Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007434.1 Corchorus capsularis cultivar CVL-1 contig07455, 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: 20390
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:52 original size:20 final size:20
Alignment explanation
Indices: 27--65 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17 AAAAAGAGCA
*
27 CCAATTTGCAAATCAAATGT
1 CCAATTCGCAAATCAAATGT
*
47 CCAATTCGTAAATCAAATG
1 CCAATTCGCAAATCAAATG
66 CCTTGTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (20 bp):
CCAATTCGCAAATCAAATGT
Found at i:599 original size:27 final size:27
Alignment explanation
Indices: 567--641 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 27
557 GAGTGGACTC
*
567 AAAATGACGAAAATGCCCCTAAATG-A
1 AAAATGACAAAAATGCCCCTAAATGTA
*
593 AAGAATGACAAAAATGCCCCCTGAATGTA
1 AA-AATGACAAAAATG-CCCCTAAATGTA
*
622 AAAATGACCAAAATGCCCCT
1 AAAATGACAAAAATGCCCCT
642 GGGTGACCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 2 0.05
27 17 0.40
28 21 0.49
29 3 0.07
ACGTcount: A:0.47, C:0.23, G:0.15, T:0.16
Consensus pattern (27 bp):
AAAATGACAAAAATGCCCCTAAATGTA
Found at i:956 original size:39 final size:39
Alignment explanation
Indices: 903--980 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
893 AGAGATCCTC
*
903 GAATAGGATCCTGAAATCCACTGATAAAACAATAATCTT
1 GAATAGGATCCTGAAATCAACTGATAAAACAATAATCTT
* * * * *
942 GAATATGATTCTGAAATTAACTGATAAAGCAATGATCTT
1 GAATAGGATCCTGAAATCAACTGATAAAACAATAATCTT
981 AAAGAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (39 bp):
GAATAGGATCCTGAAATCAACTGATAAAACAATAATCTT
Found at i:1182 original size:25 final size:25
Alignment explanation
Indices: 1154--1213 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 25
1144 TTACCAATTG
1154 CCCGGAGGACTTATCAGAATTAATA
1 CCCGGAGGACTTATCAGAATTAATA
* **
1179 CCCGGAGG--TT-TCTGAATTTGTA
1 CCCGGAGGACTTATCAGAATTAATA
1201 CCCGGAGGACTTA
1 CCCGGAGGACTTA
1214 CCAATGCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 17 0.59
23 2 0.07
24 2 0.07
25 8 0.28
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.27
Consensus pattern (25 bp):
CCCGGAGGACTTATCAGAATTAATA
Found at i:1320 original size:161 final size:166
Alignment explanation
Indices: 1031--1374 Score: 511
Period size: 161 Copynumber: 2.1 Consensus size: 166
1021 TATGAGTGTG
** *
1031 CCCGGAGGACTTGTCAATGCAAATTCTGAATAGACGCCTTCGATCAAGAATTCGAAACTTAAACA
1 CCCGGAGGACTTACCAATGCAAATTCTGAATAGACACCTTCGATCAAGAATTCGAAACTTAAACA
1096 TGAATCTTTGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAG
66 T-AA---TTGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAG
*
1161 GACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTA
127 GACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTCTA
* **
1201 CCCGGAGGACTTACCAATGCAAATTCTGAACTA-ACACCTTCGATCAAGGATTTTAAACTT-AA-
1 CCCGGAGGACTTACCAATGCAAATTCTGAA-TAGACACCTTCGATCAAGAATTCGAAACTTAAAC
* *
1263 AT-A-TGAT-AAAAACTTGATGGAATGAAATTGTACCCGGAGGTTTTACCAATTGCCCGGAGGAC
65 ATAATTGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGAC
*
1325 TTATCAGAATTAATACCCGGAGGTTTCTGAATTTCTG
130 TTATCAGAATTAATACCCGGAGGTTTCTGAATTTCTA
1362 CCCGGAGGACTTA
1 CCCGGAGGACTTA
1375 TCAGAATTAA
Statistics
Matches: 163, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
161 101 0.62
162 4 0.02
166 1 0.01
168 2 0.01
169 2 0.01
170 51 0.31
171 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (166 bp):
CCCGGAGGACTTACCAATGCAAATTCTGAATAGACACCTTCGATCAAGAATTCGAAACTTAAACA
TAATTGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGACT
TATCAGAATTAATACCCGGAGGTTTCTGAATTTCTA
Found at i:1335 original size:22 final size:24
Alignment explanation
Indices: 1313--1383 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 24
1303 TTTTACCAAT
1313 TGCCCGGAGGACTTATCAGAATTAA
1 TGCCCGGAGGACTTATCAGAATT-A
* * *
1338 TACCCGGAGG--TT-TCTGAATTTC
1 TGCCCGGAGGACTTATCAGAA-TTA
1360 TGCCCGGAGGACTTATCAGAATTA
1 TGCCCGGAGGACTTATCAGAATTA
1384 ACACTCGGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
22 14 0.39
23 4 0.11
24 4 0.11
25 14 0.39
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (24 bp):
TGCCCGGAGGACTTATCAGAATTA
Found at i:1343 original size:25 final size:25
Alignment explanation
Indices: 1315--1394 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
1305 TTACCAATTG
1315 CCCGGAGGACTTATCAGAATTAATA
1 CCCGGAGGACTTATCAGAATTAATA
* ** *
1340 CCCGGAGG--TT-TCTGAATTTCTG
1 CCCGGAGGACTTATCAGAATTAATA
*
1362 CCCGGAGGACTTATCAGAATTAACA
1 CCCGGAGGACTTATCAGAATTAATA
*
1387 CTCGGAGG
1 CCCGGAGG
1395 TTTCTGAATT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
22 16 0.38
23 2 0.05
24 2 0.05
25 22 0.52
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (25 bp):
CCCGGAGGACTTATCAGAATTAATA
Found at i:1372 original size:47 final size:47
Alignment explanation
Indices: 1313--1421 Score: 191
Period size: 47 Copynumber: 2.3 Consensus size: 47
1303 TTTTACCAAT
*
1313 TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTC
1 TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCTGAATTTC
* *
1360 TGCCCGGAGGACTTATCAGAATTAACACTCGGAGGTTTCTGAATTTG
1 TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCTGAATTTC
1407 TGCCCGGAGGACTTA
1 TGCCCGGAGGACTTA
1422 CCAATGTAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (47 bp):
TGCCCGGAGGACTTATCAGAATTAACACCCGGAGGTTTCTGAATTTC
Found at i:1414 original size:22 final size:22
Alignment explanation
Indices: 1313--1416 Score: 64
Period size: 22 Copynumber: 4.5 Consensus size: 22
1303 TTTTACCAAT
* *
1313 TGCCCGGAGGACTTATCAGAATTAA
1 TGCCCGGAGG--TT-TCTGAATTTA
* *
1338 TACCCGGAGGTTTCTGAATTTC
1 TGCCCGGAGGTTTCTGAATTTA
* *
1360 TGCCCGGAGGACTTATCAGAATTAA
1 TGCCCGGAGG--TT-TCTGAATTTA
** * *
1385 CACTCGGAGGTTTCTGAATTTG
1 TGCCCGGAGGTTTCTGAATTTA
1407 TGCCCGGAGG
1 TGCCCGGAGG
1417 ACTTACCAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
22 30 0.51
23 4 0.07
24 2 0.03
25 23 0.39
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (22 bp):
TGCCCGGAGGTTTCTGAATTTA
Found at i:2699 original size:9 final size:9
Alignment explanation
Indices: 2687--2745 Score: 70
Period size: 9 Copynumber: 6.8 Consensus size: 9
2677 TCTTTTCTTC
2687 TTTTTCATT
1 TTTTTCATT
2696 TTTTTCATT
1 TTTTTCATT
*
2705 CTTTTCATT
1 TTTTTCATT
*
2714 TTTCATCATT
1 TTT-TTCATT
2724 TTTTT-A-T
1 TTTTTCATT
2731 TTTTTC-TT
1 TTTTTCATT
2739 TTTTTCA
1 TTTTTCA
2746 CTGCACTTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
7 6 0.14
8 8 0.19
9 20 0.48
10 8 0.19
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTCATT
Found at i:2705 original size:27 final size:25
Alignment explanation
Indices: 2672--2745 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 25
2662 ACCCTAGACC
2672 TTTATTCTTTTCTTCTTTTTCATTTT
1 TTTATTCTTTTCTT-TTTTTCATTTT
*
2698 TTTCATTCTTTTCATTTTTCATCATTTT
1 TTT-ATTCTTTTC-TTTTT-TTCATTTT
2726 TTTATT-TTTTCTTTTTTTCA
1 TTTATTCTTTTCTTTTTTTCA
2746 CTGCACTTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
24 3 0.07
25 5 0.12
26 8 0.19
27 15 0.35
28 12 0.28
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTATTCTTTTCTTTTTTTCATTTT
Found at i:2708 original size:19 final size:19
Alignment explanation
Indices: 2679--2735 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
2669 ACCTTTATTC
2679 TTTTC-TTCTTTTTCATTT
1 TTTTCATTCTTTTTCATTT
2697 TTTTCATTC-TTTTCATTT
1 TTTTCATTCTTTTTCATTT
*
2715 TTCATCATT-TTTTT-ATTT
1 TT-TTCATTCTTTTTCATTT
2733 TTT
1 TTT
2736 CTTTTTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 22 0.65
19 12 0.35
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTCATTCTTTTTCATTT
Found at i:3085 original size:8 final size:8
Alignment explanation
Indices: 3046--3072 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3036 CCATTTCATC
3046 ATTTTTTT
1 ATTTTTTT
3054 ATTTTTTT
1 ATTTTTTT
3062 ATTTTTTT
1 ATTTTTTT
3070 ATT
1 ATT
3073 GATTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
ATTTTTTT
Found at i:3112 original size:13 final size:13
Alignment explanation
Indices: 3049--3117 Score: 50
Period size: 13 Copynumber: 5.0 Consensus size: 13
3039 TTTCATCATT
*
3049 TTTTTATTTTTTTA
1 TTTTT-TTTTTTGA
*
3063 -TTTTTTTATTGA
1 TTTTTTTTTTTGA
*
3075 TTTTTTTATTTGTTAA
1 -TTTTTT-TTT-TTGA
*
3091 TTTGATTTTTTTGA
1 TTT-TTTTTTTTGA
3105 TTTTTTTTTTTGA
1 TTTTTTTTTTTGA
3118 AAATTCTCGA
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
12 6 0.14
13 13 0.30
14 11 0.26
15 8 0.19
16 5 0.12
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.78
Consensus pattern (13 bp):
TTTTTTTTTTTGA
Found at i:3415 original size:83 final size:84
Alignment explanation
Indices: 3276--3444 Score: 331
Period size: 83 Copynumber: 2.0 Consensus size: 84
3266 ACTAAGAAAG
3276 AAGGCCATTTATCACTTCAAGATTGGACATCTTCATTGAAGAGGTTCCTCAGAAAAAACGGGTTT
1 AAGGCCATTTATCACTTCAAGATTGGACATCTTCATTGAAGAGGTTCCTCAGAAAAAACGGGTTT
3341 TG-AAAACCATTTTTTTGA
66 TGAAAAACCATTTTTTTGA
3359 AAGGCCATTTATCACTTCAAGATTGGACATCTTCATTGAAGAGGTTCCTCAGAAAAAACGGGTTT
1 AAGGCCATTTATCACTTCAAGATTGGACATCTTCATTGAAGAGGTTCCTCAGAAAAAACGGGTTT
3424 TGAAAAACCATTTTTTTGA
66 TGAAAAACCATTTTTTTGA
3443 AA
1 AA
3445 AACATTTGTG
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 67 0.79
84 18 0.21
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (84 bp):
AAGGCCATTTATCACTTCAAGATTGGACATCTTCATTGAAGAGGTTCCTCAGAAAAAACGGGTTT
TGAAAAACCATTTTTTTGA
Found at i:3440 original size:16 final size:15
Alignment explanation
Indices: 3421--3451 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
3411 AAAAAACGGG
3421 TTTTGAAAAACCATTT
1 TTTTGAAAAA-CATTT
3437 TTTTGAAAAACATTT
1 TTTTGAAAAACATTT
3452 GTGAAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (15 bp):
TTTTGAAAAACATTT
Found at i:3972 original size:6 final size:6
Alignment explanation
Indices: 3961--3989 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3951 ATTTCAACAA
3961 TGTTTG TGTTTG TGTTTG TGTTTG TGTTT
1 TGTTTG TGTTTG TGTTTG TGTTTG TGTTT
3990 TTGGCATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (6 bp):
TGTTTG
Found at i:8539 original size:11 final size:11
Alignment explanation
Indices: 8525--8558 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
8515 AAGAAAAGAA
8525 AAATCATTTTT
1 AAATCATTTTT
**
8536 AAATCAAGTTT
1 AAATCATTTTT
8547 AAATCATTTTT
1 AAATCATTTTT
8558 A
1 A
8559 TACAATCGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (11 bp):
AAATCATTTTT
Found at i:10962 original size:23 final size:23
Alignment explanation
Indices: 10927--10972 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
10917 GCTCAGATTT
*
10927 TTTCATATTTAGAGAGAGACAGAG
1 TTTCATATGTAGAGAGAGA-AGAG
10951 TTTC-TATGTAGAGAGAGAAGAG
1 TTTCATATGTAGAGAGAGAAGAG
10973 AGAGAGCTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 13 0.62
24 4 0.19
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (23 bp):
TTTCATATGTAGAGAGAGAAGAG
Found at i:11732 original size:27 final size:27
Alignment explanation
Indices: 11702--11757 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
11692 ATGCGTGCAT
*
11702 TTACCTTGTTGTATTGCCATGAATTGG
1 TTACCTTGCTGTATTGCCATGAATTGG
11729 TTACCTTGCTGTATTGCCATGAATTGG
1 TTACCTTGCTGTATTGCCATGAATTGG
11756 TT
1 TT
11758 TGACATATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.45
Consensus pattern (27 bp):
TTACCTTGCTGTATTGCCATGAATTGG
Found at i:12329 original size:20 final size:20
Alignment explanation
Indices: 12304--12342 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12294 AAAAAGAGCA
*
12304 CCAATTTGCAAATCAAATGT
1 CCAATTCGCAAATCAAATGT
*
12324 CCAATTCGTAAATCAAATG
1 CCAATTCGCAAATCAAATG
12343 CCTTGTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (20 bp):
CCAATTCGCAAATCAAATGT
Found at i:12876 original size:27 final size:27
Alignment explanation
Indices: 12844--12920 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 27
12834 AAGTGGACTC
*
12844 AAAATGACGAAAATGCCCCTAAATG-A
1 AAAATGACAAAAATGCCCCTAAATGTA
*
12870 AAGAATGACAAAAATGCCCCCCTGAATGTA
1 AA-AATGACAAAAATG--CCCCTAAATGTA
*
12900 AAAATGACCAAAATGCCCCTA
1 AAAATGACAAAAATGCCCCTA
12921 GGTGACCCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
26 2 0.05
27 17 0.40
29 21 0.49
30 3 0.07
ACGTcount: A:0.47, C:0.23, G:0.14, T:0.16
Consensus pattern (27 bp):
AAAATGACAAAAATGCCCCTAAATGTA
Found at i:14255 original size:2 final size:2
Alignment explanation
Indices: 14248--14277 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14238 ACATAGTATC
14248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14278 CAATAACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17545 original size:27 final size:27
Alignment explanation
Indices: 17469--17545 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
17459 ATGTGGACTT
17469 AAAATGACCAAAATGCCCCTGAGTGTGC
1 AAAATGACCAAAATGCCCCT-AGTGTGC
* *
17497 -AAATGACCAGAATGCCCTTAGTGCT-C
1 AAAATGACCAAAATGCCCCTAGTG-TGC
17523 AAAATGACCAAAATGCCCCTAGT
1 AAAATGACCAAAATGCCCCTAGT
17546 TGACCCGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
26 5 0.12
27 38 0.88
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAGTGTGC
Found at i:19896 original size:6 final size:6
Alignment explanation
Indices: 19880--19911 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
19870 AAAAGCAAGC
19880 AAATC- AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
19912 GCAGATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATCT
Found at i:19923 original size:12 final size:13
Alignment explanation
Indices: 19908--19952 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
19898 AATCTAAATC
19908 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
19920 TAAAGCAAATTAA
1 TAAAGCAGATTAA
*
19933 TAAAGTAGATTAA
1 TAAAGCAGATTAA
19946 TAAAGCA
1 TAAAGCA
19953 AACAATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:19959 original size:25 final size:25
Alignment explanation
Indices: 19908--19960 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
19898 AATCTAAATC
*
19908 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
*
19933 TAAAGTAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
19958 TAA
1 TAA
19961 TTATAAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.23
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Done.