Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012825.1 Corchorus olitorius cultivar O-4 contig12858, 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: 118067
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:204 original size:17 final size:17
Alignment explanation
Indices: 178--211 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
168 TAATCTTATT
*
178 TAATATTTATTCATATA
1 TAATAATTATTCATATA
195 TAATAATTATTCATATA
1 TAATAATTATTCATATA
212 ATGAAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATAATTATTCATATA
Found at i:535 original size:3 final size:3
Alignment explanation
Indices: 527--604 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
517 TCGGTTATGC
527 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
575 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
605 CTAATGGGGA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1257 original size:23 final size:25
Alignment explanation
Indices: 1227--1288 Score: 92
Period size: 23 Copynumber: 2.5 Consensus size: 25
1217 CTCTCCTGTT
1227 AAATTGACAGCTTTTTTTT-CCAC-
1 AAATTGACAGCTTTTTTTTGCCACA
*
1250 AAATTGACATCTTTTTTTTTGCCACA
1 AAATTGACAGC-TTTTTTTTGCCACA
1276 AAATTGACAGCTT
1 AAATTGACAGCTT
1289 AATAAACCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 10 0.29
24 8 0.24
25 6 0.18
26 10 0.29
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (25 bp):
AAATTGACAGCTTTTTTTTGCCACA
Found at i:8182 original size:13 final size:13
Alignment explanation
Indices: 8164--8190 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8154 CTACTATACT
8164 ATATATATGATAG
1 ATATATATGATAG
8177 ATATATATGATAG
1 ATATATATGATAG
8190 A
1 A
8191 ATTGGGTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (13 bp):
ATATATATGATAG
Found at i:10975 original size:29 final size:31
Alignment explanation
Indices: 10943--11009 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
10933 ATGCAATTTG
10943 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
*
10972 GGATATAACGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
11003 GGATATA
1 GGATATA
11010 GTCCGTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:11165 original size:31 final size:31
Alignment explanation
Indices: 11130--11208 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
11120 CTAACTGATT
**
11130 ATATCCTTAATTGCTTGAAATCGAAAACCTC
1 ATATCCTTAATTGCTTGAAATAAAAAACCTC
* *
11161 ATATCCTTAATTGCTTGAAATAAAAAACGTT
1 ATATCCTTAATTGCTTGAAATAAAAAACCTC
11192 ATATCCTTAATTGCTTG
1 ATATCCTTAATTGCTTG
11209 TTTTGTAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATAAAAAACCTC
Found at i:11257 original size:31 final size:29
Alignment explanation
Indices: 11185--11264 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
11175 TTGAAATAAA
***
11185 AAACGTTATATCCTTAATTGCTTGTTTTG
1 AAACGTTATATCCTTAATTGCTTGTGCAG
*
11214 TAACGTTATATCCTTAATTGCTTGTGGCAG
1 AAACGTTATATCCTTAATTGCTTGT-GCAG
* *
11244 CAAACATTATATCCTAAATTG
1 -AAACGTTATATCCTTAATTG
11265 ATTATTTGGC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 24 0.57
30 1 0.02
31 17 0.40
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (29 bp):
AAACGTTATATCCTTAATTGCTTGTGCAG
Found at i:12103 original size:16 final size:16
Alignment explanation
Indices: 12084--12114 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12074 ATATTCTAAG
12084 AATACATTTTTCTACT
1 AATACATTTTTCTACT
12100 AATACATTTTTCTAC
1 AATACATTTTTCTAC
12115 CAAGCAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (16 bp):
AATACATTTTTCTACT
Found at i:12211 original size:15 final size:17
Alignment explanation
Indices: 12186--12218 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12176 TAAAAAGTTA
12186 TTTAAATAAAA-TATTT
1 TTTAAATAAAATTATTT
12202 TTTAAA-AAAATTATTT
1 TTTAAATAAAATTATTT
12218 T
1 T
12219 CTTCTGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAATAAAATTATTT
Found at i:12286 original size:31 final size:31
Alignment explanation
Indices: 12249--12390 Score: 142
Period size: 31 Copynumber: 4.6 Consensus size: 31
12239 AGATGATAAG
* ***
12249 CAAGCAATTTAGGATATAACGTTTTCTGCCA
1 CAAGCAATTAAGGATATAACGTTTTCTAAAA
*
12280 CAAGCAATTAAGGATATAACG-TTACTAAAA
1 CAAGCAATTAAGGATATAACGTTTTCTAAAA
* * ***
12310 CAAGCAATTAAGGATATAACATTTTTTATTT
1 CAAGCAATTAAGGATATAACGTTTTCTAAAA
* * ***
12341 CAAGCAATTAAGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCTAAAA
12372 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
12391 TCAGTTAGGG
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
30 25 0.27
31 69 0.73
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCTAAAA
Found at i:12555 original size:31 final size:29
Alignment explanation
Indices: 12520--12585 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 29
12510 CCTAACGGAC
*
12520 TATATCCTTGATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCG-TTTT-GTAACGT
*
12551 TATATCCTTAATTGCTTGTTTTGTAACGT
1 TATATCCTTAATTGCTCGTTTTGTAACGT
12580 TATATC
1 TATATC
12586 TCAAATTGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 13 0.39
30 4 0.12
31 16 0.48
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (29 bp):
TATATCCTTAATTGCTCGTTTTGTAACGT
Found at i:12592 original size:29 final size:31
Alignment explanation
Indices: 12520--12594 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 31
12510 CCTAACGGAC
**
12520 TATATCCTTGATTGCTCGCTTTTCGTAACGT
1 TATATCCTAAATTGCTCGCTTTTCGTAACGT
* *
12551 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTAAATTGCTCGCTTTTCGTAACGT
12580 TATAT-CTCAAATTGC
1 TATATCCT-AAATTGC
12595 ATTTTGCAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.05
29 18 0.45
30 4 0.10
31 16 0.40
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (31 bp):
TATATCCTAAATTGCTCGCTTTTCGTAACGT
Found at i:14871 original size:40 final size:40
Alignment explanation
Indices: 14826--14906 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
14816 AGCAGCCCAT
*
14826 TGGGCTGATCTAGATCTGAAACTGTAAGAAGCCCAAATTA
1 TGGGCTGATCCAGATCTGAAACTGTAAGAAGCCCAAATTA
14866 TGGGCTGATCCAGATCTGAAACTGTAAGAAGCCCAAATTA
1 TGGGCTGATCCAGATCTGAAACTGTAAGAAGCCCAAATTA
14906 T
1 T
14907 TACATCAACG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (40 bp):
TGGGCTGATCCAGATCTGAAACTGTAAGAAGCCCAAATTA
Found at i:18832 original size:42 final size:42
Alignment explanation
Indices: 18785--18871 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
18775 CATTATCTTA
**
18785 ATTCTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAAT
1 ATTCTACTCCATCTCTAAATAATTCATCAAAATAAAGCTAAT
*
18827 ATTCTACTCCATCTCTAAATAATTCATTAAAATAAAGCTAAT
1 ATTCTACTCCATCTCTAAATAATTCATCAAAATAAAGCTAAT
18869 ATT
1 ATT
18872 AATTGTTGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.36
Consensus pattern (42 bp):
ATTCTACTCCATCTCTAAATAATTCATCAAAATAAAGCTAAT
Found at i:19364 original size:119 final size:117
Alignment explanation
Indices: 19123--19465 Score: 529
Period size: 119 Copynumber: 2.9 Consensus size: 117
19113 AACACGTTTG
19123 GGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGAAAAT
1 GGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGAAAAT
* *
19188 TTAAGGACTTG-----CCTCAAAACAATATTTATGGTTGTGGTGGAGCGTTT
66 TTGAGGACTTGAAATTCCTCAAAACAATATTTATGGTTGTGGTGGAGCCTTT
*
19235 GGAACCTAAGAATTAAGGAGTAATTTATACTATTTTTA-TGGAAGAGTTGGTTTGAAGTGGAAAA
1 GG-ATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGAAAA
*
19299 TTTGAGGACTTGAGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCCTTT
65 TTTGAGGACTT--GAAATTCCTCAAAACAATATTTATGGTTGTGGTGGAGCCTTT
* *
19354 GAGATCTAAGAATTAAGAAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAA
1 G-GATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGAAAA
*
19419 -ATGAAGGACTTGAAATTCCTCAAAACAATATTTATGGTTGTGGTGGA
65 TTTG-AGGACTTGAAATTCCTCAAAACAATATTTATGGTTGTGGTGGA
19466 TATTCTTCCA
Statistics
Matches: 211, Mismatches: 9, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
112 38 0.18
113 34 0.16
114 1 0.00
118 35 0.17
119 70 0.33
120 33 0.16
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.35
Consensus pattern (117 bp):
GGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGAAAAT
TTGAGGACTTGAAATTCCTCAAAACAATATTTATGGTTGTGGTGGAGCCTTT
Found at i:19798 original size:105 final size:105
Alignment explanation
Indices: 19678--19887 Score: 348
Period size: 105 Copynumber: 2.0 Consensus size: 105
19668 AATAAAAATT
* *
19678 TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAATACTGAGAAAATTTTAGAAAT
1 TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGAAAATTTTAGAAAT
* *
19743 TTCCCAATTAAGATTTTTGAGTTTGTGATTTTATATAGTA
66 TTCCCAATTAAAATTTTTGAGTTCGTGATTTTATATAGTA
* ***
19783 TAATGACTAATAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGGGTATTTTAGAAAT
1 TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGAAAATTTTAGAAAT
19848 TTCCCAATTAAAATTTTTGAGTTCGTGATTTTATATAGTA
66 TTCCCAATTAAAATTTTTGAGTTCGTGATTTTATATAGTA
19888 GTAAGATAAG
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
105 97 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (105 bp):
TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGAAAATTTTAGAAAT
TTCCCAATTAAAATTTTTGAGTTCGTGATTTTATATAGTA
Found at i:19914 original size:8 final size:8
Alignment explanation
Indices: 19886--19929 Score: 61
Period size: 8 Copynumber: 5.2 Consensus size: 8
19876 TTTTATATAG
19886 TAGTAAGA
1 TAGTAAGA
*
19894 TAAGATGAGA
1 T-AG-TAAGA
19904 TAGTAAGA
1 TAGTAAGA
19912 TAGTAAGA
1 TAGTAAGA
19920 TAGTAAGA
1 TAGTAAGA
19928 TA
1 TA
19930 TGGACATGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 23 0.72
9 4 0.12
10 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (8 bp):
TAGTAAGA
Found at i:21035 original size:7 final size:7
Alignment explanation
Indices: 21023--21069 Score: 94
Period size: 7 Copynumber: 6.7 Consensus size: 7
21013 TATATATGCA
21023 TGGCAAT
1 TGGCAAT
21030 TGGCAAT
1 TGGCAAT
21037 TGGCAAT
1 TGGCAAT
21044 TGGCAAT
1 TGGCAAT
21051 TGGCAAT
1 TGGCAAT
21058 TGGCAAT
1 TGGCAAT
21065 TGGCA
1 TGGCA
21070 GGCAAGCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (7 bp):
TGGCAAT
Found at i:22795 original size:16 final size:16
Alignment explanation
Indices: 22774--22806 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
22764 GAATTATAAT
22774 AGGAATTAGTGTCAGC
1 AGGAATTAGTGTCAGC
22790 AGGAATTAGTGTCAGC
1 AGGAATTAGTGTCAGC
22806 A
1 A
22807 ATGGTTGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.24
Consensus pattern (16 bp):
AGGAATTAGTGTCAGC
Found at i:25784 original size:7 final size:7
Alignment explanation
Indices: 25774--25799 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
25764 AAAACGACCC
25774 TCCCAAG
1 TCCCAAG
25781 TCCCAAG
1 TCCCAAG
25788 TCCCAAG
1 TCCCAAG
25795 TCCCA
1 TCCCA
25800 CCACAATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (7 bp):
TCCCAAG
Found at i:36522 original size:17 final size:16
Alignment explanation
Indices: 36468--36518 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
36458 ATCACCCCCC
*
36468 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
*
36485 AGATCATCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
36502 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
36518 A
1 A
36519 AGATTACATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:37235 original size:2 final size:2
Alignment explanation
Indices: 37228--37264 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
37218 TTCCCAATTG
37228 AT AT AT AT AT AT AT A- 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
37265 TAGGGTGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38394 original size:26 final size:28
Alignment explanation
Indices: 38361--38418 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
38351 ATTAACACAT
*
38361 CACA-CACATATA-AAAAAGA-GCCCAA
1 CACATCACATACACAAAAAGAGGCCCAA
* *
38386 TACATCACATGCACAAAAAGAGGCCCAA
1 CACATCACATACACAAAAAGAGGCCCAA
38414 CACAT
1 CACAT
38419 GAAAATGGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 3 0.12
26 6 0.23
27 7 0.27
28 10 0.38
ACGTcount: A:0.50, C:0.29, G:0.10, T:0.10
Consensus pattern (28 bp):
CACATCACATACACAAAAAGAGGCCCAA
Found at i:47677 original size:7 final size:7
Alignment explanation
Indices: 47661--47701 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
47651 GTCCGTTTAT
*
47661 TATAGCC
1 TATAGGC
47668 TATAGGC
1 TATAGGC
47675 TATAGGC
1 TATAGGC
47682 TATAGGC
1 TATAGGC
47689 TATAGGC
1 TATAGGC
47696 TATAGG
1 TATAGG
47702 AGTAAAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (7 bp):
TATAGGC
Found at i:48389 original size:6 final size:6
Alignment explanation
Indices: 48380--48411 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
48370 TTCAATGACA
48380 TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT TC
1 TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT TC
48412 ATTACTTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
TCCAAT
Found at i:48707 original size:22 final size:23
Alignment explanation
Indices: 48664--48708 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
48654 GATTGATTTC
*
48664 TATTAATTATACTTTTTTTTGAAA
1 TATTAATTATAC-TATTTTTGAAA
48688 TATTAATTATAC-ATTTTTGAA
1 TATTAATTATACTATTTTTGAA
48709 TTTGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
24 12 0.60
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (23 bp):
TATTAATTATACTATTTTTGAAA
Found at i:61385 original size:25 final size:29
Alignment explanation
Indices: 61337--61390 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 29
61327 ATACTTAATA
61337 AACTACATAAACTTAAACTTTTTAATATT
1 AACTACATAAACTTAAACTTTTTAATATT
61366 AACTACAT-AAC-T-AA-TTTTTAATATT
1 AACTACATAAACTTAAACTTTTTAATATT
61391 TTTTCTCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 11 0.44
26 2 0.08
27 1 0.04
28 3 0.12
29 8 0.32
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (29 bp):
AACTACATAAACTTAAACTTTTTAATATT
Found at i:62437 original size:26 final size:27
Alignment explanation
Indices: 62399--62467 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
62389 GTGTATTCAC
62399 AAAGGCAGAGAA-TTTTTTGGTGAAAT
1 AAAGGCAGAGAATTTTTTTGGTGAAAT
* * *
62425 AAAGGCTGGGAATTTTTTTTGGTGAAAAC
1 AAAGGCAGAGAA-TTTTTTTGGTG-AAAT
*
62454 AAAGGTAGAGAATT
1 AAAGGCAGAGAATT
62468 AGAGTGAGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 10 0.29
28 12 0.35
29 12 0.35
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (27 bp):
AAAGGCAGAGAATTTTTTTGGTGAAAT
Found at i:67385 original size:11 final size:11
Alignment explanation
Indices: 67369--67399 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
67359 TAATTCATTC
67369 TTTTTATTTAT
1 TTTTTATTTAT
67380 TTTTTATTTAT
1 TTTTTATTTAT
67391 TTTTT-TTTA
1 TTTTTATTTA
67400 ATTTCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:67391 original size:15 final size:15
Alignment explanation
Indices: 67371--67414 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
67361 ATTCATTCTT
67371 TTTATTTATTTTTT-A
1 TTTATTT-TTTTTTAA
67386 TTTATTTTTTTTTAA
1 TTTATTTTTTTTTAA
* *
67401 TTTCTTTCTTTTTA
1 TTTATTTTTTTTTA
67415 GATTGGGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 6 0.23
15 20 0.77
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTATTTTTTTTTAA
Found at i:67566 original size:17 final size:17
Alignment explanation
Indices: 67548--67609 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 17
67538 GCCCACGCGT
*
67548 TGGCCTAGGCCATGCGT
1 TGGCCTAGGCCATGCGC
* **
67565 TGGCCTGGGCCGCGCGC
1 TGGCCTAGGCCATGCGC
*
67582 TGGCCTGGGCCATGCGC
1 TGGCCTAGGCCATGCGC
67599 TGGCCTAGGCC
1 TGGCCTAGGCC
67610 CGCCTGGCCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.06, C:0.35, G:0.40, T:0.18
Consensus pattern (17 bp):
TGGCCTAGGCCATGCGC
Found at i:67593 original size:34 final size:33
Alignment explanation
Indices: 67543--67620 Score: 104
Period size: 34 Copynumber: 2.4 Consensus size: 33
67533 ATGAGGCCCA
* * * *
67543 CGCGTTGGCCTAGGCCATGCGTTGGCCTGGGCC
1 CGCGCTGGCCTGGGCCATGCGCTGGCCTAGGCC
67576 GCGCGCTGGCCTGGGCCATGCGCTGGCCTAGGCC
1 -CGCGCTGGCCTGGGCCATGCGCTGGCCTAGGCC
67610 CGC-CTGGCCTG
1 CGCGCTGGCCTG
67621 TTGGCTGGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 8 0.20
33 3 0.08
34 29 0.73
ACGTcount: A:0.05, C:0.37, G:0.40, T:0.18
Consensus pattern (33 bp):
CGCGCTGGCCTGGGCCATGCGCTGGCCTAGGCC
Found at i:80143 original size:28 final size:27
Alignment explanation
Indices: 80112--80215 Score: 88
Period size: 28 Copynumber: 3.7 Consensus size: 27
80102 TAATTTTTTT
*
80112 AAAAAAACTTTCTTCTTTTTGCGATTTA
1 AAAAAAAATTTCTTCTTTTTGCGA-TTA
80140 AAAAAAAATGTTTCTTTTCTTTTTGCGA-T-
1 AAAAAAAA--TTTC--TTCTTTTTGCGATTA
* *
80169 AAAAAAATTTCTCTGTTTTTTTGCG-TTA
1 AAAAAAAATT-TCT-TCTTTTTGCGATTA
*
80197 AAAAAAAATTTCTTGTTTT
1 AAAAAAAATTTCTTCTTTT
80216 CAGTTTTTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
26 6 0.10
27 15 0.24
28 18 0.29
29 7 0.11
30 5 0.08
32 12 0.19
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.48
Consensus pattern (27 bp):
AAAAAAAATTTCTTCTTTTTGCGATTA
Found at i:80154 original size:30 final size:28
Alignment explanation
Indices: 80112--80210 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 28
80102 TAATTTTTTT
80112 AAAAAAACTTTC-TTCTTTTTGCGATTTAA
1 AAAAAAACTTTCTTTCTTTTTGCGA--TAA
*
80141 AAAAAAATGTTTCTTTTCTTTTTGCGAT--
1 AAAAAAA-CTTTC-TTTCTTTTTGCGATAA
* *
80169 AAAAAAA-TTTCTCTGTTTTTTTGCGTTAA
1 AAAAAAACTTTCT-T-TCTTTTTGCGATAA
80198 AAAAAAA-TTTCTT
1 AAAAAAACTTTCTT
80211 GTTTTCAGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
25 1 0.02
26 5 0.08
27 10 0.17
28 8 0.13
29 19 0.32
30 5 0.08
32 12 0.20
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.46
Consensus pattern (28 bp):
AAAAAAACTTTCTTTCTTTTTGCGATAA
Found at i:80165 original size:32 final size:31
Alignment explanation
Indices: 80124--80213 Score: 104
Period size: 28 Copynumber: 3.1 Consensus size: 31
80114 AAAAACTTTC
*
80124 TTCTTTTTGCGATTTAAAAAAAAATGTT-TCTT
1 TTCTTTTTGCGA-TTAAAAAAAAAT-TTCTCTG
80156 TTCTTTTTGCGA-T--AAAAAAATTTCTCTG
1 TTCTTTTTGCGATTAAAAAAAAATTTCTCTG
80184 TT-TTTTTGCG-TTAAAAAAAAATTTCT-TG
1 TTCTTTTTGCGATTAAAAAAAAATTTCTCTG
80212 TT
1 TT
80214 TTCAGTTTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
27 11 0.21
28 17 0.32
29 12 0.23
30 1 0.02
32 12 0.23
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (31 bp):
TTCTTTTTGCGATTAAAAAAAAATTTCTCTG
Found at i:89624 original size:21 final size:21
Alignment explanation
Indices: 89581--89624 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
89571 CCAATTTAGG
*
89581 TTTAGATTTAAATTTCTTGTT
1 TTTAGATTTAAATTTATTGTT
89602 TTTAGATTTAAGATTTATT-TT
1 TTTAGATTTAA-ATTTATTGTT
89623 TT
1 TT
89625 ATGCATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTAGATTTAAATTTATTGTT
Found at i:92627 original size:13 final size:15
Alignment explanation
Indices: 92572--92622 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 15
92562 TTGGAGGTTT
92572 TTATTAATTGTTTTC
1 TTATTAATTGTTTTC
*
92587 TTGATTATTCACTGTTTTC
1 TT-ATTA---ATTGTTTTC
92606 TTATTAATTGTTTTC
1 TTATTAATTGTTTTC
92621 TT
1 TT
92623 TAATTTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 12 0.40
16 4 0.13
18 4 0.13
19 10 0.33
ACGTcount: A:0.18, C:0.10, G:0.08, T:0.65
Consensus pattern (15 bp):
TTATTAATTGTTTTC
Found at i:104178 original size:16 final size:15
Alignment explanation
Indices: 104141--104169 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
104131 GCAGAGGTTG
104141 AAAA-AAAACAATTA
1 AAAAGAAAACAATTA
104155 AAAAGAAAACAATTA
1 AAAAGAAAACAATTA
104170 TACTAGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.76, C:0.07, G:0.03, T:0.14
Consensus pattern (15 bp):
AAAAGAAAACAATTA
Found at i:107230 original size:21 final size:21
Alignment explanation
Indices: 107206--107278 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
107196 GGCTTGGAAT
*
107206 GGTGATGGCATGGGCATGGCC
1 GGTGGTGGCATGGGCATGGCC
* * **
107227 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCATGGGCATGGCC
*
107248 GGTGGTGGCATGGTGAATGGCC
1 GGTGGTGGCATGG-GCATGGCC
*
107270 GGTTGTGGC
1 GGTGGTGGC
107279 TTGGTAGTGG
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
21 28 0.70
22 12 0.30
ACGTcount: A:0.12, C:0.18, G:0.48, T:0.22
Consensus pattern (21 bp):
GGTGGTGGCATGGGCATGGCC
Found at i:108898 original size:19 final size:18
Alignment explanation
Indices: 108874--108909 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
108864 TGAAGATTTA
108874 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
108893 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
108910 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:116405 original size:22 final size:22
Alignment explanation
Indices: 116386--116439 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
116376 AGGAAAATTT
*
116386 GTCGATTAAAG-GAAGCAAATA
1 GTCGACTAAAGAGAAGCAAATA
116407 GTCGACTAAAGAGAAG-AACA-A
1 GTCGACTAAAGAGAAGCAA-ATA
*
116428 TTCGACTAAAGA
1 GTCGACTAAAGA
116440 ATTGTCGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.48, C:0.13, G:0.22, T:0.17
Consensus pattern (22 bp):
GTCGACTAAAGAGAAGCAAATA
Done.