Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017642.1 Corchorus olitorius cultivar O-4 contig17675, 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: 117105
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:722 original size:31 final size:29
Alignment explanation
Indices: 672--817 Score: 98
Period size: 31 Copynumber: 4.8 Consensus size: 29
662 TAAGAATATG
* * *
672 TCAAATAATCAATTTAGGATATAACGTTT
1 TCAAACAAGCAATTAAGGATATAACGTTT
*
701 GCTGC-AACAAGCAATTAAGGATATAATG-TT
1 --T-CAAACAAGCAATTAAGGATATAACGTTT
* *
731 ACAAAACAAACAATTAAGGATATAACGTTTT
1 TC-AAACAAGCAATTAAGGATATAACG-TTT
* ** *
762 TTATTTCAAGCAATTAAGGATATGACGTTT
1 TCA-AACAAGCAATTAAGGATATAACGTTT
**
792 TCGATTTCAAGCAATTAAGGATATAA
1 TC-A-AACAAGCAATTAAGGATATAA
818 TCAGTTAGGG
Statistics
Matches: 93, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
27 1 0.01
29 21 0.23
30 7 0.08
31 63 0.68
32 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (29 bp):
TCAAACAAGCAATTAAGGATATAACGTTT
Found at i:1010 original size:29 final size:31
Alignment explanation
Indices: 947--1010 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
937 CCTAACGGAC
*
947 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATACCCTTAATTGCTCGCTTTTCGTAACGT
*
978 TATACCCTTAATTGCTTG-TTTT-GTAACGT
1 TATACCCTTAATTGCTCGCTTTTCGTAACGT
1007 TATA
1 TATA
1011 TCCCAAATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 11 0.35
30 4 0.13
31 16 0.52
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (31 bp):
TATACCCTTAATTGCTCGCTTTTCGTAACGT
Found at i:1019 original size:29 final size:31
Alignment explanation
Indices: 947--1021 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 31
937 CCTAACGGAC
*
947 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCCTAATTGCTCGCTTTTCGTAACGT
*
978 TATA-CCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCC-TAATTGCTCGCTTTTCGTAACGT
*
1007 TATATCCCAAATTGC
1 TATATCCCTAATTGC
1022 ATTTTGCGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 17 0.44
30 9 0.23
31 13 0.33
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (31 bp):
TATATCCCTAATTGCTCGCTTTTCGTAACGT
Found at i:1180 original size:64 final size:64
Alignment explanation
Indices: 1078--1219 Score: 230
Period size: 64 Copynumber: 2.2 Consensus size: 64
1068 AAATTCTTAT
* * *
1078 ATCTGAAAACACTTTAGAAACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCAAC
1 ATCTGAAAACTCTTGAGAAACCATCTTCTAGTGTACTTCTTGACAAGATCGTCTTCCGATCAAC
* *
1142 TTCTGAAAACTCTTGAGAAATCATCTTCTAGTGTACTTCTTGACAAGATCGTCTTCCGATCAAC
1 ATCTGAAAACTCTTGAGAAACCATCTTCTAGTGTACTTCTTGACAAGATCGTCTTCCGATCAAC
*
1206 ATCTGAAAATTCTT
1 ATCTGAAAACTCTT
1220 TCTAGCAAAC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 71 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (64 bp):
ATCTGAAAACTCTTGAGAAACCATCTTCTAGTGTACTTCTTGACAAGATCGTCTTCCGATCAAC
Found at i:1271 original size:67 final size:67
Alignment explanation
Indices: 1187--1710 Score: 818
Period size: 67 Copynumber: 7.9 Consensus size: 67
1177 CTTCTTGACA
* * * * *
1187 AGATCGTCTTCCGATCAACATCTGAAAATTCTTTCTAGCAAACCGTCTTCCGATGTATTCCTTAA
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTCCTTAA
1252 TG
66 TG
* * *
1254 AGATTGTCTTCCAATCAACATTTGAAAATCCTTTCTAGCAAACCGTCTTTCGATGTACTCCTTAA
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTCCTTAA
1319 TG
66 TG
* * * ** *
1321 AGACTGTCTTCCAATCAACATTTGAAAATTCTTTCTACCAAACCGTCTTTCAATGTATTCCTTAA
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTCCTTAA
1386 TG
66 TG
* *
1388 AGATTGTCTTCCAATCAACATTTGAACATCCTTTCTAGCAAACCGTCTTCCGGTGTACTCCTTAA
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTCCTTAA
1453 TG
66 TG
* * *
1455 AGATTCTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACTGTCTTCTGGTGTACTCCTTAA
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTCCTTAA
1520 TG
66 TG
* *
1522 AGATTGTCTTCCAATCAACATTTGAACATCCTTTCTAGCAAACCGTCTTCCGGTGTACTCCTTAA
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTCCTTAA
1587 TG
66 TG
*
1589 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTT-CGGTGTAATCCTTAA
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTCCTTAA
1653 TG
66 TG
* *
1655 AGATTGTCTTCCAATCAACATTTGAAAACTC-TTCTAGCAAACCGTCTTCTGGTGTA
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTA
1711 TGCTTCTAAA
Statistics
Matches: 422, Mismatches: 34, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
65 17 0.04
66 52 0.12
67 353 0.84
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (67 bp):
AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTCCTTAA
TG
Found at i:2997 original size:20 final size:20
Alignment explanation
Indices: 2972--3010 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2962 TTTGCGGTAG
2972 TTCCAATTT-TTATGTGGTGA
1 TTCCAATTTCTT-TGTGGTGA
2992 TTCCAATTTCTTTGTGGTG
1 TTCCAATTTCTTTGTGGTG
3011 GTGACAACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (20 bp):
TTCCAATTTCTTTGTGGTGA
Found at i:7340 original size:18 final size:19
Alignment explanation
Indices: 7305--7343 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
7295 AAAATTAAAG
*
7305 TTTTTGGTCTATGATTTGA
1 TTTTTGGGCTATGATTTGA
*
7324 TTTTTGGGCT-TGTTTTGA
1 TTTTTGGGCTATGATTTGA
7342 TT
1 TT
7344 AAAGTTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.10, C:0.05, G:0.23, T:0.62
Consensus pattern (19 bp):
TTTTTGGGCTATGATTTGA
Found at i:8019 original size:19 final size:18
Alignment explanation
Indices: 7974--8010 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
7964 GTCAAAGTCG
7974 AAGAA-AAAAAATGAAAA
1 AAGAAGAAAAAATGAAAA
7991 AAGAAGAAAAAATGAAAA
1 AAGAAGAAAAAATGAAAA
8009 AA
1 AA
8011 ATCAGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (18 bp):
AAGAAGAAAAAATGAAAA
Found at i:12344 original size:11 final size:11
Alignment explanation
Indices: 12328--12353 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12318 AGATAATTTA
12328 TTTTCTTCTAG
1 TTTTCTTCTAG
12339 TTTTCTTCTAG
1 TTTTCTTCTAG
12350 TTTT
1 TTTT
12354 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:13144 original size:15 final size:15
Alignment explanation
Indices: 13114--13155 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
13104 TTACTTTGCT
13114 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
13130 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
13145 TTGCTTTCTGT
1 TTGTTTTCTGT
13156 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:16729 original size:17 final size:16
Alignment explanation
Indices: 16707--16783 Score: 75
Period size: 17 Copynumber: 4.6 Consensus size: 16
16697 GGAATTTTAG
16707 AATTAAAAAATTAAAGT
1 AATTAAAAAATT-AAGT
** *
16724 AATTAAAAAATTTTCGG
1 AATTAAAAAA-TTAAGT
16741 AATTAAAAAAATTAAGT
1 AATT-AAAAAATTAAGT
*
16758 AATT-AAAAATTTAGT
1 AATTAAAAAATTAAGT
16773 CAATTAAAAAA
1 -AATTAAAAAA
16784 AATAAAGGTG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
15 10 0.20
16 4 0.08
17 27 0.55
18 8 0.16
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
AATTAAAAAATTAAGT
Found at i:16765 original size:15 final size:16
Alignment explanation
Indices: 16747--16782 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
16737 TCGGAATTAA
16747 AAAAATTAAGT-AATT
1 AAAAATTAAGTCAATT
*
16762 AAAAATTTAGTCAATT
1 AAAAATTAAGTCAATT
16778 AAAAA
1 AAAAA
16783 AAATAAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAAATTAAGTCAATT
Found at i:16783 original size:34 final size:34
Alignment explanation
Indices: 16699--16790 Score: 111
Period size: 33 Copynumber: 2.7 Consensus size: 34
16689 CGTCACATGG
*
16699 AATTTTAGAATT-AAAAAATTAAAGTAATTAAAA
1 AATTTTCGAATTAAAAAAATTAAAGTAATTAAAA
16732 AATTTTCGGAATTAAAAAAATT-AAGTAATT-AAA
1 AATTTTC-GAATTAAAAAAATTAAAGTAATTAAAA
*
16765 AATTTAGTC-AATTAAAAAAAATAAAG
1 AATTT--TCGAATTAAAAAAATTAAAG
16791 GTGGCCATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
33 26 0.50
34 16 0.31
35 10 0.19
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.32
Consensus pattern (34 bp):
AATTTTCGAATTAAAAAAATTAAAGTAATTAAAA
Found at i:18395 original size:31 final size:31
Alignment explanation
Indices: 18307--18395 Score: 78
Period size: 30 Copynumber: 2.9 Consensus size: 31
18297 ACATTTTTGT
* *
18307 AACGTTATATCCTGAATTG-TCACCTCA-TCA
1 AACGTTATATCCTGAATTGATCA-TTTAGTCA
* * *
18337 AACATTATATCCTCAATTGGAT-TTTTAGGT-A
1 AACGTTATATCCTGAATT-GATCATTTA-GTCA
18368 AACGTTATATCCTGAATTGATCATTTAG
1 AACGTTATATCCTGAATTGATCATTTAG
18396 CCACTTTTGA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
30 22 0.48
31 22 0.48
32 2 0.04
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (31 bp):
AACGTTATATCCTGAATTGATCATTTAGTCA
Found at i:20074 original size:20 final size:20
Alignment explanation
Indices: 20046--20084 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20036 TTTTTAAAAA
*
20046 TTAATAATTAGTTACTATTT
1 TTAAAAATTAGTTACTATTT
*
20066 TTAAAAATTAGTTATTATT
1 TTAAAAATTAGTTACTATT
20085 GTTTTATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (20 bp):
TTAAAAATTAGTTACTATTT
Found at i:23573 original size:33 final size:33
Alignment explanation
Indices: 23530--23603 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
23520 CCGTTCTCCA
*
23530 GGGACAGCACCCACCGTGGTGGGCTGTCCTACG
1 GGGACGGCACCCACCGTGGTGGGCTGTCCTACG
*
23563 GGGACGGCACCCACCGTGGTGGGCTGTCCTCCG
1 GGGACGGCACCCACCGTGGTGGGCTGTCCTACG
23596 GGGACGGC
1 GGGACGGC
23604 TCCATGCCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.12, C:0.34, G:0.41, T:0.14
Consensus pattern (33 bp):
GGGACGGCACCCACCGTGGTGGGCTGTCCTACG
Found at i:26176 original size:15 final size:15
Alignment explanation
Indices: 26146--26187 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
26136 TTACTTTGTT
26146 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
26162 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
26177 TTGTTTTCTGT
1 TTGTTTTCTGT
26188 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:26593 original size:28 final size:28
Alignment explanation
Indices: 26539--26595 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
26529 GTTTTTGCGT
*** *
26539 TTTATAAAAAAAAAGGTTTTTTACGTCA
1 TTTATAAAAAAAAAAAATTTCTACGTCA
*
26567 TTTATAAAAAAAAAAAATTTCTGCGTCA
1 TTTATAAAAAAAAAAAATTTCTACGTCA
26595 T
1 T
26596 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (28 bp):
TTTATAAAAAAAAAAAATTTCTACGTCA
Found at i:28642 original size:22 final size:21
Alignment explanation
Indices: 28617--28661 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
28607 CAACCTAGCT
28617 GGCCAATACTCGG-CTATGGCCC
1 GGCC-ATACTCGGAC-ATGGCCC
*
28639 GGCCATCCTCGGACATGGCCC
1 GGCCATACTCGGACATGGCCC
28660 GG
1 GG
28662 ATAGGACCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.16, C:0.38, G:0.31, T:0.16
Consensus pattern (21 bp):
GGCCATACTCGGACATGGCCC
Found at i:29396 original size:15 final size:14
Alignment explanation
Indices: 29376--29405 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
29366 ATCTCTTTAA
29376 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
29391 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
29405 T
1 T
29406 GCTTTAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:32287 original size:15 final size:15
Alignment explanation
Indices: 32257--32298 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
32247 TTACTTTGTT
32257 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
32273 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
32288 TTGTTTTCTGT
1 TTGTTTTCTGT
32299 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:33273 original size:45 final size:45
Alignment explanation
Indices: 33209--33336 Score: 229
Period size: 45 Copynumber: 2.8 Consensus size: 45
33199 CGCAACAATT
*
33209 AATATTAACTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
* *
33254 AATATTAGCTTTATTTTGATGAATTACCTAGAGATAGAGGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
33299 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGA
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGA
33337 ATAGAATTTA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
Found at i:38368 original size:16 final size:15
Alignment explanation
Indices: 38347--38393 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
38337 AGGAATAAGC
38347 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
38362 TAATCAATCAAAGCAA
1 -AATCAATCAAAGCAA
38378 AAT-AATGCAAAG-AA
1 AATCAAT-CAAAGCAA
38392 AA
1 AA
38394 AGTAAATGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.23
15 8 0.27
16 15 0.50
ACGTcount: A:0.62, C:0.15, G:0.09, T:0.15
Consensus pattern (15 bp):
AATCAATCAAAGCAA
Found at i:44761 original size:27 final size:27
Alignment explanation
Indices: 44721--44795 Score: 132
Period size: 27 Copynumber: 2.8 Consensus size: 27
44711 AAAAATGATG
**
44721 AAATTGCTTTGACTAATAATAACAATC
1 AAATTGCTCGGACTAATAATAACAATC
44748 AAATTGCTCGGACTAATAATAACAATC
1 AAATTGCTCGGACTAATAATAACAATC
44775 AAATTGCTCGGACTAATAATA
1 AAATTGCTCGGACTAATAATA
44796 GACATAACAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (27 bp):
AAATTGCTCGGACTAATAATAACAATC
Found at i:56320 original size:15 final size:15
Alignment explanation
Indices: 56300--56329 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
56290 TCTTTGTATT
56300 TGCTTGGTCTTTTGC
1 TGCTTGGTCTTTTGC
56315 TGCTTGGTCTTTTGC
1 TGCTTGGTCTTTTGC
56330 AAGACTGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.20, G:0.27, T:0.53
Consensus pattern (15 bp):
TGCTTGGTCTTTTGC
Found at i:58240 original size:546 final size:546
Alignment explanation
Indices: 57208--58303 Score: 2007
Period size: 546 Copynumber: 2.0 Consensus size: 546
57198 CTGCTTTCCT
57208 GCATATCTCAGTCCATATCCAACAAATGATACCGATGCTTATGATGAACTTCATTGTCTCAAGTA
1 GCATATCTCAGTCCATATCCAACAAATGATACCGATGCTTATGATGAACTTCATTGTCTCAAGTA
57273 TTTCAATGACTTTTCGATCTATCATAACGATTATCTCCAACAAGCGATCGAGGAGCTAAAACAAG
66 TTTCAATGACTTTTCGATCTATCATAACGATTATCTCCAACAAGCGATCGAGGAGCTAAAACAAG
*
57338 AACATCCCAATGTGATCATTGCCTATGGGAACTACTACGATTCATTCCTCTGGCTTTTCAGCAGG
131 AACATCCCAATGTGATCATTGCCTATGGGAACTACTACGATTCATTCCTCTAGCTTTTCAGCAGG
** *
57403 GATAATATGCTTGGTAAGTGCAACTCTTGTTTGTTTGCAATAATAAATTTGAAATTCCAGTCATG
196 GATAATATGCTTGGTAAGTAAAACTCTTGTTTGTTTGCAATAATAAATTTGAAATTCCAATCATG
57468 TATTGAGAGATTGTAAAAAATGTTTACAGGTTTTGATCCGAAATCATTACAAAAAGGTTGTTGCG
261 TATTGAGAGATTGTAAAAAATGTTTACAGGTTTTGATCCGAAATCATTACAAAAAGGTTGTTGCG
* * *
57533 GAAGTGGAGGTGCAACAGTATGTTCAAACCTTGATGAACGAGTGAGTTGGGATGGAGTTCATTTG
326 GAAGTGGAGGTGCAACAATATGTTCAAACCCTGATGAACAAGTGAGTTGGGATGGAGTTCATTTG
57598 ACACAAAGGGCTTATGATTTAATGGCATCATGGCTTATCCGAGACATTTATCCGAAACTGCAATG
391 ACACAAAGGGCTTATGATTTAATGGCATCATGGCTTATCCGAGACATTTATCCGAAACTGCAATG
*
57663 CAAGCAGTTTGATTCATAAATTTCTTCTATCTAGTTTTAGATATTTTGAGACTCTGTTTGTTTAA
456 CAAGCAGTTTGATTCATAAACTTCTTCTATCTAGTTTTAGATATTTTGAGACTCTGTTTGTTTAA
57728 TTTTTATTTGCTCTTTC-GATGTAAAA
521 TTTTTATTTGCTCTTTCAG-TGTAAAA
* * *
57754 GCATATCTCGGTCGATATCCAACAAATGATACC-AGTGCTTATGATGAACTTCATTGTCTCAGGT
1 GCATATCTCAGTCCATATCCAACAAATGATACCGA-TGCTTATGATGAACTTCATTGTCTCAAGT
*
57818 ATTTCAATGACTTTTCGATCTATCATAACGATTATCTCCAACAAGTGATCGAGGAGCTAAAACAA
65 ATTTCAATGACTTTTCGATCTATCATAACGATTATCTCCAACAAGCGATCGAGGAGCTAAAACAA
*
57883 GAACATCCCAATGTGATCATTGTCTATGGGAACTACTACGATTCATTCCTCTAGCTTTTCAGCAG
130 GAACATCCCAATGTGATCATTGCCTATGGGAACTACTACGATTCATTCCTCTAGCTTTTCAGCAG
* *
57948 GGATAATATGCTTGGTAAGTAAAACTCTTGTTTGTTTGCAATAATAAATTTGAGATTGCAATCAT
195 GGATAATATGCTTGGTAAGTAAAACTCTTGTTTGTTTGCAATAATAAATTTGAAATTCCAATCAT
58013 GTATTGAGAGATTGTAAAAAATGTTTACAGGTTTTGATCCGAAATCATTACAAAAAGGTTGTTGC
260 GTATTGAGAGATTGTAAAAAATGTTTACAGGTTTTGATCCGAAATCATTACAAAAAGGTTGTTGC
58078 GGAAGTGGAGGTGCAACAATATGTTCAAACCCTGATGAACAAGTGAGTTGGGATGGAGTTCATTT
325 GGAAGTGGAGGTGCAACAATATGTTCAAACCCTGATGAACAAGTGAGTTGGGATGGAGTTCATTT
58143 GACACAAAGGGCTTATGATTTAATGGCATCATGGCTTATCCGAGACATTTATCCGAAACTGCAAT
390 GACACAAAGGGCTTATGATTTAATGGCATCATGGCTTATCCGAGACATTTATCCGAAACTGCAAT
* *
58208 GCAAGCAGTTTGATTCATATACTTCTTCTATCTAGTTTTAGATATTTTGAGATTCTGTTTGTTTA
455 GCAAGCAGTTTGATTCATAAACTTCTTCTATCTAGTTTTAGATATTTTGAGACTCTGTTTGTTTA
58273 ATTTTTATTTGCTCTTTCAGTGTAAAA
520 ATTTTTATTTGCTCTTTCAGTGTAAAA
58300 GCAT
1 GCAT
58304 TACTCCACAG
Statistics
Matches: 531, Mismatches: 17, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
545 1 0.00
546 529 1.00
547 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (546 bp):
GCATATCTCAGTCCATATCCAACAAATGATACCGATGCTTATGATGAACTTCATTGTCTCAAGTA
TTTCAATGACTTTTCGATCTATCATAACGATTATCTCCAACAAGCGATCGAGGAGCTAAAACAAG
AACATCCCAATGTGATCATTGCCTATGGGAACTACTACGATTCATTCCTCTAGCTTTTCAGCAGG
GATAATATGCTTGGTAAGTAAAACTCTTGTTTGTTTGCAATAATAAATTTGAAATTCCAATCATG
TATTGAGAGATTGTAAAAAATGTTTACAGGTTTTGATCCGAAATCATTACAAAAAGGTTGTTGCG
GAAGTGGAGGTGCAACAATATGTTCAAACCCTGATGAACAAGTGAGTTGGGATGGAGTTCATTTG
ACACAAAGGGCTTATGATTTAATGGCATCATGGCTTATCCGAGACATTTATCCGAAACTGCAATG
CAAGCAGTTTGATTCATAAACTTCTTCTATCTAGTTTTAGATATTTTGAGACTCTGTTTGTTTAA
TTTTTATTTGCTCTTTCAGTGTAAAA
Found at i:60502 original size:93 final size:93
Alignment explanation
Indices: 60417--60601 Score: 316
Period size: 93 Copynumber: 2.0 Consensus size: 93
60407 ACTTTTTAAT
* * *
60417 TAAATTAGTAATATTGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
60482 AGTTTTTAGTTGAGTAAAACTATAAAAG
66 AGTTTTTAGTTGACTAAAACTATAAAAG
* *
60510 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATGTTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
60575 AGTTTTTAGTTGACTAAAACTATAAAA
66 AGTTTTTAGTTGACTAAAACTATAAAA
60602 ATTTAAATAA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.34
Consensus pattern (93 bp):
TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:60519 original size:22 final size:22
Alignment explanation
Indices: 60494--60540 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
60484 TTTTTAGTTG
*
60494 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
60516 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
60538 AGT
1 AGT
60541 TATAAGGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:60672 original size:31 final size:31
Alignment explanation
Indices: 60637--60698 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
60627 ATATTTAAAA
60637 AATAAGGATATAATAGGCGATTCAAAAGTTT
1 AATAAGGATATAATAGGCGATTCAAAAGTTT
* *
60668 AATAAGGGTATAATAGGTGATTCAAAAGTTT
1 AATAAGGATATAATAGGCGATTCAAAAGTTT
60699 TACAAAACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (31 bp):
AATAAGGATATAATAGGCGATTCAAAAGTTT
Found at i:61171 original size:13 final size:13
Alignment explanation
Indices: 61153--61178 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61143 AGTTAATCAG
61153 TTAGGAGAAACTC
1 TTAGGAGAAACTC
61166 TTAGGAGAAACTC
1 TTAGGAGAAACTC
61179 ATACATCGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
TTAGGAGAAACTC
Found at i:61783 original size:31 final size:31
Alignment explanation
Indices: 61748--61809 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
61738 AAAAAGGGCA
61748 GGAGGAAAAGTAAGGGAGGAAATTCATCCCT
1 GGAGGAAAAGTAAGGGAGGAAATTCATCCCT
61779 GGAGGAAAAGTAAGGGAGGAAATTCATCCCT
1 GGAGGAAAAGTAAGGGAGGAAATTCATCCCT
61810 CGATTGCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.13, G:0.32, T:0.16
Consensus pattern (31 bp):
GGAGGAAAAGTAAGGGAGGAAATTCATCCCT
Found at i:63855 original size:106 final size:103
Alignment explanation
Indices: 63586--63847 Score: 343
Period size: 103 Copynumber: 2.5 Consensus size: 103
63576 ATAAGATTTT
* *
63586 AATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAAACCCTATAGCA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACA
63649 ATATTATTAATTATAGAATTTACCCTTAAAATAAAAAA
66 ATATTATTAATTATAGAATTTACCCTTAAAATAAAAAA
*** * * *
63687 AAAAATAATTTGGGGCTAAACTTAGTAAAATTAGTTTTGTATTTTATTTCTAGAACCCTATAACA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACA
* * *
63752 ATAAATTATTGATT-TTGAAATTTACCTTTAAAATAAAAATA
66 AT--ATTATTAATTATAG-AATTTACCCTTAAAATAAAAA-A
*
63793 ACATTTTAATTTGGGGCTACA-TTAGTGAAATTAGTTTTATATTTTATTTCTAAAA
1 A-ATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAA
63848 TTCTATAATA
Statistics
Matches: 136, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
101 8 0.06
102 14 0.10
103 35 0.26
104 2 0.01
105 29 0.21
106 33 0.24
107 15 0.11
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.42
Consensus pattern (103 bp):
AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACA
ATATTATTAATTATAGAATTTACCCTTAAAATAAAAAA
Found at i:68738 original size:41 final size:42
Alignment explanation
Indices: 68674--68874 Score: 237
Period size: 41 Copynumber: 4.8 Consensus size: 42
68664 TAGAGAAAAT
* *
68674 TGCCCCTGTGTTATAATTATGTTTGGGGACTTTGATATAGA-
1 TGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATAGAG
* * * * * *
68715 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTAGAGAGAAT
1 TGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATAG-AG
*
68758 TGTCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATAGA-
1 TGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATAGAG
* * * *
68799 TGGCTCTGTGTTATAAATGTGTTTGAGAACTTTGGA-ATAGAGG
1 TGCCCCTGTGTTATAAATGTGTTTGGGGACTTT-GATATAGA-G
68842 TGCCCCTGTGTTATAAATGTGTTTGGGGACTTT
1 TGCCCCTGTGTTATAAATGTGTTTGGGGACTTT
68875 TAGTTATTGG
Statistics
Matches: 134, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
41 67 0.50
42 4 0.03
43 63 0.47
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.40
Consensus pattern (42 bp):
TGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATAGAG
Found at i:68806 original size:84 final size:83
Alignment explanation
Indices: 68664--68874 Score: 314
Period size: 84 Copynumber: 2.5 Consensus size: 83
68654 GCCTTTGCCA
* * *
68664 TAGAGAAAATTGCCCCTGTGTTATAATTATGTTTGGGGACTTTGATATAGATGCCTCTGTGTTAT
1 TAGAGAGAATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTAT
*
68729 AAATGTGTTTGAGGACTTT
66 AAATGTGTTTGAGAAC-TT
* *
68748 TAGAGAGAATTGTCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATAGATGGCTCTGTGTTAT
1 TAGAGAGAATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTAT
68813 AAATGTGTTTGAGAACTT
66 AAATGTGTTTGAGAACTT
* * **
68831 TGGAATAGAGGTGCCCCTGTGTTATAAATGTGTTTGGGGACTTT
1 TAG-AGAGAATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTT
68875 TAGTTATTGG
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
83 4 0.03
84 111 0.97
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (83 bp):
TAGAGAGAATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTAT
AAATGTGTTTGAGAACTT
Found at i:70355 original size:23 final size:23
Alignment explanation
Indices: 70268--70355 Score: 61
Period size: 23 Copynumber: 3.8 Consensus size: 23
70258 GCTTCTGGGG
*
70268 CTCCCCGCGT-GCGGCAAGGTGAC
1 CTCCCCGC-TCGCGGCAAGGGGAC
* * * *
70291 CTTCTCGCTCACGTCAAGGGGAAC
1 CTCCCCGCTCGCGGCAAGGGG-AC
** * **
70315 CTCCCCATTCTCTTCAAGGGGAC
1 CTCCCCGCTCGCGGCAAGGGGAC
70338 CTCCCCGCTCGCGGCAAG
1 CTCCCCGCTCGCGGCAAG
70356 CATAGGGGAT
Statistics
Matches: 47, Mismatches: 16, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
22 1 0.02
23 29 0.62
24 17 0.36
ACGTcount: A:0.16, C:0.40, G:0.26, T:0.18
Consensus pattern (23 bp):
CTCCCCGCTCGCGGCAAGGGGAC
Found at i:75115 original size:30 final size:30
Alignment explanation
Indices: 75054--75146 Score: 134
Period size: 31 Copynumber: 3.1 Consensus size: 30
75044 AAGGGACTGA
* **
75054 TTTGTTCCAAAAGAAAAA-ATAAGAAATTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTT
75083 TTTGTCCCAAAAGAAAAACATAAGGGAGTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGA-TTT
*
75114 TTTGTCCCAAAAGAAAAACATGAGGGATTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTT
75144 TTT
1 TTT
75147 TTAGTATTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
29 17 0.29
30 12 0.21
31 29 0.50
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (30 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTT
Found at i:75441 original size:126 final size:125
Alignment explanation
Indices: 75305--75531 Score: 323
Period size: 126 Copynumber: 1.8 Consensus size: 125
75295 AATGGTAGAG
**
75305 ATAAAATAGTTATAAAAATATT-GAATTTAATTAAATAAAAATAGAATTTTTGGTAAAATAAAAC
1 ATAAAATAGTTATAAAAATATTAG-ATTTAATTAAATAAAAATAGAATTTTTAATAAAATAAAA-
* *
75369 T-GTAAAAGTTTAAATAATGTCATTTATGAAATATATTTAATTAAAATAGTAAAATGATAAAA
64 TAGTAAAAGTTTAAA-AATGACATTTAAGAAATATATTTAATTAAAATAGTAAAATGATAAAA
* * * ** *
75431 ATAAAATAGTTATAAATATATTAGATTTGATTAAATAAAAATAGAGTTTTTAATTGAGTAAAATA
1 ATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAATTTTTAATAAAATAAAATA
75496 GTAAAAGTTTAAAAATGACATTTAAGAAATATATTT
66 GTAAAAGTTTAAAAATGACATTTAAGAAATATATTT
75532 GAAAAATAAG
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
125 22 0.25
126 66 0.74
127 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.37
Consensus pattern (125 bp):
ATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAATTTTTAATAAAATAAAATA
GTAAAAGTTTAAAAATGACATTTAAGAAATATATTTAATTAAAATAGTAAAATGATAAAA
Found at i:76089 original size:7 final size:7
Alignment explanation
Indices: 76077--76109 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
76067 AAGAAGGAGA
76077 AAAAAAG
1 AAAAAAG
76084 AAAAAAG
1 AAAAAAG
76091 AAAAAAG
1 AAAAAAG
76098 -AAAAAG
1 AAAAAAG
76104 AAAAAA
1 AAAAAA
76110 ATCAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:76101 original size:13 final size:14
Alignment explanation
Indices: 76077--76109 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
76067 AAGAAGGAGA
76077 AAAAAAGAAAAAAG
1 AAAAAAGAAAAAAG
76091 AAAAAAG-AAAAAG
1 AAAAAAGAAAAAAG
76104 AAAAAA
1 AAAAAA
76110 ATCAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAAG
Found at i:76110 original size:14 final size:14
Alignment explanation
Indices: 76074--76110 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
76064 GGAAAGAAGG
76074 AGAAAAAAAGAAAA
1 AGAAAAAAAGAAAA
76088 A-AGAAAAAAGAAAA
1 AGA-AAAAAAGAAAA
76102 AGAAAAAAA
1 AGAAAAAAA
76111 TCAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.05
14 19 0.90
15 1 0.05
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAGAAAA
Found at i:76192 original size:32 final size:32
Alignment explanation
Indices: 76152--76217 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
76142 ACTAAATACT
*
76152 AAAAAAATCCCTTATGTTTTTCTTTTGGGACA
1 AAAAAAATCCCTCATGTTTTTCTTTTGGGACA
76184 AAAAAAATCCCTCATGTTTTTCTTTTGGGACA
1 AAAAAAATCCCTCATGTTTTTCTTTTGGGACA
76216 AA
1 AA
76218 TCAGTCCCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (32 bp):
AAAAAAATCCCTCATGTTTTTCTTTTGGGACA
Found at i:76409 original size:29 final size:30
Alignment explanation
Indices: 76361--76440 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
76351 CTCATTTTTG
* * *
76361 AAACGTAAGGGATTAATTTGTCCCGAAA-A
1 AAACATAAGGGATTATTTTGTCCCAAAACA
*
76390 AAATATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA-CA
76421 AAACATAAGGGAATT-TTTTG
1 AAACATAAGGG-ATTATTTTG
76441 GGTATTTAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
29 24 0.56
31 16 0.37
32 3 0.07
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (30 bp):
AAACATAAGGGATTATTTTGTCCCAAAACA
Found at i:77745 original size:30 final size:30
Alignment explanation
Indices: 77709--77827 Score: 202
Period size: 30 Copynumber: 4.0 Consensus size: 30
77699 TAAGCCAAGT
77709 GGAAGAGCAACCAACAATGGGTGGCGGCGA
1 GGAAGAGCAACCAACAATGGGTGGCGGCGA
77739 GGAAGAGCAACCAACAATGGGTGGCGGCGA
1 GGAAGAGCAACCAACAATGGGTGGCGGCGA
* *
77769 GGAAGAGCAACCATCTATGGGTGGCGGCGA
1 GGAAGAGCAACCAACAATGGGTGGCGGCGA
* *
77799 GGAAGAGCAACCATCTATGGGTGGCGGCG
1 GGAAGAGCAACCAACAATGGGTGGCGGCG
77828 GACAAGGCAC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 87 1.00
ACGTcount: A:0.29, C:0.20, G:0.40, T:0.10
Consensus pattern (30 bp):
GGAAGAGCAACCAACAATGGGTGGCGGCGA
Found at i:78509 original size:33 final size:32
Alignment explanation
Indices: 78462--78527 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 32
78452 TCAAGCGTAT
* *
78462 TATTATCTATTTATTTTGACTAAGATGGATGA
1 TATTATCAATTTATTTTGACTAAGATAGATGA
78494 TATTATCAAATTTATTTTGACTAAGATAGATGA
1 TATTATC-AATTTATTTTGACTAAGATAGATGA
78527 T
1 T
78528 CTGTAGGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (32 bp):
TATTATCAATTTATTTTGACTAAGATAGATGA
Found at i:78959 original size:22 final size:22
Alignment explanation
Indices: 78934--78981 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
78924 ACAGAAGTCG
78934 AAGATTTTAAAGGATAAAGAAA
1 AAGATTTTAAAGGATAAAGAAA
*
78956 AAGATTTTAAAGGATAAAGGAA
1 AAGATTTTAAAGGATAAAGAAA
78978 AAGA
1 AAGA
78982 AATCTGGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (22 bp):
AAGATTTTAAAGGATAAAGAAA
Found at i:85931 original size:13 final size:13
Alignment explanation
Indices: 85913--85939 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
85903 GCTCTTCAAA
85913 TGGGAGACAAGGT
1 TGGGAGACAAGGT
85926 TGGGAGACAAGGT
1 TGGGAGACAAGGT
85939 T
1 T
85940 ACCACATGGA
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:0.30, C:0.07, G:0.44, T:0.19
Consensus pattern (13 bp):
TGGGAGACAAGGT
Found at i:87173 original size:9 final size:9
Alignment explanation
Indices: 87159--87183 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
87149 AAAAGTAAAG
87159 CTTTAAATC
1 CTTTAAATC
87168 CTTTAAATC
1 CTTTAAATC
87177 CTTTAAA
1 CTTTAAA
87184 CAAAGTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (9 bp):
CTTTAAATC
Found at i:89850 original size:6 final size:6
Alignment explanation
Indices: 89772--89847 Score: 143
Period size: 6 Copynumber: 12.7 Consensus size: 6
89762 GACCAAATAT
89772 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
*
89820 ATAAAA ATAAAA ATAAAA ATAATA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
89848 TAAAAGCTTT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:99004 original size:15 final size:14
Alignment explanation
Indices: 98984--99021 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
98974 AAATGGTTGC
98984 TTTGTTTTGTTTCGG
1 TTTGTTTTGTTTC-G
98999 TTTGTTTTGTTTCG
1 TTTGTTTTGTTTCG
*
99013 TTTGCTTTG
1 TTTGTTTTG
99022 ATGTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.00, C:0.08, G:0.24, T:0.68
Consensus pattern (14 bp):
TTTGTTTTGTTTCG
Found at i:103270 original size:17 final size:17
Alignment explanation
Indices: 103247--103285 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
103237 TCCCAATAAT
*
103247 AAAAAAAGAGAAGAAAAG
1 AAAAAATGA-AAGAAAAG
*
103265 AAAAAATGAAAGAACAG
1 AAAAAATGAAAGAAAAG
103282 AAAA
1 AAAA
103286 TGGAAAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAAAATGAAAGAAAAG
Found at i:105513 original size:69 final size:69
Alignment explanation
Indices: 104927--105500 Score: 889
Period size: 69 Copynumber: 8.3 Consensus size: 69
104917 TATTTTCTAA
*
104927 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCCAAG
1 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
104992 CAGC
66 CAGC
104996 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
1 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
*
105061 CAGT
66 CAGC
*
105065 AGGGGCTTTTCCACAAGCCAAACTTGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
1 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
*
105130 CAAC
66 CAGC
* * * * *
105134 AGGGGCTTTTCCACAAGTCAAATTCGTTTCCATACTAGTCAGTTCCAGCCTTGGTTCTATCCAAG
1 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
105199 CAGC
66 CAGC
* * *
105203 ATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGGTTTAAGCCTTGGTTCCATCCAAG
1 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
*
105268 CAAC
66 CAGC
* * * * *
105272 AGTAGGCTTTTCCACAAGCTAAACTTGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAA
1 AG-GGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAA
105337 GCAGC
65 GCAGC
* *
105342 AGGGACTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATTCAAG
1 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
105407 CAGC
66 CAGC
* * *
105411 -GTAGGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCGGTTCAAGCCTTGGTTCCATCCAA
1 AG-GGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAA
105475 GCAGC
65 GCAGC
* * *
105480 ATGTGCTTTTCCATAAGCCAA
1 AGGGGCTTTTCCACAAGCCAA
105501 GTTCATTTCC
Statistics
Matches: 456, Mismatches: 46, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
68 1 0.00
69 394 0.86
70 61 0.13
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (69 bp):
AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
CAGC
Found at i:105615 original size:105 final size:105
Alignment explanation
Indices: 105430--105618 Score: 261
Period size: 105 Copynumber: 1.8 Consensus size: 105
105420 TCCACAAGCC
* * * * *
105430 AAACTCATTTCCATACGAGTCGGTTCAAGCCTTGGTTCCATCCAAGCAGCATGTGCTTTTCCATA
1 AAACTCATTTCCATACGAGTCAGTTCAAGCCTTAGTTCCATCCAAGCAGCAGGGGCTTTTCCACA
**
105495 AGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
66 AGCCAAAATCATTTCCATATGAATTCAGTCTTCCAAGACT
* * *
105535 AAACTCGTTTCCATATGAGTCAGTTTAAGCCTTAGTTCCATCCAAGCAGCAGGGGCTTTTCCACA
1 AAACTCATTTCCATACGAGTCAGTTCAAGCCTTAGTTCCATCCAAGCAGCAGGGGCTTTTCCACA
* * *
105600 TGGCAAAATCGTTTCCATA
66 AGCCAAAATCATTTCCATA
105619 CGGTGCATTA
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
105 71 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (105 bp):
AAACTCATTTCCATACGAGTCAGTTCAAGCCTTAGTTCCATCCAAGCAGCAGGGGCTTTTCCACA
AGCCAAAATCATTTCCATATGAATTCAGTCTTCCAAGACT
Found at i:107678 original size:32 final size:32
Alignment explanation
Indices: 107640--107710 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
107630 AATACCACAT
*
107640 TCTCTCTCACACATGGGATCTCCTTCATAAGC
1 TCTCTCTCACACAGGGGATCTCCTTCATAAGC
107672 TCTCTCTCACACAGGGGATCTCCTTCATAAGC
1 TCTCTCTCACACAGGGGATCTCCTTCATAAGC
107704 TCTCTCT
1 TCTCTCT
107711 GATTCTTCCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (32 bp):
TCTCTCTCACACAGGGGATCTCCTTCATAAGC
Found at i:110810 original size:16 final size:17
Alignment explanation
Indices: 110784--110824 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
110774 TATTTTCATT
*
110784 TTTTTAATAA-TTAT-A
1 TTTTAAATAATTTATAA
110799 TTATTAAATAATTTATAA
1 TT-TTAAATAATTTATAA
110817 TTTTAAAT
1 TTTTAAAT
110825 TGATGTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 2 0.09
16 7 0.32
17 10 0.45
18 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAATAATTTATAA
Found at i:111829 original size:78 final size:78
Alignment explanation
Indices: 111714--111944 Score: 333
Period size: 78 Copynumber: 3.0 Consensus size: 78
111704 GTTTTTTAAT
* * *
111714 TAAAATAGTAAAAT-AAATAGTTATAAGGGTATTAGATTTTATTAGATAAAAATAGAGTTTTTAG
1 TAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTTATTAGATAAAAATAGAGTTTTTAG
*
111778 TTGAGTAAAATAG
66 TTGAGTAAAACAG
* * * * *
111791 TAAAATGGTAAAATAAAATAGTTATAAAGATATAAGATTTAATTAAATAAAATTAGAATTTTTAG
1 TAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTTATTAGATAAAAATAGAGTTTTTAG
111856 TTGAGTAAAACAG
66 TTGAGTAAAACAG
*
111869 TAAAATGGTAAAATAAAATAGTTATAAAGATATTAGA-TTTAGTT-GAATAAAAATAGAGTTTTC
1 TAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTTA-TTAG-ATAAAAATAGAGTTTTT
111932 AGTTGAGTAAAAC
64 AGTTGAGTAAAAC
111945 TGTAGAAGTT
Statistics
Matches: 136, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
77 16 0.12
78 120 0.88
ACGTcount: A:0.49, C:0.01, G:0.15, T:0.34
Consensus pattern (78 bp):
TAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTTATTAGATAAAAATAGAGTTTTTAG
TTGAGTAAAACAG
Found at i:112409 original size:10 final size:10
Alignment explanation
Indices: 112386--112433 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 10
112376 GAAGTTCGTG
112386 ATTGAAGAATA
1 ATTGAAG-ATA
112397 ATTGAAGATA
1 ATTGAAGATA
112407 ATTTGAAGAT-
1 A-TTGAAGATA
*
112417 A-TGAAGATC
1 ATTGAAGATA
112426 ATTGAAGA
1 ATTGAAGA
112434 ATTATTTCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 11 0.32
11 15 0.44
ACGTcount: A:0.48, C:0.02, G:0.21, T:0.29
Consensus pattern (10 bp):
ATTGAAGATA
Done.