Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017194.1 Corchorus olitorius cultivar O-4 contig17227, 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: 25934
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:2524 original size:17 final size:17
Alignment explanation
Indices: 2502--2541 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2492 ATCACCCCCT
*
2502 AGATCACTAGTGAT-CAA
1 AGATCACCAGTGATGC-A
2519 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
2536 AGATCA
1 AGATCA
2542 ATGGTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:6316 original size:88 final size:88
Alignment explanation
Indices: 6217--6394 Score: 223
Period size: 88 Copynumber: 2.0 Consensus size: 88
6207 CTACCTGAGA
** * * * * *
6217 CCTTTTGTTTTTGTTTCATGTGAATATAAAATTAAATAATAGACTACACAAAAGGAGGTAGCCTT
1 CCTTTTGTTTTTCCTACATGCGAACATAAAATTAAATAATAGACTACACAAAAGAAGATAGCCTT
*
6282 CTCACATAC-CTTAACCCACTCCG
66 CTCACAT-CTCTTAACCCACCCCG
* * * *
6305 CCTTTTTTTTTTCCTACATGCGAACATGAAATTAAATGATAGGCTACACAAAAGAAGATAGCCTT
1 CCTTTTGTTTTTCCTACATGCGAACATAAAATTAAATAATAGACTACACAAAAGAAGATAGCCTT
*
6370 CTCTCATCTCTTAACCCACCCCG
66 CTCACATCTCTTAACCCACCCCG
6393 CC
1 CC
6395 CGTCTCAGGA
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
87 1 0.01
88 75 0.99
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (88 bp):
CCTTTTGTTTTTCCTACATGCGAACATAAAATTAAATAATAGACTACACAAAAGAAGATAGCCTT
CTCACATCTCTTAACCCACCCCG
Found at i:7171 original size:18 final size:18
Alignment explanation
Indices: 7117--7176 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
7107 TTGCGGTAGC
*
7117 GGAACATCCTGCGGCAAT
1 GGAACATCCTGCGGCAGT
* * ** *
7135 GCAACATTCTGTAGTAGT
1 GGAACATCCTGCGGCAGT
7153 GGAACATCCTGCGGCAGT
1 GGAACATCCTGCGGCAGT
*
7171 GTAACA
1 GGAACA
7177 ATATTTTGTA
Statistics
Matches: 30, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (18 bp):
GGAACATCCTGCGGCAGT
Found at i:8562 original size:17 final size:17
Alignment explanation
Indices: 8540--8575 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
8530 TGATTTGTAA
8540 AGTTTGTTACACCAGAT
1 AGTTTGTTACACCAGAT
* *
8557 AGTTTGTTATACTAGAT
1 AGTTTGTTACACCAGAT
8574 AG
1 AG
8576 CTCTTTGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
AGTTTGTTACACCAGAT
Found at i:9184 original size:28 final size:28
Alignment explanation
Indices: 9137--9199 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
9127 ATAAATTGGG
9137 ATAAAAT-TATAAATTGACCCATCT-AAA
1 ATAAAATATATAAATTGACCCAT-TAAAA
*
9164 ATAAAATATATATTATT-ACCCATTAAAA
1 ATAAAATATATA-AATTGACCCATTAAAA
9192 ATAAAATA
1 ATAAAATA
9200 CACTGTATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 8 0.25
28 21 0.66
29 3 0.09
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.32
Consensus pattern (28 bp):
ATAAAATATATAAATTGACCCATTAAAA
Found at i:10815 original size:297 final size:297
Alignment explanation
Indices: 10281--10871 Score: 1060
Period size: 297 Copynumber: 2.0 Consensus size: 297
10271 ATATATATAC
*
10281 TATATATTATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCTT
1 TATATATTATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCT
10346 CCTTTTGGCTTTTTTTGGTCTTTTCACACTTTTAAGGTGACTAAAAGGCCTTTGATGAATTTACT
66 CCTTTTGGCTTTTTTTGGTCTTTTCACACTTTTAAGGTGACTAAAAGGCCTTTGATGAATTTACT
*
10411 CTCTTACTTTTCCTGCGGCCCTTTTTTTGTAATTTACTATTTCTATATTTATGAGTAACTGTGTT
131 CTCTTACTTTTCCTGCGGCCCTTTTTTTGTAATCTACTATTTCTATATTTATGAGTAACTGTGTT
*
10476 TTAATTAATTACATATTAATTGTGGGTGGATATTAGGATTTACCGATTCAACTCCTCAGTCGGAA
196 TTAATTAATTACATATTAATTGTGGGTGGATATTAGGATTTACCGATTCAACTCCTCAGCCGGAA
*
10541 TTCCAAAGGATTTGTGCTATAAATGTATCTGCAAAAG
261 TTCCAAAGGATTGGTGCTATAAATGTATCTGCAAAAG
10578 TATATATTATTTTTAGTGACAATGGAAATTAC-TAAAGGCCAAATTGAGGATTAATGTGGTGCCT
1 TATATATTATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCT
* *
10642 CTTTTTGGCTTTTTTTGGTCTTTTCACAACTTTTCAGGTGACTAAAAAGGCCTTTGATGAATTTA
66 CCTTTTGGCTTTTTTTGGTCTTTTCAC-ACTTTTAAGGTGACT-AAAAGGCCTTTGATGAATTTA
* *
10707 CTCTCTTACTTTTCCTGCGGCCC-TTTTTTGTAATCTACTATTTCTATATTTATGATTAAGTGTG
129 CTCTCTTACTTTTCCTGCGGCCCTTTTTTTGTAATCTACTATTTCTATATTTATGAGTAACTGTG
* *
10771 TTTTAATTAATTACATATTAATTGTGTGTGGATATTAGGATTTACCGATTCAACTCCTCTGCCGG
194 TTTTAATTAATTACATATTAATTGTGGGTGGATATTAGGATTTACCGATTCAACTCCTCAGCCGG
10836 AATTCCAAAGGATTGGTGCTATAAATGTATCTGCAA
259 AATTCCAAAGGATTGGTGCTATAAATGTATCTGCAA
10872 TAATGGTTGA
Statistics
Matches: 282, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
296 57 0.20
297 181 0.64
298 44 0.16
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (297 bp):
TATATATTATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCT
CCTTTTGGCTTTTTTTGGTCTTTTCACACTTTTAAGGTGACTAAAAGGCCTTTGATGAATTTACT
CTCTTACTTTTCCTGCGGCCCTTTTTTTGTAATCTACTATTTCTATATTTATGAGTAACTGTGTT
TTAATTAATTACATATTAATTGTGGGTGGATATTAGGATTTACCGATTCAACTCCTCAGCCGGAA
TTCCAAAGGATTGGTGCTATAAATGTATCTGCAAAAG
Found at i:12177 original size:21 final size:22
Alignment explanation
Indices: 12152--12192 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12142 TTTGAGAGAA
*
12152 TACAAT-AATCGGAAATCTCAT
1 TACAATCAATCAGAAATCTCAT
*
12173 TACAATCAATCAGATATCTC
1 TACAATCAATCAGAAATCTC
12193 TCTTTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (22 bp):
TACAATCAATCAGAAATCTCAT
Found at i:12205 original size:3 final size:3
Alignment explanation
Indices: 12197--12228 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
12187 TATCTCTCTT
12197 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12229 CTTTTAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12220 original size:14 final size:14
Alignment explanation
Indices: 12201--12228 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12191 TCTCTTTTAT
12201 TATTATTATTATTA
1 TATTATTATTATTA
12215 TATTATTATTATTA
1 TATTATTATTATTA
12229 CTTTTAGGAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:12790 original size:12 final size:13
Alignment explanation
Indices: 12765--12796 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
12755 ATAAAATAAA
12765 ATAT-ATATATTG
1 ATATGATATATTG
12777 ATATGATATA-TG
1 ATATGATATATTG
12789 ATATGATA
1 ATATGATA
12797 ATCTTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (13 bp):
ATATGATATATTG
Found at i:15327 original size:43 final size:43
Alignment explanation
Indices: 15275--15362 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 43
15265 ACCAACAAAT
* * *
15275 TGAATTCTAATCGTAATATGTT-GCAGTTCACTTGACAAAACTA
1 TGAATTCTAATCCTAATAT-TTAACAGTTCACTTCACAAAACTA
15318 TGAATTCTAATCCTAATATTTAACAGTTCACTTCACAAAACTA
1 TGAATTCTAATCCTAATATTTAACAGTTCACTTCACAAAACTA
15361 TG
1 TG
15363 CCCTAACAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 2 0.05
43 39 0.95
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.35
Consensus pattern (43 bp):
TGAATTCTAATCCTAATATTTAACAGTTCACTTCACAAAACTA
Found at i:20560 original size:2 final size:2
Alignment explanation
Indices: 20553--20601 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
20543 TTTCAATGTG
20553 TA TA TA TA TA TA TA TA TA 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
20595 TA T- TA TA
1 TA TA TA TA
20602 CAGTTTTAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20705 original size:22 final size:22
Alignment explanation
Indices: 20663--20706 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20653 TATTCATATG
* *
20663 AAATTATGATAATCTCGCTATT
1 AAATTATAATAATCTCACTATT
20685 AAATTATAATAAT-TACACTATT
1 AAATTATAATAATCT-CACTATT
20707 TTTTATGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (22 bp):
AAATTATAATAATCTCACTATT
Found at i:20746 original size:22 final size:21
Alignment explanation
Indices: 20721--21111 Score: 196
Period size: 22 Copynumber: 17.7 Consensus size: 21
20711 ATGACATTCT
20721 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
* * *
20743 TATGAAATTTTAATAACGAT-A
1 TATGAAATTTTGATAAC-CTCC
* * **
20764 TATGGAATTTTGAGAACCTTTT
1 TATGAAATTTTGATAACC-TCC
* * ** *
20786 TATTAATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACC-TCC
*
20808 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCT-CC
* *
20830 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCTC-C
* *
20852 TATGAAAATTTGATAACTTCCC
1 TATGAAATTTTGATAACCT-CC
* *
20874 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TC-C
* *
20897 TATGAGATGTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
* * * *
20918 ATATGATATATTGATAACCACAT
1 -TATGAAATTTTGATAACCTC-C
* * *
20941 TATGAAAATTTAAAAACCTCC
1 TATGAAATTTTGATAACCTCC
* *
20962 ATAT-AAATTGTT-AGTAATCACGC
1 -TATGAAATT-TTGA-TAACCTC-C
* * * *
20985 TCTGAAATATTGATAATCACAC
1 TATGAAATTTTGATAACCTC-C
* *
21007 TATGAAATTTTAATAACCTCAT
1 TATGAAATTTTGATAACCTC-C
21029 TATGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACC-TCC
*
21052 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCT-CC
*
21075 TATAAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
*
21096 TTATGAAATCTTGATA
1 -TATGAAATTTTGATA
21112 TGATTTTTTG
Statistics
Matches: 284, Mismatches: 63, Indels: 44
0.73 0.16 0.11
Matches are distributed among these distances:
21 26 0.09
22 194 0.68
23 62 0.22
24 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:21059 original size:23 final size:23
Alignment explanation
Indices: 21033--21111 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
21023 CCTCATTATG
21033 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGATAAACCTTCCTATA
*
21056 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTTCCTATA
*
21079 AAATTTTGAT-AACC-TCCTTATG
1 AAATTTTGATAAACCTTCC-TATA
*
21101 AAATCTTGATA
1 AAATTTTGATA
21112 TGATTTTTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.04
22 16 0.32
23 32 0.64
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTTCCTATA
Found at i:21142 original size:22 final size:21
Alignment explanation
Indices: 21117--21253 Score: 100
Period size: 22 Copynumber: 6.3 Consensus size: 21
21107 TGATATGATT
21117 TTTTGATAACCTCATTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* * *
21139 TTTTGTTAATCTCCATATGAAT
1 TTTTGATAACCT-CATATGAAA
* *
21161 TTTTGATCTA-CACACTATGAAA
1 TTTTGAT-AACCTCA-TATGAAA
* *
21183 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT-CA-TATGAAA
21205 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* **
21227 TTTTGATATCCTC-CCTGAAA
1 TTTTGATAACCTCATATGAAA
21247 TTTTGAT
1 TTTTGAT
21254 TATTCCATAA
Statistics
Matches: 93, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
20 13 0.14
21 5 0.05
22 67 0.72
23 7 0.08
24 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:21165 original size:44 final size:42
Alignment explanation
Indices: 21109--21232 Score: 115
Period size: 44 Copynumber: 2.8 Consensus size: 42
21099 TGAAATCTTG
* * * **
21109 ATATGATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCC
1 ATATGAATTTTTGATAACCTCA-TATGAAATTTTG-AAAACTAA
* *
21153 ATATGAATTTTTGATCTA-CACACTATGAAATTTTGAAAACTAA
1 ATATGAATTTTTGAT-AACCTCA-TATGAAATTTTGAAAACTAA
*
21196 ACTATGAAATTTTGATAACCTTCATATGAAATTTTGA
1 A-TATGAATTTTTGATAACC-TCATATGAAATTTTGA
21233 TATCCTCCCT
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.09
44 56 0.86
45 3 0.05
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (42 bp):
ATATGAATTTTTGATAACCTCATATGAAATTTTGAAAACTAA
Found at i:21385 original size:22 final size:21
Alignment explanation
Indices: 21360--21460 Score: 71
Period size: 22 Copynumber: 4.6 Consensus size: 21
21350 ATCACATTTT
21360 GAAAATTTGATAACCTCTTTA
1 GAAAATTTGATAACCTCTTTA
*
21381 CGAAATTTTGATAACCT-TTATA
1 -GAAAATTTGATAACCTCTT-TA
* * * *
21403 TAAAATTTTGTTGACCCCTTTA
1 GAAAA-TTTGATAACCTCTTTA
*
21425 TGAAATTTTGATAACCTCGCTTT-
1 -GAAAATTTGATAACCT--CTTTA
*
21448 GAAATTTTGATAA
1 GAAAATTTGATAA
21461 GAAAACTATG
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
21 5 0.08
22 48 0.77
23 5 0.08
24 4 0.06
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (21 bp):
GAAAATTTGATAACCTCTTTA
Found at i:21453 original size:44 final size:44
Alignment explanation
Indices: 21357--21460 Score: 118
Period size: 44 Copynumber: 2.4 Consensus size: 44
21347 GTAATCACAT
* * **
21357 TTTGAAAATTTGATAACCTCTTTACGAAATTTTGATAACCTTTA
1 TTTGAAATTTTGATAACCCCTTTACGAAATTTTGATAACCTCGA
* * * * * *
21401 TATAAAATTTTGTTGACCCCTTTATGAAATTTTGATAACCTCGC
1 TTTGAAATTTTGATAACCCCTTTACGAAATTTTGATAACCTCGA
21445 TTTGAAATTTTGATAA
1 TTTGAAATTTTGATAA
21461 GAAAACTATG
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (44 bp):
TTTGAAATTTTGATAACCCCTTTACGAAATTTTGATAACCTCGA
Found at i:21529 original size:22 final size:20
Alignment explanation
Indices: 21502--21574 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 20
21492 TAATCCGATA
21502 TCTATGAAATTTCGATAATCAC
1 TCTATGAAATTT-GATAATC-C
21524 TCTATGAAATTTGATAA-CC
1 TCTATGAAATTTGATAATCC
* *
21543 TTCTATCAAATTTTGGTAATCC
1 -TCTATGAAA-TTTGATAATCC
21565 TC-ATGAAATT
1 TCTATGAAATT
21575 GAGACTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
19 3 0.07
20 14 0.31
21 14 0.31
22 14 0.31
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (20 bp):
TCTATGAAATTTGATAATCC
Found at i:21664 original size:22 final size:22
Alignment explanation
Indices: 21595--21654 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
21585 TAACCTTCAT
*
21595 ATGAAATTTTGATAACAACACC
1 ATGAAATTTTGATAACTACACC
* *
21617 GA-AAAATTTTGATAACTACACT
1 -ATGAAATTTTGATAACTACACC
21639 ATGAAATTTTGATAAC
1 ATGAAATTTTGATAAC
21655 GTCCCCATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (22 bp):
ATGAAATTTTGATAACTACACC
Found at i:21698 original size:22 final size:21
Alignment explanation
Indices: 21620--21735 Score: 63
Period size: 22 Copynumber: 5.3 Consensus size: 21
21610 CAACACCGAA
*
21620 AAATTTTGATAA-CTACACTATG
1 AAATTTTG-TAACCT-CCCTATG
* *
21642 AAATTTTGATAACGTCCCCATG
1 AAATTTTG-TAACCTCCCTATG
* * *
21664 ATATATTAGTAACCTCCTTATG
1 AAAT-TTTGTAACCTCCCTATG
* * *
21686 AAATTTTGTTAACCACACAATG
1 AAATTTTG-TAACCTCCCTATG
* * *
21708 AAATCTTATAACCTCGCTATG
1 AAATTTTGTAACCTCCCTATG
*
21729 ACATTTT
1 AAATTTT
21736 AATAATTTCT
Statistics
Matches: 70, Mismatches: 21, Indels: 7
0.71 0.21 0.07
Matches are distributed among these distances:
21 18 0.26
22 48 0.69
23 4 0.06
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (21 bp):
AAATTTTGTAACCTCCCTATG
Found at i:21729 original size:43 final size:43
Alignment explanation
Indices: 21637--21740 Score: 102
Period size: 44 Copynumber: 2.4 Consensus size: 43
21627 GATAACTACA
** * * *
21637 CTATGAAATTTTGATAACGTCCCCATGATATATTAGTAACCTC
1 CTATGAAATTTTGATAACCACACAATGAAATATTAGTAACCTC
* *
21680 CTTATGAAATTTTGTTAACCACACAATGAAATCTTA-TAACCTC
1 C-TATGAAATTTTGATAACCACACAATGAAATATTAGTAACCTC
* *
21723 GCTATGACATTTTAATAA
1 -CTATGAAATTTTGATAA
21741 TTTCTTTGAT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
43 21 0.43
44 28 0.57
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCACACAATGAAATATTAGTAACCTC
Found at i:21793 original size:44 final size:44
Alignment explanation
Indices: 21745--21886 Score: 132
Period size: 44 Copynumber: 3.2 Consensus size: 44
21735 TAATAATTTC
*
21745 TTTGATAACCTTTCTATAAAATTGTGATAACCACACTATGAAAT
1 TTTGATAACCTTCCTATAAAATTGTGATAACCACACTATGAAAT
* * *
21789 TTTGATAA-CTTCCATGTGAAATATTG-G-TAACCACACTATGGAAC
1 TTTGATAACCTTCC-TAT-AAA-ATTGTGATAACCACACTATGAAAT
* * * *
21833 TTTGATAACC-TCCTCATGAAATTATAATAACCATC-TTATGAAAT
1 TTTGATAACCTTCCT-ATAAAATTGTGATAACCA-CACTATGAAAT
21877 TTTGATAACC
1 TTTGATAACC
21887 ACACAGAGAC
Statistics
Matches: 79, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
42 3 0.04
43 7 0.09
44 59 0.75
45 6 0.08
46 4 0.05
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (44 bp):
TTTGATAACCTTCCTATAAAATTGTGATAACCACACTATGAAAT
Found at i:21862 original size:22 final size:22
Alignment explanation
Indices: 21837--21887 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
21827 TGGAACTTTG
21837 ATAACC-TCCTCATGAAATTATA
1 ATAACCAT-CTCATGAAATTATA
* * *
21859 ATAACCATCTTATGAAATTTTG
1 ATAACCATCTCATGAAATTATA
21881 ATAACCA
1 ATAACCA
21888 CACAGAGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (22 bp):
ATAACCATCTCATGAAATTATA
Found at i:24873 original size:13 final size:12
Alignment explanation
Indices: 24829--24910 Score: 119
Period size: 12 Copynumber: 6.8 Consensus size: 12
24819 TTTTTTTTGG
24829 CTTTAGGAATGA
1 CTTTAGGAATGA
* *
24841 CTTTAGGAGTGC
1 CTTTAGGAATGA
*
24853 CTTTAGGAATAA
1 CTTTAGGAATGA
24865 CTATTAGGAATGA
1 CT-TTAGGAATGA
24878 CTTTAGGAATGA
1 CTTTAGGAATGA
*
24890 CTTTAGGAATGC
1 CTTTAGGAATGA
24902 CTTTAGGAA
1 CTTTAGGAA
24911 CGAAAATATC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
12 51 0.82
13 11 0.18
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (12 bp):
CTTTAGGAATGA
Done.