Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022073.1 Corchorus olitorius cultivar O-4 contig22106, 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: 87746
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:620 original size:34 final size:34
Alignment explanation
Indices: 582--647 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
572 TTTTTAAAAT
* *
582 TAAAAAATAAGAAGGGTATTTTAGATATTTCAAA
1 TAAAAAATAAGAAAGATATTTTAGATATTTCAAA
616 TAAAAAATAAGAAAGATATTTTAGATATTTCA
1 TAAAAAATAAGAAAGATATTTTAGATATTTCA
648 GATTAAGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (34 bp):
TAAAAAATAAGAAAGATATTTTAGATATTTCAAA
Found at i:2475 original size:55 final size:55
Alignment explanation
Indices: 2391--2501 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
2381 GCTCGTGCAA
2391 CATGATAGGCAGATTTCACCGTAAAAATCCCCAACTTAGACTCCACCCAAATCAG
1 CATGATAGGCAGATTTCACCGTAAAAATCCCCAACTTAGACTCCACCCAAATCAG
2446 CATGATAGGCAGATTTCACCGTAAAAATCCCCAACTTAGACTCCACCCAAATCAG
1 CATGATAGGCAGATTTCACCGTAAAAATCCCCAACTTAGACTCCACCCAAATCAG
2501 C
1 C
2502 TTATCATCCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.36, C:0.32, G:0.13, T:0.20
Consensus pattern (55 bp):
CATGATAGGCAGATTTCACCGTAAAAATCCCCAACTTAGACTCCACCCAAATCAG
Found at i:3003 original size:25 final size:25
Alignment explanation
Indices: 2969--3017 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
2959 CCCAACAATC
2969 TTGAGCACTCTCGCTCAGTCTCTAT
1 TTGAGCACTCTCGCTCAGTCTCTAT
*
2994 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCAGTCTCTA
3018 CAAACCAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.33, G:0.18, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCAGTCTCTAT
Found at i:5295 original size:26 final size:27
Alignment explanation
Indices: 5265--5318 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
5255 ATCCCTTATG
5265 TTTTTCTTTTGGGACAAAAT-ATCCCT
1 TTTTTCTTTTGGGACAAAATAATCCCT
* *
5291 TTTTTTTTTTGGGACAAATTAATCCCT
1 TTTTTCTTTTGGGACAAAATAATCCCT
5318 T
1 T
5319 ACATTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (27 bp):
TTTTTCTTTTGGGACAAAATAATCCCT
Found at i:6094 original size:21 final size:20
Alignment explanation
Indices: 6053--6095 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
6043 CGTGAGCAAT
* *
6053 TCAAGGAGGAAAATTTGCTG
1 TCAAGGAGGAAAATCTACTG
6073 TCAAGGGAGGAAAATCTACTG
1 TCAA-GGAGGAAAATCTACTG
6094 TC
1 TC
6096 TGATTTGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (20 bp):
TCAAGGAGGAAAATCTACTG
Found at i:6355 original size:21 final size:21
Alignment explanation
Indices: 6329--6368 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6319 AAGACAATAC
6329 CCCTCATGAATCCCGAATTGT
1 CCCTCATGAATCCCGAATTGT
*
6350 CCCTCATGAATCTCGAATT
1 CCCTCATGAATCCCGAATT
6369 ATTGTCCACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.30
Consensus pattern (21 bp):
CCCTCATGAATCCCGAATTGT
Found at i:26013 original size:22 final size:21
Alignment explanation
Indices: 25988--26041 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
25978 GAAGTTCGTG
25988 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
26010 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
26029 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
26042 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:28833 original size:80 final size:81
Alignment explanation
Indices: 28642--28862 Score: 223
Period size: 80 Copynumber: 2.7 Consensus size: 81
28632 AGAAATTATT
* * * *
28642 CTTCTCATTTTCTTAACCAAAAATCTAAACTTTAACTTAAAAAACCAATCTTTAAACAAAAATCT
1 CTTCACATTTTC-TAAACAAAAATCTAAACTTTAAATTAAAAAACCAATCTTTAAACAAAAACCT
28707 AAACCATGAAATCTAAA
65 AAACCATGAAATCTAAA
* * * ** ** *
28724 CTCCATATTTCCTAAGTAAAAATCTAAACTTTAAATTAAAAAGTCAAT-TTTCAAAC-AAACCCT
1 CTTCACATTTTCTAAACAAAAATCTAAACTTTAAATTAAAAAACCAATCTTT-AAACAAAAACCT
**
28787 AATTCATGAAAAT-TAAA
65 AAACCATG-AAATCTAAA
* * * * *
28804 CTTCACATTTTCTAAACAAAAATCCAAACTTTAAGTTAAAGAACTAATCTTTAGACAAA
1 CTTCACATTTTCTAAACAAAAATCTAAACTTTAAATTAAAAAACCAATCTTTAAACAAA
28863 TCCCAACCTA
Statistics
Matches: 110, Mismatches: 25, Indels: 9
0.76 0.17 0.06
Matches are distributed among these distances:
80 58 0.53
81 44 0.40
82 8 0.07
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (81 bp):
CTTCACATTTTCTAAACAAAAATCTAAACTTTAAATTAAAAAACCAATCTTTAAACAAAAACCTA
AACCATGAAATCTAAA
Found at i:34762 original size:113 final size:105
Alignment explanation
Indices: 34625--34873 Score: 273
Period size: 113 Copynumber: 2.3 Consensus size: 105
34615 TTTTATTTTC
* * **
34625 CCTATAATAATAAATCATTGATTTCACAATATACCCTTGAAATGAATTATTTTTTTTTTAACTTT
1 CCTATAATAATAAATCTTTAATTTCACAATATACCCTTGAAATGAATTA--AATTTTTTAA-TTT
*
34690 GGAGCTAAACCTAGTGAAATTGATATTTTTTTATTTTTTCCCCTAAAA
63 GGAGCTAAACCTAGTGAAATTGAT-TATTTTTA-TTTTT---CTAAAA
* *
34738 CCTATAATAATAAATCTTTAATTTCACGACTTTTACCCTTGAAATGAATTAAATTTTTTAATTTG
1 CCTATAATAATAAATCTTTAATTTCAC-A-ATATACCCTTGAAATGAATTAAATTTTTTAATTTG
* *** * *
34803 GGGCTAAGTTTAGTGAAATTGGTTATTTTTATTTTTCTAAAT
64 GAGCTAAACCTAGTGAAATTGATTATTTTTATTTTTCTAAAA
* *
34845 CTTATAATAGTAAATCTTTAATTTCACAA
1 CCTATAATAATAAATCTTTAATTTCACAA
34874 AGTTTAACCC
Statistics
Matches: 118, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
106 1 0.01
107 30 0.25
110 5 0.04
111 7 0.06
112 22 0.19
113 33 0.28
114 1 0.01
115 19 0.16
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (105 bp):
CCTATAATAATAAATCTTTAATTTCACAATATACCCTTGAAATGAATTAAATTTTTTAATTTGGA
GCTAAACCTAGTGAAATTGATTATTTTTATTTTTCTAAAA
Found at i:35954 original size:21 final size:21
Alignment explanation
Indices: 35928--35989 Score: 61
Period size: 26 Copynumber: 2.7 Consensus size: 21
35918 GTTTCACTTG
35928 TTTGATGGAATATTACAATTA
1 TTTGATGGAATATTACAATTA
* *
35949 TTTGATGAAATTGTGTATTACAATTG
1 TTTGATGGAA-----TATTACAATTA
35975 TTTGATGGAATATTA
1 TTTGATGGAATATTA
35990 TATCATCTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
21 14 0.42
26 19 0.58
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (21 bp):
TTTGATGGAATATTACAATTA
Found at i:37470 original size:21 final size:21
Alignment explanation
Indices: 37444--37505 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 21
37434 GTTTCACTTC
37444 TTTGATGGAATATTACAATTG
1 TTTGATGGAATATTACAATTG
*
37465 TTTGATGAAATTGTGTATTACAATTG
1 TTTGATGGAA-----TATTACAATTG
37491 TTTGATGGAATATTA
1 TTTGATGGAATATTA
37506 TATCATCTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
21 14 0.41
26 20 0.59
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (21 bp):
TTTGATGGAATATTACAATTG
Found at i:38437 original size:21 final size:21
Alignment explanation
Indices: 38411--38475 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 21
38401 CTGGTTTCAC
38411 TTGTTTGATGGAATATTACAA
1 TTGTTTGATGGAATATTACAA
38432 TTGTTTGAT-GACATTGTGTATTACAA
1 TTGTTTGATGGA-A-----TATTACAA
38458 TTGTTTGATGGAATATTA
1 TTGTTTGATGGAATATTA
38476 TATGTGAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
20 2 0.05
21 15 0.41
26 18 0.49
27 2 0.05
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.46
Consensus pattern (21 bp):
TTGTTTGATGGAATATTACAA
Found at i:39688 original size:20 final size:20
Alignment explanation
Indices: 39663--39700 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39653 TATAAATTTT
39663 AATTTTT-GATCTAAAGTTTG
1 AATTTTTAGAT-TAAAGTTTG
39683 AATTTTTAGATTAAAGTT
1 AATTTTTAGATTAAAGTT
39701 AGCTTGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (20 bp):
AATTTTTAGATTAAAGTTTG
Found at i:45520 original size:48 final size:48
Alignment explanation
Indices: 45463--45629 Score: 218
Period size: 49 Copynumber: 3.5 Consensus size: 48
45453 AGATGCGAAT
* * *
45463 TTTTTTGTTTTCTTTCATAAAATGCCCTTCCCGAATGGAAAGCACTAA
1 TTTTCTGTTTTCTTTCCTAAAATGCCCTTCCCGAATGGAAGGCACTAA
* * *
45511 TTTTCTGTTTTATTTCCTAAAATGCCCATCCC-AGATGGAAGGCACTAGT
1 TTTTCTGTTTTCTTTCCTAAAATGCCCTTCCCGA-ATGGAAGGCACTA-A
45560 TTTTCTGTTTTCTTTCCTAAAATGCCCTTCCCTG-ATGGAAGGCACTAA
1 TTTTCTGTTTTCTTTCCTAAAATGCCCTTCCC-GAATGGAAGGCACTAA
45608 -TTT-T-TTTTCTTTCCTAAAATGC
1 TTTTCTGTTTTCTTTCCTAAAATGC
45630 TCTTTTTGCA
Statistics
Matches: 106, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
45 18 0.17
46 1 0.01
47 4 0.04
48 40 0.38
49 43 0.41
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.41
Consensus pattern (48 bp):
TTTTCTGTTTTCTTTCCTAAAATGCCCTTCCCGAATGGAAGGCACTAA
Found at i:45643 original size:45 final size:45
Alignment explanation
Indices: 45465--45656 Score: 151
Period size: 49 Copynumber: 4.1 Consensus size: 45
45455 ATGCGAATTT
* *
45465 TTTTGTTTTCTTTCATAAAATGCCCTTCCC-GAATGGAAAG-CACTAA
1 TTTT-TTTTCTTTCCTAAAATGCCCTTCCCTG-ATGGAAGGTC-CTAA
* * * *
45511 TTTTCTGTTTTATTTCCTAAAATGCCCATCCCAGATGGAAGG-CACTAGTT
1 -TTT-T-TTTTCTTTCCTAAAATGCCCTTCCCTGATGGAAGGTC-CTA--A
45561 TTTCTGTTTTCTTTCCTAAAATGCCCTTCCCTGATGGAAGG-CACTAA
1 TTT-T-TTTTCTTTCCTAAAATGCCCTTCCCTGATGGAAGGTC-CTAA
* **
45608 TTTTTTTTCTTTCCTAAAATGCTCTT-TTTGCATGGAAGGTCCTAA
1 TTTTTTTTCTTTCCTAAAATGCCCTTCCCTG-ATGGAAGGTCCTAA
45653 TTTT
1 TTTT
45657 ACTCTTTTTT
Statistics
Matches: 127, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
44 2 0.02
45 37 0.29
46 2 0.02
47 6 0.05
48 36 0.28
49 44 0.35
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (45 bp):
TTTTTTTTCTTTCCTAAAATGCCCTTCCCTGATGGAAGGTCCTAA
Found at i:47818 original size:33 final size:33
Alignment explanation
Indices: 47756--47818 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
47746 ATATATAATT
*
47756 AGAGAGAAATAACTCACAAAACTAGAGGAGGAG
1 AGAGAGAAATAACTCACAAAACTAAAGGAGGAG
* *
47789 AGAGAGAAATAACTCACCAAGCTAAAGGAG
1 AGAGAGAAATAACTCACAAAACTAAAGGAG
47819 TTGTAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.51, C:0.14, G:0.25, T:0.10
Consensus pattern (33 bp):
AGAGAGAAATAACTCACAAAACTAAAGGAGGAG
Found at i:52121 original size:23 final size:23
Alignment explanation
Indices: 52095--52139 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
52085 CAACATTACA
*
52095 ATCACTAAACAAACAAACAAACG
1 ATCACCAAACAAACAAACAAACG
* *
52118 ATCACCAAACAAAGAAATAAAC
1 ATCACCAAACAAACAAACAAAC
52140 AGTTCATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.62, C:0.24, G:0.04, T:0.09
Consensus pattern (23 bp):
ATCACCAAACAAACAAACAAACG
Found at i:52174 original size:30 final size:30
Alignment explanation
Indices: 52140--52200 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
52130 AGAAATAAAC
* *
52140 AGTTCATGAACACCTATAGTTCTAAAGTTA
1 AGTTCATGAACACCTACAGTTCTAAAATTA
52170 AGTTCATGAACACCTACAGTTCTAAAATTA
1 AGTTCATGAACACCTACAGTTCTAAAATTA
52200 A
1 A
52201 CATTTGCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31
Consensus pattern (30 bp):
AGTTCATGAACACCTACAGTTCTAAAATTA
Found at i:55189 original size:2 final size:2
Alignment explanation
Indices: 55182--55218 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
55172 ACATAATTAT
55182 TA TA TA TA TA T- TA TA TA -A TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55219 AACGAACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:55193 original size:11 final size:11
Alignment explanation
Indices: 55179--55218 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
55169 AAAACATAAT
55179 TATTATATATA
1 TATTATATATA
55190 TATTATATA-A
1 TATTATATATA
55200 TA-TATATATA
1 TATTATATATA
*
55210 TATAATATA
1 TATTATATA
55219 AACGAACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 6 0.23
10 6 0.23
11 14 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TATTATATATA
Found at i:55207 original size:20 final size:20
Alignment explanation
Indices: 55182--55219 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55172 ACATAATTAT
*
55182 TATATATATATTATATAATA
1 TATATATATATAATATAATA
55202 TATATATATATAATATAA
1 TATATATATATAATATAA
55220 ACGAACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATATATATATAATATAATA
Found at i:55207 original size:22 final size:22
Alignment explanation
Indices: 55174--55218 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
55164 AAATTAAAAC
*
55174 ATAATTATTATATATATATTAT
1 ATAATTATTATATATATAATAT
55196 ATAA-TATATATATATATAATAT
1 ATAATTAT-TATATATATAATAT
55218 A
1 A
55219 AACGAACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATTATTATATATATAATAT
Found at i:55242 original size:11 final size:11
Alignment explanation
Indices: 55215--55269 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
55205 ATATATATAA
55215 TATAAACGAAC
1 TATAAACGAAC
*
55226 -ATAAACGAGC
1 TATAAACGAAC
*
55236 TATAAACGATC
1 TATAAACGAAC
55247 TATTAAACGAAC
1 TA-TAAACGAAC
55259 -ACTAAACGAAC
1 TA-TAAACGAAC
55270 ATTAATCGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.24
11 21 0.55
12 8 0.21
ACGTcount: A:0.51, C:0.20, G:0.11, T:0.18
Consensus pattern (11 bp):
TATAAACGAAC
Found at i:56146 original size:19 final size:20
Alignment explanation
Indices: 56109--56151 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
56099 GATGTTAATG
*
56109 TAATTGATTTGATTATTTTC
1 TAATTGATTTGAGTATTTTC
*
56129 TAATTGATTT-AGTATTTTG
1 TAATTGATTTGAGTATTTTC
56148 TAAT
1 TAAT
56152 CAATACTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (20 bp):
TAATTGATTTGAGTATTTTC
Found at i:62590 original size:23 final size:23
Alignment explanation
Indices: 62564--62615 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
62554 GACCAAAAAG
62564 AGCATGGAAAGAATGTGCATTGA
1 AGCATGGAAAGAATGTGCATTGA
62587 AGCATGGAAAGAATGTGCATTGA
1 AGCATGGAAAGAATGTGCATTGA
62610 AGCATG
1 AGCATG
62616 AAGATGCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (23 bp):
AGCATGGAAAGAATGTGCATTGA
Found at i:62953 original size:22 final size:22
Alignment explanation
Indices: 62928--62970 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
62918 GAACTTCAGA
*
62928 ACAAGTCCTGCCCAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
62950 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
62971 TTGCTGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTGG
Found at i:63664 original size:12 final size:12
Alignment explanation
Indices: 63644--63672 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
63634 GGTTATATCG
63644 AAAAA-AATTAA
1 AAAAATAATTAA
63655 AAAAATAATTAA
1 AAAAATAATTAA
63667 AAAAAT
1 AAAAAT
63673 TTCGACCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAATAATTAA
Found at i:66429 original size:54 final size:54
Alignment explanation
Indices: 66331--66968 Score: 655
Period size: 53 Copynumber: 11.9 Consensus size: 54
66321 TCCTTAAAAC
* *
66331 GACCGCACTGGATCAAAT-TGGAGATTAACTCTGATCATCG-AAACTTCTTGGAAC
1 GACCGCACTGGATC--ATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
* * * * * *
66385 GACCGCACTAGATTAAT-TGGAGATCAACTTTGATCATCGAAAACTTTTTGAAAC
1 GACCGCACTGGA-TCATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
* * * *
66439 GACCACACTGGATCATCTGGAGATAAACTCTGATCAT-GAAAAACTTCTTAGAAC
1 GACCGCACTGGATCATCTGGAGATCAACTCTGATCATCG-AAAACTTCTTGGAAT
* * *
66493 GACCGCACTGGATCATCTGGAGATCAACTCTAATCATTGAAAACTTCTTGGAGT
1 GACCGCACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
* ** *
66547 GACGGCACTGGATCATCT-G-GATCAACTCTGATCAAAGAAAACTTCTTGCAAT
1 GACCGCACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
** *
66599 GACCGCACTGGATCATCTGG-GATCAACTCTGATCA-CTGAAAACTTCTTCAAAC
1 GACCGCACTGGATCATCTGGAGATCAACTCTGATCATC-GAAAACTTCTTGGAAT
* * *
66652 GACCGCACTAGATCATCTAGGA-ATCAACTCTGATCGTTGAAAACTTCTTCGGAAT
1 GACCGCACTGGATCATCT-GGAGATCAACTCTGATCATCGAAAACTTCTT-GGAAT
* * *
66707 GACCGCACTGGATTATCTAGG-GATCAACTCTGATC-TCTAAAAACTTCTTCGAAT
1 GACCGCACTGGATCATCT-GGAGATCAACTCTGATCATC-GAAAACTTCTTGGAAT
* * * **
66761 GACCGCACTGGGTCATCTAGA-ATCAGCTCTGATCAAAGAAAACTTCTTGGAAT
1 GACCGCACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
*
66814 GACCGCACTGGATCATCTGG-GATCAACTCTGATCA-CTGAAAACTTTTTGGAAT
1 GACCGCACTGGATCATCTGGAGATCAACTCTGATCATC-GAAAACTTCTTGGAAT
** * * ** *
66867 GACCTAACTAGG-TCATCT-AAGATCAACTTTGATCAAAGAAAAGTTCTTGGAAT
1 GACCGCACT-GGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
* *
66920 GACTGCACTGGATCATCTACG-GATCAACTCTGATCATCG-AAACTTCTTG
1 GACCGCACTGGATCATCT-GGAGATCAACTCTGATCATCGAAAACTTCTTG
66969 AAAGGAGATC
Statistics
Matches: 491, Mismatches: 70, Indels: 47
0.81 0.12 0.08
Matches are distributed among these distances:
52 47 0.10
53 208 0.42
54 190 0.39
55 46 0.09
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (54 bp):
GACCGCACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
Found at i:66847 original size:268 final size:267
Alignment explanation
Indices: 66331--66971 Score: 739
Period size: 268 Copynumber: 2.4 Consensus size: 267
66321 TCCTTAAAAC
*
66331 GACCGCACTGGATCAAAT-TGGAGATTAACTCTGATCATCG-AAACTTCTTGGAACGACCGCACT
1 GACCGCACTGGATC--ATCTGG-GATCAACTCTGATCAT-GAAAACTTCTTGGAACGACCGCACT
* * *
66394 AGATTAAT-T-GGAGATCAACTTTGATCATCGAAAACTT-TTTGAAACGACCACACTGGATCATC
62 AGA-TCATCTAGGA-ATCAACTCTGATCATCGAAAACTTCTTCGAAACGACCACACTGGATCATC
*
66456 TGGAGATAAACTCTGATCATGAAAAACTTCTTAGAACGACCGCACTGGATCATCTGGAGATCAAC
125 TGGAGATAAACTCTGATCATGAAAAACTTCTTAGAACGACCGCACTGGATCATCTAGAGATCAAC
** * *
66521 TCTAATCATTGAAAACTTCTTGGAGTGACGGCACTGGATCATCTGGATCAACTCTGATCAAAGAA
190 TCTAATCAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGATCAACTCTGATCAAAGAA
66586 AACTTCTTGCAAT
255 AACTTCTTGCAAT
**
66599 GACCGCACTGGATCATCTGGGATCAACTCTGATCACTGAAAACTTCTTCAAACGACCGCACTAGA
1 GACCGCACTGGATCATCTGGGATCAACTCTGATCA-TGAAAACTTCTTGGAACGACCGCACTAGA
* * * * * *
66664 TCATCTAGGAATCAACTCTGATCGTTGAAAACTTCTTCGGAATGACCGCACTGGATTATCTAGG-
65 TCATCTAGGAATCAACTCTGATCATCGAAAACTTCTTCGAAACGACCACACTGGATCATCT-GGA
* * * * * *
66728 GATCAACTCTGATC-TCTAAAAACTTCTTCGAATGACCGCACTGGGTCATCTAGA-ATCAGCTCT
129 GATAAACTCTGATCAT-GAAAAACTTCTTAGAACGACCGCACTGGATCATCTAGAGATCAACTCT
* **
66791 GATCAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGGATCAACTCTGATCACTGAAAA
193 AATCAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCT-GGATCAACTCTGATCAAAGAAAA
* *
66856 CTTTTTGGAAT
257 CTTCTTGCAAT
** ** * * * * * *
66867 GACCTAACTAGG-TCATCTAAGATCAACTTTGATCAAAGAAAAGTTCTTGGAATGACTGCACTGG
1 GACCGCACT-GGATCATCTGGGATCAACTCTGATC-ATGAAAACTTCTTGGAACGACCGCACTAG
66931 ATCATCTACGG-ATCAACTCTGATCATCG-AAACTTCTT-GAAA
64 ATCATCTA-GGAATCAACTCTGATCATCGAAAACTTCTTCGAAA
66972 GGAGATCAAC
Statistics
Matches: 318, Mismatches: 43, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
266 23 0.07
267 104 0.33
268 184 0.58
269 7 0.02
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (267 bp):
GACCGCACTGGATCATCTGGGATCAACTCTGATCATGAAAACTTCTTGGAACGACCGCACTAGAT
CATCTAGGAATCAACTCTGATCATCGAAAACTTCTTCGAAACGACCACACTGGATCATCTGGAGA
TAAACTCTGATCATGAAAAACTTCTTAGAACGACCGCACTGGATCATCTAGAGATCAACTCTAAT
CAAAGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGATCAACTCTGATCAAAGAAAACTTC
TTGCAAT
Found at i:67005 original size:35 final size:35
Alignment explanation
Indices: 66941--67322 Score: 613
Period size: 35 Copynumber: 10.9 Consensus size: 35
66931 ATCATCTACG
*
66941 GATCAACTCTGATCATCG-AAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
*
66975 GATCAACTATGATCATCGAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* *
67010 GATCAACTCTGATCATCGAAAACTTCTTGGAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
*
67045 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* * *
67080 GATCAACTCTGATCATCGAAAACTTCTTCAAAGGC
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
*
67115 GATCAACTCTGATCATCGAAAAATTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
*
67150 GATCAACTCTGATCATCGAAAACTTCTTGACACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
*
67185 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
*
67220 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* *
67255 GATCAACTCTGATCATGGAAAACTTCTTGAAACAA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
*
67290 GATCAACTCTGATCATCAAAAACTTCTATGAAA
1 GATCAACTCTGATCATCGAAAACTTCT-TGAAA
67323 GACCACACTG
Statistics
Matches: 323, Mismatches: 23, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
34 17 0.05
35 301 0.93
36 5 0.02
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (35 bp):
GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
Found at i:67372 original size:54 final size:54
Alignment explanation
Indices: 67308--67422 Score: 212
Period size: 54 Copynumber: 2.1 Consensus size: 54
67298 CTGATCATCA
*
67308 AAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATTTGTTTAGATCTCTG
1 AAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTGTTTAGATCTCTG
*
67362 AAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTGTTTCGATCTCTG
1 AAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTGTTTAGATCTCTG
67416 AAAACTT
1 AAAACTT
67423 TAAAAGATCG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (54 bp):
AAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTGTTTAGATCTCTG
Found at i:67514 original size:22 final size:21
Alignment explanation
Indices: 67486--67536 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
67476 AACACCTGTA
* *
67486 CTTGACTCTTCATCTATCCTTT
1 CTTGACTCTTC-TCTACCCATT
*
67508 CTTGACTTCTTCTTTACCCATT
1 CTTGAC-TCTTCTCTACCCATT
67530 CTTGACT
1 CTTGACT
67537 ATTGTCTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.76
23 5 0.20
ACGTcount: A:0.14, C:0.31, G:0.06, T:0.49
Consensus pattern (21 bp):
CTTGACTCTTCTCTACCCATT
Found at i:75941 original size:2 final size:2
Alignment explanation
Indices: 75934--75961 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
75924 AACCGAATAG
75934 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
75962 TCGTTATAAG
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:77740 original size:23 final size:23
Alignment explanation
Indices: 77709--77752 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
77699 TTTTTGGGAC
* * *
77709 GAAACAAAAAAGTAAATAAAACA
1 GAAAAAAAAAAGAAAAGAAAACA
77732 GAAAAAAAAAAGAAAAGAAAA
1 GAAAAAAAAAAGAAAAGAAAA
77753 GAAAAGTCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.80, C:0.05, G:0.11, T:0.05
Consensus pattern (23 bp):
GAAAAAAAAAAGAAAAGAAAACA
Found at i:77740 original size:634 final size:636
Alignment explanation
Indices: 76786--78056 Score: 2271
Period size: 637 Copynumber: 2.0 Consensus size: 636
76776 TAAGTAGAGT
** *
76786 CAGTGTTACCAGGATCGATAGATCTGGTGCGATCCTCGATCTGGTACGAACGTACCGGATCGCGG
1 CAGTGTTACCAGGATCGATAGATCTGGTGCGATCCTCGATCTGGTACGAACAAACCAGATCGCGG
*
76851 AACATTTCCGACCCTGGAATGGTGGGAACGGGTTCCAAATCGCTGGAACCGGCGTTCCAGATTAG
66 AACATTTCCGACCCTGAAATGGTGGGAACGGGTTCCAAATCGCTGGAACCGGCGTTCCAGATTAG
* * *
76916 TCGGAGATTGTAAACAGTGGCACTGCGTCTTTATCGACCAAAGAAGAAGAAAACTAAAAGGAAAA
131 CCGGAGATTGTAAACAGCGGCACTGCGTCTTTATCGACCAAAGAAAAAGAAAACTAAAAGGAAAA
*
76981 AGAAGGGGACAATATTGATGATAGCTTACTTCACGTGGGACCTATAAAACTTTCTAAAGAAAAAG
196 AGAAGGGGACAATATTGATGATAGCTTACTTCACGTGGGACCCATAAAACTTTCTAAAGAAAAAG
*
77046 CAACAAAAAAAGTAATTTTCTTTTTGGGAAGAAACAAAAAAGTAAATAAAACGGAAAAAAAAAG-
261 CAACAAAAAAAGTAATTTTCTTTTTGGGAAGAAACAAAAAAGTAAATAAAACGAAAAAAAAAAGA
*
77110 AGA-AAAAGAAAAAGTCTAGTATGTAGGTAAAGTAGGATAATTATTTTTTTTAAGACATCTAATT
326 AAAGAAAAG-AAAAGTCTAGTATGTAGGTAAAGTAGGATAATTATTTTTTTTAAGACATCTAATT
77174 CTAATTACTAAATA-CTCCATATTAAGATTATTATTACTATTATAAAATAATAACAACACTAAAA
390 CTAATTACTAAATACCTCCATATTAAGATTATTATTACTATTATAAAATAATAACAACACTAAAA
*
77238 CAATTTTTAATCTTAATATATTTTTATAAAATCGATCCGAATGTAATTTTTAACCATACCGCGAT
455 CAATTTTTAATATTAATATATTTTTATAAAATCGATCCGAATGTAATTTTTAACCATACCGCGAT
77303 CCGAACAAACGTACCGGAGAAGACTACCCCCAACGTATCTCGTACCAATCAACCTACGATCCTCG
520 CCGAACAAACGTACCGGAGAAGACTACCCCCAACGTATCTCGTACCAATCAACCTACGATCCTCG
77368 TACCCGCATCCGTTCCGCAACCCGGATCGTACCCCGATCCAGGTAACATTGA
585 TACCCGCATCCGTTCCGCAACCCGGATCGTACCCCGATCCAGGTAACATTGA
*
77420 CAGTGTTACCAGGATCGATAGATCTGGTGCGATCCTCGATCTGGTATGAACAAACCAGATCGCGG
1 CAGTGTTACCAGGATCGATAGATCTGGTGCGATCCTCGATCTGGTACGAACAAACCAGATCGCGG
*
77485 AACATTTCCGACCCTGAAATGGTGGGAACGGGTTCCAAATCGCTGGAATCGGCGTTCCAGATTAG
66 AACATTTCCGACCCTGAAATGGTGGGAACGGGTTCCAAATCGCTGGAACCGGCGTTCCAGATTAG
*
77550 CCGGAGATTGTAAACAGCGGCACTGTGTCTTTATCGACCAAAGAAAAAGAAAACTAAAAGG-AAA
131 CCGGAGATTGTAAACAGCGGCACTGCGTCTTTATCGACCAAAGAAAAAGAAAACTAAAAGGAAAA
* *
77614 ATAAGGGGACAATATTGATGATAGCTTACTTCACGTGGGACCCATAAAACTTTCTAAAGGAAAAG
196 AGAAGGGGACAATATTGATGATAGCTTACTTCACGTGGGACCCATAAAACTTTCTAAAGAAAAAG
*
77679 CAACAAAAAAAGTAATTTTCTTTTTGGGACGAAACAAAAAAGTAAATAAAACAGAAAAAAAAAAG
261 CAACAAAAAAAGTAATTTTCTTTTTGGGAAGAAACAAAAAAGTAAATAAAAC-GAAAAAAAAAAG
*
77744 AAAAGAAAAGAAAAGTCTAGTATGTAGGTAAAGTAGGGTAATTATTTTTTTTAAGACATCTAATT
325 AAAAGAAAAGAAAAGTCTAGTATGTAGGTAAAGTAGGATAATTATTTTTTTTAAGACATCTAATT
77809 CTAATTACTAAATACTCTCCATATTAAGATTATTATTACTATTATAAAATAATAACAACACTAAA
390 CTAATTACTAAATAC-CTCCATATTAAGATTATTATTACTATTATAAAATAATAACAACACTAAA
* *
77874 ATAATTTTTAATATTAATATATTTTTATAAAATCGATCCGAATGTAATTTTTAACCGTACCGCGA
454 ACAATTTTTAATATTAATATATTTTTATAAAATCGATCCGAATGTAATTTTTAACCATACCGCGA
* *
77939 TCCGAACAAACGTACCGGAGAAGACTACCCCCAACGTATCTCGTATCGATCAACCTACGATCCTC
519 TCCGAACAAACGTACCGGAGAAGACTACCCCCAACGTATCTCGTACCAATCAACCTACGATCCTC
* *
78004 GTACCCGGATCCGTTCCGCGACCCGGATCGTACCCCGATCCAGGTAACATTGA
584 GTACCCGCATCCGTTCCGCAACCCGGATCGTACCCCGATCCAGGTAACATTGA
78057 GTAGAGTTTT
Statistics
Matches: 608, Mismatches: 24, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
633 116 0.19
634 192 0.32
635 70 0.12
636 5 0.01
637 225 0.37
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (636 bp):
CAGTGTTACCAGGATCGATAGATCTGGTGCGATCCTCGATCTGGTACGAACAAACCAGATCGCGG
AACATTTCCGACCCTGAAATGGTGGGAACGGGTTCCAAATCGCTGGAACCGGCGTTCCAGATTAG
CCGGAGATTGTAAACAGCGGCACTGCGTCTTTATCGACCAAAGAAAAAGAAAACTAAAAGGAAAA
AGAAGGGGACAATATTGATGATAGCTTACTTCACGTGGGACCCATAAAACTTTCTAAAGAAAAAG
CAACAAAAAAAGTAATTTTCTTTTTGGGAAGAAACAAAAAAGTAAATAAAACGAAAAAAAAAAGA
AAAGAAAAGAAAAGTCTAGTATGTAGGTAAAGTAGGATAATTATTTTTTTTAAGACATCTAATTC
TAATTACTAAATACCTCCATATTAAGATTATTATTACTATTATAAAATAATAACAACACTAAAAC
AATTTTTAATATTAATATATTTTTATAAAATCGATCCGAATGTAATTTTTAACCATACCGCGATC
CGAACAAACGTACCGGAGAAGACTACCCCCAACGTATCTCGTACCAATCAACCTACGATCCTCGT
ACCCGCATCCGTTCCGCAACCCGGATCGTACCCCGATCCAGGTAACATTGA
Found at i:87236 original size:29 final size:28
Alignment explanation
Indices: 87147--87246 Score: 128
Period size: 29 Copynumber: 3.5 Consensus size: 28
87137 CTTTGCTTCT
*
87147 CATTTTGGTCATTTTACATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
* * * *
87175 CATTTTGGTCATTTTGTCAGGACCAAGGT
1 CATTTTGGTCATTTT-TCATGTCCAGGGG
*
87204 CATTTTGGTCATTTTTCATGTTCAGGGGG
1 CATTTTGGTCATTTTTCATGTCCA-GGGG
87233 CATTTTGGTCATTT
1 CATTTTGGTCATTT
87247 CAAGTGTACT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
28 21 0.35
29 39 0.65
ACGTcount: A:0.17, C:0.16, G:0.24, T:0.43
Consensus pattern (28 bp):
CATTTTGGTCATTTTTCATGTCCAGGGG
Done.