Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2154
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: 98853
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6875 original size:13 final size:13
Alignment explanation
Indices: 6857--6882 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6847 TACACCAAGT
6857 ATGTATCGATACA
1 ATGTATCGATACA
6870 ATGTATCGATACA
1 ATGTATCGATACA
6883 CCAAAAATTG
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:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:6880 original size:32 final size:33
Alignment explanation
Indices: 6839--6902 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
6829 TAGCCAAACT
**
6839 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
6871 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
6903 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:8528 original size:21 final size:21
Alignment explanation
Indices: 8502--8543 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8492 AATCAATCGT
* *
8502 TCAAGATGATGATGAAGATGA
1 TCAAGAGGATGATGAAAATGA
*
8523 TCAAGAGGTTGATGAAAATGA
1 TCAAGAGGATGATGAAAATGA
8544 AGAAATGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (21 bp):
TCAAGAGGATGATGAAAATGA
Found at i:12447 original size:32 final size:33
Alignment explanation
Indices: 12406--12469 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
12396 TAGCCAAACT
**
12406 TGTATCGATACACCAAGTATT-TATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
12438 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
12470 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:15881 original size:19 final size:19
Alignment explanation
Indices: 15853--15921 Score: 111
Period size: 19 Copynumber: 3.6 Consensus size: 19
15843 TTTTTACCCA
15853 GATGTATCGATATATTTTC
1 GATGTATCGATATATTTTC
* *
15872 GATCTATCGATATATTTTT
1 GATGTATCGATATATTTTC
*
15891 GATGTATCCATATATTTTC
1 GATGTATCGATATATTTTC
15910 GATGTATCGATA
1 GATGTATCGATA
15922 CATGTATGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (19 bp):
GATGTATCGATATATTTTC
Found at i:17434 original size:13 final size:13
Alignment explanation
Indices: 17394--17435 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
17384 CGTTTAAGGT
17394 AATGTATTGATAC
1 AATGTATTGATAC
*
17407 -ATGATTATCGATAC
1 AATG--TATTGATAC
17421 AATGTATTGATAC
1 AATGTATTGATAC
17434 AA
1 AA
17436 GGTGCCATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 3 0.12
13 10 0.42
14 8 0.33
15 3 0.12
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (13 bp):
AATGTATTGATAC
Found at i:19993 original size:27 final size:27
Alignment explanation
Indices: 19940--19994 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
19930 TTTATTGAAA
* **
19940 AATGGGGTTGGAGTATCCTCTCGGATG
1 AATGGGGTTGGAGTATCCCCAAGGATG
* *
19967 AATGGGGTTGGAGTGTCCCCAATGATG
1 AATGGGGTTGGAGTATCCCCAAGGATG
19994 A
1 A
19995 CAATTTAAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.22, C:0.15, G:0.36, T:0.27
Consensus pattern (27 bp):
AATGGGGTTGGAGTATCCCCAAGGATG
Found at i:20194 original size:97 final size:97
Alignment explanation
Indices: 19947--20183 Score: 368
Period size: 97 Copynumber: 2.4 Consensus size: 97
19937 AAAAATGGGG
* * * *
19947 TTGGAGTATCCTCTCGGATGAATGGGGTTGGAGTGTCCCCAATGATGACAATTTAAGTGAGAATA
1 TTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGATGATGACAATTTAAGTGAGAATA
* *
20012 AAATTTGAACTTTGATGCGTTTAAAAGCAGGG
66 AAATTTAAACTTTGATGCGTTTAAAAGCAGGA
20044 TTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGATGATGACAATTTAAGTGAGAATA
1 TTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGATGATGACAATTTAAGTGAGAATA
* *
20109 AGATTTAAACTTTGATGTGTTTAAAAGC-GAGA
66 AAATTTAAACTTTGATGCGTTTAAAAGCAG-GA
* *
20141 TTGGAGTATCCCCTCGGAGGAATAGGGTTGAAGTATCCCCGAT
1 TTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGAT
20184 AAATAAAATT
Statistics
Matches: 129, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
96 1 0.01
97 128 0.99
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (97 bp):
TTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGATGATGACAATTTAAGTGAGAATA
AAATTTAAACTTTGATGCGTTTAAAAGCAGGA
Found at i:22413 original size:20 final size:20
Alignment explanation
Indices: 22390--22455 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
22380 GAATGTATGG
22390 ATACATTGAAAAAAGTATCA
1 ATACATTGAAAAAAGTATCA
* * * * *
22410 ATACATTCATACATGTATCG
1 ATACATTGAAAAAAGTATCA
22430 ATACATTGAAAAAAGTATCA
1 ATACATTGAAAAAAGTATCA
22450 ATACAT
1 ATACAT
22456 CTGGGTAAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (20 bp):
ATACATTGAAAAAAGTATCA
Found at i:23196 original size:48 final size:48
Alignment explanation
Indices: 23134--23257 Score: 167
Period size: 48 Copynumber: 2.6 Consensus size: 48
23124 AGAGGAGTGC
** * *
23134 CAATGTGCCAATTCAAGGCCAATGACATCAAGCTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAACGACATCAAGCTAAGGGAAAAGTAGA
** *
23182 CAATGTGCTGATTCAAGGCCAACGACATTGAGTTAAGGGAAAAGTAGA
1 CAATGTGCTGATTCAAGGCCAACGACATCAAGCTAAGGGAAAAGTAGA
* *
23230 CAATGTGCTGATTCAAGACCAGCGACAT
1 CAATGTGCTGATTCAAGGCCAACGACAT
23258 TGAGCTAATA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (48 bp):
CAATGTGCTGATTCAAGGCCAACGACATCAAGCTAAGGGAAAAGTAGA
Found at i:23421 original size:28 final size:28
Alignment explanation
Indices: 23371--23600 Score: 210
Period size: 28 Copynumber: 8.0 Consensus size: 28
23361 CTTTTAAAAT
* * *
23371 AAAGGTGCCACTAACTTATGTGGGCTTTAA
1 AAAGATGCCACTGAC-T-TGTGGGCTTTGA
*
23401 AAAGATGCCACTAACTTGTGGG-TTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* * * *
23428 AGAGATGCTGCCACTAACTCGTGGGCTTTGG
1 A-A-A-GATGCCACTGACTTGTGGGCTTTGA
* **
23459 AAGGATGCCACTGACTCATGGGCTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* * *
23487 AAAGGTGCCATTGACTTGTGGGCTTGGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
*
23515 AAAGATGCCATTGACTTGTGGGCTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* * *
23543 AATGATGCCAGTGACTTGTGGTCTTTTGA
1 AAAGATGCCACTGACTTGTGGGC-TTTGA
* * *
23572 AGAGATGCCACTGACTCGTGGACTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
23600 A
1 A
23601 GAGGTCACAA
Statistics
Matches: 169, Mismatches: 26, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
27 5 0.03
28 102 0.60
29 25 0.15
30 32 0.19
31 5 0.03
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (28 bp):
AAAGATGCCACTGACTTGTGGGCTTTGA
Found at i:29948 original size:97 final size:97
Alignment explanation
Indices: 29765--29997 Score: 322
Period size: 97 Copynumber: 2.4 Consensus size: 97
29755 TTTTTTATTG
* * * * *
29765 AAAAACGGGGTTAGAGTATCTCCTCGGAGGAATGGGGTTGGAGTGTCCTCGATGATGACAATTTA
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGATGATGACAATTTA
* * *
29830 AGTGAGAATAAAATTTGAACTTTGATGCGTTT
66 AGTAAGAATAAAATTTAAACTTTGATACGTTT
* *
29862 AAAAGCGGGGTTGGAGTATCCCCTCGAAGGAATGGGGTTGAAGTGTCCCCGATGGTGACAATTTA
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGATGATGACAATTTA
* * *
29927 AGTAAGAATCAGATTTAAACTTTGATATGTTT
66 AGTAAGAATAAAATTTAAACTTTGATACGTTT
* * *
29959 AAAAGCGAGATTGGAGTATCCCCTCGGAGGAATAGGGTT
1 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTT
29998 AGAGTATCCC
Statistics
Matches: 119, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 119 1.00
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.28
Consensus pattern (97 bp):
AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGATGATGACAATTTA
AGTAAGAATAAAATTTAAACTTTGATACGTTT
Found at i:32175 original size:20 final size:20
Alignment explanation
Indices: 32146--32314 Score: 90
Period size: 20 Copynumber: 7.8 Consensus size: 20
32136 AAAAAAAGAT
*
32146 AGAATATATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
32166 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
32186 TA-CATGTCTCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
32206 AAAATGTATCCATACATCTAGGTAAAAAAAA
1 AGAATGTATCGATACAT-T--G--------A
* *
32237 TAGAATGTTTCAATACATTGA
1 -AGAATGTATCGATACATTGA
*
32258 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
32278 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
32298 AAAATGTATCAATACAT
1 AGAATGTATCGATACAT
32315 ACTTTTTCAT
Statistics
Matches: 115, Mismatches: 18, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
19 2 0.02
20 91 0.79
21 4 0.03
23 1 0.01
29 1 0.01
31 2 0.02
32 14 0.12
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:32261 original size:92 final size:92
Alignment explanation
Indices: 32118--32314 Score: 315
Period size: 92 Copynumber: 2.1 Consensus size: 92
32108 CATTTTTCTT
* *
32118 TGTATCGATACATCTGGAAAAAAAAGATAGAATATATCGATACATTGAAGAATGTATCGATACAT
1 TGTATCAATACATCTGGAAAAAAAAGATAGAATATATCAATACATTGAAGAATGTATCGATACAT
*
32183 TCATACATGTCTCGATACATTGAAAAA
66 TCATACATGTATCGATACATTGAAAAA
* * * *
32210 TGTATCCATACATCTAGGTAAAAAAA-ATAGAATGTTTCAATACATTGAAGAATGTATCGATACA
1 TGTATCAATACATCT-GGAAAAAAAAGATAGAATATATCAATACATTGAAGAATGTATCGATACA
32274 TTCATACATGTATCGATACATTGAAAAA
65 TTCATACATGTATCGATACATTGAAAAA
32302 TGTATCAATACAT
1 TGTATCAATACAT
32315 ACTTTTTCAT
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
92 88 0.91
93 9 0.09
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (92 bp):
TGTATCAATACATCTGGAAAAAAAAGATAGAATATATCAATACATTGAAGAATGTATCGATACAT
TCATACATGTATCGATACATTGAAAAA
Found at i:37453 original size:33 final size:33
Alignment explanation
Indices: 37416--37482 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
37406 TTCAACGATT
37416 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
37449 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
37482 T
1 T
37483 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:37454 original size:13 final size:13
Alignment explanation
Indices: 37436--37460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37426 CATAAAATGT
37436 TGTATCGATACAA
1 TGTATCGATACAA
37449 TGTATCGATACA
1 TGTATCGATACA
37461 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:37541 original size:13 final size:13
Alignment explanation
Indices: 37523--37547 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37513 ATTACTCAAA
37523 TGTATCGATACAT
1 TGTATCGATACAT
37536 TGTATCGATACA
1 TGTATCGATACA
37548 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:37649 original size:52 final size:52
Alignment explanation
Indices: 37556--37683 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
37546 CACTGATCTT
*
37556 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
37607 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
37659 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
37684 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:42304 original size:15 final size:15
Alignment explanation
Indices: 42286--42320 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
42276 CGAGTCAACT
42286 TCATCATTATCATT-A
1 TCATCATTATC-TTCA
42301 TCATCATTATCTTCA
1 TCATCATTATCTTCA
42316 TCATC
1 TCATC
42321 TTTGATGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.46
Consensus pattern (15 bp):
TCATCATTATCTTCA
Found at i:44578 original size:20 final size:19
Alignment explanation
Indices: 44551--44674 Score: 74
Period size: 20 Copynumber: 6.8 Consensus size: 19
44541 ATCACTGTTC
44551 ATGTATCGATACATTGTGA
1 ATGTATCGATACATTGTGA
**
44570 ATAGTATCGATACATCACTGTTC
1 AT-GTATCGATACAT---TGTGA
44593 ATGTATCGATACA---T--
1 ATGTATCGATACATTGTGA
*
44607 -TGTATCGATACATTATGA
1 ATGTATCGATACATTGTGA
44625 ATAGTATCGATACA----G-
1 AT-GTATCGATACATTGTGA
*
44640 -TGTATCGATACATTATGA
1 ATGTATCGATACATTGTGA
44658 ATAGTATCGATACATTG
1 AT-GTATCGATACATTG
44675 AGTCCAACGG
Statistics
Matches: 84, Mismatches: 3, Indels: 35
0.69 0.02 0.29
Matches are distributed among these distances:
13 23 0.27
14 1 0.01
16 3 0.04
17 1 0.01
19 4 0.05
20 36 0.43
22 11 0.13
23 5 0.06
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACATTGTGA
Found at i:44601 original size:22 final size:22
Alignment explanation
Indices: 44541--44606 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
44531 TTCACTGTTG
44541 ATCACTGTTCATGTATCGATAC
1 ATCACTGTTCATGTATCGATAC
**
44563 AT---TGTGAATAGTATCGATAC
1 ATCACTGTTCAT-GTATCGATAC
44583 ATCACTGTTCATGTATCGATAC
1 ATCACTGTTCATGTATCGATAC
44605 AT
1 AT
44607 TGTATCGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 5 0.14
20 12 0.33
22 14 0.39
23 5 0.14
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCACTGTTCATGTATCGATAC
Found at i:44612 original size:13 final size:13
Alignment explanation
Indices: 44594--44653 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
44584 TCACTGTTCA
44594 TGTATCGATACAT
1 TGTATCGATACAT
44607 TGTATCGATACA-
1 TGTATCGATACAT
44619 T-TAT-G--A-AT
1 TGTATCGATACAT
* *
44627 AGTATCGATACAG
1 TGTATCGATACAT
44640 TGTATCGATACAT
1 TGTATCGATACAT
44653 T
1 T
44654 ATGAATAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.08
10 2 0.05
11 3 0.08
12 2 0.05
13 25 0.68
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:44637 original size:33 final size:33
Alignment explanation
Indices: 44595--44674 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
44585 CACTGTTCAT
44595 GTATCGATACATTGTATCGATACATTATGAATA
1 GTATCGATACATTGTATCGATACATTATGAATA
*
44628 GTATCGATACAGTGTATCGATACATTATGAATA
1 GTATCGATACATTGTATCGATACATTATGAATA
44661 GTATCGATACATTG
1 GTATCGATACATTG
44675 AGTCCAACGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (33 bp):
GTATCGATACATTGTATCGATACATTATGAATA
Found at i:44755 original size:20 final size:21
Alignment explanation
Indices: 44709--44755 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
44699 AATTTCAAAT
*
44709 GTATGTATCGATACATTATGA
1 GTATGTATCGATACATTAGGA
*
44730 AT-TGTATCGATACA-TAGGA
1 GTATGTATCGATACATTAGGA
44749 GTATGTA
1 GTATGTA
44756 AGTGCGGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.23
20 16 0.73
21 1 0.05
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (21 bp):
GTATGTATCGATACATTAGGA
Found at i:49091 original size:167 final size:166
Alignment explanation
Indices: 48645--49192 Score: 530
Period size: 167 Copynumber: 3.3 Consensus size: 166
48635 TTTTAATAAC
* *** * * * * **
48645 AATATTAGATGAATTTTAAAAATTTTAAACCGAGAAAAATCCCCC-AAAAAAAATTACGAAGGAG
1 AATATTTGATGAATTTTAAAAATAAAAAACCAAGAAAAATCCCCCGAAAACAATTTATGAAATAG
* * * * * * * * *
48709 AAAACTCGGTTTCTCG-AATAAAGGGAATTACAAAG-AAAACTTCAAAACTCATGAAAATGAATG
66 AAAACTCGATTTTTCGAAAAAAAGGGCATTTCAAAGAAAAAATCCAAAACTTATGAAAATGAATT
* *
48772 AATTTTTCAAAAC-TGAATTT-A-A-GAGTTTAATGAC-
131 AATTTTT-TAAACTTG-ATTTAATATGAGTTAAATG-CT
* * *** * * * * * ** *
48806 AATATTAGATAAATTTTAAAAATTTTACATCGAG-AAAACCCCCCGAAAAC-CTTTATGGGATCG
1 AATATTTGATGAATTTTAAAAATAAAAAACCAAGAAAAATCCCCCGAAAACAATTTATGAAATAG
* * * *
48869 GAAACTCAATTTTTC-AAAAAAAAGGCATTTCAAAGAAAAAATCCAAAAATTATGAAAATGAATT
66 AAAACTCGATTTTTCGAAAAAAAGGGCATTTCAAAGAAAAAATCCAAAACTTATGAAAATGAATT
48933 AATTTTTTAAACTTGATTTAATATGAGTTAAATGCT
131 AATTTTTTAAACTTGATTTAATATGAGTTAAATGCT
*
48969 AATATTTTATGAATTTTAAAAATAAAAAACCAAGAAAAATCCCCC-AAAACAATTTATGAAATAG
1 AATATTTGATGAATTTTAAAAATAAAAAACCAAGAAAAATCCCCCGAAAACAATTTATGAAATAG
49033 AAAACTCGATTTTTCGAAAAAAACGGGCATTTCAAAGAAAAAAATCCAAAACTTATGAAAATGAA
66 AAAACTCGATTTTTCGAAAAAAA-GGGCATTTCAAAG-AAAAAATCCAAAACTTATGAAAATGAA
* * * *
49098 TTAATTTTTTAAAATTAATTTAATATAAGTTAAATGAT
129 TTAATTTTTTAAACTTGATTTAATATGAGTTAAATGCT
* *
49136 GATATTTGATGAATTTTAAAAATAAAAAATCAA-AAAGAATCCTCCCGAAAA-AATTTA
1 AATATTTGATGAATTTTAAAAATAAAAAACCAAGAAA-AATCC-CCCGAAAACAATTTA
49193 CAGAGTAAAA
Statistics
Matches: 318, Mismatches: 53, Indels: 25
0.80 0.13 0.06
Matches are distributed among these distances:
160 48 0.15
161 68 0.21
162 2 0.01
163 39 0.12
164 31 0.10
165 7 0.02
166 15 0.05
167 95 0.30
168 9 0.03
169 4 0.01
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (166 bp):
AATATTTGATGAATTTTAAAAATAAAAAACCAAGAAAAATCCCCCGAAAACAATTTATGAAATAG
AAAACTCGATTTTTCGAAAAAAAGGGCATTTCAAAGAAAAAATCCAAAACTTATGAAAATGAATT
AATTTTTTAAACTTGATTTAATATGAGTTAAATGCT
Found at i:49377 original size:47 final size:46
Alignment explanation
Indices: 49249--50144 Score: 615
Period size: 47 Copynumber: 19.0 Consensus size: 46
49239 GTCAAATGAT
* * *
49249 GGTG-GAAAGAGTTTGACTAGGTCTTAATGCCAATACAGTTAAACAA
1 GGTGAGAAA-AGTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
* * *
49295 GGT-AAAAAGAGTTTGACCT-GGTCCTAATGCCAATACAGTCAAATAA
1 GGTGAGAAA-AGTTTGA-CTAGGTCCTAATGCCAATATAGTCAAACAA
* * * * *
49341 TGGTGAGAAAAGTTTGACTAGGTTCTAACGCTAATACAATCAAACAA
1 -GGTGAGAAAAGTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
*
49388 GG-GTA-AAAAGTGTTTGACTAAGTCCTAATGCCAATATAGTCAAACAA
1 GGTG-AGAAAA--GTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
** *
49435 GG-GTA-AAAAGTGTTTGACTAGGTCCTAACACCAATATAATCAAACAA
1 GGTG-AGAAAA--GTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
* * * **
49482 GGTGACAAGAGTTTGACCAAATCCTAATGCCAATATAGTCAAACAA
1 GGTGAGAAAAGTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
* * * *
49528 GAGTG-GAAAGAGTTTGACTAGATCC-AACAGCCAATATAGTCAAATGAT
1 G-GTGAGAAA-AGTTTGACTAGGTCCTAA-TGCCAATATAGTCAAA-CAA
* * * * *
49576 GGT-AGAATTTGAGTTTGACTAGATCCAAATGCCAATAAAGTCAAATAA
1 GGTGAGAA---AAGTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
* * * *
49624 GGTTGAGAAAAGTTTGACTAGGTTCTAACGCCAATATAATCAAACGA
1 GG-TGAGAAAAGTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
* * *
49671 GG-GTA-AAAACTGTTTGATTAGGTCCTAATGCCAATATAGTTAAATAA
1 GGTG-AGAAAA--GTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
* * * * ***
49718 GGTGAGAAGAGTTTGACTAGATCCTAACGCCAATACAGTCAAGTGA
1 GGTGAGAAAAGTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
* * *
49764 GAGT-AGAAGGAGTTTGACTTGGTCCTAATGCCAATATAGTCAAACGAT
1 G-GTGAGAA-AAGTTTGACTAGGTCCTAATGCCAATATAGTCAAAC-AA
* * *
49812 GGTG-GAATTTGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGAT
1 GGTGAGAA---AAGTTTGACTAGGTCCTAATGCCAATATAGTCAAAC-AA
* * * * *
49861 GGTG-GAATTTAAGTTTGACCAGGTCCTAACGCCAATACAGTTAAATAA
1 GGTGAGAA---AAGTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
* * * * *
49909 GGGTAAGAAAAGTTTGACCAGGTTCTAATGTCAATATAGTCAAATAA
1 -GGTGAGAAAAGTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
* * * *
49956 GG-GTA-AAAAGTGTTTGACTAGGTCCCAATGCTAATACAGTTAAACAA
1 GGTG-AGAAAA--GTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
* * * * * *
50003 GGTGAGAAGAGTTTGACCATGCCCTAACGCCAATTTAGTCAAACAA
1 GGTGAGAAAAGTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
* * *
50049 GAGTG-GAAAGAGTTTGACTAGGTCTTAATGCCAATACAGTCAAACGAT
1 G-GTGAGAAA-AGTTTGACTAGGTCCTAATGCCAATATAGTCAAAC-AA
** *
50097 GGTG-GTATTTGAGTTTGACCAGGTCCTAATGCCAATATAGTCAAACAA
1 GGTGAG-A--AAAGTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
50145 TCATGAAATT
Statistics
Matches: 685, Mismatches: 120, Indels: 88
0.77 0.13 0.10
Matches are distributed among these distances:
45 14 0.02
46 147 0.21
47 345 0.50
48 27 0.04
49 143 0.21
50 9 0.01
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (46 bp):
GGTGAGAAAAGTTTGACTAGGTCCTAATGCCAATATAGTCAAACAA
Found at i:49525 original size:93 final size:93
Alignment explanation
Indices: 49254--50092 Score: 623
Period size: 93 Copynumber: 8.9 Consensus size: 93
49244 ATGATGGTGG
* * * * *
49254 AAAGAGTTTGACTAGGTCTTAATGCCAATACAGTTAAACAAGGTAAAAAGAGTTTGACCT-GGTC
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAATCAAACAAGGTAAAAAGAGTTTGA-CTAGGTC
* * *
49318 CTAATGCCAATACAGTCAAATAATGGTGAG
65 CTAATGCCAATATAGTCAAATAAGGGT-AA
* * * * *
49348 AAA-AGTTTGACTAGGTTCTAACGCTAATACAATCAAACAAGGGTAAAAAGTGTTTGACTAAGTC
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAATCAAACAA-GGTAAAAAGAGTTTGACTAGGTC
*
49412 CTAATGCCAATATAGTCAAACAAGGGTAA
65 CTAATGCCAATATAGTCAAATAAGGGTAA
* * * * * **
49441 AAAGTGTTTGACTAGGTCCTAACACCAATATAATCAAACAAGGTGACAAGAGTTTGACCAAATCC
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAATCAAACAAGGTAAAAAGAGTTTGACTAGGTCC
* * **
49506 TAATGCCAATATAGTCAAACAAGAGTGG
66 TAATGCCAATATAGTCAAATAAGGGTAA
* * * * **
49534 AAAGAGTTTGACTAGATCC-AACAGCCAATATAGTCAAATGATGGTAGAATTTGAGTTTGACTAG
1 AAAGAGTTTGACTAGGTCCTAAC-GCCAATATAATCAAA-CAAGGTA-AA-AAGAGTTTGACTAG
* * * * *
49598 ATCCAAATGCCAATAAAGTCAAATAAGGTTGAG
62 GTCCTAATGCCAATATAGTCAAATAAGGGT-AA
* * ** *
49631 AAA-AGTTTGACTAGGTTCTAACGCCAATATAATCAAACGAGGGTAAAAACTGTTTGATTAGGTC
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAATCAAAC-AAGGTAAAAAGAGTTTGACTAGGTC
* *
49695 CTAATGCCAATATAGTTAAATAA-GGTGA
65 CTAATGCCAATATAGTCAAATAAGGGTAA
* * * * *** * * *
49723 GAAGAGTTTGACTAGATCCTAACGCCAATACAGTCAAGTGAGAGTAGAAGGAGTTTGACTTGGTC
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAATCAAACAAG-GTAAAAAGAGTTTGACTAGGTC
* * *
49788 CTAATGCCAATATAGTCAAACGATGGTGGAA
65 CTAATGCCAATATAGTCAAA-TAAGG-GTAA
*** * * * * ** *
49819 TTTGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGATGGTGGAATTTA-AGTTTGACCAG
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAATCAAAC-AAGGT--AA-AAAGAGTTTGACTAG
* * *
49883 GTCCTAACGCCAATACAGTTAAATAAGGGTAA
62 GTCCTAATGCCAATATAGTCAAATAAGGGTAA
* * * * * * *
49915 GAAA-AGTTTGACCAGGTTCTAATGTCAATATAGTCAAATAAGGGTAAAAAGTGTTTGACTAGGT
1 -AAAGAGTTTGACTAGGTCCTAACGCCAATATAATCAAACAA-GGTAAAAAGAGTTTGACTAGGT
* * * * * *
49979 CCCAATGCTAATACAGTTAAACAA-GGTGA
64 CCTAATGCCAATATAGTCAAATAAGGGTAA
* * * * * * **
50008 GAAGAGTTTGACCATGCCCTAACGCCAATTTAGTCAAACAAGAGTGGAAAGAGTTTGACTAGGTC
1 AAAGAGTTTGACTAGGTCCTAACGCCAATATAATCAAACAAG-GTAAAAAGAGTTTGACTAGGTC
* *
50073 TTAATGCCAATACAGTCAAA
65 CTAATGCCAATATAGTCAAA
50093 CGATGGTGGT
Statistics
Matches: 587, Mismatches: 134, Indels: 49
0.76 0.17 0.06
Matches are distributed among these distances:
92 9 0.02
93 247 0.42
94 146 0.25
95 5 0.01
96 139 0.24
97 11 0.02
98 30 0.05
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (93 bp):
AAAGAGTTTGACTAGGTCCTAACGCCAATATAATCAAACAAGGTAAAAAGAGTTTGACTAGGTCC
TAATGCCAATATAGTCAAATAAGGGTAA
Found at i:49676 original size:236 final size:236
Alignment explanation
Indices: 49277--49856 Score: 638
Period size: 236 Copynumber: 2.5 Consensus size: 236
49267 AGGTCTTAAT
* * * * * **
49277 GCCAATACAGTTAAACAAG-GTAAAAAGAGTTTGACCT-GGTCCTAATGCCAATACAGTCAAATA
1 GCCAATACAGTCAAACAAGAGTAGAAAGAGTTTGA-CTAGATCCTAAAGCCAATATAGTCAAACG
* * * * * * * *
49340 ATGGTGAGAA---AAGTTTGACTAGGTTCTAACGCTAATACAA-TCAAACAAGGGT-A-AAAAGT
65 ATGGT-AGAATTTGAGTTTGACTAGATCCAAATGCCAATA-AAGTCAAATAAGGTTGAGAAAA--
* * *
49399 GTTTGACTAAGTCCTAATGCCAATATAGTCAAACAAGGGTAAAAAGTGTTTGACTAGGTCCTAAC
126 GTTTGACTAAGTCCTAACGCCAATATAATCAAACAAGGGTAAAAACTGTTTGACTAGGTCCTAAC
*
49464 ACCAATATAATCAAACAAGGTGACAAGAGTTTGACCAAATCCTAAT
191 ACCAATATAATCAAACAAGGTGACAAGAGTTTGACCAAATCCTAAC
* * *
49510 GCCAATATAGTCAAACAAGAGTGGAAAGAGTTTGACTAGATCC-AACAGCCAATATAGTCAAATG
1 GCCAATACAGTCAAACAAGAGTAGAAAGAGTTTGACTAGATCCTAA-AGCCAATATAGTCAAACG
49574 ATGGTAGAATTTGAGTTTGACTAGATCCAAATGCCAATAAAGTCAAATAAGGTTGAGAAAAGTTT
65 ATGGTAGAATTTGAGTTTGACTAGATCCAAATGCCAATAAAGTCAAATAAGGTTGAGAAAAGTTT
* * * * **
49639 GACTAGGTTCTAACGCCAATATAATCAAACGAGGGTAAAAACTGTTTGATTAGGTCCTAATGCCA
130 GACTAAGTCCTAACGCCAATATAATCAAACAAGGGTAAAAACTGTTTGACTAGGTCCTAACACCA
* * * * * *
49704 ATATAGTTAAATAAGGTGAGAAGAGTTTGACTAGATCCTAAC
195 ATATAATCAAACAAGGTGACAAGAGTTTGACCAAATCCTAAC
*** * * * *
49746 GCCAATACAGTCAAGTGAGAGTAGAAGGAGTTTGACTTGGTCCTAATGCCAATATAGTCAAACGA
1 GCCAATACAGTCAAACAAGAGTAGAAAGAGTTTGACTAGATCCTAAAGCCAATATAGTCAAACGA
* * * *
49811 TGGTGGAATTTGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAA
66 TGGTAGAATTTGAGTTTGACTAGATCCAAATGCCAATAAAGTCAAA
49857 CGATGGTGGA
Statistics
Matches: 291, Mismatches: 46, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
233 25 0.09
234 37 0.13
235 2 0.01
236 220 0.76
237 3 0.01
238 4 0.01
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.25
Consensus pattern (236 bp):
GCCAATACAGTCAAACAAGAGTAGAAAGAGTTTGACTAGATCCTAAAGCCAATATAGTCAAACGA
TGGTAGAATTTGAGTTTGACTAGATCCAAATGCCAATAAAGTCAAATAAGGTTGAGAAAAGTTTG
ACTAAGTCCTAACGCCAATATAATCAAACAAGGGTAAAAACTGTTTGACTAGGTCCTAACACCAA
TATAATCAAACAAGGTGACAAGAGTTTGACCAAATCCTAAC
Found at i:49946 original size:285 final size:280
Alignment explanation
Indices: 49232--50213 Score: 1091
Period size: 285 Copynumber: 3.5 Consensus size: 280
49222 GAGAGAATTT
* * * * *
49232 CAATATGGTCAAATGATGGTGGAAAGAGTTTGACTAGGTCTTAATGCCAATACAGTTAAAC-AAG
1 CAATATAGTCAAACGATGGTGGAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGATG
** * * * *
49296 GT--AA-AAAGAGTTTGACCTGGTCCTAATGCCAATACAGTCAAATAATGGTGAGAAAAGTTTGA
66 GTGGAATTTA-AGTTTGACCAGATCCTAATGCCAATACAGTCAAATAAGGGTAAGAAAAGTTTGA
* * *
49358 CTAGGTTCTAACGCTAATACAATCAAACAAGGGTAAAAAGTGTTTGACTAAGTCCTAATGCCAAT
130 CCAGGTTCTAACGC-AATATAATCAAACAAGGGTAAAAAGTGTTTGACTAGGTCCTAATGCCAAT
* * * * * *
49423 ATAGTCAAACAAGGGTAAAAAGTGTTTGACTAGGTCCTAACACCAATATAATCAAACAAG-GTGA
194 ATAGTTAAACAA-GGTGAGAAGAGTTTGACTA-GTCCTAACGCCAATATAGTCAAACAAGAGTGA
* **
49487 CAAGAGTTTGACCAAATCCTAATGC
257 -AAGAGTTTGACTAGGTCCTAATGC
* * * * *
49512 CAATATAGTCAAAC-AAGAGTGGAAAGAGTTTGACTAGATCC-AACAGCCAATATAGTCAAATGA
1 CAATATAGTCAAACGATG-GTGGAAAGAGTTTGACTAGGTCCTAA-TGCCAATACAGTCAAACGA
* * * * * * *
49575 TGGTAGAATTTGAGTTTGACTAGATCCAAATGCCAATAAAGTCAAATAAGGTTGAGAAAAGTTTG
64 TGGTGGAATTTAAGTTTGACCAGATCCTAATGCCAATACAGTCAAATAAGGGTAAGAAAAGTTTG
* * * *
49640 ACTAGGTTCTAACGCCAATATAATCAAACGAGGGTAAAAACTGTTTGATTAGGTCCTAATGCCAA
129 ACCAGGTTCTAACG-CAATATAATCAAACAAGGGTAAAAAGTGTTTGACTAGGTCCTAATGCCAA
* * ***
49705 TATAGTTAAATAAGGTGAGAAGAGTTTGACTAGATCCTAACGCCAATACAGTCAAGTGAGAGTAG
193 TATAGTTAAACAAGGTGAGAAGAGTTTGACTAG-TCCTAACGCCAATATAGTCAAACAAGAGT-G
* *
49770 AAGGAGTTTGACTTGGTCCTAATGC
256 AAAGAGTTTGACTAGGTCCTAATGC
*
49795 CAATATAGTCAAACGATGGTGGAATTTGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGA
1 CAATATAGTCAAACGATGGTGGAA--AGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGA
* * *
49860 TGGTGGAATTTAAGTTTGACCAGGTCCTAACGCCAATACAGTTAAATAAGGGTAAGAAAAGTTTG
64 TGGTGGAATTTAAGTTTGACCAGATCCTAATGCCAATACAGTCAAATAAGGGTAAGAAAAGTTTG
* * * * *
49925 ACCAGGTTCTAATGTCAATATAGTCAAATAAGGGTAAAAAGTGTTTGACTAGGTCCCAATGCTAA
129 ACCAGGTTCTAACG-CAATATAATCAAACAAGGGTAAAAAGTGTTTGACTAGGTCCTAATGCCAA
* * * *
49990 TACAGTTAAACAAGGTGAGAAGAGTTTGACCATGCCCTAACGCCAATTTAGTCAAACAAGAGTGG
193 TATAGTTAAACAAGGTGAGAAGAGTTTGACTA-GTCCTAACGCCAATATAGTCAAACAAGAGT-G
*
50055 AAAGAGTTTGACTAGGTCTTAATGC
256 AAAGAGTTTGACTAGGTCCTAATGC
* ** * * *
50080 CAATACAGTCAAACGATGGTGGTATTTGAGTTTGACCAGGTCCTAATGCCAATATAGTCAAACAA
1 CAATATAGTCAAACGATGGTGG-A-AAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGA
** * * * *
50145 TCATGAAATTTGAGTTTGACCA-ATCCTAATGCCAATACAATTAAATAAGGGTGAA-AAAAGTTT
64 TGGTGGAATTTAAGTTTGACCAGATCCTAATGCCAATACAGTCAAATAAGGGT-AAGAAAAGTTT
50208 GACCAG
128 GACCAG
50214 ATATAGTGAA
Statistics
Matches: 592, Mismatches: 92, Indels: 32
0.83 0.13 0.04
Matches are distributed among these distances:
279 4 0.01
280 46 0.08
281 5 0.01
282 36 0.06
283 158 0.27
284 46 0.08
285 293 0.49
286 4 0.01
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (280 bp):
CAATATAGTCAAACGATGGTGGAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACGATG
GTGGAATTTAAGTTTGACCAGATCCTAATGCCAATACAGTCAAATAAGGGTAAGAAAAGTTTGAC
CAGGTTCTAACGCAATATAATCAAACAAGGGTAAAAAGTGTTTGACTAGGTCCTAATGCCAATAT
AGTTAAACAAGGTGAGAAGAGTTTGACTAGTCCTAACGCCAATATAGTCAAACAAGAGTGAAAGA
GTTTGACTAGGTCCTAATGC
Found at i:50200 original size:48 final size:49
Alignment explanation
Indices: 50058--50185 Score: 125
Period size: 49 Copynumber: 2.6 Consensus size: 49
50048 AGAGTGGAAA
* * * * * * **
50058 GAGTTTGACTAGGTCTTAATGCCAATACAGTCAAACGATG-GTGGTATTT
1 GAGTTTGACCAGATCCTAATGCCAATACAATCAAAC-AAGCATGAAATTT
* * * *
50107 GAGTTTGACCAGGTCCTAATGCCAATATAGTCAAACAATCATGAAATTT
1 GAGTTTGACCAGATCCTAATGCCAATACAATCAAACAAGCATGAAATTT
50156 GAGTTTGACCA-ATCCTAATGCCAATACAAT
1 GAGTTTGACCAGATCCTAATGCCAATACAAT
50186 TAAATAAGGG
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
48 17 0.25
49 50 0.75
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (49 bp):
GAGTTTGACCAGATCCTAATGCCAATACAATCAAACAAGCATGAAATTT
Found at i:52174 original size:20 final size:20
Alignment explanation
Indices: 52128--52188 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
52118 CAACACCTTT
* **
52128 TTCAATGTATCGATATATGG
1 TTCAATGTATCGATACATTC
* *
52148 ATGAATGTATCGATACATTC
1 TTCAATGTATCGATACATTC
52168 TTCAATGTATCGATACATTC
1 TTCAATGTATCGATACATTC
52188 T
1 T
52189 ACCCTGATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (20 bp):
TTCAATGTATCGATACATTC
Found at i:52202 original size:23 final size:20
Alignment explanation
Indices: 52151--52208 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
52141 TATATGGATG
*
52151 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTCC
52171 AATGTATCGATACATTCTACCC
1 AATGTATCGATACATTCT--CC
*
52193 TGATGTATCGATACAT
1 -AATGTATCGATACAT
52209 CTAGTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 18 0.55
22 1 0.03
23 14 0.42
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCTCC
Found at i:63841 original size:20 final size:20
Alignment explanation
Indices: 63778--63851 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
63768 TTTTAACTAG
*
63778 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAAAA
* * * * *
63798 ATGAATTGATAAATTCAAAC
1 ATGTATCGATACATTGAAAA
63818 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
63838 ATGTATCGATACAT
1 ATGTATCGATACAT
63852 ATGGGTAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:64844 original size:28 final size:28
Alignment explanation
Indices: 64765--65386 Score: 658
Period size: 28 Copynumber: 21.9 Consensus size: 28
64755 TAAAAAAAAT
*
64765 GTGCCACTAACTTGTGTGGGCTTTGAAAAGAG
1 GTGCCACTGAC-T-TGTGGGCTTTG-AAAG-G
* *
64797 TTGCCACCGACTTCTGTGGGCTTTGAAAGG
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGG
* **
64827 GTGCCACTAACTTGTGGGCTTTGATGGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
64855 GTGCCACTGACTTGTGGGCTTTGAAGGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
64883 GTACCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * * * *
64911 GTACTATTGACTTGTGGGATTCGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * *
64939 GTACCACTAACTTATGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
**
64967 GTATCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
64995 GTGCCACTAACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
65023 GTGCCACTGACTTGTGGGATTTGGAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
65051 GTGCCACTGATTTGTGCGGGCTTTGAAAGAG
1 GTGCCACTGACTTGT--GGGCTTTGAAAG-G
* **
65082 TATGCCACTGACTTGTGGGCTTTGAAACA
1 -GTGCCACTGACTTGTGGGCTTTGAAAGG
*
65111 GTGCCACTAACTTGTGGGCTTTGTAAA-G
1 GTGCCACTGACTTGTGGGCTTTG-AAAGG
* * *
65139 ATGCCACTGACTTGTGGTCTTTTG-AAGAA
1 GTGCCACTGACTTGTGGGC-TTTGAAAG-G
* * * *
65168 ATGCCACTAACTTATGGGTTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
65196 ATGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * * *
65224 ATGCCACTAACTTGTAGGCTTTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
65252 GTGCCACTGACTTATGGGCTTTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * *
65280 ATGCCACT-ACTTATGGGCTTTCAAA-G
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * **
65306 ATGCCACTAACTTGTGGGCTTTGAAATT
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
65334 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
65362 ATGCCACTGACCTGTGGGCTTTGAA
1 GTGCCACTGACTTGTGGGCTTTGAA
65387 GAGATGAACG
Statistics
Matches: 507, Mismatches: 72, Indels: 26
0.84 0.12 0.04
Matches are distributed among these distances:
26 9 0.02
27 33 0.07
28 370 0.73
29 26 0.05
30 30 0.06
31 5 0.01
32 34 0.07
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (28 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGG
Found at i:73384 original size:21 final size:21
Alignment explanation
Indices: 73343--73386 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
73333 CTCTCCTTTA
* *
73343 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
73364 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
73385 TC
1 TC
73387 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:75215 original size:13 final size:13
Alignment explanation
Indices: 75197--75222 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
75187 ATAATCACCC
75197 TGTATCGATACAA
1 TGTATCGATACAA
75210 TGTATCGATACAA
1 TGTATCGATACAA
75223 AGAAAAATGT
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:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:77314 original size:15 final size:15
Alignment explanation
Indices: 77294--77324 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
77284 GTTTCGTTTG
*
77294 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
77309 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
77324 G
1 G
77325 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:79157 original size:21 final size:21
Alignment explanation
Indices: 79128--79172 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
79118 AAGTTTTCAT
*
79128 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
79148 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
79170 TTT
1 TTT
79173 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:84574 original size:33 final size:32
Alignment explanation
Indices: 84530--84594 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
84520 CACACCCAGA
* * *
84530 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCAATACATG-TGCATTGTATCAATACAT
*
84563 TGTATCAATACATGTTCATTGTATCAATACAT
1 TGTATCAATACATGTGCATTGTATCAATACAT
84595 GGACAAATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (32 bp):
TGTATCAATACATGTGCATTGTATCAATACAT
Found at i:89998 original size:17 final size:17
Alignment explanation
Indices: 89978--90036 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 17
89968 CATCCTTCTT
89978 AAAAAAAACAAAAAACA
1 AAAAAAAACAAAAAACA
89995 AAAAAAAACAAAAAAACA
1 AAAAAAAAC-AAAAAACA
90013 AAAAACAAA-AGAAAACACA
1 AAAAA-AAACA-AAAA-ACA
90032 AAAAA
1 AAAAA
90037 TGAGGGGCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.26
18 17 0.45
19 11 0.29
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (17 bp):
AAAAAAAACAAAAAACA
Found at i:90007 original size:25 final size:25
Alignment explanation
Indices: 89979--90036 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
89969 ATCCTTCTTA
89979 AAAAAAACAAAAAACAAAAAAAAAC
1 AAAAAAACAAAAAACAAAAAAAAAC
*
90004 AAAAAAACAAAAAACAAAAGAAAAC
1 AAAAAAACAAAAAACAAAAAAAAAC
90029 ACAAAAAA
1 A-AAAAAA
90037 TGAGGGGCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 25 0.81
26 6 0.19
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (25 bp):
AAAAAAACAAAAAACAAAAAAAAAC
Found at i:90034 original size:7 final size:7
Alignment explanation
Indices: 89980--90022 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
89970 TCCTTCTTAA
89980 AAAAAAC
1 AAAAAAC
89987 AAAAAAC
1 AAAAAAC
89994 -AAAAA-
1 AAAAAAC
*
89999 AAAACA-
1 AAAAAAC
90005 AAAAAAC
1 AAAAAAC
90012 AAAAAAC
1 AAAAAAC
90019 AAAA
1 AAAA
90023 GAAAACACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 14 0.44
7 18 0.56
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:91278 original size:25 final size:27
Alignment explanation
Indices: 91223--91285 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 27
91213 TAATTTGCCA
*
91223 TTTGTCAAGAATTTATCATCAAGAACT
1 TTTGTCAAGAATGTATCATCAAGAACT
*
91250 TTTGTCAAGAATGT-TCAT-TAGAAAC-
1 TTTGTCAAGAATGTATCATCAAG-AACT
91275 TTTGTCAAGAA
1 TTTGTCAAGAA
91286 ATTTTTGCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 13 0.39
26 7 0.21
27 13 0.39
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (27 bp):
TTTGTCAAGAATGTATCATCAAGAACT
Found at i:91326 original size:29 final size:29
Alignment explanation
Indices: 91293--91850 Score: 574
Period size: 29 Copynumber: 19.6 Consensus size: 29
91283 GAAATTTTTG
*
91293 CCTTTTTAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
91322 CCTTTTAAAAGCCCACAAGTCCA-TGGCAT
1 CCTTTTAAAAGCCCACAAGT-CAGTGGCAT
*
91351 CC-TTTCAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* *
91379 CCTTTCAAAAGCCCACAAGTCAATGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
*
91408 CCTTTCAAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* *
91437 CCTTTTAAAAGCTCACAAGTCAATGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
*
91466 CCTTTCAAAAGCCCACAAGTCCA-TGGCAT
1 CCTTTTAAAAGCCCACAAGT-CAGTGGCAT
* *
91495 TC-TTTCAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
*
91523 CC-TTTCAAAGCCCACAAGTCTA-TGGCAT
1 CCTTTTAAAAGCCCACAAGTC-AGTGGCAT
* * * ** *
91551 CC-TTTCAAAGCCCATAAATGGGTGGCGT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* * *
91579 CCTTTCAAAAGCCCATAAGTCAATGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* * *
91608 CCTTTCAAAAGCCCATAAGTCAATGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* * *
91637 CC-TTCAAAAGCCTACAAGTTAGTGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
*
91665 CCTTTT-AAAGCCCATAAGTCAGTGGCA-
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* *
91692 CC-TTTCAAAGCCCACAAGTTAGTGGCA-
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
*
91719 -CTTTTCAAAAGCCAACAAGTCAGTGGCA-
1 CCTTTT-AAAAGCCCACAAGTCAGTGGCAT
* * *
91747 CCTTTTAAAAGCCAACAAGTCAATCGCA-
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* *
91775 CATTTTCAAAAG-CCACCAAGTCAATGGCA-
1 CCTTTT-AAAAGCCCA-CAAGTCAGTGGCAT
* * * *
91804 CCTTTTCAAAGCCTACAAGTCAGTGACAAC
1 CCTTTTAAAAGCCCACAAGTCAGTGGC-AT
*
91834 CCTTTTCAAAGCCCACA
1 CCTTTTAAAAGCCCACA
91851 CAAGTTGGTG
Statistics
Matches: 460, Mismatches: 51, Indels: 35
0.84 0.09 0.06
Matches are distributed among these distances:
26 4 0.01
27 28 0.06
28 196 0.43
29 212 0.46
30 20 0.04
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (29 bp):
CCTTTTAAAAGCCCACAAGTCAGTGGCAT
Found at i:91389 original size:57 final size:57
Alignment explanation
Indices: 91300--91850 Score: 615
Period size: 57 Copynumber: 9.7 Consensus size: 57
91290 TTGCCTTTTT
* *
91300 AAAGCCCACAAGTCAGTGGCATCCTTTTAAAAGCCCACAAGTCCATGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAATGGCATCCTTTC
91357 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAATGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAATGGCATCCTTTC
* *
91414 AAAAGCCCACAAGTCAGTGGCATCCTTTTAAAAGCTCACAAGTCAATGGCATCCTTTC
1 -AAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAATGGCATCCTTTC
* *
91472 AAAAGCCCACAAGTCCA-TGGCATTCTTTC-AAAGCCCACAAGTCAGTGGCATCCTTTC
1 -AAAGCCCACAAGT-CAGTGGCATCCTTTCAAAAGCCCACAAGTCAATGGCATCCTTTC
* * *** *
91529 AAAGCCCACAAGTCTA-TGGCATCCTTTC-AAAGCCCATAAATGGGTGGCGTCCTTTC
1 AAAGCCCACAAGTC-AGTGGCATCCTTTCAAAAGCCCACAAGTCAATGGCATCCTTTC
* * *
91585 AAAAGCCCATAAGTCAATGGCATCCTTTCAAAAGCCCATAAGTCAATGGCATCC-TTC
1 -AAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAATGGCATCCTTTC
* * * * *
91642 AAAAGCCTACAAGTTAGTGGCATCCTTT-TAAAGCCCATAAGTCAGTGGCA-CCTTTC
1 -AAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAATGGCATCCTTTC
* * * * *
91698 AAAGCCCACAAGTTAGTGGCA-CTTTTCAAAAGCCAACAAGTCAGTGGCA-CCTTTTA
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAATGGCATCC-TTTC
* * * *
91754 AAAGCCAACAAGTCAATCGCA-CATTTTCAAAAG-CCACCAAGTCAATGGCA-CCTTTTC
1 AAAGCCCACAAGTCAGTGGCATC-CTTTCAAAAGCCCA-CAAGTCAATGGCATCC-TTTC
* * *
91811 AAAGCCTACAAGTCAGTGACAACCCTTTTC-AAAGCCCACA
1 AAAGCCCACAAGTCAGTGGC-ATCC-TTTCAAAAGCCCACA
91851 CAAGTTGGTG
Statistics
Matches: 435, Mismatches: 44, Indels: 29
0.86 0.09 0.06
Matches are distributed among these distances:
54 4 0.01
55 44 0.10
56 95 0.22
57 177 0.41
58 105 0.24
59 10 0.02
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAATGGCATCCTTTC
Found at i:93339 original size:11 final size:11
Alignment explanation
Indices: 93323--93367 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
93313 AGGTTCAACT
93323 AAAAAAAAGA-
1 AAAAAAAAGAG
93333 AAAAAAAGAGAG
1 AAAAAAA-AGAG
*
93345 AAAAAAAGGAG
1 AAAAAAAAGAG
*
93356 AAAGAAAAGAG
1 AAAAAAAAGAG
93367 A
1 A
93368 GAAGAAATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
10 7 0.23
11 16 0.53
12 7 0.23
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:93346 original size:13 final size:13
Alignment explanation
Indices: 93330--93370 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 13
93320 ACTAAAAAAA
93330 AGAAAAAAAAGAG
1 AGAAAAAAAAGAG
93343 AG-AAAAAAAG-G
1 AGAAAAAAAAGAG
*
93354 AGAAAGAAAAGAG
1 AGAAAAAAAAGAG
93367 AGAA
1 AGAA
93371 GAAATAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 3 0.12
12 15 0.60
13 7 0.28
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAGAG
Found at i:93357 original size:24 final size:22
Alignment explanation
Indices: 93323--93397 Score: 73
Period size: 24 Copynumber: 3.4 Consensus size: 22
93313 AGGTTCAACT
93323 AAAAAAAAGAAAAAAAAGAGAG
1 AAAAAAAAGAAAAAAAAGAGAG
*
93345 AAAAAAAGGAGAAAGAAAAGAGAG
1 AAAAAAA--AGAAAAAAAAGAGAG
* * *
93369 AAGAAATAG-AAACAAAGAG-G
1 AAAAAAAAGAAAAAAAAGAGAG
93389 TAAAAAAAA
1 -AAAAAAAA
93398 TAAGGTTAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
20 1 0.02
21 14 0.33
22 9 0.21
24 19 0.44
ACGTcount: A:0.75, C:0.01, G:0.21, T:0.03
Consensus pattern (22 bp):
AAAAAAAAGAAAAAAAAGAGAG
Found at i:93372 original size:12 final size:12
Alignment explanation
Indices: 93336--93374 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
93326 AAAAAGAAAA
*
93336 AAAAGAGAGAAA
1 AAAAGAGAGAAG
93348 AAAAG-GAGAAAG
1 AAAAGAGAG-AAG
93360 AAAAGAGAGAAG
1 AAAAGAGAGAAG
93372 AAA
1 AAA
93375 TAGAAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 3 0.12
12 18 0.75
13 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
AAAAGAGAGAAG
Found at i:95949 original size:13 final size:12
Alignment explanation
Indices: 95922--95973 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
95912 TTTGTTTCTA
*
95922 TTTTCTTCT-TC
1 TTTTTTTCTCTC
95933 TTTTCTTTCTC-C
1 TTTT-TTTCTCTC
95945 TTTTTTTCTCTC
1 TTTTTTTCTCTC
95957 TTTTTTT-TCT-
1 TTTTTTTCTCTC
95967 TTTTTTT
1 TTTTTTT
95974 TAGTTGAACC
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
10 7 0.19
11 13 0.35
12 17 0.46
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTTCTCTC
Found at i:95958 original size:24 final size:22
Alignment explanation
Indices: 95916--95974 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
95906 TACCTCTTTG
* *
95916 TTTCTATTTTCTTCTTCTTTTC
1 TTTCTCTTTTTTTCTTCTTTTC
*
95938 TTTCTCCTTTTTTTCTCTCTTTTT
1 TTTCT-CTTTTTTTCT-TCTTTTC
*
95962 TTTCTTTTTTTTT
1 TTTCTCTTTTTTT
95975 AGTTGAACCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 5 0.16
23 15 0.48
24 11 0.35
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTCTCTTTTTTTCTTCTTTTC
Found at i:95973 original size:22 final size:22
Alignment explanation
Indices: 95899--95973 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
95889 ACTAACCTTA
*
95899 TTTTTTTTAC-CTC-TTTGTTTC
1 TTTTTTTT-CTCTCTTTTTTTTC
*
95920 TATTTTCTTCT-TCTTTTCTTTCTC
1 T-TTTTTTTCTCTCTTTT-TTT-TC
*
95944 CTTTTTTTCTCTCTTTTTTTTC
1 TTTTTTTTCTCTCTTTTTTTTC
95966 TTTTTTTT
1 TTTTTTTT
95974 TAGTTGAACC
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
21 4 0.09
22 18 0.42
23 13 0.30
24 8 0.19
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (22 bp):
TTTTTTTTCTCTCTTTTTTTTC
Found at i:97418 original size:32 final size:32
Alignment explanation
Indices: 97382--97459 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
97372 CGGACATAGG
**
97382 TGCCACTAACTTGTGTGGGCGTTGACTAGGGT
1 TGCCACTAACTTGTGTGGGCGTTGAAAAGGGT
* *
97414 TGCCACCAACTTGTGTGGGCTTTGAAAAGGGT
1 TGCCACTAACTTGTGTGGGCGTTGAAAAGGGT
* *
97446 TGTCACTGACTTGT
1 TGCCACTAACTTGT
97460 AGGCTTTGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (32 bp):
TGCCACTAACTTGTGTGGGCGTTGAAAAGGGT
Found at i:97539 original size:28 final size:29
Alignment explanation
Indices: 97427--97970 Score: 530
Period size: 28 Copynumber: 19.3 Consensus size: 29
97417 CACCAACTTG
* *
97427 TGTGGGC-TTTGAAAAGGGTTGTCACTGACT
1 TGTGGGCTTTTG-AAA-GGATGCCACTGACT
* * *
97457 TGTAGGC-TTTGAAAAG-TGCCATTGACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACT
* * *
97484 TG-GTGGCTTTTGAAAATG-TGCGATTGACT
1 TGTG-GGCTTTTG-AAAGGATGCCACTGACT
* *
97513 TGTTGGCTTTTAAAAGG-TGCCACTGACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACT
* * *
97541 TGTTGG--TTTGAAAAG-TGCCACTAACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACT
97567 TGTGGGGC-TTTGAAAGG-TGCCACTGACT
1 TGT-GGGCTTTTGAAAGGATGCCACTGACT
* * *
97595 TATGGGC-TTTAAAAGGATGCCACTAACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACT
* *
97623 TGTAGGCTTTTG-AAGGATGCCATTGACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACT
* *
97651 TATGGGCTTTTGAAAGGATGCCATTGACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACT
* * ** *
97680 TATGGGCTTTTTGAAAGGACGCCACCCATT
1 TGTGGGC-TTTTGAAAGGATGCCACTGACT
*
97710 TATGGGC-TTTGAAAGGATGCCA-TAGACT
1 TGTGGGCTTTTGAAAGGATGCCACT-GACT
97738 TGTGGGC-TTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACT
*
97766 TGTGGGC-TTTGAAAGAATGCCA-TGGACT
1 TGTGGGCTTTTGAAAGGATGCCACT-GACT
*
97794 TGTGGGCTTTTGAAAGGATGCCATTGACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACT
* *
97823 TGTGAGCTTTTAAAAGGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACT
*
97852 TGT-GGC-TTTGAAAGGATGCCATTGACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACT
97879 TGTGGGC-TTTGAAAGGATGCCACTGGACT
1 TGTGGGCTTTTGAAAGGATGCCACT-GACT
97908 TGTGGGC-TTTGAAAGG-TGCC-CTGGACT
1 TGTGGGCTTTTGAAAGGATGCCACT-GACT
97935 TGTGGGCTTTT-AAAGG-TGCCA-TGACT
1 TGTGGGCTTTTGAAAGGATGCCACTGACT
97961 TGTGGGCTTT
1 TGTGGGCTTT
97971 AAAAAGGCAA
Statistics
Matches: 448, Mismatches: 47, Indels: 42
0.83 0.09 0.08
Matches are distributed among these distances:
26 34 0.08
27 75 0.17
28 184 0.41
29 120 0.27
30 35 0.08
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.32
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAGGATGCCACTGACT
Done.