Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1793
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: 126524
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:10413 original size:27 final size:28
Alignment explanation
Indices: 10311--10413 Score: 129
Period size: 27 Copynumber: 3.8 Consensus size: 28
10301 GGAATAAAGC
*** *
10311 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
10339 CGGGGTTGGAGTAT-CCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* * *
10366 CGAGGTTGGAGTATCCTCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
10393 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
10414 TGTGAAGAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 45 0.69
28 20 0.31
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:10497 original size:51 final size:53
Alignment explanation
Indices: 10401--10519 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
10391 AACGGGGTTG
* * *
10401 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
10455 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
10506 GAATATCCCCGATT
1 GAGTATCCCCGATT
10520 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:12909 original size:13 final size:13
Alignment explanation
Indices: 12891--12916 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12881 ACAAAGATCC
12891 ATGTATCGATACA
1 ATGTATCGATACA
12904 ATGTATCGATACA
1 ATGTATCGATACA
12917 CAGAAAAATG
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:12912 original size:33 final size:33
Alignment explanation
Indices: 12870--12936 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12860 AAAATTTCCA
***
12870 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
12903 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
12936 A
1 A
12937 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:12980 original size:19 final size:18
Alignment explanation
Indices: 12956--13023 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
12946 CAATAGCTAA
12956 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
12975 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
12990 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
13007 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
13024 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:12996 original size:13 final size:13
Alignment explanation
Indices: 12978--13002 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12968 ACAATACTTA
12978 TGTATCGATACAT
1 TGTATCGATACAT
12991 TGTATCGATACA
1 TGTATCGATACA
13003 AAACTTATGT
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:13000 original size:32 final size:32
Alignment explanation
Indices: 12959--13021 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
12949 TAGCTAATTA
*
12959 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
12991 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
13022 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:18420 original size:20 final size:20
Alignment explanation
Indices: 18395--18446 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
18385 TACAAGCCAA
**
18395 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
18415 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
18434 TGTATCGATACAA
1 TGTATCGATACAA
18447 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:20551 original size:21 final size:20
Alignment explanation
Indices: 20522--20564 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
20512 GGCTAGTGTG
* *
20522 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
20543 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
20563 GG
1 GG
20565 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:23121 original size:15 final size:15
Alignment explanation
Indices: 23101--23141 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
23091 GTTCATCGAT
23101 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
23116 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
*
23131 CTCAATTTGGA
1 TTC-ATTTGGA
23142 CATTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:31570 original size:13 final size:13
Alignment explanation
Indices: 31552--31577 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31542 ACAATATTCT
31552 TTGTATCGATACA
1 TTGTATCGATACA
31565 TTGTATCGATACA
1 TTGTATCGATACA
31578 AAGGTTACTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:32172 original size:22 final size:20
Alignment explanation
Indices: 32144--32187 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
32134 TTTTTAACCG
*
32144 TTTATCAATGAGGAGAAATTTT
1 TTTATCAAAGA-GA-AAATTTT
32166 TTTATCAAAGAGAAAATTTT
1 TTTATCAAAGAGAAAATTTT
32186 TT
1 TT
32188 AACGAGAGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 2 0.10
22 10 0.48
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (20 bp):
TTTATCAAAGAGAAAATTTT
Found at i:32182 original size:50 final size:49
Alignment explanation
Indices: 32094--32190 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 49
32084 AAAATAAATT
* **
32094 TTTATCAATGGGGAGAAAATCTTTTTAATCGTAAAAAATCTTTTTAACCG
1 TTTATCAATGAGGAGAAAATCTTTTTAATCAAAAAAAAT-TTTTTAACCG
*
32144 TTTATCAATGAGGAG-AAAT-TTTTTTATCAAAGAGAAAATTTTTTAAC
1 TTTATCAATGAGGAGAAAATCTTTTTAATCAAA-A-AAAATTTTTTAAC
32191 GAGAGCCTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
48 9 0.22
49 13 0.32
50 19 0.46
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.39
Consensus pattern (49 bp):
TTTATCAATGAGGAGAAAATCTTTTTAATCAAAAAAAATTTTTTAACCG
Found at i:35126 original size:20 final size:19
Alignment explanation
Indices: 35086--35135 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
35076 CGATACTTTA
* *
35086 TATCGATACATATTCATTG
1 TATCGATACATAATAATTG
35105 TATCGATACATACATAATTG
1 TATCGATACATA-ATAATTG
35125 TATCGATACAT
1 TATCGATACAT
35136 GAAACTGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
TATCGATACATAATAATTG
Found at i:37684 original size:2 final size:2
Alignment explanation
Indices: 37677--37705 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
37667 TTGTTTTGGC
37677 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
37706 GAGTATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38061 original size:1 final size:1
Alignment explanation
Indices: 38055--38079 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
38045 GGAAATTGTT
38055 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
38080 GAATCTCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:44973 original size:2 final size:2
Alignment explanation
Indices: 44968--44995 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44958 TATATATATA
44968 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
44996 CAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:50702 original size:30 final size:30
Alignment explanation
Indices: 50668--50730 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
50658 GGTTTGGTTA
*
50668 CAGGTGTAGAAACGGGTTTAGACACAAGTT
1 CAGGTGTAGAAACGGGTTCAGACACAAGTT
*
50698 CAGGTGTAGAAACGGGTTCATACACAAGTT
1 CAGGTGTAGAAACGGGTTCAGACACAAGTT
50728 CAG
1 CAG
50731 ACACGGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (30 bp):
CAGGTGTAGAAACGGGTTCAGACACAAGTT
Found at i:53776 original size:2 final size:2
Alignment explanation
Indices: 53769--53803 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53759 TGCTTGTACC
53769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53804 GTTAGGTCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60826 original size:12 final size:12
Alignment explanation
Indices: 60809--60835 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
60799 TTACAATTTG
60809 CAGCCAAGCTGA
1 CAGCCAAGCTGA
60821 CAGCCAAGCTGA
1 CAGCCAAGCTGA
60833 CAG
1 CAG
60836 GAACTCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.26, T:0.07
Consensus pattern (12 bp):
CAGCCAAGCTGA
Found at i:64696 original size:156 final size:155
Alignment explanation
Indices: 64496--64815 Score: 367
Period size: 156 Copynumber: 2.1 Consensus size: 155
64486 AGTATTTCAA
* * ** * * *
64496 TAACCCTAAAGGACATG-AAAGGATTATAAAAGGATGAACCTATCCTAAATATTTACCTTTGGCA
1 TAACCCTAAAGAACACGAAAAATATTATAAAAGAATGAACCTATCCTAAATATATACATTTGGCA
* ** * *
64560 TAAAAATGACATGGTGACAA-TCTAAGACTCGATTCTACAAAAAATTACCTAAATGCCTCTAAAG
66 TAAAAACGACATAATGACAACT-TAAGACTCGATTCTA-AAAAAATTACCAAAATACCTCTAAAG
*
64624 TATA-CATTCGACGTGAAAGTATCCTAG
129 TATACCA-TCGACATGAAAGTATCCTAG
* *
64651 TAATCCTAAAGAACACGAAAAATATTATAAAAGAATGAACCTATCCTAAATGTATACATTTGGCA
1 TAACCCTAAAGAACACGAAAAATATTATAAAAGAATGAACCTATCCTAAATATATACATTTGGCA
* * * * * * * **
64716 TGAAAGCGACTTAATGACTACTTAGGATTCGATTTTAAAAAAATTACCAAAATACCTCTGGAGTA
66 TAAAAACGACATAATGACAACTTAAGACTCGATTCTAAAAAAATTACCAAAATACCTCTAAAGTA
*
64781 TACCATCGACATTAAAGTATCCTAG
131 TACCATCGACATGAAAGTATCCTAG
64806 TAACCCTAAA
1 TAACCCTAAA
64816 AGATACAAAA
Statistics
Matches: 136, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
155 67 0.49
156 68 0.50
157 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (155 bp):
TAACCCTAAAGAACACGAAAAATATTATAAAAGAATGAACCTATCCTAAATATATACATTTGGCA
TAAAAACGACATAATGACAACTTAAGACTCGATTCTAAAAAAATTACCAAAATACCTCTAAAGTA
TACCATCGACATGAAAGTATCCTAG
Found at i:64818 original size:156 final size:156
Alignment explanation
Indices: 64496--64815 Score: 369
Period size: 155 Copynumber: 2.1 Consensus size: 156
64486 AGTATTTCAA
* * ** * * *
64496 TAACCCTAAAGGACATG-AAAGGATTATAAAAGGATGAACCTATCCTAAATATTTACCTTTGGCA
1 TAACCCTAAAGAACACGAAAAATATTATAAAAGAATGAACCTATCCTAAATATATACATTTGGCA
* ** * *
64560 TAAAAATGACATGGTGACAATCTAAGACTCGATTCTACAAAAAATTACCTAAATGCCTCTAAAGT
66 TAAAAACGACATAATGACAATCTAAGACTCGATTCTACAAAAAATTACCAAAATACCTCTAAAGT
*
64625 ATACATTCGACGTGAAAGTATCCTAG
131 ATACATTCGACATGAAAGTATCCTAG
* *
64651 TAATCCTAAAGAACACGAAAAATATTATAAAAGAATGAACCTATCCTAAATGTATACATTTGGCA
1 TAACCCTAAAGAACACGAAAAATATTATAAAAGAATGAACCTATCCTAAATATATACATTTGGCA
* * * * * * * **
64716 TGAAAGCGACTTAATGACTA-CTTAGGATTCGATTTTA-AAAAAATTACCAAAATACCTCTGGAG
66 TAAAAACGACATAATGACAATC-TAAGACTCGATTCTACAAAAAATTACCAAAATACCTCTAAAG
*
64779 TATACCA-TCGACATTAAAGTATCCTAG
130 TATA-CATTCGACATGAAAGTATCCTAG
64806 TAACCCTAAA
1 TAACCCTAAA
64816 AGATACAAAA
Statistics
Matches: 136, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
155 68 0.50
156 68 0.50
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (156 bp):
TAACCCTAAAGAACACGAAAAATATTATAAAAGAATGAACCTATCCTAAATATATACATTTGGCA
TAAAAACGACATAATGACAATCTAAGACTCGATTCTACAAAAAATTACCAAAATACCTCTAAAGT
ATACATTCGACATGAAAGTATCCTAG
Found at i:65820 original size:2 final size:2
Alignment explanation
Indices: 65813--65846 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
65803 GAACATGGAC
65813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65847 GAAAAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66496 original size:5 final size:6
Alignment explanation
Indices: 66437--66495 Score: 66
Period size: 6 Copynumber: 9.8 Consensus size: 6
66427 TGAAACTAGT
* * **
66437 TAAAAA T-AAAA TAAAAT TAAAATT TCCAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAA-A TAAAAA TAAAAA TAAAAA TAAAAA
66485 TAAAAA TAAAA
1 TAAAAA TAAAA
66496 TTATTAATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
5 5 0.11
6 36 0.80
7 4 0.09
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (6 bp):
TAAAAA
Found at i:67875 original size:41 final size:40
Alignment explanation
Indices: 67802--67907 Score: 124
Period size: 41 Copynumber: 2.6 Consensus size: 40
67792 CGAAATTGAC
** * *
67802 AAGTCAACAATTAAAAAATGTTGACCGAGACAAAACCTAT
1 AAGTCAACAAAGAAAAAAGGTTGACCGAGACAAAACCAAT
67842 AAGTCAACAAAGAATAAAAGGTTGACC-AGGACAAAACCAAT
1 AAGTCAACAAAGAA-AAAAGGTTGACCGA-GACAAAACCAAT
* *
67883 AAGTCAATAAATGAAAAAGGGTTGA
1 AAGTCAACAAA-GAAAAAAGGTTGA
67908 GTAACATTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
40 13 0.23
41 41 0.72
42 3 0.05
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (40 bp):
AAGTCAACAAAGAAAAAAGGTTGACCGAGACAAAACCAAT
Found at i:68473 original size:75 final size:76
Alignment explanation
Indices: 68367--68589 Score: 229
Period size: 76 Copynumber: 2.9 Consensus size: 76
68357 ATCAATGGCT
** *
68367 AAAACAAACTGCTAACAAGCT-AAAGTGAAAGATCATGATAAGGAATATGT-TTTCTGCAATTTC
1 AAAACAAACTAATAACAAGCTGAAA-TAAAAGATCATGATAAGGAATATGTGTTTCTGCAATTTC
68430 CCATTAATAGCC
65 CCATTAATAGCC
* * * *
68442 AAAATAAACT-ATCAACAAGCTGAAATAAAAGATCATGATGAGGAATATATGATTCTGCAATTTC
1 AAAACAAACTAAT-AACAAGCTGAAATAAAAGATCATGATAAGGAATATGTGTTTCTGCAATTTC
* *
68506 CCATCAATAGCT
65 CCATTAATAGCC
* * * * * * **
68518 GAAACAAACTAATAATAAGTTGAAATAGAAGAACATGACATA-GAATATGTGTTTGCTAAAATTT
1 AAAACAAACTAATAACAAGCTGAAATAAAAGATCATGATA-AGGAATATGTGTTT-CTGCAATTT
68582 CCCATTAA
64 CCCATTAA
68590 CATAAATAAA
Statistics
Matches: 121, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
74 1 0.01
75 39 0.32
76 64 0.53
77 17 0.14
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (76 bp):
AAAACAAACTAATAACAAGCTGAAATAAAAGATCATGATAAGGAATATGTGTTTCTGCAATTTCC
CATTAATAGCC
Found at i:77614 original size:110 final size:108
Alignment explanation
Indices: 77489--77838 Score: 355
Period size: 110 Copynumber: 3.2 Consensus size: 108
77479 ACTTTATGTG
* * *
77489 AAAAATGAATTATCCTATGTAAAGGGCGTTCGTACGTCACTTTATGACTTTGGACAATGACCTAT
1 AAAAATGAATTATCCTATATAAAGAGCGTTCGTACGTCACTTTATGACTTTAGACAATGACCTAT
* * **
77554 TTCAAGACCAATCCTTTGGTACCCGAATCTATGTAATTAATGC
66 TTCAAGACCAATCCCTTAGTACCCGAATCTACATAATTAATGC
* * * * * *
77597 AATTAATTGAATTATCCTACATAAAGTGCGTTCATACGCCATTTTAT-AGCTTTAGACAATGACC
1 AA--AAATGAATTATCCTATATAAAGAGCGTTCGTACGTCACTTTATGA-CTTTAGACAATGACC
* * **
77661 TATTTCAAGGCCAATCCCTTAGTGCCTTAATCTACATAATTAATGC
63 TATTTCAAGACCAATCCCTTAGTACCCGAATCTACATAATTAATGC
* * * *
77707 AAAAAT-AAGTTATCCTATATAAAAAACATTCGTACGTCACTTTATGACTCTAGACAATGA-CTA
1 AAAAATGAA-TTATCCTATATAAAGAGCGTTCGTACGTCACTTTATGACTTTAGACAATGACCTA
** * * * * *
77770 TTTCAAGGTCAATCTCTTAGTGCTCGAATCTACCTAATTTATGC
65 TTTCAAGACCAATCCCTTAGTACCCGAATCTACATAATTAATGC
* *
77814 AAAAAAATGAGTTATCTTATATAAA
1 --AAAAATGAATTATCCTATATAAA
77839 AGGCATTCAT
Statistics
Matches: 199, Mismatches: 35, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
107 42 0.21
108 45 0.23
109 21 0.11
110 91 0.46
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (108 bp):
AAAAATGAATTATCCTATATAAAGAGCGTTCGTACGTCACTTTATGACTTTAGACAATGACCTAT
TTCAAGACCAATCCCTTAGTACCCGAATCTACATAATTAATGC
Found at i:77874 original size:109 final size:108
Alignment explanation
Indices: 77526--77903 Score: 305
Period size: 110 Copynumber: 3.5 Consensus size: 108
77516 GTTCGTACGT
** * * * * * * **
77526 CACTTTATGACTTTGGACAATGACCTATTTCAAGACCAATCCTTTGGTACCCGAATCTATGTAAT
1 CACTTTATGACCCTAGACAATGACCTATTTCAAGGCCAATCCCTTAGTGCCTGAATCTACATAAT
* * *** * *
77591 TAATGCAATTAATTGAA-TTATCCTACATAAAGTGCGTTCATACGC
66 TAATGCAA--AAAT-AAGTTATCCTATATAAAAAACATTCATACAC
* ** *
77636 CATTTTAT-AGCTTTAGACAATGACCTATTTCAAGGCCAATCCCTTAGTGCCTTAATCTACATAA
1 CACTTTATGA-CCCTAGACAATGACCTATTTCAAGGCCAATCCCTTAGTGCCTGAATCTACATAA
* **
77700 TTAATGCAAAAATAAGTTATCCTATATAAAAAACATTCGTACGT
65 TTAATGCAAAAATAAGTTATCCTATATAAAAAACATTCATACAC
* * * *
77744 CACTTTATGACTCTAGACAATGA-CTATTTCAAGGTCAATCTCTTAGTG-CTCGAATCTACCTAA
1 CACTTTATGACCCTAGACAATGACCTATTTCAAGGCCAATCCCTTAGTGCCT-GAATCTACATAA
* * * **
77807 TTTATGCAAAAAAATGAGTTATCTTATATAAAAGGCATTCATACAC
65 TTAATGC--AAAAATAAGTTATCCTATATAAAAAACATTCATACAC
* ** ** * *
77853 CACTTTATTACCCTAGACAATGATTTATTTTGAGGCCAATCCTTTGGTGCC
1 CACTTTATGACCCTAGACAATGACCTATTTCAAGGCCAATCCCTTAGTGCC
77904 CAAACGCTAC
Statistics
Matches: 219, Mismatches: 41, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
106 2 0.01
107 41 0.19
108 43 0.20
109 53 0.24
110 79 0.36
111 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.34
Consensus pattern (108 bp):
CACTTTATGACCCTAGACAATGACCTATTTCAAGGCCAATCCCTTAGTGCCTGAATCTACATAAT
TAATGCAAAAATAAGTTATCCTATATAAAAAACATTCATACAC
Found at i:78735 original size:12 final size:12
Alignment explanation
Indices: 78718--78809 Score: 60
Period size: 12 Copynumber: 7.2 Consensus size: 12
78708 ATCCACCCTA
78718 TTTTCTTTTTTT
1 TTTTCTTTTTTT
78730 TTTTCTTTTTCTT
1 TTTTCTTTTT-TT
*
78743 TTCTTATTCCTTCTTT
1 TT-TTCTT--TT-TTT
* *
78759 CTTTCTTTCTTT
1 TTTTCTTTTTTT
*
78771 CTTTCTTTCTTTT
1 TTTTCTTT-TTTT
**
78784 TTTTC-TTCCTT
1 TTTTCTTTTTTT
*
78795 TTTCCTTTTTTT
1 TTTTCTTTTTTT
78807 TTT
1 TTT
78810 CTCTCTTCCT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
11 6 0.10
12 30 0.48
13 12 0.19
14 4 0.06
15 4 0.06
16 5 0.08
17 1 0.02
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:78738 original size:8 final size:8
Alignment explanation
Indices: 78718--78806 Score: 56
Period size: 8 Copynumber: 10.5 Consensus size: 8
78708 ATCCACCCTA
78718 TTTTCTTT
1 TTTTCTTT
78726 TTTT-TTT
1 TTTTCTTT
*
78733 TCTTT-TTC
1 T-TTTCTTT
78741 TTTTCTTAT
1 TTTTCTT-T
*
78750 TCCTTCTTT
1 T-TTTCTTT
*
78759 CTTTCTTT
1 TTTTCTTT
*
78767 CTTTCTTT
1 TTTTCTTT
*
78775 CTTTCTTTT
1 TTTTC-TTT
78784 TTTTCTTCCT
1 TTTTCTT--T
78794 TTTTCCTTT
1 TTTT-CTTT
78803 TTTT
1 TTTT
78807 TTTCTCTCTT
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
7 7 0.10
8 33 0.49
9 14 0.21
10 10 0.15
11 3 0.04
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTCTTT
Found at i:78762 original size:4 final size:4
Alignment explanation
Indices: 78753--78782 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
78743 TTCTTATTCC
78753 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
78783 TTTTTCTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:78822 original size:22 final size:22
Alignment explanation
Indices: 78780--78823 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
78770 TCTTTCTTTC
**
78780 TTTTTTTTCTTCCTTTTTCCTT
1 TTTTTTTTCTTCCTTCCTCCTT
78802 TTTTTTTTC-TCTCTTCCTCCTT
1 TTTTTTTTCTTC-CTTCCTCCTT
78824 CCTTCTCCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTTTTTCTTCCTTCCTCCTT
Found at i:78825 original size:26 final size:24
Alignment explanation
Indices: 78775--78827 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
78765 TTCTTTCTTT
**
78775 CTTTCTTTTTTTTCTTCCTTTTTC
1 CTTTCTTTTTTTTCTTCCTCCTTC
*
78799 CTTTTTTTTTTCTCTCTTCCTCCTTC
1 CTTTCTTTTTT-T-TCTTCCTCCTTC
78825 CTT
1 CTT
78828 CTCCTCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 10 0.42
25 1 0.04
26 13 0.54
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (24 bp):
CTTTCTTTTTTTTCTTCCTCCTTC
Found at i:80635 original size:2 final size:2
Alignment explanation
Indices: 80628--80666 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
80618 ATAAGACTTG
80628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80667 TAAAAATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:84692 original size:2 final size:2
Alignment explanation
Indices: 84685--84741 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
84675 TGATTATTAG
*
84685 CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
84727 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
84742 ACCGAAATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:91891 original size:2 final size:2
Alignment explanation
Indices: 91879--91908 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
91869 CTAGTATTAG
*
91879 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
91909 CATAACACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:92901 original size:56 final size:56
Alignment explanation
Indices: 92793--92907 Score: 142
Period size: 56 Copynumber: 2.1 Consensus size: 56
92783 AAAGGCAATA
* * * *
92793 AAAAGTAAAAAGTTAATTTAAAAATCGAAGATGAAGTGTTTGCAATTAGAGGTTGT
1 AAAAGTAAAAAGTTAATTTAAAAATCAAAGATGAAGAGTTTGCAATGAGAGGTCGT
* * * *
92849 AAAAGTGAAAA-TTCAATTTAAAAGTCAAAGATTAAGAGTTTGCAATGGGAGGTCGT
1 AAAAGTAAAAAGTT-AATTTAAAAATCAAAGATGAAGAGTTTGCAATGAGAGGTCGT
92905 AAA
1 AAA
92908 GGATTCGAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
55 2 0.04
56 48 0.96
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.28
Consensus pattern (56 bp):
AAAAGTAAAAAGTTAATTTAAAAATCAAAGATGAAGAGTTTGCAATGAGAGGTCGT
Found at i:96109 original size:31 final size:32
Alignment explanation
Indices: 96074--96152 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 32
96064 TATTTTTCAT
96074 TATATCGATACATTCTGAG-TTTTGACCCAAA
1 TATATCGATACATTCTGAGTTTTTGACCCAAA
* *
96105 TATATTGATACATTCTGGGTTTTTGACCCAAA
1 TATATCGATACATTCTGAGTTTTTGACCCAAA
**
96137 TGCATCGATACATTCT
1 TATATCGATACATTCT
96153 TCAATGTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 17 0.40
32 25 0.60
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (32 bp):
TATATCGATACATTCTGAGTTTTTGACCCAAA
Found at i:98721 original size:81 final size:79
Alignment explanation
Indices: 98496--98855 Score: 365
Period size: 81 Copynumber: 4.5 Consensus size: 79
98486 AAATTTTTCC
* * * *
98496 TTCACAAATATCGA-TTTTCATC-TCGGAGATACTCCAATCCCATCATTTTCGAG-GGAATACTC
1 TTCA-AAATATCAATTTTTCACCATCGGGGATACTCCAACCCCATCATTTTCGAGAGG-ATACTC
**
98558 CAACCTTGTTTTTACT
64 CAACCCCGTTTTTACT
* * * * *
98574 TTCAAAATATCGAATTTTTAACCATCGAGAATACTCCAACCTCATCATTTTCGAGAGGATATTCC
1 TTCAAAATATC-AATTTTTCACCATCGGGGATACTCCAACCCCATCATTTTCGAGAGGATACTCC
98639 AACCCCGTTTTTACT
65 AACCCCGTTTTTACT
* * * * * * *
98654 TTTAAAAGCATCAAAATGTTCACCATCGGGGATACTTCAACCCCATTATTTTCAAG-GAGATACT
1 TTCAAAA-TATC-AATTTTTCACCATCGGGGATACTCCAACCCCATCATTTTCGAGAG-GATACT
98718 CCAACCCCGTTTTT--T
63 CCAACCCCGTTTTTACT
*
98733 TTCAAAATATCAATTTTTCACCATTGGGGATACTCCAACCCCATCATTTTCGAGAGGATACTCCA
1 TTCAAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCATCATTTTCGAGAGGATACTCCA
* *
98798 ACCCCCTTCTTACT
66 ACCCCGTTTTTACT
* * * *
98812 TTGAAAATATTAAATTTTTTTCATC-TCGGGGATATTCCAACCCC
1 TTCAAAATA-TCAA--TTTTTCACCATCGGGGATACTCCAACCCC
98856 GATTTTCACC
Statistics
Matches: 231, Mismatches: 39, Indels: 21
0.79 0.13 0.07
Matches are distributed among these distances:
77 62 0.27
78 9 0.04
79 22 0.10
80 55 0.24
81 75 0.32
82 8 0.03
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (79 bp):
TTCAAAATATCAATTTTTCACCATCGGGGATACTCCAACCCCATCATTTTCGAGAGGATACTCCA
ACCCCGTTTTTACT
Found at i:101418 original size:24 final size:24
Alignment explanation
Indices: 101386--101433 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
101376 CCCATTTACA
101386 TCATCCGACCTCTTAGTCAAGAAG
1 TCATCCGACCTCTTAGTCAAGAAG
101410 TCATCCGACCTCTTAGTCAAGAAG
1 TCATCCGACCTCTTAGTCAAGAAG
101434 AAAGATAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (24 bp):
TCATCCGACCTCTTAGTCAAGAAG
Found at i:103937 original size:34 final size:34
Alignment explanation
Indices: 103894--103961 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
103884 ATGTAAAAAA
103894 GCATTCTTGATGTCTAGCTCATGCAAGGGCCAAT
1 GCATTCTTGATGTCTAGCTCATGCAAGGGCCAAT
103928 GCATTCTTGATGTCTAGCTCATGCAAGGGCCAAT
1 GCATTCTTGATGTCTAGCTCATGCAAGGGCCAAT
103962 TAGGAATGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (34 bp):
GCATTCTTGATGTCTAGCTCATGCAAGGGCCAAT
Found at i:106522 original size:28 final size:28
Alignment explanation
Indices: 106441--106522 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
106431 TTTTGGAGAT
*
106441 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
106469 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
106497 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
106523 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:106661 original size:51 final size:51
Alignment explanation
Indices: 106505--106675 Score: 216
Period size: 51 Copynumber: 3.3 Consensus size: 51
106495 GAAATAACGA
* * *
106505 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * *
106557 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* *
106610 GGTTGGAGTATCCCCGATTATGAAAAATTGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
106661 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
106676 TCAGAAATAA
Statistics
Matches: 100, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
51 41 0.41
52 16 0.16
53 33 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:106721 original size:27 final size:28
Alignment explanation
Indices: 106658--106733 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
106648 AAAATAAAGT
*
106658 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
106686 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
106713 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
106734 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:106819 original size:212 final size:212
Alignment explanation
Indices: 106449--106840 Score: 556
Period size: 212 Copynumber: 1.8 Consensus size: 212
106439 ATAATAACGA
* * * *
106449 GGTTGGAGTGTTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
* *
106514 ATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTAAA
66 ATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCAATTAAA
** * *
106579 GGAGAAATTGGTGTTGTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTATGAAAAATTGATAT
131 GGAGAAATTAATGTTGTGAAAATAAAATCGGAGTTGGAATATCCCCGATTATGAAAAATTGATAT
106644 TTTGAAAATAAAGTCGG
196 TTTGAAAATAAAGTCGG
* *
106661 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
* * *
106725 GTCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCAATT
66 ATCCCCGATTGTGAA-AAATT-G-GTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCAATT
* * * * *
106790 ATA-TA-AAATTAATGTTTTGAAAGTAAAATCGGAGTTGGAATATCCTCGATT
128 AAAGGAGAAATTAATGTTGTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
106841 GTGGAGAATT
Statistics
Matches: 157, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
211 28 0.18
212 87 0.55
213 2 0.01
214 40 0.25
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (212 bp):
GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
ATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCAATTAAA
GGAGAAATTAATGTTGTGAAAATAAAATCGGAGTTGGAATATCCCCGATTATGAAAAATTGATAT
TTTGAAAATAAAGTCGG
Found at i:108935 original size:13 final size:13
Alignment explanation
Indices: 108917--108942 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
108907 ACAAAGATCC
108917 ATGTATCGATACA
1 ATGTATCGATACA
108930 ATGTATCGATACA
1 ATGTATCGATACA
108943 CAGAAAAATG
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:108938 original size:33 final size:33
Alignment explanation
Indices: 108896--108962 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
108886 AAAATTTCCA
***
108896 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
108929 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
108962 A
1 A
108963 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:109006 original size:19 final size:18
Alignment explanation
Indices: 108982--109049 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
108972 CAGTAGCTAA
108982 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
109001 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
109016 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
109033 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
109050 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:109022 original size:13 final size:13
Alignment explanation
Indices: 109004--109028 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
108994 ACAATACTTA
109004 TGTATCGATACAT
1 TGTATCGATACAT
109017 TGTATCGATACA
1 TGTATCGATACA
109029 AAACTTATGT
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:109026 original size:32 final size:32
Alignment explanation
Indices: 108985--109047 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
108975 TAGCTAATTA
*
108985 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
109017 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
109048 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:109111 original size:21 final size:21
Alignment explanation
Indices: 109085--109158 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
109075 GTTGGGACCC
109085 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
109106 TGTATCGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
109126 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
109147 TGTATCGATACA
1 TGTATCGATACA
109159 AAATTTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 3 0.06
20 15 0.31
21 31 0.63
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:109958 original size:55 final size:54
Alignment explanation
Indices: 109883--111487 Score: 2185
Period size: 55 Copynumber: 29.0 Consensus size: 54
109873 TGAGGAGTAA
* *
109883 AAAG-TGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACTG
* *
109937 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACTG
* * *
109992 AAAGGTGCCACCAACTTGTGTAGGCTTTGAAA-ATAAAAAGCATCCTGCTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGT-----G--TCCTGCTCTTTGAGGACTG
* *
110053 AAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACT-G
* *
110109 AAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTCGGGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACTG
* *
110163 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAA-ATAAAAAGCATCCTGCTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGT-----G--TCCTGCTCTTTGAGGACTG
* *
110224 AAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACT-G
* *
110280 AAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTCGGGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACTG
* *
110334 AAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACTG
* **
110389 GAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACT-G
* *
110445 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACTG
*
110500 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACT-G
*
110556 AAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGTTCTTTGAGGACTAG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACT-G
* *
110611 AAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGATTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACTG
*
110665 AAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACT-G
*
110721 AAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACTG
*
110775 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTAG
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACT-G
* *
110831 AAA-ATGCCACCAACTTGGGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACTG
*
110885 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACT-G
*
110941 AAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGTTCTTTGAGGACTAG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACT-G
*
110996 AAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACTG
*
111050 AAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACTG
* * *
111105 AAAAATGCCACCAACTTGTATGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACTG
*
111160 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTAG
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACT-G
* *
111216 AAA-ATGCCACCAACTTGGGTGGGCTTTGAAAGGTGT-CTGCTCTTTGGGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACTG
*
111269 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACT-G
*
111325 AAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTACTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACTG
* *
111379 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCTTGCTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACTG
* *
111434 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGACGTGTCCTGCTCTTTGAGGACT
1 AAAGATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACT
111488 AAAAAGCGGA
Statistics
Matches: 1417, Mismatches: 82, Indels: 103
0.88 0.05 0.06
Matches are distributed among these distances:
53 6 0.00
54 92 0.06
55 1123 0.79
56 100 0.07
57 2 0.00
59 2 0.00
61 90 0.06
62 2 0.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (54 bp):
AAAGATGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:109997 original size:26 final size:26
Alignment explanation
Indices: 109909--109998 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
109899 GTGTGGGCTT
* *
109909 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
109935 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
109962 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
109990 TGAAAGGTG
1 TGAAAGGTG
109999 CCACCAACTT
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.34
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:110810 original size:29 final size:29
Alignment explanation
Indices: 110725--110810 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
110715 GACTGGAAAA
110725 TGCCACCAACTTGTGTGGGCTTTAAGAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGG
** * *
110754 TGTCCTGC-TCTT-TG-GGGAC-TGAA-AGG
1 TG-CCACCAACTTGTGTGGG-CTTTAAGAGG
110780 TGCCACCAACTTGTGTGGGCTTTAAGAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGG
110809 TG
1 TG
110811 TCCTGCTCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
25 3 0.07
26 8 0.19
27 9 0.21
28 9 0.21
29 10 0.24
30 3 0.07
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.29
Consensus pattern (29 bp):
TGCCACCAACTTGTGTGGGCTTTAAGAGG
Found at i:112474 original size:1 final size:1
Alignment explanation
Indices: 112470--112522 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
112460 CTTTTCTCTC
* * * * **
112470 TTTTTCTTTGTTTTGTTTTTTTGTTTTTTTTTTTTTTTGCTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
112523 GAAGAGAAGG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.89
Consensus pattern (1 bp):
T
Found at i:112489 original size:16 final size:14
Alignment explanation
Indices: 112470--112523 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 14
112460 CTTTTCTCTC
*
112470 TTTTTCTTTGTTTT
1 TTTTTTTTTGTTTT
112484 GTTTTTTTGTT-TTTT
1 -TTTTTTT-TTGTTTT
112499 TTTTTTTTTGCTTTT
1 TTTTTTTTTG-TTTT
112514 TTTTTTTTTG
1 TTTTTTTTTG
112524 AAGAGAAGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
13 2 0.06
14 7 0.20
15 24 0.69
16 2 0.06
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (14 bp):
TTTTTTTTTGTTTT
Found at i:112500 original size:17 final size:16
Alignment explanation
Indices: 112470--112522 Score: 70
Period size: 17 Copynumber: 3.2 Consensus size: 16
112460 CTTTTCTCTC
* *
112470 TTTTTCTTTGTTTTGTT
1 TTTTTGTTT-TTTTTTT
112487 TTTTTGTTTTTTTTTT
1 TTTTTGTTTTTTTTTT
112503 TTTTTGCTTTTTTTTTT
1 TTTTTG-TTTTTTTTTT
112520 TTT
1 TTT
112523 GAAGAGAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.36
17 21 0.64
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.89
Consensus pattern (16 bp):
TTTTTGTTTTTTTTTT
Found at i:125523 original size:9 final size:9
Alignment explanation
Indices: 125504--125546 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
125494 ACAGGGGAAC
125504 AACATAAAAA
1 AACA-AAAAA
125514 AACAAAAAA
1 AACAAAAAA
125523 AACAACAAAA
1 AACAA-AAAA
*
125533 AA-AACAAA
1 AACAAAAAA
125541 AACAAA
1 AACAAA
125547 CCAAGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 5 0.17
9 14 0.48
10 10 0.34
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (9 bp):
AACAAAAAA
Found at i:125526 original size:22 final size:22
Alignment explanation
Indices: 125501--125559 Score: 84
Period size: 21 Copynumber: 2.6 Consensus size: 22
125491 AAAACAGGGG
125501 AACAACATAAAAAAACAAAAA-A
1 AACAACA-AAAAAAACAAAAACA
125523 AACAACAAAAAAAACAAAAACA
1 AACAACAAAAAAAACAAAAACA
*
125545 AACCAAGAAAAAAAA
1 AA-CAACAAAAAAAA
125560 AAGCATCGCG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 13 0.38
22 10 0.29
23 11 0.32
ACGTcount: A:0.81, C:0.15, G:0.02, T:0.02
Consensus pattern (22 bp):
AACAACAAAAAAAACAAAAACA
Found at i:125529 original size:12 final size:12
Alignment explanation
Indices: 125509--125559 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
125499 GGAACAACAT
125509 AAAAA-AACAAA
1 AAAAACAACAAA
125520 AAAAACAACAAA
1 AAAAACAACAAA
125532 AAAAACAA-AAA
1 AAAAACAACAAA
* * *
125543 CAAACCAAGAAA
1 AAAAACAACAAA
125555 AAAAA
1 AAAAA
125560 AAGCATCGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.41
12 20 0.59
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAACAACAAA
Found at i:125559 original size:18 final size:17
Alignment explanation
Indices: 125511--125561 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
125501 AACAACATAA
125511 AAAAACAAAAAAAACAAC
1 AAAAA-AAAAAAAACAAC
125529 AAAAAAAACAAAAACAAACC
1 AAAAAAAA-AAAAAC-AA-C
*
125549 AAGAAAAAAAAAA
1 AAAAAAAAAAAAA
125562 GCATCGCGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 3 0.10
18 11 0.38
19 7 0.24
20 8 0.28
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAACAAC
Done.