Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002404.1 Hibiscus syriacus cultivar Beakdansim tig00004919_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 175399
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1033 original size:13 final size:13
Alignment explanation
Indices: 1015--1046 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1005 CGACGGTCAA
1015 CGGGTCAACGGGT
1 CGGGTCAACGGGT
1028 CGGGTCAACGGGT
1 CGGGTCAACGGGT
1041 CGGGTC
1 CGGGTC
1047 GGGTCATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:6816 original size:17 final size:16
Alignment explanation
Indices: 6790--6830 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
6780 TTTTATTTAA
6790 AAAT-ATAATAATAAAT
1 AAATCATAATAA-AAAT
6806 AAATCATAATAAAAAT
1 AAATCATAATAAAAAT
6822 AATATCATA
1 AA-ATCATA
6831 GTGTCTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATCATAATAAAAAT
Found at i:27465 original size:53 final size:53
Alignment explanation
Indices: 27367--27519 Score: 193
Period size: 53 Copynumber: 2.9 Consensus size: 53
27357 CAAATGATGA
* *
27367 GTTCGCTCCCTCTTG-TTCATGGATTAAGGAACTCGAACAATCTTCT-AAAAGCGG
1 GTTCGCTCCCTCTTGCTTCAAGGAGT-A-GAACTCGAACAATCTTCTGAAAA-CGG
* * * ***
27421 GTTCGCTCCCTATTGCTTCAGGGAGTAGAACTTGAACAATCTTCTGCCTACGG
1 GTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGAAAACGG
27474 GTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTG
1 GTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTG
27520 GTGTGATTCT
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
53 63 0.72
54 16 0.18
55 8 0.09
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (53 bp):
GTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGAAAACGG
Found at i:36232 original size:45 final size:47
Alignment explanation
Indices: 36164--36274 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 47
36154 CCATGCTTTG
36164 TTATTCACAAAAAGAAATCCTAACCACATGATATCTAATTCGCATGC-
1 TTATTCA-AAAAAGAAATCCTAACCACATGATATCTAATTCGCATGCA
* * *
36211 TTATTCAAAAAATAAAT-CTAACCGCATGATATCTAGTTCGCATGCA
1 TTATTCAAAAAAGAAATCCTAACCACATGATATCTAATTCGCATGCA
*
36257 TTTATTCGAAAAACGAAA
1 -TTATTC-AAAAAAGAAA
36275 ATAATTGACT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
45 26 0.46
46 9 0.16
47 13 0.23
48 8 0.14
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (47 bp):
TTATTCAAAAAAGAAATCCTAACCACATGATATCTAATTCGCATGCA
Found at i:43141 original size:16 final size:18
Alignment explanation
Indices: 43110--43145 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
43100 AGATCATGTG
43110 ATAATTAATAAAATTAAT
1 ATAATTAATAAAATTAAT
43128 ATAA-TAAT-AAATTAAT
1 ATAATTAATAAAATTAAT
43144 AT
1 AT
43146 GGAATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 4 0.22
18 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATTAATAAAATTAAT
Found at i:43151 original size:18 final size:17
Alignment explanation
Indices: 43110--43160 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
43100 AGATCATGTG
43110 ATAATTAATAAAATTAAT
1 ATAA-TAATAAAATTAAT
43128 ATAATAAT-AAATTAAT
1 ATAATAATAAAATTAAT
43144 ATGGAAT-ATAAAATTAA
1 AT--AATAATAAAATTAA
43161 AATCTATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.33
17 6 0.20
18 14 0.47
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (17 bp):
ATAATAATAAAATTAAT
Found at i:47275 original size:21 final size:21
Alignment explanation
Indices: 47251--47291 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
47241 ATGTAAGTGT
47251 GTTAGTTCACGAGCCTCGAGA
1 GTTAGTTCACGAGCCTCGAGA
47272 GTTAGTTCACGAGCCTCGAG
1 GTTAGTTCACGAGCCTCGAG
47292 TTTTCAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.24
Consensus pattern (21 bp):
GTTAGTTCACGAGCCTCGAGA
Found at i:49748 original size:24 final size:24
Alignment explanation
Indices: 49716--49770 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
49706 TGGAAGCTAA
49716 ATGATCAGAAGTAGGTTAAATCCG
1 ATGATCAGAAGTAGGTTAAATCCG
49740 ATGATCAGAAGTAGGTTAAATCCG
1 ATGATCAGAAGTAGGTTAAATCCG
49764 ATGATCA
1 ATGATCA
49771 ACATGTATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (24 bp):
ATGATCAGAAGTAGGTTAAATCCG
Found at i:62590 original size:131 final size:131
Alignment explanation
Indices: 62380--62631 Score: 459
Period size: 131 Copynumber: 1.9 Consensus size: 131
62370 TTTGAAGCAG
* *
62380 TTGGAGATGTTTTCTCTACAAAATAAAACTACCCAGGATAAGGAGTATCGATACTCCTATAATGA
1 TTGGAGATGTTTTCTCTACAAAATAAAACTACCCAAGATAAGGAGTATCGATAATCCTATAATGA
*
62445 GTATCGGTAATTCCTTTGTTATTTTTAAATAAAACTAACCGTTAAAGACCGTTGGGAGTGATTTG
66 GTATCGGTAATTCCTTTGTTATTTTTAAATAAAACTAACCGTTAAAGACCATTGGGAGTGATTTG
62510 A
131 A
*
62511 TTGGAGATGTTTTCTCTACAAAATAAAACTGCCCAAGATAAGGAGTATCGATAATCCTATAATGA
1 TTGGAGATGTTTTCTCTACAAAATAAAACTACCCAAGATAAGGAGTATCGATAATCCTATAATGA
*
62576 GTATCGGTATTTCCTTTGTTATTTTTAAATAAAACTAACCGTTAAAGACCATTGGG
66 GTATCGGTAATTCCTTTGTTATTTTTAAATAAAACTAACCGTTAAAGACCATTGGG
62632 CTTGACGGTA
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
131 116 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (131 bp):
TTGGAGATGTTTTCTCTACAAAATAAAACTACCCAAGATAAGGAGTATCGATAATCCTATAATGA
GTATCGGTAATTCCTTTGTTATTTTTAAATAAAACTAACCGTTAAAGACCATTGGGAGTGATTTG
A
Found at i:63087 original size:23 final size:23
Alignment explanation
Indices: 63053--63121 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
63043 CACCACAGCT
* *
63053 CGTATAAATGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
63076 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
63099 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
63122 TATAAGGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:63597 original size:2 final size:2
Alignment explanation
Indices: 63590--63622 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
63580 TTCATCTTCC
63590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
63623 CATTTTTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64762 original size:24 final size:20
Alignment explanation
Indices: 64705--64782 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
64695 TTTCCCTTGA
*
64705 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
64725 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
*
64748 ATGTGCATCGATGCACTCCT-T
1 A-GTGCATCGATGCA-TCCTAC
64769 A-TGCATCGATGCAT
1 AGTGCATCGATGCAT
64783 TAATTGCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
18 1 0.02
19 12 0.24
20 14 0.29
21 2 0.04
22 1 0.02
23 4 0.08
24 14 0.29
25 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:66587 original size:13 final size:13
Alignment explanation
Indices: 66569--66595 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
66559 ATTATGTTAA
66569 TATTTTTATTTTT
1 TATTTTTATTTTT
66582 TATTTTTATTTTT
1 TATTTTTATTTTT
66595 T
1 T
66596 TTTCGTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:78001 original size:19 final size:19
Alignment explanation
Indices: 77978--78026 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
77968 AAATAAAAGA
77978 GAAAAAATGAAAAAATGA-
1 GAAAAAATGAAAAAATGAT
77996 GAAAAAA-G-AAAAATGAT
1 GAAAAAATGAAAAAATGAT
78013 GGAAAAAATGAAAA
1 -GAAAAAATGAAAA
78027 GAAAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 8 0.30
17 1 0.04
18 14 0.52
19 1 0.04
20 3 0.11
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.10
Consensus pattern (19 bp):
GAAAAAATGAAAAAATGAT
Found at i:78033 original size:7 final size:7
Alignment explanation
Indices: 78023--78093 Score: 52
Period size: 7 Copynumber: 8.9 Consensus size: 7
78013 GGAAAAAATG
78023 AAAAGAA
1 AAAAGAA
78030 AAAAGAA
1 AAAAGAA
78037 AAAAGGGAA
1 AAAA--GAA
78046 AAGGGAAGAA
1 AA---AAGAA
78056 AAAATGAA
1 AAAA-GAA
*
78064 AAATGAA
1 AAAAGAA
78071 ATAAAGAGA
1 A-AAAGA-A
78080 AAAATGAA
1 AAAA-GAA
78088 AAAAGA
1 AAAAGA
78094 GAAATAAAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 18
0.73 0.03 0.25
Matches are distributed among these distances:
7 19 0.36
8 18 0.34
9 9 0.17
10 5 0.09
12 2 0.04
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (7 bp):
AAAAGAA
Found at i:79528 original size:55 final size:54
Alignment explanation
Indices: 79463--79843 Score: 344
Period size: 55 Copynumber: 6.9 Consensus size: 54
79453 GTTGAAGATT
* * ***
79463 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAATTCGTTGAAGATTGTTC
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCCGTT-GTTGAAGATTGTTC
* *
79518 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTT-TCATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCCGTTGT--TGAAGATTGTTC
* * * * * *
79573 GAGTTCTATACTCTCTGAAGGAATAGAGAACGAACACGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCCGTTGT-TGAAGATTGTTC
*
79628 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAA-GGAATAGGGAGCGGACCCGTTGT-TGAAGATTGTTC
* * *
79683 GAGTTCTATACTCCCTGAACGG-ATAGGGAGTGGACCCGTTTGTCGAAGATTATTC
1 GAGTTCTATACTCCCTGAA-GGAATAGGGAGCGGACCCG-TTGTTGAAGATTGTTC
* ** * *
79738 GAG-TCTTATACTCCCTGAACGAATAGGGAGTAGACAC-AT-TTGCCAAGGATTGTTC
1 GAGTTC-TATACTCCCTGAAGGAATAGGGAGCGGACCCGTTGTTG--AA-GATTGTTC
* * * * *
79793 GAG-TCTTATACTCCTTGAAAGAAAAGGGAGCAGACCCGTTATTTGAAGATT
1 GAGTTC-TATACTCCCTGAAGGAATAGGGAGCGGACCCGTT-GTTGAAGATT
79844 TTTCAAGTAT
Statistics
Matches: 284, Mismatches: 29, Indels: 26
0.84 0.09 0.08
Matches are distributed among these distances:
52 2 0.01
53 2 0.01
54 5 0.02
55 263 0.93
56 9 0.03
58 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (54 bp):
GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCCGTTGTTGAAGATTGTTC
Found at i:79661 original size:110 final size:109
Alignment explanation
Indices: 79463--79767 Score: 391
Period size: 110 Copynumber: 2.8 Consensus size: 109
79453 GTTGAAGATT
* ** *
79463 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAATTCGTTGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTT-TTTGAAGATTGTTCGAGTTCTATA
* *
79528 CTCTCTGAA-GGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTC
65 CTCCCTGAACGG-ATAGGGAGCGGACCCGTTTCATGAAGATTGTTC
* * *
79573 GAGTTCTATACTCTCTGAAGGAATAGAGAACGAACACGTTTTATGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTT-TGAAGATTGTTCGAGTTCTATA
*
79638 CTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
65 CTCCCTGAACGGATAGGGAGCGGACCCGTTTCATGAAGATTGTTC
* * * * *
79683 GAGTTCTATACTCCCTGAACGG-ATAGGGAGTGGACCCGTTTGTCGAAGATTATTCGAG-TCTTA
1 GAGTTCTATACTCTCTGAA-GGAATAGGGAGCGGACACGTTT-TTGAAGATTGTTCGAGTTC-TA
*
79746 TACTCCCTGAACGAATAGGGAG
63 TACTCCCTGAACGGATAGGGAG
79768 TAGACACATT
Statistics
Matches: 171, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
109 3 0.02
110 163 0.95
111 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (109 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTTTGAAGATTGTTCGAGTTCTATAC
TCCCTGAACGGATAGGGAGCGGACCCGTTTCATGAAGATTGTTC
Found at i:79741 original size:165 final size:165
Alignment explanation
Indices: 79463--79763 Score: 405
Period size: 165 Copynumber: 1.8 Consensus size: 165
79453 GTTGAAGATT
*
79463 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAATTCGTTGAAGATTGTTCGAGTTCTATA
1 GAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACAAATTCGTTGAAGATTGTTCGAGTTCTATA
* * *
79528 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTCGAGT-TCTATACTCTCTGAA
66 CTCCCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTATTCGAGTCT-TATACTCCCTGAA
*
79592 GGAATAGAGAACGAACACGTTTTATGAAGATTGTTC
130 CGAATAGAGAACGAACACGTTTTATGAAGATTGTTC
* *** *
79628 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACCCGTT-TTATGAAGATTGTTCGAGTTCTA
1 GAGTCCTATACTCCCTGAA-GGAATAGGGAGCGGACAAATTCGT-TGAAGATTGTTCGAGTTCTA
* * *
79691 TACTCCCTGAACGG-ATAGGGAGTGGACCCGTTT-GTCGAAGATTATTCGAGTCTTATACTCCCT
64 TACTCCCTGAA-GGAATAGAGAGCGGACCCGTTTCAT-GAAGATTATTCGAGTCTTATACTCCCT
79754 GAACGAATAG
127 GAACGAATAG
79764 GGAGTAGACA
Statistics
Matches: 118, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
164 2 0.02
165 111 0.94
166 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (165 bp):
GAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACAAATTCGTTGAAGATTGTTCGAGTTCTATA
CTCCCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTATTCGAGTCTTATACTCCCTGAAC
GAATAGAGAACGAACACGTTTTATGAAGATTGTTC
Found at i:79791 original size:165 final size:164
Alignment explanation
Indices: 79463--79843 Score: 400
Period size: 165 Copynumber: 2.3 Consensus size: 164
79453 GTTGAAGATT
* * *** **
79463 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAATTCGTTGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCCCTGAAGG-ATAGGGAGCGGACCCGTTATTTGAAGATTGTTCGAGTTCTATA
* * * *
79528 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTCGAGTTCTATACTCTCTGAAG
65 CTCCCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTATTCGAGTTCTATACTCCCTGAAC
* **
79593 GAATAGAGAACGAACACGTTTTATGAAGATTGTTC
130 GAATAGAGAACGAACACGATTTACCAAGATTGTTC
79628 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTT-TTATGAAGATTGTTCGAGTTCTAT
1 GAGTTCTATACTCCCTGAA-GGATAGGGAGCGGACCCGTTATT-TGAAGATTGTTCGAGTTCTAT
* * *
79692 ACTCCCTGAACGG-ATAGGGAGTGGACCCGTTT-GTCGAAGATTATTCGAG-TCTTATACTCCCT
64 ACTCCCTGAA-GGAATAGAGAGCGGACCCGTTTCAT-GAAGATTATTCGAGTTC-TATACTCCCT
* *
79754 GAACGAATAG-GGA-GTAGACAC-ATTTGCCAAGGATTGTTC
126 GAACGAATAGAGAACG-A-ACACGATTTACCAA-GATTGTTC
* * * *
79793 GAG-TCTTATACTCCTTGAAAGAAAAGGGAGCAGACCCGTTATTTGAAGATT
1 GAGTTC-TATACTCCCTG-AAGGATAGGGAGCGGACCCGTTATTTGAAGATT
79844 TTTCAAGTAT
Statistics
Matches: 183, Mismatches: 22, Indels: 22
0.81 0.10 0.10
Matches are distributed among these distances:
163 1 0.01
164 14 0.08
165 160 0.87
166 8 0.04
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (164 bp):
GAGTTCTATACTCCCTGAAGGATAGGGAGCGGACCCGTTATTTGAAGATTGTTCGAGTTCTATAC
TCCCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTATTCGAGTTCTATACTCCCTGAACG
AATAGAGAACGAACACGATTTACCAAGATTGTTC
Found at i:81661 original size:7 final size:7
Alignment explanation
Indices: 81649--81680 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
81639 TATGTTAATA
81649 TTTTTAT
1 TTTTTAT
81656 TTTTTAT
1 TTTTTAT
81663 TTTTTA-
1 TTTTTAT
81669 TTTTTAT
1 TTTTTAT
81676 TTTTT
1 TTTTT
81681 TTTCGTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:81681 original size:14 final size:14
Alignment explanation
Indices: 81649--81680 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
81639 TATGTTAATA
81649 TTTTTATTTTTTAT
1 TTTTTATTTTTTAT
81663 TTTTTA-TTTTTAT
1 TTTTTATTTTTTAT
81676 TTTTT
1 TTTTT
81681 TTTCGTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTATTTTTTAT
Found at i:86022 original size:23 final size:23
Alignment explanation
Indices: 85985--86048 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
85975 CAGGTTGTAT
* *
85985 AAATGCATCGAAGTGCTACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
86008 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
86031 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
86049 TATAAGGTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:87683 original size:24 final size:20
Alignment explanation
Indices: 87626--87703 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
87616 TTTCCCTTGA
*
87626 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
87646 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
87669 ATGTGCATCGATGCACTCCT--
1 A-GTGCATCGATGCA-TCCTAC
*
87689 TGTGCATCGATGCAT
1 AGTGCATCGATGCAT
87704 TAATTGCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
18 1 0.02
19 13 0.27
20 14 0.29
21 1 0.02
22 1 0.02
23 4 0.08
24 14 0.29
25 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:98360 original size:26 final size:25
Alignment explanation
Indices: 98329--98378 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
98319 AGAATTTTCC
98329 AAAAAATT-TTGAATTTTCGAAATTAA
1 AAAAAATTGTTG-ATTTTC-AAATTAA
*
98355 AAAAAATTGTTGTTTTTCAAATTA
1 AAAAAATTGTTGATTTTCAAATTA
98379 TTGTGTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 13 0.59
27 3 0.14
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (25 bp):
AAAAAATTGTTGATTTTCAAATTAA
Found at i:103850 original size:20 final size:20
Alignment explanation
Indices: 103825--103864 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
103815 GGCTTGATTT
103825 TACTGTAGCA-GTATCGATAC
1 TACTGTAG-AGGTATCGATAC
103845 TACTGTAGAGGTATCGATAC
1 TACTGTAGAGGTATCGATAC
103865 CTATTTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (20 bp):
TACTGTAGAGGTATCGATAC
Found at i:109935 original size:24 final size:24
Alignment explanation
Indices: 109890--109935 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
109880 TTTAGTCCAT
*
109890 TTTTATATTAATATCAGCTTCACA
1 TTTTATATTAATATCAACTTCACA
*
109914 TTTTATAATTAAT-TCAATTTCA
1 TTTTAT-ATTAATATCAACTTCA
109936 TCCCTCATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTATATTAATATCAACTTCACA
Found at i:110053 original size:22 final size:21
Alignment explanation
Indices: 110028--110153 Score: 77
Period size: 22 Copynumber: 5.8 Consensus size: 21
110018 ATATATAAAC
110028 TATAAACTATAAAGTATAAGTA
1 TATAAA-TATAAAGTATAAGTA
110050 TATATATATATAAAGTAT-A-TAA
1 TATA-A-ATATAAAGTATAAGT-A
*
110072 TATAAAGTATTAAACTAT-A-TAA
1 TATAAA-TA-TAAAGTATAAGT-A
*
110094 TATAAGTATTAAA-TATAAAGTA
1 TATAAATA-TAAAGTAT-AAGTA
*
110116 T-TAAAGTATATAAATATAAGTA
1 TATAAA-TATA-AAGTATAAGTA
110138 T-TAAATATAAAGTATA
1 TATAAATATAAAGTATA
110154 TTAATTATCA
Statistics
Matches: 89, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
20 10 0.11
21 20 0.22
22 43 0.48
23 15 0.17
24 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.37
Consensus pattern (21 bp):
TATAAATATAAAGTATAAGTA
Found at i:110059 original size:14 final size:14
Alignment explanation
Indices: 110050--110184 Score: 52
Period size: 14 Copynumber: 9.4 Consensus size: 14
110040 AGTATAAGTA
110050 TATATATATATAAAG
1 TATATATATAT-AAG
110065 TATATA-ATATAAAG
1 TATATATATAT-AAG
*
110079 TATTAAACTATATAA-
1 TA-TATA-TATATAAG
*
110094 TATA-AGTAT-TAAA
1 TATATA-TATATAAG
*
110107 TATAAAGTAT-TAAAG
1 TATATA-TATAT-AAG
*
110122 TATATAAATATAAG
1 TATATATATATAAG
*
110136 TAT-TAAATATAAAG
1 TATATATATAT-AAG
*
110150 TATATTAATTATCATAAT
1 TATA-T-A-TAT-ATAAG
110168 TA-ATATAT-TAAG
1 TATATATATATAAG
110180 TATAT
1 TATAT
110185 TTATTAATTT
Statistics
Matches: 98, Mismatches: 8, Indels: 30
0.72 0.06 0.22
Matches are distributed among these distances:
12 8 0.08
13 17 0.17
14 35 0.36
15 20 0.20
16 4 0.04
17 6 0.06
18 6 0.06
19 2 0.02
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (14 bp):
TATATATATATAAG
Found at i:110091 original size:35 final size:36
Alignment explanation
Indices: 110012--110152 Score: 155
Period size: 37 Copynumber: 3.9 Consensus size: 36
110002 TTGGTACTTC
* * *
110012 ATATACATATATAAACTA-TAAACTATAAAGTA-TAAGT
1 ATATATATATAT-AAGTATTAAA-TATAAAGTATTAA-A
110049 ATATATATATATAAAGTA-TATAATATAAAGTATTAAA
1 ATATATATATAT-AAGTATTA-AATATAAAGTATTAAA
*
110086 CTATATA-ATATAAGTATTAAATATAAAGTATTAAA
1 ATATATATATATAAGTATTAAATATAAAGTATTAAA
* *
110121 GTATATAAATATAAGTATTAAATATAAAGTAT
1 ATATATATATATAAGTATTAAATATAAAGTAT
110153 ATTAATTATC
Statistics
Matches: 95, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
35 27 0.28
36 30 0.32
37 33 0.35
38 5 0.05
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (36 bp):
ATATATATATATAAGTATTAAATATAAAGTATTAAA
Found at i:110137 original size:57 final size:52
Alignment explanation
Indices: 110020--110153 Score: 159
Period size: 57 Copynumber: 2.5 Consensus size: 52
110010 TCATATACAT
* *
110020 ATATAAACTA-TAAACTATAAAGTATAAGTATATATATATATAAAGTATATA
1 ATATAAAGTATTAAACTATAAAGTATAAGTATATATAAATATAAAGTATATA
110071 ATATAAAGTATTAAACTATATAA-TATAAGTATTAAATATAAAGTATTAAAGTATATA
1 ATATAAAGTATTAAACTATA-AAGTATAAGTA-T--ATATAAA-TA-TAAAGTATATA
110128 A-ATATAAGTATTAAA-TATAAAGTATA
1 ATATA-AAGTATTAAACTATAAAGTATA
110154 TTAATTATCA
Statistics
Matches: 72, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
51 9 0.12
52 17 0.24
53 3 0.04
55 8 0.11
56 13 0.18
57 22 0.31
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (52 bp):
ATATAAAGTATTAAACTATAAAGTATAAGTATATATAAATATAAAGTATATA
Found at i:110176 original size:21 final size:21
Alignment explanation
Indices: 110150--110220 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
110140 AAATATAAAG
110150 TATATTAATTATCATAATTAA
1 TATATTAATTATCATAATTAA
* *
110171 TATATTAAGTAT-AT--TTAT
1 TATATTAATTATCATAATTAA
110189 TA-ATTTAATTATCATAATTAA
1 TATA-TTAATTATCATAATTAA
*
110210 TAT-TTTATTAT
1 TATATTAATTAT
110221 AACATTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
17 1 0.03
18 12 0.30
19 2 0.05
20 9 0.22
21 16 0.40
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (21 bp):
TATATTAATTATCATAATTAA
Found at i:110208 original size:18 final size:19
Alignment explanation
Indices: 110151--110213 Score: 67
Period size: 18 Copynumber: 3.3 Consensus size: 19
110141 AATATAAAGT
110151 ATATTAATTATCATAATTAA
1 ATATTAATTATCATAATT-A
* *
110171 TATATTAAGTAT-ATTTATTA
1 -ATATTAATTATCA-TAATTA
110191 AT-TTAATTATCATAATTA
1 ATATTAATTATCATAATTA
110209 ATATT
1 ATATT
110214 TTATTATAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 14 0.40
19 5 0.14
20 2 0.06
21 14 0.40
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (19 bp):
ATATTAATTATCATAATTA
Found at i:110340 original size:16 final size:16
Alignment explanation
Indices: 110315--110372 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
110305 CAATGATAAT
110315 ATAT-AAGTCAGGTAA
1 ATATCAAGTCAGGTAA
*
110330 ATGTCAAGTCAGGTAA
1 ATATCAAGTCAGGTAA
* * *
110346 ATATCAAATCATGTCA
1 ATATCAAGTCAGGTAA
*
110362 ATAACAAGTCA
1 ATATCAAGTCA
110373 TATCATTTAC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
15 3 0.09
16 32 0.91
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.26
Consensus pattern (16 bp):
ATATCAAGTCAGGTAA
Found at i:110730 original size:21 final size:21
Alignment explanation
Indices: 110704--110747 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
110694 AGGATATAAG
*
110704 AACCTCATCACTAGTTACTTC
1 AACCTCATCACCAGTTACTTC
*
110725 AACCTCATCACCAGTTATTTC
1 AACCTCATCACCAGTTACTTC
110746 AA
1 AA
110748 TAGTGCAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32
Consensus pattern (21 bp):
AACCTCATCACCAGTTACTTC
Found at i:115619 original size:40 final size:40
Alignment explanation
Indices: 115564--115683 Score: 222
Period size: 40 Copynumber: 3.0 Consensus size: 40
115554 GTTGTAGGTT
*
115564 ATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGTA
1 ATACACTTCGGTGTATATGGTGGGCATGACCTTATGTGTA
115604 ATACACTTCGGTGTATATGGTGGGCATGACCTTATGTGTA
1 ATACACTTCGGTGTATATGGTGGGCATGACCTTATGTGTA
*
115644 ATACACTTCGATGTATATGGTGGGCATGACCTTATGTGTA
1 ATACACTTCGGTGTATATGGTGGGCATGACCTTATGTGTA
115684 GCATTACGGT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
ATACACTTCGGTGTATATGGTGGGCATGACCTTATGTGTA
Found at i:115883 original size:47 final size:46
Alignment explanation
Indices: 115827--115956 Score: 192
Period size: 47 Copynumber: 2.8 Consensus size: 46
115817 AGTATATGGG
115827 TAAAATAAGCTTACGAGCTTATGAGATTAAATGGTAAGTATTTTGTA
1 TAAAATAAGCTTACGAGCTTATGAGATTAAATGGTAAGTATTTTG-A
* *
115874 TAAAATAAGCTTATGAGCTTAT-AGAATTTAAATGGTAAGTATTTTGG
1 TAAAATAAGCTTACGAGCTTATGAG-A-TTAAATGGTAAGTATTTTGA
*
115921 TAAAATAAGCTTACGAGCTTATGGGA-TAAATGGTAA
1 TAAAATAAGCTTACGAGCTTATGAGATTAAATGGTAA
115957 AAGATTTTAT
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
45 10 0.13
46 2 0.03
47 44 0.58
48 20 0.26
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (46 bp):
TAAAATAAGCTTACGAGCTTATGAGATTAAATGGTAAGTATTTTGA
Found at i:120700 original size:27 final size:27
Alignment explanation
Indices: 120664--120729 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
120654 CCTCAATCAG
120664 TATATATTA-TTATTAAGA-ATAATATTA
1 TATATATTATTTATT-AGATAT-ATATTA
*
120691 TATATCTTATTTATTAGATATATATTA
1 TATATATTATTTATTAGATATATATTA
120718 T-T-TATTATTTAT
1 TATATATTATTTAT
120730 ATATTATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 9 0.26
26 1 0.03
27 18 0.51
28 7 0.20
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (27 bp):
TATATATTATTTATTAGATATATATTA
Found at i:120713 original size:18 final size:18
Alignment explanation
Indices: 120690--120739 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
120680 GAATAATATT
*
120690 ATATATCTTATTTATTAG
1 ATATATATTATTTATTAG
*
120708 ATATATATTATTTATTAT
1 ATATATATTATTTATTAG
*
120726 TTATATATTATTTA
1 ATATATATTATTTA
120740 AATAATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
ATATATATTATTTATTAG
Found at i:120860 original size:29 final size:30
Alignment explanation
Indices: 120800--120861 Score: 99
Period size: 29 Copynumber: 2.0 Consensus size: 30
120790 ACAAGGGCTT
120800 ATTTGATCCGATCGTACAACATAATCCTTTAA
1 ATTTGATCCGATCGT--AACATAATCCTTTAA
120832 ATTTGATCCGATCGT-ACATAATCCTTTAA
1 ATTTGATCCGATCGTAACATAATCCTTTAA
120861 A
1 A
120862 AAGTGTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 15 0.50
32 15 0.50
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (30 bp):
ATTTGATCCGATCGTAACATAATCCTTTAA
Found at i:133387 original size:17 final size:20
Alignment explanation
Indices: 133365--133405 Score: 61
Period size: 17 Copynumber: 2.2 Consensus size: 20
133355 AAATAGGTAT
133365 TTAAGTTT-ATAT-TTA-TA
1 TTAAGTTTCATATATTATTA
133382 TTAAGTTTCATATATTATTA
1 TTAAGTTTCATATATTATTA
133402 TTAA
1 TTAA
133406 ATTTTGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 3 0.14
20 6 0.29
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAAGTTTCATATATTATTA
Found at i:139880 original size:60 final size:59
Alignment explanation
Indices: 139811--140054 Score: 201
Period size: 60 Copynumber: 4.1 Consensus size: 59
139801 GAGTCCATAC
* * * * * *
139811 TGAGTGAAAAACATAGATTTTCAGCTTCAGCTACACGATTAAGCTAAAGATCGTCAAAT
1 TGAGTGAAAAACATAGATTCTCAGTTTCAGCTATAAGATTAAGCTAAATAGCGTCAAAT
* * * * *
139870 TAGAGTGAAAAAAAAAGATTCACAGTTTCAGCTTTAAGA-TAGAGCTAAATAGCGTCAACAC
1 T-GAGTGAAAAACATAGATTCTCAGTTTCAGCTATAAGATTA-AGCTAAATAGCGTCAA-AT
* * * * *
139931 TGAGTGAAAAACATATAGATTTTCAGATTCATCTA-AACGATTAAGCTAAAAAGCGTTAAAT
1 TGAGTGAAAAAC--ATAGATTCTCAGTTTCAGCTATAA-GATTAAGCTAAATAGCGTCAAAT
* * *
139992 TGGAGTG--AAATA-AGTATTCTCAGTTTCAGCTATAAGATAAAGCTAAATATCGTCAAAAT
1 T-GAGTGAAAAACATAG-ATTCTCAGTTTCAGCTATAAGATTAAGCTAAATAGCGTC-AAAT
140051 TGAG
1 TGAG
140055 ACAAAAAGAC
Statistics
Matches: 145, Mismatches: 29, Indels: 23
0.74 0.15 0.12
Matches are distributed among these distances:
57 2 0.01
58 33 0.23
59 10 0.07
60 56 0.39
61 6 0.04
62 36 0.25
63 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (59 bp):
TGAGTGAAAAACATAGATTCTCAGTTTCAGCTATAAGATTAAGCTAAATAGCGTCAAAT
Found at i:139935 original size:120 final size:119
Alignment explanation
Indices: 139809--140047 Score: 320
Period size: 120 Copynumber: 2.0 Consensus size: 119
139799 AAGAGTCCAT
* * * *
139809 ACTGAGTGAAAAAC-ATAGATTTTCAGCTTCAGCTACACGATTAAGCTAAAGATCGTCAAATTAG
1 ACTGAGTGAAAAACAATAGATTTTCAGATTCAGCTAAACGATTAAGCTAAAAAGCGTCAAATTAG
* *
139873 AGTGAAAAAAAAAG-ATTCACAGTTTCAGCTTTAAGATAGAGCTAAATAGCGTCAAC
66 AGTG---AAAAAAGTATTCACAGTTTCAGCTATAAGATAAAGCTAAATAGCGTCAAC
* * *
139929 ACTGAGTGAAAAACATATAGATTTTCAGATTCATCTAAACGATTAAGCTAAAAAGCGTTAAATTG
1 ACTGAGTGAAAAACA-ATAGATTTTCAGATTCAGCTAAACGATTAAGCTAAAAAGCGTCAAATTA
* * *
139994 GAGTGAAATAAGTATTCTCAGTTTCAGCTATAAGATAAAGCTAAATATCGTCAA
65 GAGTGAAAAAAGTATTCACAGTTTCAGCTATAAGATAAAGCTAAATAGCGTCAA
140048 AATTGAGACA
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
119 6 0.06
120 51 0.49
122 47 0.45
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (119 bp):
ACTGAGTGAAAAACAATAGATTTTCAGATTCAGCTAAACGATTAAGCTAAAAAGCGTCAAATTAG
AGTGAAAAAAGTATTCACAGTTTCAGCTATAAGATAAAGCTAAATAGCGTCAAC
Found at i:140402 original size:60 final size:59
Alignment explanation
Indices: 140333--140576 Score: 199
Period size: 60 Copynumber: 4.1 Consensus size: 59
140323 GAGTCCATAC
* * * * *
140333 TGAGTGAAAAACATAGATTTTCAGCTTCAGCTACACGATTAAGCTAAAGATCGTCAAAT
1 TGAGTGAAAAACATAGATTCTCAGTTTCAGCTATACGATTAAGCTAAATAGCGTCAAAT
* * * * * *
140392 TAGAGTGAAAAAAAAAGATTCACAGTTTCAGCTTTATGA-TAGAGCTAAATAGCGTCAACAC
1 T-GAGTGAAAAACATAGATTCTCAGTTTCAGCTATACGATTA-AGCTAAATAGCGTCAA-AT
* * * * * *
140453 TGAGTGAAAAACATATAGATTTTCAGATTCATCTAAACGATTAAGCTAAAAAGCGTTAAAT
1 TGAGTGAAAAAC--ATAGATTCTCAGTTTCAGCTATACGATTAAGCTAAATAGCGTCAAAT
* * * *
140514 TGGAGTG--AAATA-AGTATTCTCAGTTTCAGCTATAAGATAAAGCTAAATATCGTCAAAAT
1 T-GAGTGAAAAACATAG-ATTCTCAGTTTCAGCTATACGATTAAGCTAAATAGCGTC-AAAT
140573 TGAG
1 TGAG
140577 ACAAAAAGAC
Statistics
Matches: 143, Mismatches: 33, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
57 2 0.01
58 34 0.24
59 8 0.06
60 56 0.39
61 4 0.03
62 37 0.26
63 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (59 bp):
TGAGTGAAAAACATAGATTCTCAGTTTCAGCTATACGATTAAGCTAAATAGCGTCAAAT
Found at i:140458 original size:120 final size:119
Alignment explanation
Indices: 140309--140569 Score: 314
Period size: 120 Copynumber: 2.2 Consensus size: 119
140299 TTTCATTAAA
* * * * *
140309 ATGATAGAGCT-AA-AGAGTCCATACTGAGTGAAAAAC-ATAGATTTTCAGCTTCAGCTACACGA
1 ATGATAGAGCTAAATAGCGTCAACACTGAGTGAAAAACAATAGATTTTCAGATTCAGCTAAACGA
* * *
140371 TTAAGCTAAAGATCGTCAAATTAGAGTGAAAAAAAAAG-ATTCACAGTTTCAGCTTT
66 TTAAGCTAAAAAGCGTCAAATTAGAGTG---AAAAAAGTATTCACAGTTTCAGCTAT
*
140427 ATGATAGAGCTAAATAGCGTCAACACTGAGTGAAAAACATATAGATTTTCAGATTCATCTAAACG
1 ATGATAGAGCTAAATAGCGTCAACACTGAGTGAAAAACA-ATAGATTTTCAGATTCAGCTAAACG
* * * *
140492 ATTAAGCTAAAAAGCGTTAAATTGGAGTGAAATAAGTATTCTCAGTTTCAGCTAT
65 ATTAAGCTAAAAAGCGTCAAATTAGAGTGAAAAAAGTATTCACAGTTTCAGCTAT
* * *
140547 AAGATAAAGCTAAATATCGTCAA
1 ATGATAGAGCTAAATAGCGTCAA
140570 AATTGAGACA
Statistics
Matches: 122, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
118 11 0.09
119 8 0.07
120 56 0.46
122 47 0.39
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (119 bp):
ATGATAGAGCTAAATAGCGTCAACACTGAGTGAAAAACAATAGATTTTCAGATTCAGCTAAACGA
TTAAGCTAAAAAGCGTCAAATTAGAGTGAAAAAAGTATTCACAGTTTCAGCTAT
Found at i:140532 original size:522 final size:522
Alignment explanation
Indices: 139548--140591 Score: 2070
Period size: 522 Copynumber: 2.0 Consensus size: 522
139538 CCATTGATCT
139548 TCACTTACAGCAGGAAAAGCAAATTCAACTGAATAACTACAGAGGCTTCTTTCCTAATAATTACA
1 TCACTTACAGCAGGAAAAGCAAATTCAACTGAATAACTACAGAGGCTTCTTTCCTAATAATTACA
139613 TTTCCTAAGAAGTTCTACTAAAGAACCAGGAAAAAATCAGAGAGACCGAGTAAGTTTCAGACTTT
66 TTTCCTAAGAAGTTCTACTAAAGAACCAGGAAAAAATCAGAGAGACCGAGTAAGTTTCAGACTTT
139678 TAGCTAAAAGATAAATTGAAATAATTGACTAATTGAGTGGAAAACAGAAAATTGAGCTAAATAGC
131 TAGCTAAAAGATAAATTGAAATAATTGACTAATTGAGTGGAAAACAGAAAATTGAGCTAAATAGC
139743 GTCAAAAGGAGTAAAAAAATTAAAAGAAATTCAGTTTCATTAAAATGATAGAGCTAAAGAGTCCA
196 GTCAAAAGGAGTAAAAAAATTAAAAGAAATTCAGTTTCATTAAAATGATAGAGCTAAAGAGTCCA
139808 TACTGAGTGAAAAACATAGATTTTCAGCTTCAGCTACACGATTAAGCTAAAGATCGTCAAATTAG
261 TACTGAGTGAAAAACATAGATTTTCAGCTTCAGCTACACGATTAAGCTAAAGATCGTCAAATTAG
139873 AGTGAAAAAAAAAGATTCACAGTTTCAGCTTTAAGATAGAGCTAAATAGCGTCAACACTGAGTGA
326 AGTGAAAAAAAAAGATTCACAGTTTCAGCTTTAAGATAGAGCTAAATAGCGTCAACACTGAGTGA
139938 AAAACATATAGATTTTCAGATTCATCTAAACGATTAAGCTAAAAAGCGTTAAATTGGAGTGAAAT
391 AAAACATATAGATTTTCAGATTCATCTAAACGATTAAGCTAAAAAGCGTTAAATTGGAGTGAAAT
140003 AAGTATTCTCAGTTTCAGCTATAAGATAAAGCTAAATATCGTCAAAATTGAGACAAAAAGACAAA
456 AAGTATTCTCAGTTTCAGCTATAAGATAAAGCTAAATATCGTCAAAATTGAGACAAAAAGACAAA
140068 AA
521 AA
140070 TCACTTACAGCAGGAAAAGCAAATTCAACTGAATAACTACAGAGGCTTCTTTCCTAATAATTACA
1 TCACTTACAGCAGGAAAAGCAAATTCAACTGAATAACTACAGAGGCTTCTTTCCTAATAATTACA
140135 TTTCCTAAGAAGTTCTACTAAAGAACCAGGAAAAAATCAGAGAGACCGAGTAAGTTTCAGACTTT
66 TTTCCTAAGAAGTTCTACTAAAGAACCAGGAAAAAATCAGAGAGACCGAGTAAGTTTCAGACTTT
140200 TAGCTAAAAGATAAATTGAAATAATTGACTAATTGAGTGGAAAACAGAAAATTGAGCTAAATAGC
131 TAGCTAAAAGATAAATTGAAATAATTGACTAATTGAGTGGAAAACAGAAAATTGAGCTAAATAGC
*
140265 GTCAAATGGAGTAAAAAAATTAAAAGAAATTCAGTTTCATTAAAATGATAGAGCTAAAGAGTCCA
196 GTCAAAAGGAGTAAAAAAATTAAAAGAAATTCAGTTTCATTAAAATGATAGAGCTAAAGAGTCCA
140330 TACTGAGTGAAAAACATAGATTTTCAGCTTCAGCTACACGATTAAGCTAAAGATCGTCAAATTAG
261 TACTGAGTGAAAAACATAGATTTTCAGCTTCAGCTACACGATTAAGCTAAAGATCGTCAAATTAG
*
140395 AGTGAAAAAAAAAGATTCACAGTTTCAGCTTTATGATAGAGCTAAATAGCGTCAACACTGAGTGA
326 AGTGAAAAAAAAAGATTCACAGTTTCAGCTTTAAGATAGAGCTAAATAGCGTCAACACTGAGTGA
140460 AAAACATATAGATTTTCAGATTCATCTAAACGATTAAGCTAAAAAGCGTTAAATTGGAGTGAAAT
391 AAAACATATAGATTTTCAGATTCATCTAAACGATTAAGCTAAAAAGCGTTAAATTGGAGTGAAAT
140525 AAGTATTCTCAGTTTCAGCTATAAGATAAAGCTAAATATCGTCAAAATTGAGACAAAAAGACAAA
456 AAGTATTCTCAGTTTCAGCTATAAGATAAAGCTAAATATCGTCAAAATTGAGACAAAAAGACAAA
140590 AA
521 AA
140592 GATTTTTAGT
Statistics
Matches: 520, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
522 520 1.00
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.25
Consensus pattern (522 bp):
TCACTTACAGCAGGAAAAGCAAATTCAACTGAATAACTACAGAGGCTTCTTTCCTAATAATTACA
TTTCCTAAGAAGTTCTACTAAAGAACCAGGAAAAAATCAGAGAGACCGAGTAAGTTTCAGACTTT
TAGCTAAAAGATAAATTGAAATAATTGACTAATTGAGTGGAAAACAGAAAATTGAGCTAAATAGC
GTCAAAAGGAGTAAAAAAATTAAAAGAAATTCAGTTTCATTAAAATGATAGAGCTAAAGAGTCCA
TACTGAGTGAAAAACATAGATTTTCAGCTTCAGCTACACGATTAAGCTAAAGATCGTCAAATTAG
AGTGAAAAAAAAAGATTCACAGTTTCAGCTTTAAGATAGAGCTAAATAGCGTCAACACTGAGTGA
AAAACATATAGATTTTCAGATTCATCTAAACGATTAAGCTAAAAAGCGTTAAATTGGAGTGAAAT
AAGTATTCTCAGTTTCAGCTATAAGATAAAGCTAAATATCGTCAAAATTGAGACAAAAAGACAAA
AA
Found at i:140583 original size:120 final size:120
Alignment explanation
Indices: 140345--140583 Score: 291
Period size: 122 Copynumber: 2.0 Consensus size: 120
140335 AGTGAAAAAC
* * * *
140345 ATAGATTTTCAGCTTCAGCTACACGATTAAGCTAAAGATCGTCAAATTAGAGTGAAAAAAAAAGA
1 ATAGATTTTCAGATTCAGCTAAACGATTAAGCTAAAAAGCGTCAAATTAGAGTG--AAAAAAAGA
* * * * **
140410 TTCACAGTTTCAGCTTTATGATAGAGCTAAATAGCGTCAACACTGAGTGAAAAACAT
64 TTCACAGTTTCAGCTATAAGATAAAGCTAAATAGCGTCAAAACTGAGACAAAAACAT
* * * *
140467 ATAGATTTTCAGATTCATCTAAACGATTAAGCTAAAAAGCGTTAAATTGGAGTG-AAATAAGTAT
1 ATAGATTTTCAGATTCAGCTAAACGATTAAGCTAAAAAGCGTCAAATTAGAGTGAAAAAAAG-AT
* * *
140531 TCTCAGTTTCAGCTATAAGATAAAGCTAAATATCGTCAAAATTGAGACAAAAA
65 TCACAGTTTCAGCTATAAGATAAAGCTAAATAGCGTCAAAACTGAGACAAAAA
140584 GACAAAAAGA
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
119 6 0.06
120 46 0.46
122 47 0.47
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (120 bp):
ATAGATTTTCAGATTCAGCTAAACGATTAAGCTAAAAAGCGTCAAATTAGAGTGAAAAAAAGATT
CACAGTTTCAGCTATAAGATAAAGCTAAATAGCGTCAAAACTGAGACAAAAACAT
Found at i:140595 original size:122 final size:120
Alignment explanation
Indices: 140347--140611 Score: 282
Period size: 122 Copynumber: 2.2 Consensus size: 120
140337 TGAAAAACAT
* * * *
140347 AGATTTTCAGCTTCAGCTACACGATTAAGCTAAAGATCGTCAAATTAGAGTGAAAAAAAAAGATT
1 AGATTTTCAGATTCAGCTAAACGATTAAGCTAAAAAGCGTCAAATTAGAGTG--AAAAAAAGATT
* * * * ** * *
140412 CACAGTTTCAGCTTTATGATAGAGCTAAATAGCGTCAACACTGAGTGAAAAACATAT
64 CACAGTTTCAGCTATAAGATAAAGCTAAATAGCGTCAAAACTGAGCAAAAAACAAAA
* * * *
140469 AGATTTTCAGATTCATCTAAACGATTAAGCTAAAAAGCGTTAAATTGGAGTG-AAATAAGTATTC
1 AGATTTTCAGATTCAGCTAAACGATTAAGCTAAAAAGCGTCAAATTAGAGTGAAAAAAAG-ATTC
* * *
140533 TCAGTTTCAGCTATAAGATAAAGCTAAATATCGTCAAAATTGAGACAAAAAGACAAAA
65 ACAGTTTCAGCTATAAGATAAAGCTAAATAGCGTCAAAACTGAG-CAAAAA-ACAAAA
*
140591 AGATTTTTAG-TTACAGCTAAA
1 AGATTTTCAGATT-CAGCTAAA
140612 AGATAGAGCT
Statistics
Matches: 118, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
119 6 0.05
120 41 0.35
121 6 0.05
122 65 0.55
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (120 bp):
AGATTTTCAGATTCAGCTAAACGATTAAGCTAAAAAGCGTCAAATTAGAGTGAAAAAAAGATTCA
CAGTTTCAGCTATAAGATAAAGCTAAATAGCGTCAAAACTGAGCAAAAAACAAAA
Found at i:141111 original size:2 final size:2
Alignment explanation
Indices: 141104--141128 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
141094 AACCTGCAAA
141104 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
141129 TGGGGGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:155373 original size:17 final size:18
Alignment explanation
Indices: 155351--155400 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
155341 GTCATGTTCA
155351 ATTTTTAAAAAATA-TAT
1 ATTTTTAAAAAATATTAT
*
155368 ATTTTTAAATAAA-ATTTT
1 ATTTTTAAA-AAATATTAT
155386 ATTTTTGAAAAAATA
1 ATTTTT-AAAAAATA
155401 AAAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 10 0.36
18 14 0.50
19 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATTTTTAAAAAATATTAT
Found at i:155938 original size:21 final size:23
Alignment explanation
Indices: 155901--155970 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 23
155891 AGTTTTTGAG
*
155901 TTAATA-ATTAT-TATTTAAAAT
1 TTAATATATTATATTTTTAAAAT
**
155922 TTAA-ATA-TATATTTTTATTAT
1 TTAATATATTATATTTTTAAAAT
155943 TTAATATATTATAACTTTTTAATAAT
1 TTAATATATTAT-A-TTTTTAA-AAT
155969 TT
1 TT
155971 TTGTAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
20 4 0.11
21 16 0.43
22 3 0.08
23 3 0.08
24 1 0.03
25 6 0.16
26 4 0.11
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (23 bp):
TTAATATATTATATTTTTAAAAT
Found at i:165256 original size:112 final size:110
Alignment explanation
Indices: 165057--165269 Score: 408
Period size: 112 Copynumber: 1.9 Consensus size: 110
165047 GAAGATCGGC
165057 TTTAATAGCCATCCAATCACCTTAAGATTATTAATTATACAACGATCATCCCACCATAATTATTT
1 TTTAATAGCCATCCAATCACCTTAAGATTATTAATTATACAACGATCATCCCACCATAATTATTT
165122 TTGGGGTTAGGCACTGCAAACGATTTACTTTCTACTTTTTGAAGA
66 TTGGGGTTAGGCACTGCAAACGATTTACTTTCTACTTTTTGAAGA
165167 TTTAATAGCCATCCAATCACCTTAAGATTATTTAATTATACAACGATCATCCCACCATTAATTAT
1 TTTAATAGCCATCCAATCACCTTAAGATTA-TTAATTATACAACGATCATCCCACCA-TAATTAT
165232 TTTTGGGGTTAGGCACTGCAAACGATTTACTTTCTACT
64 TTTTGGGGTTAGGCACTGCAAACGATTTACTTTCTACT
165270 AAATGACTTA
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
110 30 0.30
111 26 0.26
112 45 0.45
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (110 bp):
TTTAATAGCCATCCAATCACCTTAAGATTATTAATTATACAACGATCATCCCACCATAATTATTT
TTGGGGTTAGGCACTGCAAACGATTTACTTTCTACTTTTTGAAGA
Found at i:167378 original size:12 final size:12
Alignment explanation
Indices: 167357--167399 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
167347 AGAAGAGAAG
167357 AGAA-AAAAACA
1 AGAAGAAAAACA
167368 AGAAGAAAAACA
1 AGAAGAAAAACA
*
167380 AGAAGAAAAAGA
1 AGAAGAAAAACA
167392 AGAAGAAA
1 AGAAGAAA
167400 GAGGTAGGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 4 0.13
12 26 0.87
ACGTcount: A:0.77, C:0.05, G:0.19, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAACA
Found at i:167902 original size:20 final size:20
Alignment explanation
Indices: 167879--167928 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
167869 GCAAAAGTTG
167879 ATTTTGAAAATCAAAATGAA
1 ATTTTGAAAATCAAAATGAA
167899 ATTTTGAAAATCAAAATGAA
1 ATTTTGAAAATCAAAATGAA
167919 ATTTTGAAAA
1 ATTTTGAAAA
167929 ATAATTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.32
Consensus pattern (20 bp):
ATTTTGAAAATCAAAATGAA
Found at i:169506 original size:20 final size:21
Alignment explanation
Indices: 169465--169515 Score: 95
Period size: 20 Copynumber: 2.5 Consensus size: 21
169455 CACTTAGGGA
169465 ACCGATTCCCTATGAGGGGGT
1 ACCGATTCCCTATGAGGGGGT
169486 ACCGATTCCCTATGA-GGGGT
1 ACCGATTCCCTATGAGGGGGT
169506 ACCGATTCCC
1 ACCGATTCCC
169516 CCCACGCTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.24
Consensus pattern (21 bp):
ACCGATTCCCTATGAGGGGGT
Found at i:169575 original size:21 final size:20
Alignment explanation
Indices: 169549--169604 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
169539 AATTGATTCT
169549 CATCCCTAAACGGCTCCAAAA
1 CATCCC-AAACGGCTCCAAAA
* *
169570 CATCCCCAAACAGCTTCAAAA
1 CAT-CCCAAACGGCTCCAAAA
*
169591 CATCCCCAACGGCT
1 CATCCCAAACGGCT
169605 ATATACGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 9 0.30
21 18 0.60
22 3 0.10
ACGTcount: A:0.36, C:0.41, G:0.09, T:0.14
Consensus pattern (20 bp):
CATCCCAAACGGCTCCAAAA
Found at i:170114 original size:24 final size:24
Alignment explanation
Indices: 170056--170115 Score: 95
Period size: 23 Copynumber: 2.5 Consensus size: 24
170046 TCCCTAAACA
170056 CAAAACCGTTCCGACTCCTCTTTG
1 CAAAACCGTTCCGACTCCTCTTTG
*
170080 C-AAACCATTCCGACTCCTCTTTG
1 CAAAACCGTTCCGACTCCTCTTTG
*
170103 CAAAACTGTTCCG
1 CAAAACCGTTCCG
170116 CTTGTCGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.23, C:0.37, G:0.12, T:0.28
Consensus pattern (24 bp):
CAAAACCGTTCCGACTCCTCTTTG
Done.