Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015767.1 Corchorus olitorius cultivar O-4 contig15800, 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: 83354
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:147 original size:17 final size:17
Alignment explanation
Indices: 127--206 Score: 58
Period size: 17 Copynumber: 5.3 Consensus size: 17
117 GCTGGTCCGC
127 GCGCTTGGCTGGCCCAA
1 GCGCTTGGCTGGCCCAA
144 GCGC-TGG-T--CCGC--
1 GCGCTTGGCTGGCC-CAA
156 GCGCTTGGCTGGCCCAA
1 GCGCTTGGCTGGCCCAA
173 GCGC-T-G--GGCCGC--
1 GCGCTTGGCTGGCC-CAA
185 GCGCTTGGCTGGCCCAA
1 GCGCTTGGCTGGCCCAA
202 GCGCT
1 GCGCT
207 GGGCCGCGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 28
0.64 0.00 0.36
Matches are distributed among these distances:
12 8 0.16
13 10 0.20
14 4 0.08
15 4 0.08
16 10 0.20
17 13 0.27
ACGTcount: A:0.07, C:0.38, G:0.39, T:0.16
Consensus pattern (17 bp):
GCGCTTGGCTGGCCCAA
Found at i:152 original size:29 final size:29
Alignment explanation
Indices: 110--240 Score: 226
Period size: 29 Copynumber: 4.5 Consensus size: 29
100 CCAGGAGCGA
110 CCCAAGCGCTGGTCCGCGCGCTTGGCTGG
1 CCCAAGCGCTGGTCCGCGCGCTTGGCTGG
139 CCCAAGCGCTGGTCCGCGCGCTTGGCTGG
1 CCCAAGCGCTGGTCCGCGCGCTTGGCTGG
*
168 CCCAAGCGCTGGGCCGCGCGCTTGGCTGG
1 CCCAAGCGCTGGTCCGCGCGCTTGGCTGG
* *
197 CCCAAGCGCTGGGCCGCGCACTTGGCTGG
1 CCCAAGCGCTGGTCCGCGCGCTTGGCTGG
*
226 CCCAAGCGTTGGTCC
1 CCCAAGCGCTGGTCC
241 AGCCGCTGGG
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 98 1.00
ACGTcount: A:0.08, C:0.38, G:0.37, T:0.16
Consensus pattern (29 bp):
CCCAAGCGCTGGTCCGCGCGCTTGGCTGG
Found at i:1291 original size:26 final size:26
Alignment explanation
Indices: 1257--1310 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1247 GAAAAATAGT
1257 AAAATGGTAAAAATAAAGTAATTATA
1 AAAATGGTAAAAATAAAGTAATTATA
1283 AAAATGGTAAAAATAAAGTAATTATA
1 AAAATGGTAAAAATAAAGTAATTATA
1309 AA
1 AA
1311 GATATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (26 bp):
AAAATGGTAAAAATAAAGTAATTATA
Found at i:4753 original size:121 final size:112
Alignment explanation
Indices: 4547--4776 Score: 309
Period size: 121 Copynumber: 2.0 Consensus size: 112
4537 CAGGGGCGCC
*
4547 TTCTTTTAAATTGATGATGATACCCTTAATTATTTAAAATATTTCTAAAACGTCATTATTTGCTT
1 TTCTTTTAAATTGATGATGATACCCTTAATTATTTAAAATATTTATAAAACGTCATTATTTGCTT
* *
4612 TATTTTTAAGTTGGGCTTAAATTATGTTAAAGGTTATTTTTAATATT
66 TATTTTTAAGTTGGCCTTAAATTATGTAAAAGGTTATTTTTAATATT
* * *
4659 TTCTTTTAGATTGATGATGATACCCTTAATTTTTTAAAAATATTTATAAAACGTTATTACTTAAT
1 TTCTTTTAAATTGATGATGATACCCTTAATTATTT-AAAATATTTATAAAACG---TCA-TT-AT
4724 ATTGGCCTTTATTTTTAAGTT-GCCTTTAAATTATGTAAAAGGTTATTTTTAAT
60 -TT-G-CTTTATTTTTAAGTTGGCC-TTAAATTATGTAAAAGGTTATTTTTAAT
4777 TTCATTTTTT
Statistics
Matches: 102, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
112 33 0.32
113 16 0.16
116 2 0.02
117 2 0.02
118 2 0.02
119 2 0.02
120 3 0.03
121 42 0.41
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (112 bp):
TTCTTTTAAATTGATGATGATACCCTTAATTATTTAAAATATTTATAAAACGTCATTATTTGCTT
TATTTTTAAGTTGGCCTTAAATTATGTAAAAGGTTATTTTTAATATT
Found at i:5190 original size:22 final size:22
Alignment explanation
Indices: 5165--5399 Score: 82
Period size: 22 Copynumber: 10.6 Consensus size: 22
5155 GAGAAATTAT
* *
5165 CAAAATTTCATAGTATGGTTAC
1 CAAAATTTCATAGGAAGGTTAC
* *
5187 CAAAATTTCATAGGAAGTTTAT
1 CAAAATTTCATAGGAAGGTTAC
* * *
5209 CAAAATTTCATTCTGG--GGTAAT
1 CAAAATTTCA-T-AGGAAGGTTAC
* * *
5231 CAAAATTTCTTAGTGAGGGTTAA
1 CAAAATTTCATAG-GAAGGTTAC
* ** *
5254 CAAAATTTGATAGGCTGGTTAT
1 CAAAATTTCATAGGAAGGTTAC
* * * * *
5276 CGAAATTTCAAAGGGAGATTAG
1 CAAAATTTCATAGGAAGGTTAC
* * * * *
5298 TAAAATTTTATAGGGAGTTTAT
1 CAAAATTTCATAGGAAGGTTAC
* *
5320 CAAAATTTCATAAGG-AGATTAT
1 CAAAATTTCAT-AGGAAGGTTAC
* * * *
5342 CGAAATTTTATAGTGTA-GTTAT
1 CAAAATTTCATAG-GAAGGTTAC
* * **
5364 CAAAATTTCATAGTATGGTTTT
1 CAAAATTTCATAGGAAGGTTAC
*
5386 CAAAATTTCGTAGG
1 CAAAATTTCATAGG
5400 GTAATTAACA
Statistics
Matches: 161, Mismatches: 43, Indels: 18
0.73 0.19 0.08
Matches are distributed among these distances:
20 1 0.01
21 4 0.02
22 134 0.83
23 20 0.12
24 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAC
Found at i:5214 original size:44 final size:44
Alignment explanation
Indices: 5160--5394 Score: 161
Period size: 44 Copynumber: 5.3 Consensus size: 44
5150 ATAGGGAGAA
*
5160 ATTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAGGAAG
1 ATTATCAAAATTTCATAGTATGGTTATCAAAATTTCATAGGAAG
* ** ** * * *
5204 TTTATCAAAATTTCATTCTGGGGTAATCAAAATTTCTTAGTGAGG
1 ATTATCAAAATTTCATAGTATGGTTATCAAAATTTCATAG-GAAG
* * * ** * * *
5249 GTTAACAAAATTTGATAGGCTGGTTATCGAAATTTCAAAGGGAG
1 ATTATCAAAATTTCATAGTATGGTTATCAAAATTTCATAGGAAG
* * *
5293 ATTAGT-AAAATTTTATAGGGA-GTTTATCAAAATTTCATAAGG-AG
1 ATTA-TCAAAATTTCATA-GTATGGTTATCAAAATTTCAT-AGGAAG
* * * * * *
5337 ATTATCGAAATTTTATAGTGTAGTTATCAAAATTTCATAGTATG
1 ATTATCAAAATTTCATAGTATGGTTATCAAAATTTCATAGGAAG
* *
5381 GTTTTCAAAATTTC
1 ATTATCAAAATTTC
5395 GTAGGGTAAT
Statistics
Matches: 143, Mismatches: 41, Indels: 14
0.72 0.21 0.07
Matches are distributed among these distances:
43 4 0.03
44 103 0.72
45 36 0.25
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (44 bp):
ATTATCAAAATTTCATAGTATGGTTATCAAAATTTCATAGGAAG
Found at i:5257 original size:23 final size:23
Alignment explanation
Indices: 5165--5266 Score: 86
Period size: 22 Copynumber: 4.6 Consensus size: 23
5155 GAGAAATTAT
* *
5165 CAAAATTTCATAGT-ATGGTTAC
1 CAAAATTTCATAGTGAGGGTTAA
* * *
5187 CAAAATTTCATAG-GAAGTTTAT
1 CAAAATTTCATAGTGAGGGTTAA
**
5209 CAAAATTTCATTCTG-GGG-TAA
1 CAAAATTTCATAGTGAGGGTTAA
*
5230 TCAAAATTTCTTAGTGAGGGTTAA
1 -CAAAATTTCATAGTGAGGGTTAA
*
5254 CAAAATTTGATAG
1 CAAAATTTCATAG
5267 GCTGGTTATC
Statistics
Matches: 62, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
21 2 0.03
22 42 0.68
23 15 0.24
24 3 0.05
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (23 bp):
CAAAATTTCATAGTGAGGGTTAA
Found at i:5389 original size:66 final size:66
Alignment explanation
Indices: 5161--5399 Score: 200
Period size: 66 Copynumber: 3.6 Consensus size: 66
5151 TAGGGAGAAA
* * * * ** *
5161 TTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAGGAAGTTTATCAAAATTTCATTCTGGG
1 TTATCAAAATTTCATAGTAGGGTTATCAAAATTTCATAGGAAGATTATCGAAATTTCATAGTGGA
5226 G
66 G
* * * * ** * *
5227 TAATCAAAATTTCTTAGTGAGGGTTAACAAAATTTGATAGGCTGGTTATCGAAATTTCAAAG-GG
1 TTATCAAAATTTCATAGT-AGGGTTATCAAAATTTCATAGGAAGATTATCGAAATTTCATAGTGG
5291 AG
65 AG
* *
5293 ATTAGT-AAAATTTTATAG--GGAGTTTATCAAAATTTCATAAGG-AGATTATCGAAATTTTATA
1 -TTA-TCAAAATTTCATAGTAGG-G-TTATCAAAATTTCAT-AGGAAGATTATCGAAATTTCATA
*
5354 GTGTAG
61 GTGGAG
* * *
5360 TTATCAAAATTTCATAGTATGGTTTTCAAAATTTCGTAGG
1 TTATCAAAATTTCATAGTAGGGTTATCAAAATTTCATAGG
5400 GTAATTAACA
Statistics
Matches: 136, Mismatches: 27, Indels: 21
0.74 0.15 0.11
Matches are distributed among these distances:
64 2 0.01
65 5 0.04
66 75 0.55
67 52 0.38
68 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (66 bp):
TTATCAAAATTTCATAGTAGGGTTATCAAAATTTCATAGGAAGATTATCGAAATTTCATAGTGGA
G
Found at i:5450 original size:21 final size:21
Alignment explanation
Indices: 5411--5496 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 21
5401 TAATTAACAA
*
5411 ATAAGGAGATTATCAAAAATTT
1 ATAAGGAGGTTATC-AAAATTT
*
5433 AT-AGAGAGGTTATTAAAATTTT
1 ATAAG-GAGGTTATCAAAA-TTT
*
5455 ATAAGGTGGTTATCAAAATTT
1 ATAAGGAGGTTATCAAAATTT
*
5476 -TACAGCAAGGTT-TCAAAATTT
1 ATA-AG-GAGGTTATCAAAATTT
5497 CATAGTGAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
20 2 0.04
21 20 0.38
22 29 0.55
23 2 0.04
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (21 bp):
ATAAGGAGGTTATCAAAATTT
Found at i:5487 original size:44 final size:43
Alignment explanation
Indices: 5411--5496 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 43
5401 TAATTAACAA
* *
5411 ATAAGGAGATTATCAAAAATTTATAGAGAGGTTATTAAAATTTT
1 ATAAGGAGATTATCAAAAATTTACAGAGAGGTT-TCAAAATTTT
* * *
5455 ATAAGGTGGTTATCAAAATTTTACAGCA-AGGTTTCAAAATTT
1 ATAAGGAGATTATCAAAAATTTACAG-AGAGGTTTCAAAATTT
5497 CATAGTGAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 8 0.22
44 27 0.75
45 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (43 bp):
ATAAGGAGATTATCAAAAATTTACAGAGAGGTTTCAAAATTTT
Found at i:21380 original size:58 final size:60
Alignment explanation
Indices: 21312--21447 Score: 195
Period size: 64 Copynumber: 2.2 Consensus size: 60
21302 CCAATAACAA
*
21312 TTCAAGATCAAGTCGCCAAGACCTTTGAATCAA-ATC-ATCAAGCTCTCAAATTATCAAG
1 TTCAAGATCAAGTCGCCAAGACCCTTGAATCAATATCAATCAAGCTCTCAAATTATCAAG
* *
21370 TTCAAGATCAAGTCGTCAAGACCCTTGAATCAAGTTATCAAAATCAAGTTCTCAAATTATCAAG
1 TTCAAGATCAAGTCGCCAAGACCCTTGAATCAA--TATC--AATCAAGCTCTCAAATTATCAAG
21434 TTCAAGATCAAGTC
1 TTCAAGATCAAGTC
21448 ATTCGACCCT
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
58 31 0.45
61 3 0.04
64 35 0.51
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.27
Consensus pattern (60 bp):
TTCAAGATCAAGTCGCCAAGACCCTTGAATCAATATCAATCAAGCTCTCAAATTATCAAG
Found at i:21414 original size:14 final size:14
Alignment explanation
Indices: 21397--21435 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
21387 AAGACCCTTG
21397 AATCAAGTTATCAA
1 AATCAAGTTATCAA
*
21411 AATCAAGTTCTCAA
1 AATCAAGTTATCAA
21425 ATTATCAAGTT
1 A--ATCAAGTT
21436 CAAGATCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.64
16 8 0.36
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (14 bp):
AATCAAGTTATCAA
Found at i:21734 original size:22 final size:22
Alignment explanation
Indices: 21630--21733 Score: 66
Period size: 22 Copynumber: 4.7 Consensus size: 22
21620 TGTATACAGT
*
21630 GAGGTTATCAAAATTTCACAAG
1 GAGGTTATCAAAATTTCATAAG
* * * *
21652 AAAGTTATCACAATTTGAT-AG
1 GAGGTTATCAAAATTTCATAAG
* * *
21673 TGTGGTTATCAAAATATCATAAT
1 -GAGGTTATCAAAATTTCATAAG
* ** * * *
21696 GTGAATACCAACATTTTATAAG
1 GAGGTTATCAAAATTTCATAAG
21718 GAGGTTATCAAAATTT
1 GAGGTTATCAAAATTT
21734 TGTAGTGTGC
Statistics
Matches: 56, Mismatches: 24, Indels: 4
0.67 0.29 0.05
Matches are distributed among these distances:
21 2 0.04
22 53 0.95
23 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAAG
Found at i:27471 original size:159 final size:159
Alignment explanation
Indices: 27182--27818 Score: 967
Period size: 159 Copynumber: 4.0 Consensus size: 159
27172 GGAAGACCTA
* * *
27182 GAAAGAAGCCAATTGAGGGATCTCAACTAGATCAGGTTAAGAGGCCCAAAGGTAGACCTAGAAAG
1 GAAAGAAGCCAATTGAGGAATCTCAACTAGATCAAGTTAAGAGGCCAAAAGGTAGACCTAGAAAG
* * *
27247 AAACCAATTGGTGAATCTCTTAGTGGCGATCAGCCTCTTGCTATACAGTACCCAGAAGTTTCCTT
66 AAACCAATTGGTGAATCTCTTAGTGGTGATCAGCCTCTTGCTGTACAGTACACAGAAGTTTCCTT
* *
27312 TGAGCCAATCGCTGCAGACAGTGCTCGTG
131 TGAGCCAATCGCTGTAGACAGTGCTCCTG
* **
27341 GAAAGAAGCCAACTGAGGAATCTCAACTAGATCTTGTTAAGAGGCCAAAAGGTAGACCTAGAAAG
1 GAAAGAAGCCAATTGAGGAATCTCAACTAGATCAAGTTAAGAGGCCAAAAGGTAGACCTAGAAAG
* *
27406 AAACCAATTGGTGAATCTCTTAGTGGTGATCAGCCTCTTGTTGTACACTACACAGAAGTTTCCTT
66 AAACCAATTGGTGAATCTCTTAGTGGTGATCAGCCTCTTGCTGTACAGTACACAGAAGTTTCCTT
27471 TGAGCCAATCGCTGTAGACAGTGCTCCTG
131 TGAGCCAATCGCTGTAGACAGTGCTCCTG
* *
27500 GAAAGAAGCCAATTGAGGAATCTCAACTAGATCACG--AA-AGGCCAAAAGGGAGACCTAGAAAG
1 GAAAGAAGCCAATTGAGGAATCTCAACTAGATCAAGTTAAGAGGCCAAAAGGTAGACCTAGAAAG
* ** * *
27562 AAACCAATTGGGGTTTCTCTTAGTGGTGATCAGCCTCTTGCTGTACAGTACACTGAAGTTTCCCT
66 AAACCAATTGGTGAATCTCTTAGTGGTGATCAGCCTCTTGCTGTACAGTACACAGAAGTTTCCTT
* *
27627 TGAGCCAATTGCTGTAGACACTGCTCCTG
131 TGAGCCAATCGCTGTAGACAGTGCTCCTG
* *
27656 GAAAGAAGCCAATTGAGGAATCTCAACTAGATC-AGCTTAAGAGGCCAACAGGTAGATCTAGAAA
1 GAAAGAAGCCAATTGAGGAATCTCAACTAGATCAAG-TTAAGAGGCCAAAAGGTAGACCTAGAAA
* * *
27720 GAAACCGATTGGTGAATCTCTTAGTAGTGATCAGCCTCTTGCTGTACAGTACCCAGAAGTTTCCT
65 GAAACCAATTGGTGAATCTCTTAGTGGTGATCAGCCTCTTGCTGTACAGTACACAGAAGTTTCCT
* * *
27785 TTGAGCCAATTGCTATAAACAGTGCTCCTG
130 TTGAGCCAATCGCTGTAGACAGTGCTCCTG
27815 GAAA
1 GAAA
27819 TACGCAAGAA
Statistics
Matches: 434, Mismatches: 40, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
155 1 0.00
156 141 0.32
157 2 0.00
158 2 0.00
159 288 0.66
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (159 bp):
GAAAGAAGCCAATTGAGGAATCTCAACTAGATCAAGTTAAGAGGCCAAAAGGTAGACCTAGAAAG
AAACCAATTGGTGAATCTCTTAGTGGTGATCAGCCTCTTGCTGTACAGTACACAGAAGTTTCCTT
TGAGCCAATCGCTGTAGACAGTGCTCCTG
Found at i:27809 original size:315 final size:317
Alignment explanation
Indices: 27182--27818 Score: 983
Period size: 315 Copynumber: 2.0 Consensus size: 317
27172 GGAAGACCTA
* * * *
27182 GAAAGAAGCCAATTGAGGGATCTCAACTAGATCAGGTTAAGAGGCCCAAAGGTAGACCTAGAAAG
1 GAAAGAAGCCAATTGAGGAATCTCAACTAGATCACG-TAAGAGGCCAAAAGGGAGACCTAGAAAG
* * *
27247 AAACCAATTGGTGAATCTCTTAGTGGCGATCAGCCTCTTGCTATACAGTACCCAGAAGTTTCCTT
65 AAACCAATTGGGGAATCTCTTAGTGGCGATCAGCCTCTTGCTATACAGTACACAGAAGTTTCCCT
* * *
27312 TGAGCCAATCGCTGCAGACAGTGCTCGTGGAAAGAAGCCAACTGAGGAATCTCAACTAGATCTTG
130 TGAGCCAATCGCTGCAGACACTGCTCCTGGAAAGAAGCCAACTGAGGAATCTCAACTAGATCTAG
*
27377 TTAAGAGGCCAAAAGGTAGACCTAGAAAGAAACCAATTGGTGAATCTCTTAGTGGTGATCAGCCT
195 TTAAGAGGCCAAAAGGTAGACCTAGAAAGAAACCAATTGGTGAATCTCTTAGTAGTGATCAGCCT
* * *
27442 CTTGTTGTACACTACACAGAAGTTTCCTTTGAGCCAATCGCTGTAGACAGTGCTCCTG
260 CTTGCTGTACACTACACAGAAGTTTCCTTTGAGCCAATCGCTATAAACAGTGCTCCTG
27500 GAAAGAAGCCAATTGAGGAATCTCAACTAGATCACG-AA-AGGCCAAAAGGGAGACCTAGAAAGA
1 GAAAGAAGCCAATTGAGGAATCTCAACTAGATCACGTAAGAGGCCAAAAGGGAGACCTAGAAAGA
** * * *
27563 AACCAATTGGGGTTTCTCTTAGTGGTGATCAGCCTCTTGCTGTACAGTACACTGAAGTTTCCCTT
66 AACCAATTGGGGAATCTCTTAGTGGCGATCAGCCTCTTGCTATACAGTACACAGAAGTTTCCCTT
* * *
27628 GAGCCAATTGCTGTAGACACTGCTCCTGGAAAGAAGCCAATTGAGGAATCTCAACTAGATC-AGC
131 GAGCCAATCGCTGCAGACACTGCTCCTGGAAAGAAGCCAACTGAGGAATCTCAACTAGATCTAG-
* * *
27692 TTAAGAGGCCAACAGGTAGATCTAGAAAGAAACCGATTGGTGAATCTCTTAGTAGTGATCAGCCT
195 TTAAGAGGCCAAAAGGTAGACCTAGAAAGAAACCAATTGGTGAATCTCTTAGTAGTGATCAGCCT
* * *
27757 CTTGCTGTACAGTACCCAGAAGTTTCCTTTGAGCCAATTGCTATAAACAGTGCTCCTG
260 CTTGCTGTACACTACACAGAAGTTTCCTTTGAGCCAATCGCTATAAACAGTGCTCCTG
27815 GAAA
1 GAAA
27819 TACGCAAGAA
Statistics
Matches: 290, Mismatches: 28, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
314 1 0.00
315 253 0.87
316 2 0.01
318 34 0.12
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (317 bp):
GAAAGAAGCCAATTGAGGAATCTCAACTAGATCACGTAAGAGGCCAAAAGGGAGACCTAGAAAGA
AACCAATTGGGGAATCTCTTAGTGGCGATCAGCCTCTTGCTATACAGTACACAGAAGTTTCCCTT
GAGCCAATCGCTGCAGACACTGCTCCTGGAAAGAAGCCAACTGAGGAATCTCAACTAGATCTAGT
TAAGAGGCCAAAAGGTAGACCTAGAAAGAAACCAATTGGTGAATCTCTTAGTAGTGATCAGCCTC
TTGCTGTACACTACACAGAAGTTTCCTTTGAGCCAATCGCTATAAACAGTGCTCCTG
Found at i:45410 original size:1 final size:1
Alignment explanation
Indices: 45404--45439 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
45394 TGTGCACGTT
45404 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
45440 TGAAGAGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:49573 original size:16 final size:16
Alignment explanation
Indices: 49552--49582 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
49542 AAGTTAAGCA
49552 ATTAACATATTAGGCG
1 ATTAACATATTAGGCG
49568 ATTAACATATTAGGC
1 ATTAACATATTAGGC
49583 AACCCCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (16 bp):
ATTAACATATTAGGCG
Found at i:51812 original size:2 final size:2
Alignment explanation
Indices: 51805--51838 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
51795 GCTCAATAGG
51805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51839 TTTTAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56740 original size:12 final size:13
Alignment explanation
Indices: 56723--56751 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
56713 TTAATTTACG
56723 TTTTGTTAT-TTT
1 TTTTGTTATGTTT
56735 TTTTGTTATGTTT
1 TTTTGTTATGTTT
56748 TTTT
1 TTTT
56752 TTGTTCCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (13 bp):
TTTTGTTATGTTT
Found at i:56835 original size:31 final size:32
Alignment explanation
Indices: 56770--56836 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
56760 ACAATGACGG
* *
56770 AACTGGTCATTTCTCCAGTCTTGTCGCTGAAT
1 AACTGGTCATGTCTCCAGTCTTGTCGCGGAAT
* *
56802 AACTGGTCATGT-TCCAGTCTTGTTGCGGCAT
1 AACTGGTCATGTCTCCAGTCTTGTCGCGGAAT
56833 AACT
1 AACT
56837 AGTCCATTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 20 0.65
32 11 0.35
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (32 bp):
AACTGGTCATGTCTCCAGTCTTGTCGCGGAAT
Found at i:64246 original size:21 final size:21
Alignment explanation
Indices: 64198--64246 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
64188 AGTAACAATA
*
64198 AAATAAA-TAAGCAAGAAAAT
1 AAATAAATTAAGCAACAAAAT
*
64218 -AATAAAATTAAGCAACAAGAT
1 AAAT-AAATTAAGCAACAAAAT
64239 AAATAAAT
1 AAATAAAT
64247 ACTCCAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
21 15 0.62
22 3 0.12
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.18
Consensus pattern (21 bp):
AAATAAATTAAGCAACAAAAT
Found at i:68126 original size:22 final size:23
Alignment explanation
Indices: 68090--68134 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
68080 CTCGATAGTT
*
68090 TTTTGTTCAATTAACAATTGTCC
1 TTTTGTTCAAGTAACAATTGTCC
68113 TTTT-TTCAAGTAACAATTGTCC
1 TTTTGTTCAAGTAACAATTGTCC
68135 CTCAACAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.47
Consensus pattern (23 bp):
TTTTGTTCAAGTAACAATTGTCC
Found at i:68764 original size:21 final size:21
Alignment explanation
Indices: 68716--68764 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
68706 AGTAACAATA
*
68716 AAATAAA-TAAGCAAGAAAAT
1 AAATAAATTAAGCAACAAAAT
*
68736 -AATAAAATTAAGCAACAAGAT
1 AAAT-AAATTAAGCAACAAAAT
68757 AAATAAAT
1 AAATAAAT
68765 ACTCCAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
21 15 0.62
22 3 0.12
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.18
Consensus pattern (21 bp):
AAATAAATTAAGCAACAAAAT
Found at i:74573 original size:34 final size:34
Alignment explanation
Indices: 74535--74610 Score: 152
Period size: 34 Copynumber: 2.2 Consensus size: 34
74525 AAAAATATTA
74535 TATGTATAGATGAATCATTTATATATATTTATCG
1 TATGTATAGATGAATCATTTATATATATTTATCG
74569 TATGTATAGATGAATCATTTATATATATTTATCG
1 TATGTATAGATGAATCATTTATATATATTTATCG
74603 TATGTATA
1 TATGTATA
74611 TAAAAAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (34 bp):
TATGTATAGATGAATCATTTATATATATTTATCG
Found at i:74576 original size:17 final size:17
Alignment explanation
Indices: 74556--74612 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
74546 GAATCATTTA
74556 TATATATTTATCGTATG
1 TATATATTTATCGTATG
* ** * * *
74573 TATAGATGAATCATTTA
1 TATATATTTATCGTATG
74590 TATATATTTATCGTATG
1 TATATATTTATCGTATG
74607 TATATA
1 TATATA
74613 AAAAATATTA
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (17 bp):
TATATATTTATCGTATG
Found at i:79942 original size:19 final size:19
Alignment explanation
Indices: 79918--79954 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
79908 AAATAAAAAA
79918 ACCTCATTTGTTTTTATGC
1 ACCTCATTTGTTTTTATGC
79937 ACCTCATTTGTTTTTATG
1 ACCTCATTTGTTTTTATG
79955 TATACAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.11, T:0.54
Consensus pattern (19 bp):
ACCTCATTTGTTTTTATGC
Found at i:81206 original size:24 final size:24
Alignment explanation
Indices: 81174--81219 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
81164 CAAATTACTC
*
81174 AGTCGACAAGTCCTCCAGATATTT
1 AGTCGACAAGTCCTCCAAATATTT
81198 AGTCGACAAGTCCTCCAAATAT
1 AGTCGACAAGTCCTCCAAATAT
81220 CGATTCTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (24 bp):
AGTCGACAAGTCCTCCAAATATTT
Found at i:82719 original size:290 final size:293
Alignment explanation
Indices: 82166--82750 Score: 962
Period size: 290 Copynumber: 2.0 Consensus size: 293
82156 TTTTTAGTGA
82166 CTATGAAAATTACTTAAAGGCCAAATTGAGGATTAATGCGGTGCCTCCTTTTGGCTTTTTTTGAT
1 CTATGAAAATTACTTAAAGGCCAAATTGAGGATTAATGCGGTGCCTCCTTTTGGCTTTTTTT-AT
* * **
82231 CTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTTGATGAATTTCTTTTCTTACTTTTCCTCCTG
65 CTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTCCTG
* **
82296 CCCTTTTTTGTAATTTACTATTTTTTGTATTTATGATTAAGTGTGTTTTAATTATGTATTAATTG
130 CCCTTTTTTGTAATTTACTATTTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTG
* * * * *
82361 TGTGTGGATATTAGGATTTACCGGTTCAACTCTTCTGTCGGAATTCCGAAGGATTGGTGCTATAA
195 TGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGATATAA
82426 ATGTATCTACCCGAGTTCATTAATTTAACAATTG
260 ATGTATCTACCCGAGTTCATTAATTTAACAATTG
* *
82460 CTATGGAAATTACTTAAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGGCTTTTTTT-T
1 CTATGAAAATTACTT-AAAGGCCAAATTGAGGATTAATGCGGTGCCTCCTTTTGGCTTTTTTTAT
*
82524 -TTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTGCTG
65 CTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTCCTG
*
82588 -CCTTTTTTGTAATTTACTA-TTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTGATTG
130 CCCTTTTTTGTAATTTACTATTTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTG
*
82651 TGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGATGTAA
195 TGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGATATAA
*
82716 ATGTGTCTACCCGAGTTCATTAATTTAACAATTG
260 ATGTATCTACCCGAGTTCATTAATTTAACAATTG
82750 C
1 C
82751 AATCAAGATT
Statistics
Matches: 272, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
290 133 0.49
291 19 0.07
292 59 0.22
293 1 0.00
294 14 0.05
295 46 0.17
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (293 bp):
CTATGAAAATTACTTAAAGGCCAAATTGAGGATTAATGCGGTGCCTCCTTTTGGCTTTTTTTATC
TTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTCCTGC
CCTTTTTTGTAATTTACTATTTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGT
GTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGATATAAA
TGTATCTACCCGAGTTCATTAATTTAACAATTG
Found at i:83108 original size:42 final size:43
Alignment explanation
Indices: 83057--83150 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
83047 AGTGCATTAC
* *
83057 CTAA-ATTCTA-CTCCATCTCTAGGTAATTTATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
83098 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
83143 CTAATATT
1 CTAATATT
83151 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Done.