Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023220.1 Corchorus olitorius cultivar O-4 contig23253, 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: 41541
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2000 original size:178 final size:178
Alignment explanation
Indices: 1784--2112 Score: 444
Period size: 178 Copynumber: 1.8 Consensus size: 178
1774 AATAACAAAC
*
1784 TTTTCAGAAGCATTTTTGATACTTGAAACATCAAATTTAGCTTTCGAGTCCTTCATGAAAGTTGT
1 TTTTCAGAAGCATTTTTGATACTTGAAACATCAAATTTAGCTTTCAAGTCCTTCATGAAAGTTGT
* * * * *
1849 AGGTTATGGAACAACCTTTTAATAAACACTTGAATCACCTCAATCGGACATCTGGAGCAAAAATT
66 AGATCATGGAACAACCTTTTAAGAAACACTCGAATCACCTCAATCGGACATCCGGAGCAAAAATT
* *
1914 ATGTAATATTAAGTAGACCGTCCATTCCCATTAACTGAAACAACTAAT
131 ATATAATATTAAATAGACCGTCCATTCCCATTAACTGAAACAACTAAT
* * * * *
1962 TTTTCGGAAGCATTTTTGATACTTGAAA-ATTTAAATTTAGTTTTCAAGTTCTTTATGAAAGTTG
1 TTTTCAGAAGCATTTTTGATACTTGAAACA-TCAAATTTAGCTTTCAAGTCCTTCATGAAAGTTG
* ** ** * *
2026 TAGATCATGGGACAACCTTTTAAGATGCACTCGAATCACCTTTATCGGATATCCGTAGCAAAAAT
65 TAGATCATGGAACAACCTTTTAAGAAACACTCGAATCACCTCAATCGGACATCCGGAGCAAAAAT
* *
2091 TATATGATGTTAAATAGACCGT
130 TATATAATATTAAATAGACCGT
2113 TCAACAAAAC
Statistics
Matches: 128, Mismatches: 22, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
177 1 0.01
178 127 0.99
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (178 bp):
TTTTCAGAAGCATTTTTGATACTTGAAACATCAAATTTAGCTTTCAAGTCCTTCATGAAAGTTGT
AGATCATGGAACAACCTTTTAAGAAACACTCGAATCACCTCAATCGGACATCCGGAGCAAAAATT
ATATAATATTAAATAGACCGTCCATTCCCATTAACTGAAACAACTAAT
Found at i:2513 original size:236 final size:228
Alignment explanation
Indices: 2108--2567 Score: 681
Period size: 236 Copynumber: 2.0 Consensus size: 228
2098 TGTTAAATAG
*
2108 ACCGTTCAACAAAACTACTTATAAATATGTTATTTTATATTATATTATAATTTAAAAATGCTAGA
1 ACCGTTCAACAAAACCACTTATAAATATGTTATTTTATATTATATTATAATTTAAAAATGCTAGA
** * *
2173 AAGTCAAAATGCCCTCAAAGGTTTGTGAGAATAACAAAAAAGCCAAAGTTAAAATGACTAAAAAC
66 AAGTCAAAAAACCCTCAAAGGTTTGTGAGAATAACAAAAAAGCCAAAGCTAAAATGACTAAAAAA
*
2238 CCAAGATGAATAGTAACAAAATGAATATAGTGATTAGGTCAGGAAAATTTTTGAGGGTACTTTAG
131 CCAAGATGAATAGTAACAAAATGAATATAGTGATTAGGTCAAGAAAATTTTTGAGGGTACTTTAG
*
2303 TAATTGTACTTCTTACTATTAGTGTTTTTATAA
196 TAATTGCACTTCTTACTATTAGTGTTTTTATAA
* *
2336 ACCGTTCAACCAAACCACTTATAAATATGTTATATGTTATATTATATTATAATTTAGAAATGCTA
1 ACCGTTCAACAAAACCACTTATAAATATGTTAT-T-TTATATTATATTATAATTTAAAAATGCTA
* *
2401 GAAAGTCAAAAAAACCCTCAATGGTTTGTGAGAATAAC-AAAAAGACCAAAGCTGAAATGA-TAA
64 GAAAGTC-AAAAAACCCTCAAAGGTTTGTGAGAATAACAAAAAAG-CCAAAGCTAAAATGACT--
* *
2464 AAAAAAAAACCAATGGTGAATAGTAACAAAATGAATGTAGTGATTAGGTCAAGAAAATTTTTGAG
125 ---AAAAAACCAA-GATGAATAGTAACAAAATGAATATAGTGATTAGGTCAAGAAAATTTTTGAG
* *
2529 GGTATTTTAGTAATTGCATTTCTTACTATTAGTGTTTTT
186 GGTACTTTAGTAATTGCACTTCTTACTATTAGTGTTTTT
2568 TTATTCATTT
Statistics
Matches: 207, Mismatches: 15, Indels: 12
0.88 0.06 0.05
Matches are distributed among these distances:
228 31 0.15
229 1 0.00
230 42 0.20
231 40 0.19
235 9 0.04
236 84 0.41
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (228 bp):
ACCGTTCAACAAAACCACTTATAAATATGTTATTTTATATTATATTATAATTTAAAAATGCTAGA
AAGTCAAAAAACCCTCAAAGGTTTGTGAGAATAACAAAAAAGCCAAAGCTAAAATGACTAAAAAA
CCAAGATGAATAGTAACAAAATGAATATAGTGATTAGGTCAAGAAAATTTTTGAGGGTACTTTAG
TAATTGCACTTCTTACTATTAGTGTTTTTATAA
Found at i:4315 original size:24 final size:23
Alignment explanation
Indices: 4249--4315 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
4239 GACAAGATTG
* *
4249 AAACCCCATCTATAGAGGAAGAAA
1 AAACCCCATC-AAAAAGGAAGAAA
4273 AAACCCCATCAAAAGAGGAA-AAGA
1 AAACCCCATCAAAA-AGGAAGAA-A
4297 AAACCCCATCAACAAAGGA
1 AAACCCCATCAA-AAAGGA
4316 CTCGAAAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.11
24 32 0.84
25 2 0.05
ACGTcount: A:0.54, C:0.24, G:0.15, T:0.07
Consensus pattern (23 bp):
AAACCCCATCAAAAAGGAAGAAA
Found at i:4328 original size:24 final size:24
Alignment explanation
Indices: 4249--4308 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
4239 GACAAGATTG
* *
4249 AAACCCCATCTATAGAGGAAGAA-A
1 AAACCCCATCAAAAGAGGAA-AAGA
4273 AAACCCCATCAAAAGAGGAAAAGA
1 AAACCCCATCAAAAGAGGAAAAGA
4297 AAACCCCATCAA
1 AAACCCCATCAA
4309 CAAAGGACTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 2 0.06
24 31 0.94
ACGTcount: A:0.53, C:0.25, G:0.13, T:0.08
Consensus pattern (24 bp):
AAACCCCATCAAAAGAGGAAAAGA
Found at i:4885 original size:105 final size:106
Alignment explanation
Indices: 4703--4964 Score: 377
Period size: 107 Copynumber: 2.5 Consensus size: 106
4693 AATTTTTCTA
* * ** * * *
4703 ACCCTTAAAATATAATTTTAATTTTAATTT-GGGCTAAAATTAATG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATCTTA
*
4766 TTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* *
4806 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTCTATCTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATCTTA
*
4871 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
* *
4913 AACCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
4965 AGGCTAAACT
Statistics
Matches: 142, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
103 26 0.18
104 13 0.09
105 36 0.25
107 67 0.47
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATCTTA
TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:5837 original size:16 final size:16
Alignment explanation
Indices: 5819--5894 Score: 82
Period size: 16 Copynumber: 4.8 Consensus size: 16
5809 AATTTTGGGT
*
5819 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAATG
* *
5835 ACCCGAATCC-AAACG
1 ACCCGAACCCGAAATG
*
5850 ATCCGAACCCGAAAATG
1 ACCCGAACCCG-AAATG
* *
5867 ACCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
5883 ACCCGAACCCGA
1 ACCCGAACCCGA
5895 TCAACCCGAC
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
15 11 0.23
16 24 0.51
17 12 0.26
ACGTcount: A:0.41, C:0.38, G:0.13, T:0.08
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:7540 original size:15 final size:17
Alignment explanation
Indices: 7510--7542 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
7500 AAAACGACGC
7510 AACCCAAAATTGACCCG
1 AACCCAAAATTGACCCG
7527 AACCC-AAA-TGACCCG
1 AACCCAAAATTGACCCG
7542 A
1 A
7543 TATTTGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.42, C:0.36, G:0.12, T:0.09
Consensus pattern (17 bp):
AACCCAAAATTGACCCG
Found at i:8465 original size:25 final size:25
Alignment explanation
Indices: 8420--8468 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
8410 TTTTGAACTC
*
8420 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
8445 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
8469 ACATCTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:8468 original size:21 final size:21
Alignment explanation
Indices: 8420--8469 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
8410 TTTTGAACTC
8420 ATTATT-TATTATTTAAAATAT
1 ATTATTAT-TTATTTAAAATAT
8441 ATTTATTATTTATTTAATAATAT
1 A-TTATTATTTATTTAA-AATAT
8464 A-TATTA
1 ATTATTA
8470 CATCTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 6 0.23
22 13 0.50
23 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTATTATTTATTTAAAATAT
Found at i:9760 original size:21 final size:21
Alignment explanation
Indices: 9734--9776 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
9724 CTTCTTGTAT
*
9734 ATAATTAAATAAAAGTACTAC
1 ATAATTAAATAAAACTACTAC
9755 ATAATTAAATAAAACTACTAC
1 ATAATTAAATAAAACTACTAC
9776 A
1 A
9777 GGTATCTTAT
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:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (21 bp):
ATAATTAAATAAAACTACTAC
Found at i:15418 original size:7 final size:8
Alignment explanation
Indices: 15403--15428 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
15393 TCTCTTGAAT
15403 ATAAAAAA
1 ATAAAAAA
15411 ATAAAAAA
1 ATAAAAAA
15419 ATAAAAAA
1 ATAAAAAA
15427 AT
1 AT
15429 GCTGATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
ATAAAAAA
Found at i:20714 original size:5 final size:5
Alignment explanation
Indices: 20704--20736 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
20694 CTTTGTGCCA
*
20704 AAAAT AAAAT AAAAC AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
20737 TCATTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:21190 original size:77 final size:78
Alignment explanation
Indices: 21042--21197 Score: 199
Period size: 77 Copynumber: 2.0 Consensus size: 78
21032 AAACATGGTA
* * * * *
21042 ATCTTATTCTCACAAAAATAAAAAAATTATATTTTCCCACTAAAATAGCATTTCTAGGAAAGTAG
1 ATCTTATTCCCACAAAAATAAAAAAATTATATTTTCCCACTAAAACAGCATTCCTAAGAAAGTAA
* *
21107 TGTGAATGTCATT
66 TATGAATGACATT
** *
21120 ATCTTATTCCCATTAAAAT-AAAAAATTATATTTTCTCACTAAAACAGCATTCCTAAGATAA-TA
1 ATCTTATTCCCACAAAAATAAAAAAATTATATTTTCCCACTAAAACAGCATTCCTAAGA-AAGTA
21183 ATATGAATGACATT
65 ATATGAATGACATT
21197 A
1 A
21198 CCACGTAACA
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
77 49 0.73
78 18 0.27
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.35
Consensus pattern (78 bp):
ATCTTATTCCCACAAAAATAAAAAAATTATATTTTCCCACTAAAACAGCATTCCTAAGAAAGTAA
TATGAATGACATT
Found at i:32946 original size:23 final size:23
Alignment explanation
Indices: 32916--32972 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
32906 TATTGTTCAT
*
32916 TTAAGTGTTCACGAACATGCTCG
1 TTAAGTGTTCACGAACAGGCTCG
32939 TTAAGTGTTCACGAACAGGCTCG
1 TTAAGTGTTCACGAACAGGCTCG
* *
32962 TTTATTGTTCA
1 TTAAGTGTTCA
32973 TTTAAGTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (23 bp):
TTAAGTGTTCACGAACAGGCTCG
Found at i:33007 original size:58 final size:58
Alignment explanation
Indices: 32887--33007 Score: 134
Period size: 58 Copynumber: 2.1 Consensus size: 58
32877 GTTCGTTTAT
** ** * **
32887 GTTCACGAACAGGCTCGTTTATTGTTCATTTAAGTGTTCACGAACATGCTCGTTAAGT
1 GTTCACGAACAGGCTCGTTTATTGTTCATTTAAGTGTTCACGAACATAATAATCAAAC
**** *
32945 GTTCACGAACAGGCTCGTTTATTGTTCATTTAAGTGTTCGTTTATATAATAATCAAAC
1 GTTCACGAACAGGCTCGTTTATTGTTCATTTAAGTGTTCACGAACATAATAATCAAAC
33003 GTTCA
1 GTTCA
33008 TTTATTATAT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (58 bp):
GTTCACGAACAGGCTCGTTTATTGTTCATTTAAGTGTTCACGAACATAATAATCAAAC
Found at i:33046 original size:16 final size:16
Alignment explanation
Indices: 33025--33056 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33015 TATAATTATT
33025 TATATATTAATAATAA
1 TATATATTAATAATAA
*
33041 TATATATTATTAATAA
1 TATATATTAATAATAA
33057 AAATTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:33051 original size:19 final size:19
Alignment explanation
Indices: 33009--33056 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
32999 AAACGTTCAT
* *
33009 TTATTATATAATTATTTATA
1 TTATTA-ATAATAATATATA
33029 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
33047 TTATTAATAA
1 TTATTAATAA
33057 AAATTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:33211 original size:18 final size:18
Alignment explanation
Indices: 33184--33218 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33174 AATTATTACA
*
33184 TTGTTCATGAATAATTTT
1 TTGTTCATGAACAATTTT
*
33202 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
33219 CAATTTTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:33624 original size:53 final size:52
Alignment explanation
Indices: 33503--33661 Score: 183
Period size: 52 Copynumber: 3.0 Consensus size: 52
33493 AGTCGTGCAC
* * * *
33503 CTTTTTCTTTCCTTTTTTTTTCCTGGTTTTGCTTCACTCATCGAAGGAAATTT
1 CTTTTT-TTTTCTTTTTTTTTCCTGATTTTGCTTTACTCATCGAAGGAGATTT
* ** * *
33556 CTTTTTTCTTCTTTTTTTCCCCTGATTTTGCTTTGCTCATGGAAGGAGATTT
1 CTTTTTTTTTCTTTTTTTTTCCTGATTTTGCTTTACTCATCGAAGGAGATTT
* * * *
33608 CTTTTTTTTTCTTTTTTTTTTCTGGTTTTTGCTTTACTCATTGAAGGGGATTT
1 CTTTTTTTTTCTTTTTTTTTCCT-GATTTTGCTTTACTCATCGAAGGAGATTT
33661 C
1 C
33662 CATACCAGAG
Statistics
Matches: 88, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
52 56 0.64
53 32 0.36
ACGTcount: A:0.11, C:0.18, G:0.14, T:0.57
Consensus pattern (52 bp):
CTTTTTTTTTCTTTTTTTTTCCTGATTTTGCTTTACTCATCGAAGGAGATTT
Found at i:34174 original size:22 final size:22
Alignment explanation
Indices: 34132--34254 Score: 108
Period size: 22 Copynumber: 5.6 Consensus size: 22
34122 TAATTTTGGG
* *
34132 GGTTATCAAAA-TTTATTGTGT
1 GGTTACCAAAATTTTATAGTGT
34153 GGTTTA-CAAAATTTTATAGTGT
1 GG-TTACCAAAATTTTATAGTGT
* *
34175 GGTTATCAAAATTTTATAGTGA
1 GGTTACCAAAATTTTATAGTGT
*
34197 GGTTACCAAAATTTTGTAG-GT
1 GGTTACCAAAATTTTATAGTGT
* **
34218 AGGATATTAAAATTTTATAGTGT
1 -GGTTACCAAAATTTTATAGTGT
* * *
34241 AGTTATCACAATTT
1 GGTTACCAAAATTT
34255 CATGGGATGT
Statistics
Matches: 84, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
21 11 0.13
22 71 0.85
23 2 0.02
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (22 bp):
GGTTACCAAAATTTTATAGTGT
Found at i:34294 original size:22 final size:22
Alignment explanation
Indices: 34175--34524 Score: 220
Period size: 22 Copynumber: 15.8 Consensus size: 22
34165 TTTATAGTGT
*
34175 GGTTATCAAAATTTTAT-AGTGA
1 GGTTATCAAAATTTCATAAG-GA
* **
34197 GGTTACCAAAATTTTGT-AGGTA
1 GGTTATCAAAATTTCATAAGG-A
* * *
34219 GGATATTAAAATTTTAT-AGTGTA
1 GGTTATCAAAATTTCATAAG-G-A
* *
34242 -GTTATCACAATTTCAT-GGGA
1 GGTTATCAAAATTTCATAAGGA
*
34262 TGTTATCAAAATTTCATAAGGA
1 GGTTATCAAAATTTCATAAGGA
*
34284 GGTTATTAAAATAAAATTTCATAAGGA
1 GGTTA-T----CAAAATTTCATAAGGA
* *
34311 TGTTATCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAAGGA
*
34333 GGTTATCAAAATTTCACAAGGA
1 GGTTATCAAAATTTCATAAGGA
* *
34355 GATTATCGAAA-TTCAT--GGAA
1 GGTTATCAAAATTTCATAAGG-A
34375 GGTTATCAAAATTTCAT-AGGAA
1 GGTTATCAAAATTTCATAAGG-A
* ****
34397 AGTTA-CTAAAATTTCATACTCT
1 GGTTATC-AAAATTTCATAAGGA
34419 GGTTATCAAAATTTCAT-AGGAA
1 GGTTATCAAAATTTCATAAGG-A
* * * *
34441 GGCTAACAAAATTTCATAGGGC
1 GGTTATCAAAATTTCATAAGGA
* * * *
34463 GATTAGCAAAATTTTATATGGA
1 GGTTATCAAAATTTCATAAGGA
34485 GGTTATCAAAATTTCAT-AGGAA
1 GGTTATCAAAATTTCATAAGG-A
*
34507 GATTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
34525 CTGTGCTTAT
Statistics
Matches: 258, Mismatches: 51, Indels: 37
0.75 0.15 0.11
Matches are distributed among these distances:
19 2 0.01
20 11 0.04
21 29 0.11
22 189 0.73
23 7 0.03
26 1 0.00
27 19 0.07
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGGA
Found at i:34321 original size:49 final size:48
Alignment explanation
Indices: 34250--34344 Score: 154
Period size: 49 Copynumber: 2.0 Consensus size: 48
34240 TAGTTATCAC
* *
34250 AATTTCATGGGATGTTATCAAAATTTCATAAGGAGGTTATTAAAATAA
1 AATTTCATAGGATGTTATCAAAATTTCATAAGGAGGTTATCAAAATAA
*
34298 AATTTCATAAGGATGTTATCAAAATTTCATATGGAGGTTATCAAAAT
1 AATTTCAT-AGGATGTTATCAAAATTTCATAAGGAGGTTATCAAAAT
34345 TTCACAAGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
48 8 0.19
49 35 0.81
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (48 bp):
AATTTCATAGGATGTTATCAAAATTTCATAAGGAGGTTATCAAAATAA
Found at i:34347 original size:44 final size:43
Alignment explanation
Indices: 34132--34524 Score: 250
Period size: 44 Copynumber: 8.9 Consensus size: 43
34122 TAATTTTGGG
* * *
34132 GGTTATCAAAATTT-AT-TGTGTGGTT-TACAAAATTTTATAGTGT
1 GGTTATCAAAATTTCATATG-GAGGTTAT-CAAAATTTCATAG-GA
* * **
34175 GGTTATCAAAATTTTATA-GTGAGGTTACCAAAATTTTGTAGGTA
1 GGTTATCAAAATTTCATATG-GAGGTTATCAAAATTTCATAGG-A
* * * * * *
34219 GGATATTAAAATTTTATAGTGTA-GTTATCACAATTTCATGGGA
1 GGTTATCAAAATTTCATA-TGGAGGTTATCAAAATTTCATAGGA
* * *
34262 TGTTATCAAAATTTCATAAGGAGGTTATTAAAATAAAATTTCATAAGGA
1 GGTTATCAAAATTTCATATGGAGGTTA-T----CAAAATTTCAT-AGGA
* *
34311 TGTTATCAAAATTTCATATGGAGGTTATCAAAATTTCACAAGGA
1 GGTTATCAAAATTTCATATGGAGGTTATCAAAATTTCA-TAGGA
* *
34355 GATTATCGAAA-TTC--ATGGAAGGTTATCAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATATGG-AGGTTATCAAAATTTCATAGG-A
* **
34397 AGTTA-CTAAAATTTCATACT-CTGGTTATCAAAATTTCATAGGAA
1 GGTTATC-AAAATTTCATA-TGGAGGTTATCAAAATTTCATAGG-A
* * * * * * *
34441 GGCTAACAAAATTTCATAGGGCGATTAGCAAAATTTTATATGGA
1 GGTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATA-GGA
*
34485 GGTTATCAAAATTTCATA-GGAAGATTATCAAAATTTCATA
1 GGTTATCAAAATTTCATATGG-AGGTTATCAAAATTTCATA
34525 CTGTGCTTAT
Statistics
Matches: 279, Mismatches: 46, Indels: 49
0.75 0.12 0.13
Matches are distributed among these distances:
41 8 0.03
42 26 0.09
43 42 0.15
44 157 0.56
45 5 0.02
46 2 0.01
48 10 0.04
49 29 0.10
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (43 bp):
GGTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGGA
Found at i:34541 original size:66 final size:64
Alignment explanation
Indices: 34133--34524 Score: 257
Period size: 66 Copynumber: 6.0 Consensus size: 64
34123 AATTTTGGGG
* * * *
34133 GTTATCAAAATTT-AT-TGTGTGGTT-TACAAAATTTTATAGTG-TGGTTATCAAAATTTTATAG
1 GTTATCAAAATTTCATATG-GAGGTTAT-CAAAATTTCATAG-GAAGGTTATCAAAATTTCATAG
34194 TGA
63 -GA
* ** * * * * * *
34197 GGTTACCAAAATTTTGTA-GGTAGGATATTAAAATTTTATAGTGTA-GTTATCACAATTTCATGG
1 -GTTATCAAAATTTCATATGG-AGGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAG
34260 GA
63 GA
* * *
34262 TGTTATCAAAATTTCATAAGGAGGTTATTAAAATAAAATTTCATAAGG-ATGTTATCAAAATTTC
1 -GTTATCAAAATTTCATATGGAGGTTA-T----CAAAATTTCAT-AGGAAGGTTATCAAAATTTC
34326 ATATGGA
59 ATA-GGA
* * * *
34333 GGTTATCAAAATTTCACAAGGAGATTATCGAAA-TTCAT-GGAAGGTTATCAAAATTTCATAGGA
1 -GTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGG-
34396 AA
64 -A
** * *
34398 GTTA-CTAAAATTTCATACT-CTGGTTATCAAAATTTCATAGGAAGGCTAACAAAATTTCATAGG
1 GTTATC-AAAATTTCATA-TGGAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA-G
*
34461 GC
63 GA
* * *
34463 GATTAGCAAAATTTTATATGGAGGTTATCAAAATTTCATAGGAAGATTATCAAAATTTCATA
1 G-TTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
34525 CTGTGCTTAT
Statistics
Matches: 264, Mismatches: 38, Indels: 49
0.75 0.11 0.14
Matches are distributed among these distances:
63 5 0.02
64 41 0.16
65 47 0.18
66 110 0.42
67 4 0.02
69 1 0.00
70 27 0.10
71 29 0.11
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (64 bp):
GTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGGA
Found at i:34657 original size:22 final size:22
Alignment explanation
Indices: 34630--34681 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
34620 TAGAGGTAAA
*
34630 CAAAATTTCATG-GGGAGGTTAT
1 CAAAATTTCA-GAGGGAGATTAT
* *
34652 CGAAATTTTAGAGGGAGATTAT
1 CAAAATTTCAGAGGGAGATTAT
34674 CAAAATTT
1 CAAAATTT
34682 TATTGTGTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.33
Consensus pattern (22 bp):
CAAAATTTCAGAGGGAGATTAT
Found at i:34682 original size:22 final size:22
Alignment explanation
Indices: 34642--34683 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
34632 AAATTTCATG
* *
34642 GGGAGGTTATCGAAATTTTAGA
1 GGGAGATTATCAAAATTTTAGA
34664 GGGAGATTATCAAAATTTTA
1 GGGAGATTATCAAAATTTTA
34684 TTGTGTGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (22 bp):
GGGAGATTATCAAAATTTTAGA
Found at i:34712 original size:22 final size:22
Alignment explanation
Indices: 34670--34714 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
34660 TAGAGGGAGA
**
34670 TTATCAAAATTTTATTGTGTGG
1 TTATCAAAATTTTATAATGTGG
34692 TTATCAAAATTTTATAATGTGG
1 TTATCAAAATTTTATAATGTGG
34714 T
1 T
34715 ATTTCAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (22 bp):
TTATCAAAATTTTATAATGTGG
Found at i:34783 original size:22 final size:21
Alignment explanation
Indices: 34758--34829 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
34748 TGTGGTAATT
*
34758 AAAATTTCATAATGAGTTTATC
1 AAAATTT-ATAATGAGATTATC
* *
34780 AAAATTTATAGTGAGATTAAC
1 AAAATTTATAATGAGATTATC
* * *
34801 AAAATTTGATAATGTGGTTCTC
1 AAAATTT-ATAATGAGATTATC
34823 AAAATTT
1 AAAATTT
34830 TATAGGAAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 18 0.44
22 23 0.56
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (21 bp):
AAAATTTATAATGAGATTATC
Found at i:34803 original size:21 final size:22
Alignment explanation
Indices: 34758--34814 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
34748 TGTGGTAATT
* *
34758 AAAATTTCATAATGAGTTTATC
1 AAAATTTCATAATGAGATTAAC
*
34780 AAAATTT-ATAGTGAGATTAAC
1 AAAATTTCATAATGAGATTAAC
*
34801 AAAATTTGATAATG
1 AAAATTTCATAATG
34815 TGGTTCTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (22 bp):
AAAATTTCATAATGAGATTAAC
Found at i:34813 original size:43 final size:44
Alignment explanation
Indices: 34758--34855 Score: 119
Period size: 43 Copynumber: 2.2 Consensus size: 44
34748 TGTGGTAATT
*
34758 AAAATTTCATAATGAGTTTATCAAAA-TTTATAGTG-AGATTAAC
1 AAAATTTCATAATGAGGTTATCAAAATTTTATAG-GAAGATTAAC
* * * *
34801 AAAATTTGATAATGTGGTTCTCAAAATTTTATAGGAAGATTAAT
1 AAAATTTCATAATGAGGTTATCAAAATTTTATAGGAAGATTAAC
*
34845 GAAATTTCATA
1 AAAATTTCATA
34856 GGTAAGTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
43 23 0.50
44 23 0.50
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (44 bp):
AAAATTTCATAATGAGGTTATCAAAATTTTATAGGAAGATTAAC
Found at i:34931 original size:23 final size:23
Alignment explanation
Indices: 34895--34973 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 23
34885 TTTAGTTATC
* *
34895 AAAATTTAAT-AGGAAGTTAATT
1 AAAATTTTATAAGGAAGTTAATA
* *
34917 TAAATTTTATAAGGAGGTT-ATA
1 AAAATTTTATAAGGAAGTTAATA
* * **
34939 AAAAATTTATAAGGATGTT-ACC
1 AAAATTTTATAAGGAAGTTAATA
34961 AAAATTTTATAAG
1 AAAATTTTATAAG
34974 ATGGTTATCA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
22 39 0.85
23 7 0.15
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.37
Consensus pattern (23 bp):
AAAATTTTATAAGGAAGTTAATA
Found at i:34950 original size:22 final size:22
Alignment explanation
Indices: 34922--35027 Score: 80
Period size: 22 Copynumber: 5.0 Consensus size: 22
34912 TAATTTAAAT
*
34922 TTTATAAGGAGGTTATAAAAAA
1 TTTATAAGGAGGTTATCAAAAA
* * *
34944 TTTATAAGGATGTTACCAAAAT
1 TTTATAAGGAGGTTATCAAAAA
34966 TTTATAA-GATGGTTATC-AAAA
1 TTTATAAGGA-GGTTATCAAAAA
* * *
34987 TTTCATGAGGTGGTTTTC-AAAA
1 TTT-ATAAGGAGGTTATCAAAAA
35009 TTTCAT---GAGGTTATCAAAA
1 TTT-ATAAGGAGGTTATCAAAA
35028 TTTCAAATCG
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
19 7 0.10
20 3 0.04
21 8 0.12
22 49 0.72
23 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (22 bp):
TTTATAAGGAGGTTATCAAAAA
Found at i:35008 original size:44 final size:43
Alignment explanation
Indices: 34918--35032 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 43
34908 AAGTTAATTT
*
34918 AAATTTTATAAGGAGGTTATAAAAAATTT-ATAAGGATGTTACCA
1 AAATTTTATAA-GAGGTTAT-CAAAATTTCATAAGGATGTTACCA
* **
34962 AAATTTTATAAGATGGTTATCAAAATTTCATGAGG-TGGTTTTCA
1 AAATTTTATAAGA-GGTTATCAAAATTTCATAAGGAT-GTTACCA
*
35006 AAATTTCAT--GAGGTTATCAAAATTTCA
1 AAATTTTATAAGAGGTTATCAAAATTTCA
35033 AATCGAGGTC
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
41 16 0.25
42 2 0.03
43 10 0.16
44 35 0.56
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (43 bp):
AAATTTTATAAGAGGTTATCAAAATTTCATAAGGATGTTACCA
Found at i:35040 original size:22 final size:20
Alignment explanation
Indices: 34976--35033 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
34966 TTTATAAGAT
34976 GGTTATCAAAATTTC-ATGA
1 GGTTATCAAAATTTCAATGA
*
34995 GGTGGTTTTCAAAATTTC-ATGA
1 ---GGTTATCAAAATTTCAATGA
35017 GGTTATCAAAATTTCAA
1 GGTTATCAAAATTTCAA
35034 ATCGAGGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.42
20 1 0.03
22 18 0.55
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (20 bp):
GGTTATCAAAATTTCAATGA
Found at i:35166 original size:22 final size:22
Alignment explanation
Indices: 35140--35208 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
35130 GCTTACCAAT
35140 TTTCATTGGGAGGTTATTAAAA
1 TTTCATTGGGAGGTTATTAAAA
* * *
35162 TTTCATAGGGTGGTTATCAAAA
1 TTTCATTGGGAGGTTATTAAAA
*
35184 TTTCATTAGGTA-GTTATTAAAA
1 TTTCATT-GGGAGGTTATTAAAA
35206 TTT
1 TTT
35209 TATAGCGAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 37 0.95
23 2 0.05
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (22 bp):
TTTCATTGGGAGGTTATTAAAA
Found at i:35227 original size:22 final size:22
Alignment explanation
Indices: 35202--35252 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
35192 GGTAGTTATT
**
35202 AAAATTTTAT-AGCGAGTATAAC
1 AAAATTTTATAAGAAAGT-TAAC
35224 AAAATTTTATAAGAAAGTTAAC
1 AAAATTTTATAAGAAAGTTAAC
35246 AAAATTT
1 AAAATTT
35253 CATATGGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (22 bp):
AAAATTTTATAAGAAAGTTAAC
Found at i:35349 original size:20 final size:19
Alignment explanation
Indices: 35290--35352 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
35280 TATCGTCATA
35290 AAAACTTTATAGTGTAATTATC
1 AAAA-TTTATAGTG-AA-TATC
* * *
35312 AAAA-TTATGGAGATTATC
1 AAAATTTATAGTGAATATC
35330 AAAATTTTATAGTGAATATC
1 AAAA-TTTATAGTGAATATC
35350 AAA
1 AAA
35353 TTTCATAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
18 8 0.24
19 1 0.03
20 20 0.61
22 4 0.12
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (19 bp):
AAAATTTATAGTGAATATC
Found at i:36266 original size:22 final size:23
Alignment explanation
Indices: 36227--36272 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
36217 AATTTACTAT
36227 TTTTATATTTATGATTAAGTGTG
1 TTTTATATTTATGATTAAGTGTG
*
36250 TTTTA-ATTATAT-ATTAATTGTG
1 TTTTATATT-TATGATTAAGTGTG
36272 T
1 T
36273 GTGGATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (23 bp):
TTTTATATTTATGATTAAGTGTG
Found at i:41200 original size:21 final size:21
Alignment explanation
Indices: 41162--41201 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41152 TCCCCATACA
*
41162 CAATACATACACATTCCAAAC
1 CAATACATACACAATCCAAAC
41183 CAAT-CATACTACAATCCAA
1 CAATACATAC-ACAATCCAA
41202 TTAGTCTCGA
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:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (21 bp):
CAATACATACACAATCCAAAC
Done.