Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008279.1 Corchorus capsularis cultivar CVL-1 contig08300, 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: 62619
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:1163 original size:21 final size:22
Alignment explanation
Indices: 1137--1181 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1127 ACTTTCTGAA
*
1137 TTGCTAAACACCGTCTCA-TTT
1 TTGCTAAACACCGTCCCACTTT
**
1158 TTGCTATTCACCGTCCCACTTT
1 TTGCTAAACACCGTCCCACTTT
1180 TT
1 TT
1182 ACACTTTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.18, C:0.31, G:0.09, T:0.42
Consensus pattern (22 bp):
TTGCTAAACACCGTCCCACTTT
Found at i:4645 original size:22 final size:22
Alignment explanation
Indices: 4619--4672 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
4609 TTTTGGGTTT
4619 GGCTGTGCCGTCCTCTTGGGGC
1 GGCTGTGCCGTCCTCTTGGGGC
*
4641 GGCTGTGCTGTCCTCTTGGGGC
1 GGCTGTGCCGTCCTCTTGGGGC
*
4663 GGCTTTGCCG
1 GGCTGTGCCG
4673 CGGCATGGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.00, C:0.30, G:0.41, T:0.30
Consensus pattern (22 bp):
GGCTGTGCCGTCCTCTTGGGGC
Found at i:4728 original size:33 final size:33
Alignment explanation
Indices: 4691--4757 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4681 CGCCCCGGTG
* *
4691 GGACGGCTTAGCCACGACTTTGCCGCCCTACTA
1 GGACGGCTTAGCCACGACTGTGCCGCCCCACTA
* *
4724 GGACGGCTTTGCCACGGCTGTGCCGCCCCACTA
1 GGACGGCTTAGCCACGACTGTGCCGCCCCACTA
4757 G
1 G
4758 AGCGGCAAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.15, C:0.37, G:0.28, T:0.19
Consensus pattern (33 bp):
GGACGGCTTAGCCACGACTGTGCCGCCCCACTA
Found at i:5154 original size:12 final size:12
Alignment explanation
Indices: 5137--5164 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5127 CTTTAGAGGG
5137 AGAGAGAGGCTC
1 AGAGAGAGGCTC
5149 AGAGAGAGGCTC
1 AGAGAGAGGCTC
5161 AGAG
1 AGAG
5165 GGAGAGAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.14, G:0.43, T:0.07
Consensus pattern (12 bp):
AGAGAGAGGCTC
Found at i:5191 original size:30 final size:30
Alignment explanation
Indices: 5131--5191 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
5121 GCTGAGCTTT
*
5131 AGAGGGAGAGAGAGGCTCAGAGAGAGGCTC
1 AGAGGGAGAGAGAGGCTCAGAGACAGGCTC
*
5161 AGAGGGAGAGAGA-GCTTCAGAGACATGCTC
1 AGAGGGAGAGAGAGGC-TCAGAGACAGGCTC
5191 A
1 A
5192 AATTCTGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.34, C:0.15, G:0.41, T:0.10
Consensus pattern (30 bp):
AGAGGGAGAGAGAGGCTCAGAGACAGGCTC
Found at i:5450 original size:12 final size:12
Alignment explanation
Indices: 5435--5502 Score: 57
Period size: 12 Copynumber: 5.4 Consensus size: 12
5425 ATTTGTTACA
5435 AATTTAGTTATT
1 AATTTAGTTATT
*
5447 AATTTTATATTATT
1 AA-TTTA-GTTATT
*
5461 AGA-TTAGTAAATT
1 A-ATTTAGT-TATT
5474 AATTTAGTTATT
1 AATTTAGTTATT
* *
5486 AATTCATTTATT
1 AATTTAGTTATT
5498 AATTT
1 AATTT
5503 TAGGGATTAC
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
12 21 0.48
13 16 0.36
14 6 0.14
15 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (12 bp):
AATTTAGTTATT
Found at i:12115 original size:26 final size:26
Alignment explanation
Indices: 12086--12137 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
12076 TGAATTGTAA
*
12086 TGAGATTTCATTGGGTTTGTTTGTTG
1 TGAGATTTCATTGGGTTTATTTGTTG
12112 TGAGATTTCATTGGGTTTATTTGTTG
1 TGAGATTTCATTGGGTTTATTTGTTG
12138 GCTTATATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.04, G:0.29, T:0.54
Consensus pattern (26 bp):
TGAGATTTCATTGGGTTTATTTGTTG
Found at i:12224 original size:46 final size:46
Alignment explanation
Indices: 12169--12262 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
12159 AGTAATCTGC
12169 TAATCATGTAGCGGTGTTTTGAATTGTAATGAGATTTCATTGGGTT
1 TAATCATGTAGCGGTGTTTTGAATTGTAATGAGATTTCATTGGGTT
12215 TAATCATGTAGCGGTGTTTTGAATTGTAATGAGATTTCATTGGGTT
1 TAATCATGTAGCGGTGTTTTGAATTGTAATGAGATTTCATTGGGTT
12261 TA
1 TA
12263 TTTGTTGGCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (46 bp):
TAATCATGTAGCGGTGTTTTGAATTGTAATGAGATTTCATTGGGTT
Found at i:12438 original size:2 final size:2
Alignment explanation
Indices: 12415--12461 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
12405 AAATAAATCA
12415 AT AT AT -T AT AT -T A- AT -T AT -T 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
12452 AT A- AT AT AT A
1 AT AT AT AT AT A
12462 ACATAATTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
1 6 0.15
2 33 0.85
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12458 original size:21 final size:20
Alignment explanation
Indices: 12414--12461 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
12404 TAAATAAATC
12414 AATATAT-TATATTAATTAT
1 AATATATATATATTAATTAT
*
12433 TATATATATATA-TATATATAT
1 AATATATATATATTA-AT-TAT
12454 AATATATA
1 AATATATA
12462 ACATAATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.33
20 6 0.25
21 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATATATATATATTAATTAT
Found at i:20965 original size:30 final size:31
Alignment explanation
Indices: 20905--20979 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
20895 AAAATTGGTG
20905 AGGGACCCAATTGCTCAATTAACTCAACTTC
1 AGGGACCCAATTGCTCAATTAACTCAACTTC
* *
20936 AGGGACTCAATTGCTC-ATTAAGTTC-ACTTC
1 AGGGACCCAATTGCTCAATTAA-CTCAACTTC
* *
20966 AAGGACCCATTTGC
1 AGGGACCCAATTGC
20980 ATATTCGCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 21 0.55
31 17 0.45
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (31 bp):
AGGGACCCAATTGCTCAATTAACTCAACTTC
Found at i:23198 original size:20 final size:20
Alignment explanation
Indices: 23173--23212 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
23163 CCGTTAATTA
*
23173 AAACGTGTCACTCGTGTCTT
1 AAACGTGTCAATCGTGTCTT
*
23193 AAACGTGTTAATCGTGTCTT
1 AAACGTGTCAATCGTGTCTT
23213 GACACGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
AAACGTGTCAATCGTGTCTT
Found at i:23271 original size:42 final size:43
Alignment explanation
Indices: 23200--23282 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
23190 CTTAAACGTG
* *
23200 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACAATTACGACACGAAACACGATAATC
*
23243 TTAATCGTGTC-CGACACAATT-CAGACACGAGACACGATAA
1 TTAATCGTGTCTCGACACAATTAC-GACACGAAACACGATAA
23283 GCCAAACACG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 1 0.03
42 24 0.67
43 11 0.31
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACAATTACGACACGAAACACGATAATC
Found at i:26112 original size:106 final size:106
Alignment explanation
Indices: 25946--26204 Score: 380
Period size: 108 Copynumber: 2.4 Consensus size: 106
25936 TTTCTAACCT
* **
25946 TTAAAATAAAATTTTAATTTTAATTTGGGCTAAACTTAGTG-AATTAGTTATATATTTTATTTCT
1 TTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTCT
* *
26010 AAAACCCTATAACAAT-A-TTATTAATTATGGAATTTATCC
66 AAAACCCTATAACAATAATTTATTAATTATGAAATTTACCC
* *
26049 TTAAAATAAAAATAAAATTTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTT
1 TTAAAATAAAAATAAAA-TTTTAATTT-GGGCTAAACTTAGTGAAATTAGTTATATATTTTATTT
* * *
26114 CTAAAATCCTATAATAATAATTTATTAATTTTGAAATTTACCC
64 CTAAAACCCTATAACAATAATTTATTAATTATGAAATTTACCC
26157 TTAAAATAAAAATAAAATTTTAATTTAGGGCTAAACTTAGTGAAATTA
1 TTAAAATAAAAATAAAATTTTAATTT-GGGCTAAACTTAGTGAAATTA
26205 AGACTAAACT
Statistics
Matches: 140, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
103 14 0.10
104 9 0.06
105 15 0.11
106 35 0.25
107 31 0.22
108 36 0.26
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.43
Consensus pattern (106 bp):
TTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTCT
AAAACCCTATAACAATAATTTATTAATTATGAAATTTACCC
Found at i:32751 original size:21 final size:21
Alignment explanation
Indices: 32725--32766 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
32715 GATCGGTCCA
32725 AAGAAAATGTTTCAAGTCTAC
1 AAGAAAATGTTTCAAGTCTAC
32746 AAGAAAATGTTTCAAGTCTAC
1 AAGAAAATGTTTCAAGTCTAC
32767 TTTATATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (21 bp):
AAGAAAATGTTTCAAGTCTAC
Found at i:33381 original size:30 final size:31
Alignment explanation
Indices: 33323--33387 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
33313 AACTTTATGT
*
33323 TTTCCGATTGTACCCTTATTTTTAAAATATA
1 TTTCCAATTGTACCCTTATTTTTAAAATATA
*
33354 TTTCCAATTGTACCCTT-TTTTTTAAATATA
1 TTTCCAATTGTACCCTTATTTTTAAAATATA
33384 TTTC
1 TTTC
33388 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAATATA
Found at i:33394 original size:31 final size:31
Alignment explanation
Indices: 33329--33394 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
33319 ATGTTTTCCG
*
33329 ATTGTACCCTTATTTTTAAAATATATTTCCA
1 ATTGTACCCTTATTTTTAAAATATATTTCAA
*
33360 ATTGTACCCTT-TTTTTTAAATATATTTCTAA
1 ATTGTACCCTTATTTTTAAAATATATTTC-AA
33391 ATTG
1 ATTG
33395 CCATTGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.52
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAATATATTTCAA
Found at i:33459 original size:15 final size:16
Alignment explanation
Indices: 33439--33472 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
33429 TTTAATCATA
*
33439 AATTATTCGATTAT-T
1 AATTATTAGATTATAT
33454 AATTATTAGATTATAT
1 AATTATTAGATTATAT
33470 AAT
1 AAT
33473 ACGTATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
AATTATTAGATTATAT
Found at i:33651 original size:22 final size:22
Alignment explanation
Indices: 33582--33828 Score: 166
Period size: 22 Copynumber: 11.3 Consensus size: 22
33572 TAAAAGTCTC
* *
33582 AATTTCATA-AGAAG-TACCAA
1 AATTTCATAGAGAGGTTATCAA
*
33602 AATTTGATAGA-AGGTTATC-A
1 AATTTCATAGAGAGGTTATCAA
* * *
33622 AATCTCATAGAGTGGTTATCGA
1 AATTTCATAGAGAGGTTATCAA
* *
33644 AATTTCATATAGATCAGATTATCAA
1 AATTTC--ATAGA-GAGGTTATCAA
* *
33669 AATTT-ATAG-GAAGATTATTAA
1 AATTTCATAGAG-AGGTTATCAA
* **
33690 AATTTCATAGTGTTGTTATCAA
1 AATTTCATAGAGAGGTTATCAA
* *
33712 AATTTCAAAGCGAGGTTATCAA
1 AATTTCATAGAGAGGTTATCAA
* * *
33734 AATTACATA-ATGTGATTATCAA
1 AATTTCATAGA-GAGGTTATCAA
* * *
33756 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGAGGTTATCAA
* * *
33778 AATTTTATAAAGAGATTATCAA
1 AATTTCATAGAGAGGTTATCAA
*
33800 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAGAGAGGTTATCAA
*
33822 ATTTTCA
1 AATTTCA
33829 AAATGTGATT
Statistics
Matches: 175, Mismatches: 40, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
20 20 0.11
21 25 0.14
22 111 0.63
23 2 0.01
24 5 0.03
25 12 0.07
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
AATTTCATAGAGAGGTTATCAA
Found at i:33684 original size:21 final size:23
Alignment explanation
Indices: 33637--33855 Score: 100
Period size: 22 Copynumber: 9.8 Consensus size: 23
33627 CATAGAGTGG
*
33637 TTATCGAAATTTCATA-TAGATCAGA
1 TTATCAAAATTTCATAGT-GA--AGA
33662 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGTGAAGA
* **
33683 TTATTAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAGTGAAGA
* * *
33705 TTATCAAAATTTCAAAGCG-AGG
1 TTATCAAAATTTCATAGTGAAGA
* * *
33727 TTATCAAAATTACATAATG-TGA
1 TTATCAAAATTTCATAGTGAAGA
* * *
33749 TTATCAAAATTTCATAGAG-GGG
1 TTATCAAAATTTCATAGTGAAGA
* * * **
33771 TCAACAAAATTTTATAAAG-AGA
1 TTATCAAAATTTCATAGTGAAGA
** *
33793 TTATCAAAATTTCATAAAG-AGG
1 TTATCAAAATTTCATAGTGAAGA
* * * *
33815 TTATCAAATTTTCAAAATG-TGA
1 TTATCAAAATTTCATAGTGAAGA
33837 TTA-CAAAAATTTCATAGTG
1 TTATC-AAAATTTCATAGTG
33856 GTACTTCTGG
Statistics
Matches: 152, Mismatches: 37, Indels: 13
0.75 0.18 0.06
Matches are distributed among these distances:
21 16 0.11
22 118 0.78
23 4 0.03
24 3 0.02
25 11 0.07
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.35
Consensus pattern (23 bp):
TTATCAAAATTTCATAGTGAAGA
Found at i:33851 original size:44 final size:44
Alignment explanation
Indices: 33705--33852 Score: 151
Period size: 44 Copynumber: 3.4 Consensus size: 44
33695 CATAGTGTTG
* * * *
33705 TTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGTGA
* * * * *
33749 TTATCAAAATTTCATAGAGGGGTCAACAAAATTTT-ATAAA-GAGA
1 TTATCAAAATTTCATAAAGAGGTTATC-AAATTTTCA-AAATGTGA
33793 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGA
33837 TTA-CAAAAATTTCATA
1 TTATC-AAAATTTCATA
33853 GTGGTACTTC
Statistics
Matches: 84, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
43 11 0.13
44 65 0.77
45 8 0.10
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (44 bp):
TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGA
Found at i:34002 original size:22 final size:22
Alignment explanation
Indices: 33977--34144 Score: 92
Period size: 22 Copynumber: 7.5 Consensus size: 22
33967 AGTTTAGTTT
33977 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAGGGTTA
** *
33999 TCAAAATTAAATAAG-GAGATTA
1 TCAAAATTTCATAAGAG-GGTTA
*
34021 ACAAAATTTCATAATGA-GGTTA
1 TCAAAATTTCATAA-GAGGGTTA
** * *
34043 TCAAAAAATCATAGGGAGGTTTTA
1 TCAAAATTTCATA-AGAGG-GTTA
* * **
34067 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATAAG-AGGGTTA
* *
34090 TTAAAATATCATAACGA-GGTTA
1 TCAAAATTTCATAA-GAGGGTTA
* * *
34112 TCACAATTTCAT-AGTGTGATTA
1 TCAAAATTTCATAAGAG-GGTTA
34134 TCAAAATTTCA
1 TCAAAATTTCA
34145 GAGTGTGATT
Statistics
Matches: 108, Mismatches: 28, Indels: 20
0.69 0.18 0.13
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 70 0.65
23 19 0.18
24 16 0.15
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.33
Consensus pattern (22 bp):
TCAAAATTTCATAAGAGGGTTA
Found at i:34149 original size:22 final size:22
Alignment explanation
Indices: 34109--34155 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
34099 CATAACGAGG
* *
34109 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
34131 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
34153 TTA
1 TTA
34156 CTAACAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:34166 original size:22 final size:23
Alignment explanation
Indices: 34109--34164 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
34099 CATAACGAGG
*
34109 TTATC-ACAATTTCATAGTGTGA
1 TTATCAACAATTTCAGAGTGTGA
34131 TTATCAA-AATTTCAGAGTGTGA
1 TTATCAACAATTTCAGAGTGTGA
34153 TTA-CTAACAATT
1 TTATC-AACAATT
34165 CATATGGAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 1 0.03
22 24 0.80
23 5 0.17
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (23 bp):
TTATCAACAATTTCAGAGTGTGA
Found at i:34211 original size:22 final size:22
Alignment explanation
Indices: 34186--34248 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
34176 TTTTAAATTT
*
34186 TCATAACGTGGTTATCAATATA
1 TCATAACGTGGTTATCAACATA
** * *
34208 TCATATGGAGGTTATCAACATC
1 TCATAACGTGGTTATCAACATA
**
34230 TCATAGTGTTGGTTATCAA
1 TCATAACG-TGGTTATCAA
34249 AATTTAATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 23 0.72
23 9 0.28
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (22 bp):
TCATAACGTGGTTATCAACATA
Found at i:34234 original size:44 final size:45
Alignment explanation
Indices: 34164--34248 Score: 102
Period size: 44 Copynumber: 1.9 Consensus size: 45
34154 TACTAACAAT
* * *
34164 TCATATGGAGGTTTTTAAATTTTCATAACG-TGGTTATCAATATA
1 TCATATGGAGGTTATCAAATTCTCATAACGTTGGTTATCAATATA
**
34208 TCATATGGAGGTTATCAACA-TCTCATAGTGTTGGTTATCAA
1 TCATATGGAGGTTATCAA-ATTCTCATAACGTTGGTTATCAA
34249 AATTTAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 23 0.68
45 11 0.32
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.40
Consensus pattern (45 bp):
TCATATGGAGGTTATCAAATTCTCATAACGTTGGTTATCAATATA
Found at i:34247 original size:23 final size:22
Alignment explanation
Indices: 34193--34248 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
34183 TTTTCATAAC
*
34193 GTGGTTATCAATATATCATATG
1 GTGGTTATCAACATATCATATG
* *
34215 GAGGTTATCAACATCTCATAGTG
1 GTGGTTATCAACATATCATA-TG
*
34238 TTGGTTATCAA
1 GTGGTTATCAA
34249 AATTTAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (22 bp):
GTGGTTATCAACATATCATATG
Found at i:34292 original size:21 final size:22
Alignment explanation
Indices: 34268--34339 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 22
34258 TTAAGGTCTT
**
34268 CAAAATTCAT-AGGGAGGTTAA
1 CAAAATTCATAAGAAAGGTTAA
34289 CAAAATTTCATAAGAAAGGTTAA
1 CAAAA-TTCATAAGAAAGGTTAA
* *
34312 AAAAATT-ATAA-AAAGGTTAT
1 CAAAATTCATAAGAAAGGTTAA
*
34332 CGAAATTC
1 CAAAATTC
34340 CATAGTATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 13 0.31
21 9 0.21
22 7 0.17
23 13 0.31
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.26
Consensus pattern (22 bp):
CAAAATTCATAAGAAAGGTTAA
Found at i:34326 original size:20 final size:23
Alignment explanation
Indices: 34269--34330 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 23
34259 TAAGGTCTTC
**
34269 AAAATTCAT-AGGGAGGTTAACA
1 AAAATTCATAAGAAAGGTTAACA
*
34291 AAATTTCATAAGAAAGGTTAA-A
1 AAAATTCATAAGAAAGGTTAACA
34313 AAAATT-ATAA-AAAGGTTA
1 AAAATTCATAAGAAAGGTTA
34331 TCGAAATTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 8 0.23
21 4 0.11
22 14 0.40
23 9 0.26
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (23 bp):
AAAATTCATAAGAAAGGTTAACA
Found at i:36725 original size:2 final size:2
Alignment explanation
Indices: 36718--36747 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
36708 AGCTCAAAGA
36718 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
36748 GCATAAAGTT
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:37499 original size:2 final size:2
Alignment explanation
Indices: 37492--37520 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
37482 TTTATTGTAC
37492 GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
37521 CTACGGGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:37512 original size:13 final size:13
Alignment explanation
Indices: 37494--37519 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37484 TATTGTACGA
37494 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
37507 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
37520 ACTACGGGTG
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:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (13 bp):
GAGAGAGAGAGAG
Found at i:37512 original size:15 final size:15
Alignment explanation
Indices: 37492--37520 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
37482 TTTATTGTAC
37492 GAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAG
37507 GAGAGAGAGAGAGA
1 GAGAGAGAGAGAGA
37521 CTACGGGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (15 bp):
GAGAGAGAGAGAGAG
Found at i:58507 original size:11 final size:11
Alignment explanation
Indices: 58491--58533 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
58481 CTATATATAT
58491 CTAATTAATAG
1 CTAATTAATAG
*
58502 CTAATTAATAT
1 CTAATTAATAG
58513 CTAATTAATAG
1 CTAATTAATAG
*
58524 TTAATTAATA
1 CTAATTAATA
58534 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:58512 original size:22 final size:22
Alignment explanation
Indices: 58487--58533 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
58477 TATACTATAT
58487 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
58509 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
58531 ATA
1 ATA
58534 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:60915 original size:39 final size:39
Alignment explanation
Indices: 60861--60982 Score: 171
Period size: 39 Copynumber: 3.2 Consensus size: 39
60851 GCTACGTGCT
60861 GGTGGCA-TGCGCAGTGGTGGAGGAAGAGGTATTGGTAGA
1 GGTGGCAGTG-GCAGTGGTGGAGGAAGAGGTATTGGTAGA
* **
60900 GGTGGCAGTGGCAGTGGTGGAGGAAGAGGAAGAGGTAGA
1 GGTGGCAGTGGCAGTGGTGGAGGAAGAGGTATTGGTAGA
*
60939 GGTGGCAGT---AGTGGTGGAGGAAGAGGTCTTGGTAGA
1 GGTGGCAGTGGCAGTGGTGGAGGAAGAGGTATTGGTAGA
60975 GGTGGCAG
1 GGTGGCAG
60983 CGCTGCGGCC
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
36 31 0.41
39 42 0.56
40 2 0.03
ACGTcount: A:0.24, C:0.07, G:0.52, T:0.18
Consensus pattern (39 bp):
GGTGGCAGTGGCAGTGGTGGAGGAAGAGGTATTGGTAGA
Done.