Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011581.1 Corchorus capsularis cultivar CVL-1 contig11602, 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: 56806
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:974 original size:34 final size:35
Alignment explanation
Indices: 918--988 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
908 TTGGAATAGT
* *
918 AGAGAGTCATGGTTTTC-AAAAAATGTTTTTCAAA
1 AGAGAGCCATGGTTTTCAAAAAAAAGTTTTTCAAA
* **
952 AGAGAGCCATGTTTTTTTAAAAAAAGTTTTTCAAA
1 AGAGAGCCATGGTTTTCAAAAAAAAGTTTTTCAAA
987 AG
1 AG
989 TCATTTTCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 14 0.44
35 18 0.56
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.35
Consensus pattern (35 bp):
AGAGAGCCATGGTTTTCAAAAAAAAGTTTTTCAAA
Found at i:1156 original size:2 final size:2
Alignment explanation
Indices: 1149--1209 Score: 85
Period size: 2 Copynumber: 32.0 Consensus size: 2
1139 CGGCCCCGAA
1149 AT AT AT AT AT AT AT AT AT AT AT CA- AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
1190 AT AT AT AT AT -T A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1210 GTTTTTTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.07
2 49 0.91
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1188 original size:29 final size:29
Alignment explanation
Indices: 1152--1209 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1142 CCCCGAAATA
1152 TATATATATATATATATATCAATATATAT
1 TATATATATATATATATATCAATATATAT
*
1181 TATATATATATATATATATTAATATATAT
1 TATATATATATATATATATCAATATATAT
1210 GTTTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
TATATATATATATATATATCAATATATAT
Found at i:1328 original size:18 final size:18
Alignment explanation
Indices: 1281--1338 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1271 TCAGATATGT
*
1281 TTTACTAAAAAATAATAATA
1 TTTACTAATAAAT-A-AATA
* *
1301 TATACCAATAAATAAATA
1 TTTACTAATAAATAAATA
1319 TTTACTAATAATATAAATA
1 TTTACTAATAA-ATAAATA
1338 T
1 T
1339 ATATTGTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 13 0.41
19 9 0.28
20 10 0.31
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTACTAATAAATAAATA
Found at i:3011 original size:30 final size:30
Alignment explanation
Indices: 2975--3032 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
2965 GGTCTGCAGG
*
2975 AGCGTTAACGTTTTGGTCTACAGGAGCGTT
1 AGCGTTAACGTTTGGGTCTACAGGAGCGTT
*
3005 AGCGTTAACGTTTGGGTCTGCAGGAGCG
1 AGCGTTAACGTTTGGGTCTACAGGAGCG
3033 CTACAGGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.34, T:0.29
Consensus pattern (30 bp):
AGCGTTAACGTTTGGGTCTACAGGAGCGTT
Found at i:3032 original size:24 final size:24
Alignment explanation
Indices: 2951--3010 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
2941 GAGGATTTGC
*
2951 AGCGTTAACGTTTGGGTCTGCAGG
1 AGCGTTAACGTTTGGGTCTACAGG
*
2975 AGCGTTAACGTTTTGGTCTACAGG
1 AGCGTTAACGTTTGGGTCTACAGG
*
2999 AGCGTTAGCGTT
1 AGCGTTAACGTT
3011 AACGTTTGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.18, C:0.17, G:0.33, T:0.32
Consensus pattern (24 bp):
AGCGTTAACGTTTGGGTCTACAGG
Found at i:3049 original size:41 final size:41
Alignment explanation
Indices: 2992--3072 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
2982 ACGTTTTGGT
2992 CTACAGGAGCGTTAGCGTTAACGTTTGGGTCTGCAGGAGCG
1 CTACAGGAGCGTTAGCGTTAACGTTTGGGTCTGCAGGAGCG
* **
3033 CTACAGGAGTGTTAGCGTTTGCGTTTGGGTCTGCAGGAGC
1 CTACAGGAGCGTTAGCGTTAACGTTTGGGTCTGCAGGAGC
3073 ATTAGTGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.17, C:0.19, G:0.37, T:0.27
Consensus pattern (41 bp):
CTACAGGAGCGTTAGCGTTAACGTTTGGGTCTGCAGGAGCG
Found at i:3332 original size:8 final size:8
Alignment explanation
Indices: 3319--3351 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
3309 ACGTGTGTTC
3319 CATCTTCT
1 CATCTTCT
3327 CATCTTCT
1 CATCTTCT
*
3335 CA-GTTCT
1 CATCTTCT
3342 CATCTTCT
1 CATCTTCT
3350 CA
1 CA
3352 GGTCTCCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.15, C:0.36, G:0.03, T:0.45
Consensus pattern (8 bp):
CATCTTCT
Found at i:3343 original size:15 final size:15
Alignment explanation
Indices: 3323--3357 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3313 GTGTTCCATC
3323 TTCTCATCTTCTCAG
1 TTCTCATCTTCTCAG
3338 TTCTCATCTTCTCAG
1 TTCTCATCTTCTCAG
*
3353 GTCTC
1 TTCTC
3358 CAAGACTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.34, G:0.09, T:0.46
Consensus pattern (15 bp):
TTCTCATCTTCTCAG
Found at i:3421 original size:31 final size:31
Alignment explanation
Indices: 3386--3445 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
3376 CATGATATCA
3386 GTTTCAGTGGCTCCACCATCACCATCAAGGG
1 GTTTCAGTGGCTCCACCATCACCATCAAGGG
3417 GTTTCAGTGGCTCCACCATCACCATCAAG
1 GTTTCAGTGGCTCCACCATCACCATCAAG
3446 CATCTACGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.23
Consensus pattern (31 bp):
GTTTCAGTGGCTCCACCATCACCATCAAGGG
Found at i:3564 original size:20 final size:20
Alignment explanation
Indices: 3539--3579 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3529 TGTCTAATTC
*
3539 TAACCCAATATCCTTTATCA
1 TAACCCAAAATCCTTTATCA
3559 TAACCCAAAATCCTTTATCA
1 TAACCCAAAATCCTTTATCA
3579 T
1 T
3580 GTCCTACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (20 bp):
TAACCCAAAATCCTTTATCA
Found at i:3600 original size:25 final size:25
Alignment explanation
Indices: 3572--3624 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
3562 CCCAAAATCC
3572 TTTATCATGTCCTACATCACCTCAA
1 TTTATCATGTCCTACATCACCTCAA
*
3597 TTTATCATGTCCTACATCATCTCAA
1 TTTATCATGTCCTACATCACCTCAA
3622 TTT
1 TTT
3625 CTGTTCAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.26, C:0.28, G:0.04, T:0.42
Consensus pattern (25 bp):
TTTATCATGTCCTACATCACCTCAA
Found at i:6429 original size:27 final size:27
Alignment explanation
Indices: 6398--6453 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
6388 GTGAATTTAA
6398 TAAATACAAAAATTTTTGGACAAATAT
1 TAAATACAAAAATTTTTGGACAAATAT
*
6425 TAAATACAAAACTTTTTGGACAAATAT
1 TAAATACAAAAATTTTTGGACAAATAT
6452 TA
1 TA
6454 TGAAGAAGAT
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:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (27 bp):
TAAATACAAAAATTTTTGGACAAATAT
Found at i:26493 original size:2 final size:2
Alignment explanation
Indices: 26481--26512 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
26471 TGGATTAGAG
26481 AT AT AT A- AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26513 CAAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:26499 original size:13 final size:13
Alignment explanation
Indices: 26481--26512 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
26471 TGGATTAGAG
26481 ATATATAATATAT
1 ATATATAATATAT
26494 ATATATAATATAT
1 ATATATAATATAT
26507 ATATAT
1 ATATAT
26513 CAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATAATATAT
Found at i:32182 original size:29 final size:29
Alignment explanation
Indices: 32149--32214 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
32139 CTTATACCGT
* *
32149 CAAATAAGCCTCTGGATTATTATTTCGGC
1 CAAATAAGCCCCTGGACTATTATTTCGGC
32178 CAAATAAGCCCCTGGACTATTATTTCGGC
1 CAAATAAGCCCCTGGACTATTATTTCGGC
32207 CAAATAAG
1 CAAATAAG
32215 TCCTGTTGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (29 bp):
CAAATAAGCCCCTGGACTATTATTTCGGC
Found at i:34222 original size:2 final size:2
Alignment explanation
Indices: 34210--34251 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
34200 ATGGACATGC
*
34210 AT AT AT GT AT AT 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 AT AT AT AT AT AT
34252 GAACATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34676 original size:13 final size:13
Alignment explanation
Indices: 34658--34682 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34648 TATTATAGCT
34658 TTTAATAATTAAG
1 TTTAATAATTAAG
34671 TTTAATAATTAA
1 TTTAATAATTAA
34683 TTGAAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TTTAATAATTAAG
Found at i:38858 original size:23 final size:21
Alignment explanation
Indices: 38806--38847 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
38796 CCCCTGCCTA
38806 ACAAATACATAAACAAACACT
1 ACAAATACATAAACAAACACT
38827 ACATAAATACATAAACAAACA
1 AC--AAATACATAAACAAACA
38848 AATTACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.11
23 17 0.89
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.14
Consensus pattern (21 bp):
ACAAATACATAAACAAACACT
Found at i:40452 original size:2 final size:2
Alignment explanation
Indices: 40445--40478 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40435 ACAAAGCTAC
40445 AT AT 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 AT AT
40479 TCATATTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43225 original size:1 final size:1
Alignment explanation
Indices: 43219--43243 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
43209 TTCAATCAAG
43219 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
43244 GCCATCCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:47926 original size:123 final size:122
Alignment explanation
Indices: 47707--47948 Score: 369
Period size: 123 Copynumber: 2.0 Consensus size: 122
47697 TTTGGTTAAT
* * *
47707 AATTTTAAATTTAAGTTAAAATATAATTCGATCGGTTGATTGATATATTTCGGTTTGGTTAATGT
1 AATTTTAAATTCAAGTTAAAATATAATTCGATCGGTTAATTGAAATATTTCGGTTTGGTTAATGT
*
47772 TCGGAATAAGATACTTCAGTTCGATTAATGTTTTACAAAAAATAGTATTCGGTTCATA
66 TCGGAATAAGATACTTCAGTTCAATTAATGTTTTAC-AAAAATAGTATTCGGTTCATA
* * * *
47830 AATTTTAAATTCATGTTAAAATATCATTTGGTCGGTTAATTGAAATATTTCGGTTTGGTTAATGT
1 AATTTTAAATTCAAGTTAAAATATAATTCGATCGGTTAATTGAAATATTTCGGTTTGGTTAATGT
* *
47895 TCGGAATAGGATACTTC-GTTTCAATTAATGTTTTACAAAAATAGTTTTCGGTTC
66 TCGGAATAAGATACTTCAG-TTCAATTAATGTTTTACAAAAATAGTATTCGGTTC
47949 GTTCGGTTAA
Statistics
Matches: 108, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
122 18 0.17
123 90 0.83
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.43
Consensus pattern (122 bp):
AATTTTAAATTCAAGTTAAAATATAATTCGATCGGTTAATTGAAATATTTCGGTTTGGTTAATGT
TCGGAATAAGATACTTCAGTTCAATTAATGTTTTACAAAAATAGTATTCGGTTCATA
Found at i:48719 original size:104 final size:104
Alignment explanation
Indices: 48546--48747 Score: 368
Period size: 104 Copynumber: 1.9 Consensus size: 104
48536 AAATTGTGCG
* * * *
48546 GATTAACTACTAACCTAATCAGTTGGACTTTCCTAGCACAAGTTTTGGCAAGACATGGGTTCTCA
1 GATTAACTACTAACCTAATCAGCTGAACTTTCCTAGCACAACTTTTGGCAAGACATGGGTTCCCA
48611 TATAAGTGGATTAACTACATTCTAACTTGTGTTTGTGTT
66 TATAAGTGGATTAACTACATTCTAACTTGTGTTTGTGTT
48650 GATTAACTACTAACCTAATCAGCTGAACTTTCCTAGCACAACTTTTGGCAAGACATGGGTTCCCA
1 GATTAACTACTAACCTAATCAGCTGAACTTTCCTAGCACAACTTTTGGCAAGACATGGGTTCCCA
48715 TATAAGTGGATTAACTACATTCTAACTTGTGTT
66 TATAAGTGGATTAACTACATTCTAACTTGTGTT
48748 ACAACTATTA
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 94 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (104 bp):
GATTAACTACTAACCTAATCAGCTGAACTTTCCTAGCACAACTTTTGGCAAGACATGGGTTCCCA
TATAAGTGGATTAACTACATTCTAACTTGTGTTTGTGTT
Found at i:49646 original size:10 final size:9
Alignment explanation
Indices: 49631--49694 Score: 53
Period size: 10 Copynumber: 7.1 Consensus size: 9
49621 CATTATTCAG
49631 ACTAATTAA
1 ACTAATTAA
49640 CACTAA-TAA
1 -ACTAATTAA
49649 ACTAA-TAA
1 ACTAATTAA
*
49657 AATAA-TAA
1 ACTAATTAA
49665 ACTAATTAA
1 ACTAATTAA
*
49674 CAATAATTAA
1 -ACTAATTAA
*
49684 CCTTAATTAA
1 AC-TAATTAA
49694 A
1 A
49695 TTTCAAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
8 19 0.42
9 6 0.13
10 20 0.44
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (9 bp):
ACTAATTAA
Found at i:49654 original size:8 final size:8
Alignment explanation
Indices: 49631--49679 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
49621 CATTATTCAG
49631 ACTAATTAA
1 ACTAA-TAA
49640 CACTAATAA
1 -ACTAATAA
49649 ACTAATAA
1 ACTAATAA
*
49657 AATAATAA
1 ACTAATAA
*
49665 ACTAATTA
1 ACTAATAA
49673 AC-AATAA
1 ACTAATAA
49680 TTAACCTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
7 4 0.11
8 23 0.66
9 3 0.09
10 5 0.14
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (8 bp):
ACTAATAA
Found at i:49664 original size:16 final size:18
Alignment explanation
Indices: 49631--49680 Score: 77
Period size: 16 Copynumber: 2.9 Consensus size: 18
49621 CATTATTCAG
*
49631 ACTAATTAACACTAATAA
1 ACTAATTAACAATAATAA
49649 ACTAA-TAA-AATAATAA
1 ACTAATTAACAATAATAA
49665 ACTAATTAACAATAAT
1 ACTAATTAACAATAAT
49681 TAACCTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 12 0.41
17 6 0.21
18 11 0.38
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (18 bp):
ACTAATTAACAATAATAA
Found at i:52001 original size:25 final size:25
Alignment explanation
Indices: 51959--52007 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
51949 TCTTTATAGT
*
51959 TTTTGAAGGGGGTATCGACATCCCTC
1 TTTTGAAGAGGGTATCGACA-CCCTC
*
51985 TTTTG-AGAGGGTGTCGACACCCT
1 TTTTGAAGAGGGTATCGACACCCT
52008 AGTTGATGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 12 0.57
26 5 0.24
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (25 bp):
TTTTGAAGAGGGTATCGACACCCTC
Found at i:54334 original size:4 final size:4
Alignment explanation
Indices: 54325--54358 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
54315 GTTTCAGGGT
*
54325 TTTC TTTC TTTC TTTC TTTC TTTC TTTC CTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
54359 CTTCTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:54361 original size:3 final size:3
Alignment explanation
Indices: 54353--54388 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
54343 TCTTTCTTTC
54353 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
54389 TTAAAGTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:55924 original size:22 final size:21
Alignment explanation
Indices: 55894--55934 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
55884 ATGTGATTGT
55894 TGTTATTTTTGACTATATCTTG
1 TGTTATTTTT-ACTATATCTTG
*
55916 TGTTGTTTTTACTATATCT
1 TGTTATTTTTACTATATCT
55935 GAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.61
Consensus pattern (21 bp):
TGTTATTTTTACTATATCTTG
Found at i:56400 original size:466 final size:465
Alignment explanation
Indices: 55767--56806 Score: 1999
Period size: 466 Copynumber: 2.2 Consensus size: 465
55757 TTTTCTCTTA
* *
55767 TACTTCAGTTTCTTCGTGAGGAGAAATTCAAAGATACTGTTCACATGTAAGTAAGCTTGCTTTCT
1 TACTTCAGTTTCTTCGTGAGGAGAAATTCAAAGATACTGTTCACATGTAAGTAAGTTTGTTTTCT
* *
55832 GTTTTTTGTTCTCTTCATTTGAACTTTGAAGTTTTTGAAATTGTAAGTTTTAATGTGATTGTTGT
66 GTTTTTTGTTCTCTTCATTTGAACTTTGAAGTTTTTGAAATTGTAACTTTTAATGTGATGGTTGT
55897 TATTTTTGACTATATCTTGTGTTGTTTTTACTATATCTGAAAATAAAAACAAATTGGAGAAAGAG
131 TATTTTTGACTATATCTTGTGTTGTTTTTACTATATCTGAAAATAAAAACAAATTGGAGAAAGAG
55962 TCTGGTTTTTTCTTCGATATGAGACATTTTGGAGACTATGTAACCAATGGAGATAGGGACGAAGA
196 TCTGGTTTTTTCTTCGATATGAGACATTTTGGAGACTATGTAACCAATGGAGATAGGGACGAAGA
56027 CAGGGGCGGAGCCAAGAAATTCCTTAATAAGTCTTTCTCTCTCTCAATCTGCGCTACGCTCTTTC
261 CAGGGGCGGAGCCAAGAAATTCCTTAATAAGTCTTTCTCTCTCTCAATCTGCGCTACGCTCTTTC
56092 TGTTTTCTTATTGTCATTATTTTCTTTTGTTTTAATTGAGATTTTCTTAATCGATTTCTTTGCTT
326 TGTTTTCTTATTGTCATTATTTTCTTTTGTTTTAATTGAGATTTTCTTAATCGATTTCTTTGCTT
56157 TTTCCTCTTTATTTGCACTGAGGAGTCAGAACGAAGAAATGTCTTTGATGATGAGTAGAGAATTA
391 TTTCCTCTTTATTTGCACTGAGGAGTCAGAACGAAGAAATGTCTTTGATGATGAGTAGAGAATTA
56222 GTATTTCCTC
456 GTATTTCCTC
56232 TACTTCAGTTTCTTCGTGAGGAGAAATTCAAAGATACTGTTCACATGTAAGTAAGTTTGTTTTCT
1 TACTTCAGTTTCTTCGTGAGGAGAAATTCAAAGATACTGTTCACATGTAAGTAAGTTTGTTTTCT
56297 GTTTTTTGTTCTCTTCAATTTGAACTTTGAAGTTTTTGAAATTGTAACTTTTAATGTGATGGTTG
66 GTTTTTTGTTCTCTTC-ATTTGAACTTTGAAGTTTTTGAAATTGTAACTTTTAATGTGATGGTTG
*
56362 TTATTTTTTACTATATCTTGTGTTGTTTTTACTATATCTGAAAATAAAAACAAATTGGAGAAAGA
130 TTATTTTTGACTATATCTTGTGTTGTTTTTACTATATCTGAAAATAAAAACAAATTGGAGAAAGA
*
56427 GTCTGGTTTTTTCTTCGATATGAGACATTTTGGAGACTGTGTAACCAATGGAGATAGGGACGAAG
195 GTCTGGTTTTTTCTTCGATATGAGACATTTTGGAGACTATGTAACCAATGGAGATAGGGACGAAG
*
56492 ACAGGGGCGGAGCCAGGAAATTCCTTAATAAGTCTTTCTCTCTCTCAATCTGCGCTACGCTCTTT
260 ACAGGGGCGGAGCCAAGAAATTCCTTAATAAGTCTTTCTCTCTCTCAATCTGCGCTACGCTCTTT
56557 CTGTTTTCTTATTGTCATTATTTTCTTTTGTTTTAATTGAGATTTTCTTAATCGATTTCTTTGCT
325 CTGTTTTCTTATTGTCATTATTTTCTTTTGTTTTAATTGAGATTTTCTTAATCGATTTCTTTGCT
56622 TTTTCCTCTTTATTTGCACTGAGGAGTCAGAACGAAGAAATGTCTTTGATGATGAGTAGAGAATT
390 TTTTCCTCTTTATTTGCACTGAGGAGTCAGAACGAAGAAATGTCTTTGATGATGAGTAGAGAATT
56687 AGTATTTCCTC
455 AGTATTTCCTC
*
56698 TACTTCAGTTTCTTCGTGAGGAGAAATTCAAAGATATTGTTCACATGTAAGTAAGTTTGTTTTCT
1 TACTTCAGTTTCTTCGTGAGGAGAAATTCAAAGATACTGTTCACATGTAAGTAAGTTTGTTTTCT
56763 GTTTTTTGTTCTCTTCATTTGAACTTTGAAGTTTTTGAAATTGT
66 GTTTTTTGTTCTCTTCATTTGAACTTTGAAGTTTTTGAAATTGT
Statistics
Matches: 566, Mismatches: 8, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
465 107 0.19
466 459 0.81
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (465 bp):
TACTTCAGTTTCTTCGTGAGGAGAAATTCAAAGATACTGTTCACATGTAAGTAAGTTTGTTTTCT
GTTTTTTGTTCTCTTCATTTGAACTTTGAAGTTTTTGAAATTGTAACTTTTAATGTGATGGTTGT
TATTTTTGACTATATCTTGTGTTGTTTTTACTATATCTGAAAATAAAAACAAATTGGAGAAAGAG
TCTGGTTTTTTCTTCGATATGAGACATTTTGGAGACTATGTAACCAATGGAGATAGGGACGAAGA
CAGGGGCGGAGCCAAGAAATTCCTTAATAAGTCTTTCTCTCTCTCAATCTGCGCTACGCTCTTTC
TGTTTTCTTATTGTCATTATTTTCTTTTGTTTTAATTGAGATTTTCTTAATCGATTTCTTTGCTT
TTTCCTCTTTATTTGCACTGAGGAGTCAGAACGAAGAAATGTCTTTGATGATGAGTAGAGAATTA
GTATTTCCTC
Done.