Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007089.1 Corchorus capsularis cultivar CVL-1 contig07110, 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: 38692
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:627 original size:21 final size:21
Alignment explanation
Indices: 603--668 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
593 TATGTTTTTC
603 TTGTTCCCATGCTTGTGTGTT
1 TTGTTCCCATGCTTGTGTGTT
**
624 TTGTTCCCAT-C--GCT-TACT
1 TTGTTCCCATGCTTG-TGTGTT
642 TTGTTCCCATGCTTGTGTGTT
1 TTGTTCCCATGCTTGTGTGTT
663 TTGTTC
1 TTGTTC
669 TCTGTAGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
18 13 0.36
19 2 0.06
20 2 0.06
21 19 0.53
ACGTcount: A:0.06, C:0.23, G:0.20, T:0.52
Consensus pattern (21 bp):
TTGTTCCCATGCTTGTGTGTT
Found at i:1461 original size:27 final size:27
Alignment explanation
Indices: 1425--1541 Score: 180
Period size: 27 Copynumber: 4.3 Consensus size: 27
1415 TCCGTCTCTC
1425 CCCACTTCGACCCCAGAAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
* *
1452 CCCACTTCGACCCCAGAAGTCGAACCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
* * *
1479 CCTACTTCGACCCAAGTAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
*
1506 CCCACTTCGACCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
1533 CCCACTTCG
1 CCCACTTCG
1542 CCTTGGGTCG
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 80 1.00
ACGTcount: A:0.21, C:0.42, G:0.17, T:0.20
Consensus pattern (27 bp):
CCCACTTCGACCCCAGAAGTGGATCCT
Found at i:3490 original size:12 final size:12
Alignment explanation
Indices: 3469--3513 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
3459 CGAATACTAG
*
3469 TGGCGGTGGCGA
1 TGGCGATGGCGA
*
3481 TGGCGATGGCGG
1 TGGCGATGGCGA
* *
3493 TGACGATGGAGA
1 TGGCGATGGCGA
3505 TGGCGATGG
1 TGGCGATGG
3514 TGGTAATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.16, C:0.13, G:0.53, T:0.18
Consensus pattern (12 bp):
TGGCGATGGCGA
Found at i:3492 original size:18 final size:18
Alignment explanation
Indices: 3469--3509 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
3459 CGAATACTAG
* *
3469 TGGCGGTGGCGATGGCGA
1 TGGCGGTGACGATGGAGA
3487 TGGCGGTGACGATGGAGA
1 TGGCGGTGACGATGGAGA
3505 TGGCG
1 TGGCG
3510 ATGGTGGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.54, T:0.17
Consensus pattern (18 bp):
TGGCGGTGACGATGGAGA
Found at i:3689 original size:2 final size:2
Alignment explanation
Indices: 3682--3709 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3672 AACAATTTTC
3682 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
3710 GCTACTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3944 original size:32 final size:32
Alignment explanation
Indices: 3875--3937 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
3865 GGGTATACCT
*
3875 TTATATAGCGGCGTCTAAAGAACAAAACGCCC
1 TTATATAGCGCCGTCTAAAGAACAAAACGCCC
*
3907 TTATATAGCGCCGTCTAACGAA-ACAAACGCC
1 TTATATAGCGCCGTCTAAAGAACA-AAACGCC
3938 ACTATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (32 bp):
TTATATAGCGCCGTCTAAAGAACAAAACGCCC
Found at i:4018 original size:24 final size:24
Alignment explanation
Indices: 3986--4054 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 24
3976 TAAATTGCAT
*
3986 ATAGCGGCGTCTAGACGCCGCCAA
1 ATAGGGGCGTCTAGACGCCGCCAA
4010 ATAGGGGCGTCTAGACGCCGCCAA
1 ATAGGGGCGTCTAGACGCCGCCAA
* *
4034 ATAGGGGCATCCAGACGCCGC
1 ATAGGGGCGTCTAGACGCCGC
4055 AATATTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.25, C:0.32, G:0.32, T:0.12
Consensus pattern (24 bp):
ATAGGGGCGTCTAGACGCCGCCAA
Found at i:5254 original size:422 final size:427
Alignment explanation
Indices: 4402--5264 Score: 1045
Period size: 422 Copynumber: 2.0 Consensus size: 427
4392 CAATTAAGGT
* ** *
4402 AATTCAGGTGTCTATTAAAAGGTAATGTCATGATCTACAACTTTCATTAAGGACCACCCACAAGT
1 AATTAAGGTGTCTATTAAAAAATAATGTCATAATCTACAACTTTCATTAAGGACCA--CACAAGT
* * ** *
4467 CAATTTTTATGTTTCAATTCAAAAAAATGCTTCTGAAATTTTGTGGTTTCGATTGCCCGTCTATT
64 CAATTTTTATGTTTCAATTCAAAAAAATGCTTCTCAAATTTGGCCGTCTCGATTGCCCGTCTATT
*
4532 TAATATCATAAAATTTTCGATCCACATGTCCGATGAAAGTTATTAAAGTGTCGGTGAGAAGATTA
129 TAATAGCATAAAATTTTCGATCCACATGTCCGATGAAAGTTATTAAAG-GTC-GTGAGAAGATTA
* * * * *
4597 TTGCATGATCTACGTCTTTCATGAAGGACCCGAAAGTTAAATTTGATTTACGAGTTTCATGAAGG
192 TTGCATGATCTACATCTTTCATGAAAGACCCGAAAGTTAAATTTGATCTACAAGTTTCATGAAGA
*
4662 GCTCAAAAGGGAATTTTTTATGTTTCAAGATCCCATCAGCAAACATTTTCTTATTTGAATTATTT
257 GCTCAAAAGGGAATTTTTTATGTTTCAAGATCCCATCAACAAACATTTTCTTATTTGAATTATTT
* * * * **
4727 TTTAAATGATCCTCATATTTTAGTACTTTATACTGCACAGTCCTTTACTGATTCTATCTTGATCG
322 ATCAAATGACCCTCATATTTTAGTACTTTATACTACACAGTCCTTTACAAATTCTATCTTGATC-
* * * *
4792 ATCAGATTTGTTTATTTTTTTTATTTTTTATTATATTTGTCT
386 ATCAGATTTGTTCACTTTTTTTATTCTTTATTATATTTGTCC
* * *
4834 GATTAAGGTGTCTATTAAAAAATAATTTCATAATCTACAACTTTCATTAATGACTCA-A-AAGTC
1 AATTAAGGTGTCTATTAAAAAATAATGTCATAATCTACAACTTTCATTAAGGAC-CACACAAGTC
* * *
4897 AATTTTTATGTTTCAATTCAAAAAAATTCTTCTCAAATTTGGCCGTCTCGGTTGCCGGTCTATTT
65 AATTTTTATGTTTCAATTCAAAAAAATGCTTCTCAAATTTGGCCGTCTCGATTGCCCGTCTATTT
* * * * *
4962 AATAGCATATAATTTTTGATCCACATGTCTGATTAAAGTTATTCAA-GT-GT-A-AAG-TTATTG
130 AATAGCATAAAATTTTCGATCCACATGTCCGATGAAAGTTATTAAAGGTCGTGAGAAGATTATTG
* *
5022 CATGATCTACAAT-TTTCATGAAAGACCCGAAA-TCTAAATTTGATCTACAAGTTTGATGAATAG
195 CATGATCTAC-ATCTTTCATGAAAGACCCGAAAGT-TAAATTTGATCTACAAGTTTCATGAAGAG
* * *
5085 TTCAAAAGGGAA-TTTTTATGTTTCTAGATCTCCATCAACAAACATTTTCTTATTTGGATTATTT
258 CTCAAAAGGGAATTTTTTATGTTTCAAGATC-CCATCAACAAACATTTTCTTATTTGAATTATTT
** ***
5149 ATCAAATGACCCTCATACTTTTTTTACTTTATACTACTTTGTCCTTTACAAATTCTATCTT-A-C
322 ATCAAATGACCCTCATA-TTTTAGTACTTTATACTACACAGTCCTTTACAAATTCTATCTTGATC
* *
5212 -TC-GATTTAACGCTTCAGCTTTTTTT-TTCTTTGTTCTATTTGTCC
386 ATCAGATTT---G-TTCA-CTTTTTTTATTCTTTATTATATTTGTCC
5256 AATTAAGGT
1 AATTAAGGT
5265 AATTCATGTG
Statistics
Matches: 371, Mismatches: 50, Indels: 30
0.82 0.11 0.07
Matches are distributed among these distances:
418 5 0.01
419 2 0.01
421 20 0.05
422 141 0.38
423 46 0.12
424 1 0.00
425 2 0.01
427 2 0.01
429 102 0.27
430 1 0.00
432 47 0.13
433 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (427 bp):
AATTAAGGTGTCTATTAAAAAATAATGTCATAATCTACAACTTTCATTAAGGACCACACAAGTCA
ATTTTTATGTTTCAATTCAAAAAAATGCTTCTCAAATTTGGCCGTCTCGATTGCCCGTCTATTTA
ATAGCATAAAATTTTCGATCCACATGTCCGATGAAAGTTATTAAAGGTCGTGAGAAGATTATTGC
ATGATCTACATCTTTCATGAAAGACCCGAAAGTTAAATTTGATCTACAAGTTTCATGAAGAGCTC
AAAAGGGAATTTTTTATGTTTCAAGATCCCATCAACAAACATTTTCTTATTTGAATTATTTATCA
AATGACCCTCATATTTTAGTACTTTATACTACACAGTCCTTTACAAATTCTATCTTGATCATCAG
ATTTGTTCACTTTTTTTATTCTTTATTATATTTGTCC
Found at i:12168 original size:22 final size:22
Alignment explanation
Indices: 12142--12306 Score: 133
Period size: 22 Copynumber: 7.5 Consensus size: 22
12132 TGTATATTTT
12142 TATGAAATTTTGATAACC-ACGC
1 TATGAAATTTTGATAACCTAC-C
** *
12164 TATGAAATTTTGATAATTTACG
1 TATGAAATTTTGATAACCTACC
* * *
12186 TATAAAATTGTGATAAACT-CC
1 TATGAAATTTTGATAACCTACC
* * *
12207 ATATGATACTTTGATAACCTAAC
1 -TATGAAATTTTGATAACCTACC
* *
12230 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AACCTACC
*
12253 TATGAAATTTT-ATAACCTTCC
1 TATGAAATTTTGATAACCTACC
*
12274 TATG-ATTTTTGATAACCT-CC
1 TATGAAATTTTGATAACCTACC
*
12294 TTATGAGATTTTG
1 -TATGAAATTTTG
12307 TTAATCTCCC
Statistics
Matches: 114, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
20 7 0.06
21 24 0.21
22 63 0.55
23 20 0.18
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTACC
Found at i:13085 original size:2 final size:2
Alignment explanation
Indices: 13080--13114 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
13070 CCACACACAC
*
13080 TA TA TA GA 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 T
13115 CGAGAACTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13486 original size:29 final size:29
Alignment explanation
Indices: 13452--13550 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
13442 CCAAAATGCT
13452 CAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGTCTGATCTTTTAATTTGGC
* * * **
13481 CAAATAAGGGCCT-AACGTTATCGAAAAT-GC
1 CAAATAAGGGTCTGATC-TT-T-TAATTTGGC
*
13511 TCAAATAAGGGTCTGATCTTTTAATTTGAC
1 -CAAATAAGGGTCTGATCTTTTAATTTGGC
13541 CAAATAAGGG
1 CAAATAAGGG
13551 CCTAACGTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 2 0.04
29 27 0.51
30 5 0.09
31 17 0.32
32 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (29 bp):
CAAATAAGGGTCTGATCTTTTAATTTGGC
Found at i:13508 original size:60 final size:60
Alignment explanation
Indices: 13425--13581 Score: 271
Period size: 60 Copynumber: 2.6 Consensus size: 60
13415 ATTGCTCGAC
* * *
13425 TAAGGGCCTAAGGTT-TGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGCCAAA
1 TAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGACCAAA
13485 TAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGACCAAA
1 TAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGACCAAA
13545 TAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGG
1 TAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGG
13582 CATGGCGTCA
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
60 92 0.99
61 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (60 bp):
TAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGACCAAA
Found at i:13519 original size:31 final size:31
Alignment explanation
Indices: 13481--13582 Score: 113
Period size: 31 Copynumber: 3.4 Consensus size: 31
13471 TTAATTTGGC
13481 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * **
13512 CAAATAAGGGTCTGATC-TT-T-TAATTTGAC-
1 CAAATAAGGGCCT-AACGTTATCGAAAATG-CT
13541 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
13572 CAAATAAGGGC
1 CAAATAAGGGC
13583 ATGGCGTCAG
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
28 2 0.04
29 18 0.33
30 4 0.07
31 29 0.53
32 2 0.04
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:13848 original size:213 final size:213
Alignment explanation
Indices: 13481--13894 Score: 650
Period size: 213 Copynumber: 1.9 Consensus size: 213
13471 TTAATTTGGC
13481 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGACCAAAT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGACCAAAT
** * * * *
13546 AAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCATGGCGTCAGTTTGGATCACGCATAAGA
66 AAGAACCTAACATTATCGAAAATGCTCAAATAAGAGCATGCCGTAAGTTTGGATCACGCATAAGA
* *
13611 AATTTCGACGCTAGGCCCTTATTTGAGCATTTTCGATAAGGATAGGCCCTTATTTGGCCAAATTA
131 AATTTCGACGCCAGGCCCTTATTTGAGCATTTTCGATAACGATAGGCCCTTATTTGGCCAAATTA
13676 AAAGATAAACTAATTGCT
196 AAAGATAAACTAATTGCT
* *
13694 CAAATAAGGGCCTAACGTT-TGCTAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGCCCAAA
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGACCAAA
* * * ** *
13758 TAAGAACCTAACATTATTGAAAATGCTCAAATAAGAGCCTGCCGTAAGTTTGGATGACGTGTGAG
65 TAAGAACCTAACATTATCGAAAATGCTCAAATAAGAGCATGCCGTAAGTTTGGATCACGCATAAG
* *
13823 AATTTTCGACGCCAGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATT
130 AAATTTCGACGCCAGGCCCTTATTTGAGCATTTTCGATAACGATAGGCCCTTATTTGGCCAAATT
13888 AAAAGAT
195 AAAAGAT
13895 TGGGCCCTTA
Statistics
Matches: 182, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
212 1 0.01
213 181 0.99
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (213 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGACCAAAT
AAGAACCTAACATTATCGAAAATGCTCAAATAAGAGCATGCCGTAAGTTTGGATCACGCATAAGA
AATTTCGACGCCAGGCCCTTATTTGAGCATTTTCGATAACGATAGGCCCTTATTTGGCCAAATTA
AAAGATAAACTAATTGCT
Found at i:13874 original size:31 final size:31
Alignment explanation
Indices: 13836--13939 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
13826 TTTCGACGCC
13836 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
** *
13867 AGGCCCTTATTTG-GCCAAATT--A-AAAGATT
1 AGGCCCTTATTTGAG-CATTTTCGATAACG-TT
*
13896 GGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
* *
13927 AAGCTCTTATTTG
1 AGGCCCTTATTTG
13940 GCCAAATTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 3 0.05
29 19 0.33
30 2 0.04
31 30 0.53
32 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTCGATAACGTT
Found at i:13936 original size:60 final size:60
Alignment explanation
Indices: 13835--14123 Score: 259
Period size: 60 Copynumber: 4.8 Consensus size: 60
13825 TTTTCGACGC
*
13835 CAGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTCGATAACGTTAAGCCCTTATTTGGCCAAATTAAAAGAT
** *
13895 TGGGCCCTTATTTGAGCATTTTCGATAACGTTAAGCTCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTCGATAACGTTAAGCCCTTATTTGGCCAAATTAAAAGAT
* * * **
13955 CATGCCCTTATTTTAGCATTTTGGCA-AATATT-AGACCCTTATTTGAG-C-AATTAGCCTAAAT
1 CAGGCCCTTATTTGAGCATTTTCG-ATAACGTTAAG-CCCTTATTTG-GCCAAATTA----AAA-
14016 GAT
58 GAT
* * ** * *
14019 CGGGCCCTTATTTGATCATTTAGGATAACATTAGGCCCTTATTTGG-CACAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTCGATAACGTTAAGCCCTTATTTGGCCA-AATTAAAAGAT
* * * *
14079 CCA-GTCCTTATTTGAGCATTTTGGCA-AACCTTAGGCCCTTATTTG
1 -CAGGCCCTTATTTGAGCATTTTCG-ATAACGTTAAGCCCTTATTTG
14124 AGCAATTAAC
Statistics
Matches: 191, Mismatches: 24, Indels: 28
0.79 0.10 0.12
Matches are distributed among these distances:
59 7 0.04
60 128 0.67
61 7 0.04
63 6 0.03
64 37 0.19
65 6 0.03
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTCGATAACGTTAAGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:14060 original size:124 final size:124
Alignment explanation
Indices: 13838--14131 Score: 343
Period size: 124 Copynumber: 2.4 Consensus size: 124
13828 TCGACGCCAG
* * * * *
13838 GCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG-GCCAA--A--TTAAAAGATTG
1 GCCCTTATTTGAGCATTTTGGCA-AACATTAGACCCTTATTTGAG-CAATTAGCCTAAAAGATCG
* * *
13897 GGCCCTTATTTGAGCATTTTCGATAACGTTAAGCTCTTATTTGGC-CAAATTAAAAGAT-CA
64 GGCCCTTATTTGAGCATTTACGATAACATTAAGCCCTTATTTGGCAC-AATTAAAAGATCCA
* * *
13957 TGCCCTTATTTTAGCATTTTGGCAAATATTAGACCCTTATTTGAGCAATTAGCCTAAATGATCGG
1 -GCCCTTATTTGAGCATTTTGGCAAACATTAGACCCTTATTTGAGCAATTAGCCTAAAAGATCGG
* * *
14022 GCCCTTATTTGATCATTTAGGATAACATTAGGCCCTTATTTGGCACAATTAAAAGATCCA
65 GCCCTTATTTGAGCATTTACGATAACATTAAGCCCTTATTTGGCACAATTAAAAGATCCA
* * *
14082 GTCCTTATTTGAGCATTTTGGCAAACCTTAGGCCCTTATTTGAGCAATTA
1 GCCCTTATTTGAGCATTTTGGCAAACATTAGACCCTTATTTGAGCAATTA
14132 ACTGTACTTT
Statistics
Matches: 147, Mismatches: 19, Indels: 12
0.83 0.11 0.07
Matches are distributed among these distances:
120 38 0.26
121 2 0.01
122 1 0.01
124 103 0.70
125 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (124 bp):
GCCCTTATTTGAGCATTTTGGCAAACATTAGACCCTTATTTGAGCAATTAGCCTAAAAGATCGGG
CCCTTATTTGAGCATTTACGATAACATTAAGCCCTTATTTGGCACAATTAAAAGATCCA
Found at i:24805 original size:42 final size:42
Alignment explanation
Indices: 24758--24843 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
24748 TGTCTTTTAC
* * * *
24758 TTATTCCTGATTTTGTAACTTGTTTTGTGGAAATGGGCTCAT
1 TTATTCCTGATTTTGTAACTTCTTTGGTCGAAATGAGCTCAT
24800 TTATTCCTGATTTTGTAACTTCTTTGGTCGAAATGAGCTCAT
1 TTATTCCTGATTTTGTAACTTCTTTGGTCGAAATGAGCTCAT
24842 TT
1 TT
24844 GAAGAGTACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.48
Consensus pattern (42 bp):
TTATTCCTGATTTTGTAACTTCTTTGGTCGAAATGAGCTCAT
Found at i:26981 original size:28 final size:28
Alignment explanation
Indices: 26941--27003 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
26931 CGTTTAAAGC
*
26941 ACTTTCTCTCTCTCTCTCTCTCATTATA
1 ACTTTCTCTCTCTCTCCCTCTCATTATA
26969 ACTTTCTCTCTCTCTCCCTCTCATTATA
1 ACTTTCTCTCTCTCTCCCTCTCATTATA
26997 ACTTTCT
1 ACTTTCT
27004 ACCTTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.14, C:0.37, G:0.00, T:0.49
Consensus pattern (28 bp):
ACTTTCTCTCTCTCTCCCTCTCATTATA
Found at i:27524 original size:31 final size:31
Alignment explanation
Indices: 27446--27558 Score: 111
Period size: 31 Copynumber: 3.7 Consensus size: 31
27436 TGGCATGTAT
* * *
27446 CTTTTT-GTGCACGTGACATGCCACGTGCCA
1 CTTTTTGGTACACGTGGCATGCCACGTGTCA
* ** *
27476 TTTTTTGAAACATGTGGCATGCCACGTGTCA
1 CTTTTTGGTACACGTGGCATGCCACGTGTCA
* * *
27507 CTTTTTGGTACACGTGGCGTGACATGTGTCA
1 CTTTTTGGTACACGTGGCATGCCACGTGTCA
**
27538 CTTTTTGGTACATATGGCATG
1 CTTTTTGGTACACGTGGCATG
27559 ACTTTTTTGT
Statistics
Matches: 65, Mismatches: 17, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
30 5 0.08
31 60 0.92
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (31 bp):
CTTTTTGGTACACGTGGCATGCCACGTGTCA
Found at i:27562 original size:22 final size:22
Alignment explanation
Indices: 27537--27601 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
27527 GACATGTGTC
*
27537 ACTTTTTGGTACATATGGCATG
1 ACTTTTTGGTACATGTGGCATG
* *
27559 ACTTTTTTGTACATGTGGCACG
1 ACTTTTTGGTACATGTGGCATG
*
27581 -CTTTTTGGTACACGTGGCATG
1 ACTTTTTGGTACATGTGGCATG
27602 CCACGTCGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 18 0.49
22 19 0.51
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (22 bp):
ACTTTTTGGTACATGTGGCATG
Found at i:30736 original size:12 final size:13
Alignment explanation
Indices: 30704--30745 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
30694 ACAAATATTC
30704 AATAACTTAATAA
1 AATAACTTAATAA
* *
30717 AATTACTTCA-AA
1 AATAACTTAATAA
*
30729 AATAACTTAGTAA
1 AATAACTTAATAA
30742 AATA
1 AATA
30746 GTAATAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (13 bp):
AATAACTTAATAA
Done.