Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016228.1 Corchorus capsularis cultivar CVL-1 contig16249, 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: 60024
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:994 original size:29 final size:29
Alignment explanation
Indices: 962--1032 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 29
952 CCCTAATTTT
962 AAAAACGGAAAAATA-TTTTTTTTTTTAGA
1 AAAAACGGAAAAA-ACTTTTTTTTTTTAGA
*
991 AAAATCGGAAAAAACTTTTTTTTTTTTAGA
1 AAAAACGGAAAAAAC-TTTTTTTTTTTAGA
1021 AAAAACGGAAAA
1 AAAAACGGAAAA
1033 TCAAAAACTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 1 0.03
29 12 0.32
30 25 0.66
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (29 bp):
AAAAACGGAAAAAACTTTTTTTTTTTAGA
Found at i:1329 original size:6 final size:6
Alignment explanation
Indices: 1320--1358 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
1310 AAAGCAAAGC
1320 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1359 GCAGATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:1370 original size:12 final size:12
Alignment explanation
Indices: 1355--1399 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
1345 AATCTAAATC
1355 TAAAGCAGATTA
1 TAAAGCAGATTA
* *
1367 TAAAGCAAAATAA
1 TAAAGC-AGATTA
1380 TAAAGCAGATTAA
1 TAAAGCAGATT-A
1393 TAAAGCA
1 TAAAGCA
1400 AACAATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.58, C:0.09, G:0.13, T:0.20
Consensus pattern (12 bp):
TAAAGCAGATTA
Found at i:1406 original size:25 final size:25
Alignment explanation
Indices: 1355--1407 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
1345 AATCTAAATC
*
1355 TAAAGCAGATTATAAAGCAAAATAA
1 TAAAGCAGATTATAAAGCAAAACAA
1380 TAAAGCAGATTAATAAAGC-AAACAA
1 TAAAGCAGATT-ATAAAGCAAAACAA
1405 TAA
1 TAA
1408 TTAAAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.19
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAAACAA
Found at i:13510 original size:21 final size:21
Alignment explanation
Indices: 13484--13539 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
13474 TGACCAGCCA
* **
13484 CATGCCCGTCCATCTCCATCG
1 CATGCCCGACCATCAACATCG
13505 CATGCCCGACCATCAACATCG
1 CATGCCCGACCATCAACATCG
*
13526 CATGACCCGGCCAT
1 CATG-CCCGACCAT
13540 GCCTAAGCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 22 0.73
22 8 0.27
ACGTcount: A:0.21, C:0.45, G:0.16, T:0.18
Consensus pattern (21 bp):
CATGCCCGACCATCAACATCG
Found at i:20613 original size:16 final size:16
Alignment explanation
Indices: 20592--20624 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20582 AGCCCGTTCC
*
20592 AAAAAAAAATTAATTA
1 AAAAAAAAACTAATTA
20608 AAAAAAAAACTAATTA
1 AAAAAAAAACTAATTA
20624 A
1 A
20625 TTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAAAAAACTAATTA
Found at i:21573 original size:15 final size:15
Alignment explanation
Indices: 21553--21586 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
21543 ATTGGATTTA
21553 TTATTACTAA-TTGTT
1 TTATTA-TAACTTGTT
21568 TTATTATAACTTGTT
1 TTATTATAACTTGTT
21583 TTAT
1 TTAT
21587 AAGTTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (15 bp):
TTATTATAACTTGTT
Found at i:25456 original size:1 final size:1
Alignment explanation
Indices: 25450--25479 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
25440 CCTAAACTGC
25450 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25480 GTCACAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:25748 original size:16 final size:16
Alignment explanation
Indices: 25727--25757 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
25717 TTCGCCACAT
25727 GAAAAGGAAGCACCAC
1 GAAAAGGAAGCACCAC
25743 GAAAAGGAAGCACCA
1 GAAAAGGAAGCACCA
25758 GAGAAGGTAG
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:0.52, C:0.23, G:0.26, T:0.00
Consensus pattern (16 bp):
GAAAAGGAAGCACCAC
Found at i:25828 original size:16 final size:16
Alignment explanation
Indices: 25807--25838 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25797 CACGCCATTC
25807 CACAAAGCTGAAGCAA
1 CACAAAGCTGAAGCAA
25823 CACAAAGCTGAAGCAA
1 CACAAAGCTGAAGCAA
25839 GAGGTAGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.19, T:0.06
Consensus pattern (16 bp):
CACAAAGCTGAAGCAA
Found at i:25910 original size:45 final size:45
Alignment explanation
Indices: 25846--25932 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
25836 CAAGAGGTAG
**
25846 AGGGTGATAAAAAAAAATGATACACCCTGCCATTCCACAAAGCTA
1 AGGGTGATAAAAAAAAATGATACACCCCACCATTCCACAAAGCTA
* *
25891 AGGGTGATCAATAAAAATGATACACCCCACCATTCCACAAAG
1 AGGGTGATAAAAAAAAATGATACACCCCACCATTCCACAAAG
25933 TTGGGAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.17
Consensus pattern (45 bp):
AGGGTGATAAAAAAAAATGATACACCCCACCATTCCACAAAGCTA
Found at i:26916 original size:399 final size:399
Alignment explanation
Indices: 26178--27149 Score: 1676
Period size: 399 Copynumber: 2.4 Consensus size: 399
26168 GAAATTGAAC
26178 TGTTGAGGATTTACATGTGAGGGAACATCCCACATCATGAAGAGATGGGTTGTTAGAGTAGCTTA
1 TGTTGAGGATTTACATGTGAGGGAACATCCCACATCATGAAGAGATGGGTTGTTAGAGTAGCTTA
*
26243 TATACATGAAAGACCCAAGAAACCATCAGTCTAGGCTTTTGGGTTCGGATTGGTGTCCGGCATGT
66 TATACATGAAAGACCCAAGAAACCATCAGTCTAGGCTTTTGGGTTCGGATTGGTGTCCGACATGT
* *
26308 ATATGGGTTGCTCGGTGGGCCTTGCTGAAGCAGACAAGGTCCAGTTCCTCTCCCAACAAGTGGTA
131 ATATGGGTTGCTCGGTGGGCCTTGCTGAAGCAGACAGGGCCCAGTTCCTCTCCCAACAAGTGGTA
*
26373 TCAGAGCCTGGTTGAACTTGATCAGTGTGGCCCATGAGCACGGTAAACCTGGTTAGCCGCACGAC
196 TCAGAGCCTGGTTGAACTCGATCAGTGTGGCCCATGAGCACGGTAAACCTGGTTAGCCGCACGAC
* ** *
26438 AGGGGCGTGCGATTGTGGAGTGTTCGTAGCTTGCACCACTTGAGGGGTTAAGTCTTAGATGGCCG
261 AAGGGCGTGCGATTGTGGAGTGTTCGTAGCTTGCACCACTCCAAGGGTTAAGTCTTAGATGGCCG
26503 GTAATTGGCTTAAGACTTGACGGGTTGGGCCGCACGGGGGAGAGATGAGGACTCACATGTAAATC
326 GTAATTGGCTTAAGACTTGACGGGTTGGGCCGCACGGGGGAGAGATGAGGACTCACATGTAAATC
26568 GGGGGAGAT
391 GGGGGAGAT
* *
26577 TGTTGAGGATTTACATGTGAGGGAACATCCCACATCATGAAGAGATGGGTTGTTGGAATAGCTTA
1 TGTTGAGGATTTACATGTGAGGGAACATCCCACATCATGAAGAGATGGGTTGTTAGAGTAGCTTA
*
26642 TATACATGAAAGACCCAAGAAATCATCAGTCTAGGCTTTTGGGTTCGGATTGGTGTCCGACATGT
66 TATACATGAAAGACCCAAGAAACCATCAGTCTAGGCTTTTGGGTTCGGATTGGTGTCCGACATGT
26707 ATATGGGTTGCTCGGTGGGCCTTGCTGAAGCAGACAGGGCCCAGTTCCTCTCCCAACAAGTGGTA
131 ATATGGGTTGCTCGGTGGGCCTTGCTGAAGCAGACAGGGCCCAGTTCCTCTCCCAACAAGTGGTA
* *
26772 TCAGAGCCTGGTTGAACTCGATCAGTGTGGCCCATGAGCACGGTAAACCTGGTTGGCCGCACGAG
196 TCAGAGCCTGGTTGAACTCGATCAGTGTGGCCCATGAGCACGGTAAACCTGGTTAGCCGCACGAC
*
26837 AAGGGCGTGCGATTGTGGAGTGTTCGTAGCTTGCACCACTCCAAGGGTTAAGTCTTGGATGGCCG
261 AAGGGCGTGCGATTGTGGAGTGTTCGTAGCTTGCACCACTCCAAGGGTTAAGTCTTAGATGGCCG
26902 GTAATTGGCTTAAGACTTGACGGGTTGGGCCGCACGGGGGAGAGATGAGGACTCACATGTAAATC
326 GTAATTGGCTTAAGACTTGACGGGTTGGGCCGCACGGGGGAGAGATGAGGACTCACATGTAAATC
*
26967 GGGGTAGAT
391 GGGGGAGAT
* * * * *
26976 TGTTGAGGATTTACATGTGAGGAAACATCCCACATCAT-AAAAGGATGGGTTTTTTTGAGTAGCA
1 TGTTGAGGATTTACATGTGAGGGAACATCCCACATCATGAAGA-GATGGG-TTGTTAGAGTAGCT
*
27040 TATATACATGAAGGACCCAAGAAACCATCAGTCTAGGCTTTTGGGTTCGGATTGGTGTCCGACAT
64 TATATACATGAAAGACCCAAGAAACCATCAGTCTAGGCTTTTGGGTTCGGATTGGTGTCCGACAT
* * * ** *
27105 GTATATGGGCTACTCGATGGGCCTTGCTGGTGTAGACAGGGCCCA
129 GTATATGGGTTGCTCGGTGGGCCTTGCTGAAGCAGACAGGGCCCA
27150 CCGAGTATCC
Statistics
Matches: 542, Mismatches: 29, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
398 3 0.01
399 427 0.79
400 112 0.21
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (399 bp):
TGTTGAGGATTTACATGTGAGGGAACATCCCACATCATGAAGAGATGGGTTGTTAGAGTAGCTTA
TATACATGAAAGACCCAAGAAACCATCAGTCTAGGCTTTTGGGTTCGGATTGGTGTCCGACATGT
ATATGGGTTGCTCGGTGGGCCTTGCTGAAGCAGACAGGGCCCAGTTCCTCTCCCAACAAGTGGTA
TCAGAGCCTGGTTGAACTCGATCAGTGTGGCCCATGAGCACGGTAAACCTGGTTAGCCGCACGAC
AAGGGCGTGCGATTGTGGAGTGTTCGTAGCTTGCACCACTCCAAGGGTTAAGTCTTAGATGGCCG
GTAATTGGCTTAAGACTTGACGGGTTGGGCCGCACGGGGGAGAGATGAGGACTCACATGTAAATC
GGGGGAGAT
Found at i:30508 original size:18 final size:18
Alignment explanation
Indices: 30485--30591 Score: 74
Period size: 18 Copynumber: 5.4 Consensus size: 18
30475 TTCATATTTA
30485 TTTGTGTCTTGGATACTT
1 TTTGTGTCTTGGATACTT
*
30503 TTTGTGT-TTAGGGTTCATATTT
1 TTTGTGTCTT--GG---ATACTT
30525 ATTTGTGTCTTGGATACTT
1 -TTTGTGTCTTGGATACTT
*
30544 TTTGTGT-TTAGGGTTCATATTT
1 TTTGTGTCTT--GG---ATACTT
30566 ATTTGTGTCTTGGATACTT
1 -TTTGTGTCTTGGATACTT
30585 TTTGTGT
1 TTTGTGT
30592 TTAGGGTTTG
Statistics
Matches: 71, Mismatches: 4, Indels: 28
0.69 0.04 0.27
Matches are distributed among these distances:
17 4 0.06
18 21 0.30
19 14 0.20
22 14 0.20
23 14 0.20
24 4 0.06
ACGTcount: A:0.13, C:0.07, G:0.22, T:0.57
Consensus pattern (18 bp):
TTTGTGTCTTGGATACTT
Found at i:30532 original size:41 final size:41
Alignment explanation
Indices: 30475--30599 Score: 250
Period size: 41 Copynumber: 3.0 Consensus size: 41
30465 CAAATTAGTA
30475 TTCATATTTATTTGTGTCTTGGATACTTTTTGTGTTTAGGG
1 TTCATATTTATTTGTGTCTTGGATACTTTTTGTGTTTAGGG
30516 TTCATATTTATTTGTGTCTTGGATACTTTTTGTGTTTAGGG
1 TTCATATTTATTTGTGTCTTGGATACTTTTTGTGTTTAGGG
30557 TTCATATTTATTTGTGTCTTGGATACTTTTTGTGTTTAGGG
1 TTCATATTTATTTGTGTCTTGGATACTTTTTGTGTTTAGGG
30598 TT
1 TT
30600 TGTTTAGTGG
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.14, C:0.07, G:0.22, T:0.57
Consensus pattern (41 bp):
TTCATATTTATTTGTGTCTTGGATACTTTTTGTGTTTAGGG
Found at i:34881 original size:2 final size:2
Alignment explanation
Indices: 34876--34908 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34866 TTTTTTTTTC
34876 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
34909 ATAAGCACTC
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:35241 original size:109 final size:109
Alignment explanation
Indices: 35050--35270 Score: 370
Period size: 109 Copynumber: 2.0 Consensus size: 109
35040 ACTTACACAT
* *
35050 TTAAGGTGCCTTGCATACTCGTAATTTTGGGTCATGACTGACGCGAAGGTTGATATTTGTGATAC
1 TTAAGATGCCTTGCATACTCATAATTTTGGGTCATGACTGACGCGAAGGTTGATATTTGTGATAC
*
35115 CGAACCCCGGGTGCTCCACTTCCCAAAAACAGCGGAGTAATTTA
66 CGAACCCCGGGTGCTCCACTCCCCAAAAACAGCGGAGTAATTTA
* * *
35159 TTAAGATGCTTTGCATACTCATAATTTTGGTTCGTGACTGACGCGAAGGTTGATATTTGTGATAC
1 TTAAGATGCCTTGCATACTCATAATTTTGGGTCATGACTGACGCGAAGGTTGATATTTGTGATAC
* *
35224 CGAACCCCGTGTGCTCCACTCCCCAAAAACAGCGGAGTAGTTTA
66 CGAACCCCGGGTGCTCCACTCCCCAAAAACAGCGGAGTAATTTA
35268 TTA
1 TTA
35271 GATTCCTCTT
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
109 104 1.00
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (109 bp):
TTAAGATGCCTTGCATACTCATAATTTTGGGTCATGACTGACGCGAAGGTTGATATTTGTGATAC
CGAACCCCGGGTGCTCCACTCCCCAAAAACAGCGGAGTAATTTA
Found at i:38259 original size:3 final size:3
Alignment explanation
Indices: 38251--38280 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
38241 TCGACCAACC
38251 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
38281 TATGGTTCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:38474 original size:68 final size:66
Alignment explanation
Indices: 38314--38494 Score: 201
Period size: 68 Copynumber: 2.7 Consensus size: 66
38304 TTGAAGAATG
* *
38314 AAAAGAGAAGATATTTGATTTGAGGGAAAAAATTGAGT-A--G-AGAGATTGAAGAATTATTAGA
1 AAAAGAG-AGAAATTTGATTTGAGGGAAAAAATTGAGTAACGGCAGAGATTGAAGAATGA-TAGA
38375 TTA
64 TTA
*
38378 AAAAGGGAGAAATTTGAATTTGAGGGAAACAAATTGAGTAACGGGCAGAGATTGAAGAATGA-AG
1 AAAAGAGAGAAATTTG-ATTTGAGGGAAA-AAATTGAGTAAC-GGCAGAGATTGAAGAATGATAG
38442 ATTA
63 ATTA
* * * *
38446 AGAAGATACGAGATTTGATTTCAGGGAAAAAATTTGAGTAACGGCAGAG
1 AAAAGAGA-GAAATTTGATTTGAGGGAAAAAA-TTGAGTAACGGCAGAG
38495 TTGGGAAGAA
Statistics
Matches: 100, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
63 8 0.08
64 18 0.18
65 9 0.09
66 1 0.01
67 10 0.10
68 31 0.31
69 8 0.08
70 15 0.15
ACGTcount: A:0.45, C:0.04, G:0.28, T:0.24
Consensus pattern (66 bp):
AAAAGAGAGAAATTTGATTTGAGGGAAAAAATTGAGTAACGGCAGAGATTGAAGAATGATAGATT
A
Found at i:38931 original size:31 final size:31
Alignment explanation
Indices: 38893--38992 Score: 114
Period size: 31 Copynumber: 3.3 Consensus size: 31
38883 AGTACCTAAA
* *
38893 TAGTCCCTGTACTATTGAAAAAAGATCATTT
1 TAGTCCCTCTACTATTGAAAAAAGATCAATT
* * * *
38924 TAGTCCCTCCATTA-TGAAAGATG-TCAATT
1 TAGTCCCTCTACTATTGAAAAAAGATCAATT
*
38953 TAGTCCCTCTACTATTGAAAAGAGATCAATT
1 TAGTCCCTCTACTATTGAAAAAAGATCAATT
*
38984 TAGTTCCTC
1 TAGTCCCTC
38993 CATGAAATGG
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
29 17 0.31
30 13 0.24
31 25 0.45
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (31 bp):
TAGTCCCTCTACTATTGAAAAAAGATCAATT
Found at i:41367 original size:237 final size:237
Alignment explanation
Indices: 40950--41393 Score: 753
Period size: 237 Copynumber: 1.9 Consensus size: 237
40940 ATGAATTAAA
*
40950 AATTAAAAATTAGAATTTTGAAGAAAAAAAATTCGGAAGTTTTAAATAAAAAATTAATTTACACG
1 AATTAAAAATTAGAATTTTGAAGAAAAAAAATTCGGAACTTTTAAATAAAAAATTAATTTACACG
* * * *
41015 TGGCATGCTGTGATTGGGTCACGCCATCCATCTTAGAAAAGTAAAGCAACTTAACGACCACGTCA
66 TGGCATGATATGATTGAGTCACGCCATCCATCTTAGAAAACTAAAGCAACTTAACGACCACGTCA
* * *
41080 GCAAAATTGACAGTCCCATTTCACAGAAGGACTAAATTGACTTGTTTTCAATAGTAGAGTGACTA
131 GCAAAATTGACAGCCCCATTTCACAGAAGGACTAAATTGACCTCTTTTCAATAGTAGAGTGACTA
*
41145 AATTGATAGATTTTAGAATGAATTAAAAAATTTAAATAAATG
196 AATTAATAGATTTTAGAATGAATTAAAAAATTTAAATAAATG
* * *
41187 AATTAAAAATTAGAATTTTGAAGAAAAAAATTTTGGATCTTTTAAATAAAAAATTAATTTACACG
1 AATTAAAAATTAGAATTTTGAAGAAAAAAAATTCGGAACTTTTAAATAAAAAATTAATTTACACG
*
41252 TGGCATGATATGATTGAGTCACGCCATCCATCTTAGAAGACTAAAGCAACTTAACGACCACGTCA
66 TGGCATGATATGATTGAGTCACGCCATCCATCTTAGAAAACTAAAGCAACTTAACGACCACGTCA
* *
41317 GCAAAATTGACAGCCCCATTTCACAGAGGGACTAAATTGACCTCTTTTCAATAGTAGAGTGTCTA
131 GCAAAATTGACAGCCCCATTTCACAGAAGGACTAAATTGACCTCTTTTCAATAGTAGAGTGACTA
41382 AATTAATAGATT
196 AATTAATAGATT
41394 CCATATGGAG
Statistics
Matches: 192, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
237 192 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (237 bp):
AATTAAAAATTAGAATTTTGAAGAAAAAAAATTCGGAACTTTTAAATAAAAAATTAATTTACACG
TGGCATGATATGATTGAGTCACGCCATCCATCTTAGAAAACTAAAGCAACTTAACGACCACGTCA
GCAAAATTGACAGCCCCATTTCACAGAAGGACTAAATTGACCTCTTTTCAATAGTAGAGTGACTA
AATTAATAGATTTTAGAATGAATTAAAAAATTTAAATAAATG
Found at i:47352 original size:53 final size:55
Alignment explanation
Indices: 47248--47358 Score: 190
Period size: 53 Copynumber: 2.0 Consensus size: 55
47238 CCCATGTACA
*
47248 TATATACTTAACATAAAATACATAGTATAATAAAACTAAAGCCCACTGGACCCAAC
1 TATATACTTAACATAAAATACA-AGTACAATAAAACTAAAGCCCACTGGACCCAAC
47304 TATATACTTAACATAAAATAC-A-TACAATAAAACTAAAGCCCACTGGACCCAAC
1 TATATACTTAACATAAAATACAAGTACAATAAAACTAAAGCCCACTGGACCCAAC
47357 TA
1 TA
47359 AGGGATAAGA
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
53 32 0.59
54 1 0.02
56 21 0.39
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.23
Consensus pattern (55 bp):
TATATACTTAACATAAAATACAAGTACAATAAAACTAAAGCCCACTGGACCCAAC
Found at i:48730 original size:437 final size:435
Alignment explanation
Indices: 47750--48730 Score: 1153
Period size: 437 Copynumber: 2.2 Consensus size: 435
47740 TGGGTCTCGC
* * * *
47750 TCTCAATAAACAAATAATTTTTTTGCTGGATTATTTATCAAATGATCC-CTATACTTTTATAATT
1 TCTCCATAAACAAAT-ATTTTTTT--TGGAATAATTATCAAATGATCCTC-ATACTTTTAT-GTT
** * * * * * ** * *
47814 TATGTTATTTAGTCCCTCACAGATTCA-GGGTTGGATGATCGAACGTTTCGACTTTAATTTTTTT
61 TATACTATTGAATCCTTTACA-ATT-ATAGGTTGGATGATTTAACGCTTCGACTTTAATTTTTGT
* * * ****
47878 ATTTTTTGTTTTGCTTGTCCGATCAAGGTGATTCATGTGTCTATTAAAAGGTTACTTCACGATCT
124 ATTTTTTGTTCTACTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAACCAGACTTCACGATCT
* * **
47943 ACAACTTTCATGAATGACTCAAAAGCCAATTTTAATATTTTCATTCTAAAAATTGCTTCTGAAAT
189 ACAACTTTCATAAAGGACTCAAAAGCCAATTTTAATATTTTCATTCTAAAAATTGCTTCCAAAAT
* * * * *
48008 TTTGTGCTTTCGATTGCCGGTCTATCTAATATTGTATAACTTTCGGTCCACTTGTTCGATTGAGG
254 TTTGTGCTCTCGATTGCCCGTCTATCTAATATCGTATAACTTTCGGTCCAATTGTCCGATTGAGG
* *
48073 TTGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACAACTTTCGTTAAGGACCTCAAAGCTG
319 TTATTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACAACTTTCATTAAGGACCTCAAAGCTG
* * * *
48138 GATTTGATTAATGAGTTTCGTGGACGGTTCAAAAATGAATTTTTATGTTCGG
384 AATTTGATTAATGAGTTTCGTGAACGGTTCAAAAAGGAATTTTTATGTTCAG
* * *
48190 TCTCCATAAACAAAATATTTTTTTTGGATTATTTATCAAATGATCCTCATACTTTTATGTTTATG
1 TCTCCATAAAC-AAATATTTTTTTTGGAATAATTATCAAATGATCCTCATACTTTTATGTTTATA
* * * * *
48255 CTATTGAATGCTTTACAATTATTGTGTTGGACGATTTAACGCTTCGGCTTTTATTTTTGTATTTT
65 CTATTGAATCCTTTACAATTATAG-GTTGGATGATTTAACGCTTCGACTTTAATTTTTGTATTTT
* * * *
48320 TTGTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAACCAGATTTCATGATCTACAAC
129 TTGTTCTACTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAACCAGACTTCACGATCTACAAC
* * * * * *
48385 TTTCATAAAGGGCTCAGAAGCCAATTTTAATGTTTTGATTTTTAAGAA-TGCTTCCAAAATTTTG
194 TTTCATAAAGGACTCAAAAGCCAATTTTAATATTTTCA-TTCTAAAAATTGCTTCCAAAATTTTG
* * *
48449 TGGTCTCGATTGCCCGTCTATTTAATATCGTATAATTTTCGGTCCAATTGTCCGATTGAGGTTAT
258 TGCTCTCGATTGCCCGTCTATCTAATATCGTATAACTTTCGGTCCAATTGTCCGATTGAGGTTAT
* * * *
48514 TCAAGTGTTGGTTAAAAGGTTATTGTGTGATTTACAACTTTCATTAAGGGCCTGAAAGCTGAATT
323 TCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACAACTTTCATTAAGGACCTCAAAGCTGAATT
* * * *
48579 TGATTAATGAGTTTCGTGAAGGGTTCAAGAGGGAATTTTTATGTTTAG
388 TGATTAATGAGTTTCGTGAACGGTTCAAAAAGGAATTTTTATGTTCAG
* * * **
48627 TCTCTATAAAC-TATTTTTTTTTCCTGGAATAATTATTTAATGA-CCATCATACTTTTATGCTTT
1 TCTCCATAAACAAATATTTTTTT--TGGAATAATTATCAAATGATCC-TCATACTTTTATG-TTT
*
48690 ATACTATTGAATCCTTTATAATTATAGGTTGGATGATTTAA
62 ATACTATTGAATCCTTTACAATTATAGGTTGGATGATTTAA
48731 TGCTCACTAC
Statistics
Matches: 461, Mismatches: 71, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
435 10 0.02
436 6 0.01
437 357 0.77
438 65 0.14
439 1 0.00
440 18 0.04
441 4 0.01
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.43
Consensus pattern (435 bp):
TCTCCATAAACAAATATTTTTTTTGGAATAATTATCAAATGATCCTCATACTTTTATGTTTATAC
TATTGAATCCTTTACAATTATAGGTTGGATGATTTAACGCTTCGACTTTAATTTTTGTATTTTTT
GTTCTACTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAACCAGACTTCACGATCTACAACTT
TCATAAAGGACTCAAAAGCCAATTTTAATATTTTCATTCTAAAAATTGCTTCCAAAATTTTGTGC
TCTCGATTGCCCGTCTATCTAATATCGTATAACTTTCGGTCCAATTGTCCGATTGAGGTTATTCA
AGTGTCGGTTAAAAGGTTATTGTGTGATCTACAACTTTCATTAAGGACCTCAAAGCTGAATTTGA
TTAATGAGTTTCGTGAACGGTTCAAAAAGGAATTTTTATGTTCAG
Found at i:55871 original size:32 final size:32
Alignment explanation
Indices: 55793--55904 Score: 118
Period size: 32 Copynumber: 3.5 Consensus size: 32
55783 TGCTAAAAAG
* * *
55793 AGCGGCGTCTAATGAATTAAACGCCACTATTT
1 AGCGGCGCCTAATGAATTAGACGCCGCTATTT
* * *
55825 AGCGGTGCTTAATGAAATAGACGCCGCTATTT
1 AGCGGCGCCTAATGAATTAGACGCCGCTATTT
* *
55857 AGCGGCGCCCAATG-ATTCAGACACCGCTATTT
1 AGCGGCGCCTAATGAATT-AGACGCCGCTATTT
* *
55889 AGCGGCGTCTACTGAA
1 AGCGGCGCCTAATGAA
55905 AGAAACACCG
Statistics
Matches: 64, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
31 2 0.03
32 61 0.95
33 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (32 bp):
AGCGGCGCCTAATGAATTAGACGCCGCTATTT
Found at i:56612 original size:11 final size:12
Alignment explanation
Indices: 56552--56617 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 12
56542 AAGTCTTCCA
56552 TTCCTTT-TCCTT
1 TTCCTTTCTCC-T
56564 TTCCTTT-TCCT
1 TTCCTTTCTCCT
*
56575 TCCGTCTGTTCTCCT
1 TTC--CT-TTCTCCT
56590 TTCCTTTTCTCCT
1 TTCC-TTTCTCCT
56603 TTCC-TTCTCCT
1 TTCCTTTCTCCT
56614 TTCC
1 TTCC
56618 ATCCGTTCGA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
11 14 0.30
12 10 0.21
13 14 0.30
14 3 0.06
15 6 0.13
ACGTcount: A:0.00, C:0.39, G:0.03, T:0.58
Consensus pattern (12 bp):
TTCCTTTCTCCT
Found at i:57061 original size:2 final size:2
Alignment explanation
Indices: 57054--57085 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
57044 ATTAGCCATG
57054 AT AT AT AT 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
57086 TACCAAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58653 original size:27 final size:28
Alignment explanation
Indices: 58539--58653 Score: 132
Period size: 27 Copynumber: 4.2 Consensus size: 28
58529 TCGGGCCCTC
*
58539 CCCACTT-CGACCCCAGAAGTGGATCCT
1 CCCACTTGCGACCCAAGAAGTGGATCCT
*
58566 CCCAC-TGCGACCCAATAAGTGGATCCT
1 CCCACTTGCGACCCAAGAAGTGGATCCT
* *
58593 --CTCTGTGCAACCCAAGAAGTGGATCCT
1 CCCACT-TGCGACCCAAGAAGTGGATCCT
* *
58620 CCCACTTG-GACCCCAGCAGTGGATCCT
1 CCCACTTGCGACCCAAGAAGTGGATCCT
58647 CCCACTT
1 CCCACTT
58654 CGCCTCGGGT
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
25 2 0.03
26 1 0.01
27 66 0.89
28 2 0.03
29 3 0.04
ACGTcount: A:0.23, C:0.38, G:0.19, T:0.20
Consensus pattern (28 bp):
CCCACTTGCGACCCAAGAAGTGGATCCT
Done.