Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019720.1 Corchorus olitorius cultivar O-4 contig19753, 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: 141169
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1161 original size:36 final size:36
Alignment explanation
Indices: 1114--1183 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1104 TTCAATAACC
* *
1114 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
1150 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
1184 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:2213 original size:25 final size:24
Alignment explanation
Indices: 2179--2225 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
2169 ATGTCTGCAC
2179 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
2204 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
2226 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:3408 original size:86 final size:86
Alignment explanation
Indices: 3309--3476 Score: 300
Period size: 86 Copynumber: 2.0 Consensus size: 86
3299 CTATCATTCA
3309 GAGACAAATTTGTTTCGTCTCTGAGCCTTAGCAACGCGGGGTTTCAAGACGCATTGTAAAACTGT
1 GAGACAAATTTGTTTCGTCTCTGAGCCTTAGCAACGCGGGGTTTCAAGACGCATTGTAAAACTGT
3374 CTCAAATTTTGTTTCTAGTTC
66 CTCAAATTTTGTTTCTAGTTC
* * * *
3395 GAGACAGATTTGTTTCGTTTCTGAGCCTTAGCAACGTGGGTTTTCAAGACGCATTGTAAAACTGT
1 GAGACAAATTTGTTTCGTCTCTGAGCCTTAGCAACGCGGGGTTTCAAGACGCATTGTAAAACTGT
3460 CTCAAATTTTGTTTCTA
66 CTCAAATTTTGTTTCTA
3477 ATTCTTTTAG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 78 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (86 bp):
GAGACAAATTTGTTTCGTCTCTGAGCCTTAGCAACGCGGGGTTTCAAGACGCATTGTAAAACTGT
CTCAAATTTTGTTTCTAGTTC
Found at i:3522 original size:13 final size:13
Alignment explanation
Indices: 3504--3530 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3494 AAAATGTCTC
3504 TATTTTCCATTTT
1 TATTTTCCATTTT
3517 TATTTTCCATTTT
1 TATTTTCCATTTT
3530 T
1 T
3531 TTAGTGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TATTTTCCATTTT
Found at i:5636 original size:116 final size:116
Alignment explanation
Indices: 5432--5783 Score: 686
Period size: 116 Copynumber: 3.0 Consensus size: 116
5422 GGTTGTTTCC
5432 TTCCTCTTTTCATCTTATTTTCTTTCTCTTCTAAACCCTTTTTTGAAGAACTTCTCACCGATATT
1 TTCCTCTTTTCATCTTATTTTCTTTCTCTTCTAAACCCTTTTTTGAAGAACTTCTCACCGATATT
5497 CATGATATGTAGGAAAATTTATTGGTTTAACAGTTGAAACTTATCTAAAAT
66 CATGATATGTAGGAAAATTTATTGGTTTAACAGTTGAAACTTATCTAAAAT
5548 TTCCTCTTTTCATCTTATTTTCTTTCTCTTCTAAACCCTTTTTTGAAGAACTTCTCACCGATATT
1 TTCCTCTTTTCATCTTATTTTCTTTCTCTTCTAAACCCTTTTTTGAAGAACTTCTCACCGATATT
5613 CATGATATGTAGGAAAATTTATTGGTTTAACAGTTGAAACTTATCTAAAAT
66 CATGATATGTAGGAAAATTTATTGGTTTAACAGTTGAAACTTATCTAAAAT
5664 TTCCTCTTTTCATCTTATTTTCTTTCTCTTCTAAACCCTTTTTTTGAAGAACTTCTCACCGATAT
1 TTCCTCTTTTCATCTTATTTTCTTTCTCTTCTAAACCC-TTTTTTGAAGAACTTCTCACCGATAT
*
5729 TCATGATATGTAGGAAAATTTATTGGTTTAACAGTTAAAACTTATCTAAAAT
65 TCATGATATGTAGGAAAATTTATTGGTTTAACAGTTGAAACTTATCTAAAAT
5781 TTC
1 TTC
5784 AAACTATGAA
Statistics
Matches: 234, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
116 154 0.66
117 80 0.34
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (116 bp):
TTCCTCTTTTCATCTTATTTTCTTTCTCTTCTAAACCCTTTTTTGAAGAACTTCTCACCGATATT
CATGATATGTAGGAAAATTTATTGGTTTAACAGTTGAAACTTATCTAAAAT
Found at i:6209 original size:58 final size:58
Alignment explanation
Indices: 6113--6227 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
6103 ATTAATCAAA
*
6113 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCGAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGGCT
* * *
6171 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACCGAGGC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGGC
6228 ATGATGCTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 37 0.71
59 15 0.29
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGGCT
Found at i:7543 original size:36 final size:36
Alignment explanation
Indices: 7496--7565 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
7486 TTCAATAACC
*
7496 TTACATCTTTTGT-GATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAG-TTTTGATTATCATATTTCTTA
*
7532 TTACATTTTTTGTAGTTTTGATTATCATATTTCT
1 TTACATCTTTTGTAGTTTTGATTATCATATTTCT
7566 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAGTTTTGATTATCATATTTCTTA
Found at i:8452 original size:205 final size:200
Alignment explanation
Indices: 8083--8492 Score: 757
Period size: 205 Copynumber: 2.0 Consensus size: 200
8073 GCTTAATAAC
8083 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
*
8148 ATACAACACATTATTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGA
66 ATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGA
8213 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
131 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTC-AAATTATAAAAGATATTAAAGATCC
8278 GATTTA
195 GATTTA
8284 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAA-TTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
8349 GATACAACACATTACTATTATATATATAGAACTATACCTAAAAAAAATTAGTTGAACATTAGTGG
65 GATACAACACATTACTATTATATATA-A-AACTATACC-AAAAAAAATTAGTTGAACATTAGTGG
*
8414 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAATTATAAAAGATATTAAATA
127 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAATTATAAAAGATATTAAAGA
8479 TCCGATTTA
192 TCCGATTTA
8488 TTTAT
1 TTTAT
8493 TATTAAGGAA
Statistics
Matches: 203, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
201 24 0.12
202 65 0.32
203 1 0.00
204 44 0.22
205 69 0.34
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (200 bp):
TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
ATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGA
TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAATTATAAAAGATATTAAAGATCCG
ATTTA
Found at i:30800 original size:13 final size:13
Alignment explanation
Indices: 30782--30807 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30772 AACTATAAAC
30782 TCTTAATTTCAAT
1 TCTTAATTTCAAT
30795 TCTTAATTTCAAT
1 TCTTAATTTCAAT
30808 GATTATGATT
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:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
TCTTAATTTCAAT
Found at i:41346 original size:13 final size:13
Alignment explanation
Indices: 41328--41355 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41318 GGGCCCAACA
41328 TGCCTTTGTTTAT
1 TGCCTTTGTTTAT
41341 TGCCTTTGTTTAT
1 TGCCTTTGTTTAT
41354 TG
1 TG
41356 GGCCTTGCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.18, T:0.61
Consensus pattern (13 bp):
TGCCTTTGTTTAT
Found at i:41694 original size:17 final size:16
Alignment explanation
Indices: 41654--41704 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
41644 CATGTAATCT
*
41654 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
41670 TTGTATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
41687 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
41704 T
1 T
41705 GGGGGGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:49211 original size:5 final size:5
Alignment explanation
Indices: 49201--49228 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
49191 ACGTAATTCA
49201 TAAAT TAAAT TAAAT TAAAT TAAAT TAA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAA
49229 TCACCATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAAAT
Found at i:50635 original size:26 final size:26
Alignment explanation
Indices: 50599--50651 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
50589 CCTTGCGTTA
50599 TGCTTTGTGTATATTGGATGCATCTT
1 TGCTTTGTGTATATTGGATGCATCTT
*
50625 TGCTTTGTGTATATTGGATGCTTCTT
1 TGCTTTGTGTATATTGGATGCATCTT
50651 T
1 T
50652 ATATCTAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.13, C:0.11, G:0.23, T:0.53
Consensus pattern (26 bp):
TGCTTTGTGTATATTGGATGCATCTT
Found at i:51421 original size:35 final size:35
Alignment explanation
Indices: 51375--51444 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
51365 GAACGATTGG
51375 ATTCAAATATGTGGAGTTGATTCAGACAATCTTGC
1 ATTCAAATATGTGGAGTTGATTCAGACAATCTTGC
51410 ATTCAAATATGTGGAGTTGATTCAGACAATCTTGC
1 ATTCAAATATGTGGAGTTGATTCAGACAATCTTGC
51445 CATTTGCCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (35 bp):
ATTCAAATATGTGGAGTTGATTCAGACAATCTTGC
Found at i:77780 original size:26 final size:27
Alignment explanation
Indices: 77743--77799 Score: 107
Period size: 26 Copynumber: 2.1 Consensus size: 27
77733 TCCCAAGTTC
77743 TATGCATATTCATTATTTGTGTATAAA
1 TATGCATATTCATTATTTGTGTATAAA
77770 TATGC-TATTCATTATTTGTGTATAAA
1 TATGCATATTCATTATTTGTGTATAAA
77796 TATG
1 TATG
77800 GACAAAATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 25 0.83
27 5 0.17
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (27 bp):
TATGCATATTCATTATTTGTGTATAAA
Found at i:80896 original size:26 final size:25
Alignment explanation
Indices: 80850--80902 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
80840 TAAAAGATAG
80850 TAGTACCCTTGTTCTCAAAAAAAAGA
1 TAGTACCCTTGTTCTC-AAAAAAAGA
* *
80876 TAGTACCCTT-TTGTACCAAAAAAGA
1 TAGTACCCTTGTTCT-CAAAAAAAGA
80901 TA
1 TA
80903 CTCCTAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (25 bp):
TAGTACCCTTGTTCTCAAAAAAAGA
Found at i:81388 original size:14 final size:14
Alignment explanation
Indices: 81364--81398 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
81354 GGTTGGTGAG
81364 ATTCA-TTCATTCA
1 ATTCATTTCATTCA
81377 ATTCATTTCATTCA
1 ATTCATTTCATTCA
*
81391 ATTGATTT
1 ATTCATTT
81399 TGATTCTACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.29, C:0.17, G:0.03, T:0.51
Consensus pattern (14 bp):
ATTCATTTCATTCA
Found at i:94610 original size:14 final size:15
Alignment explanation
Indices: 94585--94618 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
94575 ATTTCTTTGA
*
94585 ATTTTTATTTTATTT
1 ATTTTTATTTTATAT
94600 ATTTTTA-TTTATAT
1 ATTTTTATTTTATAT
94614 ATTTT
1 ATTTT
94619 GTCAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTTATTTTATAT
Found at i:99679 original size:31 final size:31
Alignment explanation
Indices: 99644--99716 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
99634 TTTTTTGTAG
*
99644 AAAGTTGAAATTAAGATTGACAAAAAATGAA
1 AAAGTAGAAATTAAGATTGACAAAAAATGAA
99675 AAAGTAGAAATTAAGATTGACAAAAAATGAA
1 AAAGTAGAAATTAAGATTGACAAAAAATGAA
99706 AAAGTAGAAAT
1 AAAGTAGAAAT
99717 CAAAACTCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.60, C:0.03, G:0.16, T:0.21
Consensus pattern (31 bp):
AAAGTAGAAATTAAGATTGACAAAAAATGAA
Found at i:100117 original size:125 final size:125
Alignment explanation
Indices: 99890--100138 Score: 363
Period size: 125 Copynumber: 2.0 Consensus size: 125
99880 AACTAAACTC
* * * *
99890 ACATTTTATGAGACCTCAATTCAGAATTTTATGATTCAGACACGATACATTCGCTAATTGAATTA
1 ACATTATATGAAACCTCAATTCAGAATTTCATGATTCAGACACGATACACTCGCTAATTGAATTA
* * **
99955 ATAACTAAGATGCAAATCAAAGCTAAAACTCTATTGAGTTAGGCAAACACCGAGAAAAAT
66 ACAACTAAGATGCAAATCAAAACTAAAACTCTATTGAGTTAGGCAAACAAAGAGAAAAAT
* ** *
100015 ACATTATATGAAACCTGAATTCAGAATTTCATGATTCAGACACGATGTACTCGCTAATTGAATTG
1 ACATTATATGAAACCTCAATTCAGAATTTCATGATTCAGACACGATACACTCGCTAATTGAATTA
* * *
100080 ACAACTAAGATGTAAATCAAAACTAAAACTCTGTTGAGTTAGGCGAACAAAGAGAAAAA
66 ACAACTAAGATGCAAATCAAAACTAAAACTCTATTGAGTTAGGCAAACAAAGAGAAAAA
100139 ATGAGAAGGT
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
125 109 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (125 bp):
ACATTATATGAAACCTCAATTCAGAATTTCATGATTCAGACACGATACACTCGCTAATTGAATTA
ACAACTAAGATGCAAATCAAAACTAAAACTCTATTGAGTTAGGCAAACAAAGAGAAAAAT
Found at i:122026 original size:18 final size:18
Alignment explanation
Indices: 121975--122028 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
121965 CAATTTTTAA
121975 TTAATTAATTTATTTT-T
1 TTAATTAATTTATTTTGT
* *
121992 ATTTATTAATTCA-TTTGT
1 -TTAATTAATTTATTTTGT
122010 TTAATTAATTTATTTTGT
1 TTAATTAATTTATTTTGT
122028 T
1 T
122029 AATCATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (18 bp):
TTAATTAATTTATTTTGT
Found at i:122093 original size:14 final size:15
Alignment explanation
Indices: 122059--122101 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
122049 ATTGTTGCTG
122059 TTTAAAATTCAAAAT
1 TTTAAAATTCAAAAT
* *
122074 TTTAAAATTGATAA-
1 TTTAAAATTCAAAAT
122088 TTTAAAATTTCAAA
1 TTTAAAA-TTCAAA
122102 CACATAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (15 bp):
TTTAAAATTCAAAAT
Found at i:129337 original size:14 final size:15
Alignment explanation
Indices: 129318--129347 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
129308 GAAAATCTTG
129318 TAATATCAA-AATTT
1 TAATATCAAGAATTT
129332 TAATATCAAGAATTT
1 TAATATCAAGAATTT
129347 T
1 T
129348 TTGAAGCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (15 bp):
TAATATCAAGAATTT
Found at i:130434 original size:143 final size:144
Alignment explanation
Indices: 130173--130464 Score: 541
Period size: 143 Copynumber: 2.0 Consensus size: 144
130163 TCAATTGTTA
*
130173 AAAATTGTTGATGTAGTATGACATTAATGCATTATGCCACATCAACATTTCTTATGGAGAAATTA
1 AAAATTATTGATGTAGTATGAC--TAATGCATTATGCCACATCAACATTTCTTATGGAGAAATTA
130238 TTCCGATTTTAATAGTTAATTTAAGAACTGAAAGTGCAATAGAAGGTAAAAGTTTAGGAGGTAAA
64 TTCCGATTTTAATAGTTAATTTAAGAACTGAAAGTGCAATAGAAGGTAAAAGTTTAGGAGGTAAA
130303 TGGGTTTTAGTTTAAC
129 TGGGTTTTAGTTTAAC
130319 AAAATTATTGATGTAGTATGAC-AATGCATTATGCCACATCAACATTTCTTATGGAGAAATTATT
1 AAAATTATTGATGTAGTATGACTAATGCATTATGCCACATCAACATTTCTTATGGAGAAATTATT
*
130383 CCGATTTTGATAGTTAATTTAAGAACTGAAAGTGCAATAGAAGGTAAAAGTTTAGGAGGTAAATG
66 CCGATTTTAATAGTTAATTTAAGAACTGAAAGTGCAATAGAAGGTAAAAGTTTAGGAGGTAAATG
130448 GGTTTTAGTTTAAC
131 GGTTTTAGTTTAAC
130462 AAA
1 AAA
130465 TGAAAACGTA
Statistics
Matches: 144, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
143 123 0.85
146 21 0.15
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (144 bp):
AAAATTATTGATGTAGTATGACTAATGCATTATGCCACATCAACATTTCTTATGGAGAAATTATT
CCGATTTTAATAGTTAATTTAAGAACTGAAAGTGCAATAGAAGGTAAAAGTTTAGGAGGTAAATG
GGTTTTAGTTTAAC
Found at i:130945 original size:121 final size:121
Alignment explanation
Indices: 130729--130969 Score: 464
Period size: 121 Copynumber: 2.0 Consensus size: 121
130719 TAACAATCTC
130729 CCCCGATTCACTTGTAAGTCCTCATCTCTCCCCCGTGCGGCCTAACCCGTTAAGTCTTAAGTCAA
1 CCCCGATTCACTTGTAAGTCCTCATCTCTCCCCCGTGCGGCCTAACCCGTTAAGTCTTAAGTCAA
130794 TTACCGGCCATCCAAGACTTTACCCATATAGTGCAAGGGTCCAAATCTCTCCCCCT
66 TTACCGGCCATCCAAGACTTTACCCATATAGTGCAAGGGTCCAAATCTCTCCCCCT
*
130850 CCCCGATTCACTTGTAAGTCCTCATTTCTCCCCCGTGCGGCCTAACCCGTTAAGTCTTAAGTCAA
1 CCCCGATTCACTTGTAAGTCCTCATCTCTCCCCCGTGCGGCCTAACCCGTTAAGTCTTAAGTCAA
*
130915 TTACCGGCCATCCAAGACTTTACCCGTATAGTGCAAGGGTCCAAATCTCTCCCCC
66 TTACCGGCCATCCAAGACTTTACCCATATAGTGCAAGGGTCCAAATCTCTCCCCC
130970 GTACGGCCTA
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 118 1.00
ACGTcount: A:0.22, C:0.36, G:0.15, T:0.27
Consensus pattern (121 bp):
CCCCGATTCACTTGTAAGTCCTCATCTCTCCCCCGTGCGGCCTAACCCGTTAAGTCTTAAGTCAA
TTACCGGCCATCCAAGACTTTACCCATATAGTGCAAGGGTCCAAATCTCTCCCCCT
Found at i:131021 original size:86 final size:86
Alignment explanation
Indices: 130876--131044 Score: 293
Period size: 86 Copynumber: 2.0 Consensus size: 86
130866 AGTCCTCATT
*
130876 TCTCCCCCGTGCGGCCTAACCCGTTAAGTCTTAAGTCAATTACCGGCCATCCAAGACTTTACCCG
1 TCTCCCCCGTACGGCCTAACCCGTTAAGTCTTAAGTCAATTACCGGCCATCCAAGACTTTACCCG
*
130941 TATAGTGCAAGGGTCCAAATC
66 TATAATGCAAGGGTCCAAATC
* * *
130962 TCTCCCCCGTACGGCCTAACCCGTTAAGTCTTAAGTCAATTACTGGTCATTCAAGACTTTACCCG
1 TCTCCCCCGTACGGCCTAACCCGTTAAGTCTTAAGTCAATTACCGGCCATCCAAGACTTTACCCG
131027 TATAATGCAAGGGTCCAA
66 TATAATGCAAGGGTCCAA
131045 CACTTCAATT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 78 1.00
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (86 bp):
TCTCCCCCGTACGGCCTAACCCGTTAAGTCTTAAGTCAATTACCGGCCATCCAAGACTTTACCCG
TATAATGCAAGGGTCCAAATC
Found at i:132711 original size:21 final size:22
Alignment explanation
Indices: 132679--132719 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
132669 GTCCTCAGCC
132679 ACATTAATTTGAAGAAAAGAAG
1 ACATTAATTTGAAGAAAAGAAG
*
132701 ACATT-ATTTGAAGATAAGA
1 ACATTAATTTGAAGAAAAGA
132720 TATGAAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (22 bp):
ACATTAATTTGAAGAAAAGAAG
Found at i:133141 original size:19 final size:19
Alignment explanation
Indices: 133117--133153 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
133107 GTACAGTACC
*
133117 TAATCTAATCTGTACAATG
1 TAATCTAATATGTACAATG
*
133136 TAATCTCATATGTACAAT
1 TAATCTAATATGTACAAT
133154 TTGCTAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (19 bp):
TAATCTAATATGTACAATG
Done.