Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1464.1
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: 445533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 5946 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:702 original size:88 final size:88
Alignment explanation
Indices: 602--777 Score: 343
Period size: 88 Copynumber: 2.0 Consensus size: 88
592 TTTGGGTGGG
*
602 GGGGGGGGGGGGAGAGGCGTTGCCCTTGACTCAATACAAAACCTATACAAGTCTATCAAATATAT
1 GGGGGGGAGGGGAGAGGCGTTGCCCTTGACTCAATACAAAACCTATACAAGTCTATCAAATATAT
667 AAGAGTTTCAAGACTTGCTAACA
66 AAGAGTTTCAAGACTTGCTAACA
690 GGGGGGGAGGGGAGAGGCGTTGCCCTTGACTCAATACAAAACCTATACAAGTCTATCAAATATAT
1 GGGGGGGAGGGGAGAGGCGTTGCCCTTGACTCAATACAAAACCTATACAAGTCTATCAAATATAT
755 AAGAGTTTCAAGACTTGCTAACA
66 AAGAGTTTCAAGACTTGCTAACA
778 TACTAGAGGT
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.23
Consensus pattern (88 bp):
GGGGGGGAGGGGAGAGGCGTTGCCCTTGACTCAATACAAAACCTATACAAGTCTATCAAATATAT
AAGAGTTTCAAGACTTGCTAACA
Found at i:3256 original size:20 final size:22
Alignment explanation
Indices: 3217--3256 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3207 ACACTTCTCG
*
3217 AGGTATCACGATATCCACCTCT
1 AGGTATCACGACATCCACCTCT
3239 AGGTATC-CGACA-CCACCT
1 AGGTATCACGACATCCACCT
3257 TCGTCAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 4 0.24
22 7 0.41
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (22 bp):
AGGTATCACGACATCCACCTCT
Found at i:11420 original size:31 final size:31
Alignment explanation
Indices: 11376--11441 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
11366 TTAATATAAT
* * *
11376 ATTTGGTAATTGAATTTGACAATTTTTTTTA
1 ATTTGATAATTGAACTTGACAATTTTTCTTA
* *
11407 ATTTGATATTTGAACTTGACTATTTTTCTTA
1 ATTTGATAATTGAACTTGACAATTTTTCTTA
11438 ATTT
1 ATTT
11442 AGTACTTGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.06, G:0.11, T:0.56
Consensus pattern (31 bp):
ATTTGATAATTGAACTTGACAATTTTTCTTA
Found at i:12615 original size:18 final size:18
Alignment explanation
Indices: 12592--12634 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12582 GAATAGGTTT
12592 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
12610 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
12628 TTAATTA
1 TTAATTA
12635 CACTTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:28178 original size:19 final size:19
Alignment explanation
Indices: 28154--28191 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28144 GCTTCCTTGC
28154 CATAGAAAATAAGCCTATT
1 CATAGAAAATAAGCCTATT
28173 CATAGAAAATAAGCCTATT
1 CATAGAAAATAAGCCTATT
28192 TCAGCTACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
CATAGAAAATAAGCCTATT
Found at i:29307 original size:14 final size:14
Alignment explanation
Indices: 29288--29315 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29278 ACAACCCCAG
29288 AACAATAGAAGAGT
1 AACAATAGAAGAGT
29302 AACAATAGAAGAGT
1 AACAATAGAAGAGT
29316 TAAGTTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
AACAATAGAAGAGT
Found at i:36393 original size:20 final size:21
Alignment explanation
Indices: 36352--36398 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
36342 GGCCCGGTCC
36352 ATTTTTTAATAAAATACTAAAA
1 ATTTTTTAATAAAATAC-AAAA
36374 ATTTATTTAA-AAAATA-AAAA
1 ATTT-TTTAATAAAATACAAAA
36394 ATTTT
1 ATTTT
36399 AAAAAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 8 0.33
22 10 0.42
23 5 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTTTTTAATAAAATACAAAA
Found at i:37669 original size:18 final size:18
Alignment explanation
Indices: 37642--37678 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
37632 ATAGCAAAAC
* *
37642 ATGCATAAACAACACTAA
1 ATGCAAAAACAAAACTAA
37660 ATGCAAAAACAAAACTAA
1 ATGCAAAAACAAAACTAA
37678 A
1 A
37679 ACACAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.19, G:0.05, T:0.14
Consensus pattern (18 bp):
ATGCAAAAACAAAACTAA
Found at i:40140 original size:6 final size:6
Alignment explanation
Indices: 40129--40153 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40119 ACCATACGCA
40129 TGCATC TGCATC TGCATC TGCATC T
1 TGCATC TGCATC TGCATC TGCATC T
40154 TCAACTCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (6 bp):
TGCATC
Found at i:44828 original size:21 final size:22
Alignment explanation
Indices: 44799--44845 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
44789 CAGAAGGAGT
*
44799 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
44821 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
44842 GAGT
1 GAGT
44846 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:46638 original size:13 final size:13
Alignment explanation
Indices: 46622--46647 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46612 TTATAACTTG
46622 AATTTAATATTTA
1 AATTTAATATTTA
46635 AATTTAATATTTA
1 AATTTAATATTTA
46648 TTTTTCAATT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTAATATTTA
Found at i:48403 original size:15 final size:16
Alignment explanation
Indices: 48383--48419 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
48373 GATTTTTCCC
*
48383 TAAAAA-AATCAAATA
1 TAAAAATAATAAAATA
48398 TAAAAATAATAAAATA
1 TAAAAATAATAAAATA
48414 TAAAAA
1 TAAAAA
48420 GCATCAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (16 bp):
TAAAAATAATAAAATA
Found at i:56801 original size:17 final size:17
Alignment explanation
Indices: 56776--56810 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
56766 TCACTGGAAA
56776 ATTAAATTTTAACAACT
1 ATTAAATTTTAACAACT
* *
56793 ATTAGATTTTAGCAACT
1 ATTAAATTTTAACAACT
56810 A
1 A
56811 AGAGTACGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (17 bp):
ATTAAATTTTAACAACT
Found at i:57776 original size:51 final size:51
Alignment explanation
Indices: 57721--57817 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
57711 GTTGTTGCTT
* *
57721 TGGTTAAGATACTTAGTAGTTTGTTTTAATTTTTGAAGATTTTATGGCTAG
1 TGGTTAAGATACTTAGTAATTTGTTTTAATTATTGAAGATTTTATGGCTAG
* * *
57772 TGGTTAAGTTACTTATTAATTTGTTTTAGTTATTGAAGATTTTATG
1 TGGTTAAGATACTTAGTAATTTGTTTTAATTATTGAAGATTTTATG
57818 TCTCAATACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.26, C:0.03, G:0.20, T:0.52
Consensus pattern (51 bp):
TGGTTAAGATACTTAGTAATTTGTTTTAATTATTGAAGATTTTATGGCTAG
Found at i:58448 original size:13 final size:13
Alignment explanation
Indices: 58430--58454 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58420 AATATTGCCT
58430 TTATTATTATTTG
1 TTATTATTATTTG
58443 TTATTATTATTT
1 TTATTATTATTT
58455 TTTAGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTATTATTATTTG
Found at i:59120 original size:25 final size:27
Alignment explanation
Indices: 59091--59144 Score: 94
Period size: 25 Copynumber: 2.1 Consensus size: 27
59081 GTATCCCAAT
59091 AAATAAATATTATATC-AAA-ACATAA
1 AAATAAATATTATATCAAAATACATAA
59116 AAATAAATATTATATCAAAATACATAA
1 AAATAAATATTATATCAAAATACATAA
59143 AA
1 AA
59145 TTATATACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 16 0.59
26 3 0.11
27 8 0.30
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (27 bp):
AAATAAATATTATATCAAAATACATAA
Found at i:59299 original size:18 final size:16
Alignment explanation
Indices: 59276--59311 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
59266 ATAGGGTTTT
59276 TAAAAGTATATTATAAAA
1 TAAAAGT-TATTA-AAAA
59294 TAAAAGTTATTAAAAA
1 TAAAAGTTATTAAAAA
59310 TA
1 TA
59312 TATTATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAAAGTTATTAAAAA
Found at i:59396 original size:39 final size:38
Alignment explanation
Indices: 59352--59427 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 38
59342 CATCACAAAG
* * *
59352 TTAAAATAATAATGTATGATAATAATAAAATAAAATAAT
1 TTAAAATAATAATGCATAATAA-AATAAAAAAAAATAAT
* *
59391 TTAAAATAATAGTGCATAATAAAGTAAAAAAAAATAA
1 TTAAAATAATAATGCATAATAAAATAAAAAAAAATAA
59428 GTAACTGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
38 13 0.41
39 19 0.59
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (38 bp):
TTAAAATAATAATGCATAATAAAATAAAAAAAAATAAT
Found at i:59492 original size:23 final size:23
Alignment explanation
Indices: 59466--59510 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
59456 ATAATGTCAA
59466 TAATAATAATAATAA-TAATAAAT
1 TAATAATAA-AATAATTAATAAAT
* *
59489 TAATATTAAACTAATTAATAAA
1 TAATAATAAAATAATTAATAAA
59511 ACAATGGGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TAATAATAAAATAATTAATAAAT
Found at i:60435 original size:11 final size:11
Alignment explanation
Indices: 60415--60481 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
60405 CAAAAATTAA
60415 AAAAAGTATTTT
1 AAAAA-TATTTT
60427 AAAAATATTTT
1 AAAAATATTTT
60438 --AAA-A-TTT
1 AAAAATATTTT
* *
60445 AAAAA-AATTA
1 AAAAATATTTT
60455 AAAAAGTATTTT
1 AAAAA-TATTTT
*
60467 AAAAAAATTTT
1 AAAAATATTTT
60478 AAAA
1 AAAA
60482 TTAAAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
7 3 0.07
8 1 0.02
9 7 0.15
10 7 0.15
11 15 0.33
12 13 0.28
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:60442 original size:43 final size:42
Alignment explanation
Indices: 60388--60533 Score: 199
Period size: 43 Copynumber: 3.5 Consensus size: 42
60378 ACCAAAAATT
60388 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAA-AAAAATTAAAAAAAGTATTTTAAAAA
*
60432 TATTTTAAAATT-TAAAAAAATT-AAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAAATTAAAAAAAGTATTTTAAAAA
* * *
60472 AATTTTAAAATTAAAAAAATTAA-AAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAA--AATTAAAAAAAGTATTTTAAAAA
60515 TATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
60534 TAAAAATATT
Statistics
Matches: 92, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
40 29 0.32
41 12 0.13
42 2 0.02
43 43 0.47
44 6 0.07
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.34
Consensus pattern (42 bp):
TATTTTAAAATTAAAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:60455 original size:9 final size:9
Alignment explanation
Indices: 60438--60499 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
60428 AAAATATTTT
*
60438 AAAATTTAA
1 AAAAATTAA
60447 AAAAATTAA
1 AAAAATTAA
60456 AAAAGTATTTTAA
1 AAAA--A--TTAA
*
60469 AAAAATT-T
1 AAAAATTAA
*
60477 TAAAATTAA
1 AAAAATTAA
60486 AAAAATTAA
1 AAAAATTAA
60495 AAAAA
1 AAAAA
60500 AAAGTATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
8 6 0.14
9 27 0.63
11 2 0.05
13 8 0.19
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAAATTAA
Found at i:60498 original size:17 final size:17
Alignment explanation
Indices: 60465--60498 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
60455 AAAAAGTATT
**
60465 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTAAAAAA
60482 TTAAAAAAATTAAAAAA
1 TTAAAAAAATTAAAAAA
60499 AAAAGTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAAAAAAATTAAAAAA
Found at i:60513 original size:11 final size:11
Alignment explanation
Indices: 60499--60524 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
60489 AATTAAAAAA
60499 AAAAGTATTTT
1 AAAAGTATTTT
60510 AAAAGTATTTT
1 AAAAGTATTTT
60521 AAAA
1 AAAA
60525 TTAAAAAAAT
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:73342 original size:19 final size:19
Alignment explanation
Indices: 73318--73468 Score: 212
Period size: 19 Copynumber: 7.8 Consensus size: 19
73308 AATTTTTGAG
73318 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
73337 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
73356 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
73377 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
** *
73396 GATATATAATTTTAGATAT
1 GATATGCAATCTTAGATAT
*
73415 GATATGCAATCTTAGAGAT
1 GATATGCAATCTTAGATAT
**
73434 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
73453 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
73469 ATATATGATT
Statistics
Matches: 114, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
19 97 0.85
21 17 0.15
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:73363 original size:40 final size:38
Alignment explanation
Indices: 73325--73468 Score: 234
Period size: 38 Copynumber: 3.7 Consensus size: 38
73315 GAGGATATGC
**
73325 AATCTTAGATATGATATGCAATCCAAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
73363 GCAATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 --AATCTTAGATATGATATGCAATCTTAGATATGATATAT
* *
73403 AATTTTAGATATGATATGCAATCTTAGAGATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
73441 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
73469 ATATATGATT
Statistics
Matches: 99, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
38 63 0.64
40 36 0.36
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATGATATAT
Found at i:74896 original size:98 final size:98
Alignment explanation
Indices: 74776--74972 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
74766 TAAAAAATAA
* *
74776 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
74841 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
74874 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
74939 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
74972 T
1 T
74973 TTTATTGTAC
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:79071 original size:12 final size:12
Alignment explanation
Indices: 79055--79103 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
79045 AAAATATTTC
*
79055 AAAAAAAAAGAGG
1 AAAAAGAAA-AGG
79068 AAAAAGAAAAGG
1 AAAAAGAAAAGG
*
79080 AAAAAGGAAAAAAG
1 AAAAA-G-AAAAGG
79094 AAAAAGAAAA
1 AAAAAGAAAA
79104 AGTAAAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 12 0.38
13 10 0.31
14 10 0.31
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGG
Found at i:79086 original size:7 final size:7
Alignment explanation
Indices: 79060--79110 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
79050 ATTTCAAAAA
79060 AAAAGAGG
1 AAAA-AGG
79068 AAAAA-G
1 AAAAAGG
79074 -AAAAGG
1 AAAAAGG
79080 AAAAAGG
1 AAAAAGG
*
79087 AAAAAAG
1 AAAAAGG
79094 AAAAA-G
1 AAAAAGG
*
79100 AAAAAGT
1 AAAAAGG
79107 AAAA
1 AAAA
79111 GGAGAGGCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 4 0.11
6 8 0.21
7 22 0.58
8 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (7 bp):
AAAAAGG
Found at i:79091 original size:20 final size:20
Alignment explanation
Indices: 79055--79110 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
79045 AAAATATTTC
79055 AAAAA-AAAAGAGG-AAAAAG
1 AAAAAGAAAA-AGGAAAAAAG
*
79074 AAAAGGAAAAAGGAAAAAAG
1 AAAAAGAAAAAGGAAAAAAG
*
79094 AAAAAGAAAAAGTAAAA
1 AAAAAGAAAAAGGAAAA
79111 GGAGAGGCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.22
20 25 0.78
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAAGGAAAAAAG
Found at i:80560 original size:132 final size:132
Alignment explanation
Indices: 80318--80802 Score: 839
Period size: 132 Copynumber: 3.7 Consensus size: 132
80308 AACAGATCAG
* *
80318 TGAAAATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATC-AACGACGGCGAATCTTATC
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA-GACAGCGAATCTTATC
*
80382 TTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAA
65 TTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAA
80447 GGT
130 GGT
* *
80450 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACAGCGAATCTTATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCT
80515 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
80580 GT
131 GT
*
80582 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC-GACGAATCTTATA
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAG-CGAATCTTATC
* *
80646 TTTCCAAGATAGTGGGAAGCAGATTTAAGCCATCAAGCCTTGTCTCCCTGAGCAGCCGCGGAGAA
65 TTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAA
80711 GGT
130 GGT
* * *
80714 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGACAACAAATCTTATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCT
80779 TTCCAAGATAGTGGGAAGCAGATT
66 TTCCAAGATAGTGGGAAGCAGATT
80803 AAAGTCGACA
Statistics
Matches: 336, Mismatches: 14, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
131 1 0.00
132 333 0.99
133 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (132 bp):
TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCT
TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
GT
Found at i:80642 original size:44 final size:44
Alignment explanation
Indices: 80330--80827 Score: 137
Period size: 44 Copynumber: 11.3 Consensus size: 44
80320 AAAATTGTAG
* * *
80330 ATCTTATCTCCCTAAACAGTAGTGGAGCAGA-TCAACGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAA-GACGACGA
* * * *
80374 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGACGA
* * * * * * *
80417 AGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTA-G-
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CG-ACGA
* *
80462 ATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGAC-AGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGA-CGA
* * * *
80506 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGACGA
* * * * * * * * *
80549 AGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAAATTGTA-G-
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CG-ACGA
*
80594 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGACGA
* * * *
80638 ATCTTATATTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCATC-A
1 ATCTTAT-CTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGA-CGA
* * * ** * * * * *
80681 AGCCTTGTCTCCCTGAGCAGCCGCGGAGAAGGTTGAAAATTGTA-G-
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CG-ACGA
* * * *
80726 ATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGACAACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGACGA
* * *
80770 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTAAAGTCGAC-A
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGACGA
*
80813 ATCCTATCTCCCTAA
1 ATCTTATCTCCCTAA
80828 AGTTGCAGTG
Statistics
Matches: 314, Mismatches: 95, Indels: 91
0.63 0.19 0.18
Matches are distributed among these distances:
41 1 0.00
42 21 0.07
43 44 0.14
44 213 0.68
45 27 0.09
46 5 0.02
47 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGACGA
Found at i:80915 original size:40 final size:40
Alignment explanation
Indices: 80858--81003 Score: 152
Period size: 40 Copynumber: 3.5 Consensus size: 40
80848 AAATCATAGA
*
80858 TCTTATCCCTCTGAAGTTGCAGAGAGCAAATCGCATCTAG
1 TCTTATCCCTCTAAAGTTGCAGAGAGCAAATCGCATCTAG
* * * ***
80898 TCTTATCTCC-CTAAAGTTGCAGTGGAGCGGATTAAAATCATAG
1 TCTTATC-CCTCTAAAGTTGCAG-AGAGC-AAATCGCATC-TAG
*
80941 ATCTTATCCCTCTGAAGTTGCAGAGAGCAAATCGCATCTAG
1 -TCTTATCCCTCTAAAGTTGCAGAGAGCAAATCGCATCTAG
80982 TCTTATCTCC-CTAAAGTTGCAG
1 TCTTATC-CCTCTAAAGTTGCAG
81004 TGGAGCAGAC
Statistics
Matches: 84, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
40 36 0.43
41 11 0.13
42 10 0.12
43 9 0.11
44 18 0.21
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (40 bp):
TCTTATCCCTCTAAAGTTGCAGAGAGCAAATCGCATCTAG
Found at i:81043 original size:84 final size:84
Alignment explanation
Indices: 80817--81009 Score: 386
Period size: 84 Copynumber: 2.3 Consensus size: 84
80807 TCGACAATCC
80817 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCATAGATCTTATCCCTCTGAAGTTGCAGAG
1 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCATAGATCTTATCCCTCTGAAGTTGCAGAG
80882 AGCAAATCGCATCTAGTCT
66 AGCAAATCGCATCTAGTCT
80901 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCATAGATCTTATCCCTCTGAAGTTGCAGAG
1 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCATAGATCTTATCCCTCTGAAGTTGCAGAG
80966 AGCAAATCGCATCTAGTCT
66 AGCAAATCGCATCTAGTCT
80985 TATCTCCCTAAAGTTGCAGTGGAGC
1 TATCTCCCTAAAGTTGCAGTGGAGC
81010 AGACTAAGTA
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 109 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (84 bp):
TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCATAGATCTTATCCCTCTGAAGTTGCAGAG
AGCAAATCGCATCTAGTCT
Found at i:81137 original size:217 final size:217
Alignment explanation
Indices: 80901--81313 Score: 684
Period size: 217 Copynumber: 1.9 Consensus size: 217
80891 CATCTAGTCT
* *
80901 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCATAGATCTTATCCCTCTGAAGTTGCAGAG
1 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCAGAGATCTTATCCCTCTGAAGTTACAGAG
*
80966 AGCAAATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGC-AGACTAAGTAAACAAGTCTT
66 AGCAAATCGCATCTAATCTTATCTCCCTAAAGTTGCAGTGGA-CAAGACTAAGTAAACAAGTCTT
* *
81030 ATCCTTCTAAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTGAAGTTGCAGTG
130 ATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTG
81095 GAGCAGATTAAAGCCGACAATCC
195 GAGCAGATTAAAGCCGACAATCC
* *
81118 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATTAGAGATCTTATCTCTCTGAAGTTACAGAG
1 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCAGAGATCTTATCCCTCTGAAGTTACAGAG
* * * * *
81183 AGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCGGTGGACAAGGCTAAGTAAGCAAGTCTTA
66 AGCAAATCGCATCTAATCTTATCTCCCTAAAGTTGCAGTGGACAAGACTAAGTAAACAAGTCTTA
* *
81248 TCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCGGTGG
131 TCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGG
81313 A
196 A
81314 CAAGGCTAAG
Statistics
Matches: 181, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
216 1 0.01
217 180 0.99
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (217 bp):
TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCAGAGATCTTATCCCTCTGAAGTTACAGAG
AGCAAATCGCATCTAATCTTATCTCCCTAAAGTTGCAGTGGACAAGACTAAGTAAACAAGTCTTA
TCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGG
AGCAGATTAAAGCCGACAATCC
Found at i:81166 original size:44 final size:43
Alignment explanation
Indices: 80795--81224 Score: 228
Period size: 44 Copynumber: 10.0 Consensus size: 43
80785 GATAGTGGGA
* *
80795 AGCAGATTAAAGTCGACA-ATCCTATCTCCCTAAAGTTGCAGTGG
1 AGCAGATTAAAATC-A-AGATCTTATCTCCCTAAAGTTGCAGTGG
* * *
80839 AGCGGATTAAAATCATAGATCTTATC-CCTCTGAAGTTGCAG-AG
1 AGCAGATTAAAATCA-AGATCTTATCTCC-CTAAAGTTGCAGTGG
* *** *
80882 AGCA-AATCGCATCTAG-TCTTATCTCCCTAAAGTTGCAGTGG
1 AGCAGATTAAAATCAAGATCTTATCTCCCTAAAGTTGCAGTGG
* * *
80923 AGCGGATTAAAATCATAGATCTTATC-CCTCTGAAGTTGCAG-AG
1 AGCAGATTAAAATCA-AGATCTTATCTCC-CTAAAGTTGCAGTGG
* *** *
80966 AGCA-AATCGCATCTAG-TCTTATCTCCCTAAAGTTGCAGTGG
1 AGCAGATTAAAATCAAGATCTTATCTCCCTAAAGTTGCAGTGG
* * * *
81007 AGCAGACTAAGTAAACAAG-TCTTATC-CTTCTAAAGTTACAGT-G
1 AGCAGATTAA--AATCAAGATCTTATCTC-CCTAAAGTTGCAGTGG
* * * *
81050 AGGCAGACTGAAGATGGCAA-ATCTTATCTTCCTGAAGTTGCAGTGG
1 A-GCAGA-TTAAAAT--CAAGATCTTATCTCCCTAAAGTTGCAGTGG
** *
81096 AGCAGATTAAAGCCGACA-ATCCTATCTCCCTAAAGTTGCAGTGG
1 AGCAGATTAAAATC-A-AGATCTTATCTCCCTAAAGTTGCAGTGG
* * * * * *
81140 AGCGGATTAAAATTAGAGATCTTATCTCTCTGAAGTTACAG-AG
1 AGCAGATTAAAATCA-AGATCTTATCTCCCTAAAGTTGCAGTGG
*** * * *
81183 AGCAGA-TCGCATCTA-ATCTTATCTCCCTGAAGTTGCGGTGG
1 AGCAGATTAAAATCAAGATCTTATCTCCCTAAAGTTGCAGTGG
81224 A
1 A
81225 CAAGGCTAAG
Statistics
Matches: 288, Mismatches: 73, Indels: 53
0.70 0.18 0.13
Matches are distributed among these distances:
40 56 0.19
41 20 0.07
42 21 0.07
43 29 0.10
44 132 0.46
45 28 0.10
46 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
AGCAGATTAAAATCAAGATCTTATCTCCCTAAAGTTGCAGTGG
Found at i:81308 original size:89 final size:89
Alignment explanation
Indices: 81197--81491 Score: 581
Period size: 89 Copynumber: 3.3 Consensus size: 89
81187 GATCGCATCT
81197 AATCTTATCTCCCTGAAGTTGCGGTGGACAAGGCTAAGTAAGCAAGTCTTATCCTCCTGAAGTTA
1 AATCTTATCTCCCTGAAGTTGCGGTGGACAAGGCTAAGTAAGCAAGTCTTATCCTCCTGAAGTTA
81262 CAGTGAGGCAGACTGAAGATGGCA
66 CAGTGAGGCAGACTGAAGATGGCA
81286 AATCTTATCTCCCTGAAGTTGCGGTGGACAAGGCTAAGTAAGCAAGTCTTATCCTCCTGAAGTTA
1 AATCTTATCTCCCTGAAGTTGCGGTGGACAAGGCTAAGTAAGCAAGTCTTATCCTCCTGAAGTTA
81351 CAGTGAGGCAGACTGAAGATGGCA
66 CAGTGAGGCAGACTGAAGATGGCA
81375 AATCTTATCTCCCTGAAGTTGCGGTGGACAAGGCTAAGTAAGCAAGTCTTATCCTCCTGAAGTTA
1 AATCTTATCTCCCTGAAGTTGCGGTGGACAAGGCTAAGTAAGCAAGTCTTATCCTCCTGAAGTTA
81440 CAGTGAGGCAGACTGAAGATGGCA
66 CAGTGAGGCAGACTGAAGATGGCA
*
81464 AATCTTATCTCCCTGAAGTTGCAGTGGA
1 AATCTTATCTCCCTGAAGTTGCGGTGGA
81492 GTATATTGAA
Statistics
Matches: 205, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 205 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (89 bp):
AATCTTATCTCCCTGAAGTTGCGGTGGACAAGGCTAAGTAAGCAAGTCTTATCCTCCTGAAGTTA
CAGTGAGGCAGACTGAAGATGGCA
Found at i:81502 original size:45 final size:45
Alignment explanation
Indices: 81197--81492 Score: 238
Period size: 45 Copynumber: 6.6 Consensus size: 45
81187 GATCGCATCT
* * * *
81197 AATCTTATCTCCCTGAAGTTGCGGTGGACAAGGCT-AAG-TAAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAAGAT-GGCA
* * *
81241 AGTCTTATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGGCA
1 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GAAGACTGAAGATGGCA
* * * *
81286 AATCTTATCTCCCTGAAGTTGCGGTGGACAAGGCT-AAG-TAAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAAGAT-GGCA
* * *
81330 AGTCTTATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGGCA
1 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GAAGACTGAAGATGGCA
* * * *
81375 AATCTTATCTCCCTGAAGTTGCGGTGGACAAGGCT-AAG-TAAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAAGAT-GGCA
* * *
81419 AGTCTTATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGGCA
1 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GAAGACTGAAGATGGCA
81464 AATCTTATCTCCCTGAAGTTGCAGTGGAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG
81493 TATATTGAAG
Statistics
Matches: 195, Mismatches: 37, Indels: 39
0.72 0.14 0.14
Matches are distributed among these distances:
43 11 0.06
44 84 0.43
45 88 0.45
46 12 0.06
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (45 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTGAAGATGGCA
Found at i:81730 original size:19 final size:19
Alignment explanation
Indices: 81706--81818 Score: 154
Period size: 19 Copynumber: 5.8 Consensus size: 19
81696 AATTTTTGAG
*
81706 GATATGCAATTTTAGATAT
1 GATATGCAATCTTAGATAT
**
81725 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
81744 GATAGATGCAATCTTAGATAT
1 GAT--ATGCAATCTTAGATAT
*
81765 GATATGCAATCTTAGAGAT
1 GATATGCAATCTTAGATAT
**
81784 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
81803 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
81819 ATATATGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
19 64 0.79
21 17 0.21
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:81804 original size:38 final size:39
Alignment explanation
Indices: 81712--81818 Score: 153
Period size: 40 Copynumber: 2.7 Consensus size: 39
81702 TGAGGATATG
* ** *
81712 CAATTTTAGATATGATATGCAATCCAAGATATGATAGAT
1 CAATCTTAGATATGATATGCAATCTTAGAGATGATAGAT
*
81751 GCAATCTTAGATATGATATGCAATCTTAGAGATGATATAT
1 -CAATCTTAGATATGATATGCAATCTTAGAGATGATAGAT
81791 -AATCTTAGATATGATATGCAATCTTAGA
1 CAATCTTAGATATGATATGCAATCTTAGA
81819 ATATATGATT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 28 0.45
40 34 0.55
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (39 bp):
CAATCTTAGATATGATATGCAATCTTAGAGATGATAGAT
Found at i:93225 original size:5 final size:5
Alignment explanation
Indices: 93211--93271 Score: 115
Period size: 5 Copynumber: 12.4 Consensus size: 5
93201 AATTATTAAG
93211 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
93260 TATAT TATAT TA
1 TATAT TATAT TA
93272 CAATAAAACA
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.07
5 52 0.93
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:93305 original size:21 final size:21
Alignment explanation
Indices: 93273--93314 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
93263 ATTATATTAC
* *
93273 AATAAAACAAAATAAATAAAG
1 AATAAAACAAAAGAAAGAAAG
93294 AATAAATA-AAAAGAAAGAAAG
1 AATAAA-ACAAAAGAAAGAAAG
93315 GTACTTAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (21 bp):
AATAAAACAAAAGAAAGAAAG
Found at i:94636 original size:45 final size:45
Alignment explanation
Indices: 94577--94686 Score: 115
Period size: 45 Copynumber: 2.6 Consensus size: 45
94567 TTTGGTTCGC
* *
94577 TGTATTGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
* * ***
94622 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
94666 TG--A---AATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
94687 TAATGGAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
39 15 0.27
42 1 0.02
44 18 0.33
45 21 0.38
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (45 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
Found at i:94853 original size:18 final size:17
Alignment explanation
Indices: 94832--94866 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
94822 TTATTATTAA
*
94832 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
94850 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
94867 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:94999 original size:16 final size:16
Alignment explanation
Indices: 94980--95010 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
94970 TTTAAACATA
*
94980 ATAATTATAATATATT
1 ATAATTAAAATATATT
94996 ATAATTAAAATATAT
1 ATAATTAAAATATAT
95011 AATTTAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:95033 original size:157 final size:157
Alignment explanation
Indices: 94720--95035 Score: 537
Period size: 159 Copynumber: 2.0 Consensus size: 157
94710 AGAATACCCG
* *
94720 TAGCATAAATTTGTTTTGGTAAATGGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAT
1 TAGCAGAAATTTGTTTTGGTAAATGGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAA
* * *
94785 TATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAAT
94850 ATATAATTTAATAAAATTCTTAATAAT
131 ATATAATTTAATAAAATTCTTAATAAT
**
94877 TAGCAGAAATTTGTTTTGGTAAATTATTTTATTGTTATTGTTATTTAAATTTTAATAAGATTATT
1 TAGCAGAAATTTGTTTTGGTAAA-T-GGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATT
94942 AATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTA-T-AATATATTATAATTAAA
64 AATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAA
95005 ATATATAATTTAATAAAATTCTTAATAAT
129 ATATATAATTTAATAAAATTCTTAATAAT
95034 TA
1 TA
95036 ATATTCTTAT
Statistics
Matches: 150, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
157 69 0.46
158 2 0.01
159 79 0.53
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TAGCAGAAATTTGTTTTGGTAAATGGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAA
TATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAATAAT
Found at i:95120 original size:120 final size:121
Alignment explanation
Indices: 94969--95264 Score: 478
Period size: 120 Copynumber: 2.5 Consensus size: 121
94959 ATTTAATCAT
* *
94969 ATTTAAACATAATAATTA-T-AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
95032 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
95089 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
95152 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* * *
95208 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
95265 TAAAATAATT
Statistics
Matches: 166, Mismatches: 5, Indels: 10
0.92 0.03 0.06
Matches are distributed among these distances:
118 12 0.07
119 10 0.06
120 142 0.86
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:95137 original size:14 final size:15
Alignment explanation
Indices: 95088--95139 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
95078 GTAAAATATA
95088 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
95103 TATTAAATATATTAT
1 AATTAAATATATTAT
95118 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
95131 AATTTAATA
1 AATTAAATA
95140 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:95351 original size:24 final size:25
Alignment explanation
Indices: 95305--95352 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
95295 TATGAATTTG
95305 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
95331 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
95353 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:95356 original size:92 final size:92
Alignment explanation
Indices: 95260--95488 Score: 236
Period size: 92 Copynumber: 2.5 Consensus size: 92
95250 TGATTTAATA
* * *
95260 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
95322 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
95352 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
95417 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
95442 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
95489 CTAAAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 81 0.68
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:101176 original size:24 final size:24
Alignment explanation
Indices: 101149--101195 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
101139 ATTGAAATGG
101149 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
101173 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
101196 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:101193 original size:15 final size:15
Alignment explanation
Indices: 101173--101222 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
101163 TGATGAATTT
101173 ATTGAATTTATATTG
1 ATTGAATTTATATTG
101188 ATTGAATTGGTATATATAG
1 ATTGAATT--TATAT-T-G
101207 ATTGAA--TATATTG
1 ATTGAATTTATATTG
101220 ATT
1 ATT
101223 ATTTGAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 4 0.13
14 1 0.03
15 13 0.42
17 5 0.16
18 1 0.03
19 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:101453 original size:40 final size:41
Alignment explanation
Indices: 101358--101459 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
101348 ACTTCGAGTC
* * * * *
101358 GATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTT
1 GATGAGGCACTGGGTGTCAAATTACTACTTCGAATTAATCT
*
101399 GATGAGGCACTGGGTGTCAAATTATTACTTCGAATT-ATCT
1 GATGAGGCACTGGGTGTCAAATTACTACTTCGAATTAATCT
*
101439 GATGAGGCACTGGGTGCCAAA
1 GATGAGGCACTGGGTGTCAAA
101460 CTGGTGTGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 23 0.43
41 31 0.57
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (41 bp):
GATGAGGCACTGGGTGTCAAATTACTACTTCGAATTAATCT
Found at i:101944 original size:28 final size:27
Alignment explanation
Indices: 101894--101948 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
101884 TACTTAACTT
* *
101894 TTAAGTTTTAATATTATAATATATATA
1 TTAACTTTAAATATTATAATATATATA
101921 TTAACTTTAAATATTTATAATATATATA
1 TTAACTTTAAATA-TTATAATATATATA
101949 CTCTTATGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TTAACTTTAAATATTATAATATATATA
Found at i:104803 original size:60 final size:60
Alignment explanation
Indices: 104668--104803 Score: 148
Period size: 60 Copynumber: 2.3 Consensus size: 60
104658 CTAAATATAA
* * * * ** **
104668 AAAAAATCAACAAATTTAGCACTCAATATTTACAAAATTTTTCATTTTAGTTTTAATTCT
1 AAAAAATCAAAAAATTTACCACTCAATATTTACAAAATCTATCATTTTAGTCCTAACACT
** *
104728 AAAAGTTCAATAAATTTGACCA-TCAATATTTACAAAATCTATCATTTTAGTCCTAACACT
1 AAAAAATCAAAAAATTT-ACCACTCAATATTTACAAAATCTATCATTTTAGTCCTAACACT
*
104788 AAAAAATAAAAAAATT
1 AAAAAATCAAAAAATT
104804 ATAAAAAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
60 58 0.95
61 3 0.05
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (60 bp):
AAAAAATCAAAAAATTTACCACTCAATATTTACAAAATCTATCATTTTAGTCCTAACACT
Found at i:107719 original size:10 final size:10
Alignment explanation
Indices: 107687--107730 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
107677 AAAATTTTAA
107687 TAAATTATAAT
1 TAAATTAT-AT
107698 TATAATTAATAT
1 TA-AATT-ATAT
107710 TAAATTATAT
1 TAAATTATAT
*
107720 TATATTATAT
1 TAAATTATAT
107730 T
1 T
107731 TTAATATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 14 0.47
11 6 0.20
12 8 0.27
13 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAAATTATAT
Found at i:113389 original size:19 final size:20
Alignment explanation
Indices: 113365--113403 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
113355 ATATTTTATA
113365 TTAAAA-TTTAATAATTTTT
1 TTAAAATTTTAATAATTTTT
*
113384 TTAAAATTTTATTAATTTTT
1 TTAAAATTTTAATAATTTTT
113404 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAAAATTTTAATAATTTTT
Found at i:113393 original size:11 final size:12
Alignment explanation
Indices: 113371--113421 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
113361 TATATTAAAA
113371 TTTAATAATTTT
1 TTTAATAATTTT
113383 TTTAA-AATTTT
1 TTTAATAATTTT
* **
113394 ATTAATTTTTATT
1 TTTAATAATT-TT
*
113407 TTTTATAATTTT
1 TTTAATAATTTT
113419 TTT
1 TTT
113422 GCCACATGCC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
11 10 0.33
12 12 0.40
13 8 0.27
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTAATAATTTT
Found at i:115860 original size:56 final size:56
Alignment explanation
Indices: 115793--115904 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
115783 TATAAATTTC
* *
115793 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCGTGTGTCAATTCAAA
1 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
115849 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
1 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
115905 CATTACATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.25, C:0.36, G:0.04, T:0.36
Consensus pattern (56 bp):
ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
Found at i:126588 original size:22 final size:22
Alignment explanation
Indices: 126561--126615 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
126551 ATAATAACAA
*
126561 CAAAATAGTAACAATACAATAG
1 CAAAATAGTAACAAAACAATAG
*
126583 CGAAAT-GATAACAAAACAATAG
1 CAAAATAG-TAACAAAACAATAG
*
126605 CAAAAAAGTAA
1 CAAAATAGTAA
126616 AACAACAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.62, C:0.13, G:0.11, T:0.15
Consensus pattern (22 bp):
CAAAATAGTAACAAAACAATAG
Found at i:129802 original size:27 final size:27
Alignment explanation
Indices: 129752--129830 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
129742 TTGGGGTCTT
* **
129752 CCTCATCTTCTTCCTCAGTTGAAGAC-
1 CCTCTTCTTCTTCCTCAGAAGAAGACA
*
129778 CCTTCTTCTTCTTCCTCAGAAGAAGTCA
1 CC-TCTTCTTCTTCCTCAGAAGAAGACA
* * *
129806 CCTCTTCATCTTCTTCAGAGGAAGA
1 CCTCTTCTTCTTCCTCAGAAGAAGA
129831 AGCGGCTGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 2 0.05
27 39 0.91
28 2 0.05
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.34
Consensus pattern (27 bp):
CCTCTTCTTCTTCCTCAGAAGAAGACA
Found at i:130081 original size:9 final size:9
Alignment explanation
Indices: 130067--130131 Score: 94
Period size: 9 Copynumber: 7.2 Consensus size: 9
130057 ATTCGGCCGG
130067 TTAACCGAA
1 TTAACCGAA
*
130076 TTAACCTAA
1 TTAACCGAA
*
130085 TTACCCGAA
1 TTAACCGAA
130094 TTAACCGAA
1 TTAACCGAA
130103 TTAACCGAA
1 TTAACCGAA
*
130112 TTACCCGAA
1 TTAACCGAA
*
130121 TTAACCAAA
1 TTAACCGAA
130130 TT
1 TT
130132 GAATTACTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.26
Consensus pattern (9 bp):
TTAACCGAA
Found at i:130097 original size:27 final size:27
Alignment explanation
Indices: 130067--130131 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
130057 ATTCGGCCGG
*
130067 TTAACCGAATTAACCTAATTACCCGAA
1 TTAACCGAATTAACCGAATTACCCGAA
130094 TTAACCGAATTAACCGAATTACCCGAA
1 TTAACCGAATTAACCGAATTACCCGAA
*
130121 TTAACCAAATT
1 TTAACCGAATT
130132 GAATTACTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.26
Consensus pattern (27 bp):
TTAACCGAATTAACCGAATTACCCGAA
Found at i:130266 original size:18 final size:18
Alignment explanation
Indices: 130226--130269 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
130216 AATTTTTATG
**
130226 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
130244 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
130262 CTTGGGTT
1 ATTGGGTT
130270 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:130799 original size:9 final size:9
Alignment explanation
Indices: 130777--130989 Score: 92
Period size: 9 Copynumber: 22.2 Consensus size: 9
130767 ATGATTAAAA
*
130777 ATAAAAATCA
1 ATAAAAAT-T
*
130787 ATAAAAGTT
1 ATAAAAATT
130796 ATAAAAATT
1 ATAAAAATT
130805 ATAAAAATTT
1 ATAAAAA-TT
130815 AATAAAAATT
1 -ATAAAAATT
130825 ATAAAAA-T
1 ATAAAAATT
130833 ATTAAAAATT
1 A-TAAAAATT
* *
130843 AGAAAAGTT
1 ATAAAAATT
* *
130852 TTAAAATTAT
1 ATAAAAAT-T
130862 ATAAAAATT
1 ATAAAAATT
* *
130871 GTAAAAA-A
1 ATAAAAATT
130879 ATGATAAAATAT
1 AT-A-AAAAT-T
130891 ATAAAAATAT
1 ATAAAAAT-T
*
130901 AGGAAAAAATT
1 A--TAAAAATT
*
130912 TTAAAATATT
1 ATAAAA-ATT
* *
130922 AT-AAAGTC
1 ATAAAAATT
130930 ATAAGAAAATT
1 AT-A-AAAATT
*
130941 ATAAAAAAT
1 ATAAAAATT
* *
130950 GTAAAGAAAT
1 ATAAA-AATT
130960 AT-AAAATT
1 ATAAAAATT
*
130968 CGTAAAAAATT
1 -AT-AAAAATT
*
130979 ATAAACATT
1 ATAAAAATT
130988 AT
1 AT
130990 CGTACTAAAA
Statistics
Matches: 155, Mismatches: 29, Indels: 39
0.70 0.13 0.17
Matches are distributed among these distances:
8 9 0.06
9 74 0.48
10 43 0.28
11 21 0.14
12 8 0.05
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:130818 original size:29 final size:30
Alignment explanation
Indices: 130777--130898 Score: 123
Period size: 29 Copynumber: 4.3 Consensus size: 30
130767 ATGATTAAAA
* *
130777 ATAAAAA-TCAATAAAAGTTATAAAAAT-T
1 ATAAAAATTTAATAAAAATTATAAAAATAT
130805 ATAAAAATTTAATAAAAATTATAAAAATAT
1 ATAAAAATTTAATAAAAATTATAAAAATAT
* * * *
130835 -TAAAAA-TT-AGAAAAGTTTTAAAATTAT
1 ATAAAAATTTAATAAAAATTATAAAAATAT
*
130862 ATAAAAATTGTAA-AAAAATGAT-AAAATAT
1 ATAAAAATT-TAATAAAAATTATAAAAATAT
130891 ATAAAAAT
1 ATAAAAAT
130899 ATAGGAAAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
27 15 0.19
28 15 0.19
29 39 0.50
30 8 0.10
31 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (30 bp):
ATAAAAATTTAATAAAAATTATAAAAATAT
Found at i:130819 original size:20 final size:20
Alignment explanation
Indices: 130796--130887 Score: 86
Period size: 20 Copynumber: 4.8 Consensus size: 20
130786 AATAAAAGTT
130796 ATAAAAATTATAAAAATTTA
1 ATAAAAATTATAAAAATTTA
130816 ATAAAAATTATAAAAA--TA
1 ATAAAAATTATAAAAATTTA
* * *
130834 TTAAAAATTAGAAAAGTTT-
1 ATAAAAATTATAAAAATTTA
*
130853 -TAAAATTATATAAAAATTGTA
1 ATAAAAAT-TATAAAAATT-TA
*
130874 A-AAAAATGATAAAA
1 ATAAAAATTATAAAA
130888 TATATAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
18 21 0.36
19 8 0.14
20 24 0.41
21 5 0.09
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (20 bp):
ATAAAAATTATAAAAATTTA
Found at i:130907 original size:29 final size:27
Alignment explanation
Indices: 130835--130926 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 27
130825 ATAAAAATAT
* *
130835 TAAAAATTAGAAAAGTTTTAAAATTATA
1 TAAAAATTAGAAAAATTATAAAA-TATA
* *
130863 TAAAAATTGTAAAAAAATGATAAAATATA
1 TAAAAA-T-TAGAAAAATTATAAAATATA
*
130892 TAAAAATATAGGAAAAAATTTTAAAATATTA
1 TAAAAAT-TA-G-AAAAATTATAAAATA-TA
130923 TAAA
1 TAAA
130927 GTCATAAGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
28 9 0.18
29 11 0.22
30 25 0.49
31 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.32
Consensus pattern (27 bp):
TAAAAATTAGAAAAATTATAAAATATA
Found at i:130983 original size:10 final size:10
Alignment explanation
Indices: 130789--130983 Score: 69
Period size: 10 Copynumber: 20.2 Consensus size: 10
130779 AAAAATCAAT
*
130789 AAAAGTTAT-
1 AAAAATTATA
130798 AAAAATTATA
1 AAAAATTATA
*
130808 AAAATTTA-A
1 AAAAATTATA
130817 TAAAAATTAT-
1 -AAAAATTATA
*
130827 AAAAA-TATT
1 AAAAATTATA
*
130836 AAAAATTA-G
1 AAAAATTATA
*
130845 AAAAGTT-T-
1 AAAAATTATA
*
130853 TAAAATTATA
1 AAAAATTATA
*
130863 TAAAAATTGTAA
1 -AAAAATTAT-A
*
130875 AAAAATGATA
1 AAAAATTATA
*
130885 AAATA-TAT-
1 AAAAATTATA
*
130893 AAAAATATAGGA
1 AAAAAT-TA-TA
*
130905 AAAAATTTTA
1 AAAAATTATA
*
130915 AAATATTAT-
1 AAAAATTATA
* *
130924 -AAAGTCATA
1 AAAAATTATA
130933 AGAAAATTATA
1 A-AAAATTATA
130944 AAAAATGTA-A
1 AAAAAT-TATA
*
130954 AGAAA-TAT-
1 AAAAATTATA
*
130962 -AAAATTCGTA
1 AAAAATT-ATA
130972 AAAAATTATA
1 AAAAATTATA
130982 AA
1 AA
130984 CATTATCGTA
Statistics
Matches: 135, Mismatches: 28, Indels: 45
0.65 0.13 0.22
Matches are distributed among these distances:
7 3 0.02
8 20 0.15
9 29 0.21
10 45 0.33
11 31 0.23
12 7 0.05
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (10 bp):
AAAAATTATA
Found at i:131031 original size:20 final size:17
Alignment explanation
Indices: 131006--131055 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 17
130996 AAAAGAAGCA
131006 TTTTATAATTTTTCTATAAT
1 TTTTATAATTTTT-TAT--T
131026 TTTTATAATTTTTTATT
1 TTTTATAATTTTTTATT
131043 TTTTATCAATTTT
1 TTTTAT-AATTTT
131056 CGACACATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.24
18 6 0.21
19 3 0.10
20 13 0.45
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATAATTTTTTATT
Found at i:131032 original size:9 final size:9
Alignment explanation
Indices: 131006--131055 Score: 57
Period size: 10 Copynumber: 5.3 Consensus size: 9
130996 AAAAGAAGCA
131006 TTTTATAATT
1 TTTTATAA-T
131016 TTTCTATAAT
1 TTT-TATAAT
131026 TTTTATAAT
1 TTTTATAAT
*
131035 TTTT-TATT
1 TTTTATAAT
131043 TTTTATCAAT
1 TTTTAT-AAT
131053 TTT
1 TTT
131056 CGACACATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 7 0.20
9 11 0.31
10 12 0.34
11 5 0.14
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTATAAT
Found at i:131211 original size:8 final size:8
Alignment explanation
Indices: 131200--131247 Score: 69
Period size: 8 Copynumber: 5.8 Consensus size: 8
131190 TTTTAAAAAA
131200 TTTTATAT
1 TTTTATAT
131208 TTTTATATT
1 TTTTATA-T
*
131217 TTTTCTAAT
1 TTTTAT-AT
131226 TTTTATAT
1 TTTTATAT
131234 TTTTATAT
1 TTTTATAT
131242 TTTTAT
1 TTTTAT
131248 TAAAATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
8 23 0.64
9 12 0.33
10 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTATAT
Found at i:131217 original size:26 final size:26
Alignment explanation
Indices: 131170--131264 Score: 100
Period size: 26 Copynumber: 3.5 Consensus size: 26
131160 TTTTTTATGC
131170 ATTTTATAATTTTTTATCATTTTTAAAAA
1 ATTTTAT-A-TTTTTAT-ATTTTTAAAAA
***
131199 ATTTTATATTTTTATATTTTTTCTAA
1 ATTTTATATTTTTATATTTTTAAAAA
* *
131225 TTTTTATATTTTTATATTTTTATTAAA
1 ATTTTATATTTTTATATTTTTA-AAAA
*
131252 ATTTAATATTTTT
1 ATTTTATATTTTT
131265 TATAACTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 28 0.50
27 20 0.36
28 1 0.02
29 7 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (26 bp):
ATTTTATATTTTTATATTTTTAAAAA
Found at i:131300 original size:10 final size:9
Alignment explanation
Indices: 131171--131286 Score: 76
Period size: 9 Copynumber: 12.7 Consensus size: 9
131161 TTTTTATGCA
131171 TTTTATAATT
1 TTTTATAA-T
*
131181 TTTTATCAT
1 TTTTATAAT
* *
131190 TTTTAAAAAA
1 TTTT-ATAAT
131200 TTTTAT-AT
1 TTTTATAAT
*
131208 TTTTATATT
1 TTTTATAAT
*
131217 TTTTCTAAT
1 TTTTATAAT
131226 TTTTAT-AT
1 TTTTATAAT
131234 TTTTAT-AT
1 TTTTATAAT
*
131242 TTTTATTAAAA
1 TTTTA-T-AAT
* *
131253 TTTAATATT
1 TTTTATAAT
*
131262 TTTTATAAC
1 TTTTATAAT
*
131271 TTTTATTTAT
1 TTTTA-TAAT
131281 TTTTAT
1 TTTTAT
131287 TTTTATAAAT
Statistics
Matches: 81, Mismatches: 19, Indels: 13
0.72 0.17 0.12
Matches are distributed among these distances:
8 22 0.27
9 33 0.41
10 21 0.26
11 5 0.06
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTATAAT
Found at i:140668 original size:39 final size:40
Alignment explanation
Indices: 140614--140691 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 40
140604 CTTTATATTG
140614 CCAAAAAGAAAAATAGAAATCCC-CCCAAATCCCTTTTTT
1 CCAAAAAGAAAAATAGAAATCCCTCCCAAATCCCTTTTTT
*
140653 CCAAAAAGAAAAATAGAAATCCCTCCTAAATCCCTTTTT
1 CCAAAAAGAAAAATAGAAATCCCTCCCAAATCCCTTTTT
140692 AACGTTTTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 23 0.62
40 14 0.38
ACGTcount: A:0.44, C:0.27, G:0.05, T:0.24
Consensus pattern (40 bp):
CCAAAAAGAAAAATAGAAATCCCTCCCAAATCCCTTTTTT
Found at i:142466 original size:90 final size:90
Alignment explanation
Indices: 142372--142538 Score: 212
Period size: 90 Copynumber: 1.9 Consensus size: 90
142362 TTAGTGGCTA
* * * * **
142372 ATCCTATAAATTCGGTAG-GTTTATCAAGTCTATCTCAATAGGACCACCCAAACTCT-AGGCTGT
1 ATCCTATAAATTCGG-AGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTATGA-GCAAT
142435 GAACTCATTAAGAGCTTCTAGTAGTTC
64 GAACTCATTAAGAGCTTCTAGTAGTTC
* * * *
142462 ATCCTATAAATTTGGAGAATTCATCAAGTCCGTCTTAGTAGGACCACCCAAACTATGAGCAATGA
1 ATCCTATAAATTCGGAGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTATGAGCAATGA
142527 ACTCATTAAGAG
66 ACTCATTAAGAG
142539 TAACAAACTC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
89 2 0.03
90 62 0.95
91 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (90 bp):
ATCCTATAAATTCGGAGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTATGAGCAATGA
ACTCATTAAGAGCTTCTAGTAGTTC
Found at i:142981 original size:15 final size:15
Alignment explanation
Indices: 142957--142986 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
142947 ATTTTATGGT
142957 GGAGCAAGCAACACA
1 GGAGCAAGCAACACA
*
142972 GGAGCGAGCAACACA
1 GGAGCAAGCAACACA
142987 CGTCTGTTTA
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:0.30, T:0.00
Consensus pattern (15 bp):
GGAGCAAGCAACACA
Found at i:159008 original size:16 final size:15
Alignment explanation
Indices: 158987--159016 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
158977 ACACTATGCT
158987 TTTTCTTTTTCTTTTC
1 TTTTCTTTTT-TTTTC
159003 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
159017 ATATCATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTCTTTTTTTTTC
Found at i:159422 original size:33 final size:33
Alignment explanation
Indices: 159380--159444 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
159370 TGAGATTGAA
*
159380 TCATAAAAATTGTCTACTAATGGTGTATGTAGT
1 TCATAAAAATTGTCTACTAATGGTGTACGTAGT
159413 TCATAAAAATTGTCTACTAATGGTGTACGTAG
1 TCATAAAAATTGTCTACTAATGGTGTACGTAG
159445 ATAATAGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (33 bp):
TCATAAAAATTGTCTACTAATGGTGTACGTAGT
Found at i:164447 original size:18 final size:18
Alignment explanation
Indices: 164426--164464 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
164416 TCTAAATAAT
164426 ATATAAATAAAATT-AAAA
1 ATATAAA-AAAATTCAAAA
164444 ATATAAAAAAATTCAAAA
1 ATATAAAAAAATTCAAAA
164462 ATA
1 ATA
164465 ATAATTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
ATATAAAAAAATTCAAAA
Found at i:164685 original size:15 final size:15
Alignment explanation
Indices: 164665--164700 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
164655 AAATAATTTC
164665 ACTCGATTCAATTCA
1 ACTCGATTCAATTCA
* *
164680 ATTCGATTCGATTCA
1 ACTCGATTCAATTCA
164695 ACTCGA
1 ACTCGA
164701 CTTGAATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (15 bp):
ACTCGATTCAATTCA
Found at i:168547 original size:15 final size:16
Alignment explanation
Indices: 168520--168549 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
168510 AAATATCATA
168520 AGCCCGAGCCCGGCCT
1 AGCCCGAGCCCGGCCT
168536 AGCCCG-GCCCGGCC
1 AGCCCGAGCCCGGCC
168550 CGGCCCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.53, G:0.33, T:0.03
Consensus pattern (16 bp):
AGCCCGAGCCCGGCCT
Found at i:173669 original size:12 final size:11
Alignment explanation
Indices: 173652--173684 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
173642 TTAATACAAA
173652 AAATATGATTTT
1 AAATAT-ATTTT
173664 AAATATA-TTT
1 AAATATATTTT
173674 AAATATATTTT
1 AAATATATTTT
173685 TTTTATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 4 0.20
12 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
AAATATATTTT
Found at i:174480 original size:23 final size:24
Alignment explanation
Indices: 174454--174503 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
174444 TAGTTGACTT
*
174454 AAATTTTTAAA-CTCGAAAAATAA
1 AAATTATTAAATCTCGAAAAATAA
* *
174477 AAA-TATTAAATTTCTAAAAATAA
1 AAATTATTAAATCTCGAAAAATAA
174500 AAAT
1 AAAT
174504 ATAAAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATTATTAAATCTCGAAAAATAA
Found at i:174485 original size:22 final size:23
Alignment explanation
Indices: 174460--174505 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
174450 ACTTAAATTT
174460 TTAAA-CTCGAAAAATAAAAATA
1 TTAAATCTCGAAAAATAAAAATA
* *
174482 TTAAATTTCTAAAAATAAAAATA
1 TTAAATCTCGAAAAATAAAAATA
174505 T
1 T
174506 AAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (23 bp):
TTAAATCTCGAAAAATAAAAATA
Found at i:183199 original size:6 final size:6
Alignment explanation
Indices: 183190--183223 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
183180 CACCGATCTT
*
183190 CCCTTT CCCTTC CCCTTC CCCTTC CCCTTC CCCT
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCT
183224 ATCCTTGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CCCTTC
Found at i:186120 original size:20 final size:20
Alignment explanation
Indices: 186095--186136 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
186085 TTTCTGTTTA
186095 ATATATAAATTTATTAATAT
1 ATATATAAATTTATTAATAT
186115 ATATATAAATTTATTAATAT
1 ATATATAAATTTATTAATAT
186135 AT
1 AT
186137 GTAAAAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATAAATTTATTAATAT
Found at i:186389 original size:21 final size:21
Alignment explanation
Indices: 186364--186405 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
186354 CCTTTCTCTT
186364 TCAGTTATATGGAGGAGTGAG
1 TCAGTTATATGGAGGAGTGAG
186385 TCAGTTATATGGAGGAGTGAG
1 TCAGTTATATGGAGGAGTGAG
186406 AGCTTAGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.38, T:0.29
Consensus pattern (21 bp):
TCAGTTATATGGAGGAGTGAG
Found at i:193612 original size:16 final size:15
Alignment explanation
Indices: 193571--193613 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
193561 TTTTTACAAT
*
193571 TATTTTAATTTTATT
1 TATTTTAATTTTATA
193586 TATTTTTAATTTTATCA
1 TA-TTTTAATTTTAT-A
*
193603 TATTTAAATTT
1 TATTTTAATTT
193614 CCTTTTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 20 0.83
17 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTAATTTTATA
Found at i:195186 original size:40 final size:39
Alignment explanation
Indices: 195067--195199 Score: 171
Period size: 40 Copynumber: 3.4 Consensus size: 39
195057 GTTCGAGTTC
* * *
195067 ATGAGACACTGGGTGTCAATCTATCACTTCAGATTTATTTG
1 ATGAGGCACTGGGTGTCAATTTAT-ACTTC-GATTTATCTG
* *
195108 ATGAGGCACTGGGTGCCAA-TT-TACTTCGATTTAACTG
1 ATGAGGCACTGGGTGTCAATTTATACTTCGATTTATCTG
*
195145 ATGAGGCACTGGGTGTCAATTTACTACTTCGAATTATCTG
1 ATGAGGCACTGGGTGTCAATTTA-TACTTCGATTTATCTG
195185 ATGAGGCACTGGGTG
1 ATGAGGCACTGGGTG
195200 CCAAATTGGT
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
37 26 0.32
38 7 0.09
39 1 0.01
40 30 0.37
41 17 0.21
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (39 bp):
ATGAGGCACTGGGTGTCAATTTATACTTCGATTTATCTG
Found at i:196672 original size:31 final size:32
Alignment explanation
Indices: 196613--196677 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
196603 GGCAAATTAC
196613 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
196645 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
196676 AA
1 AA
196678 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:202410 original size:98 final size:98
Alignment explanation
Indices: 202241--202431 Score: 346
Period size: 98 Copynumber: 1.9 Consensus size: 98
202231 ATACAATAAA
*
202241 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
202306 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* *
202339 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
202404 CCTTTAGAATCTCAAACTCGGAATATTT
66 CCTTTAGAATCCCAAACTCGGAATATTT
202432 TCTTCATGAT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:203532 original size:19 final size:19
Alignment explanation
Indices: 203499--203590 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
203489 AATCATATAT
*
203499 TCTAAGATTGCATATCATA
1 TCTAATATTGCATATCATA
**
203518 TCTAATATTATATATCATA
1 TCTAATATTGCATATCATA
203537 TCTAATATTGCATATCATA
1 TCTAATATTGCATATCATA
**
203556 TCTAGGATTGCATATCATA
1 TCTAATATTGCATATCATA
*
203575 TCTAAGATTGCATATC
1 TCTAATATTGCATATC
203591 CTCAAAAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 65 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (19 bp):
TCTAATATTGCATATCATA
Found at i:203547 original size:38 final size:38
Alignment explanation
Indices: 203476--203590 Score: 140
Period size: 38 Copynumber: 2.9 Consensus size: 38
203466 AAATTAAATC
*
203476 TCTAAGATTACAAAATCATATATTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATC--ATA-TCTAAGATTGCATATCATA
* * *
203518 TCTAATATTATATATCATATCTAATATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
203556 TCTAGGATTGCATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
203591 CTCAAAAATT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
38 48 0.75
39 3 0.05
41 4 0.06
42 9 0.14
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:204061 original size:132 final size:132
Alignment explanation
Indices: 203819--205001 Score: 1793
Period size: 132 Copynumber: 9.0 Consensus size: 132
203809 CTGCAACTGC
* * * * **
203819 AGGGAGATAATA-CTTACAATCTTCAACCTATTCCACTGCTAACCAGGG-AGATAGAATTACT-G
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGCCCAGGGAAG-TAGAATTACTAG
** *
203881 ACTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTACCATCTTCGATCTACTCCACTAC
64 -CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAC
203946 TGCTT
128 TGCTT
* * *
203951 AGGGAGATAAGATCT-ACCATCTTCAACCTATTCCACTGTTGCCTAGGGAAGTAGAATTACTAGC
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGC
* *
204015 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCAATCTTCAATCTGCTCCACTACTG
65 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
204080 CTT
130 CTT
* *
204083 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCTAGGG-AGATAGAATTACT-GA
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAG-TAGAATTACTAG-
* *
204146 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACT
64 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACT
204211 GCTT
129 GCTT
* * *
204215 AGGGAGATAAGATCTGAAATCTTCAATCTATTTCACTATTGCCCAGGGAGGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
* * *
204280 TCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCCGCAATCTTCAATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
204345 TT
131 TT
* * *
204347 AGGGAGATAAGATCTGAAATCTTCAATTTATTCCACTATTGCCTAGGGAAGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
* * * **
204412 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACTATCTTTGATCTATTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
204477 TT
131 TT
* * *
204479 AGGGAGATAAGATCTGAAATCTTCAATTTATTCCACTATTGCCTAGGGAAGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
* *
204544 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCAATCTTCAATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
204609 TT
131 TT
* *
204611 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
* * *
204676 TCAATGTACTCCACTATAACCACATGGAGGTAAAATCCGTCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
204741 TT
131 TT
*
204743 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
* * * * *
204808 TCAATGTACTCTACTATAACTATAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
204873 TT
131 TT
* *
204875 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
* * *
204940 TCAATGTACTCCATTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCGACTAC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAC
205002 AAACGAGGAA
Statistics
Matches: 974, Mismatches: 69, Indels: 16
0.92 0.07 0.02
Matches are distributed among these distances:
131 3 0.00
132 963 0.99
133 8 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (132 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTAGCT
TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TT
Found at i:204426 original size:43 final size:44
Alignment explanation
Indices: 204367--204558 Score: 142
Period size: 44 Copynumber: 4.4 Consensus size: 44
204357 GATCTGAAAT
*
204367 CTTCAATTTATTCCACTATTGCCTAGGGAAGTAGAAT-TACTAG
1 CTTCAATGTATTCCACTATTGCCTAGGGAAGTAGAATCTACTAG
* * ** * * * * *
204410 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACTAT
1 CTTCAATGTATTCCACTATTGCC-TAGGGAAGTAGAATCTACTAG
** * * * * *
204455 CTTTGATCTATTCCACTACTGCTTAGGG-AGATA-AGATCTGA-AAT
1 CTTCAATGTATTCCACTATTGCCTAGGGAAG-TAGA-ATCT-ACTAG
*
204499 CTTCAATTTATTCCACTATTGCCTAGGGAAGTAGAAT-TACTAG
1 CTTCAATGTATTCCACTATTGCCTAGGGAAGTAGAATCTACTAG
*
204542 CTTCAATGTACTCCACT
1 CTTCAATGTATTCCACT
204559 GTAACCACAG
Statistics
Matches: 109, Mismatches: 32, Indels: 16
0.69 0.20 0.10
Matches are distributed among these distances:
42 1 0.01
43 37 0.34
44 49 0.45
45 22 0.20
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (44 bp):
CTTCAATGTATTCCACTATTGCCTAGGGAAGTAGAATCTACTAG
Found at i:206260 original size:6 final size:6
Alignment explanation
Indices: 206251--206292 Score: 68
Period size: 6 Copynumber: 7.0 Consensus size: 6
206241 TCACTTTCAT
206251 TTTTTG TTTTTG TTTTTG TTTTTTG TTTTTG TTTTT- TTTTTG
1 TTTTTG TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG
206293 AATTTGAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.15
6 23 0.68
7 6 0.18
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:206266 original size:13 final size:13
Alignment explanation
Indices: 206251--206291 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
206241 TCACTTTCAT
206251 TTTTTG-TTTTTG
1 TTTTTGTTTTTTG
206263 TTTTTGTTTTTTG
1 TTTTTGTTTTTTG
206276 TTTTTGTTTTTT-
1 TTTTTGTTTTTTG
206288 TTTT
1 TTTT
206292 GAATTTGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTGTTTTTTG
Found at i:206272 original size:19 final size:18
Alignment explanation
Indices: 206250--206291 Score: 75
Period size: 19 Copynumber: 2.3 Consensus size: 18
206240 TTCACTTTCA
206250 TTTTTTGTTTTTGTTTTT
1 TTTTTTGTTTTTGTTTTT
206268 GTTTTTTGTTTTTGTTTTT
1 -TTTTTTGTTTTTGTTTTT
206287 TTTTT
1 TTTTT
206292 GAATTTGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (18 bp):
TTTTTTGTTTTTGTTTTT
Found at i:210650 original size:37 final size:37
Alignment explanation
Indices: 210549--210651 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
210539 TTTGAGTACT
**
210549 TCTGATCAAGAAACAAAGTGATAAGTGACTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
210586 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
** *
210623 TCTGATCAAGTGATAAAGTGATAAGTGGT
1 TCTGATCAAGAAACAAAGTGATAAGTGGT
210652 AGCTTCAGCT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
Found at i:210668 original size:46 final size:44
Alignment explanation
Indices: 210615--210736 Score: 174
Period size: 46 Copynumber: 2.7 Consensus size: 44
210605 GATAAGTGGT
*
210615 TACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCAGC
1 TACACTTATCTGATCAAGTGA-AAAGTGATAAGTGGTAGCCT-AGC
*
210661 TACACTTATCTGATCAAGTAGCAAAGTGATAAGTGGTAGCCTAGC
1 TACACTTATCTGATCAAGT-GAAAAGTGATAAGTGGTAGCCTAGC
* *
210706 TACATTTATCTGATCAAG-GACAAGTGATAAG
1 TACACTTATCTGATCAAGTGAAAAGTGATAAG
210737 AGGTCATATG
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
43 11 0.16
45 20 0.29
46 38 0.54
47 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (44 bp):
TACACTTATCTGATCAAGTGAAAAGTGATAAGTGGTAGCCTAGC
Found at i:218213 original size:37 final size:37
Alignment explanation
Indices: 218172--218422 Score: 439
Period size: 37 Copynumber: 6.8 Consensus size: 37
218162 TTTGAGTACT
218172 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
* *
218209 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
218246 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
218283 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
218320 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
* *
218357 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
** *
218394 TCTGATCAAGTGATAAAGTGATAAGTGGT
1 TCTGATCAAGAAACAAAGTGATAAGTGGT
218423 AGCTTCAGCT
Statistics
Matches: 205, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 205 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
Found at i:218493 original size:45 final size:46
Alignment explanation
Indices: 218384--218507 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
218374 GTGATAAGTG
* *
218384 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
218430 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
218475 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
218508 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:220489 original size:98 final size:98
Alignment explanation
Indices: 220320--220710 Score: 737
Period size: 98 Copynumber: 4.0 Consensus size: 98
220310 ATACAATAAA
*
220320 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
220385 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
220418 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
220483 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
220516 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
220581 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* *
220614 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
* *
220679 CCTTTAGGATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
220711 CATGATTTTT
Statistics
Matches: 288, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 288 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:221800 original size:19 final size:19
Alignment explanation
Indices: 221776--221867 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
221766 AATCATATAT
*
221776 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
**
221795 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
221814 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
221833 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
221852 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
221868 CTCAAAAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 68 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:221823 original size:38 final size:38
Alignment explanation
Indices: 221753--221867 Score: 149
Period size: 38 Copynumber: 2.9 Consensus size: 38
221743 AAATTAAATC
* *
221753 TCTAAGATTACAAAATCATATATTCTAAGATTGTATATCATA
1 TCTAAGATTAC-ATATC--ATA-TCTAAGATTGCATATCATA
*
221795 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
221833 TCTAGGATTGCATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
221868 CTCAAAAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
38 50 0.75
39 3 0.04
41 4 0.06
42 10 0.15
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:223195 original size:40 final size:40
Alignment explanation
Indices: 223138--223248 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
223128 GTTTGGATAA
* * *
223138 AAAATGCCACTAAAGATCGAGCATTAGCGGCGCTCTTTGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCAGCGCTCTTTGG
* *
223178 AAAACGCCGCTAAAGATCGAGTATTAGCAGCGCTTTTTGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCAGCGCTCTTTGG
* *
223218 AAAACGCCGCTAAA-AACAAGCATTAGCAGCG
1 AAAACGCCGCTAAAGATCGAGCATTAGCAGCG
223249 TTTTCCAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 14 0.22
40 49 0.78
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGCATTAGCAGCGCTCTTTGG
Found at i:223383 original size:41 final size:41
Alignment explanation
Indices: 223311--223642 Score: 423
Period size: 41 Copynumber: 8.1 Consensus size: 41
223301 CTTTGGGGGT
* * *
223311 TTTAGCGGCGTTTTTGAGAAAGCGACGCTAATGCTCAGGAC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
* * *
223352 TTTAGCGGCGTTTTTGGGAAATCGCCACTAATGCTCAGGGA
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
* *
223393 TTTAGCGGCATTTTTGGGAAAGCGCCGCTTATGCTCAGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
* * ** *
223434 TTTAGCGACATTTTTGTAAAAGCGCTGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
* *
223475 TTTAACGGCGTTTTTGGTAAAGCGCCGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
* *
223516 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGT
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
** *
223557 TTTAGCGGCGTTTTTGTTAAAGCGCCGCGAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
* * ** *
223598 TTTAGCGACATTTTCTAAG-AAGCGCCGCTAATGCTCAGGGA
1 TTTAGCGGCGTTTT-TGGGAAAGCGCCGCTAATGCTCAGGGC
223639 TTTA
1 TTTA
223643 AAATAATTTA
Statistics
Matches: 253, Mismatches: 37, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
41 252 1.00
42 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
Found at i:223887 original size:7 final size:7
Alignment explanation
Indices: 223860--223978 Score: 55
Period size: 7 Copynumber: 16.4 Consensus size: 7
223850 GGTTTATAAA
223860 TTATGGGT
1 TTAT-GGT
* *
223868 TTAGGGG
1 TTATGGT
223875 TTATGGT
1 TTATGGT
223882 TTATGGT
1 TTATGGT
*
223889 TTATGAT
1 TTATGGT
* *
223896 TTAAAGGC
1 TT-ATGGT
*
223904 TTAAGGT
1 TTATGGT
*
223911 TTA-GAGG
1 TTATG-GT
223918 TTAT-GT
1 TTATGGT
*
223924 GTTAAGAGT
1 -TTATG-GT
223933 TTATGGTT
1 TTATGG-T
223941 TTATGGTT
1 TTATGG-T
223949 TTATGGT
1 TTATGGT
*
223956 TTA-AGT
1 TTATGGT
*
223962 TTGTGGT
1 TTATGGT
*
223969 TTAGGGT
1 TTATGGT
223976 TTA
1 TTA
223979 GATTAACTAG
Statistics
Matches: 85, Mismatches: 18, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
6 6 0.07
7 51 0.60
8 26 0.31
9 2 0.02
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (7 bp):
TTATGGT
Found at i:223945 original size:8 final size:8
Alignment explanation
Indices: 223932--223957 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
223922 GTGTTAAGAG
223932 TTTATGGT
1 TTTATGGT
223940 TTTATGGT
1 TTTATGGT
223948 TTTATGGT
1 TTTATGGT
223956 TT
1 TT
223958 AAGTTTGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.23, T:0.65
Consensus pattern (8 bp):
TTTATGGT
Found at i:225902 original size:50 final size:47
Alignment explanation
Indices: 225838--225934 Score: 158
Period size: 50 Copynumber: 2.0 Consensus size: 47
225828 GTTTTTCTTT
225838 TCCCTACATGAGTATATGACAATTGGATTTTTTTTTTTGAATAAAAACA
1 TCCCTACATGAGTATATGACAATTGGA--TTTTTTTTTGAATAAAAACA
*
225887 NTCCCTACATGAGTATATGTCAATTGGATTTTTTTTTGAATAAAAACA
1 -TCCCTACATGAGTATATGACAATTGGATTTTTTTTTGAATAAAAACA
225935 ATGCATTTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 20 0.43
50 26 0.57
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.40
Consensus pattern (47 bp):
TCCCTACATGAGTATATGACAATTGGATTTTTTTTTGAATAAAAACA
Found at i:229033 original size:16 final size:16
Alignment explanation
Indices: 229012--229079 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
229002 GATTTGCTAT
229012 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
229028 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
229044 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
*
229060 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
229076 TACA
1 TACA
229080 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:233011 original size:43 final size:43
Alignment explanation
Indices: 232950--233036 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
232940 CAATGATGTA
* * *
232950 CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
* *
232993 CAAGATTTACTTGATTAAGAAAATGCATTTTATGTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
233036 C
1 C
233037 TTGCATATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.45
Consensus pattern (43 bp):
CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
Found at i:233235 original size:24 final size:22
Alignment explanation
Indices: 233208--233259 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
233198 TAATATTTTT
* *
233208 TATTTATTCTTAAAACATATATAA
1 TATTTA-TCATAAAA-ATAAATAA
*
233232 TATTTATCATAAAAATAAATAT
1 TATTTATCATAAAAATAAATAA
233254 TATTTA
1 TATTTA
233260 AAAAAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.48
23 7 0.28
24 6 0.24
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTTATCATAAAAATAAATAA
Found at i:233341 original size:43 final size:43
Alignment explanation
Indices: 233294--233516 Score: 383
Period size: 43 Copynumber: 5.2 Consensus size: 43
233284 GTTTTTAGTA
233294 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
1 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
* *
233337 GCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
1 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
** * * *
233380 GTATTTGTGGGAGAAGCGCCGCTAAAGGTCTTGTTCTATAGTG
1 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
233423 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
1 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
233466 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
1 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
233509 GCGTTTGT
1 GCGTTTGT
233517 TTCTAAAAAC
Statistics
Matches: 170, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 170 1.00
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (43 bp):
GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTTGTTCTATAGCG
Found at i:245101 original size:21 final size:21
Alignment explanation
Indices: 245075--245115 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
245065 ATCTGCTCAA
* *
245075 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
245096 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
245116 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:250457 original size:19 final size:20
Alignment explanation
Indices: 250435--250474 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
250425 TTTTTTAGAT
250435 AATT-ACATTTATTTTTTTA
1 AATTAACATTTATTTTTTTA
*
250454 AATTAAGATTTATTTTTTTA
1 AATTAACATTTATTTTTTTA
250474 A
1 A
250475 TTTCATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (20 bp):
AATTAACATTTATTTTTTTA
Found at i:251258 original size:20 final size:19
Alignment explanation
Indices: 251229--251266 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
251219 AAATATCTTG
*
251229 ATATTTTTTAGTTAAAATT
1 ATATTTTTTAATTAAAATT
251248 ATATATTTTTAATTAAAAT
1 ATAT-TTTTTAATTAAAAT
251267 AATAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATATTTTTTAATTAAAATT
Found at i:251276 original size:21 final size:20
Alignment explanation
Indices: 251233--251272 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
251223 ATCTTGATAT
* * *
251233 TTTTTAGTTAAAATTATATA
1 TTTTTAATTAAAATAATAAA
251253 TTTTTAATTAAAATAATAAA
1 TTTTTAATTAAAATAATAAA
251273 ATTTACAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTTAATTAAAATAATAAA
Found at i:251577 original size:42 final size:42
Alignment explanation
Indices: 251531--251610 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
251521 AGCTAGACAC
* *
251531 GCTTTCTGCATAGTTAGT-AGAAAAGCTCGTACAGCTGGGCAA
1 GCTTTCTGCATAATTA-TCAGAAAAGCTCATACAGCTGGGCAA
* * *
251573 GCTTTTTGCATAATTATCAGGAAAGCTCATTCAGCTGG
1 GCTTTCTGCATAATTATCAGAAAAGCTCATACAGCTGG
251611 ATGAGCTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.03
42 31 0.97
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (42 bp):
GCTTTCTGCATAATTATCAGAAAAGCTCATACAGCTGGGCAA
Done.