Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013910.1 Corchorus capsularis cultivar CVL-1 contig13931, 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: 78041
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1348 original size:13 final size:13
Alignment explanation
Indices: 1327--1371 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1317 AATTATTGTT
1327 TGCTTTATTAATC
1 TGCTTTATTAATC
* * *
1340 TGTTTTATTGATT
1 TGCTTTATTAATC
1353 TGCTTTA-TAATC
1 TGCTTTATTAATC
1365 TGCTTTA
1 TGCTTTA
1372 GATTTAGATT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.58
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:1363 original size:25 final size:25
Alignment explanation
Indices: 1319--1371 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
1309 TGCTTTATAA
*
1319 TTATTGTTTGCTTTATTAATCTGTT
1 TTATTGTTTGCTTTATTAATCTGCT
1344 TTATTGATTTGCTTTA-TAATCTGCT
1 TTATTG-TTTGCTTTATTAATCTGCT
1369 TTA
1 TTA
1372 GATTTAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.19, C:0.09, G:0.11, T:0.60
Consensus pattern (25 bp):
TTATTGTTTGCTTTATTAATCTGCT
Found at i:1443 original size:14 final size:15
Alignment explanation
Indices: 1415--1447 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1405 ATTTTTAGTT
*
1415 TAATTGTTTTCTTCA
1 TAATTGTTATCTTCA
1430 TAATTGTTAT-TTCA
1 TAATTGTTATCTTCA
1444 TAAT
1 TAAT
1448 CCCTGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (15 bp):
TAATTGTTATCTTCA
Found at i:3107 original size:42 final size:42
Alignment explanation
Indices: 3059--3145 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
3049 ACGCATGGGA
* *
3059 CATCGCACGGGGCATCGCACAAGCCTTCCGGCCACAACCGGC
1 CATCGCACGGGCCATCGCACAAGCCATCCGGCCACAACCGGC
**
3101 CATCGCACGGGCCATCGCACGGGCCATCCGGCCACAACCGGC
1 CATCGCACGGGCCATCGCACAAGCCATCCGGCCACAACCGGC
3143 CAT
1 CAT
3146 TCGATCCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.21, C:0.44, G:0.26, T:0.09
Consensus pattern (42 bp):
CATCGCACGGGCCATCGCACAAGCCATCCGGCCACAACCGGC
Found at i:3115 original size:12 final size:12
Alignment explanation
Indices: 3098--3128 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3088 GGCCACAACC
3098 GGCCATCGCACG
1 GGCCATCGCACG
3110 GGCCATCGCACG
1 GGCCATCGCACG
3122 GGCCATC
1 GGCCATC
3129 CGGCCACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.42, G:0.32, T:0.10
Consensus pattern (12 bp):
GGCCATCGCACG
Found at i:10893 original size:15 final size:15
Alignment explanation
Indices: 10868--10915 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
10858 GTTGAAACTC
*
10868 GCTGCTAGGAAGCTT
1 GCTGCCAGGAAGCTT
** *
10883 GCTGCGGGGAAGCTC
1 GCTGCCAGGAAGCTT
*
10898 ACTGCCAGGAAGCTT
1 GCTGCCAGGAAGCTT
10913 GCT
1 GCT
10916 AACGCTCGCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (15 bp):
GCTGCCAGGAAGCTT
Found at i:13454 original size:12 final size:13
Alignment explanation
Indices: 13425--13477 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
13415 CATTCATTAT
*
13425 ATTATATATAAAAT
1 ATTA-ATATAAAAA
13439 ATTAATA-AAAAA
1 ATTAATATAAAAA
* *
13451 ATTAGTATGAAAA
1 ATTAATATAAAAA
*
13464 ATTAATCTAAAAA
1 ATTAATATAAAAA
13477 A
1 A
13478 CTAAAGAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
12 10 0.31
13 18 0.56
14 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (13 bp):
ATTAATATAAAAA
Found at i:13579 original size:27 final size:25
Alignment explanation
Indices: 13544--13593 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
13534 TTTATATTTT
13544 TTTTCAATATTATAATATATATAATTAA
1 TTTTCAATATTA-AATA-AT-TAATTAA
13572 TTTT-AATATTAAATAATTAATT
1 TTTTCAATATTAAATAATTAATT
13594 TAATGATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.23
25 2 0.09
26 4 0.18
27 7 0.32
28 4 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTCAATATTAAATAATTAATTAA
Found at i:13580 original size:19 final size:18
Alignment explanation
Indices: 13556--13610 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
13546 TTCAATATTA
13556 TAATATATATAATTAATTT
1 TAATATATATAATTAA-TT
*
13575 TAATATTAAATAATTAATT
1 TAATA-TATATAATTAATT
*
13594 TAATGATATTTAATTAA
1 TAAT-ATATATAATTAA
13611 ATTATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TAATATATATAATTAATT
Found at i:17271 original size:130 final size:130
Alignment explanation
Indices: 17038--17298 Score: 522
Period size: 130 Copynumber: 2.0 Consensus size: 130
17028 CTCTAGGAAA
17038 AATATTTAGTAATGTTGAAGTTTTATCGATATGATCAAAGATTCTGGATCAACTAATTAAAATCT
1 AATATTTAGTAATGTTGAAGTTTTATCGATATGATCAAAGATTCTGGATCAACTAATTAAAATCT
17103 TATGTGCATAATGCATATGAAAAAAATATTAAATTCATAATTTTTAAAAATATTAACCATAAATT
66 TATGTGCATAATGCATATGAAAAAAATATTAAATTCATAATTTTTAAAAATATTAACCATAAATT
17168 AATATTTAGTAATGTTGAAGTTTTATCGATATGATCAAAGATTCTGGATCAACTAATTAAAATCT
1 AATATTTAGTAATGTTGAAGTTTTATCGATATGATCAAAGATTCTGGATCAACTAATTAAAATCT
17233 TATGTGCATAATGCATATGAAAAAAATATTAAATTCATAATTTTTAAAAATATTAACCATAAATT
66 TATGTGCATAATGCATATGAAAAAAATATTAAATTCATAATTTTTAAAAATATTAACCATAAATT
17298 A
1 A
17299 TTTATAAAAA
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 131 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (130 bp):
AATATTTAGTAATGTTGAAGTTTTATCGATATGATCAAAGATTCTGGATCAACTAATTAAAATCT
TATGTGCATAATGCATATGAAAAAAATATTAAATTCATAATTTTTAAAAATATTAACCATAAATT
Found at i:17511 original size:20 final size:21
Alignment explanation
Indices: 17488--17530 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
17478 TAACCGTGTC
*
17488 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
17508 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
17529 AA
1 AA
17531 TTAACGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:17905 original size:12 final size:12
Alignment explanation
Indices: 17888--17918 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
17878 TACCCTATTT
17888 AAACACGACACG
1 AAACACGACACG
17900 AAACACGACACG
1 AAACACGACACG
17912 AAACACG
1 AAACACG
17919 GATTGTGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:19687 original size:435 final size:434
Alignment explanation
Indices: 18834--19728 Score: 1036
Period size: 435 Copynumber: 2.1 Consensus size: 434
18824 TCATGAATTT
* * * *
18834 CCTTAATTGGACAAATAGAACAAAGAAAAAAAAACTGAAGTGTTAAATTGAGTAAGATAAATTTT
1 CCTTAATCGGACAAATAGAACAAA-AAAAAAAAACTGAAGCGTTAAATTGAGTAAGATAAAATTA
* * * * * *
18899 GTAAAGGACTAAGTAGTGATAAGTAGAAAAGTTTGAGGGTCATCTGTTAGATAATCCAAATAAGA
65 GTAAAGGACTAAATAGTGATAAGTAGAAAAATATGAGAGTCATCTGATAAATAATCCAAATAAGA
* * * * * *
18964 AAATGTGTGTTGATAGATATCTTGAAACATACAAATTTCCTTCTGAACCTTTCATGAAACTTGTA
130 AAATATGTGTTGACAGAGATCTTGAAACATAAAAATTTCCTTCTGAACCTTTAATGAAACTCGTA
* * * **
19029 GATCAAATTTAGTTTTCGGGTACTTCATGAAAGTTGTAGATCACACAATAACCTTTTAACCGACA
195 GATCAAATTTAGCTTTCAGGTACTTCACGAAAGTCATAGATCACACAATAACCTTTTAACCGACA
* * * * * *
19094 CTTAAATAACTTTAATTGGACATGTGGATCCAAAATTATATAGTATTGAATAGATCGGCAATCGA
260 CTTAAATAACATTAATCGGACATGTGGATCCAAAATAATATAGTATTAAATAGACCGGCAATCAA
* * * *
19159 AAACACATAATTTTGTAAGCATTTTTTTAATTGAAACATAAAAATTGAATTTTGAGTCCTTCATG
325 AAACACATAATTTCGGAAGCATTTTTTGAATTGAAACATAAAAATTGAATTTTGAGTCCTTCACG
* * *
19224 GAAGTTGGAGATCATGAAATCACCTTTTAATAGACCACCTGAATCA
390 AAAGTTGGAAATCATGAAATCACCTTTTAATAGA-CACCTAAATCA
* * ** *
19270 CCTTGATCGGACAAATAAAACAAAAAAAATAAAGTTGAAGCG-TAAATTGATTAAGATAAAATTA
1 CCTTAATCGGACAAATAGAACAAAAAAAA-AAAACTGAAGCGTTAAATTGAGTAAGATAAAATTA
* * * * *
19334 GTAAATGACTAAATA-TTATAAAGTATAAAAATATGAGAGTCATTTGATAAATAATTCAAATAAG
65 GTAAAGGACTAAATAGTGAT-AAGTAGAAAAATATGAGAGTCATCTGATAAATAATCCAAATAAG
* * * *
19398 AAAATATTTGTTGACGGAGATTTTGAAACATAAAAA-TTCTCTTTTGAA-CTCTTAATGAAACTC
129 AAAATATGTGTTGACAGAGATCTTGAAACATAAAAATTTC-CTTCTGAACCT-TTAATGAAACTC
* * * **
19461 GT-GATCAAATTTAGCTTTCAGGTTCTTCACGAATGTCATAGATGATGCAATAACCTTTTAACCG
192 GTAGATCAAATTTAGCTTTCAGGTACTTCACGAAAGTCATAGATCACACAATAACCTTTTAACCG
* * *
19525 ACACTTCAATAACATTAATCGGACATGTGGA-CTGAAAATAATAT-GATATTAAATAGACCGGTA
257 ACACTTAAATAACATTAATCGGACATGTGGATC-CAAAATAATATAG-TATTAAATAGACCGGCA
* **
19588 AT-AAAAATCACCA-AATTTCGGAAGTATTTTTTGGAATTGAAACATAAAAATTGGTTTTTGAGT
320 ATCAAAAA-CA-CATAATTTCGGAAGCATTTTTT-GAATTGAAACATAAAAATTGAATTTTGAGT
* * * *
19651 TCTTTACGAAAGTTGTAAATCATGAAATTACCTTTTAATAGACACCTAAATCA
382 CCTTCACGAAAGTTGGAAATCATGAAATCACCTTTTAATAGACACCTAAATCA
* *
19704 CTTTAATCGAACAAATAGAA-AAAAA
1 CCTTAATCGGACAAATAGAACAAAAA
19729 TATTAAAAAC
Statistics
Matches: 383, Mismatches: 67, Indels: 21
0.81 0.14 0.04
Matches are distributed among these distances:
433 11 0.03
434 157 0.41
435 185 0.48
436 30 0.08
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.31
Consensus pattern (434 bp):
CCTTAATCGGACAAATAGAACAAAAAAAAAAAACTGAAGCGTTAAATTGAGTAAGATAAAATTAG
TAAAGGACTAAATAGTGATAAGTAGAAAAATATGAGAGTCATCTGATAAATAATCCAAATAAGAA
AATATGTGTTGACAGAGATCTTGAAACATAAAAATTTCCTTCTGAACCTTTAATGAAACTCGTAG
ATCAAATTTAGCTTTCAGGTACTTCACGAAAGTCATAGATCACACAATAACCTTTTAACCGACAC
TTAAATAACATTAATCGGACATGTGGATCCAAAATAATATAGTATTAAATAGACCGGCAATCAAA
AACACATAATTTCGGAAGCATTTTTTGAATTGAAACATAAAAATTGAATTTTGAGTCCTTCACGA
AAGTTGGAAATCATGAAATCACCTTTTAATAGACACCTAAATCA
Found at i:25817 original size:29 final size:27
Alignment explanation
Indices: 25772--25825 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
25762 GTCCCTCTTA
*
25772 AAAAGAAAAAAATGAGTGTTAGTAACCTC
1 AAAAGAAAAAAA-G-GAGTTAGTAACCTC
*
25801 AAAAGAAAAAAGGGAGTTAGTAACC
1 AAAAGAAAAAAAGGAGTTAGTAACC
25826 CCTAAATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 1 0.04
29 11 0.48
ACGTcount: A:0.54, C:0.09, G:0.20, T:0.17
Consensus pattern (27 bp):
AAAAGAAAAAAAGGAGTTAGTAACCTC
Found at i:29717 original size:26 final size:27
Alignment explanation
Indices: 29648--29721 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 27
29638 AAAAGTGGAT
*
29648 TGAAAACGACCAAAATGCCCCTGAATG
1 TGAAAATGACCAAAATGCCCCTGAATG
* * *
29675 TGCAAATGACCAGAATGCCCCT-AGTG
1 TGAAAATGACCAAAATGCCCCTGAATG
29701 T-AAAGATGACCAAAATGCCCC
1 TGAAA-ATGACCAAAATGCCCC
29722 CTAGGTGACC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 2 0.05
26 19 0.47
27 19 0.47
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (27 bp):
TGAAAATGACCAAAATGCCCCTGAATG
Found at i:29722 original size:27 final size:26
Alignment explanation
Indices: 29648--29729 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 26
29638 AAAAGTGGAT
* *
29648 TGAAAACGACCAAAATGCCCCTGAATG
1 TGAAAATGACCAAAATGCCCCT-AGTG
* *
29675 TGCAAATGACCAGAATGCCCCTAGTG
1 TGAAAATGACCAAAATGCCCCTAGTG
29701 T-AAAGATGACCAAAATGCCCCCTAG-G
1 TGAAA-ATGACCAAAATG-CCCCTAGTG
29727 TGA
1 TGA
29730 CCCTAATGCC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
25 2 0.04
26 17 0.37
27 27 0.59
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.17
Consensus pattern (26 bp):
TGAAAATGACCAAAATGCCCCTAGTG
Found at i:33109 original size:22 final size:22
Alignment explanation
Indices: 33070--33111 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
33060 CGATTCTGTT
* *
33070 TCAACCTTTATGGAGGTCAACG
1 TCAACCTTCAAGGAGGTCAACG
*
33092 TCAACCTTCAAGGGGGTCAA
1 TCAACCTTCAAGGAGGTCAA
33112 ATCAGAAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (22 bp):
TCAACCTTCAAGGAGGTCAACG
Found at i:39157 original size:29 final size:27
Alignment explanation
Indices: 39100--39151 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
39090 ATGATTTAGG
* *
39100 GGTTACTAACTCCCTTTTTTCTTTTGA
1 GGTTACTAACACCATTTTTTCTTTTGA
39127 GGTTACTAACACTCATTTTTT-TTTT
1 GGTTACTAACAC-CATTTTTTCTTTT
39152 CAGAGGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.54
Consensus pattern (27 bp):
GGTTACTAACACCATTTTTTCTTTTGA
Found at i:40692 original size:21 final size:21
Alignment explanation
Indices: 40645--40695 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
40635 ATGCTTGGTA
40645 CCTGGGTGCTCAGGCCTATGG
1 CCTGGGTGCTCAGGCCTATGG
** * * *
40666 GTTGGGTGTTCAGGCTTTTGG
1 CCTGGGTGCTCAGGCCTATGG
40687 CCTGGGTGC
1 CCTGGGTGC
40696 CCTACTAGAG
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.06, C:0.22, G:0.41, T:0.31
Consensus pattern (21 bp):
CCTGGGTGCTCAGGCCTATGG
Found at i:49617 original size:2 final size:2
Alignment explanation
Indices: 49610--49642 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49600 TTGTCCTCCT
49610 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 T
49643 TGTTGTGGTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54707 original size:72 final size:72
Alignment explanation
Indices: 54584--54859 Score: 342
Period size: 72 Copynumber: 3.8 Consensus size: 72
54574 GTACTAGCAT
* * * *
54584 GGATTGTGCGAAGGACTGCC-AATGTAGGAACTGCCTCGACTACAGTCGCAATGAGGAAGATTAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTACCTCGGCTACAATCGCAATGAGGAAGATTAT
**
54648 CACATAA
66 CATGTAA
** *
54655 GGATTGTGCGAAGGACTGCCAAACATGGGAACTACCTCGGCTACAACCGCAAT-ATGGAAGATTA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTACCTCGGCTACAATCGCAATGA-GGAAGATTA
*
54719 TCATGGAA
65 TCATGTAA
* * * *
54727 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTACCTCGGTTACAATCGCAATAAAGG-TGATGA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTACCTCGGCTACAATCGCAAT-GAGGAAGATTA
54791 TCATGTAA
65 TCATGTAA
* * * * *
54799 GGATTATGCGAAGGGCTGCCAAATGTGGGAACTACCTCGGCTAAAATCACAATGAAGAAGA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTACCTCGGCTACAATCGCAATGAGGAAGA
54860 AGACCATGGG
Statistics
Matches: 175, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
71 23 0.13
72 149 0.85
73 2 0.01
74 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (72 bp):
GGATTGTGCGAAGGACTGCCAAATGTGGGAACTACCTCGGCTACAATCGCAATGAGGAAGATTAT
CATGTAA
Found at i:59596 original size:2 final size:2
Alignment explanation
Indices: 59589--59631 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
59579 CAGACATAAG
* * *
59589 TA TA TA TA TA CA TA TA CA TA CA 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
59631 T
1 T
59632 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:67323 original size:15 final size:15
Alignment explanation
Indices: 67303--67333 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
67293 TTTTATTTCT
67303 TTTCAAATAAGTCCC
1 TTTCAAATAAGTCCC
*
67318 TTTCAATTAAGTCCC
1 TTTCAAATAAGTCCC
67333 T
1 T
67334 GAAACGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (15 bp):
TTTCAAATAAGTCCC
Found at i:69791 original size:35 final size:35
Alignment explanation
Indices: 69745--69823 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
69735 CCTTTCTCTC
*
69745 TTTCCGTGATTTAAGCCTCTAAAACTCTCATCTAG
1 TTTCCGCGATTTAAGCCTCTAAAACTCTCATCTAG
* *
69780 TTTCCGCGATTTAAGCCTCTAAATCTCTCATCTGG
1 TTTCCGCGATTTAAGCCTCTAAAACTCTCATCTAG
*
69815 TTTCTGCGA
1 TTTCCGCGA
69824 AAATCTCTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.38
Consensus pattern (35 bp):
TTTCCGCGATTTAAGCCTCTAAAACTCTCATCTAG
Found at i:72466 original size:2 final size:2
Alignment explanation
Indices: 72459--72500 Score: 59
Period size: 2 Copynumber: 20.5 Consensus size: 2
72449 AATTTCTAAG
72459 AT AT AT AT GAT GAT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT -AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
72501 AATTAAACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.84
3 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:72689 original size:5 final size:5
Alignment explanation
Indices: 72678--72710 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
72668 AAGAGAAATG
72678 GAAAA -AAAA -AAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
72711 AAGATATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:72981 original size:2 final size:2
Alignment explanation
Indices: 72974--72999 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
72964 CCTGCCCCAA
72974 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
73000 ACATTCACAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:75048 original size:20 final size:18
Alignment explanation
Indices: 75023--75060 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
75013 ATATATATAG
75023 TCTTTTCTTTCTAGTTTTTT
1 TCTTTTCTTT-T-GTTTTTT
75043 TCTTTTCTTTTGTTTTTT
1 TCTTTTCTTTTGTTTTTT
75061 ATTTTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 10 0.56
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (18 bp):
TCTTTTCTTTTGTTTTTT
Done.