Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007182.1 Corchorus capsularis cultivar CVL-1 contig07203, 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: 30109
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:12168 original size:29 final size:28
Alignment explanation
Indices: 12117--12176 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
12107 AAAACGTCCC
* *
12117 AAATTGAAGTTCAGGAGGTAAAATATCCA
1 AAATTGAAGTTCAGGAGGCAAAACAT-CA
**
12146 AAATTGAAGTTCATTAGGCAAAACATCA
1 AAATTGAAGTTCAGGAGGCAAAACATCA
12174 AAA
1 AAA
12177 CACTACAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (28 bp):
AAATTGAAGTTCAGGAGGCAAAACATCA
Found at i:17001 original size:18 final size:18
Alignment explanation
Indices: 16980--17016 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16970 TGTGGTGGCG
* *
16980 GCGGTTGTGTTGGTGCTT
1 GCGGTGGTGGTGGTGCTT
16998 GCGGTGGTGGTGGTGCTT
1 GCGGTGGTGGTGGTGCTT
17016 G
1 G
17017 TGGCGGTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.51, T:0.38
Consensus pattern (18 bp):
GCGGTGGTGGTGGTGCTT
Found at i:17024 original size:18 final size:18
Alignment explanation
Indices: 16990--17024 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16980 GCGGTTGTGT
*
16990 TGGTGCTTGCGGTGGTGG
1 TGGTGCTTGCGGCGGTGG
*
17008 TGGTGCTTGTGGCGGTG
1 TGGTGCTTGCGGCGGTG
17025 TTGGGGGTTG
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:0.00, C:0.11, G:0.54, T:0.34
Consensus pattern (18 bp):
TGGTGCTTGCGGCGGTGG
Found at i:18702 original size:2 final size:2
Alignment explanation
Indices: 18695--18727 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18685 TCCATTGCAA
18695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18728 GAATCAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19095 original size:5 final size:5
Alignment explanation
Indices: 19085--19120 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
19075 TTAGGGAGAG
19085 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
19121 TCTTGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:21486 original size:32 final size:31
Alignment explanation
Indices: 21422--21488 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 31
21412 AACTTTATGT
*
21422 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
21453 TTTCCAATTGTACCCTT-TTTTTAGAAAACATA
1 TTTCCAATTGTACCCTTATTTTT--AAAACATA
21485 TTTC
1 TTTC
21489 TAAATTACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 5 0.15
31 16 0.48
32 12 0.36
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.46
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:21562 original size:15 final size:15
Alignment explanation
Indices: 21514--21575 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
21504 AAATAATATT
*
21514 TTAATTATTCCATTA
1 TTAATTATTACATTA
*
21529 TT--TT-TTA-ATCA
1 TTAATTATTACATTA
*
21540 TAAATTATTACATTA
1 TTAATTATTACATTA
*
21555 TTAATTATTAAATTA
1 TTAATTATTACATTA
21570 TATAAT
1 T-TAAT
21576 ACGTATATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
11 4 0.11
12 2 0.06
13 4 0.11
14 3 0.08
15 19 0.53
16 4 0.11
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATTATTACATTA
Found at i:22430 original size:22 final size:22
Alignment explanation
Indices: 22402--22577 Score: 101
Period size: 22 Copynumber: 7.7 Consensus size: 22
22392 TGTCTCTATG
22402 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* *
22424 TGGTTATTATATATAATTTCATGAGGA
1 TGGTTA-T-CA-A-AATTTCAT-AAGA
*
22451 -GGTTATCAAAATTCCATATA-A
1 TGGTTATCAAAATTTCATA-AGA
** *
22472 AAGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
22494 TGGTTACCAAAATTTCATATA-A
1 TGGTTATCAAAATTTCATA-AGA
** *
22516 AAGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
22538 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
*
22560 TCAGGTTATTAAAATTTC
1 T--GGTTATCAAAATTTC
22578 TTAGGTTGAT
Statistics
Matches: 115, Mismatches: 23, Indels: 30
0.68 0.14 0.18
Matches are distributed among these distances:
20 2 0.02
21 2 0.02
22 74 0.64
23 3 0.03
24 16 0.14
25 2 0.02
26 13 0.11
27 3 0.03
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:22505 original size:44 final size:44
Alignment explanation
Indices: 22438--22556 Score: 195
Period size: 44 Copynumber: 2.7 Consensus size: 44
22428 TATTATATAT
* * *
22438 AATTTCATGAG-GAGGTTATCAAAATTCCATATAAAAGTTATCAA
1 AATTTCAT-AGTGTGGTTACCAAAATTTCATATAAAAGTTATCAA
22482 AATTTCATAGTGTGGTTACCAAAATTTCATATAAAAGTTATCAA
1 AATTTCATAGTGTGGTTACCAAAATTTCATATAAAAGTTATCAA
22526 AATTTCATAGTGTGGTTACCAAAATTTCATA
1 AATTTCATAGTGTGGTTACCAAAATTTCATA
22557 GGATCAGGTT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
43 2 0.03
44 69 0.97
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (44 bp):
AATTTCATAGTGTGGTTACCAAAATTTCATATAAAAGTTATCAA
Found at i:22573 original size:24 final size:22
Alignment explanation
Indices: 22519--22604 Score: 66
Period size: 22 Copynumber: 3.8 Consensus size: 22
22509 CATATAAAAG
* *
22519 TTATCAAAATTTCATAGTGT-GG
1 TTATTAAAATTTCATAG-GTAGA
** *
22541 TTACCAAAATTTCATAGGATCAGG
1 TTATTAAAATTTCATAGG-T-AGA
* *
22565 TTATTAAAATTTCTTAGGTTGA
1 TTATTAAAATTTCATAGGTAGA
*
22587 TTATTGAAATTTCATAGG
1 TTATTAAAATTTCATAGG
22605 GTGGTTAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.02
22 34 0.64
23 1 0.02
24 17 0.32
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (22 bp):
TTATTAAAATTTCATAGGTAGA
Found at i:22746 original size:22 final size:22
Alignment explanation
Indices: 22647--22996 Score: 135
Period size: 22 Copynumber: 15.7 Consensus size: 22
22637 ATCAAAGAGA
* *
22647 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGGGAGG
*
22669 TTAT-AAGAATTTCATAGGGTGG
1 TTATCAA-AATTTCATAGGGAGG
*
22691 TTAAT-AAAATTTCATTA-GTAGG
1 TT-ATCAAAATTTCA-TAGGGAGG
* *
22713 TTACTC-ATATTTCATGGGGAGG
1 TTA-TCAAAATTTCATAGGGAGG
* * *
22735 TTATCAAAATTTTATATGAAGG
1 TTATCAAAATTTCATAGGGAGG
* *
22757 TTATAAAAGTCTCAATTTCATAAGGA-G
1 TTAT-CAA-----AATTTCATAGGGAGG
* *
22784 -TATCAAAATTTGATA-GAAGG
1 TTATCAAAATTTCATAGGGAGG
* * * *
22804 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGGGAGG
* * * *
22825 TTATCGAAATCTCATAGAGATCAGA
1 TTATCAAAATTTCATAG-G--GAGG
* * *
22850 TTATCGAAATTT-ATAGGAAGA
1 TTATCAAAATTTCATAGGGAGG
* **
22871 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGGGAGG
* *
22893 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGGGAGG
* ** * *
22915 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGGGAGG
* *
22937 TTATCAGAATTTCATAAAGG-GG
1 TTATCAAAATTTCAT-AGGGAGG
* * * **
22959 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGGGAGG
22981 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
22997 AAGAGTTTAT
Statistics
Matches: 246, Mismatches: 59, Indels: 46
0.70 0.17 0.13
Matches are distributed among these distances:
19 2 0.01
20 17 0.07
21 33 0.13
22 149 0.61
23 12 0.05
24 4 0.02
25 15 0.06
26 3 0.01
27 1 0.00
28 10 0.04
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGG
Found at i:22871 original size:21 final size:23
Alignment explanation
Indices: 22823--22887 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 23
22813 CTCATAGAGT
*
22823 GATTATCGAAATCTCATAGAGATCA
1 GATTATCGAAAT-TTATAGAGA-CA
22848 GATTATCGAAATTTATAG-GA-A
1 GATTATCGAAATTTATAGAGACA
*
22869 GATTATCAAAATTTCATAG
1 GATTATCGAAATTT-ATAG
22888 TGTTGTTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
21 14 0.38
22 4 0.11
23 2 0.05
24 5 0.14
25 12 0.32
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (23 bp):
GATTATCGAAATTTATAGAGACA
Found at i:23015 original size:22 final size:22
Alignment explanation
Indices: 22892--23016 Score: 85
Period size: 22 Copynumber: 5.7 Consensus size: 22
22882 TCATAGTGTT
* *
22892 GTTATCAAAATTTCA-AAGCGAG
1 GTTATCAAATTTTCATAA-AGAG
* * * *
22914 GTTATCAAAATTACATAATGTG
1 GTTATCAAATTTTCATAAAGAG
* *
22936 ATTATCAGAA-TTTCATAAAGGG
1 GTTATCA-AATTTTCATAAAGAG
* *
22958 GTCAACAAAATTTT-ATAAAGAG
1 GTTATC-AAATTTTCATAAAGAG
*
22980 GTTATCAAAATTTCATAAAGAG
1 GTTATCAAATTTTCATAAAGAG
* *
23002 TTTATCAATTTTTCA
1 GTTATCAAATTTTCA
23017 AAATGTGATT
Statistics
Matches: 81, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
21 6 0.07
22 67 0.83
23 8 0.10
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
GTTATCAAATTTTCATAAAGAG
Found at i:23083 original size:22 final size:21
Alignment explanation
Indices: 23056--23523 Score: 207
Period size: 22 Copynumber: 21.9 Consensus size: 21
23046 ATTTCTGGGG
23056 AGGTTATCAAAATTTCATAGT
1 AGGTTATCAAAATTTCATAGT
* *
23077 ATGGTTA-CAAAA-TT-A-GGA
1 A-GGTTATCAAAATTTCATAGT
* * *
23095 AGGTTATTAAACTTTTATTA-T
1 AGGTTATCAAAATTTCA-TAGT
* * *
23116 GGAGTAATCAAAATTTCAGAG-
1 AG-GTTATCAAAATTTCATAGT
* * *
23137 AGGATATCAAAATTTCA-GGG
1 AGGTTATCAAAATTTCATAGT
* *
23157 AGGATATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GT
*
23179 AGGTTATCAAAATTTCATAGGG
1 AGGTTATCAAAATTTCATA-GT
* * *
23201 AGATTAACAAAATTTCATAAT
1 AGGTTATCAAAATTTCATAGT
** *
23222 GAGGTTATCAAAAAATCATAGGG
1 -AGGTTATCAAAATTTCATA-GT
23245 AGGTTATCAAAA-TT--T-GT
1 AGGTTATCAAAATTTCATAGT
* *
23262 A-GTTATCAAGATTTCATAAGA
1 AGGTTATCAAAATTTCAT-AGT
* * *
23283 AAGTTATCAAAATTTTATAGGC
1 AGGTTATCAAAATTTCATA-GT
* *
23305 AGGTTTATCAAAATTTTATAGGA
1 AGG-TTATCAAAATTTCATA-GT
*
23328 AGATTTATCAAAATTTCATAG-
1 AG-GTTATCAAAATTTCATAGT
* *
23349 CGAGTTATCACAATTTCATAGT
1 AG-GTTATCAAAATTTCATAGT
*
23371 -GTGATTATCAAAATTTCAGAGT
1 AG-G-TTATCAAAATTTCATAGT
23393 -GTGATTA-CTAACAATTT-ATATGT
1 AG-G-TTATC-AA-AATTTCATA-GT
* * *
23416 AGGTTTTTAAATTTTCATAACGT
1 AGGTTATCAAAATTTCAT-A-GT
* *
23439 -GGTTATCAAAATATCATATGG
1 AGGTTATCAAAATTTCATA-GT
* *
23460 AGGTTATCAACATCTCATAGT
1 AGGTTATCAAAATTTCATAGT
* *
23481 ATTGGTTATCAAAATTTCATTGGG
1 A--GGTTATCAAAATTTCA-TAGT
*
23505 AAGTTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
23524 TTGAGGACTT
Statistics
Matches: 344, Mismatches: 68, Indels: 70
0.71 0.14 0.15
Matches are distributed among these distances:
16 9 0.03
17 9 0.03
18 5 0.01
19 6 0.02
20 33 0.10
21 43 0.12
22 175 0.51
23 60 0.17
24 4 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGT
Found at i:23147 original size:20 final size:20
Alignment explanation
Indices: 23122--23195 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
23112 TTATGGAGTA
23122 ATCAAAATTTCAGAGAGGAT
1 ATCAAAATTTCAGAGAGGAT
*
23142 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAGAGAGGAT
* *
23162 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCAGA-G-AGGAT
23184 ATCAAAATTTCA
1 ATCAAAATTTCA
23196 TAGGGAGATT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 31 0.65
21 1 0.02
22 16 0.33
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (20 bp):
ATCAAAATTTCAGAGAGGAT
Found at i:23214 original size:44 final size:43
Alignment explanation
Indices: 23122--23529 Score: 243
Period size: 44 Copynumber: 9.4 Consensus size: 43
23112 TTATGGAGTA
* *
23122 ATCAAAATTTCAGA-GAGGATATCAAAATTTC--AGGGAGGA-T
1 ATCAAAATTTCATATGAGGTTATCAAAATTTCATAGGGA-GATT
23162 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATG-AGGTTATCAAAATTTCATAGGGAGATT
* ** *
23206 AACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCAT-ATGAGGTTATCAAAATTTCATAGGGAGATT
* * * *
23250 ATCAAAA-TT--TGT-A-GTTATCAAGATTTCATA-AGAAAGTT
1 ATCAAAATTTCATATGAGGTTATCAAAATTTCATAGGGAGA-TT
* * * *
23288 ATCAAAATTTTATAGGCAGGTTTATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATATG-AGG-TTATCAAAATTTCATAGGGAGA-TT
* * * *
23334 ATCAAAATTTCATA-GCGAGTTATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATATGAG-GTTATCAAAATTTCATAGGGAGATT
* * * * * *
23377 ATCAAAATTTCAGAGTGTGATTA-CTAACAATTT-ATATGTAGGTT
1 ATCAAAATTTCATA-TGAGGTTATC-AA-AATTTCATAGGGAGATT
* * * * * * * *
23421 TTTAAATTTTCATAACGTGGTTATCAAAATATCATATGGAGGTT
1 ATCAAAATTTCAT-ATGAGGTTATCAAAATTTCATAGGGAGATT
* * *
23465 ATCAACATCTCATA-GTATTGGTTATCAAAATTTCATTGGGA-AGTT
1 ATCAAAATTTCATATG-A--GGTTATCAAAATTTCATAGGGAGA-TT
23510 ATCAAAATTTCATATTGAGG
1 ATCAAAATTTCATA-TGAGG
23530 ACTTCAAAAT
Statistics
Matches: 281, Mismatches: 58, Indels: 54
0.72 0.15 0.14
Matches are distributed among these distances:
37 2 0.01
38 23 0.08
39 3 0.01
40 14 0.05
41 3 0.01
42 16 0.06
43 26 0.09
44 114 0.41
45 61 0.22
46 18 0.06
47 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (43 bp):
ATCAAAATTTCATATGAGGTTATCAAAATTTCATAGGGAGATT
Found at i:23316 original size:23 final size:23
Alignment explanation
Indices: 23264--23348 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
23254 AAATTTGTAG
* * * *
23264 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* *
23286 TTATCAAAATTTTATAGGCAGGT
1 TTATCAAAATTTTATAGGAAGAT
23309 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
*
23332 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
23349 CGAGTTATCA
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:23511 original size:45 final size:45
Alignment explanation
Indices: 23438--23523 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
23428 TTTCATAACG
* *
23438 TGGTTATCAAAATATCATATGGAGGTTATCAACATCTCATAGTAT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTAT
* *
23483 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
23524 TTGAGGACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 1 0.03
45 35 0.97
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTAT
Found at i:23580 original size:22 final size:22
Alignment explanation
Indices: 23552--23600 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
23542 CTTAGGGATC
* * *
23552 AGGTTAACAATATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAAA
*
23574 AGGTTAAAAAAATTTTATAAAA
1 AGGTTAAAAAAATTTCATAAAA
23596 AGGTT
1 AGGTT
23601 CTCGAAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAAA
Found at i:29529 original size:23 final size:23
Alignment explanation
Indices: 29498--29582 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
29488 GATAACCTCG
*
29498 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
*
29521 CTATAAAATTTTGATAAA-CCTC
1 CTATAAAATTTTGATAAATCTTC
29543 CTTATAAAATTTTGATAAAT-TTC
1 C-TATAAAATTTTGATAAATCTTC
* * *
29566 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
29583 CTACAAATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
22 18 0.33
23 36 0.67
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:29581 original size:45 final size:45
Alignment explanation
Indices: 29459--29582 Score: 132
Period size: 45 Copynumber: 2.8 Consensus size: 45
29449 TCACACTCTG
* *
29459 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCGCTATA
*
29503 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTC-CTTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCGC-TATA
*
29549 AAATTTTGATAAAT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
29583 CTACAAATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
44 11 0.16
45 32 0.46
46 26 0.38
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCGCTATA
Found at i:29675 original size:44 final size:44
Alignment explanation
Indices: 29323--29751 Score: 208
Period size: 44 Copynumber: 9.8 Consensus size: 44
29313 AAGACCTCAA
* * *
29323 TATGAAATTTTGATAACTTCCCAATGAAATTTTTATAACCA-ACAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-CATA-AC
* * ** * *
29368 TATGAGATGTTGATAACCTCCAAATGATATATTGATAAC--AAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATAAC
* * * *
29410 GTTATGAAAATTT-AAAACCTCCATATG-AATTGTT-AGTAATCA-CAC
1 --TATGAAATTTTGATAACCTCCCTATGAAATT-TTGA-TAA-CATAAC
* * * * * * **
29455 TCTGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATAAC
* * * * *
29499 TATGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCT-CC
1 TATGAAATTTTGAT-AACCTCCCTATGAAATTTTGAT-AACATAAC
* ** * * *
29544 TTATAAAATTTTGATAAATTTCTTATGAAATCTTGATAAC-T-AC
1 -TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATAAC
** * *
29587 ----AAATTTTGATAACCTCCCTATGATTTTTTGATAACTTAAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATAAC
* * *
29627 TATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGAT-AACATAAC
* * *
29671 TATGAAATTTTGATAACC-CTCTTGTGAAATTTTGAAAAC-TAAAC
1 TATGAAATTTTGATAACCTC-CCTATGAAATTTTGATAACAT-AAC
* * * *
29715 TATTAAATTTTGATAACCTTCATATGAAGTTTTGATA
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATA
29752 TCCTCCCTGA
Statistics
Matches: 294, Mismatches: 66, Indels: 49
0.72 0.16 0.12
Matches are distributed among these distances:
38 28 0.10
39 1 0.00
40 1 0.00
42 6 0.02
43 33 0.11
44 131 0.45
45 76 0.26
46 18 0.06
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATAAC
Found at i:29747 original size:22 final size:22
Alignment explanation
Indices: 29192--29751 Score: 151
Period size: 22 Copynumber: 25.7 Consensus size: 22
29182 ATGACCCCAT
29192 TATGAAATTTTGATAACCTTTC-
1 TATGAAATTTTGATAACC-TTCA
* **
29214 TATGAAATTTTAATAA-CGACA
1 TATGAAATTTTGATAACCTTCA
* * * **
29235 CTATGGAATTTCGAGAACCTTTT
1 -TATGAAATTTTGATAACCTTCA
* ** *
29258 TAT-AATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCA
** * * *
29279 TATGAAATTCGGTTAACCTCCT
1 TATGAAATTTTGATAACCTTCA
* *
29301 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-A
29323 TATGAAATTTTGATAA-CTTCCCA
1 TATGAAATTTTGATAACCTT--CA
* **
29346 -ATGAAATTTTTATAACCAACA
1 TATGAAATTTTGATAACCTTCA
* * *
29367 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTTCA
* * * *
29390 AATGATATATTGATAACAACGT--
1 TATGAAATTTTGATAAC--CTTCA
* * *
29412 TATGAAAATTT-AAAACCTCCA
1 TATGAAATTTTGATAACCTTCA
* *
29433 TATG-AATTGTT-AGTAATC-ACA
1 TATGAAATT-TTGA-TAACCTTCA
* * *
29454 CTCTGAAATTTTGATAATC-ACA
1 -TATGAAATTTTGATAACCTTCA
* *
29476 CTATGAAATTGTGATAACC-TCGC
1 -TATGAAATTTTGATAACCTTC-A
* *
29499 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCA
* * *
29522 TATAAAATTTTGATAAACCTCCT
1 TATGAAATTTTGAT-AACCTTCA
* ** *
29545 TATAAAATTTTGATAAATTTCT
1 TATGAAATTTTGATAACCTTCA
*
29567 TATGAAATCTTGATAA----C-
1 TATGAAATTTTGATAACCTTCA
* * *
29584 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCA
** *
29605 TATGATTTTTTGATAA-CTTAA
1 TATGAAATTTTGATAACCTTCA
* * * *
29626 TTATGAAATTTTGTTAATCTCCC
1 -TATGAAATTTTGATAACCTTCA
* * *
29649 TATGAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTTCA
* *
29671 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCA
* * **
29693 TGTGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTTCA
*
29714 CTATTAAATTTTGATAACCTTCA
1 -TATGAAATTTTGATAACCTTCA
*
29737 TATGAAGTTTTGATA
1 TATGAAATTTTGATA
29752 TCCTCCCTGA
Statistics
Matches: 392, Mismatches: 109, Indels: 74
0.68 0.19 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
19 1 0.00
20 5 0.01
21 43 0.11
22 253 0.65
23 72 0.18
24 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:29900 original size:22 final size:22
Alignment explanation
Indices: 29875--29926 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
29865 TAATCACATT
*
29875 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTAATAACCTCTTTA
*
29897 TGAAATTTTAATAACCTCTTTA
1 TGAAAATTTAATAACCTCTTTA
29919 T-AAAATTT
1 TGAAAATTT
29927 TGTTGACCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (22 bp):
TGAAAATTTAATAACCTCTTTA
Found at i:30073 original size:22 final size:23
Alignment explanation
Indices: 30044--30098 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
30034 AAATTGAGAC
* *
30044 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACCTACACTATAAAA
30065 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
*
30087 TTTCGATAACCT
1 TTTTGATAACCT
30099 CCCCATGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:30109 original size:22 final size:22
Alignment explanation
Indices: 30059--30109 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
30049 TAACCTTCAT
* *
30059 ATGAAATTTTGATAACCACACT
1 ATGAAATTTCGATAACCACACC
* * *
30081 ATAAAATTTCGATAACCTCCCC
1 ATGAAATTTCGATAACCACACC
30103 ATGAAAT
1 ATGAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (22 bp):
ATGAAATTTCGATAACCACACC
Done.