Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008116.1 Corchorus capsularis cultivar CVL-1 contig08137, 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: 78252
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:759 original size:80 final size:80
Alignment explanation
Indices: 626--773 Score: 287
Period size: 80 Copynumber: 1.9 Consensus size: 80
616 TTGGTATACA
626 TATTTACTGCCTGTTCTTTTGCATCATCAAATTAAGAGTATATTGTGCATCAGTAACATTTTGTA
1 TATTTACTGCCTGTTCTTTTGCATCATCAAATTAAGAGTATATTGTGCATCAGTAACATTTTGTA
691 ACACATTTTTTAACC
66 ACACATTTTTTAACC
*
706 TATTTACTGCCTGTTCTTTTGCATCATCAACTTAAGAGTATATTGTGCATCAGTAACATTTTGTA
1 TATTTACTGCCTGTTCTTTTGCATCATCAAATTAAGAGTATATTGTGCATCAGTAACATTTTGTA
771 ACA
66 ACA
774 TGTTTCCTCA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (80 bp):
TATTTACTGCCTGTTCTTTTGCATCATCAAATTAAGAGTATATTGTGCATCAGTAACATTTTGTA
ACACATTTTTTAACC
Found at i:8853 original size:31 final size:31
Alignment explanation
Indices: 8817--8915 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
8807 TTTTGTGCAC
* * **
8817 GTGGCATGTCACGTGCCACTTTTTGAAACAT
1 GTGGCATGACACGTGTCACTTTTTGGTACAT
* *
8848 GTGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCATGACACGTGTCACTTTTTGGTACAT
* *
8879 GTGGCGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATGACACGTGTCACTTTTTGGTACAT
8910 GTGGCA
1 GTGGCA
8916 CGACTTTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.33
Consensus pattern (31 bp):
GTGGCATGACACGTGTCACTTTTTGGTACAT
Found at i:8924 original size:22 final size:22
Alignment explanation
Indices: 8896--8937 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
8886 GACATGTGTC
*
8896 ACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACATATGGCACG
*
8918 ACTTTTTTGTACATATGGCA
1 ACTTTTTGGTACATATGGCA
8938 TGCCCCATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (22 bp):
ACTTTTTGGTACATATGGCACG
Found at i:8930 original size:53 final size:53
Alignment explanation
Indices: 8865--8967 Score: 125
Period size: 53 Copynumber: 1.9 Consensus size: 53
8855 GCCACGTGTC
* * ** *
8865 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACATGGCATGACACATGTCACTTTTTGGTACACGTGGCACG
* * * *
8918 ACTTTTTTGTACATATGGCATGCCCCATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACATGGCATGACACATGTCACTTTTTGGTACACGTGGC
8968 GTGCCACGTC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 41 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.37
Consensus pattern (53 bp):
ACTTTTTGGTACACATGGCATGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:9747 original size:2 final size:2
Alignment explanation
Indices: 9742--9779 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
9732 AAATCCTCTC
9742 AT AT 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
9780 GGAGTAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19277 original size:24 final size:24
Alignment explanation
Indices: 19249--19297 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
19239 GGTTATGTCA
19249 CCTCCTGCGTCTGAAAACTTATGC
1 CCTCCTGCGTCTGAAAACTTATGC
19273 CCTCCTGCGTCTGAAAACTTATGC
1 CCTCCTGCGTCTGAAAACTTATGC
19297 C
1 C
19298 GCACTGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.35, G:0.16, T:0.29
Consensus pattern (24 bp):
CCTCCTGCGTCTGAAAACTTATGC
Found at i:23715 original size:31 final size:31
Alignment explanation
Indices: 23679--23758 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 31
23669 CGTGGCCCAT
* *
23679 TTTTTGAAACATGTGGCATGCCACGTGTCAC
1 TTTTTGAAACACGTGGCATGACACGTGTCAC
** * *
23710 TTTTTGGTACACGTGGCGTGACATGTGTCAC
1 TTTTTGAAACACGTGGCATGACACGTGTCAC
**
23741 TTTTTGGTACACGTGGCA
1 TTTTTGAAACACGTGGCA
23759 CGATTTTTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (31 bp):
TTTTTGAAACACGTGGCATGACACGTGTCAC
Found at i:23780 original size:53 final size:53
Alignment explanation
Indices: 23710--23810 Score: 157
Period size: 53 Copynumber: 1.9 Consensus size: 53
23700 CACGTGTCAC
* **
23710 TTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACACGTGGCACGAT
1 TTTTTGGTACACATGGCGTGACACATGTCACTTTTTGGTACACGTGGCACGAT
* *
23763 TTTTTGGTACATATGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 TTTTTGGTACACATGGCGTGACACATGTCACTTTTTGGTACACGTGGC
23811 GTGCCACGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.37
Consensus pattern (53 bp):
TTTTTGGTACACATGGCGTGACACATGTCACTTTTTGGTACACGTGGCACGAT
Found at i:24038 original size:13 final size:13
Alignment explanation
Indices: 24020--24045 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24010 GTTAAAAGGG
24020 AAAACATTATAGT
1 AAAACATTATAGT
24033 AAAACATTATAGT
1 AAAACATTATAGT
24046 GCTTCAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
AAAACATTATAGT
Found at i:25565 original size:5 final size:5
Alignment explanation
Indices: 25555--25590 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
25545 ACTTAGAATC
25555 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA T
25591 GCAGCATCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:31117 original size:21 final size:21
Alignment explanation
Indices: 31091--31159 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
31081 TCTCGTTTAA
* *
31091 CCACCGCTGCTCTTCTCGTAG
1 CCACCGTTGCTCTTCCCGTAG
*
31112 CCACCGTTGCTCTTCCCGCAG
1 CCACCGTTGCTCTTCCCGTAG
* *
31133 CCAGCGTTGCTCTTCGCGTAG
1 CCACCGTTGCTCTTCCCGTAG
31154 CCACCG
1 CCACCG
31160 GATTTCTTCG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.10, C:0.43, G:0.22, T:0.25
Consensus pattern (21 bp):
CCACCGTTGCTCTTCCCGTAG
Found at i:42925 original size:735 final size:735
Alignment explanation
Indices: 41503--42979 Score: 2537
Period size: 735 Copynumber: 2.0 Consensus size: 735
41493 GAATGGTCGA
*
41503 AGCATGGATAGGAAATTTCTTCCGAGTAAATCATAGAAAATGTTGAGAAACCATGAGAAATGCGG
1 AGCATGGATAAGAAATTTCTTCCGAGTAAATCATAGAAAATGTTGAGAAACCATGAGAAATGCGG
41568 AGACATCATGAATAACATTGCATCTTTGGCTTGAATTGCAATCATGTGAAAACTTCGTACGACAG
66 AGACATCATGAATAACATTGCATCTTTGGCTTGAATTGCAATCATGTG---ACTTCGTACGACAG
* * *
41633 TTATTCAGACAACGTTCGCTCCATGTGTAGTGTTCGTACAAGTTTTATTTTTCTTTATTTTAGTG
128 TCATTCAGACAACGTGCACTCCATGTGTAGTGTTCGTACAAGTTTTATTTTTCTTTATTTTAGTG
* * *
41698 TTTTAATTATTTTAGTGTACAATTCACGAGTTCGCAGATTCCAAGTATAGGCAAAACCATTGATG
193 TTTTAATTATTCTAGTGTACAATTCACGAGCTCGCAGATTCCAAGTATAGACAAAACCATTGATG
*
41763 TTAAGGTTATGATTTCGGGGTCTTTTGTGAAGATGGTAGCCCATTTTTTCCCTACCAGTATAGCA
258 TTAAGGTTATGATTTCGGGGTCTTTTGTGAAGAAGGTAGCCCATTTTTTCCCTACCAGTATAGCA
* *
41828 AAAACCAAGGCTGAAAATCCAAGGATGAAGCTTGAGGAAAGTCCAACGATTACAGCCAGCTTTGC
323 AAAACCAAGGCTGAAAATCCAAGGATAAAGCTTGAAGAAAGTCCAACGATTACAGCCAGCTTTGC
* *
41893 CTTCAGGGGATTGTTAGCTCCAAGCTCATTCCCGACCCCGATTGACACGCCAAAACTTAGGGATG
388 CTTCAAGGGATTGTTAGCTCCAAGCTCATTCCCAACCCCGATTGACACGCCAAAACTTAGGGATG
* * *
41958 ACGGGAGAATATATATCAGAGAAGTCGTTTGAATTAGAATCCCCATTGAAGCCACGGTTGCTTGT
453 ACGGGAAAATATATATCAGAGAAGTCGTCTGAATCAGAATCCCCATTGAAGCCACGGTTGCTTGT
42023 GGATTTAATAACAAGCCACATAGTAGCGTTATTATTTCATACCACCACCATTCCAAGCAAACTGA
518 GGATTTAATAACAAGCCACATAGTAGCGTTATTATTTCATACCACCACCATTCCAAGCAAACTGA
*
42088 GATGCAGCTTGGAATGGATAAATTCAACAAGCTCCTCCAGCCTCTGAAGCAGTCCCAAGAAATCC
583 GATGCAGCTTGGAATGGATAAATTCAACAAGCTCCTCCAGCCTCTGAAGCACTCCCAAGAAATCC
* * *
42153 CACTCCACGTTCTCTTGTAAACTCCTGAAATTTTGAGATAAATAATCAACGAACCAACGAGATTG
648 AACTCCACGTTCTCTTGTAAACTCCCGAAACTTTGAGATAAATAATCAACGAACCAACGAGATTG
*
42218 ATGCTGGTCGAAGTAGAGCCGAG
713 ATGCTGGTCCAAGTAGAGCCGAG
*
42241 AGCATGGATAAGAAATTTCTTCCGAGTAAATCATAGAAAATGTTGAGAAACCATGAGAAATGTGG
1 AGCATGGATAAGAAATTTCTTCCGAGTAAATCATAGAAAATGTTGAGAAACCATGAGAAATGCGG
*
42306 AGACATCATGAATAACATTGCATCTTTGGCTTGAATTGCAATCATGTG-C-TCGTACGACAGTCG
66 AGACATCATGAATAACATTGCATCTTTGGCTTGAATTGCAATCATGTGACTTCGTACGACAGTCA
42369 TGT-AGACAACGTGCACTCCATGTGTAGTGTTCGTACAAGTTTTATTTTTCTTTATTTTAGTGTT
131 T-TCAGACAACGTGCACTCCATGTGTAGTGTTCGTACAAGTTTTATTTTTCTTTATTTTAGTGTT
* *
42433 TTAATTATTCTAGTGTACAATTCCCGAGCTCGCAGATTTCAAGTATAGACAAAACCATTGATGTT
195 TTAATTATTCTAGTGTACAATTCACGAGCTCGCAGATTCCAAGTATAGACAAAACCATTGATGTT
42498 AAGGTTATGATTTCGGGGTCTTTTGTGAAGAAGGTAGCCCATTTTTTTCCCTACCAGTATAGCAA
260 AAGGTTATGATTTCGGGGTCTTTTGTGAAGAAGGTAGCCCA-TTTTTTCCCTACCAGTATAGCAA
* * *
42563 AAACCAAGGCTGAAAAATCCAAGGATAAATCTTGAAGAAAGTCCAACGATTACATCCAGTTTTGC
324 AAACCAAGGCTG-AAAATCCAAGGATAAAGCTTGAAGAAAGTCCAACGATTACAGCCAGCTTTGC
* * * *
42628 TTTCAAGGGATTGTTAGCTCCTAGCTCATTCCCAACCCTGGTTGACACGCCAAAACTTAGGGATG
388 CTTCAAGGGATTGTTAGCTCCAAGCTCATTCCCAACCCCGATTGACACGCCAAAACTTAGGGATG
* ** * *
42693 ATGGGAAAATATATATCAGATTAGTCGTCTGAATCAGAATCCCTATTGAAGCCACTGTTGCTTGT
453 ACGGGAAAATATATATCAGAGAAGTCGTCTGAATCAGAATCCCCATTGAAGCCACGGTTGCTTGT
42758 GGATTTAATAACAAGCCACATAGTAGCGTTATTATTTCATACCACCACCATTCCAAGCAAACTGA
518 GGATTTAATAACAAGCCACATAGTAGCGTTATTATTTCATACCACCACCATTCCAAGCAAACTGA
*
42823 GATGCAGCTTGGAATGGATGAATTCAACAAGCTCCTCCAGCCTCTGAAGCACTCCCAAGAAATCC
583 GATGCAGCTTGGAATGGATAAATTCAACAAGCTCCTCCAGCCTCTGAAGCACTCCCAAGAAATCC
42888 AACTCCACGTTCTCTTGTAAACTCCCGAAACTTTGAGATAAATAATCAACGAACCAACGAGATTG
648 AACTCCACGTTCTCTTGTAAACTCCCGAAACTTTGAGATAAATAATCAACGAACCAACGAGATTG
*
42953 ATGCTGGTCCAAGTATAGCCGAG
713 ATGCTGGTCCAAGTAGAGCCGAG
42976 AGCA
1 AGCA
42980 ACACCTCTAA
Statistics
Matches: 698, Mismatches: 38, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
733 172 0.25
734 37 0.05
735 378 0.54
738 111 0.16
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (735 bp):
AGCATGGATAAGAAATTTCTTCCGAGTAAATCATAGAAAATGTTGAGAAACCATGAGAAATGCGG
AGACATCATGAATAACATTGCATCTTTGGCTTGAATTGCAATCATGTGACTTCGTACGACAGTCA
TTCAGACAACGTGCACTCCATGTGTAGTGTTCGTACAAGTTTTATTTTTCTTTATTTTAGTGTTT
TAATTATTCTAGTGTACAATTCACGAGCTCGCAGATTCCAAGTATAGACAAAACCATTGATGTTA
AGGTTATGATTTCGGGGTCTTTTGTGAAGAAGGTAGCCCATTTTTTCCCTACCAGTATAGCAAAA
ACCAAGGCTGAAAATCCAAGGATAAAGCTTGAAGAAAGTCCAACGATTACAGCCAGCTTTGCCTT
CAAGGGATTGTTAGCTCCAAGCTCATTCCCAACCCCGATTGACACGCCAAAACTTAGGGATGACG
GGAAAATATATATCAGAGAAGTCGTCTGAATCAGAATCCCCATTGAAGCCACGGTTGCTTGTGGA
TTTAATAACAAGCCACATAGTAGCGTTATTATTTCATACCACCACCATTCCAAGCAAACTGAGAT
GCAGCTTGGAATGGATAAATTCAACAAGCTCCTCCAGCCTCTGAAGCACTCCCAAGAAATCCAAC
TCCACGTTCTCTTGTAAACTCCCGAAACTTTGAGATAAATAATCAACGAACCAACGAGATTGATG
CTGGTCCAAGTAGAGCCGAG
Found at i:48081 original size:2 final size:2
Alignment explanation
Indices: 48042--48072 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
48032 ATTTTTATTG
48042 AT AT A- 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
48073 TGCATATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48711 original size:107 final size:105
Alignment explanation
Indices: 48480--48742 Score: 386
Period size: 107 Copynumber: 2.5 Consensus size: 105
48470 AATTTTTCTA
* **
48480 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
*
48543 TTTCTAAAACCCTATAACAATACTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATACTATTAATTATGAAATTT
* * * * *
48583 ACCCTTAAAATGAAAATAAAATTTTAATTTGGGGCTAAATTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
* *
48648 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT--ACTATTAATTATGAAATTT
*
48690 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTGAACTTAGTGAAATTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
48743 GGCTAAACTT
Statistics
Matches: 141, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
103 26 0.18
104 14 0.10
105 36 0.26
107 65 0.46
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
TTTCTAAAACCCTATAACAATACTATTAATTATGAAATTT
Found at i:57494 original size:30 final size:30
Alignment explanation
Indices: 57447--57532 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 30
57437 GATGTACAGG
*
57447 CAGATGCTCCACTGCCGCAGGATTTACAAA
1 CAGATGATCCACTGCCGCAGGATTTACAAA
* * * *
57477 CTGATGATCCTCTGCCGCAGGATGTACAGA
1 CAGATGATCCACTGCCGCAGGATTTACAAA
* *
57507 CAGATGTTCCAGTGCCGCAGGATTTA
1 CAGATGATCCACTGCCGCAGGATTTA
57533 TAGCTAGCTG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (30 bp):
CAGATGATCCACTGCCGCAGGATTTACAAA
Found at i:59200 original size:17 final size:17
Alignment explanation
Indices: 59178--59210 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
59168 ATTTGTAAAG
59178 TTGTTACACCAGATAGT
1 TTGTTACACCAGATAGT
*
59195 TTGTTACACTAGATAG
1 TTGTTACACCAGATAG
59211 CTCTATGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (17 bp):
TTGTTACACCAGATAGT
Found at i:60130 original size:17 final size:17
Alignment explanation
Indices: 60108--60160 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
60098 ATTTCAGGAG
*
60108 TAATTATTGAATAATAA
1 TAATTATTCAATAATAA
*
60125 TAATTATTTC-ATAATTA
1 TAATTA-TTCAATAATAA
*
60142 TTATTAGTTCAATAATAA
1 TAATTA-TTCAATAATAA
60160 T
1 T
60161 GGTCTGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 20 0.69
18 9 0.31
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (17 bp):
TAATTATTCAATAATAA
Found at i:60778 original size:11 final size:11
Alignment explanation
Indices: 60762--60793 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
60752 GAAGTTCGTG
60762 TTTGAAGATTA
1 TTTGAAGATTA
*
60773 TTTGAAGATAA
1 TTTGAAGATTA
60784 TTTGAAGATT
1 TTTGAAGATT
60794 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:60790 original size:22 final size:22
Alignment explanation
Indices: 60762--60821 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
60752 GAAGTTCGTG
*
60762 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
60784 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
60803 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
60822 AGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:60796 original size:19 final size:18
Alignment explanation
Indices: 60772--60809 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
60762 TTTGAAGATT
*
60772 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
60791 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
60809 A
1 A
60810 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:62158 original size:6 final size:6
Alignment explanation
Indices: 62147--62177 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
62137 ATAATTGCTA
62147 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
62178 CTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:64752 original size:51 final size:51
Alignment explanation
Indices: 64676--64780 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
64666 TTGTGGGAGG
64676 AGAATAACCATAAACAGCCTCAAATGGTGTCATGCCAATAGCCGAGTGCCA
1 AGAATAACCATAAACAGCCTCAAATGGTGTCATGCCAATAGCCGAGTGCCA
*
64727 AGAATAACCATAAACAGCCTCAAATGGTGTCATGCCAATAGCCTAGTGCCA
1 AGAATAACCATAAACAGCCTCAAATGGTGTCATGCCAATAGCCGAGTGCCA
64778 AGA
1 AGA
64781 GCTGTTATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (51 bp):
AGAATAACCATAAACAGCCTCAAATGGTGTCATGCCAATAGCCGAGTGCCA
Found at i:74248 original size:16 final size:15
Alignment explanation
Indices: 74221--74250 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
74211 TTTGGGAAAG
74221 GAAAAGAGAAAAGAT
1 GAAAAGAGAAAAGAT
74236 GAAAAGAAGAAAAGA
1 GAAAAG-AGAAAAGA
74251 AAAAGGGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (15 bp):
GAAAAGAGAAAAGAT
Found at i:76665 original size:31 final size:30
Alignment explanation
Indices: 76630--76693 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
76620 ATTTTTTAGA
76630 GGGGGCAAAACATCCAAAATTGAGAGTTCAT
1 GGGGGCAAAACATCCAAAATTGA-AGTTCAT
* * *
76661 GGGGGTAAAACGTCCAAAATTGAAGTTTAT
1 GGGGGCAAAACATCCAAAATTGAAGTTCAT
76691 GGG
1 GGG
76694 ACAAAACGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (30 bp):
GGGGGCAAAACATCCAAAATTGAAGTTCAT
Found at i:76707 original size:29 final size:31
Alignment explanation
Indices: 76643--76707 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
76633 GGCAAAACAT
** *
76643 CCAAAATTGAGAGTTCATGGGGGTAAAACGT
1 CCAAAATTGAGAGTTCATGGGGACAAAACGG
*
76674 CCAAAATTGA-AGTTTAT-GGGACAAAACGG
1 CCAAAATTGAGAGTTCATGGGGACAAAACGG
76703 CCAAA
1 CCAAA
76708 CGCTACAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.47
30 6 0.20
31 10 0.33
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (31 bp):
CCAAAATTGAGAGTTCATGGGGACAAAACGG
Done.