Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006687.1 Corchorus capsularis cultivar CVL-1 contig06708, 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: 24024
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:90 original size:15 final size:14
Alignment explanation
Indices: 55--107 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 14
45 AATTAAATTC
55 TAACGTTATATA-T
1 TAACGTTATATATT
68 TAACGTTATATATT
1 TAACGTTATATATT
* *
82 TAATTGTTATTTATTTT
1 TAA-CGTTA--TATATT
99 TAACGTTAT
1 TAACGTTAT
108 GTAAATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 12 0.36
14 5 0.15
15 4 0.12
16 4 0.12
17 8 0.24
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.55
Consensus pattern (14 bp):
TAACGTTATATATT
Found at i:204 original size:23 final size:23
Alignment explanation
Indices: 160--204 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
150 TATATAACGT
* **
160 TATATTTAATTCTTAAGGTTATA
1 TATATTAAATTCTTAACATTATA
183 TATATTAAATTCTTAACATTAT
1 TATATTAAATTCTTAACATTAT
205 GTTTAGGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (23 bp):
TATATTAAATTCTTAACATTATA
Found at i:2666 original size:1 final size:1
Alignment explanation
Indices: 2660--2687 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2650 TCACAAATGT
2660 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
2688 GCGTTCGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4675 original size:43 final size:44
Alignment explanation
Indices: 4601--4688 Score: 144
Period size: 43 Copynumber: 2.0 Consensus size: 44
4591 TAAGGAGTGA
4601 GCTAGTATAGCGGTGGTTACTGGATAGGCTACACTAATGTCAGAC
1 GCTAGTATAGCGGTGG-TACTGGATAGGCTACACTAATGTCAGAC
4646 GCTAGTATA-CGGGTGG-ACTGGATAGGCTACACTAATGTCAGAC
1 GCTAGTATAGC-GGTGGTACTGGATAGGCTACACTAATGTCAGAC
4689 TTAATAGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
43 27 0.64
44 1 0.02
45 14 0.33
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (44 bp):
GCTAGTATAGCGGTGGTACTGGATAGGCTACACTAATGTCAGAC
Found at i:7139 original size:30 final size:29
Alignment explanation
Indices: 7105--7184 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
7095 CGGGGCTGTT
*
7105 AAGTTGAGGAGCCAAAACGTCCCAAAATTG
1 AAGTTCAGGAGCCAAAACGT-CCAAAATTG
* * * *
7135 AAGTTCAGGGGGCAAAATGTCCAAGATTG
1 AAGTTCAGGAGCCAAAACGTCCAAAATTG
* * *
7164 AAGTTCGGGGGGCAAAACGTC
1 AAGTTCAGGAGCCAAAACGTC
7185 TAAACGCTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 27 0.63
30 16 0.37
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.17
Consensus pattern (29 bp):
AAGTTCAGGAGCCAAAACGTCCAAAATTG
Found at i:7165 original size:29 final size:29
Alignment explanation
Indices: 7117--7211 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 29
7107 GTTGAGGAGC
*
7117 CAAAACGTCCCAAAATTGAAGTTCAGGGGG
1 CAAAACGT-CCAAGATTGAAGTTCAGGGGG
* *
7147 CAAAATGTCCAAGATTGAAGTTCGGGGGG
1 CAAAACGTCCAAGATTGAAGTTCAGGGGG
* * **
7176 CAAAACGTCTAAACGCTACAAGTTCAGGGGG
1 CAAAACGTC-CAA-GATTGAAGTTCAGGGGG
7207 CAAAA
1 CAAAA
7212 TGGTAGATTA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
29 27 0.50
30 9 0.17
31 18 0.33
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (29 bp):
CAAAACGTCCAAGATTGAAGTTCAGGGGG
Found at i:11795 original size:15 final size:16
Alignment explanation
Indices: 11764--11797 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11754 TAATATATAA
11764 AAACTGTTAAGAACTT
1 AAACTGTTAAGAACTT
*
11780 AAACTGTT-ATAACTT
1 AAACTGTTAAGAACTT
11795 AAA
1 AAA
11798 ATAATGGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (16 bp):
AAACTGTTAAGAACTT
Found at i:19496 original size:29 final size:31
Alignment explanation
Indices: 19456--19521 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
19446 CCCAAATCAA
*
19456 AAAGTTTAGGCACTGATTTGACC-TTTT-CC
1 AAAGTTTAGGCACTGATATGACCATTTTGCC
* * *
19485 AAAGTTTGGGCACTTATATGACCATTTTGGC
1 AAAGTTTAGGCACTGATATGACCATTTTGCC
19516 AAAGTT
1 AAAGTT
19522 CAAGGCCCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 20 0.65
30 4 0.13
31 7 0.23
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (31 bp):
AAAGTTTAGGCACTGATATGACCATTTTGCC
Found at i:19791 original size:1 final size:1
Alignment explanation
Indices: 19785--19811 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
19775 ATCAAATCTC
19785 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
19812 ATGAAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:22671 original size:30 final size:31
Alignment explanation
Indices: 22636--22701 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
22626 ATGACAATTT
*
22636 AGAAATATA-TTTTTAAAAAAGGGTATAATC
1 AGAAATATATTTTTTAAAAAAGGGTACAATC
*
22666 GGAAATATATTTTTTAAAAAAGGGTACAATC
1 AGAAATATATTTTTTAAAAAAGGGTACAATC
22697 AGAAA
1 AGAAA
22702 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (31 bp):
AGAAATATATTTTTTAAAAAAGGGTACAATC
Found at i:22964 original size:22 final size:22
Alignment explanation
Indices: 22917--22965 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
22907 AGATTTCGAG
* **
22917 AACCTTTTTATAAATTTTTTTC
1 AACCTTCTTATAAATTTAGTTC
22939 AACCTTCTTATAAAATTTAGTT-
1 AACCTTCTTAT-AAATTTAGTTC
22961 AACCT
1 AACCT
22966 CCCTAAGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.33, C:0.16, G:0.02, T:0.49
Consensus pattern (22 bp):
AACCTTCTTATAAATTTAGTTC
Found at i:23026 original size:23 final size:22
Alignment explanation
Indices: 22990--23054 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
22980 GAAGACCTCA
*
22990 ATATGAAATTTTGATAACCAAC
1 ATATGAAATATTGATAACCAAC
* * **
23012 ACTATGAGATGTTGATAACCTCC
1 A-TATGAAATATTGATAACCAAC
*
23035 ATATGATATATTGATAACCA
1 ATATGAAATATTGATAACCA
23055 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
ATATGAAATATTGATAACCAAC
Found at i:23048 original size:22 final size:22
Alignment explanation
Indices: 22984--23230 Score: 87
Period size: 22 Copynumber: 11.1 Consensus size: 22
22974 AATTTTGAAG
* *
22984 ACCTCAATATGAAATTTTGATA
1 ACCTCCATATGAAATATTGATA
** * *
23006 ACCAACACTATGAGATGTTGATA
1 ACCTCCA-TATGAAATATTGATA
*
23029 ACCTCCATATGATATATTGATA
1 ACCTCCATATGAAATATTGATA
* ** * *
23051 ACCACGTTATGAAA-ATTTAAAA
1 ACCTCCATATGAAATA-TTGATA
* *
23073 ACCTCCATATGAATTGTT-AGTA
1 ACCTCCATATGAAATATTGA-TA
* *
23095 A--TCACACTTTGAAATTTTGATA
1 ACCTC-CA-TATGAAATATTGATA
*
23117 A--TCACACTATGAAATTTTGATA
1 ACCTC-CA-TATGAAATATTGATA
*
23139 ACCTCGC-TATGAAATTTTGATAA
1 ACCTC-CATATGAAATATTGAT-A
* * *
23162 ATCTTCC-TATAAAATTTTGATAA
1 A-CCTCCATATGAAATATTGAT-A
* * *
23185 ACCTCCCTATAAAATTTTGATA
1 ACCTCCATATGAAATATTGATA
* * * *
23207 ACTTTCTTATGAAATCTTGATA
1 ACCTCCATATGAAATATTGATA
23229 AC
1 AC
23231 TACAAATTTT
Statistics
Matches: 179, Mismatches: 34, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.01
21 4 0.02
22 115 0.64
23 52 0.29
24 6 0.03
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (22 bp):
ACCTCCATATGAAATATTGATA
Found at i:23152 original size:44 final size:42
Alignment explanation
Indices: 22991--23420 Score: 184
Period size: 44 Copynumber: 10.0 Consensus size: 42
22981 AAGACCTCAA
* * * *
22991 TATGAAATTTTGATAACCAACACTATGAGATGTTGATAACCTCC
1 TATGAAATTTTGATAACC-TC-CTATGAAATTTTGATAATCTCC
* * * * * * * *
23035 ATATGATATATTGATAACCACGTTATGAAAATTTAAAAACCTCC
1 -TATGAAATTTTGATAACCTC-CTATGAAATTTTGATAATCTCC
* * * *
23079 ATATG-AATTGTT-AGTAATCACACTTTGAAATTTTGATAATCACAC
1 -TATGAAATT-TTGA-TAACCTC-CTATGAAATTTTGATAATCTC-C
23124 TATGAAATTTTGATAACCTCGCTATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGATAACCTC-CTATGAAATTTTGAT-AATC-TCC
* * * *
23169 TATAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGAT-AACCT-CCTATGAAATTTTGATAA-TCTCC
* * *
23214 TATGAAATCTTGATAA----CTA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCTATGAAATTTTGATAATCT-CC
** * * *
23252 TATGATTTTTTGATAATCTCATTATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTC-CTATGAAATTTTGATAATCT-CC
* * * * * *
23296 TATGAAATTTTGATCTACATACTATGAAAATTTGATAACCCTCT
1 TATGAAATTTTGAT-AACCTCCTATGAAATTTTGATAA-TCTCC
* * * * **
23340 TTTAAAATTTT-AAAAACTAAAATATGAAATTTTGAT-ATCCTCC
1 TATGAAATTTTGATAACCT--CCTATGAAATTTTGATAAT-CTCC
* *
23383 -CTG-AATTTTGATATCCTCCT-TGAAATTTTGATAA-CTCC
1 TATGAAATTTTGATAACCTCCTATGAAATTTTGATAATCTCC
23421 ATAATAAAAG
Statistics
Matches: 291, Mismatches: 70, Indels: 55
0.70 0.17 0.13
Matches are distributed among these distances:
37 1 0.00
38 30 0.10
39 15 0.05
40 2 0.01
41 6 0.02
42 7 0.02
43 10 0.03
44 138 0.47
45 60 0.21
46 21 0.07
47 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (42 bp):
TATGAAATTTTGATAACCTCCTATGAAATTTTGATAATCTCC
Found at i:23176 original size:23 final size:23
Alignment explanation
Indices: 23104--23309 Score: 120
Period size: 22 Copynumber: 9.5 Consensus size: 23
23094 AATCACACTT
*
23104 TGAAATTTTGAT-AATC-ACACTA
1 TGAAATTTTGATAAATCTTC-CTA
*
23126 TGAAATTTTGAT-AA-CCTCGCTA
1 TGAAATTTTGATAAATCTTC-CTA
23148 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGATAAATCTTCCTA
* * *
23171 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGATAAATCTTCCTA
* * *
23194 TAAAATTTTGATAACT-TTCTTA
1 TGAAATTTTGATAAATCTTCCTA
*
23216 TGAAATCTTGAT-AA-----CTA
1 TGAAATTTTGATAAATCTTCCTA
* * *
23233 -CAAATTTTGATA-ACCTCCCTA
1 TGAAATTTTGATAAATCTTCCTA
** *
23254 TGATTTTTTGAT-AATC-TCATTA
1 TGAAATTTTGATAAATCTTC-CTA
* *
23276 TGAAATTTTG-TTAATCTCCCTA
1 TGAAATTTTGATAAATCTTCCTA
23298 TGAAATTTTGAT
1 TGAAATTTTGAT
23310 CTACATACTA
Statistics
Matches: 143, Mismatches: 26, Indels: 29
0.72 0.13 0.15
Matches are distributed among these distances:
16 10 0.07
17 2 0.01
21 7 0.05
22 80 0.56
23 41 0.29
24 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (23 bp):
TGAAATTTTGATAAATCTTCCTA
Found at i:23227 original size:45 final size:46
Alignment explanation
Indices: 23106--23229 Score: 148
Period size: 45 Copynumber: 2.8 Consensus size: 46
23096 TCACACTTTG
* * *
23106 AAATTTTGAT-AATC-ACACTATGAAATTTTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATTTTGATAAACCTCCCTATA
*
23150 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAATTTTGATAAACCTCCCTATA
* * *
23196 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAATTTTGATAA
23230 CTACAAATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
44 10 0.14
45 35 0.51
46 24 0.35
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (46 bp):
AAATTTTGATAAATCTTCCTATGAAATTTTGATAAACCTCCCTATA
Found at i:23411 original size:20 final size:20
Alignment explanation
Indices: 23364--23415 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
23354 AACTAAAATA
23364 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
23384 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
23403 TGAAATTTTGATA
1 TGAAATTTTGATA
23416 ACTCCATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:23636 original size:66 final size:66
Alignment explanation
Indices: 23539--23667 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
23529 GATAACCTCT
* * * ** *
23539 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGCTGACCCCTCTATGAAATTCTGATAATCAC
1 TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
23604 A
66 A
* * *
23605 TTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACACTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATC
23668 TTTCTATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 51 0.96
67 2 0.04
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
A
Found at i:23655 original size:22 final size:22
Alignment explanation
Indices: 23493--23735 Score: 121
Period size: 22 Copynumber: 11.0 Consensus size: 22
23483 CCAGAAATAC
**
23493 CACTATGAAATTTTTG-TAATAA
1 CACTATGAAA-TTTTGATAACCA
* * * *
23515 CATTTTGAAAATTTGATAACCT
1 CACTATGAAATTTTGATAACCA
** *
23537 CTTTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
** * * * *
23559 CTTTATAAAATTTTGCTGACCC
1 CACTATGAAATTTTGATAACCA
* * *
23581 CTCTATGAAATTCTGATAATCA
1 CACTATGAAATTTTGATAACCA
* * *
23603 CATTATGTAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* * *
23625 CGCTTTGAAATTTTGATAACAA
1 CACTATGAAATTTTGATAACCA
* *
23647 CACTATGAAATTTTGATAATCT
1 CACTATGAAATTTTGATAACCA
** *
23669 TTCTAT-AAATTTTGATAATCTGA
1 CACTATGAAATTTTGATAA-C-CA
** **
23692 TGTCTATGAAATTTTGATAGTCA
1 -CACTATGAAATTTTGATAACCA
* *
23715 CTCTATGAGATTTTGATAACC
1 CACTATGAAATTTTGATAACC
23736 TTCTATCAAA
Statistics
Matches: 166, Mismatches: 50, Indels: 10
0.73 0.22 0.04
Matches are distributed among these distances:
21 16 0.10
22 133 0.80
23 1 0.01
24 5 0.03
25 11 0.07
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCA
Found at i:23658 original size:88 final size:88
Alignment explanation
Indices: 23495--23661 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 88
23485 AGAAATACCA
* * * **
23495 CTATGAAATTTTTGTAATAACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTCTGTAATAACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
23560 TTTATAAAATTTTGCTGACCCCT
66 ACTATAAAATTTTGCTGACCCCT
* * *
23583 CTATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTCTG-TAATAACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
23646 ACACTATGAAATTTTG
64 ACACTATAAAATTTTG
23662 ATAATCTTTC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 4 0.06
88 60 0.91
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATAACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGCTGACCCCT
Found at i:23680 original size:21 final size:22
Alignment explanation
Indices: 23520--23750 Score: 123
Period size: 22 Copynumber: 10.5 Consensus size: 22
23510 AATAACATTT
* *
23520 TGAAAATTTGATAACCTCTT-TA
1 TGAAATTTTGATAATCT-TTCTA
*
23542 TGAAATTTTGATAACCTCTT-TA
1 TGAAATTTTGATAATCT-TTCTA
* * * * **
23564 TAAAATTTTGCTGACCCCTCTA
1 TGAAATTTTGATAATCTTTCTA
* **
23586 TGAAATTCTGATAATCACAT-TA
1 TGAAATTTTGATAATC-TTTCTA
* * ** *
23608 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAATCTTTCTA
***
23630 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAATC-TTTCTA
23652 TGAAATTTTGATAATCTTTCTA
1 TGAAATTTTGATAATCTTTCTA
23674 T-AAATTTTGATAATCTGATGTCTA
1 TGAAATTTTGATAATCT--T-TCTA
* **
23698 TGAAATTTTGATAGTCACTCTA
1 TGAAATTTTGATAATCTTTCTA
* *
23720 TGAGATTTTGATAA-CCTTCTA
1 TGAAATTTTGATAATCTTTCTA
*
23741 TCAAATTTTG
1 TGAAATTTTG
23751 GTACTTCTTA
Statistics
Matches: 165, Mismatches: 35, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
21 30 0.18
22 113 0.68
23 4 0.02
24 5 0.03
25 13 0.08
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAATCTTTCTA
Found at i:24009 original size:24 final size:22
Alignment explanation
Indices: 23945--24010 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
23935 TTGTAATAAT
* *
23945 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
23967 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTATGAAATTTTAA
23989 TAA-CATGATCCTATGAAATTTT
1 TAACCA--A-CCTATGAAATTTT
24011 GGTAACCACA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 21 0.60
23 1 0.03
24 11 0.31
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Done.