Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008271.1 Corchorus capsularis cultivar CVL-1 contig08292, 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: 79315
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3264 original size:3 final size:3
Alignment explanation
Indices: 3258--3294 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3248 GATGATGATG
3258 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3295 GATGTATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:8064 original size:2 final size:2
Alignment explanation
Indices: 8037--8113 Score: 53
Period size: 2 Copynumber: 42.0 Consensus size: 2
8027 TAATAAATAA
* *
8037 AT AT AT -T AT AT TT A- AT -T AT TT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
8075 GT AT AT -T AT AT TT A- AT -T AGT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
8114 TAGAAATCTG
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
1 8 0.14
2 49 0.84
3 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (2 bp):
AT
Found at i:8089 original size:38 final size:39
Alignment explanation
Indices: 8038--8113 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 39
8028 AATAAATAAA
*
8038 TATATTATATTTAATTATTTATATATATATAT-TATATG
1 TATATTATATTTAATTAGTTATATATATATATATATATG
8076 TATATTATATTTAATTAGTTATATATATATATATATAT
1 TATATTATATTTAATTAGTTATATATATATATATATAT
8114 TAGAAATCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 31 0.86
39 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (39 bp):
TATATTATATTTAATTAGTTATATATATATATATATATG
Found at i:9570 original size:70 final size:69
Alignment explanation
Indices: 9453--9643 Score: 255
Period size: 70 Copynumber: 2.8 Consensus size: 69
9443 AAACTTTTTT
* *
9453 TTCAAAGCTATTGCCAATTCAAGAGAGGGAAACGTGAAATTGGAATTCATGAGGAGAGATGAAAA
1 TTCAAAGCTATTACCAATTC-AGAGAGGGAAACGTAAAATTGGAATTCATGAGGAGAGATGAAAA
9518 AAAAA
65 AAAAA
* *
9523 TTCAAAGCTATTACCAATTCAGTAGAGGGAAACGTAAAATTGAAATTCATAAGGAGAGATGAAAA
1 TTCAAAGCTATTACCAATTCAG-AGAGGGAAACGTAAAATTGGAATTCATGAGGAGAGATGAAAA
9588 AAAAA
65 AAAAA
* * * *
9593 TTCGAAGC---TACCAATTCAGGACATGGAAACGTAAAA-TGGAATTGATGAGGA
1 TTCAAAGCTATTACCAATTCA-GAGAGGGAAACGTAAAATTGGAATTCATGAGGA
9644 ATTGATGAGG
Statistics
Matches: 109, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
66 12 0.11
67 24 0.22
68 1 0.01
69 2 0.02
70 70 0.64
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.21
Consensus pattern (69 bp):
TTCAAAGCTATTACCAATTCAGAGAGGGAAACGTAAAATTGGAATTCATGAGGAGAGATGAAAAA
AAAA
Found at i:9646 original size:11 final size:11
Alignment explanation
Indices: 9630--9654 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9620 AACGTAAAAT
9630 GGAATTGATGA
1 GGAATTGATGA
9641 GGAATTGATGA
1 GGAATTGATGA
9652 GGA
1 GGA
9655 GAGATAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.24
Consensus pattern (11 bp):
GGAATTGATGA
Found at i:11764 original size:14 final size:15
Alignment explanation
Indices: 11745--11776 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
11735 ATTTTCTTAT
11745 ATTATTATAT-ATTA
1 ATTATTATATAATTA
11759 ATTATTATATAATTA
1 ATTATTATATAATTA
11774 ATT
1 ATT
11777 TGGATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTATTATATAATTA
Found at i:12403 original size:62 final size:63
Alignment explanation
Indices: 12293--12420 Score: 231
Period size: 62 Copynumber: 2.0 Consensus size: 63
12283 GATCGCATGA
12293 ACAACTTCTTTTTCTTCAATCATCAATGGGGTTTAATTAATATTAGTATATATATTTTTTTCTAT
1 ACAACTTCTTTTTCTTCAATCAT--ATGGGGTTTAATTAATATTAGTATATATATTTTTTTCTAT
12358 ACAACTTCTTTTTCTTCAATCAT-TGGGGTTTAATTAATATTAGTATATATATTTTTTTCTAT
1 ACAACTTCTTTTTCTTCAATCATATGGGGTTTAATTAATATTAGTATATATATTTTTTTCTAT
12420 A
1 A
12421 TTTTTGTAGT
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
62 40 0.63
65 23 0.37
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.52
Consensus pattern (63 bp):
ACAACTTCTTTTTCTTCAATCATATGGGGTTTAATTAATATTAGTATATATATTTTTTTCTAT
Found at i:13024 original size:13 final size:13
Alignment explanation
Indices: 13006--13031 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12996 GGTCTTTAGT
13006 TCTCTCAATTTCA
1 TCTCTCAATTTCA
13019 TCTCTCAATTTCA
1 TCTCTCAATTTCA
13032 CTAATTGAGA
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:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (13 bp):
TCTCTCAATTTCA
Found at i:13326 original size:53 final size:53
Alignment explanation
Indices: 13260--13365 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
13250 AAAGTTCGAA
13260 AGTACTATAATTTTAAATGTGTTGCATCTTTAAAAGGTTATACTATTAACATT
1 AGTACTATAATTTTAAATGTGTTGCATCTTTAAAAGGTTATACTATTAACATT
*
13313 AGTACTATGATTTTAAATGTGTTGCATCTTTAAAAGGTTATACTATTAACATT
1 AGTACTATAATTTTAAATGTGTTGCATCTTTAAAAGGTTATACTATTAACATT
13366 GAGCATACGC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (53 bp):
AGTACTATAATTTTAAATGTGTTGCATCTTTAAAAGGTTATACTATTAACATT
Found at i:13577 original size:19 final size:19
Alignment explanation
Indices: 13553--13611 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
13543 TTTATTATAA
13553 AATTTATGTTATAACATTG
1 AATTTATGTTATAACATTG
*
13572 AATTTATG-T-GAAC----
1 AATTTATGTTATAACATTG
13585 -ATTTATGTTATAACATTG
1 AATTTATGTTATAACATTG
13603 AATTTATGT
1 AATTTATGT
13612 GAAAGGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
12 7 0.23
13 1 0.03
14 3 0.10
17 3 0.10
18 1 0.03
19 16 0.52
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (19 bp):
AATTTATGTTATAACATTG
Found at i:13587 original size:17 final size:17
Alignment explanation
Indices: 13565--13614 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
13555 TTTATGTTAT
13565 AACATTGAATTTATGTG
1 AACATTGAATTTATGTG
*
13582 AACATT-TATGTTA--T-
1 AACATTGAAT-TTATGTG
13596 AACATTGAATTTATGTG
1 AACATTGAATTTATGTG
13613 AA
1 AA
13615 AGGAAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
14 9 0.35
15 3 0.12
16 3 0.12
17 11 0.42
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (17 bp):
AACATTGAATTTATGTG
Found at i:13589 original size:31 final size:31
Alignment explanation
Indices: 13554--13614 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
13544 TTATTATAAA
13554 ATTTATGTTATAACATTGAATTTATGTGAAC
1 ATTTATGTTATAACATTGAATTTATGTGAAC
13585 ATTTATGTTATAACATTGAATTTATGTGAA
1 ATTTATGTTATAACATTGAATTTATGTGAA
13615 AGGAAATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (31 bp):
ATTTATGTTATAACATTGAATTTATGTGAAC
Found at i:18349 original size:20 final size:22
Alignment explanation
Indices: 18321--18360 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18311 TTTCATTTAT
18321 ATAAAT-AAAATTAT-AAAATC
1 ATAAATAAAAATTATGAAAATC
*
18341 ATAACTAAAAATTATGAAAA
1 ATAAATAAAAATTATGAAAA
18361 AAGTATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (22 bp):
ATAAATAAAAATTATGAAAATC
Found at i:18943 original size:3 final size:3
Alignment explanation
Indices: 18935--18973 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
18925 CCTTTACTGT
18935 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
18974 ATATATGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18958 original size:17 final size:17
Alignment explanation
Indices: 18936--18970 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
18926 CTTTACTGTT
18936 TATTATTATTATTATTA
1 TATTATTATTATTATTA
18953 TATTATTATTATTATTA
1 TATTATTATTATTATTA
18970 T
1 T
18971 TATATATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:18960 original size:20 final size:20
Alignment explanation
Indices: 18935--18975 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
18925 CCTTTACTGT
18935 TTATTATTATTATTATTATA
1 TTATTATTATTATTATTATA
18955 TTATTATTATTATTATTATA
1 TTATTATTATTATTATTATA
18975 T
1 T
18976 ATATGGTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTATTATTATTATTATA
Found at i:20266 original size:13 final size:13
Alignment explanation
Indices: 20248--20279 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
20238 CGGTTGGTTT
20248 TCGGTTTTTTTAG
1 TCGGTTTTTTTAG
20261 TCGG--TTTTTAG
1 TCGGTTTTTTTAG
20272 TCGGTTTT
1 TCGGTTTT
20280 AATTTTGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.65
13 6 0.35
ACGTcount: A:0.06, C:0.09, G:0.25, T:0.59
Consensus pattern (13 bp):
TCGGTTTTTTTAG
Found at i:20280 original size:10 final size:11
Alignment explanation
Indices: 20254--20279 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20244 GTTTTCGGTT
20254 TTTTTAGTCGG
1 TTTTTAGTCGG
20265 TTTTTAGTCGG
1 TTTTTAGTCGG
20276 TTTT
1 TTTT
20280 AATTTTGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.23, T:0.62
Consensus pattern (11 bp):
TTTTTAGTCGG
Found at i:20812 original size:14 final size:13
Alignment explanation
Indices: 20789--20824 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
20779 ATTTTTTAAC
20789 ATAATGAATAAATA
1 ATAAT-AATAAATA
20803 ATAAATAATAAATA
1 AT-AATAATAAATA
20817 ATAATAAT
1 ATAATAAT
20825 TAATTAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.29
14 12 0.57
15 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
ATAATAATAAATA
Found at i:20828 original size:7 final size:7
Alignment explanation
Indices: 20795--20824 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
20785 TAACATAATG
20795 AATAAAT
1 AATAAAT
20802 AATAAAT
1 AATAAAT
20809 AATAAAT
1 AATAAAT
20816 AAT-AAT
1 AATAAAT
20822 AAT
1 AAT
20825 TAATTAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATAAAT
Found at i:20835 original size:17 final size:17
Alignment explanation
Indices: 20789--20828 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
20779 ATTTTTTAAC
*
20789 ATAATGAATAAATAATAA
1 ATAATAAAT-AATAATAA
20807 ATAATAAATAATAATAA
1 ATAATAAATAATAATAA
*
20824 TTAAT
1 ATAAT
20829 TAGTAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATAATAAATAATAATAA
Found at i:21887 original size:21 final size:20
Alignment explanation
Indices: 21854--21894 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
21844 TCGCTCAGTC
*
21854 TCTACAAACTAATCATCACA
1 TCTACAAACTAATCACCACA
*
21874 TCTACCAAAGTAATCACCACA
1 TCTA-CAAACTAATCACCACA
21895 GCAAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.22
Consensus pattern (20 bp):
TCTACAAACTAATCACCACA
Found at i:23239 original size:26 final size:26
Alignment explanation
Indices: 23210--23277 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
23200 TTCCTTCATT
23210 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
23236 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
23262 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
23278 AAACTAAGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:23277 original size:15 final size:15
Alignment explanation
Indices: 23210--23281 Score: 63
Period size: 11 Copynumber: 5.4 Consensus size: 15
23200 TTCCTTCATT
*
23210 TTAATCATAAACTAA
1 TTAAACATAAACTAA
23225 TT-AA-AT--ACTAA
1 TTAAACATAAACTAA
*
23236 TTAATCATAAACTAA
1 TTAAACATAAACTAA
23251 TT-AA-AT--ACTAA
1 TTAAACATAAACTAA
23262 TTAAACATAAACTAA
1 TTAAACATAAACTAA
23277 -TAAAC
1 TTAAAC
23282 TAAGTAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 17
0.70 0.05 0.26
Matches are distributed among these distances:
11 14 0.30
12 3 0.07
13 8 0.17
14 7 0.15
15 14 0.30
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAACATAAACTAA
Found at i:23330 original size:52 final size:49
Alignment explanation
Indices: 23211--23330 Score: 113
Period size: 52 Copynumber: 2.4 Consensus size: 49
23201 TCCTTCATTT
* * *
23211 TAATCATAAACTAATTAA-ATACTAATTAATCATAAACTAATTAAATAC
1 TAATCATAAACTAATTAATAAACTAAGTAATAATAAACTAATTAAATAC
* *
23259 TAAT--TAAACATAAACTAATAAACTAAGTAATTTGAATTAACTAATTTAAA-AC
1 TAATCATAAAC-T-AATTAATAAACTAAGTAA--T-AATAAACTAA-TTAAATAC
23311 TAATCATAAACTAATTAATA
1 TAATCATAAACTAATTAATA
23331 TTAAAAAATG
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
46 5 0.09
47 1 0.02
48 9 0.16
49 9 0.16
51 1 0.02
52 21 0.37
53 6 0.11
54 5 0.09
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (49 bp):
TAATCATAAACTAATTAATAAACTAAGTAATAATAAACTAATTAAATAC
Found at i:23584 original size:20 final size:20
Alignment explanation
Indices: 23559--23601 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
23549 AAAAATTATA
23559 AAAAGGGGACGGTATTTAGC
1 AAAAGGGGACGGTATTTAGC
* *
23579 AAAAGGGGGCGGTGTTTAGC
1 AAAAGGGGACGGTATTTAGC
23599 AAA
1 AAA
23602 CCCCATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.09, G:0.37, T:0.19
Consensus pattern (20 bp):
AAAAGGGGACGGTATTTAGC
Found at i:24326 original size:29 final size:30
Alignment explanation
Indices: 24258--24326 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
24248 GAGTTTTTTA
**
24258 CCAAACTATAACAGTTTAGAAACTTATTTC
1 CCAAACTATAACACATTAGAAACTTATTTC
*
24288 CCAATA-TATAATACATTA-AAACTTATTTC
1 CCAA-ACTATAACACATTAGAAACTTATTTC
24317 CCAAACTATA
1 CCAAACTATA
24327 TCAATTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 1 0.03
29 19 0.56
30 13 0.38
31 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.33
Consensus pattern (30 bp):
CCAAACTATAACACATTAGAAACTTATTTC
Found at i:25476 original size:17 final size:17
Alignment explanation
Indices: 25454--25489 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
25444 AAGCAGCAAC
25454 AAGTCTTACAATATACA
1 AAGTCTTACAATATACA
25471 AAGTCTTACAATATACA
1 AAGTCTTACAATATACA
25488 AA
1 AA
25490 TTACATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (17 bp):
AAGTCTTACAATATACA
Found at i:29557 original size:24 final size:24
Alignment explanation
Indices: 29530--29577 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
29520 ATGTATCATA
29530 TAATCACCCTTTAAAAATTAAATG
1 TAATCACCCTTTAAAAATTAAATG
29554 TAATCACCCTTTAAAAATTAAATG
1 TAATCACCCTTTAAAAATTAAATG
29578 AAGCAAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (24 bp):
TAATCACCCTTTAAAAATTAAATG
Found at i:31005 original size:14 final size:14
Alignment explanation
Indices: 30986--31015 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
30976 AATGATCCTC
30986 ATTATTTCTACTAT
1 ATTATTTCTACTAT
31000 ATTATTTCTACTAT
1 ATTATTTCTACTAT
31014 AT
1 AT
31016 ACTACTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTATTTCTACTAT
Found at i:31602 original size:12 final size:12
Alignment explanation
Indices: 31585--31610 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31575 TACATAATTA
31585 TTGGTGTTTATT
1 TTGGTGTTTATT
31597 TTGGTGTTTATT
1 TTGGTGTTTATT
31609 TT
1 TT
31611 ATCAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.23, T:0.69
Consensus pattern (12 bp):
TTGGTGTTTATT
Found at i:38335 original size:4 final size:4
Alignment explanation
Indices: 38326--38360 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
38316 CATTTGAACA
*
38326 AAAT AAAT AAAT ATAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
38361 AAGTGGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:38948 original size:49 final size:49
Alignment explanation
Indices: 38856--38952 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 49
38846 AATTATACCT
* * *
38856 TTTTTTTAAATTTATTTCTAAATTTCCATTTTTAAAAATTAATATATTAC
1 TTTTTTCAAATATATTTCTAAATTTCCA-TATTAAAAATTAATATATTAC
*
38906 TTTTTTCAAATATATTTCTAAATTTCACA-ATTAAGAATTAATATATT
1 TTTTTTCAAATATATTTCTAAATTTC-CATATTAAAAATTAATATATT
38953 TTTATTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
49 16 0.38
50 24 0.57
51 2 0.05
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (49 bp):
TTTTTTCAAATATATTTCTAAATTTCCATATTAAAAATTAATATATTAC
Found at i:39409 original size:21 final size:21
Alignment explanation
Indices: 39378--39455 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
39368 GGTGTAGTTG
*
39378 AAAATTTCATTAGATGGTAATC
1 AAAA-TTCATTAGAAGGTAATC
* *
39400 AAAATTCATTCGAAGGTTATC
1 AAAATTCATTAGAAGGTAATC
*
39421 AAAATTTTC-GTAGTAAGGTAATC
1 AAAA--TTCATTAG-AAGGTAATC
*
39444 AAAATTCCTTAG
1 AAAATTCATTAG
39456 GGAAGTTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
21 21 0.47
22 9 0.20
23 15 0.33
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (21 bp):
AAAATTCATTAGAAGGTAATC
Found at i:39528 original size:22 final size:23
Alignment explanation
Indices: 39503--39568 Score: 93
Period size: 22 Copynumber: 3.0 Consensus size: 23
39493 ACATAATGTC
* *
39503 GTTATCAAAATTTTATAGA-AAT
1 GTTATCAAAATTTCATAAAGAAT
39525 GTTATCAAAATTTCATAAAGAAT
1 GTTATCAAAATTTCATAAAGAAT
39548 -TTATCAAAATTTCAT-AAGAAT
1 GTTATCAAAATTTCATAAAGAAT
39569 ATTTAAGTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
21 6 0.15
22 32 0.78
23 3 0.07
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (23 bp):
GTTATCAAAATTTCATAAAGAAT
Found at i:39535 original size:11 final size:10
Alignment explanation
Indices: 39504--39559 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 10
39494 CATAATGTCG
39504 TTATCAAAATT
1 TTATCAAAA-T
39515 TTAT-AGAAAT
1 TTATCA-AAAT
39525 GTTATCAAAAT
1 -TTATCAAAAT
*
39536 TTCATAAAGAAT
1 TT-ATCAA-AAT
39548 TTATCAAAAT
1 TTATCAAAAT
39558 TT
1 TT
39560 CATAAGAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 9 0.24
11 23 0.61
12 6 0.16
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (10 bp):
TTATCAAAAT
Found at i:45305 original size:33 final size:33
Alignment explanation
Indices: 45261--45347 Score: 147
Period size: 33 Copynumber: 2.6 Consensus size: 33
45251 ATTAGAAAAA
*
45261 GACAATCGGGTAAGTCCTTTCTACTTTATGTCT
1 GACAATCGGGTAAGTCCTTTCTACTTTATCTCT
* *
45294 GACAATTGGGTAAGTGCTTTCTACTTTATCTCT
1 GACAATCGGGTAAGTCCTTTCTACTTTATCTCT
45327 GACAATCGGGTAAGTCCTTTC
1 GACAATCGGGTAAGTCCTTTC
45348 AAGTGAGTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (33 bp):
GACAATCGGGTAAGTCCTTTCTACTTTATCTCT
Found at i:48205 original size:2 final size:2
Alignment explanation
Indices: 48184--48223 Score: 53
Period size: 2 Copynumber: 19.0 Consensus size: 2
48174 ACTATGTAAA
*
48184 AT AT AA AT AT GAT CAT 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 AT AT
48224 GATGGTAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 30 0.88
3 4 0.12
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:48312 original size:29 final size:29
Alignment explanation
Indices: 48262--48321 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
48252 TAATCATTAA
* *
48262 AATTTCATCTACCAATATACGTGGTACAT
1 AATTCCATCTACCAATAAACGTGGTACAT
** *
48291 AATTCCATCTACTGATAAACGTGTTACAT
1 AATTCCATCTACCAATAAACGTGGTACAT
48320 AA
1 AA
48322 ATCTTTAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (29 bp):
AATTCCATCTACCAATAAACGTGGTACAT
Found at i:55241 original size:32 final size:32
Alignment explanation
Indices: 55205--55273 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
55195 TACATAGGAT
* * **
55205 CAAAAATGCCACATGGCAATGTCACGTCGGAC
1 CAAAAATACCACATAGCAATACCACGTCGGAC
*
55237 CAAAAATACCATATAGCAATACCACGTCGGAC
1 CAAAAATACCACATAGCAATACCACGTCGGAC
55269 CAAAA
1 CAAAA
55274 CACTATGTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.42, C:0.28, G:0.16, T:0.14
Consensus pattern (32 bp):
CAAAAATACCACATAGCAATACCACGTCGGAC
Found at i:56208 original size:16 final size:16
Alignment explanation
Indices: 56187--56220 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
56177 ATTTTATTTT
56187 TGCCTTGTTAGTTGGA
1 TGCCTTGTTAGTTGGA
56203 TGCCTTGTTAGTTGGA
1 TGCCTTGTTAGTTGGA
56219 TG
1 TG
56221 ATTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.32, T:0.44
Consensus pattern (16 bp):
TGCCTTGTTAGTTGGA
Found at i:57268 original size:27 final size:28
Alignment explanation
Indices: 57224--57278 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
57214 TCTCGTTTTC
*
57224 AAAAGTTAAGGGATCAATTTGTCCCAAA
1 AAAAGTTAAGGGAGCAATTTGTCCCAAA
57252 AAAAGTTAAGGG-GCAATTTGTCCCAAA
1 AAAAGTTAAGGGAGCAATTTGTCCCAAA
57279 GTGGATAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.24
Consensus pattern (28 bp):
AAAAGTTAAGGGAGCAATTTGTCCCAAA
Found at i:75989 original size:20 final size:20
Alignment explanation
Indices: 75951--75988 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
75941 GAATTTATAA
75951 ATAACCTTATAATTGTTTTG
1 ATAACCTTATAATTGTTTTG
75971 ATAACC-TATAATTGTTTT
1 ATAACCTTATAATTGTTTT
75989 TTAGTAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (20 bp):
ATAACCTTATAATTGTTTTG
Found at i:79057 original size:2 final size:2
Alignment explanation
Indices: 79050--79084 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
79040 TTAGCTAGTG
79050 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
79085 CAAAGCCTTG
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.