Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013128.1 Corchorus capsularis cultivar CVL-1 contig13149, 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: 41963
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:449 original size:220 final size:219
Alignment explanation
Indices: 49--629 Score: 869
Period size: 220 Copynumber: 2.6 Consensus size: 219
39 TGATATAGTT
* *
49 ATCATACCCAAATCATCATATGCACCATTCCCAAATTCTTTAGAAATTGACA-TTTCTCATATAC
1 ATCATCCCCAAATAATCATATGCACCATTCCCAAATTCTTTAGAAATTGACATTTTCTCATATAC
* * *
113 ACAAATTTGACTTTAAAAAGTGCTTTAATCTATATTTTAGGGATCCAATTAATTGAATAAACTAC
66 ACAAATTTGACTTTAAAAAGTGCTTTAATCCATATTTTA--GATCTAATTAATTGAATAAACCAC
*
178 GTCTATATGATTTTAGCGCCGTCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAATGA
129 GTCTATATGATTTTAGCGCCATCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAATGA
* *
243 TATACTTTATACCCAAATCATTTTTC
194 TATAATTTATACCCAAATCATTTCTC
* * * *
269 ATCATCCCCAATTAATCTTATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTCTCATATAC
1 ATCATCCCCAAATAATCATATGCACCATTCCCAAATTCTTTAGAAATTGACATTTTCTCATATAC
* * ** *
334 ACAAATTGGACTTTAAAAAGTGGTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCACA
66 ACAAATTTGACTTTAAAAAGTGCTTTAATCCATATTTTAGA-TCTAATTAATTGAATAAACCACG
* ** * *
399 TCTATATGATTTTAGCGTCATCTCATAATTAAACAAAATGTGAAATTCAGTATCCCCAAACTTAT
130 TCTATATGATTTTAGCGCCATCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAATGAT
464 ATAATTTATACCCAAATCATTTCTC
195 ATAATTTATACCCAAATCATTTCTC
* *
489 ACCATCCCCAAATAATCATACGCACCATTCCCAAATTCTTTAGAAATTG-CTATTTTCTCATATA
1 ATCATCCCCAAATAATCATATGCACCATTCCCAAATTCTTTAGAAATTGAC-ATTTTCTCATATA
*
553 CACAAATTTGACTTTAAAAAGTGTTTTAATCCATATTTTAGAGATCTAATTAATTGAATAAACCA
65 CACAAATTTGACTTTAAAAAGTGCTTTAATCCATATTTT--AGATCTAATTAATTGAATAAACCA
618 CGTCTATATGAT
128 CGTCTATATGAT
630 GGTGGAAAAT
Statistics
Matches: 323, Mismatches: 33, Indels: 9
0.88 0.09 0.02
Matches are distributed among these distances:
219 2 0.01
220 241 0.75
221 79 0.24
222 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (219 bp):
ATCATCCCCAAATAATCATATGCACCATTCCCAAATTCTTTAGAAATTGACATTTTCTCATATAC
ACAAATTTGACTTTAAAAAGTGCTTTAATCCATATTTTAGATCTAATTAATTGAATAAACCACGT
CTATATGATTTTAGCGCCATCTCATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAATGATA
TAATTTATACCCAAATCATTTCTC
Found at i:811 original size:21 final size:21
Alignment explanation
Indices: 784--856 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
774 GAAAAAATTT
784 AAGAAAAGAAATTGATAAAAG
1 AAGAAAAGAAATTGATAAAAG
* * *
805 CAGAAAAGGAAGA-AGAAAAGGAAG
1 AAGAAAA-GAA-ATTGATAA--AAG
829 AAGAAAAGAAATTGATAAAAG
1 AAGAAAAGAAATTGATAAAAG
*
850 TAGAAAA
1 AAGAAAA
857 CGGAGAAGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
21 15 0.38
22 8 0.20
23 8 0.20
24 9 0.22
ACGTcount: A:0.66, C:0.01, G:0.23, T:0.10
Consensus pattern (21 bp):
AAGAAAAGAAATTGATAAAAG
Found at i:823 original size:12 final size:12
Alignment explanation
Indices: 806--881 Score: 72
Period size: 12 Copynumber: 6.6 Consensus size: 12
796 TGATAAAAGC
806 AGAAAAGGAAGA
1 AGAAAAGGAAGA
818 AGAAAAGGAAGA
1 AGAAAAGGAAGA
830 AGAAAA-GAA-A
1 AGAAAAGGAAGA
* * *
840 TTGATAA--AAGT
1 -AGAAAAGGAAGA
851 AGAAAACGG-AGA
1 AGAAAA-GGAAGA
863 AGAAAAGGAAGA
1 AGAAAAGGAAGA
875 AGAAAAG
1 AGAAAAG
882 AAATTTGGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
10 7 0.13
11 9 0.17
12 36 0.69
ACGTcount: A:0.64, C:0.01, G:0.29, T:0.05
Consensus pattern (12 bp):
AGAAAAGGAAGA
Found at i:833 original size:45 final size:45
Alignment explanation
Indices: 784--886 Score: 181
Period size: 45 Copynumber: 2.3 Consensus size: 45
774 GAAAAAATTT
784 AAGAAAAGAAATTGATAAAAGCAGAAAA-GGAAGAAGAAAAGGAAG
1 AAGAAAAGAAATTGATAAAAGCAGAAAACGG-AGAAGAAAAGGAAG
*
829 AAGAAAAGAAATTGATAAAAGTAGAAAACGGAGAAGAAAAGGAAG
1 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
874 AAGAAAAGAAATT
1 AAGAAAAGAAATT
887 TGGGAAAATA
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
45 54 0.96
46 2 0.04
ACGTcount: A:0.64, C:0.02, G:0.25, T:0.09
Consensus pattern (45 bp):
AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
Found at i:2096 original size:25 final size:24
Alignment explanation
Indices: 2079--2126 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
2069 AATGAATTAA
2079 TTTAATAGTAATAATAATGGTAAG
1 TTTAATAGTAATAATAATGGTAAG
*
2103 TTTTAATAGTAATAATAATAGTAA
1 -TTTAATAGTAATAATAATGGTAA
2127 TAATAATGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (24 bp):
TTTAATAGTAATAATAATGGTAAG
Found at i:2101 original size:12 final size:12
Alignment explanation
Indices: 2081--2138 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
2071 TGAATTAATT
2081 TAATAGTAATAA
1 TAATAGTAATAA
* **
2093 TAATGGTAAGTTT
1 TAATAGTAA-TAA
2106 TAATAGTAATAA
1 TAATAGTAATAA
2118 TAATAGTAATAA
1 TAATAGTAATAA
*
2130 TAATGGTAA
1 TAATAGTAA
2139 GTTAGGCGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
12 29 0.76
13 9 0.24
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (12 bp):
TAATAGTAATAA
Found at i:11421 original size:127 final size:129
Alignment explanation
Indices: 11170--11431 Score: 342
Period size: 127 Copynumber: 2.1 Consensus size: 129
11160 TCTCACTTGG
*
11170 TTTA-TTACTAAGAAGACTCTCAATTAGTTTCTCACCATTCGCCTCTCCTCCAACCCTTTTTTTG
1 TTTATTTACTAAGAAGACTCTCAATTAGTTTCTCACCATTCGCCTCTCCTCCAACCCTTATTTTG
* * * * * * *
11234 TAATTGCAAGGGTTTTTAACTAGTTGAATGTGAAAGCATTTATTGACCATAAAATCATGTATTA
66 TAATTACAAAGGATTTCAACTAGTTCAATGTGAAAACATTTATTGACCATAAAATCATGTACTA
* *
11298 TTTATTTACTAAGAAG-GTCCTCAATTAGTTTCTCACCATTC-CTTCTTCCTCC-A-CCTTATTT
1 TTTATTTACTAAGAAGACT-CTCAATTAGTTTCTCACCATTCGCCTC-TCCTCCAACCCTTATTT
11359 TGTAATTACAAAGGATTTCAA-TCAGTTCAATGT-AAACACATTTATTGACCATAAAATCATGTA
64 TGTAATTACAAAGGATTTCAACT-AGTTCAATGTGAAA-ACATTTATTGACCATAAAATCATGTA
11422 CTA
127 CTA
11425 -TTATTTA
1 TTTATTTA
11432 TTCTCTTCAT
Statistics
Matches: 119, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
126 11 0.09
127 60 0.50
128 9 0.08
129 39 0.33
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (129 bp):
TTTATTTACTAAGAAGACTCTCAATTAGTTTCTCACCATTCGCCTCTCCTCCAACCCTTATTTTG
TAATTACAAAGGATTTCAACTAGTTCAATGTGAAAACATTTATTGACCATAAAATCATGTACTA
Found at i:13518 original size:157 final size:158
Alignment explanation
Indices: 13305--13623 Score: 577
Period size: 157 Copynumber: 2.0 Consensus size: 158
13295 CCCAGTGGTT
*
13305 AAGAGTTTGAGATTTCTTGTGGGAGGTCTCGTGTTCAAAACCTGGGATGAGTGGGGTGGGATTAT
1 AAGAGTTTGAGATTTCTTGTGGGAGGTCTCGTGTTCAAAACCTGGGATGAGCGGGGTGGGATTAT
* *
13370 GGGAAAGGAGAGGAATACCTCCTATTGTGTAGTCCATTTCAATATCATGTTCATGAGTAG-ACAA
66 GGGAAAGGAGAGGAATACCTCCTATTGTATAGTCCATTTCAATATCATGTTCATGAGTAGAAAAA
13434 AAAAAAAAAACAATAACAACAAAAATAG
131 AAAAAAAAAACAATAACAACAAAAATAG
*
13462 AAGAGTTTGAGATTTCTTGTGGGAGGTCTCGTGTTCGAAACCTGGGATGAGCGGGGTGGGATTAT
1 AAGAGTTTGAGATTTCTTGTGGGAGGTCTCGTGTTCAAAACCTGGGATGAGCGGGGTGGGATTAT
13527 GGGAAAGGAGAGGAATACCTCCTATTGTATAGTCCATTTCAATATCATGTTCATGAGTAGAAAAA
66 GGGAAAGGAGAGGAATACCTCCTATTGTATAGTCCATTTCAATATCATGTTCATGAGTAG--AAA
13592 AAAAAAAAAAAACAATAACAACAAAAATAG
129 AAAAAAAAAAAACAATAACAACAAAAATAG
13622 AA
1 AA
13624 AGTGCAACCC
Statistics
Matches: 155, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
157 122 0.79
160 33 0.21
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (158 bp):
AAGAGTTTGAGATTTCTTGTGGGAGGTCTCGTGTTCAAAACCTGGGATGAGCGGGGTGGGATTAT
GGGAAAGGAGAGGAATACCTCCTATTGTATAGTCCATTTCAATATCATGTTCATGAGTAGAAAAA
AAAAAAAAAACAATAACAACAAAAATAG
Found at i:14854 original size:19 final size:19
Alignment explanation
Indices: 14832--14869 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
14822 TTTTTATGAG
14832 TAATTTTTACACTATACAA
1 TAATTTTTACACTATACAA
14851 TAATTTTTACACTATACAA
1 TAATTTTTACACTATACAA
14870 GTGGTACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATTTTTACACTATACAA
Found at i:16939 original size:29 final size:29
Alignment explanation
Indices: 16904--16982 Score: 115
Period size: 29 Copynumber: 2.7 Consensus size: 29
16894 AATCATTGTG
16904 GCCCCTAAACTTTTAAAATTTGATATTTT
1 GCCCCTAAACTTTTAAAATTTGATATTTT
16933 GCCCCTAAAC-TTTAAAATCTTGATATTTT
1 GCCCCTAAACTTTTAAAAT-TTGATATTTT
* * *
16962 ACCTCTAAACTTTCAAAATTT
1 GCCCCTAAACTTTTAAAATTT
16983 TTGTTGACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 8 0.18
29 30 0.67
30 7 0.16
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (29 bp):
GCCCCTAAACTTTTAAAATTTGATATTTT
Found at i:19700 original size:16 final size:16
Alignment explanation
Indices: 19661--19735 Score: 91
Period size: 16 Copynumber: 4.8 Consensus size: 16
19651 ATTGGGCGGG
* *
19661 TTCGGGCTCGGGT-TC
1 TTCGGGTTCGGGTATT
19676 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
19692 TTTGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
19708 TTCAGGTTCGGGT-TT
1 TTCGGGTTCGGGTATT
19723 TGTCGGGTTCGGG
1 T-TCGGGTTCGGG
19736 CTCGGATCGG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
15 15 0.29
16 37 0.71
ACGTcount: A:0.04, C:0.15, G:0.40, T:0.41
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:20395 original size:19 final size:19
Alignment explanation
Indices: 20371--20407 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
20361 CTTGGACTTA
20371 TTTATTT-ATATGTAAAAGC
1 TTTATTTAATAT-TAAAAGC
20390 TTTATTTAATATTAAAAG
1 TTTATTTAATATTAAAAG
20408 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (19 bp):
TTTATTTAATATTAAAAGC
Found at i:20487 original size:20 final size:18
Alignment explanation
Indices: 20441--20488 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
20431 AATAATGAAA
*
20441 AATTTTTATTTTATAAAT
1 AATTTTGATTTTATAAAT
*
20459 AATTCTTGATTTTTTAAAT
1 AATT-TTGATTTTATAAAT
20478 ATTATTTTGAT
1 A--ATTTTGAT
20489 CTCGGGCTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 4 0.16
19 13 0.52
20 5 0.20
21 3 0.12
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
AATTTTGATTTTATAAAT
Found at i:20525 original size:16 final size:16
Alignment explanation
Indices: 20504--20551 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
20494 GCTCGGGTTG
20504 GGTTCGGGCGGGTTCA
1 GGTTCGGGCGGGTTCA
**** *
20520 GGTTCGGGTAATTTCG
1 GGTTCGGGCGGGTTCA
20536 GGTTCGGGCGGGTTCA
1 GGTTCGGGCGGGTTCA
20552 AGACGTTGAC
Statistics
Matches: 22, Mismatches: 10, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.08, C:0.17, G:0.46, T:0.29
Consensus pattern (16 bp):
GGTTCGGGCGGGTTCA
Found at i:30106 original size:2 final size:2
Alignment explanation
Indices: 30099--30132 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
30089 GTAAGATAAG
30099 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30133 GGATAATAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31704 original size:78 final size:78
Alignment explanation
Indices: 31553--31708 Score: 179
Period size: 78 Copynumber: 2.0 Consensus size: 78
31543 CAGGAGAGAA
* * ** * * **
31553 GTCGACAATAGGAAGCCAAGGGTGGAGATGACTCATGGTGGTTCTATTGAAAAATCTGTATTTGT
1 GTCGACAATAGAAAGCCAAGGGTGGAAATGACTCATGGTGGCCCTATTGAAAAACCTGAACATGT
*
31618 TTGCAGAAATCCT
66 TCGCAGAAATCCT
* * *
31631 GTCGACAATAGAAAGTCAGGGGTGGAAAT-AGCTCATGGTGGCCCTATTGAAAGACCTGAACATG
1 GTCGACAATAGAAAGCCAAGGGTGGAAATGA-CTCATGGTGGCCCTATTGAAAAACCTGAACATG
*
31695 TTCGTAGAAATCCT
65 TTCGCAGAAATCCT
31709 ATCTATGATG
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
77 1 0.02
78 63 0.98
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (78 bp):
GTCGACAATAGAAAGCCAAGGGTGGAAATGACTCATGGTGGCCCTATTGAAAAACCTGAACATGT
TCGCAGAAATCCT
Found at i:38297 original size:16 final size:17
Alignment explanation
Indices: 38276--38320 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
38266 TGATGCTCTC
38276 AACCATAAAG-GAAGCT
1 AACCATAAAGAGAAGCT
38292 AACCATGCAAAGATGAAGCT
1 AACCAT--AAAGA-GAAGCT
38312 AACCATAAA
1 AACCATAAA
38321 AGAGTGAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.24
18 7 0.28
20 12 0.48
ACGTcount: A:0.51, C:0.20, G:0.16, T:0.13
Consensus pattern (17 bp):
AACCATAAAGAGAAGCT
Found at i:38913 original size:13 final size:13
Alignment explanation
Indices: 38895--38926 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
38885 TGCTACATGA
38895 CCCTCCAATTTGT
1 CCCTCCAATTTGT
*
38908 CCCTCCATTTTGT
1 CCCTCCAATTTGT
38921 CCCTCC
1 CCCTCC
38927 TGACGTGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.09, C:0.47, G:0.06, T:0.38
Consensus pattern (13 bp):
CCCTCCAATTTGT
Found at i:39084 original size:40 final size:40
Alignment explanation
Indices: 39027--39103 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
39017 TTTATAACTA
39027 GGGGCTAAACCTAGATTTAATTTCTTACCTTAATTATCAG
1 GGGGCTAAACCTAGATTTAATTTCTTACCTTAATTATCAG
* * *
39067 GGGGCTAAACCTGGATTTAATTTGTTTCCTTAATTAT
1 GGGGCTAAACCTAGATTTAATTTCTTACCTTAATTAT
39104 TAGGAGGGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (40 bp):
GGGGCTAAACCTAGATTTAATTTCTTACCTTAATTATCAG
Found at i:39505 original size:66 final size:70
Alignment explanation
Indices: 39428--39566 Score: 214
Period size: 73 Copynumber: 2.0 Consensus size: 70
39418 AGAAATTGTA
*
39428 AAGCAGAGAACAATTAACACAATTTAT-CA-A-CA-TCATCCCCAATTTATTTCATCTATAACAT
1 AAGCAGAGAACAATTAACACAATTTATACACATCATTCATCCCCAATTTATCTCATCTATAACAT
39489 ATTTC
66 ATTTC
39494 AAGCAGAGAACAATTAACACAATTTATCAACATCATCATTCATCCCCAATTTATCTCATCTATAA
1 AAGCAGAGAACAATTAACACAATTTAT--ACA-CATCATTCATCCCCAATTTATCTCATCTATAA
39559 CATATTTC
63 CATATTTC
39567 CTAGAACTTG
Statistics
Matches: 65, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
66 27 0.42
69 2 0.03
71 1 0.02
72 2 0.03
73 33 0.51
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (70 bp):
AAGCAGAGAACAATTAACACAATTTATACACATCATTCATCCCCAATTTATCTCATCTATAACAT
ATTTC
Found at i:39610 original size:21 final size:21
Alignment explanation
Indices: 39584--39632 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
39574 TTGTAAAGCA
* *
39584 GAGAACAATTAATAATTGATC
1 GAGAACAATTAACAATTGACC
*
39605 GAGAACAATTAACAGTTGACC
1 GAGAACAATTAACAATTGACC
39626 GAGAACA
1 GAGAACA
39633 GAGAACAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.20
Consensus pattern (21 bp):
GAGAACAATTAACAATTGACC
Found at i:41023 original size:13 final size:14
Alignment explanation
Indices: 41005--41037 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40995 TTCTACAACA
41005 CCCTCCA-ATTTGT
1 CCCTCCATATTTGT
*
41018 CCCTCCATTTTTGT
1 CCCTCCATATTTGT
41032 CCCTCC
1 CCCTCC
41038 TGACGTGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.09, C:0.45, G:0.06, T:0.39
Consensus pattern (14 bp):
CCCTCCATATTTGT
Found at i:41203 original size:271 final size:268
Alignment explanation
Indices: 40533--41236 Score: 1054
Period size: 270 Copynumber: 2.6 Consensus size: 268
40523 TCCCAACCCT
* *
40533 ACCCTATTCAATAATAGGCTAAAATCAAGGGATTTACCCTGCAAACTCTCCATATTTATATCTAG
1 ACCCTATTCAATAATAGCCTAAAATCAAGGGATTTACCCTGCAAACTCTCCATATTTATAACTAG
* *
40598 GGGCTAAACCTGGATTTAATTTCTACCTTAATTATCAGGGGTGCTAAGCCTGGATTTAATTTGTT
66 GGGCTAAACCTGGATTTAATTTCTACCTTAATTATCAGGGGGGCTAAACCT-GATTTAATTTGTT
* *
40663 TCCTTAATTATTAGGAGGGGCAAATTGGAGGGTCAAATAGAATTATCCTAAGAAAATAGTATTGC
130 TCCTTAATTATTAGGAGGGACAAATTGGAGGGTCAAATAGAATTATCCTAAGAAAAGAGTATTGC
**
40728 TACATGACCCTACAATTTGTCCCTCAATTTTGTCCCTCCTGACGTGTCATTAGAAAACTTACTAT
195 TACAACACCCTACAATTTGTCCCTCAATTTTGTCCCTCCTGACGTGTCATTAGAAAACTTACTAT
40793 AATTTCTAA
260 AATTTCTAA
* *
40802 ACCATATTCAATAATAGCCTAAAATTAAGGGATTTACCCTGCAAACTCTCCATATTT-TAACTAG
1 ACCCTATTCAATAATAGCCTAAAATCAAGGGATTTACCCTGCAAACTCTCCATATTTATAACTAG
* * *
40866 GAGCTAAACATGGATTTAATTTCTTCCCTTAATTATCAGAGGGGGCTAAACCTTGATTTAATTTG
66 GGGCTAAACCTGGATTTAATTTC-TACCTTAATTATCAG-GGGGGCTAAACC-TGATTTAATTTG
* * *
40931 TTTCCTTAATTATAAGGAGCGACAAATTGGAGGGTCAAATAGAATTATCGTAAGAAAAGAGTATT
128 TTTCCTTAATTATTAGGAGGGACAAATTGGAGGGTCAAATAGAATTATCCTAAGAAAAGAGTATT
* * * *
40996 TCTACAACACCCTCCAATTTGTCCCTCCATTTTTGTCCCTCCTGACGTGTCATTAGAAAACTTAT
193 GCTACAACACCCTACAATTTGTCCCT-CAATTTTGTCCCTCCTGACGTGTCATTAGAAAACTTAC
41061 TATAATTTCTAAA
257 TATAATTTCT-AA
* * * *
41074 ACCCTATTCAATAACAGCCTAAAATCAAGAGATTTACCCTAG-AAACTCACCGTATTTATAACTA
1 ACCCTATTCAATAATAGCCTAAAATCAAGGGATTTACCCT-GCAAACTCTCCATATTTATAACTA
* *
41138 GGGGCTAAACCTGAATTTAATTTCTACATTAATTATCAGGGGGGCTAAACCTGAATTTAATTTGT
65 GGGGCTAAACCTGGATTTAATTTCTACCTTAATTATCAGGGGGGCTAAACCTG-ATTTAATTTGT
* *
41203 TTCCGTT-ATTATTAGGGGGGACAAATTGAAGGGT
129 TTCC-TTAATTATTAGGAGGGACAAATTGGAGGGT
41237 GATCGGTCGT
Statistics
Matches: 391, Mismatches: 35, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
268 27 0.07
269 68 0.17
270 105 0.27
271 97 0.25
272 66 0.17
273 28 0.07
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (268 bp):
ACCCTATTCAATAATAGCCTAAAATCAAGGGATTTACCCTGCAAACTCTCCATATTTATAACTAG
GGGCTAAACCTGGATTTAATTTCTACCTTAATTATCAGGGGGGCTAAACCTGATTTAATTTGTTT
CCTTAATTATTAGGAGGGACAAATTGGAGGGTCAAATAGAATTATCCTAAGAAAAGAGTATTGCT
ACAACACCCTACAATTTGTCCCTCAATTTTGTCCCTCCTGACGTGTCATTAGAAAACTTACTATA
ATTTCTAA
Done.