Period size: 59 Copynumber: 1.9 Consensus size: 59
25186 ATAAATACCG
*
25196 TGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACTACGCCA
1 TGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCATGTGGGGGATGCCCACTACGCCA
25255 TGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCATGTGGGGGATGCCCACT
1 TGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCATGTGGGGGATGCCCACT
25308 CGGTCGTATG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.27
Consensus pattern (59 bp):
TGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCATGTGGGGGATGCCCACTACGCCA
Found at i:29693 original size:31 final size:31
Alignment explanation
Indices: 29658--29772 Score: 176
Period size: 31 Copynumber: 3.7 Consensus size: 31
29648 GCATGTCACG
*
29658 TGTACCAAAAAGTGACACGTGTCACACCACA
1 TGTACCAAAAAGTGACACGTGTCACGCCACA
*
29689 TGTACCAAAAAGTGACACGTGGCACGCCACA
1 TGTACCAAAAAGTGACACGTGTCACGCCACA
*
29720 TGTACCAAAAAGTGACATGTGTCACGCCACA
1 TGTACCAAAAAGTGACACGTGTCACGCCACA
* *
29751 TGTGTCAAAAAAGTGACACGTG
1 TGT-ACCAAAAAGTGACACGTG
29773 GCATGCCTCG
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
31 61 0.80
32 15 0.20
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (31 bp):
TGTACCAAAAAGTGACACGTGTCACGCCACA
Found at i:29742 original size:62 final size:63
Alignment explanation
Indices: 29643--29801 Score: 198
Period size: 62 Copynumber: 2.6 Consensus size: 63
29633 ACGATGTTCG
* * * *
29643 ACGTGGCATGTCACGTGTACCAAAAAGTGACACGTGTCACACCACATGT-ACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGACACGTGTCACACCACATGTGACAAAAAAGTGAC
* * *
29705 ACGTGGCACGCCACATGTACCAAAAAGTGACATGTGTCACGCCACATGTGTCAAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGACACGTGTCACACCACATGTGACAAAAAAGTGAC
* * * *
29768 ACGTGGCATGCCTCGTGCA-CAAAAAG-GACACGTG
1 ACGTGGCACGCCACATGTACCAAAAAGTGACACGTG
29802 CTACGTGTCA
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
61 7 0.08
62 51 0.61
63 26 0.31
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (63 bp):
ACGTGGCACGCCACATGTACCAAAAAGTGACACGTGTCACACCACATGTGACAAAAAAGTGAC
Found at i:29791 original size:31 final size:31
Alignment explanation
Indices: 29643--29801 Score: 171
Period size: 31 Copynumber: 5.2 Consensus size: 31
29633 ACGATGTTCG
* *
29643 ACGTGGCATGTCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * *
29674 ACGTGTCACACCACATGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
*
29705 ACGTGGCACGCCACATGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * *
29736 ATGTGTCACGCCACATGTGT-CAAAAAAGTGAC
1 ACGTGGCACGCCAC--GTGTACCAAAAAGTGAC
* * *
29768 ACGTGGCATGCCTCGTGCA-CAAAAAG-GAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
29797 ACGTG
1 ACGTG
29802 CTACGTGTCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.07
30 9 0.08
31 67 0.62
32 21 0.19
33 3 0.03
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:30977 original size:3 final size:3
Alignment explanation
Indices: 30971--31014 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
30961 ATAGGTTTTT
* *
30971 TTC TTC TTC TTT TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
31015 TTGAGCACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:30986 original size:15 final size:15
Alignment explanation
Indices: 30966--31016 Score: 75
Period size: 15 Copynumber: 3.2 Consensus size: 15
30956 CAAATATAGG
30966 TTTTTTTCTTCTTCT
1 TTTTTTTCTTCTTCT
30981 TTTTTTTCTTCTTCT
1 TTTTTTTCTTCTTCT
30996 TCTTCTTCTTCTTCTTCT
1 T-TT-TT-TTCTTCTTCT
31014 TTT
1 TTT
31017 GAGCACAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 11 0.33
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTTCTTCTTCT
Found at i:30989 original size:12 final size:12
Alignment explanation
Indices: 30967--31005 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
30957 AAATATAGGT
30967 TTTTTTCTTCTTC
1 TTTTTT-TTCTTC
30980 TTTTTTTTCTTC
1 TTTTTTTTCTTC
* *
30992 TTCTTCTTCTTC
1 TTTTTTTTCTTC
31004 TT
1 TT
31006 CTTCTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 18 0.75
13 6 0.25
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTTCTTC
Found at i:37935 original size:22 final size:22
Alignment explanation
Indices: 37910--37958 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
37900 ATTTAAAAAA
* *
37910 TATATTTCGGGGACGGATATAT
1 TATATTTCGGGAACGAATATAT
37932 TATATTTCGGGAACGAATATAT
1 TATATTTCGGGAACGAATATAT
37954 TATAT
1 TATAT
37959 GTTAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (22 bp):
TATATTTCGGGAACGAATATAT
Found at i:43304 original size:253 final size:253
Alignment explanation
Indices: 42856--43340 Score: 844
Period size: 253 Copynumber: 1.9 Consensus size: 253
42846 TTAAAATTTC
42856 AATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGTCACCTGCCACGTCAGCAAAAAA
1 AATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGTCACCTGCCACGTCAGCAAAAAA
* * ** *
42921 TACGGTGTTAGTACCATGTCAGCATATTTGACGGGTCTGTCACGGCATGCTAACGTGAGAGACCT
66 GACGGTGTTAGTACCACGTCAGCATATTTGACGGGTCTGTCACGGCACACTAACATGAGAGACCT
42986 CGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAGAAAAAAAAAGTACAGGGACCAAAATC
131 CGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAGAAAAAAAAAGTACAGGGACCAAAATC
* * *
43051 AACATTTTGTATAGTACAGGGACCTCCCGGGTACTTTAACCAAAATAAATTTCAATAA
196 AACATTTCGTATAGTACAGGAACCTCCCGGATACTTTAACCAAAATAAATTTCAATAA
* *
43109 AATAAAATATATTAAAAAAATATTTAATTTTTATTTCACGTGTCACCTGCCATGTCAGCAAAAAA
1 AATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGTCACCTGCCACGTCAGCAAAAAA
* * *
43174 GACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGCACACTACCATGAGGGACCT
66 GACGGTGTTAGTACCACGTCAGCATATTTGACGGGTCTGTCACGGCACACTAACATGAGAGACCT
*
43239 CGGGTGATAGGTTCTGATAGTAGAGGGATGAATTTGTAGAAAAAAAAAGTACAGGGACCAAAATC
131 CGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAGAAAAAAAAAGTACAGGGACCAAAATC
43304 AACATTTCGTATAGTACAGGAACCTCCCGGATACTTT
196 AACATTTCGTATAGTACAGGAACCTCCCGGATACTTT
43341 TACCTATATC
Statistics
Matches: 218, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
253 218 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (253 bp):
AATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGTCACCTGCCACGTCAGCAAAAAA
GACGGTGTTAGTACCACGTCAGCATATTTGACGGGTCTGTCACGGCACACTAACATGAGAGACCT
CGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAGAAAAAAAAAGTACAGGGACCAAAATC
AACATTTCGTATAGTACAGGAACCTCCCGGATACTTTAACCAAAATAAATTTCAATAA
Found at i:44195 original size:25 final size:25
Alignment explanation
Indices: 44165--44218 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
44155 TTTTTCAAAT
44165 ATATTTCTAAAT-TGCCATTATTAAA
1 ATATTT-TAAATATGCCATTATTAAA
* *
44190 ATATTTTAATTATGTCATTATTAAA
1 ATATTTTAAATATGCCATTATTAAA
44215 ATAT
1 ATAT
44219 AATTTTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (25 bp):
ATATTTTAAATATGCCATTATTAAA
Found at i:44296 original size:25 final size:26
Alignment explanation
Indices: 44262--44317 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
44252 TTTTTCAAAT
* *
44262 ATATTTTTAAAT-TGTCATTATTAAA
1 ATATATTTAAATATGCCATTATTAAA
*
44287 ATATATTTAACTATGCCATTATTAAA
1 ATATATTTAAATATGCCATTATTAAA
44313 ATATA
1 ATATA
44318 ATAATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (26 bp):
ATATATTTAAATATGCCATTATTAAA
Found at i:44629 original size:48 final size:48
Alignment explanation
Indices: 44542--44634 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
44532 GCCAAGTCTT
* *
44542 ATTGAAATATCTATATCCATCTAACCAAATCTTACCCACACTGGACTC
1 ATTGAAATATCTATATCCATCTAACAAAATCTCACCCACACTGGACTC
** * *
44590 ATTGAAATATCTATATTTATCTAACAAAATCTCAGCCACATTGGA
1 ATTGAAATATCTATATCCATCTAACAAAATCTCACCCACACTGGA
44635 TTTAAGGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.31
Consensus pattern (48 bp):
ATTGAAATATCTATATCCATCTAACAAAATCTCACCCACACTGGACTC
Found at i:52818 original size:19 final size:19
Alignment explanation
Indices: 52794--52832 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
52784 TTCCTGAAGA
52794 ATGCGAAAACGTTAATGAT
1 ATGCGAAAACGTTAATGAT
52813 ATGCGAAAACGTTAATGAT
1 ATGCGAAAACGTTAATGAT
52832 A
1 A
52833 GAATGTCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (19 bp):
ATGCGAAAACGTTAATGAT
Found at i:52863 original size:14 final size:14
Alignment explanation
Indices: 52846--52874 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52836 TGTCGAACTC
52846 TTAATGATAGAATG
1 TTAATGATAGAATG
52860 TTAATGATAGAATG
1 TTAATGATAGAATG
52874 T
1 T
52875 CGAACTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (14 bp):
TTAATGATAGAATG
Found at i:55474 original size:29 final size:29
Alignment explanation
Indices: 55441--55604 Score: 170
Period size: 29 Copynumber: 5.6 Consensus size: 29
55431 GCTCGAGGGA
* * *
55441 ATTTTGTTCATTTTTGCATATATGGGGGC
1 ATTTTGGTCATTTTTGCACATATAGGGGC
*
55470 ATTTTGGTCATTTTTGCACATCTAGGGGC
1 ATTTTGGTCATTTTTGCACATATAGGGGC
*
55499 ATTTTGGTC-TTTTTTCACATATCCAGGGGC
1 ATTTTGGTCATTTTTGCACATAT--AGGGGC
* **
55529 ATTTTGGTCATTTTTGCATATCCAGGGGC
1 ATTTTGGTCATTTTTGCACATATAGGGGC
* * *
55558 ATTTTGGTCATCTTTACACAT-TCTGGGGC
1 ATTTTGGTCATTTTTGCACATAT-AGGGGC
* *
55587 AGTTTGGTTATTTTTGCA
1 ATTTTGGTCATTTTTGCA
55605 TACTCTAGGT
Statistics
Matches: 112, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
28 11 0.10
29 77 0.69
30 15 0.13
31 9 0.08
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.45
Consensus pattern (29 bp):
ATTTTGGTCATTTTTGCACATATAGGGGC
Found at i:55532 original size:59 final size:58
Alignment explanation
Indices: 55465--55613 Score: 201
Period size: 59 Copynumber: 2.5 Consensus size: 58
55455 TGCATATATG
* * *
55465 GGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTC-TTTTTTCACATATCCA
1 GGGGCATTTTGGTCATTTTTGCATATCTAGGGGCATTTTGGTCATCTTTACACAT-T-CA
* *
55524 GGGGCATTTTGGTCATTTTTGCATATCCAGGGGCATTTTGGTCATCTTTACACATTCT
1 GGGGCATTTTGGTCATTTTTGCATATCTAGGGGCATTTTGGTCATCTTTACACATTCA
* *
55582 GGGGCAGTTTGGTTATTTTTGCATACTCTAGG
1 GGGGCATTTTGGTCATTTTTGCATA-TCTAGG
55614 TTCTCCTTGG
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 24 0.30
59 47 0.59
60 9 0.11
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.42
Consensus pattern (58 bp):
GGGGCATTTTGGTCATTTTTGCATATCTAGGGGCATTTTGGTCATCTTTACACATTCA
Done.