Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011375.1 Corchorus capsularis cultivar CVL-1 contig11396, 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: 41146
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:1576 original size:82 final size:81
Alignment explanation
Indices: 1428--1591 Score: 256
Period size: 82 Copynumber: 2.0 Consensus size: 81
1418 GGTTTACATC
* ** *
1428 TTGGTTTGCTTCTGGCTCTATTGCTTTCTATCCCTTATAGAAAGCAGCTGAAGGAGATTTATCTG
1 TTGGTTTGCTTCTGGCTCTATTGCTTTCTATCACGGATAGAAAGCAGATGAAGGAGATTTATCTG
1493 GTAAAGCCACTTCGCT
66 GTAAAGCCACTTCGCT
* * *
1509 TTGGTTTGCTTTTGGCTCTATTGTTTTCTATCAAGGGATAGAAAGCAGATGAAGGAGATTTATCT
1 TTGGTTTGCTTCTGGCTCTATTGCTTTCTATC-ACGGATAGAAAGCAGATGAAGGAGATTTATCT
1574 GGTAAAGCCACTTCGCT
65 GGTAAAGCCACTTCGCT
1591 T
1 T
1592 ATTCAAGCAG
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
81 30 0.40
82 45 0.60
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (81 bp):
TTGGTTTGCTTCTGGCTCTATTGCTTTCTATCACGGATAGAAAGCAGATGAAGGAGATTTATCTG
GTAAAGCCACTTCGCT
Found at i:8293 original size:2 final size:2
Alignment explanation
Indices: 8286--8314 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8276 ATACCAGATT
8286 TA 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 T
8315 GTAAAGTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12779 original size:20 final size:20
Alignment explanation
Indices: 12754--12793 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12744 ATGCATCTTT
12754 ATTTTTTGTTGCAAAGAAAC
1 ATTTTTTGTTGCAAAGAAAC
12774 ATTTTTTGTTGCAAAGAAAC
1 ATTTTTTGTTGCAAAGAAAC
12794 GTGGTCGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (20 bp):
ATTTTTTGTTGCAAAGAAAC
Found at i:13737 original size:21 final size:21
Alignment explanation
Indices: 13711--13753 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
13701 TTCTGAGGAT
*
13711 TTCATCACTGAAAATAAAGCA
1 TTCATCACAGAAAATAAAGCA
13732 TTCATCACAGAAAATAAAGCA
1 TTCATCACAGAAAATAAAGCA
13753 T
1 T
13754 AGCAAGCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.19, G:0.09, T:0.23
Consensus pattern (21 bp):
TTCATCACAGAAAATAAAGCA
Found at i:15096 original size:33 final size:33
Alignment explanation
Indices: 15059--15124 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
15049 GGATGAAGTG
*
15059 AATATAAAGAGGTGAGGCAGAAGACAGAGAAGA
1 AATATAAAGAGGTGAAGCAGAAGACAGAGAAGA
15092 AATATAAAGAGGTGAAGCAGAAGACAGAGAAGA
1 AATATAAAGAGGTGAAGCAGAAGACAGAGAAGA
15125 GACCAGGCGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.53, C:0.06, G:0.32, T:0.09
Consensus pattern (33 bp):
AATATAAAGAGGTGAAGCAGAAGACAGAGAAGA
Found at i:15362 original size:112 final size:112
Alignment explanation
Indices: 15165--15390 Score: 402
Period size: 112 Copynumber: 2.0 Consensus size: 112
15155 GACGGGACTG
*
15165 TATAGGCTTGGTGTGAGGGAAGACTTGGTCGATGCTGGTGGGCCAAAAATTAACACATGCAATCA
1 TATAGGCTTGGTGTGAGGGAAGACTTGGTCGAGGCTGGTGGGCCAAAAATTAACACATGCAATCA
15230 CGATTAACCCGAACTAAATTATAGGTGAAACTCTAACTTTAAAGGGT
66 CGATTAACCCGAACTAAATTATAGGTGAAACTCTAACTTTAAAGGGT
*
15277 TATAGGCTTGGTGTGAGGGAAGAC-TGAGTCGAGGCTGGTGGGCCAAAAATTAACACATGCAATT
1 TATAGGCTTGGTGTGAGGGAAGACTTG-GTCGAGGCTGGTGGGCCAAAAATTAACACATGCAATC
15341 ACGATTAACCC-AGACTAAATTATAGGTGAAACTCTAACTTTAAAGGGT
65 ACGATTAACCCGA-ACTAAATTATAGGTGAAACTCTAACTTTAAAGGGT
15389 TA
1 TA
15391 GAACTGGCTA
Statistics
Matches: 110, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
111 3 0.03
112 107 0.97
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (112 bp):
TATAGGCTTGGTGTGAGGGAAGACTTGGTCGAGGCTGGTGGGCCAAAAATTAACACATGCAATCA
CGATTAACCCGAACTAAATTATAGGTGAAACTCTAACTTTAAAGGGT
Found at i:16128 original size:11 final size:11
Alignment explanation
Indices: 16112--16209 Score: 131
Period size: 11 Copynumber: 9.6 Consensus size: 11
16102 AAGTTAAATC
16112 TTAAATCAAAG
1 TTAAATCAAAG
16123 TTAAATCAAAG
1 TTAAATCAAAG
16134 TTAAATC----
1 TTAAATCAAAG
16141 TTAAATCAAAG
1 TTAAATCAAAG
16152 TTAAATCAAAG
1 TTAAATCAAAG
*
16163 TTGAATCAAAG
1 TTAAATCAAAG
16174 TTAAATC----
1 TTAAATCAAAG
16181 TTAAATCAAAG
1 TTAAATCAAAG
16192 TTAAATCAAAG
1 TTAAATCAAAG
16203 TTAAATC
1 TTAAATC
16210 GAGTCGGCCT
Statistics
Matches: 77, Mismatches: 2, Indels: 16
0.81 0.02 0.17
Matches are distributed among these distances:
7 14 0.18
11 63 0.82
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (11 bp):
TTAAATCAAAG
Found at i:16140 original size:29 final size:29
Alignment explanation
Indices: 16098--16198 Score: 143
Period size: 29 Copynumber: 3.5 Consensus size: 29
16088 TGACACTTGT
16098 ATCAAAGTTAAATCTTAAATCAAAGTTAA
1 ATCAAAGTTAAATCTTAAATCAAAGTTAA
16127 ATCAAAGTTAAATCTTAAATCAAAGTTAA
1 ATCAAAGTTAAATCTTAAATCAAAGTTAA
* * *
16156 ATCAAAGTTGAATC--AAAGTTAAATCTTAA
1 ATCAAAGTTAAATCTTAAA-TCAAA-GTTAA
16185 ATCAAAGTTAAATC
1 ATCAAAGTTAAATC
16199 AAAGTTAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
27 3 0.05
28 4 0.06
29 59 0.89
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (29 bp):
ATCAAAGTTAAATCTTAAATCAAAGTTAA
Found at i:16158 original size:40 final size:40
Alignment explanation
Indices: 16112--16209 Score: 187
Period size: 40 Copynumber: 2.5 Consensus size: 40
16102 AAGTTAAATC
16112 TTAAATCAAAGTTAAATCAAAGTTAAATCTTAAATCAAAG
1 TTAAATCAAAGTTAAATCAAAGTTAAATCTTAAATCAAAG
*
16152 TTAAATCAAAGTTGAATCAAAGTTAAATCTTAAATCAAAG
1 TTAAATCAAAGTTAAATCAAAGTTAAATCTTAAATCAAAG
16192 TTAAATCAAAGTTAAATC
1 TTAAATCAAAGTTAAATC
16210 GAGTCGGCCT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (40 bp):
TTAAATCAAAGTTAAATCAAAGTTAAATCTTAAATCAAAG
Found at i:16209 original size:29 final size:28
Alignment explanation
Indices: 16111--16209 Score: 86
Period size: 29 Copynumber: 3.7 Consensus size: 28
16101 AAAGTTAAAT
*
16111 CTTAAATCAAAGTTAAATC-AAAGTTAAA
1 CTTAAATCAAAGTTAAATCTAAA-TCAAA
16139 TCTTAAATCAAAG-----T-TAAATCAAA
1 -CTTAAATCAAAGTTAAATCTAAATCAAA
* *
16162 GTTGAATCAAAGTTAAATCTTAAATCAAA
1 CTTAAATCAAAGTTAAATC-TAAATCAAA
*
16191 GTTAAATCAAAGTTAAATC
1 CTTAAATCAAAGTTAAATC
16210 GAGTCGGCCT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
22 10 0.17
23 4 0.07
24 4 0.07
27 1 0.02
29 39 0.67
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (28 bp):
CTTAAATCAAAGTTAAATCTAAATCAAA
Found at i:18483 original size:21 final size:21
Alignment explanation
Indices: 18450--18498 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
18440 AAGAATTGTA
**
18450 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
18470 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
18491 GCATTCCT
1 GC-TTCCT
18499 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:22697 original size:34 final size:34
Alignment explanation
Indices: 22633--22712 Score: 110
Period size: 36 Copynumber: 2.4 Consensus size: 34
22623 AAATGGGATG
*
22633 AAAAGTAAAAAGGGTAATCAGAGTAATTAAGTTCCA
1 AAAAGTAAAAAGGGCAATCA-AGTAATTAAGTT-CA
22669 AAAAGTAAAAAGGGCAATC-AGTAATTAAGTTCA
1 AAAAGTAAAAAGGGCAATCAAGTAATTAAGTTCA
*
22702 ATAAG-AAAAAG
1 AAAAGTAAAAAG
22713 TAATTTGTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 6 0.14
33 6 0.14
34 12 0.29
36 18 0.43
ACGTcount: A:0.54, C:0.07, G:0.19, T:0.20
Consensus pattern (34 bp):
AAAAGTAAAAAGGGCAATCAAGTAATTAAGTTCA
Found at i:22797 original size:22 final size:22
Alignment explanation
Indices: 22772--22962 Score: 94
Period size: 22 Copynumber: 8.9 Consensus size: 22
22762 TGATAATCAG
*
22772 AGTAATTAAAAAAGAGTAAAAT
1 AGTAATTAGAAAAGAGTAAAAT
*
22794 AGTAATCAGTAAAA-AGT--AAT
1 AGTAATTAG-AAAAGAGTAAAAT
*
22814 -GATAATCAGTAAAAG-GTAAAAT
1 AG-TAATTAG-AAAAGAGTAAAAT
* *
22836 GGTAATTAGAAAAGGGTAAAAT
1 AGTAATTAGAAAAGAGTAAAAT
* *
22858 GGTAATTAGTAAAGAGT--AAT
1 AGTAATTAGAAAAGAGTAAAAT
* * *
22878 AGTCATCAG-TAAGAAGTAAAA-
1 AGTAATTAGAAAAG-AGTAAAAT
* * * *
22899 AGATAATCAGTAAAGGGCAAAAT
1 AG-TAATTAGAAAAGAGTAAAAT
* * *
22922 GGTAATTAGAAAAGAGCAAAGT
1 AGTAATTAGAAAAGAGTAAAAT
* * *
22944 GGTAATCAGTAAAGAGTAA
1 AGTAATTAGAAAAGAGTAA
22963 TAGTAAAAAG
Statistics
Matches: 135, Mismatches: 21, Indels: 26
0.74 0.12 0.14
Matches are distributed among these distances:
19 4 0.03
20 29 0.21
21 7 0.05
22 86 0.64
23 9 0.07
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.22
Consensus pattern (22 bp):
AGTAATTAGAAAAGAGTAAAAT
Found at i:22841 original size:42 final size:44
Alignment explanation
Indices: 22781--22962 Score: 130
Period size: 42 Copynumber: 4.2 Consensus size: 44
22771 GAGTAATTAA
22781 AAAAGAGTAAAATAGTAATCAGTAAAAAGT-AATGATAATCAGT
1 AAAAGAGTAAAATAGTAATCAGTAAAAAGTAAATGATAATCAGT
* * * * *
22824 AAAAG-GTAAAATGGTAATTAG-AAAAGGGTAAAATGGTAATTAGT
1 AAAAGAGTAAAATAGTAATCAGTAAAA-AGT-AAATGATAATCAGT
* * *
22868 -AAAGAGT--AATAGTCATCAGTAAGAAGTAAAAAGATAATCAGT
1 AAAAGAGTAAAATAGTAATCAGTAAAAAGT-AAATGATAATCAGT
* * * * * *
22910 -AAAGGGCAAAATGGTAATTAG-AAAAGAGCAAAGTGGTAATCAGT
1 AAAAGAGTAAAATAGTAATCAGTAAAA-AGTAAA-TGATAATCAGT
22954 -AAAGAGTAA
1 AAAAGAGTAA
22963 TAGTAAAAAG
Statistics
Matches: 106, Mismatches: 24, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
41 4 0.04
42 44 0.42
43 18 0.17
44 40 0.38
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.21
Consensus pattern (44 bp):
AAAAGAGTAAAATAGTAATCAGTAAAAAGTAAATGATAATCAGT
Found at i:22914 original size:64 final size:64
Alignment explanation
Indices: 22781--22956 Score: 185
Period size: 64 Copynumber: 2.7 Consensus size: 64
22771 GAGTAATTAA
* * * * * * *
22781 AAAAGAGTAAAATAGTAATCAGTAAAAAGTAATGATAATCAGTAAAAGGTAAAATGGTAATTAG
1 AAAAGGGTAAAATGGTAATTAGTAAAGAGTAATGATAATCAGTAAAAGGTAAAAAGATAATCAG
*
22845 AAAAGGGTAAAATGGTAATTAGTAAAGAGTAAT-AGTCATCAGTAAGAA-GTAAAAAGATAATCA
1 AAAAGGGTAAAATGGTAATTAGTAAAGAGTAATGA-TAATCAGTAA-AAGGTAAAAAGATAATCA
22908 G
64 G
* * * * *
22909 TAAAGGGCAAAATGGTAATTAGAAAAGAGCAAAGTGGTAATCAGTAAA
1 AAAAGGGTAAAATGGTAATTAGTAAAGAG-TAA-TGATAATCAGTAAA
22957 GAGTAATAGT
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
63 1 0.01
64 77 0.83
65 5 0.05
66 10 0.11
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.22
Consensus pattern (64 bp):
AAAAGGGTAAAATGGTAATTAGTAAAGAGTAATGATAATCAGTAAAAGGTAAAAAGATAATCAG
Found at i:22974 original size:20 final size:20
Alignment explanation
Indices: 22951--22996 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
22941 AGTGGTAATC
22951 AGTAAAGAGTAAT-AGTAAAA
1 AGTAAAG-GTAATCAGTAAAA
* *
22971 AGTAATGGTAATCAGTAGAA
1 AGTAAAGGTAATCAGTAAAA
22991 AGTAAA
1 AGTAAA
22997 AAGCTTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.54, C:0.02, G:0.22, T:0.22
Consensus pattern (20 bp):
AGTAAAGGTAATCAGTAAAA
Found at i:22975 original size:64 final size:64
Alignment explanation
Indices: 22846--22975 Score: 140
Period size: 64 Copynumber: 2.0 Consensus size: 64
22836 GGTAATTAGA
* * * * **
22846 AAAGGGTAAAATGGTAATTAGTAAAGAGTAATAGTCATCAGTAAGAAGTAAAAAGATAATCAGT
1 AAAGGGCAAAATGGTAATTAGAAAAGAGAAATAGTAATCAGTAAGAAGTAAAAAGATAAAAAGT
* *
22910 AAAGGGCAAAATGGTAATTAGAAAAGAGCAAAGTGGTAATCAGTAA-AGAGT-AATAG-TAAAAA
1 AAAGGGCAAAATGGTAATTAGAAAAGAG-AAA-TAGTAATCAGTAAGA-AGTAAAAAGATAAAAA
22972 GT
63 GT
22974 AA
1 AA
22976 TGGTAATCAG
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
64 34 0.62
65 7 0.13
66 14 0.25
ACGTcount: A:0.52, C:0.05, G:0.23, T:0.21
Consensus pattern (64 bp):
AAAGGGCAAAATGGTAATTAGAAAAGAGAAATAGTAATCAGTAAGAAGTAAAAAGATAAAAAGT
Found at i:22975 original size:86 final size:86
Alignment explanation
Indices: 22814--22975 Score: 243
Period size: 86 Copynumber: 1.9 Consensus size: 86
22804 AAAAAGTAAT
* * * *
22814 GATAATCAGTAAAAGGTAAAATGGTAATTAGAAAAGGGTAAAATGGTAATTAGTAAAGAGTAATA
1 GATAATCAGTAAAAGGCAAAATGGTAATTAGAAAAGAGCAAAATGGTAATCAGTAAAGAGTAATA
* **
22879 GTCATCAGTAAGAAGTAAAAA
66 GTAAAAAGTAAGAAGTAAAAA
* *
22900 GATAATCAGTAAAGGGCAAAATGGTAATTAGAAAAGAGCAAAGTGGTAATCAGTAAAGAGTAATA
1 GATAATCAGTAAAAGGCAAAATGGTAATTAGAAAAGAGCAAAATGGTAATCAGTAAAGAGTAATA
22965 GTAAAAAGTAA
66 GTAAAAAGTAA
22976 TGGTAATCAG
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 67 1.00
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.22
Consensus pattern (86 bp):
GATAATCAGTAAAAGGCAAAATGGTAATTAGAAAAGAGCAAAATGGTAATCAGTAAAGAGTAATA
GTAAAAAGTAAGAAGTAAAAA
Found at i:30885 original size:7 final size:7
Alignment explanation
Indices: 30873--30897 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30863 TCCTTTCCCA
30873 GTTACGG
1 GTTACGG
30880 GTTACGG
1 GTTACGG
30887 GTTACGG
1 GTTACGG
30894 GTTA
1 GTTA
30898 GGTTTGGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.40, T:0.32
Consensus pattern (7 bp):
GTTACGG
Found at i:32112 original size:49 final size:49
Alignment explanation
Indices: 32043--32141 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
32033 TAAAATTAAA
*
32043 ATTGGATTATCATGCGTCATATGCATCCATGCATTTCAAGACAAAATCC
1 ATTGGATTATCATGCATCATATGCATCCATGCATTTCAAGACAAAATCC
32092 ATTGGATTATCATGCATCATATGCATCCATGCATTTCAAGACAAAATCC
1 ATTGGATTATCATGCATCATATGCATCCATGCATTTCAAGACAAAATCC
32141 A
1 A
32142 GTGATTAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.30
Consensus pattern (49 bp):
ATTGGATTATCATGCATCATATGCATCCATGCATTTCAAGACAAAATCC
Found at i:32264 original size:43 final size:43
Alignment explanation
Indices: 32203--32544 Score: 576
Period size: 43 Copynumber: 8.0 Consensus size: 43
32193 AGGTGAATCA
32203 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTG
1 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTG
*
32246 GTAAACAACTTAATTCGGTGTAATTAAGTGAATTGGTAATTTG
1 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTG
32289 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTG
1 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTG
**
32332 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTCATAATTTG
1 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTG
32375 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTG
1 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTG
* **
32418 GTAAACAACTTAATTCAGTGTAATTAAGTAAATTGACAATTTG
1 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTG
* * * *
32461 GTAAACAACTTAATTCGTTGTAATTAAGCAAATTAGCAATTTG
1 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTG
* *
32504 GTAAACAACTTAATTCGGTGTAATTAAGAAAATTTGTAATT
1 GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATT
32545 AAGCTAAGTA
Statistics
Matches: 281, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 281 1.00
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.37
Consensus pattern (43 bp):
GTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTTG
Found at i:32552 original size:21 final size:21
Alignment explanation
Indices: 32528--32567 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
32518 TCGGTGTAAT
32528 TAAGAAAATTT-GTAATTAAGC
1 TAAG-AAATTTGGTAATTAAGC
*
32549 TAAGTAATTTGGTAATTAA
1 TAAGAAATTTGGTAATTAA
32568 ATTAGGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.38
Consensus pattern (21 bp):
TAAGAAATTTGGTAATTAAGC
Found at i:32576 original size:21 final size:20
Alignment explanation
Indices: 32534--32578 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
32524 TAATTAAGAA
*
32534 AATTTGTAATTAAGCTAAGT
1 AATTTGTAATTAAACTAAGT
* *
32554 AATTTGGTAATTAAATTAGGT
1 AATTT-GTAATTAAACTAAGT
32575 AATT
1 AATT
32579 AACTTAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (20 bp):
AATTTGTAATTAAACTAAGT
Found at i:32597 original size:19 final size:19
Alignment explanation
Indices: 32573--32634 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
32563 ATTAAATTAG
32573 GTAATTAACTTAATTCGGT
1 GTAATTAACTTAATTCGGT
* * *
32592 GTAATTAA-GTAAATC--A
1 GTAATTAACTTAATTCGGT
* *
32608 GTAGTCAACTTAATTCGGT
1 GTAATTAACTTAATTCGGT
32627 GTAATTAA
1 GTAATTAA
32635 GTAAATCAGT
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
16 6 0.20
17 5 0.17
18 5 0.17
19 14 0.47
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (19 bp):
GTAATTAACTTAATTCGGT
Found at i:32637 original size:35 final size:35
Alignment explanation
Indices: 32573--32675 Score: 152
Period size: 35 Copynumber: 2.9 Consensus size: 35
32563 ATTAAATTAG
*
32573 GTAATTAACTTAATTCGGTGTAATTAAGTAAATCA
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAATCA
*
32608 GTAGTCAACTTAATTCGGTGTAATTAAGTAAATCA
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAATCA
*** *
32643 GTAATTGGCTTAATTTGGTGTAATTAAGTAAAT
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAAT
32676 AAATGGCTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 61 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (35 bp):
GTAATCAACTTAATTCGGTGTAATTAAGTAAATCA
Found at i:32686 original size:31 final size:34
Alignment explanation
Indices: 32581--32687 Score: 130
Period size: 35 Copynumber: 3.2 Consensus size: 34
32571 AGGTAATTAA
* ***
32581 CTTAATTCGGTGTAATTAAGTAAATCAGTAGTCAA
1 CTTAATTCGGTGTAATTAAGTAAATCAG-AATTGG
32616 CTTAATTCGGTGTAATTAAGTAAATCAGTAATTGG
1 CTTAATTCGGTGTAATTAAGTAAATCAG-AATTGG
*
32651 CTTAATTTGGTGTAATTAAGTAAAT-A-AA-TGG
1 CTTAATTCGGTGTAATTAAGTAAATCAGAATTGG
32682 CTTAAT
1 CTTAAT
32688 CTAGGAGTCA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
31 9 0.13
32 2 0.03
34 1 0.01
35 55 0.82
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.37
Consensus pattern (34 bp):
CTTAATTCGGTGTAATTAAGTAAATCAGAATTGG
Found at i:33553 original size:33 final size:33
Alignment explanation
Indices: 33515--33619 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 33
33505 TTGCAAAGAG
*
33515 TGTTTTAGATGTTGTTTGCGATGACACCAAATC
1 TGTTTTAGATGTTGTTTGCGATGAAACCAAATC
* * *
33548 TGTTTTAGGTGTTGTTTGGGATGAAACAAAATC
1 TGTTTTAGATGTTGTTTGCGATGAAACCAAATC
* * ** * *
33581 TGTTTTGGATGCTAATTGTGATGAAAACAAATC
1 TGTTTTAGATGTTGTTTGCGATGAAACCAAATC
33614 TGTTTT
1 TGTTTT
33620 GGTTGATCAT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.41
Consensus pattern (33 bp):
TGTTTTAGATGTTGTTTGCGATGAAACCAAATC
Found at i:34090 original size:30 final size:30
Alignment explanation
Indices: 34029--34091 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
34019 TCTTCAAGGG
* *
34029 GGAGGGAATGATGCGCCCAAGGTTTATCAT
1 GGAGGGAATGATGCGCCCAAGGCTTACCAT
*
34059 GGAGGGAATGATGCG-TCAAGGACTTACCAT
1 GGAGGGAATGATGCGCCCAAGG-CTTACCAT
34089 GGA
1 GGA
34092 CTTGAATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.29, C:0.16, G:0.35, T:0.21
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCCAAGGCTTACCAT
Found at i:38191 original size:24 final size:24
Alignment explanation
Indices: 38164--38231 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
38154 GAAAACAAAA
* *
38164 GAGCAGCAGAAGAAGAAAAAGAGT
1 GAGCAACAGAAGAAGAAAAAGAAT
38188 GAGCAACA-ACAGAAGAAAAAGAAT
1 GAGCAACAGA-AGAAGAAAAAGAAT
*
38212 GAGCAACAGGAAAAAGAAAA
1 GAGCAACA-GAAGAAGAAAA
38232 GACTGTTAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 1 0.03
24 28 0.74
25 8 0.21
26 1 0.03
ACGTcount: A:0.60, C:0.10, G:0.26, T:0.03
Consensus pattern (24 bp):
GAGCAACAGAAGAAGAAAAAGAAT
Found at i:39169 original size:2 final size:2
Alignment explanation
Indices: 39162--39188 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39152 GAATATTCGT
39162 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 T
39189 GCTGTGGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.