Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008580.1 Corchorus capsularis cultivar CVL-1 contig08601, 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: 13275
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2510 original size:32 final size:32
Alignment explanation
Indices: 2465--2544 Score: 151
Period size: 32 Copynumber: 2.5 Consensus size: 32
2455 CGGAGCCTCC
*
2465 CCACGGCAAGCCGCCCTCATGGGGCGGCTTCG
1 CCACGGCAGGCCGCCCTCATGGGGCGGCTTCG
2497 CCACGGCAGGCCGCCCTCATGGGGCGGCTTCG
1 CCACGGCAGGCCGCCCTCATGGGGCGGCTTCG
2529 CCACGGCAGGCCGCCC
1 CCACGGCAGGCCGCCC
2545 CCAGTGGGAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.11, C:0.44, G:0.35, T:0.10
Consensus pattern (32 bp):
CCACGGCAGGCCGCCCTCATGGGGCGGCTTCG
Found at i:2633 original size:33 final size:33
Alignment explanation
Indices: 2472--2676 Score: 156
Period size: 33 Copynumber: 6.3 Consensus size: 33
2462 TCCCCACGGC
*
2472 AAGCCGCCCTCA-TGGGGCGGCTTCGCCACGG-C
1 AAGCCGCCC-CAGTGGGGCGGCTTCGCCACGGTG
* *
2504 AGGCCGCCCTCA-TGGGGCGGCTTCGCCACGG-C
1 AAGCCGCCC-CAGTGGGGCGGCTTCGCCACGGTG
* * ** *
2536 AGGCCGCCCCCAGTGGGACGGCCTT-TTCATGGTG
1 AAGCCG-CCCCAGTGGGGCGG-CTTCGCCACGGTG
* ** *
2570 AAGCCGCCCCAGTGGGGTGGCCTT-TTCATGGTG
1 AAGCCGCCCCAGTGGGGCGG-CTTCGCCACGGTG
* *
2603 AAGCCGCCCCAGTGGAGCGGCTTCGCCATGGTTG
1 AAGCCGCCCCAGTGGGGCGGCTTCGCCACGG-TG
* *
2637 -AGCCTCCCAAGTGGGGCGGCTTCGCCACGGT-
1 AAGCCGCCCCAGTGGGGCGGCTTCGCCACGGTG
2668 AAGCCGCCC
1 AAGCCGCCC
2677 TCTTGGGACG
Statistics
Matches: 148, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
32 50 0.34
33 88 0.59
34 10 0.07
ACGTcount: A:0.13, C:0.36, G:0.35, T:0.17
Consensus pattern (33 bp):
AAGCCGCCCCAGTGGGGCGGCTTCGCCACGGTG
Found at i:2875 original size:10 final size:11
Alignment explanation
Indices: 2853--2877 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2843 AGCAAAGGGC
2853 AAAAACGTAAA
1 AAAAACGTAAA
2864 AAAAACGTAAA
1 AAAAACGTAAA
2875 AAA
1 AAA
2878 TGGGGCGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAACGTAAA
Found at i:3550 original size:2 final size:2
Alignment explanation
Indices: 3545--3588 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
3535 ATCTAAGTTT
* *
3545 TA TA TA TA TA -A TA TA TA TA TA TA TC TA TA -A TA TA TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3585 TA TA
1 TA TA
3589 AACATACATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3563 original size:15 final size:15
Alignment explanation
Indices: 3545--3589 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
3535 ATCTAAGTTT
*
3545 TATATATAT-AATATA
1 TATATATATCTATA-A
3560 TATATATATCTATAA
1 TATATATATCTATAA
3575 TATATATATCTATAA
1 TATATATATCTATAA
3590 ACATACATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 25 0.89
16 3 0.11
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATATATCTATAA
Found at i:3567 original size:19 final size:19
Alignment explanation
Indices: 3545--3588 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3535 ATCTAAGTTT
3545 TATATATATAATATATATA
1 TATATATATAATATATATA
*
3564 TATATCTATAATATATATA
1 TATATATATAATATATATA
*
3583 TCTATA
1 TATATA
3589 AACATACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (19 bp):
TATATATATAATATATATA
Found at i:3719 original size:15 final size:17
Alignment explanation
Indices: 3688--3729 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
3678 TTATCAGGGG
**
3688 TATTTCGGTACTTTTG-
1 TATTTCGGTTTTTTTGT
3704 TATTT-GGTTTTTTTGT
1 TATTTCGGTTTTTTTGT
3720 TATTTCGGTT
1 TATTTCGGTT
3730 GATGGTTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 8 0.36
16 10 0.45
17 4 0.18
ACGTcount: A:0.10, C:0.07, G:0.19, T:0.64
Consensus pattern (17 bp):
TATTTCGGTTTTTTTGT
Found at i:4955 original size:15 final size:15
Alignment explanation
Indices: 4937--5004 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
4927 TATATTATAA
*
4937 TTATATATTTTTACT
1 TTATATATATTTACT
* **
4952 TTATATATA-TAAAG
1 TTATATATATTTACT
*
4966 TAATTATATATTTACT
1 TTA-TATATATTTACT
*
4982 TTATATATATTTAAT
1 TTATATATATTTACT
4997 TTATATAT
1 TTATATAT
5005 TATAATTATA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
14 4 0.10
15 33 0.80
16 4 0.10
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (15 bp):
TTATATATATTTACT
Found at i:4961 original size:30 final size:30
Alignment explanation
Indices: 4925--5005 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 30
4915 AAATATAAAT
4925 TATATATTATAATTATATATTTTTACTTTA
1 TATATATTATAATTATATATTTTTACTTTA
*
4955 TATATATAAAGTAATTATATA--TTTACTTTA
1 TATATAT-TA-TAATTATATATTTTTACTTTA
4985 TATATATT-TAATTTATATATT
1 TATATATTATAA-TTATATATT
5006 ATAATTATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
27 3 0.07
28 7 0.16
30 23 0.52
31 1 0.02
32 10 0.23
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (30 bp):
TATATATTATAATTATATATTTTTACTTTA
Found at i:4971 original size:45 final size:46
Alignment explanation
Indices: 4916--5023 Score: 132
Period size: 45 Copynumber: 2.3 Consensus size: 46
4906 AAAAATAATA
* *
4916 AATATAAATTATATATTATA-ATTATATATTTTTACTTTATATA-TAT
1 AATAT-AATTATATATT-TACATTATATATATTTAATTTATATATTAT
*
4962 AA-AGTAATTATATATTTACTTTATATATATTTAATTTATATATTAT
1 AATA-TAATTATATATTTACATTATATATATTTAATTTATATATTAT
5008 AATTATAATTATATAT
1 AA-TATAATTATATAT
5024 ATCTATACTA
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
44 2 0.04
45 32 0.59
46 8 0.15
47 11 0.20
48 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.54
Consensus pattern (46 bp):
AATATAATTATATATTTACATTATATATATTTAATTTATATATTAT
Found at i:5020 original size:12 final size:13
Alignment explanation
Indices: 4922--5020 Score: 67
Period size: 13 Copynumber: 7.1 Consensus size: 13
4912 AATAAATATA
4922 AATTATATATTAT
1 AATTATATATTAT
*
4935 AATTATATATTTTT
1 AATTATATA-TTAT
*
4949 ACTTTATATATATAAAGT
1 A-ATTATATAT-T--A-T
4967 AATTATATATT-T
1 AATTATATATTAT
* *
4979 ACTTTATATATATTT
1 A-ATTATATAT-TAT
4994 AATTTATATATTAT
1 AA-TTATATATTAT
5008 AATTATA-ATTAT
1 AATTATATATTAT
5020 A
1 A
5021 TATATCTATA
Statistics
Matches: 69, Mismatches: 7, Indels: 21
0.71 0.07 0.22
Matches are distributed among these distances:
12 8 0.12
13 22 0.32
14 10 0.14
15 18 0.26
16 1 0.01
17 8 0.12
18 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (13 bp):
AATTATATATTAT
Found at i:5035 original size:21 final size:20
Alignment explanation
Indices: 4993--5035 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
4983 TATATATATT
*
4993 TAATTTATATATTATAATTA
1 TAATTTATATATTATAACTA
5013 TAATTATATATATCTAT-ACTA
1 TAATT-TATATAT-TATAACTA
5034 TA
1 TA
5036 TATAAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 12 0.60
22 3 0.15
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATTTATATATTATAACTA
Found at i:5109 original size:31 final size:31
Alignment explanation
Indices: 5074--5136 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
5064 ATGTTTTCCG
*
5074 ATTGTACCCTTATT-TTTAAAATATATTTCTA
1 ATTGTACCCTT-TTCTTTAAAACATATTTCTA
5105 ATTGTACCCTTTTCTTTAAAACATATTTCTA
1 ATTGTACCCTTTTCTTTAAAACATATTTCTA
5136 A
1 A
5137 ATTGCCATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (31 bp):
ATTGTACCCTTTTCTTTAAAACATATTTCTA
Found at i:5473 original size:19 final size:20
Alignment explanation
Indices: 5446--5483 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5436 TACTATTATT
5446 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
5466 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
5484 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:5683 original size:22 final size:22
Alignment explanation
Indices: 5655--5762 Score: 76
Period size: 22 Copynumber: 4.9 Consensus size: 22
5645 TGTCTCTATG
*
5655 TGGTTATCAAAATTTCATAAAA
1 TGGTTATCAAAATTTCATAGAA
* * *
5677 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGAA
**
5700 -GGTTATCAAAA-TTCAATAGTG
1 TGGTTATCAAAATTTC-ATAGAA
* * **
5721 TGGTTACCAAAATTTCATGGTG
1 TGGTTATCAAAATTTCATAGAA
* *
5743 TGGTTACCATAATTTCATAG
1 TGGTTATCAAAATTTCATAG
5763 GATCAGATTA
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
21 5 0.07
22 60 0.86
23 5 0.07
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGAA
Found at i:5795 original size:22 final size:22
Alignment explanation
Indices: 5770--5816 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5760 TAGGATCAGA
* *
5770 TTATTAAAATCTCTTAGGTTGG
1 TTATTAAAATCTCATAGGGTGG
* *
5792 TTATTGAAATTTCATAGGGTGG
1 TTATTAAAATCTCATAGGGTGG
5814 TTA
1 TTA
5817 ATTATCACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (22 bp):
TTATTAAAATCTCATAGGGTGG
Found at i:5877 original size:22 final size:22
Alignment explanation
Indices: 5852--5910 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
5842 ATCAAAGAGA
*
5852 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
5874 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
*
5896 TTAACAAAATTTCAT
1 TTATCAAAATTTCAT
5911 TAAATATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:5975 original size:22 final size:22
Alignment explanation
Indices: 5916--5981 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
5906 TTCATTAAAT
* *
5916 ATTTCATGGGGAGGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
* *
5938 ATTTTATAGTGTGGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
5960 ATTTCATA-TGAAGGTTAT-AAA
1 ATTTCATAGTG-AGGTTATCAAA
5981 A
1 A
5982 GTCTCAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 6 0.16
22 31 0.84
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (22 bp):
ATTTCATAGTGAGGTTATCAAA
Found at i:6084 original size:25 final size:22
Alignment explanation
Indices: 6049--6221 Score: 79
Period size: 22 Copynumber: 7.8 Consensus size: 22
6039 TGATTAACTG
* *
6049 ATTATCGAAATTTCATAGAGATCTA
1 ATTATCAAAATTTCATAGA-A--GA
*
6074 ATTATCAAAATTT-ATAGAAGG
1 ATTATCAAAATTTCATAGAAGA
* *
6095 ATTATCAAAATTTCATAG-TGTT
1 ATTATCAAAATTTCATAGAAG-A
* * *
6117 GTTATCAAAATTTCAAAG-CGA
1 ATTATCAAAATTTCATAGAAGA
* * *
6138 GATTATCAAAATTACATA-ATGTG
1 -ATTATCAAAATTTCATAGAAG-A
* *
6161 ATTATCAGAATTTCATAGAGGA
1 ATTATCAAAATTTCATAGAAGA
* * * *
6183 GTCAACAAAATTTTATA-AAGA
1 ATTATCAAAATTTCATAGAAGA
6204 GGA-TATCAAAATTTCATA
1 --ATTATCAAAATTTCATA
6222 AAAAGGTTAT
Statistics
Matches: 112, Mismatches: 28, Indels: 19
0.70 0.18 0.12
Matches are distributed among these distances:
21 17 0.15
22 75 0.67
23 3 0.03
24 5 0.04
25 12 0.11
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (22 bp):
ATTATCAAAATTTCATAGAAGA
Found at i:6121 original size:22 final size:22
Alignment explanation
Indices: 6047--6178 Score: 108
Period size: 22 Copynumber: 5.9 Consensus size: 22
6037 AGTGATTAAC
* *
6047 TGATTATCGAAATTTCATAGAGATC
1 TGATTATCAAAATTTCAT--AG-TG
* *
6072 TAATTATCAAAATTT-ATAGAAG
1 TGATTATCAAAATTTCATAG-TG
6094 -GATTATCAAAATTTCATAGTG
1 TGATTATCAAAATTTCATAGTG
* *
6115 TTG-TTATCAAAATTTCAAAGCG
1 -TGATTATCAAAATTTCATAGTG
* * *
6137 AGATTATCAAAATTACATAATG
1 TGATTATCAAAATTTCATAGTG
*
6159 TGATTATCAGAATTTCATAG
1 TGATTATCAAAATTTCATAG
6179 AGGAGTCAAC
Statistics
Matches: 86, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
21 15 0.17
22 55 0.64
23 1 0.01
24 2 0.02
25 13 0.15
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (22 bp):
TGATTATCAAAATTTCATAGTG
Found at i:6222 original size:22 final size:23
Alignment explanation
Indices: 6074--6265 Score: 113
Period size: 22 Copynumber: 8.7 Consensus size: 23
6064 TAGAGATCTA
*
6074 ATTATCAAAATTT-ATAGA-AGG
1 ATTATCAAAATTTCATAAAGAGG
** **
6095 ATTATCAAAATTTCATAGTGTTG
1 ATTATCAAAATTTCATAAAGAGG
*
6118 -TTATCAAAATTTC--AAAGCGAG
1 ATTATCAAAATTTCATAAAGAG-G
* * *
6139 ATTATCAAAATTACATAATG-TG
1 ATTATCAAAATTTCATAAAGAGG
*
6161 ATTATCAGAATTTCAT--AGAGG
1 ATTATCAAAATTTCATAAAGAGG
* * *
6182 AGTCAACAAAATTTTATAAAGAGG
1 A-TTATCAAAATTTCATAAAGAGG
*
6206 A-TATCAAAATTTCATAAAAAGG
1 ATTATCAAAATTTCATAAAGAGG
* *
6228 -TTATCAAATTTTCA-AAATG-TG
1 ATTATCAAAATTTCATAAA-GAGG
6249 ATTA-CAAAAATTTCATA
1 ATTATC-AAAATTTCATA
6266 GTGATATTTC
Statistics
Matches: 130, Mismatches: 26, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
20 3 0.02
21 21 0.16
22 95 0.73
23 2 0.02
24 9 0.07
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (23 bp):
ATTATCAAAATTTCATAAAGAGG
Found at i:6393 original size:22 final size:20
Alignment explanation
Indices: 6347--6656 Score: 141
Period size: 22 Copynumber: 14.6 Consensus size: 20
6337 TTATGGAGTA
* *
6347 ATCAAAAGTTCA-AGGAGGAT
1 ATCAAAATTTCATA-GAGGTT
6367 ATCAAAATTTCATACGAAGGTT
1 ATCAAAATTTCATA-G-AGGTT
*
6389 ATCAAAATTTCAT--AGTTT
1 ATCAAAATTTCATAGAGGTT
* *
6407 AGT-TAAATTTCACAAGAGGGTT
1 A-TCAAAATTTCA-TAGA-GGTT
* * *
6429 ATCAAAATTTTATAGTATGTAG
1 ATCAAAATTTCATAG-AGGT-T
*
6451 ATCAAAATTTCATAAGGAGATT
1 ATCAAAATTTCAT-A-GAGGTT
*
6473 AACAAAATTTCATATTGAGGTT
1 ATCAAAATTTCATA--GAGGTT
**
6495 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATA--GAGGTT
*
6517 ATCAAAATTT-GT--A-GTT
1 ATCAAAATTTCATAGAGGTT
* * * *
6533 ATCAAGATCTCATAATAAAGTT
1 ATCAAAATTTCAT-A-GAGGTT
*
6555 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATA--GAGG-TT
* *
6578 ATCAAAATTTAATAGGAAGACTT
1 ATCAAAATTTCATA-G-AG-GTT
6601 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATA--GAGGTT
*
6623 ATCATAATTTCATAGAGTGATT
1 ATCAAAATTTCATAGAG-G-TT
6645 ATCAAAATTTCA
1 ATCAAAATTTCA
6657 GAGTGTGATT
Statistics
Matches: 221, Mismatches: 43, Indels: 50
0.70 0.14 0.16
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
18 13 0.06
19 1 0.00
20 14 0.06
21 13 0.06
22 128 0.58
23 37 0.17
24 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (20 bp):
ATCAAAATTTCATAGAGGTT
Found at i:6499 original size:44 final size:44
Alignment explanation
Indices: 6347--6838 Score: 188
Period size: 44 Copynumber: 11.3 Consensus size: 44
6337 TTATGGAGTA
* * * * *
6347 ATCAAAAGTTCA-AG-GAGGATATCAAAATTTCATACGAAGGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAAGGAGATT
* * *
6389 ATCAAAATTTCATAGT----TTAGT-TAAATTTCACAA-GAGGGTT
1 ATCAAAATTTCATAGTGAGGTTA-TCAAAATTTCATAAGGA-GATT
* * *
6429 ATCAAAATTTTATAGT-ATGTAGATCAAAATTTCATAAGGAGATT
1 ATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATAAGGAGATT
* * ** * *
6473 AACAAAATTTCATATTGAGGTTATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAAGGAGATT
* * * *
6517 ATCAAAA-TT--T-GT-A-GTTATCAAGATCTCATAA-TAAAGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAAGGAGA-TT
* * *
6555 ATCAAAATTTTATAGGGAGGTTTATCAAAATTTAAT-AGGAAGACTT
1 ATCAAAATTTCATAGTGAGG-TTATCAAAATTTCATAAGG-AGA-TT
* * *
6601 ATCAAAATTTCATAGCGAGGTTATCATAATTTCAT-AGAGTGATT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAAG-GAGATT
* * * * *
6645 ATCAAAATTTCAGAGTGTGATTA-CTAACAA-TTCATATGGAGGTT
1 ATCAAAATTTCATAGTGAGGTTATC-AA-AATTTCATAAGGAGATT
** * * * * *
6689 -TTTAAATTGTCATAATGTGCTTATCAATATATATATCATACGGAGGTT
1 ATCAAAATT-TCATAGTGAGGTTATCAA-A-AT-T-TCATAAGGAGATT
* * **
6737 ATCAACATCTCATAGT-ATTGGTTATCAAAA-TTCATTGGGA-AGTT
1 ATCAAAATTTCATAGTGA--GGTTATCAAAATTTCATAAGGAGA-TT
* * * * *
6781 ATCAAAATTTCATATTGAGGTCT-TCAAAATTCCCTAGGGAGGTT
1 ATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATAAGGAGATT
* *
6825 AACCAAATTTCATA
1 ATCAAAATTTCATA
6839 AGAAGGTTAA
Statistics
Matches: 336, Mismatches: 75, Indels: 76
0.69 0.15 0.16
Matches are distributed among these distances:
37 1 0.00
38 23 0.07
39 4 0.01
40 31 0.09
41 3 0.01
42 12 0.04
43 23 0.07
44 142 0.42
45 41 0.12
46 23 0.07
47 2 0.01
48 19 0.06
49 12 0.04
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (44 bp):
ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAAGGAGATT
Found at i:6517 original size:128 final size:129
Alignment explanation
Indices: 6349--6656 Score: 315
Period size: 128 Copynumber: 2.4 Consensus size: 129
6339 ATGGAGTAAT
* * * * *
6349 CAAAAGTTCA-AG-GAGGATATCAAAATTTCATACGAAGGTTATCAAAATTTCATAGTTTAGTTA
1 CAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAG-TTA-TCA
* ** * * *
6412 A-ATTTCACAAGAGGGTTATCAAAATTTTATA-GTATGTAGATCAAAATTTCATAAGG-AGA-TT
64 AGATCTCACAAGAAAGTTATCAAAATTTTATAGGGAGGTAGATCAAAATTTAAT-AGGAAGACTT
6473 AA
128 AA
** ** *
6475 CAAAATTTCATATTGAGGTTATCAAAAAATCATAGGGAGGTTATCAAAATTT-GTAGTTATCAAG
1 CAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTTATCAAG
* * ** *
6539 ATCTCATAATAAAGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTAATAGGAAGACTTAT
66 ATCTCACAAGAAAGTTATCAAAATTTTATAGGGAGGTAGATCAAAATTTAATAGGAAGACTTAA
* * * *
6603 CAAAATTTCATAGCGAGGTTATCATAATTTCATAGAGTGATTATCAAAATTTCA
1 CAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCA
6657 GAGTGTGATT
Statistics
Matches: 146, Mismatches: 29, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
125 3 0.02
126 40 0.27
127 23 0.16
128 80 0.55
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (129 bp):
CAAAATTTCATAGCGAGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTTATCAAG
ATCTCACAAGAAAGTTATCAAAATTTTATAGGGAGGTAGATCAAAATTTAATAGGAAGACTTAA
Found at i:6583 original size:23 final size:22
Alignment explanation
Indices: 6552--6926 Score: 138
Period size: 22 Copynumber: 16.8 Consensus size: 22
6542 TCATAATAAA
*
6552 GTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATAGGGAG
* *
6574 GTTTATCAAAATTTAATAGGAAG
1 G-TTATCAAAATTTCATAGGGAG
* *
6597 ACTTATCAAAATTTCATAGCGAG
1 -GTTATCAAAATTTCATAGGGAG
* * *
6620 GTTATCATAATTTCATAGAGTG
1 GTTATCAAAATTTCATAGGGAG
* * * *
6642 ATTATCAAAATTTCAGAGTGTG
1 GTTATCAAAATTTCATAGGGAG
* *
6664 ATTA-CTAACAA-TTCATATGGAG
1 GTTATC-AA-AATTTCATAGGGAG
** ** *
6686 GTT-TTTAAATTGTCATAATGTG
1 GTTATCAAAATT-TCATAGGGAG
* *
6708 CTTATCAATATATATATCATACGGAG
1 GTTATCAA-A-AT-T-TCATAGGGAG
* * *
6734 GTTATCAACATCTCATA-GTATTG
1 GTTATCAAAATTTCATAGGGA--G
* *
6757 GTTATCAAAA-TTCATTGGGAA
1 GTTATCAAAATTTCATAGGGAG
**
6778 GTTATCAAAATTTCATATTGAG
1 GTTATCAAAATTTCATAGGGAG
* *
6800 GTCT-TCAAAATTCCCTAGGGAG
1 GT-TATCAAAATTTCATAGGGAG
* * * *
6822 GTTAACCAAATTTCATAAGAAG
1 GTTATCAAAATTTCATAGGGAG
** ***
6844 GTTAAAAATAATTT-ATAAAAAG
1 GTTATCAA-AATTTCATAGGGAG
* * * *
6866 GTTCTCGAAA-TTCTATA-GTATC
1 GTTATCAAAATTTC-ATAGGGA-G
* *
6888 GTTATTAAAATTTCATAGGAAG
1 GTTATCAAAATTTCATAGGGAG
*
6910 GTTATCGAAATTTCATA
1 GTTATCAAAATTTCATA
6927 ATAGGATCAT
Statistics
Matches: 259, Mismatches: 71, Indels: 46
0.69 0.19 0.12
Matches are distributed among these distances:
20 4 0.02
21 19 0.07
22 152 0.59
23 64 0.25
24 3 0.01
25 2 0.01
26 15 0.06
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGAG
Found at i:6605 original size:46 final size:44
Alignment explanation
Indices: 6553--6656 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 44
6543 CATAATAAAG
* *
6553 TTATCAAAATTTTATAGGGAGGTTTATCAAAATTTAATAG-GAAGA
1 TTATCAAAATTTCATAGCGAGG-TTATCAAAATTTAATAGAG-AGA
* * *
6598 CTTATCAAAATTTCATAGCGAGGTTATCATAATTTCATAGAGTGA
1 -TTATCAAAATTTCATAGCGAGGTTATCAAAATTTAATAGAGAGA
6643 TTATCAAAATTTCA
1 TTATCAAAATTTCA
6657 GAGTGTGATT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 14 0.27
45 17 0.33
46 21 0.40
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (44 bp):
TTATCAAAATTTCATAGCGAGGTTATCAAAATTTAATAGAGAGA
Found at i:7135 original size:21 final size:22
Alignment explanation
Indices: 7109--7159 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 22
7099 ATAACCCGAC
7109 TCGACCCGAGAACCCG-CGGAA
1 TCGACCCGAGAACCCGACGGAA
7130 TCGACCCGAGAACCCGACGGAA
1 TCGACCCGAGAACCCGACGGAA
*
7152 CCGACCCG
1 TCGACCCG
7160 TCGATTCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.27, C:0.41, G:0.27, T:0.04
Consensus pattern (22 bp):
TCGACCCGAGAACCCGACGGAA
Found at i:12160 original size:21 final size:21
Alignment explanation
Indices: 12136--12175 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
12126 AGGGTTGCAG
12136 CTATAATTGTTAGAAATTGCC
1 CTATAATTGTTAGAAATTGCC
12157 CTATAATTGTTAGAAATTG
1 CTATAATTGTTAGAAATTG
12176 GCCAATTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (21 bp):
CTATAATTGTTAGAAATTGCC
Done.