Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014432.1 Corchorus capsularis cultivar CVL-1 contig14453, 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: 73598
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:117 original size:22 final size:22
Alignment explanation
Indices: 71--124 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
61 ATGATCCCAT
* * *
71 TATGAAATTTTTATAACCTTCC
1 TATGAAATTTTAATAACCATAC
*
93 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTAATAACCATAC
*
115 TATGGAATTT
1 TATGAAATTT
125 CAAGAATCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTAATAACCATAC
Found at i:168 original size:22 final size:21
Alignment explanation
Indices: 133--174 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
123 TTCAAGAATC
* *
133 TTTTTATAATTTTTTTTAACT
1 TTTTTATAAATTTTGTTAACT
154 TTTTTATGAAATTTTGTTAAC
1 TTTTTAT-AAATTTTGTTAAC
175 CTCTCTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTTTATAAATTTTGTTAACT
Found at i:260 original size:45 final size:45
Alignment explanation
Indices: 202--287 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
192 AAGACCTTAA
* * *
202 TATGAAATTTTGATAACTTTCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAAC-CTCCATATGAAATATTGATAACCAACAC
* *
247 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
288 CTTTATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 4 0.11
45 31 0.89
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:281 original size:22 final size:22
Alignment explanation
Indices: 158--636 Score: 147
Period size: 22 Copynumber: 21.9 Consensus size: 22
148 TTAACTTTTT
*
158 TATGAAATTTTGTTAACCTCTC-
1 TATGAAATTTTGATAACCTC-CA
* * **
180 TAAGGAATTTTGA-AGACCTTAA
1 TATGAAATTTTGATA-ACCTCCA
*
202 TATGAAATTTTGATAACTTTCCA
1 TATGAAATTTTGATAAC-CTCCA
**
225 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTCCA
* *
246 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTCCA
* * * **
269 TATGATATATTGATAACCACTT
1 TATGAAATTTTGATAACCTCCA
* * * *
291 TATAAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCA
313 TATG-AATTGTT-AGTAA--TCACA
1 TATGAAATT-TTGA-TAACCTC-CA
* *
334 CTTTAAAATTTTGATAA--TCACA
1 -TATGAAATTTTGATAACCTC-CA
*
356 CTATGAAATTGTGATAACCTCGC-
1 -TATGAAATTTTGATAACCTC-CA
*
379 TATGAAATTTTGATAAATCTTCC-
1 TATGAAATTTTGAT-AA-CCTCCA
* * *
402 TATAAAATTTTAATAAACAC-CCC
1 TATGAAATTTTGAT-AAC-CTCCA
* * * * *
425 TATAAAATTTTGGTAACTTTCT
1 TATGAAATTTTGATAACCTCCA
* *
447 TATGAAATCTTGAT-A---GC-
1 TATGAAATTTTGATAACCTCCA
* * *
464 TA-CAAATTTTGATAAGCTCCC
1 TATGAAATTTTGATAACCTCCA
** *
485 TATGATTTTTTGATTACCT-CA
1 TATGAAATTTTGATAACCTCCA
* * *
506 TTATGAAATTTTGTTAATCTCCC
1 -TATGAAATTTTGATAACCTCCA
* * *
529 TATGAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTCCA
*
551 TATGAAATTTTGATAACC-CTCT
1 TATGAAATTTTGATAACCTC-CA
* **
573 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTCCA
* **
594 CTATGAAAATTTGATAACCTTTA
1 -TATGAAATTTTGATAACCTCCA
* *
617 TAAGAAATTTTGATATCCTC
1 TATGAAATTTTGATAACCTC
637 ACTGAATTTC
Statistics
Matches: 335, Mismatches: 89, Indels: 66
0.68 0.18 0.13
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
18 1 0.00
20 3 0.01
21 19 0.06
22 230 0.69
23 64 0.19
24 6 0.02
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:685 original size:20 final size:19
Alignment explanation
Indices: 622--685 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
612 CTTTATAAGA
*
622 AATTTTGATATCCTCACTG
1 AATTTTGATATCCTCCCTG
* *
641 AATTTCGATATCCTCCTTG
1 AATTTTGATATCCTCCCTG
*
660 AATTTTGGTATCCTCCCTG
1 AATTTTGATATCCTCCCTG
679 AAATTTT
1 -AATTTT
686 TATTACTCCA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
19 32 0.84
20 6 0.16
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Found at i:819 original size:22 final size:22
Alignment explanation
Indices: 794--960 Score: 124
Period size: 22 Copynumber: 7.6 Consensus size: 22
784 AATCACATTT
*
794 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
816 TGAAATTTTGATAACATCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
838 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
860 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
882 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
*** **
904 TGAAATTTTGATAATAACACTA
1 TGAAATTTTGATAACCTCTTTA
*
926 TGAAATTTTGAT--CATCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
946 TATAAATTTTGATAA
1 T-GAAATTTTGATAA
961 TCTTATCTTT
Statistics
Matches: 110, Mismatches: 30, Indels: 9
0.74 0.20 0.06
Matches are distributed among these distances:
20 5 0.05
21 11 0.10
22 92 0.84
23 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:820 original size:44 final size:44
Alignment explanation
Indices: 770--962 Score: 157
Period size: 44 Copynumber: 4.4 Consensus size: 44
760 GAAATACCAC
770 TATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAA-TTTTGATAATCACATTTTGAAAATTTGATAACCTCTT
* * * *
814 TATGAAATTTTGATAA-CATC-TTTAT-AAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCA-CATTT-TGAAAA-TTTGATAACCTCTT
* * * *
858 TATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTC-TT
* * * * *
903 T-TGAAATTTTGATAATAACACTATGAAATTTTGAT--CATCTT
1 TATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTCTT
*
944 TATATAAATTTTGATAATC
1 TAT-GAAATTTTGATAATC
963 TTATCTTTAT
Statistics
Matches: 120, Mismatches: 19, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
41 2 0.02
42 4 0.03
43 27 0.22
44 80 0.67
45 7 0.06
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTCTT
Found at i:932 original size:88 final size:88
Alignment explanation
Indices: 769--935 Score: 221
Period size: 88 Copynumber: 1.9 Consensus size: 88
759 AGAAATACCA
* * *
769 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATC
1 CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
834 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* * *
857 CTATGAAA-TTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAATA
1 CTATGAAATTTTTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
920 ACACTATGAAATTTTG
64 ACACTATAAAATTTTG
936 ATCATCTTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 5 0.07
88 61 0.90
89 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (88 bp):
CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:1273 original size:24 final size:22
Alignment explanation
Indices: 1212--1372 Score: 105
Period size: 22 Copynumber: 7.2 Consensus size: 22
1202 TTGTGATAAT
* *
1212 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
1234 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
1256 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
**
1280 TAACC-ACTCTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* **
1302 TAA-CTACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
**
1324 TAACC-ACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
1346 TAA-CTACACTATGGAATTTTAA
1 TAACCAAC-CTATGAAATTTTAA
1368 TAACC
1 TAACC
1373 TCCTCATAGA
Statistics
Matches: 120, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
21 3 0.03
22 97 0.81
23 2 0.02
24 18 0.15
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:1284 original size:46 final size:43
Alignment explanation
Indices: 1219--1365 Score: 143
Period size: 44 Copynumber: 3.3 Consensus size: 43
1209 AATTAACCAC
*** *
1219 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGA
1 CCTATGAAATTTTGGTAACCACA-CTATGAAATTTTAATAA-CT-A
* **
1264 TCCTATGAAATTTTGGTAACCACTCTATGAAATTTTGGTAACTA
1 -CCTATGAAATTTTGGTAACCACACTATGAAATTTTAATAACTA
**
1308 CACTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACTA
1 C-CTATGAAATTTTGGTAACCACACTATGAAATTTTAATAACTA
*
1352 CACTATGGAATTTT
1 C-CTATGAAATTTT
1366 AATAACCTCC
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
43 1 0.01
44 55 0.61
45 2 0.02
46 32 0.36
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (43 bp):
CCTATGAAATTTTGGTAACCACACTATGAAATTTTAATAACTA
Found at i:1292 original size:68 final size:67
Alignment explanation
Indices: 1212--1372 Score: 175
Period size: 68 Copynumber: 2.4 Consensus size: 67
1202 TTGTGATAAT
* *
1212 TAACCACCCTATGAAATTTCAATAACCAAC-CTAAGAAATTTTAATAACCTGATC-CTATGAAAT
1 TAACCACACTATGAAATTTTAATAACCAACACTAAGAAATTTTAATAACC--A-CACTATGAAAT
1275 TTTGG
63 TTTGG
* ** * * **
1280 TAACCACTCTATGAAATTTTGGTAA-CTACACTATGAAATTTTGGTAACCACACTATGAAATTTT
1 TAACCACACTATGAAATTTTAATAACCAACACTAAGAAATTTTAATAACCACACTATGAAATTTT
1344 GG
66 GG
* *
1346 TAACTACACTATGGAATTTTAATAACC
1 TAACCACACTATGAAATTTTAATAACC
1373 TCCTCATAGA
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
65 1 0.01
66 35 0.45
67 4 0.05
68 37 0.48
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.33
Consensus pattern (67 bp):
TAACCACACTATGAAATTTTAATAACCAACACTAAGAAATTTTAATAACCACACTATGAAATTTT
GG
Found at i:1372 original size:44 final size:44
Alignment explanation
Indices: 1266--1365 Score: 182
Period size: 44 Copynumber: 2.3 Consensus size: 44
1256 TAACCTGATC
*
1266 CTATGAAATTTTGGTAACCACTCTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACTACA
1310 CTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACTACA
*
1354 CTATGGAATTTT
1 CTATGAAATTTT
1366 AATAACCTCC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (44 bp):
CTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACTACA
Found at i:1763 original size:32 final size:32
Alignment explanation
Indices: 1697--1759 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
1687 AATTAAGAAG
* *
1697 TATGTTTTAAAAAAAGAGGGTACAATTGGAAA
1 TATGTTTTAAAAAAAGAGGATACAATCGGAAA
*
1729 TATGTTTTAAAAATA-AGGATACAATCGGAAA
1 TATGTTTTAAAAAAAGAGGATACAATCGGAAA
1760 ATATAAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.29
Consensus pattern (32 bp):
TATGTTTTAAAAAAAGAGGATACAATCGGAAA
Found at i:1795 original size:2 final size:2
Alignment explanation
Indices: 1788--1843 Score: 85
Period size: 2 Copynumber: 27.0 Consensus size: 2
1778 TTCGTACTTT
*
1788 TA TA TA TA GTA TA TA GTA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1832 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1844 GGCAAATTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 46 0.92
3 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2273 original size:14 final size:14
Alignment explanation
Indices: 2254--2281 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2244 ATTTCCCCCC
2254 AATGGGGTAACGTT
1 AATGGGGTAACGTT
2268 AATGGGGTAACGTT
1 AATGGGGTAACGTT
2282 GATAGGCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.36, T:0.29
Consensus pattern (14 bp):
AATGGGGTAACGTT
Found at i:7157 original size:24 final size:24
Alignment explanation
Indices: 7125--7170 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
7115 ACAACGTGTT
7125 TGAACAAAATATATTTTGAAATGC
1 TGAACAAAATATATTTTGAAATGC
7149 TGAACAAAATATATTTTGAAAT
1 TGAACAAAATATATTTTGAAAT
7171 ACTTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (24 bp):
TGAACAAAATATATTTTGAAATGC
Found at i:7225 original size:17 final size:17
Alignment explanation
Indices: 7199--7250 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
7189 ATAAGAAAAC
7199 ACAAAAATTCAATTAAA
1 ACAAAAATTCAATTAAA
* *
7216 ACAAACATTCAAATAATA
1 ACAAAAATTCAATTAA-A
* *
7234 ATAAATATT-AATTAAA
1 ACAAAAATTCAATTAAA
7250 A
1 A
7251 GTGAAAGCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 2 0.07
17 19 0.66
18 8 0.28
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (17 bp):
ACAAAAATTCAATTAAA
Found at i:9314 original size:15 final size:15
Alignment explanation
Indices: 9294--9326 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
9284 ACTTTTTAAT
9294 ATAGTATAGATATAG
1 ATAGTATAGATATAG
9309 ATAGTATAGATATAG
1 ATAGTATAGATATAG
9324 ATA
1 ATA
9327 AACTCTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33
Consensus pattern (15 bp):
ATAGTATAGATATAG
Found at i:13479 original size:2 final size:2
Alignment explanation
Indices: 13431--13461 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13421 TATTCTTGCT
13431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13462 GAATGTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18115 original size:2 final size:2
Alignment explanation
Indices: 18108--18142 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
18098 AATGGATTAC
* *
18108 AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18143 ACAATTTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:30309 original size:2 final size:2
Alignment explanation
Indices: 30302--30448 Score: 294
Period size: 2 Copynumber: 73.5 Consensus size: 2
30292 TGAACAAAAG
30302 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
30344 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
30386 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
30428 AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC A
30449 TATAATTGGA
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 145 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30800 original size:2 final size:2
Alignment explanation
Indices: 30793--30818 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30783 GAATATTACA
30793 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
30819 CACCTTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31280 original size:18 final size:18
Alignment explanation
Indices: 31259--31295 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
31249 TTTTCGGTCA
31259 TTTTTCTTGTTT-TTTAT
1 TTTTTCTTGTTTATTTAT
31276 TTTTTCTTGTTTATTTAT
1 TTTTTCTTGTTTATTTAT
31294 TT
1 TT
31296 ATAATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.81
Consensus pattern (18 bp):
TTTTTCTTGTTTATTTAT
Found at i:35787 original size:1 final size:1
Alignment explanation
Indices: 35781--35815 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
35771 CCATGCATAG
35781 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35816 GGGTCAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:55453 original size:29 final size:29
Alignment explanation
Indices: 55398--55455 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
55388 ACTATCTCTT
**
55398 AACTCTATATTGTTCTTTTCCTCAAAAAA
1 AACTCTATATTGTTCTTCACCTCAAAAAA
55427 AACTCTATATTGTTCTTCACCAT-AAAAAA
1 AACTCTATATTGTTCTTCACC-TCAAAAAA
55456 GTTTCCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (29 bp):
AACTCTATATTGTTCTTCACCTCAAAAAA
Found at i:64404 original size:2 final size:2
Alignment explanation
Indices: 64397--64431 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
64387 ATTTAACTTC
64397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64432 TTCCCATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.