Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013864.1 Corchorus olitorius cultivar O-4 contig13897, 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: 69347
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:2507 original size:27 final size:29
Alignment explanation
Indices: 2465--2533 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 29
2455 ATGGGTTTAG
*
2465 ATGGTTCATC-TCCCA-ATATGTTATGGA
1 ATGGTTCATCTTCCAATATATGTTATGGA
2492 ATGGTTCATCTTCCAATATATGTTATGGA
1 ATGGTTCATCTTCCAATATATGTTATGGA
2521 ATGGTTCATCTTC
1 ATGGTTCATCTTC
2534 TTGCATTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 10 0.26
28 4 0.10
29 25 0.64
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (29 bp):
ATGGTTCATCTTCCAATATATGTTATGGA
Found at i:5174 original size:167 final size:167
Alignment explanation
Indices: 4896--5226 Score: 583
Period size: 167 Copynumber: 2.0 Consensus size: 167
4886 TTCTTAAATT
*
4896 ACATTAATTTTAGGAAGTGAAAGTACTAAAGTACAAGTCAAAAGATTTAATTTTATTAATTTGAT
1 ACATTAATTTTAGGAAGAGAAAGTACT-AAGTACAAGTCAAAAGATTTAATTTTATTAATTTGAT
* *
4961 TACTATTTAACTTGGTTTTTTCGTCATTTTAATATTGGTTTTTTCGTTATTCTCACAAACTTCTA
65 TACTATTTAACATGGTTTTTTCGTCATTTTAATATTGATTTTTTCGTTATTCTCACAAACTTCTA
*
5026 AGGGTTTTTTTTGACTTTCTAACAATTTAATATAAAAAA
130 AGGG-TATTTTTGACTTTCTAACAATTTAATATAAAAAA
5065 ACATTAATTTTAGGAAGAGAAAGTACT-AGTACAAGTCAAAAGATTTAATTTTATTAATTTGATT
1 ACATTAATTTTAGGAAGAGAAAGTACTAAGTACAAGTCAAAAGATTTAATTTTATTAATTTGATT
* *
5129 ACTATTTAGCATGGTTTTTTTGTCATTTTAATATTGATTTTTTCGTTATTCTCACAAACTTCTAA
66 ACTATTTAACATGGTTTTTTCGTCATTTTAATATTGATTTTTTCGTTATTCTCACAAACTTCTAA
5194 GGGTATTTTTGACTTTCTAACAATTTAATATAA
131 GGGTATTTTTGACTTTCTAACAATTTAATATAA
5227 CATATTTATA
Statistics
Matches: 156, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
166 29 0.19
167 101 0.65
169 26 0.17
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (167 bp):
ACATTAATTTTAGGAAGAGAAAGTACTAAGTACAAGTCAAAAGATTTAATTTTATTAATTTGATT
ACTATTTAACATGGTTTTTTCGTCATTTTAATATTGATTTTTTCGTTATTCTCACAAACTTCTAA
GGGTATTTTTGACTTTCTAACAATTTAATATAAAAAA
Found at i:6530 original size:14 final size:15
Alignment explanation
Indices: 6507--6535 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6497 TCAATAATAA
6507 AATATCTATAATTAT
1 AATATCTATAATTAT
6522 AATAT-TATAATTAT
1 AATATCTATAATTAT
6536 TATAATACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATCTATAATTAT
Found at i:7592 original size:3 final size:3
Alignment explanation
Indices: 7584--7625 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
7574 ATAATTAAAC
7584 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
7626 AATTCTTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:7609 original size:20 final size:20
Alignment explanation
Indices: 7584--7622 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
7574 ATAATTAAAC
7584 TTATTATTATTATTATTATA
1 TTATTATTATTATTATTATA
7604 TTATTATTATTATTATTAT
1 TTATTATTATTATTATTAT
7623 TATAATTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTATTATTATTATTATA
Found at i:12821 original size:29 final size:31
Alignment explanation
Indices: 12789--12855 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
12779 ATGCAATTTG
12789 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
* **
12818 GGATATAATGTTACGAAAAGTGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
12849 GGATATA
1 GGATATA
12856 GTCCGTTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
30 4 0.12
31 16 0.48
ACGTcount: A:0.48, C:0.09, G:0.19, T:0.24
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:13065 original size:31 final size:30
Alignment explanation
Indices: 12985--13125 Score: 131
Period size: 31 Copynumber: 4.6 Consensus size: 30
12975 CCCTAACTGA
* *
12985 TTATATCCTTAATTGCTTAAAATCGAAAACG
1 TTATATCCTTAATTGCTT-GAATCAAAAACG
**
13016 CCATATCCTTAATTGCTTGAAATCAAAAACG
1 TTATATCCTTAATTGCTTG-AATCAAAAACG
* ** * *
13047 TTATATCCTTAATTGCTTG-TTTTATAACA
1 TTATATCCTTAATTGCTTGAATCAAAAACG
***
13076 TTATATCCTTAATTGCTTGCGGCAGAAAACG
1 TTATATCCTTAATTGCTTGAATCA-AAAACG
*
13107 TTATATCCTAAATTGCTTG
1 TTATATCCTTAATTGCTTG
13126 CTTATCATCT
Statistics
Matches: 89, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
29 24 0.27
31 65 0.73
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (30 bp):
TTATATCCTTAATTGCTTGAATCAAAAACG
Found at i:14199 original size:31 final size:31
Alignment explanation
Indices: 14161--14236 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
14151 ACAAAACAAA
**
14161 CAATTAAGGATATAACGTTTTTTATTTCAAG
1 CAATTAAGGATATAACGTTTTCGATTTCAAG
*
14192 CAATTAAGGATATGACGTTTTCGATTTCAAG
1 CAATTAAGGATATAACGTTTTCGATTTCAAG
*
14223 TAATTAAGGATATA
1 CAATTAAGGATATA
14237 GTCAGTTTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (31 bp):
CAATTAAGGATATAACGTTTTCGATTTCAAG
Found at i:14402 original size:31 final size:29
Alignment explanation
Indices: 14367--14433 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 29
14357 CCTAACGGAC
*
14367 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCG-TTTT-GTAACAT
* *
14398 TATATCTTTAATTGCTTGTTTTGTAACAT
1 TATATCCTTAATTGCTCGTTTTGTAACAT
14427 TATATCC
1 TATATCC
14434 CAAATTGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 12 0.38
30 4 0.12
31 16 0.50
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.49
Consensus pattern (29 bp):
TATATCCTTAATTGCTCGTTTTGTAACAT
Found at i:15112 original size:29 final size:30
Alignment explanation
Indices: 15056--15113 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
15046 TATTTGGGAG
* *
15056 GTCCATGTACTGCACAAAGTGTTCAATTTC
1 GTCCATATACTGCACAAAGTGATCAATTTC
15086 GTCCATATACT-CA-AAAGGTGATCAATTT
1 GTCCATATACTGCACAAA-GTGATCAATTT
15114 AGTTCATGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 12 0.48
30 10 0.40
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (30 bp):
GTCCATATACTGCACAAAGTGATCAATTTC
Found at i:15211 original size:31 final size:31
Alignment explanation
Indices: 15170--15241 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
15160 TTTATCGATT
* *
15170 GGACTCAATTGACCCAATCTTATGAGTGCAG
1 GGACTAAATTGACCCAATCTTATGAGTACAG
* * * *
15201 GGACTAAATTGACCCAATTTTGTGAGTATAT
1 GGACTAAATTGACCCAATCTTATGAGTACAG
15232 GGACTAAATT
1 GGACTAAATT
15242 AATCGCTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (31 bp):
GGACTAAATTGACCCAATCTTATGAGTACAG
Found at i:20824 original size:18 final size:18
Alignment explanation
Indices: 20803--20838 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20793 ATTGTTTTCG
20803 TTTTATTTTATTTCATTA
1 TTTTATTTTATTTCATTA
20821 TTTTATTTTATTTCATTA
1 TTTTATTTTATTTCATTA
20839 ATTGGGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTATTTTATTTCATTA
Found at i:21498 original size:1 final size:1
Alignment explanation
Indices: 21492--21528 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
21482 TACCTTGGTG
**
21492 AAAAAAAAAAAAGCAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21529 CTCTACTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.95, C:0.03, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:22381 original size:15 final size:15
Alignment explanation
Indices: 22361--22390 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22351 ATCAGGCCGC
*
22361 CACGATACACGATAT
1 CACGATACACAATAT
22376 CACGATACACAATAT
1 CACGATACACAATAT
22391 TTCAACCGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:26470 original size:2 final size:2
Alignment explanation
Indices: 26463--26504 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
26453 TTCATCTTCA
26463 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
26505 ATTCACATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:26916 original size:3 final size:3
Alignment explanation
Indices: 26910--26953 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
26900 TAGTTTGGAC
26910 TCT TCT TCCT TCT TC- TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
26954 GCCTACTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:29667 original size:4 final size:4
Alignment explanation
Indices: 29658--29710 Score: 74
Period size: 4 Copynumber: 13.8 Consensus size: 4
29648 GCTATACGTG
* *
29658 TCTA TCTA TCTA T-AA TCTA TCTA T-GA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
29704 TCTA TCT
1 TCTA TCT
29711 TCCTAGTGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 4 0.09
4 39 0.91
ACGTcount: A:0.26, C:0.23, G:0.02, T:0.49
Consensus pattern (4 bp):
TCTA
Found at i:29677 original size:11 final size:11
Alignment explanation
Indices: 29661--29704 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
29651 ATACGTGTCT
29661 ATCTATCTATA
1 ATCTATCTATA
*
29672 ATCTATCTATG
1 ATCTATCTATA
*
29683 ATCTATCTATCT
1 ATCTATCTAT-A
29695 ATCTATCTAT
1 ATCTATCTAT
29705 CTATCTTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.48
Consensus pattern (11 bp):
ATCTATCTATA
Found at i:32671 original size:16 final size:17
Alignment explanation
Indices: 32652--32684 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
32642 CGTGTTTGTG
32652 TTTGGGTTTAA-CGTGT
1 TTTGGGTTTAATCGTGT
*
32668 TTTGTGTTTAATCGTGT
1 TTTGGGTTTAATCGTGT
32685 CAGTACGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.12, C:0.06, G:0.27, T:0.55
Consensus pattern (17 bp):
TTTGGGTTTAATCGTGT
Found at i:42011 original size:29 final size:29
Alignment explanation
Indices: 41948--42015 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
41938 ACACAAAACG
* **
41948 GTCAAATAAACCCCTGAACTCTAATTGCA
1 GTCAAATAAGCCCCTGAACTCTAAAAGCA
* *
41977 GCCAAATAAGCCCCTGAACTCCTAAAAG-T
1 GTCAAATAAGCCCCTGAACT-CTAAAAGCA
42006 GTCAAATAAG
1 GTCAAATAAG
42016 TCATTTTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.40, C:0.26, G:0.13, T:0.21
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTCTAAAAGCA
Found at i:50432 original size:20 final size:20
Alignment explanation
Indices: 50409--50448 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
50399 TGATATATCG
*
50409 GTAAATATCCATGAATATTC
1 GTAAATATCCATAAATATTC
*
50429 GTAAATATCCGTAAATATTC
1 GTAAATATCCATAAATATTC
50449 ATATTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (20 bp):
GTAAATATCCATAAATATTC
Found at i:52910 original size:2 final size:2
Alignment explanation
Indices: 52903--52931 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52893 TTTAACATGC
52903 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 A
52932 GACACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63040 original size:66 final size:67
Alignment explanation
Indices: 62934--63125 Score: 289
Period size: 66 Copynumber: 2.9 Consensus size: 67
62924 GCTGCAGCCT
* *
62934 TTTCTTCTAGGATCTCTTCTGGCATATCCAAAACCTGATCAGTTTCCTCCACAGTTTCAAACC-G
1 TTTCTTCTGGGATCTCTTCTGGCATATCCAAAACCTGATCAGTTTCCTCCACTGTTTCAAACCTG
62998 AG
66 AG
*
63000 TTTCTTCTGGGATCTCTTCTGGCATATCCAAAACTTGATCAGTTTCCTCCACTGTTTC-AACCTG
1 TTTCTTCTGGGATCTCTTCTGGCATATCCAAAACCTGATCAGTTTCCTCCACTGTTTCAAACCTG
63064 AG
66 AG
* ** * **
63066 GTTCTTCTGAAATTTCTTCTGGCAGGTCCAAAACCTGATCAGTTTCCTCCACTGTTTCAA
1 TTTCTTCTGGGATCTCTTCTGGCATATCCAAAACCTGATCAGTTTCCTCCACTGTTTCAA
63126 TCTGACCCTG
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
65 4 0.04
66 109 0.96
67 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.36
Consensus pattern (67 bp):
TTTCTTCTGGGATCTCTTCTGGCATATCCAAAACCTGATCAGTTTCCTCCACTGTTTCAAACCTG
AG
Found at i:63451 original size:45 final size:45
Alignment explanation
Indices: 63352--63454 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
63342 ATTCTTCCAG
*
63352 CATTGCCTCTTCAACCCTTTTAGGCTCCTCATAATCTGCATTTTC
1 CATTGCCTCTTCAACCCTTTTAGGCTCCTCATAAACTGCATTTTC
* *
63397 CGCTT-CCTCTTCAA-CCTTTTCTGGCTCCTCATAAACTGCATTTTC
1 C-ATTGCCTCTTCAACCCTTTT-AGGCTCCTCATAAACTGCATTTTC
63442 CATTGCCTCTTCA
1 CATTGCCTCTTCA
63455 GGTTCCCTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
44 8 0.16
45 41 0.80
46 2 0.04
ACGTcount: A:0.17, C:0.35, G:0.09, T:0.40
Consensus pattern (45 bp):
CATTGCCTCTTCAACCCTTTTAGGCTCCTCATAAACTGCATTTTC
Found at i:63564 original size:42 final size:43
Alignment explanation
Indices: 63485--63599 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 43
63475 CACTTCTGTC
* * **
63485 GGTACCTTTTCCGGTTCCTTCTCTTGGA-CAATCTCTACCCTT
1 GGTACCTTTTCAGGTTCCTTCTTTTCAACCAATCTCTACCCTT
*
63527 GGTACCTTTTCAGGTTCCTTCTTTTCAACCAAT-TCTACCTTT
1 GGTACCTTTTCAGGTTCCTTCTTTTCAACCAATCTCTACCCTT
* * *
63569 GGCACCTCTTCAGCTTCCTTCTTTTCAACCA
1 GGTACCTTTTCAGGTTCCTTCTTTTCAACCA
63600 CCTCTTCTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 60 0.94
43 4 0.06
ACGTcount: A:0.15, C:0.33, G:0.11, T:0.41
Consensus pattern (43 bp):
GGTACCTTTTCAGGTTCCTTCTTTTCAACCAATCTCTACCCTT
Found at i:64503 original size:19 final size:19
Alignment explanation
Indices: 64471--64507 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
64461 TTTAGATGTT
*
64471 ATTTAACATTAAAAAAAGA
1 ATTTAACATCAAAAAAAGA
*
64490 ATTTATCATCAAAAAAAG
1 ATTTAACATCAAAAAAAG
64508 TTTTTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.27
Consensus pattern (19 bp):
ATTTAACATCAAAAAAAGA
Found at i:64876 original size:27 final size:28
Alignment explanation
Indices: 64841--64900 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
64831 GTCCTTGTAA
*
64841 TTAC-AAAAAAAAATCAATTTAGTCCCT
1 TTACTAAAAATAAATCAATTTAGTCCCT
** *
64868 TTACTAAAAATCGATCAATTTAGTCTCT
1 TTACTAAAAATAAATCAATTTAGTCCCT
64896 TTACT
1 TTACT
64901 TACATGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 4 0.14
28 24 0.86
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (28 bp):
TTACTAAAAATAAATCAATTTAGTCCCT
Found at i:64920 original size:31 final size:31
Alignment explanation
Indices: 64882--64954 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
64872 TAAAAATCGA
64882 TCAATTTAGTCTCTTTACTTACATGTTTGAG
1 TCAATTTAGTCTCTTTACTTACATGTTTGAG
64913 TCAATTTAGTCTCTTTACTTACATGTTTGAG
1 TCAATTTAGTCTCTTTACTTACATGTTTGAG
64944 TCAATTTAGTC
1 TCAATTTAGTC
64955 CCTATCGTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.48
Consensus pattern (31 bp):
TCAATTTAGTCTCTTTACTTACATGTTTGAG
Found at i:65349 original size:15 final size:15
Alignment explanation
Indices: 65329--65359 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
65319 ATTTGGTATT
65329 ACGTTTAGGGTGAAA
1 ACGTTTAGGGTGAAA
65344 ACGTTTAGGGTGAAA
1 ACGTTTAGGGTGAAA
65359 A
1 A
65360 GCATGCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (15 bp):
ACGTTTAGGGTGAAA
Found at i:65691 original size:49 final size:47
Alignment explanation
Indices: 65600--65726 Score: 166
Period size: 49 Copynumber: 2.6 Consensus size: 47
65590 CGTGCCAATT
* * *
65600 AATTTTGTCAAAAAATTGATAAAAAGTGCAATGAAAATTAAAAGATC
1 AATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAGATC
*
65647 AATTTTGTCTTAAAAATTGAGAAAAAGGTGCAA-GTAAAAATAAAAGTTC
1 AATTTTGTC-TAAAAATTGAGAAAAA-GTGCAATG-AAAAATAAAAGATC
*
65696 AATTTTGTAGTAAAAATTGAGAAAAAGTGCA
1 AATTTTGT-CTAAAAATTGAGAAAAAGTGCA
65727 GGAAATGTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
47 9 0.13
48 20 0.28
49 42 0.59
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (47 bp):
AATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAGATC
Found at i:68354 original size:18 final size:15
Alignment explanation
Indices: 68340--68379 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
68330 TAGTAAACAC
68340 TTTCGGTGCCATAAA
1 TTTCGGTGCCATAAA
*
68355 TTTCGGTGCCAT-CA
1 TTTCGGTGCCATAAA
68369 TCTTCGGTGCC
1 T-TTCGGTGCC
68380 GTCGATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 2 0.09
15 21 0.91
ACGTcount: A:0.15, C:0.28, G:0.23, T:0.35
Consensus pattern (15 bp):
TTTCGGTGCCATAAA
Found at i:68377 original size:30 final size:30
Alignment explanation
Indices: 68341--68433 Score: 123
Period size: 30 Copynumber: 3.1 Consensus size: 30
68331 AGTAAACACT
* * *
68341 TTCGGTGCCATAAATTTCGGTGCCATCATC
1 TTCGGTGCCGTAGATTTTGGTGCCATCATC
* * *
68371 TTCGGTGCCGTCGATTTTGGTGTCGTCATC
1 TTCGGTGCCGTAGATTTTGGTGCCATCATC
*
68401 TTCGGTGCCGTTGATTTTGGTGCCATCATC
1 TTCGGTGCCGTAGATTTTGGTGCCATCATC
68431 TTC
1 TTC
68434 TTCCATGACA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.12, C:0.25, G:0.25, T:0.39
Consensus pattern (30 bp):
TTCGGTGCCGTAGATTTTGGTGCCATCATC
Found at i:68392 original size:15 final size:15
Alignment explanation
Indices: 68374--68424 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
68364 CATCATCTTC
68374 GGTGCCGTCGATTTT
1 GGTGCCGTCGATTTT
* *
68389 GGTGTCGTC-ATCTTC
1 GGTGCCGTCGAT-TTT
*
68404 GGTGCCGTTGATTTT
1 GGTGCCGTCGATTTT
68419 GGTGCC
1 GGTGCC
68425 ATCATCTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 2 0.07
15 25 0.86
16 2 0.07
ACGTcount: A:0.06, C:0.22, G:0.33, T:0.39
Consensus pattern (15 bp):
GGTGCCGTCGATTTT
Done.