Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 16 of 64
Found at i:2088206 original size:28 final size:26
Alignment explanation
Indices: 2088144--2088212 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
2088134 ATCCCTACTC
*
2088144 ATATATATAATATATTATATATATAT
1 ATATATATTATATATTATATATATAT
* * *
2088170 ATGTTTATTATATATTATATATAATGT
1 ATATATATTATATATTATATAT-ATAT
*
2088197 AATATCTATTATATAT
1 -ATATATATTATATAT
2088213 ATGCAAAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 19 0.54
27 3 0.09
28 13 0.37
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (26 bp):
ATATATATTATATATTATATATATAT
Found at i:2090062 original size:14 final size:13
Alignment explanation
Indices: 2090028--2090066 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2090018 TAATTTTTGA
*
2090028 AAAAATTAAAATT
1 AAAAATTAAAAGT
2090041 AAAAATTAAAAGT
1 AAAAATTAAAAGT
*
2090054 AATACATTAAAAG
1 AA-AAATTAAAAG
2090067 GTTTAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (13 bp):
AAAAATTAAAAGT
Found at i:2096120 original size:30 final size:30
Alignment explanation
Indices: 2096086--2096144 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2096076 CATTTGAACC
2096086 TTAAATATTTATTTTCA-TCTAATTAAATTT
1 TTAAATATTTATTTTCACTC-AATTAAATTT
2096116 TTAAATATTTATTTTCACTCAATTAAATT
1 TTAAATATTTATTTTCACTCAATTAAATT
2096145 ATAAATTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.54
Consensus pattern (30 bp):
TTAAATATTTATTTTCACTCAATTAAATTT
Found at i:2096441 original size:11 final size:11
Alignment explanation
Indices: 2096427--2096456 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2096417 AATTATATAA
2096427 TTTATTTTATT
1 TTTATTTTATT
*
2096438 TTTAATTTATT
1 TTTATTTTATT
2096449 TTTATTTT
1 TTTATTTT
2096457 TAAAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:2096445 original size:16 final size:17
Alignment explanation
Indices: 2096424--2096459 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2096414 AATAATTATA
2096424 TAATTTA-TTTTATTTT
1 TAATTTATTTTTATTTT
2096440 TAATTTATTTTTATTTT
1 TAATTTATTTTTATTTT
2096457 TAA
1 TAA
2096460 AAATATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TAATTTATTTTTATTTT
Found at i:2096474 original size:135 final size:137
Alignment explanation
Indices: 2096293--2096570 Score: 447
Period size: 135 Copynumber: 2.0 Consensus size: 137
2096283 TACCTTTTTA
2096293 TATTTTATTTTTAATTAATTTTTTATTTTTAAAAATATATTTGAAAGGATATGTGTCATTTTTTT
1 TATTTTATTTTTAATTAATTTTTTATTTTTAAAAATATATTTGAAAGGATATGTGTCATTTTTTT
*
2096358 AATTTT-TCTTGAGAAATTTAAAATTTTCACTAATAAAAAA-TGAAAAAA-ATTATAATAATAAT
66 AATTTTGT-TTGAGAAATTTAAAAATTTCACTAATAAAAAATTGAAAAAAGATTATAATAATAAT
*
2096420 TATATAATT
130 CATAT-ATT
*
2096429 TATTTTATTTTTAATTTA-TTTTTATTTTTAAAAATATATTTGAAAGGATATGTGTCATTTTTTT
1 TATTTTATTTTTAATTAATTTTTTATTTTTAAAAATATATTTGAAAGGATATGTGTCATTTTTTT
* * *
2096493 AATTTTGTTTGTGAAATTTAAAAATTTCACTAATAAAAAATTGAAAAAAGCTTTTAATAATAATC
66 AATTTTGTTTGAGAAATTTAAAAATTTCACTAATAAAAAATTGAAAAAAGATTATAATAATAATC
2096558 ATATATT
131 ATATATT
*
2096565 TTTTTT
1 TATTTT
2096571 GGTCAAAGTA
Statistics
Matches: 132, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
135 82 0.62
136 34 0.26
137 16 0.12
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (137 bp):
TATTTTATTTTTAATTAATTTTTTATTTTTAAAAATATATTTGAAAGGATATGTGTCATTTTTTT
AATTTTGTTTGAGAAATTTAAAAATTTCACTAATAAAAAATTGAAAAAAGATTATAATAATAATC
ATATATT
Found at i:2097252 original size:21 final size:21
Alignment explanation
Indices: 2097222--2097267 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
2097212 TTTTTAATTT
2097222 TTTA-ATTTTAAAACA-TTTAA
1 TTTATATTTTAAAA-ATTTTAA
2097242 TTTATATTTTAAAAATTTTAA
1 TTTATATTTTAAAAATTTTAA
2097263 TTTAT
1 TTTAT
2097268 TTATTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATATTTTAAAAATTTTAA
Found at i:2097254 original size:45 final size:45
Alignment explanation
Indices: 2097191--2097277 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
2097181 AAAAATATCT
*
2097191 ATTTAATAAATATATTAAAATTTTTTAATTT-TTTAATTTTAAAAC
1 ATTTAATAAATATATTAAAA-ATTTTAATTTATTTAATTTTAAAAC
** * *
2097236 ATTTAATTTATATTTTAAAAATTTTAATTTATTTATTTTTAA
1 ATTTAATAAATATATTAAAAATTTTAATTTATTTAATTTTAA
2097278 TAAAAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 9 0.25
45 27 0.75
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (45 bp):
ATTTAATAAATATATTAAAAATTTTAATTTATTTAATTTTAAAAC
Found at i:2100845 original size:46 final size:45
Alignment explanation
Indices: 2100760--2101005 Score: 208
Period size: 46 Copynumber: 5.6 Consensus size: 45
2100750 TCATAACTTT
*
2100760 TTAAAAGGCTTATCTCATTAGAGGCTCTACAACTATTGAAAATAAAA
1 TTAAAA-GCTTATCTCATTAGAGGCTCT-CAACTTTTGAAAATAAAA
* * *
2100807 TTAAAAGCTTATCTCATTAAAGGCCCCTTAACTTTTGAAAATAAAA
1 TTAAAAGCTTATCTCATTAGAGG-CTCTCAACTTTTGAAAATAAAA
* * *
2100853 TTAAAAACTTCTCTCATTAGAGG-TATCATAACTTTT-----T---A
1 TTAAAAGCTTATCTCATTAGAGGCTCTC--AACTTTTGAAAATAAAA
* *
2100891 --AAAGGCTTATCTCATTAGAGGCTCTACAACTATTGAAAATAAAA
1 TTAAAAGCTTATCTCATTAGAGGCTCT-CAACTTTTGAAAATAAAA
* *
2100935 TTAAAAGCTTATCTCATTAAAGGCCCCTCAACTTTTGAAAATAAAA
1 TTAAAAGCTTATCTCATTAGAGG-CTCTCAACTTTTGAAAATAAAA
* * ** *
2100981 TAAAAAACTCCTCTCACTAGAGGCT
1 TTAAAAGCTTATCTCATTAGAGGCT
2101006 TGACAACTTT
Statistics
Matches: 157, Mismatches: 26, Indels: 34
0.72 0.12 0.16
Matches are distributed among these distances:
36 24 0.15
37 2 0.01
38 2 0.01
41 2 0.01
44 2 0.01
45 1 0.01
46 112 0.71
47 12 0.08
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (45 bp):
TTAAAAGCTTATCTCATTAGAGGCTCTCAACTTTTGAAAATAAAA
Found at i:2100970 original size:82 final size:81
Alignment explanation
Indices: 2100807--2100957 Score: 205
Period size: 82 Copynumber: 1.9 Consensus size: 81
2100797 GAAAATAAAA
* * *
2100807 TTAAAAGCTTATCTCATTAAAGGCCCCTTAACTTTTGAAAATAAAATTAAAAACTTCTCTCATTA
1 TTAAAAGCTTATCTCATTAAAGGCCCCTCAACTATTGAAAATAAAATTAAAAACTTATCTCATTA
* *
2100872 GAGGTATCATAACTTT
66 AAGGTACCATAACTTT
* * *
2100888 TTAAAAGGCTTATCTCATTAGAGG-CTCTACAACTATTGAAAATAAAATTAAAAGCTTATCTCAT
1 TTAAAA-GCTTATCTCATTAAAGGCCCCT-CAACTATTGAAAATAAAATTAAAAACTTATCTCAT
2100952 TAAAGG
64 TAAAGG
2100958 CCCCTCAACT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 9 0.15
82 52 0.85
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.34
Consensus pattern (81 bp):
TTAAAAGCTTATCTCATTAAAGGCCCCTCAACTATTGAAAATAAAATTAAAAACTTATCTCATTA
AAGGTACCATAACTTT
Found at i:2101015 original size:128 final size:128
Alignment explanation
Indices: 2100725--2101003 Score: 522
Period size: 128 Copynumber: 2.2 Consensus size: 128
2100715 TTTTAATTTC
2100725 TAAAAAACTCCTCTCATTAGAGGTATCATAACTTTTTAAAAGGCTTATCTCATTAGAGGCTCTAC
1 TAAAAAACTCCTCTCATTAGAGGTATCATAACTTTTTAAAAGGCTTATCTCATTAGAGGCTCTAC
*
2100790 AACTATTGAAAATAAAATTAAAAGCTTATCTCATTAAAGGCCCCTTAACTTTTGAAAATAAAA
66 AACTATTGAAAATAAAATTAAAAGCTTATCTCATTAAAGGCCCCTCAACTTTTGAAAATAAAA
* *
2100853 TTAAAAACTTCTCTCATTAGAGGTATCATAACTTTTTAAAAGGCTTATCTCATTAGAGGCTCTAC
1 TAAAAAACTCCTCTCATTAGAGGTATCATAACTTTTTAAAAGGCTTATCTCATTAGAGGCTCTAC
2100918 AACTATTGAAAATAAAATTAAAAGCTTATCTCATTAAAGGCCCCTCAACTTTTGAAAATAAAA
66 AACTATTGAAAATAAAATTAAAAGCTTATCTCATTAAAGGCCCCTCAACTTTTGAAAATAAAA
*
2100981 TAAAAAACTCCTCTCACTAGAGG
1 TAAAAAACTCCTCTCATTAGAGG
2101004 CTTGACAACT
Statistics
Matches: 145, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 145 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (128 bp):
TAAAAAACTCCTCTCATTAGAGGTATCATAACTTTTTAAAAGGCTTATCTCATTAGAGGCTCTAC
AACTATTGAAAATAAAATTAAAAGCTTATCTCATTAAAGGCCCCTCAACTTTTGAAAATAAAA
Found at i:2101061 original size:49 final size:48
Alignment explanation
Indices: 2101001--2101305 Score: 223
Period size: 50 Copynumber: 6.1 Consensus size: 48
2100991 CTCTCACTAG
* *
2101001 AGGCTTGACAACTTTAAAAATCTTATCTTAAAAAGCTCCTTTAAATAAA
1 AGGCTCGACAACTTTAAAAATCTTATCTTAAAAAGCTCCTTTAAA-CAA
* ** *
2101050 AGGCTCGACAACTTTAAAAATCCTTATATTAAAAAATTCCTTTAAATAA
1 AGGCTCGACAACTTTAAAAAT-CTTATCTTAAAAAGCTCCTTTAAACAA
* * ** * * * *
2101099 AAGCTCGATAACTTTAAAAATAATGTCTTGGGAAAAGCTTCTTTAAACAT
1 AGGCTCGACAACTTTAAAAATCTTATCTT--AAAAAGCTCCTTTAAACAA
* * * * * *
2101149 AGACTCAACAACTTTAAAAATTTTGTCTTGGGAAAAGCTCTTTTAAACAA
1 AGGCTCGACAACTTTAAAAATCTTATCTT--AAAAAGCTCCTTTAAACAA
* * * * *
2101199 AGGCTTGACAACTTTAAAAAAATCTCATCCTAAGAAGAGCTCATTTAAATAA
1 AGGCTCGACAACTTT--AAAAATCTTATCTTAA-AA-AGCTCCTTTAAACAA
* ** * * * *
2101251 AGGTTTAACAACTTTAAAAATCCTAATATCAAAAAACTCCTTTAAACAA
1 AGGCTCGACAACTTTAAAAAT-CTTATCTTAAAAAGCTCCTTTAAACAA
2101300 AGGCTC
1 AGGCTC
2101306 TCATTTAAAT
Statistics
Matches: 201, Mismatches: 47, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
48 4 0.02
49 57 0.28
50 96 0.48
51 8 0.04
52 36 0.18
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (48 bp):
AGGCTCGACAACTTTAAAAATCTTATCTTAAAAAGCTCCTTTAAACAA
Found at i:2101095 original size:50 final size:49
Alignment explanation
Indices: 2101001--2101119 Score: 177
Period size: 49 Copynumber: 2.4 Consensus size: 49
2100991 CTCTCACTAG
* * *
2101001 AGGCTTGACAACTTTAAAAATCTTATCTTAAAAAGCTCCTTTAAATAAA
1 AGGCTCGACAACTTTAAAAATCTTATATTAAAAAACTCCTTTAAATAAA
*
2101050 AGGCTCGACAACTTTAAAAATCCTTATATTAAAAAATTCCTTTAAATAAA
1 AGGCTCGACAACTTTAAAAAT-CTTATATTAAAAAACTCCTTTAAATAAA
*
2101100 A-GCTCGATAACTTTAAAAAT
1 AGGCTCGACAACTTTAAAAAT
2101120 AATGTCTTGG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
49 38 0.59
50 26 0.41
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (49 bp):
AGGCTCGACAACTTTAAAAATCTTATATTAAAAAACTCCTTTAAATAAA
Found at i:2101309 original size:67 final size:66
Alignment explanation
Indices: 2101238--2101370 Score: 187
Period size: 67 Copynumber: 2.0 Consensus size: 66
2101228 CTAAGAAGAG
* *
2101238 CTCATTTAAATAAAGGTTTAACAACTTTAAAAATCCTAA-TATCAAAAAACTCCTTTAAACAAAG
1 CTCATTTAAATAAAGGCTTAACAACTTTAAAAATCCTAACT-T-AAAAAACTCATTTAAACAAAG
2101302 GCT
64 GCT
** * *
2101305 CTCATTTAAATAAAGGCTTGGCAACTTTAAAAATCCTAACTTAAAAAGCTTATTTAAACAAAGGC
1 CTCATTTAAATAAAGGCTTAACAACTTTAAAAATCCTAACTTAAAAAACTCATTTAAACAAAGGC
2101370 T
66 T
2101371 TGATAACTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
66 21 0.36
67 37 0.63
68 1 0.02
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.30
Consensus pattern (66 bp):
CTCATTTAAATAAAGGCTTAACAACTTTAAAAATCCTAACTTAAAAAACTCATTTAAACAAAGGC
T
Found at i:2101917 original size:15 final size:15
Alignment explanation
Indices: 2101883--2101930 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
2101873 TTCTTTTCCA
* *
2101883 TTTTTCCTTATTATT
1 TTTTTCCTTTTTTTT
*
2101898 CTTTT-CTTTTCTTTT
1 TTTTTCCTTTT-TTTT
2101913 TTTTTCCTTTTTTTT
1 TTTTTCCTTTTTTTT
2101928 TTT
1 TTT
2101931 CATTTATCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 4 0.15
15 18 0.67
16 5 0.19
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTCCTTTTTTTT
Found at i:2101925 original size:23 final size:23
Alignment explanation
Indices: 2101899--2101946 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2101889 CTTATTATTC
* * *
2101899 TTTTCTTTTCTTTTTTTTTCCTT
1 TTTTCTTTTCATTTATCTTCCTT
*
2101922 TTTTTTTTTCATTTATCTTCCTT
1 TTTTCTTTTCATTTATCTTCCTT
2101945 TT
1 TT
2101947 ATTTTTGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTCTTTTCATTTATCTTCCTT
Found at i:2102541 original size:12 final size:12
Alignment explanation
Indices: 2102524--2102588 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
2102514 AATTTAGGCC
2102524 TTTTTTTTCATT
1 TTTTTTTTCATT
**
2102536 TTTTTTATTTTTGT
1 TTTTTT-TTCAT-T
**
2102550 TTTTGTTTTTGTT
1 TTTT-TTTTCATT
*
2102563 TTTGTTTTCATT
1 TTTTTTTTCATT
2102575 TTTTTTTT-ATT
1 TTTTTTTTCATT
2102586 TTT
1 TTT
2102589 GCTTGCTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
11 6 0.14
12 19 0.44
13 7 0.16
14 9 0.21
15 2 0.05
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.85
Consensus pattern (12 bp):
TTTTTTTTCATT
Found at i:2102546 original size:18 final size:18
Alignment explanation
Indices: 2102525--2102613 Score: 58
Period size: 20 Copynumber: 4.7 Consensus size: 18
2102515 ATTTAGGCCT
2102525 TTTTTTTCATTTTTTTTA
1 TTTTTTTCATTTTTTTTA
* *
2102543 TTTTTGTT-TTTGTTTTTGTT
1 TTTTT-TTCATT-TTTTT-TA
2102563 TTTGTTTTCATTTTTTTT-
1 TTT-TTTTCATTTTTTTTA
2102581 TTATTTTTGC-TTGCTTTTTTA
1 TT-TTTTT-CATT--TTTTTTA
*
2102602 TTTTTTTTATTT
1 TTTTTTTCATTT
2102614 CTCTTCACTT
Statistics
Matches: 56, Mismatches: 4, Indels: 22
0.68 0.05 0.27
Matches are distributed among these distances:
18 16 0.29
19 10 0.18
20 24 0.43
21 6 0.11
ACGTcount: A:0.07, C:0.04, G:0.07, T:0.82
Consensus pattern (18 bp):
TTTTTTTCATTTTTTTTA
Found at i:2102606 original size:6 final size:6
Alignment explanation
Indices: 2102537--2102589 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
2102527 TTTTTCATTT
* ** *
2102537 TTTTTA TTTTTG TTTTTG TTTTTG TTTTTG TTTTCA TTTTT- TTTTTA
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
2102584 TTTTTG
1 TTTTTG
2102590 CTTGCTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
5 5 0.12
6 36 0.88
ACGTcount: A:0.06, C:0.02, G:0.09, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:2102624 original size:27 final size:26
Alignment explanation
Indices: 2102573--2102631 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
2102563 TTTGTTTTCA
* *
2102573 TTTTTTTTTTATTTTTGCTTGCTTTT
1 TTTTTTTTTTATTTCTGCTTACTTTT
2102599 TTATTTTTTTTATTTCT-CTTCACTTTT
1 TT-TTTTTTTTATTTCTGCTT-ACTTTT
2102626 TTTTTT
1 TTTTTT
2102632 GGGTTTCAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 9 0.31
27 20 0.69
ACGTcount: A:0.07, C:0.10, G:0.03, T:0.80
Consensus pattern (26 bp):
TTTTTTTTTTATTTCTGCTTACTTTT
Found at i:2115024 original size:143 final size:144
Alignment explanation
Indices: 2114592--2115014 Score: 552
Period size: 143 Copynumber: 3.0 Consensus size: 144
2114582 TAGGGAATAT
* * * * * *
2114592 TTTTATAATTTGGCC-TTCTTGAGCTCAAATTTTTATGAAACTTTTTATATCTTAATTTCATAAT
1 TTTTGTAATTT-GCCTTTCTCGAGCTCAAATTTTCATGAAACTTTTTAGATATTAATTTCATAGT
* * * * *
2114656 ATTTCATGATTTTTAGTGCATTTGAAATCATAATAATACCC-AAAAAATGTGAAATTA-TCAAAA
65 ATTTCATGATTTTTGGTGCATTTGAAATCATAGTAATACCCTAGAAAGTGTGAAAATACT-AAAA
*
2114719 TATCCCTATAAAGGTA
129 TACCCCTATAAAGGTA
* * * * *
2114735 TTTTGTAATTTGCTTTTCTCGAGCTCGAATTTTCATGAACCTTTTTAGATATTAATTTTATAGTT
1 TTTTGTAATTTGCCTTTCTCGAGCTCAAATTTTCATGAAACTTTTTAGATATTAATTTCATAGTA
* *
2114800 TTTCATGATTTTTGGTGCATTTGAAATCATAGTAATA-CCTTGAAAAGT-TTAAAATTACTAAAA
66 TTTCATGATTTTTGGTGCATTTGAAATCATAGTAATACCCTAG-AAAGTGTGAAAA-TACTAAAA
2114863 TACCCCTATAAAGGTA
129 TACCCCTATAAAGGTA
* * *
2114879 TTTTGTAATTTGCCTTTCTCGAGCTTAAATTTTCATGAAAC-TTTAAGATGTTAATTTCATAGTA
1 TTTTGTAATTTGCCTTTCTCGAGCTCAAATTTTCATGAAACTTTTTAGATATTAATTTCATAGTA
* *
2114943 TTTCATGATTTTTGGTGTATTTGAAATCATAGTAATACCCTAGGAAGTGTGAAAATACTAAAATA
66 TTTCATGATTTTTGGTGCATTTGAAATCATAGTAATACCCTAGAAAGTGTGAAAATACTAAAATA
2115008 CCCCTAT
131 CCCCTAT
2115015 TTGAGTATTT
Statistics
Matches: 242, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
142 4 0.02
143 166 0.69
144 71 0.29
145 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (144 bp):
TTTTGTAATTTGCCTTTCTCGAGCTCAAATTTTCATGAAACTTTTTAGATATTAATTTCATAGTA
TTTCATGATTTTTGGTGCATTTGAAATCATAGTAATACCCTAGAAAGTGTGAAAATACTAAAATA
CCCCTATAAAGGTA
Found at i:2123616 original size:20 final size:20
Alignment explanation
Indices: 2123593--2123631 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2123583 TTAAATTTAG
*
2123593 GGTTTGTGATTTAGGGTTTT
1 GGTTTGGGATTTAGGGTTTT
*
2123613 GGTTTGGGATTTGGGGTTT
1 GGTTTGGGATTTAGGGTTT
2123632 AAGGTTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.41, T:0.51
Consensus pattern (20 bp):
GGTTTGGGATTTAGGGTTTT
Found at i:2123670 original size:7 final size:7
Alignment explanation
Indices: 2123588--2123769 Score: 75
Period size: 7 Copynumber: 27.4 Consensus size: 7
2123578 AGGGTTTAAA
2123588 TTTAGGG
1 TTTAGGG
*
2123595 TTT-GTGA
1 TTTAG-GG
2123602 TTTAGGG
1 TTTAGGG
*
2123609 TTT-TGG
1 TTTAGGG
2123615 TTT-GGG
1 TTTAGGG
*
2123621 ATTTGGGG
1 -TTTAGGG
*
2123629 TTTAAGG
1 TTTAGGG
2123636 TTTA-GG
1 TTTAGGG
*
2123642 TTT-GGA
1 TTTAGGG
2123648 TTTAGGG
1 TTTAGGG
* *
2123655 -CTCGGG
1 TTTAGGG
2123661 TTTAGGG
1 TTTAGGG
*
2123668 TTT-GGA
1 TTTAGGG
*
2123674 TTTTGGG
1 TTTAGGG
**
2123681 TTTAGCA
1 TTTAGGG
2123688 TTTA-GG
1 TTTAGGG
2123694 TTT-GGG
1 TTTAGGG
2123700 TTTAGGG
1 TTTAGGG
*
2123707 TTT-GGA
1 TTTAGGG
*
2123713 TTTGGGG
1 TTTAGGG
* *
2123720 TTT-TGC
1 TTTAGGG
2123726 TTTAGGG
1 TTTAGGG
*
2123733 TTTAAGG
1 TTTAGGG
*
2123740 TTT-GGA
1 TTTAGGG
*
2123746 TTTTGGG
1 TTTAGGG
*
2123753 TTT-GAAG
1 TTTAG-GG
2123760 TTTAGGG
1 TTTAGGG
2123767 TTT
1 TTT
2123770 CATGGGAAAT
Statistics
Matches: 129, Mismatches: 31, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
6 48 0.37
7 76 0.59
8 5 0.04
ACGTcount: A:0.13, C:0.02, G:0.37, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:2123681 original size:13 final size:13
Alignment explanation
Indices: 2123613--2123735 Score: 99
Period size: 13 Copynumber: 9.4 Consensus size: 13
2123603 TTAGGGTTTT
*
2123613 GGTTTGGGATTTGG
1 GGTTT-GGATTTAG
2123627 GGTTTAAGG-TTTA-
1 GGTTT--GGATTTAG
2123640 GGTTTGGATTTAG
1 GGTTTGGATTTAG
* * *
2123653 GGCTCGGGTTTAG
1 GGTTTGGATTTAG
*
2123666 GGTTTGGATTTTG
1 GGTTTGGATTTAG
*
2123679 GGTTTAGCATTTA-
1 GGTTT-GGATTTAG
*
2123692 GGTTTGGGTTTAG
1 GGTTTGGATTTAG
*
2123705 GGTTTGGATTTGG
1 GGTTTGGATTTAG
* *
2123718 GGTTTTGCTTTAG
1 GGTTTGGATTTAG
2123731 GGTTT
1 GGTTT
2123736 AAGGTTTGGA
Statistics
Matches: 86, Mismatches: 18, Indels: 11
0.75 0.16 0.10
Matches are distributed among these distances:
11 2 0.02
12 9 0.10
13 60 0.70
14 13 0.15
15 2 0.02
ACGTcount: A:0.11, C:0.03, G:0.39, T:0.46
Consensus pattern (13 bp):
GGTTTGGATTTAG
Found at i:2123682 original size:52 final size:52
Alignment explanation
Indices: 2123613--2123742 Score: 145
Period size: 52 Copynumber: 2.5 Consensus size: 52
2123603 TTAGGGTTTT
* *
2123613 GGTTTGGGATTTGGGGTTTAAGGTTTAGGTTTGGATTTAGGGCTCGGGTTTAG
1 GGTTT-GGATTTAGGGTTTAAGGTTTAGGTTTGGATTTAGGGCTCGGATTTAG
* * * * * *
2123666 GGTTTGGATTTTGGGTTT-AGCATTTAGGTTTGGGTTTAGGGTTTGGATTTGG
1 GGTTTGGATTTAGGGTTTAAG-GTTTAGGTTTGGATTTAGGGCTCGGATTTAG
* *
2123718 GGTTTTGCTTTAGGGTTTAAGGTTT
1 GGTTTGGATTTAGGGTTTAAGGTTT
2123743 GGATTTTGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
51 2 0.03
52 55 0.86
53 7 0.11
ACGTcount: A:0.12, C:0.03, G:0.38, T:0.46
Consensus pattern (52 bp):
GGTTTGGATTTAGGGTTTAAGGTTTAGGTTTGGATTTAGGGCTCGGATTTAG
Found at i:2123695 original size:26 final size:25
Alignment explanation
Indices: 2123602--2123742 Score: 104
Period size: 26 Copynumber: 5.4 Consensus size: 25
2123592 GGGTTTGTGA
* *
2123602 TTTAGGGTTTTGGTTTGGGATTTGGGG
1 TTTA-GGTTTAGGTTT-GGATTTAGGG
2123629 TTTAAGGTTTAGGTTTGGATTTAGGG
1 TTT-AGGTTTAGGTTTGGATTTAGGG
* ** *
2123655 CTCGGGTTTAGGGTTTGGATTTTGGG
1 TTTAGGTTTA-GGTTTGGATTTAGGG
* *
2123681 TTTAGCATTTAGGTTTGGGTTTAGGG
1 TTTAG-GTTTAGGTTTGGATTTAGGG
* * *
2123707 TTT-GGATTTGGGGTTTTGCTTTAGGG
1 TTTAGG-TTT-AGGTTTGGATTTAGGG
2123733 TTTAAGGTTT
1 TTT-AGGTTT
2123743 GGATTTTGGG
Statistics
Matches: 91, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
25 10 0.11
26 58 0.64
27 20 0.22
28 3 0.03
ACGTcount: A:0.12, C:0.03, G:0.38, T:0.48
Consensus pattern (25 bp):
TTTAGGTTTAGGTTTGGATTTAGGG
Found at i:2123735 original size:39 final size:40
Alignment explanation
Indices: 2123647--2123735 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 40
2123637 TTAGGTTTGG
* * *
2123647 ATTTAGGGCTCGGGTTTAGGGTTTGGATTTTGGGTTTAGC
1 ATTTAGGGTTTGGGTTTAGGGTTTGGATTTGGGGTTTAGC
*
2123687 ATTTA-GGTTTGGGTTTAGGGTTTGGATTTGGGGTTTTGC
1 ATTTAGGGTTTGGGTTTAGGGTTTGGATTTGGGGTTTAGC
2123726 -TTTAGGGTTT
1 ATTTAGGGTTT
2123736 AAGGTTTGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 4 0.09
39 35 0.80
40 5 0.11
ACGTcount: A:0.11, C:0.04, G:0.37, T:0.47
Consensus pattern (40 bp):
ATTTAGGGTTTGGGTTTAGGGTTTGGATTTGGGGTTTAGC
Found at i:2124732 original size:16 final size:15
Alignment explanation
Indices: 2124707--2124736 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2124697 AAATTTGAAG
2124707 AAAAAATATAAATTC
1 AAAAAATATAAATTC
2124722 AAAAAACTATAAATT
1 AAAAAA-TATAAATT
2124737 TTCTCAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAAATATAAATTC
Found at i:2126339 original size:49 final size:48
Alignment explanation
Indices: 2126262--2126773 Score: 489
Period size: 49 Copynumber: 10.5 Consensus size: 48
2126252 GCTAAAAATT
* *
2126262 TTTAAAAA-CTCATTTTGAAAAGGCTCCTATAAACATAAGCTAGGGAAC
1 TTTAAAAATCTCATTTTGAAAAGGCTCCTATAAAAAT-AGGTAGGGAAC
* * * *
2126310 TTTAAAAATCTCATTTTGAAATGGGTCCTATAAACATAGGTAGCGAAC
1 TTTAAAAATCTCATTTTGAAAAGGCTCCTATAAAAATAGGTAGGGAAC
* *
2126358 TTTAAAAATCTCATTTTGAAATAGGCTCTTACAAAAATAGGTGAGGG-AC
1 TTTAAAAATCTCATTTTGAAA-AGGCTCCTATAAAAATAGGT-AGGGAAC
* * * * ** *
2126407 TTT-TAAATTTCATTTTGAAATGGGCTCTTATAAAAATAAGCAAGGAAAC
1 TTTAAAAATCTCATTTTGAAA-AGGCTCCTATAAAAAT-AGGTAGGGAAC
* * *
2126456 TTTAAAATTCTCATTTTTGAAAAGGGCTTCTACAAAAATAGGTAGGGAAC
1 TTTAAAAATCTCA-TTTTGAAAA-GGCTCCTATAAAAATAGGTAGGGAAC
* * * *
2126506 TCTAAAAGTCTCACTTTGAAAATGAG-TCCTATAAAAATAGGTAAAGG-AC
1 TTTAAAAATCTCATTTTGAAAA-G-GCTCCTATAAAAATAGGT-AGGGAAC
* * ***
2126555 TTTAAAATTCTCATTTTGAAAAGGACTCCTACAAAAATAGACGGGGAAC
1 TTTAAAAATCTCATTTTGAAAAGG-CTCCTATAAAAATAGGTAGGGAAC
* * * * *
2126604 TATAAAAGT-TCATTTTGAAAAAGGTTCCTATAAAAATAGGTAAGAAAC
1 TTTAAAAATCTCATTTTG-AAAAGGCTCCTATAAAAATAGGTAGGGAAC
* *
2126652 TTTAAAAATCTCATTTTTGAAAAAGGCTTCTAGAAAAATAGGTAGGGAAC
1 TTTAAAAATCTCA-TTTTG-AAAAGGCTCCTATAAAAATAGGTAGGGAAC
* * *
2126702 TTTAAAAATCTCATTTTGTAAAAGGCTCTTATAAAAATAGATCA-AGAAC
1 TTTAAAAATCTCATTTTG-AAAAGGCTCCTATAAAAATAGGT-AGGGAAC
*
2126751 TTTAAAAATCACATTTTGAAAAG
1 TTTAAAAATCTCATTTTGAAAAG
2126774 TAGTTTGATT
Statistics
Matches: 382, Mismatches: 65, Indels: 34
0.79 0.14 0.07
Matches are distributed among these distances:
47 1 0.00
48 111 0.29
49 173 0.45
50 77 0.20
51 20 0.05
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (48 bp):
TTTAAAAATCTCATTTTGAAAAGGCTCCTATAAAAATAGGTAGGGAAC
Found at i:2126691 original size:196 final size:195
Alignment explanation
Indices: 2126262--2126773 Score: 624
Period size: 196 Copynumber: 2.6 Consensus size: 195
2126252 GCTAAAAATT
* * * *
2126262 TTTAAAAA-CTCA-TTTTG-AAAAGGCTCCTATAAACATAAGCTAGGGAACTTTAAAAATCTCAT
1 TTTAAAAATCTCATTTTTGAAAAAGGCTTCTACAAAAAT-AGGTAGGGAACTTTAAAAATCTCAT
* ** *
2126324 TTTG-AAATGGGTCCTATAAACATAGGTAGCGAACTTTAAAAATCTCATTTTGAAATAGGCTCTT
65 TTTGAAAAT-GGTCCTATAAAAATAGGTAAAGAACTTTAAAAATCTCATTTTGAAA-AGGCTCCT
** * * * ** *
2126388 ACAAAAATAGGTGAGGGACTTTTAAATTTCATTTTGAAATGGGCTCTTATAAAAATAAGCAAGGA
128 ACAAAAATAGACGAGGGACTATAAAAGTTCATTTTGAAAAAGGCTCCTATAAAAATAAGCAAGGA
2126453 AAC
193 AAC
* * * * *
2126456 TTTAAAATTCTCATTTTTGAAAAGGGCTTCTACAAAAATAGGTAGGGAACTCTAAAAGTCTCACT
1 TTTAAAAATCTCATTTTTGAAAAAGGCTTCTACAAAAATAGGTAGGGAACTTTAAAAATCTCATT
* *
2126521 TTGAAAATGAGTCCTATAAAAATAGGTAAAGGACTTTAAAATTCTCATTTTGAAAAGGACTCCTA
66 TTGAAAATG-GTCCTATAAAAATAGGTAAAGAACTTTAAAAATCTCATTTTGAAAAGG-CTCCTA
* * *
2126586 CAAAAATAGACG-GGGAACTATAAAAGTTCATTTTGAAAAAGGTTCCTATAAAAATAGGTAA-GA
129 CAAAAATAGACGAGGG-ACTATAAAAGTTCATTTTGAAAAAGGCTCCTATAAAAATAAGCAAGGA
2126649 AAC
193 AAC
*
2126652 TTTAAAAATCTCATTTTTGAAAAAGGCTTCTAGAAAAATAGGTAGGGAACTTTAAAAATCTCATT
1 TTTAAAAATCTCATTTTTGAAAAAGGCTTCTACAAAAATAGGTAGGGAACTTTAAAAATCTCATT
* * * *
2126717 TTGTAAAA-GGCTCTTATAAAAATAGATCAAGAACTTTAAAAATCACATTTTGAAAAG
66 TTG-AAAATGG-TCCTATAAAAATAGGTAAAGAACTTTAAAAATCTCATTTTGAAAAG
2126774 TAGTTTGATT
Statistics
Matches: 271, Mismatches: 38, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
194 7 0.03
195 5 0.02
196 145 0.54
197 114 0.42
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (195 bp):
TTTAAAAATCTCATTTTTGAAAAAGGCTTCTACAAAAATAGGTAGGGAACTTTAAAAATCTCATT
TTGAAAATGGTCCTATAAAAATAGGTAAAGAACTTTAAAAATCTCATTTTGAAAAGGCTCCTACA
AAAATAGACGAGGGACTATAAAAGTTCATTTTGAAAAAGGCTCCTATAAAAATAAGCAAGGAAAC
Found at i:2127232 original size:19 final size:20
Alignment explanation
Indices: 2127203--2127240 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2127193 GTTTTTTTTA
*
2127203 TTTTTCACTTCATTCATTCC
1 TTTTTCACTTCAATCATTCC
2127223 TTTTTC-CTTCAATCATTC
1 TTTTTCACTTCAATCATTC
2127241 ATCATTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTCACTTCAATCATTCC
Found at i:2127435 original size:33 final size:33
Alignment explanation
Indices: 2127393--2127476 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
2127383 GGCTTAATGG
* *
2127393 TCTCATCTTGGTGGTAGCTAA-CTTGAGCTTAAA
1 TCTCATCTTGGTGCTAGCTAATCTAG-GCTTAAA
2127426 TCTCATCTTGGTGCTAGCTAATCTAGGCTTAAA
1 TCTCATCTTGGTGCTAGCTAATCTAGGCTTAAA
*
2127459 TATCATC--GGTGCTAGCTA
1 TCTCATCTTGGTGCTAGCTA
2127477 GATTCCACTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
31 11 0.23
33 33 0.70
34 3 0.06
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (33 bp):
TCTCATCTTGGTGCTAGCTAATCTAGGCTTAAA
Found at i:2127534 original size:20 final size:21
Alignment explanation
Indices: 2127511--2127562 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
2127501 TCCTTCAATC
2127511 ATTCATCATTTCCATT-TCTT-
1 ATTCATCATTTCCATTCT-TTA
2127531 ATTCA--ATTTTCCATTCTTTA
1 ATTCATCA-TTTCCATTCTTTA
2127551 ATTCATCATTTC
1 ATTCATCATTTC
2127563 ATCGTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
18 1 0.04
19 10 0.37
20 11 0.41
21 4 0.15
22 1 0.04
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTCATCATTTCCATTCTTTA
Found at i:2127697 original size:274 final size:274
Alignment explanation
Indices: 2127208--2127765 Score: 981
Period size: 274 Copynumber: 2.0 Consensus size: 274
2127198 TTTTATTTTT
2127208 CACTTCATTCATTCCTTTTTCCTTCAATCATTCATCATTTCCATTTCCTAGTCAATTTTCCATTC
1 CACTTCATTCATTCCTTTTTCCTTCAATCATTCATCATTTCCATTTCCTAGTCAATTTTCCATTC
* *
2127273 TTTAATTCATCTTTTGATCGTCATTTTTATTTCATTTATCATTTTTTTAGTTTTTTTCCCATCTC
66 TTTAATTCATCATTTCATCGTCATTTTTATTTCATTTATCATTTTTTTAGTTTTTTTCCCATCTC
*
2127338 AGTTTTTCTTTCTCCCATTTTTCTTAATTGGTACCAATTTCATTAGGCTTAATGGTCTCATCTTG
131 AGTTTTCCTTTCTCCCATTTTTCTTAATTGGTACCAATTTCATTAGGCTTAATGGTCTCATCTTG
* *
2127403 GTGGTAGCTAACTTGAGCTTAAATCTCATCTTGGTGCTAGCTAATCTAGGCTTAAATATCATCGG
196 GTGCTAGCTAACTTGAGCTTAAATCTCATCTTGGTGCTAGCTAATCTAGGCTAAAATATCATCGG
2127468 TGCTAGCTAGATTC
261 TGCTAGCTAGATTC
* *
2127482 CACTTCATTCATTCCTTTTTCCTTCAATCATTCATCATTTCCATTTCTTATTCAATTTTCCATTC
1 CACTTCATTCATTCCTTTTTCCTTCAATCATTCATCATTTCCATTTCCTAGTCAATTTTCCATTC
*
2127547 TTTAATTCATCATTTCATCGTCATTTTTATTTCATTTATCATTTTTTTAGTTTTTTTCCCATCTT
66 TTTAATTCATCATTTCATCGTCATTTTTATTTCATTTATCATTTTTTTAGTTTTTTTCCCATCTC
* *
2127612 AGTTTTCCTTTCTCCCCTTTTTCTTAATTGGTACCAATTTCATTGGGCTTAATGGTCTCATCTTG
131 AGTTTTCCTTTCTCCCATTTTTCTTAATTGGTACCAATTTCATTAGGCTTAATGGTCTCATCTTG
* * *
2127677 GTGCTAGCTAACTTGAGCTTAAATCTTATCTTGGTGCTAGCTAATCTAGGCTAAAATCTCATTGG
196 GTGCTAGCTAACTTGAGCTTAAATCTCATCTTGGTGCTAGCTAATCTAGGCTAAAATATCATCGG
*
2127742 TGCTAGCTAGATTG
261 TGCTAGCTAGATTC
*
2127756 CACTTAATTC
1 CACTTCATTC
2127766 TCCTCAATTT
Statistics
Matches: 269, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
274 269 1.00
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.48
Consensus pattern (274 bp):
CACTTCATTCATTCCTTTTTCCTTCAATCATTCATCATTTCCATTTCCTAGTCAATTTTCCATTC
TTTAATTCATCATTTCATCGTCATTTTTATTTCATTTATCATTTTTTTAGTTTTTTTCCCATCTC
AGTTTTCCTTTCTCCCATTTTTCTTAATTGGTACCAATTTCATTAGGCTTAATGGTCTCATCTTG
GTGCTAGCTAACTTGAGCTTAAATCTCATCTTGGTGCTAGCTAATCTAGGCTAAAATATCATCGG
TGCTAGCTAGATTC
Found at i:2127713 original size:33 final size:33
Alignment explanation
Indices: 2127667--2127750 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
2127657 GGCTTAATGG
* *
2127667 TCTCATCTTGGTGCTAGCTAA-CTTGAGCTTAAA
1 TCTCATCTTGGTGCTAGCTAATCTAG-GCTAAAA
*
2127700 TCTTATCTTGGTGCTAGCTAATCTAGGCTAAAA
1 TCTCATCTTGGTGCTAGCTAATCTAGGCTAAAA
2127733 TCTCA--TTGGTGCTAGCTA
1 TCTCATCTTGGTGCTAGCTA
2127751 GATTGCACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
31 13 0.28
33 30 0.65
34 3 0.07
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (33 bp):
TCTCATCTTGGTGCTAGCTAATCTAGGCTAAAA
Found at i:2127821 original size:30 final size:31
Alignment explanation
Indices: 2127777--2127852 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
2127767 CCTCAATTTG
* *
2127777 AGCTAAACTGGGCTTAA-TTCTCTAGGCACC
1 AGCTAGACTAGGCTTAATTTCTCTAGGCACC
* * ** *
2127807 AGCTAGACTAGGCTTAATTTTTCTTGGTGCT
1 AGCTAGACTAGGCTTAATTTCTCTAGGCACC
2127838 AGCTAGACTAGGCTT
1 AGCTAGACTAGGCTT
2127853 TCCATAAGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 15 0.39
31 23 0.61
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (31 bp):
AGCTAGACTAGGCTTAATTTCTCTAGGCACC
Found at i:2130752 original size:20 final size:20
Alignment explanation
Indices: 2130723--2130762 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2130713 TAAATATTTA
*
2130723 TTTCCTTTTC-TTTTCTTTTT
1 TTTCCATTTCATTTT-TTTTT
2130743 TTTCCATTTCATTTTTTTTT
1 TTTCCATTTCATTTTTTTTT
2130763 ATCTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTCCATTTCATTTTTTTTT
Found at i:2132814 original size:24 final size:24
Alignment explanation
Indices: 2132786--2132832 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2132776 CTTTTTTCTT
*
2132786 CTCTTTCGTTAGCCGAAGCTTTTC
1 CTCTTTCATTAGCCGAAGCTTTTC
* *
2132810 CTCTTTCATTAGCTGAAGGTTTT
1 CTCTTTCATTAGCCGAAGCTTTT
2132833 GCCATAATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (24 bp):
CTCTTTCATTAGCCGAAGCTTTTC
Found at i:2133861 original size:31 final size:31
Alignment explanation
Indices: 2133803--2133861 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
2133793 GATTCCATAT
** * *
2133803 CAAGGTGAATTTATATTGAGATTATTTACAC
1 CAAGGTGAATTTATATCAAAATAATTTACAC
*
2133834 CAAGGTGAATTTGTATCAAAATAATTTA
1 CAAGGTGAATTTATATCAAAATAATTTA
2133862 TATCATGGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.37
Consensus pattern (31 bp):
CAAGGTGAATTTATATCAAAATAATTTACAC
Found at i:2134020 original size:30 final size:30
Alignment explanation
Indices: 2133982--2134107 Score: 137
Period size: 30 Copynumber: 4.2 Consensus size: 30
2133972 ACTGAGGTGG
*
2133982 TCCTTTATGAAGGAATTTTGGTCGAGCTGA
1 TCCTTTATGAAGGAAATTTGGTCGAGCTGA
* * *
2134012 TTCTTTATGAAAGAAATTTGGTCGAGCTAA
1 TCCTTTATGAAGGAAATTTGGTCGAGCTGA
* * * * *
2134042 GCCTTTAT-AAGGCATTTTTGTCGAGTTGA
1 TCCTTTATGAAGGAAATTTGGTCGAGCTGA
* * *
2134071 TCCTCTATGAAGGAAATTTGGTTGAGTTGA
1 TCCTTTATGAAGGAAATTTGGTCGAGCTGA
2134101 TCCTTTA
1 TCCTTTA
2134108 AGAGGGCATT
Statistics
Matches: 76, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
29 21 0.28
30 55 0.72
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (30 bp):
TCCTTTATGAAGGAAATTTGGTCGAGCTGA
Found at i:2134106 original size:59 final size:60
Alignment explanation
Indices: 2133982--2134107 Score: 155
Period size: 59 Copynumber: 2.1 Consensus size: 60
2133972 ACTGAGGTGG
* *
2133982 TCCTTTATGAAGGAATTTTGGTCGAGCTGATTCTTTATGAAAGAAATTTGGTCGAGCTAA
1 TCCTTTATGAAGGAATTTTGGTCGAGCTGATCCTCTATGAAAGAAATTTGGTCGAGCTAA
* * * * * * * *
2134042 GCCTTTAT-AAGGCATTTTTGTCGAGTTGATCCTCTATGAAGGAAATTTGGTTGAGTTGA
1 TCCTTTATGAAGGAATTTTGGTCGAGCTGATCCTCTATGAAAGAAATTTGGTCGAGCTAA
2134101 TCCTTTA
1 TCCTTTA
2134108 AGAGGGCATT
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
59 48 0.87
60 7 0.13
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (60 bp):
TCCTTTATGAAGGAATTTTGGTCGAGCTGATCCTCTATGAAAGAAATTTGGTCGAGCTAA
Found at i:2134334 original size:48 final size:47
Alignment explanation
Indices: 2134263--2134480 Score: 145
Period size: 48 Copynumber: 4.6 Consensus size: 47
2134253 TCTTTTACTG
** * * *
2134263 AGTTGGACCATTAGGAAGACAATTTGTTGAGCTGA-CTTCTTTTGTTA
1 AGTTGGACCATTATAAAGGCAATTTGTTGAGCTAAGC-TCTTTTGTCA
* * * *
2134310 AGTTAGG-CCTTTTGTAAAGGCAATTTGTTAAGTTAAGCTCTTTTGTCA
1 AGTT-GGACC-ATTATAAAGGCAATTTGTTGAGCTAAGCTCTTTTGTCA
* *** *
2134358 AGTTGGACCATTATAAAGGTAATTTGTTGAGCTAAGCAT-TTTCACCG
1 AGTTGGACCATTATAAAGGCAATTTGTTGAGCTAAGC-TCTTTTGTCA
* * * * * * * *
2134405 AGTTTGGGCTATTATGAAGGTAATTTGTGGAGCTAAACTATTTTGCCA
1 AG-TTGGACCATTATAAAGGCAATTTGTTGAGCTAAGCTCTTTTGTCA
* * *
2134453 AGTTGGGCCCTAATAAAGGCAATTTGTT
1 AGTTGGACCATTATAAAGGCAATTTGTT
2134481 AATCTGGTCT
Statistics
Matches: 132, Mismatches: 32, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
47 58 0.44
48 73 0.55
49 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (47 bp):
AGTTGGACCATTATAAAGGCAATTTGTTGAGCTAAGCTCTTTTGTCA
Found at i:2135684 original size:21 final size:21
Alignment explanation
Indices: 2135658--2135712 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
2135648 CAAGGGTGAG
*
2135658 AGGATCGATTCGGTCCATTGA
1 AGGATCGATTCGGTCCATTCA
* **
2135679 AGGATCGATCCAATCCATTCA
1 AGGATCGATTCGGTCCATTCA
2135700 AGGATCGA-TCGGT
1 AGGATCGATTCGGT
2135713 ATATGAATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (21 bp):
AGGATCGATTCGGTCCATTCA
Found at i:2139765 original size:155 final size:155
Alignment explanation
Indices: 2139483--2139783 Score: 602
Period size: 155 Copynumber: 1.9 Consensus size: 155
2139473 ATGATTTATC
2139483 TTATGGTATTTACCATAAATATATTTGCGTAAATGATTTTGGCATGATGGAAATAATTTTGTGAT
1 TTATGGTATTTACCATAAATATATTTGCGTAAATGATTTTGGCATGATGGAAATAATTTTGTGAT
2139548 TTTATACATATTAATTTGTGATTGTTGAATATGCCTATATGATCATGTTGATTAAAATTACTCAA
66 TTTATACATATTAATTTGTGATTGTTGAATATGCCTATATGATCATGTTGATTAAAATTACTCAA
2139613 TTTGTTCTTAATGCTTTAAATATAT
131 TTTGTTCTTAATGCTTTAAATATAT
2139638 TTATGGTATTTACCATAAATATATTTGCGTAAATGATTTTGGCATGATGGAAATAATTTTGTGAT
1 TTATGGTATTTACCATAAATATATTTGCGTAAATGATTTTGGCATGATGGAAATAATTTTGTGAT
2139703 TTTATACATATTAATTTGTGATTGTTGAATATGCCTATATGATCATGTTGATTAAAATTACTCAA
66 TTTATACATATTAATTTGTGATTGTTGAATATGCCTATATGATCATGTTGATTAAAATTACTCAA
2139768 TTTGTTCTTAATGCTT
131 TTTGTTCTTAATGCTT
2139784 GGATGGTGTG
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 146 1.00
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.46
Consensus pattern (155 bp):
TTATGGTATTTACCATAAATATATTTGCGTAAATGATTTTGGCATGATGGAAATAATTTTGTGAT
TTTATACATATTAATTTGTGATTGTTGAATATGCCTATATGATCATGTTGATTAAAATTACTCAA
TTTGTTCTTAATGCTTTAAATATAT
Found at i:2140225 original size:43 final size:42
Alignment explanation
Indices: 2140177--2140292 Score: 108
Period size: 43 Copynumber: 2.7 Consensus size: 42
2140167 AAATATTTTT
*
2140177 AAATATACTTGCTCTTGTGCTCAATTGATTCATTAATTTTGTG
1 AAATAT-CTTGATCTTGTGCTCAATTGATTCATTAATTTTGTG
* * * * *
2140220 AAATATGCTT-ATTTTTGTGCTTAAATGTTTTATTAATTTTGTG
1 AAATAT-CTTGA-TCTTGTGCTCAATTGATTCATTAATTTTGTG
* *
2140263 ACATATTTTGGATCTTTGTGCTCAATTGAT
1 AAATATCTT-GATC-TTGTGCTCAATTGAT
2140293 ATATCTCTTG
Statistics
Matches: 56, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
42 2 0.04
43 41 0.73
44 13 0.23
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (42 bp):
AAATATCTTGATCTTGTGCTCAATTGATTCATTAATTTTGTG
Found at i:2152403 original size:237 final size:237
Alignment explanation
Indices: 2152060--2153020 Score: 1091
Period size: 236 Copynumber: 4.0 Consensus size: 237
2152050 TAACATCATT
* * * * * *
2152060 TAAAAG-TT-TGACATTTATATTATCATCATATAATA-CTATACACTAACGTGACAAAATTACAA
1 TAAAAGTTTGTGACATTTATGTTATCGTCATATAACATCTATACATTGACGTGACCAAATTACAA
* * *
2152122 TGTCATTAATAGTTAACTAAAATATTTAATTTGTGACAAAAATTAATAACGTCACCTAAAATCTA
66 TATCATTAATAGTTAACTAAAATATTCAATTTGTGACAAAAATTAATAACATCACCTAAAATCTA
** * *
2152187 TTAAAAAAAATTTGTCATAGATAAAATTTTAAATTTATGACAAAATTATAACATCACCTAAAATA
131 -TAAAAAAAATTCATCACAGATAAAATTTTAAATTGATGACAAAATTATAACATCACCTAAAATA
* * *
2152252 AAAAAA-GTCACAAAAAATTTTTTCACTAAATAAATTTGGCGA
195 AAAAAATGTCACAAAAAAATTTCTCACCAAATAAATTTGGCGA
* * *
2152294 TAAAAGTTTGTTACATTTATGTTATCGTCATATCACATC-ATACATTGACGTGACCAAATTGCAA
1 TAAAAGTTTGTGACATTTATGTTATCGTCATATAACATCTATACATTGACGTGACCAAATTACAA
* * * * *
2152358 TACCATTAATAGTTTAATTAAAATGTTCAATTTGTGACAAAAATTAATAACATCATCTAAAATTT
66 TATCATTAATAG-TTAACTAAAATATTCAATTTGTGACAAAAATTAATAACATCACCTAAAATCT
* * * *
2152423 ACAAAAAACAATTCATCACAAATAAAATTTTAAATTGGTGACAAAATTATAACGTCACCTATAAT
130 ATAAAAAA-AATTCATCACAGATAAAATTTTAAATTGATGACAAAATTATAACATCACC-----T
* *
2152488 GAAAATTAAAAAAATTGTCACAAAAAAATTTCTCACCAAATAAATTTGGTGG
189 -AAAA-TAAAAAAA-TGTCACAAAAAAATTTCTCACCAAATAAATTTGGCGA
* * * * **
2152540 TAAAAGTTTGTGACATTTGTGTTATCGTCATATAACA-CTATAAATTTATGTGATGAAATTACAA
1 TAAAAGTTTGTGACATTTATGTTATCGTCATATAACATCTATACATTGACGTGACCAAATTACAA
* * * * * * **
2152604 TATCATTAATAGTTAAATAAAGTGTTTAATTTATGATAAAAATTAATAATTTCACCTAAAATCTA
66 TATCATTAATAGTTAACTAAAATATTCAATTTGTGACAAAAATTAATAACATCACCTAAAATCTA
* * ** * *
2152669 TAAGAAAAAATTCGTCACAGATAAAATTTAAAATCAATGACAAAATTATAATATCACCTAAATTA
131 TAA-AAAAAATTCATCACAGATAAAATTTTAAATTGATGACAAAATTATAACATCACCTAAAATA
** * * *
2152734 AAAAAACATCACAAAAAAATTTCT-ACCAAAAAAATTTGGTGG
195 AAAAAATGTCACAAAAAAATTTCTCACCAAATAAATTTGGCGA
* * * *
2152776 TAAAAGTTTGTGACGTTTATGTTATCGTCATATAACA-CCATACATTGACATGA-CATAATTTCA
1 TAAAAGTTTGTGACATTTATGTTATCGTCATATAACATCTATACATTGACGTGACCA-AATTACA
* * * *
2152839 ATGTCATTAATAGTTAACTAAAATATTCAATTTGTGAC-GAAATTAACAACATCACCTAATATCT
65 ATATCATTAATAGTTAACTAAAATATTCAATTTGTGACAAAAATTAATAACATCACCTAAAATCT
* *
2152903 ATTAGAAAAAATTCATCACAGATAAAATTTTAAATTGATGATAAAATTATAACATCACCTAAAAT
130 A-TAAAAAAAATTCATCACAGATAAAATTTTAAATTGATGACAAAATTATAACATCACCTAAAAT
* * *
2152968 AAAAGAAAAGTCAC-AAAAAATTTCTCACCAAATGAATTTGGCTA
194 AAAA-AAATGTCACAAAAAAATTTCTCACCAAATAAATTTGGCGA
2153012 TAAAA-TTTG
1 TAAAAGTTTG
2153021 GTGGTAAGAT
Statistics
Matches: 609, Mismatches: 98, Indels: 39
0.82 0.13 0.05
Matches are distributed among these distances:
234 6 0.01
235 97 0.16
236 186 0.31
237 107 0.18
238 8 0.01
239 3 0.00
240 1 0.00
242 1 0.00
243 4 0.01
244 8 0.01
245 89 0.15
246 99 0.16
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.33
Consensus pattern (237 bp):
TAAAAGTTTGTGACATTTATGTTATCGTCATATAACATCTATACATTGACGTGACCAAATTACAA
TATCATTAATAGTTAACTAAAATATTCAATTTGTGACAAAAATTAATAACATCACCTAAAATCTA
TAAAAAAAATTCATCACAGATAAAATTTTAAATTGATGACAAAATTATAACATCACCTAAAATAA
AAAAATGTCACAAAAAAATTTCTCACCAAATAAATTTGGCGA
Found at i:2160849 original size:16 final size:16
Alignment explanation
Indices: 2160830--2160948 Score: 60
Period size: 16 Copynumber: 7.2 Consensus size: 16
2160820 TTGTTTGCTC
*
2160830 TTTAATTTTCTTGCAA
1 TTTAAATTTCTTGCAA
2160846 TTTAAATTTCATGTGCAA
1 TTTAAATTTC-T-TGCAA
** ** *
2160864 TTTATGTTTCAAGCAT
1 TTTAAATTTCTTGCAA
* **
2160880 TTTAATTTTCTATGTTA
1 TTTAAATTTCT-TGCAA
**
2160897 TTTAAATTAGTTGCAA
1 TTTAAATTTCTTGCAA
* **
2160913 TCTAAATTTCTATGTTA
1 TTTAAATTTCT-TGCAA
*
2160930 TTTAAATTT-ATGCAA
1 TTTAAATTTCTTGCAA
2160945 TTTA
1 TTTA
2160949 CTTTTCTTGT
Statistics
Matches: 72, Mismatches: 27, Indels: 9
0.67 0.25 0.08
Matches are distributed among these distances:
15 7 0.10
16 31 0.43
17 21 0.29
18 13 0.18
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.52
Consensus pattern (16 bp):
TTTAAATTTCTTGCAA
Found at i:2160937 original size:17 final size:17
Alignment explanation
Indices: 2160880--2160938 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
2160870 TTTCAAGCAT
*
2160880 TTTAATTTTCTATGTTA
1 TTTAAATTTCTATGTTA
** **
2160897 TTTAAATTAGT-TGCAA
1 TTTAAATTTCTATGTTA
*
2160913 TCTAAATTTCTATGTTA
1 TTTAAATTTCTATGTTA
2160930 TTTAAATTT
1 TTTAAATTT
2160939 ATGCAATTTA
Statistics
Matches: 30, Mismatches: 11, Indels: 2
0.70 0.26 0.05
Matches are distributed among these distances:
16 11 0.37
17 19 0.63
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (17 bp):
TTTAAATTTCTATGTTA
Found at i:2160955 original size:32 final size:32
Alignment explanation
Indices: 2160880--2160955 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 32
2160870 TTTCAAGCAT
2160880 TTTAATTTTCTATGTTATTTAAATTAGTTGCAA
1 TTTAATTTTCTATGTTATTTAAATTAG-TGCAA
* *
2160913 TCTAAATTTCTATGTTATTTAAATTTA-TGCAA
1 TTTAATTTTCTATGTTATTTAAA-TTAGTGCAA
*
2160945 TTTACTTTTCT
1 TTTAATTTTCT
2160956 TGTAATACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 13 0.35
33 21 0.57
34 3 0.08
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.55
Consensus pattern (32 bp):
TTTAATTTTCTATGTTATTTAAATTAGTGCAA
Found at i:2161050 original size:32 final size:32
Alignment explanation
Indices: 2161014--2161080 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
2161004 TACTGTTTAT
**
2161014 TTTTCATGCTCTTTACATT-TATGCAATCTAAA
1 TTTTCATGCAATTTA-ATTATATGCAATCTAAA
* *
2161046 TTTTCATGCAATTTAATTATTTGCAATTTAAA
1 TTTTCATGCAATTTAATTATATGCAATCTAAA
2161078 TTT
1 TTT
2161081 AATGTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 3 0.10
32 27 0.90
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (32 bp):
TTTTCATGCAATTTAATTATATGCAATCTAAA
Found at i:2167344 original size:21 final size:21
Alignment explanation
Indices: 2167320--2167359 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2167310 ATTAGATATA
* *
2167320 CATTTTAATTCATATTAATGT
1 CATTTCAATCCATATTAATGT
*
2167341 CATTTCAATCCATTTTAAT
1 CATTTCAATCCATATTAAT
2167360 TATTGTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.50
Consensus pattern (21 bp):
CATTTCAATCCATATTAATGT
Found at i:2169842 original size:31 final size:31
Alignment explanation
Indices: 2169807--2169866 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2169797 CACTTAACAT
*
2169807 ATCGAACATCAAAACCAATAAAAGTTAATCA
1 ATCGAACATAAAAACCAATAAAAGTTAATCA
* * *
2169838 ATCGAACATAAAAACTATTACAAGTTAAT
1 ATCGAACATAAAAACCAATAAAAGTTAAT
2169867 TAAGTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.53, C:0.17, G:0.07, T:0.23
Consensus pattern (31 bp):
ATCGAACATAAAAACCAATAAAAGTTAATCA
Found at i:2174811 original size:18 final size:18
Alignment explanation
Indices: 2174788--2174822 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2174778 AATAAAATAA
2174788 TTTAATAATAATTTAATT
1 TTTAATAATAATTTAATT
*
2174806 TTTAATAATCATTTAAT
1 TTTAATAATAATTTAAT
2174823 GTTACCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAATAATAATTTAATT
Found at i:2175608 original size:16 final size:16
Alignment explanation
Indices: 2175582--2175620 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
2175572 AATCAAACCA
*
2175582 AATTATATATATTTTTT
1 AATT-TATATATATTTT
2175599 AATTTATATATATTTT
1 AATTTATATATATTTT
2175615 AGATTT
1 A-ATTT
2175621 TTATTATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
AATTTATATATATTTT
Found at i:2175683 original size:10 final size:10
Alignment explanation
Indices: 2175644--2175685 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
2175634 ATAATTATTT
2175644 TATATT-AAA
1 TATATTAAAA
* *
2175653 TTTATTTAAA
1 TATATTAAAA
2175663 TATATTAAAAA
1 TATATT-AAAA
2175674 TATATTAAAA
1 TATATTAAAA
2175684 TA
1 TA
2175686 ATAAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 5 0.18
10 14 0.50
11 9 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TATATTAAAA
Found at i:2175933 original size:2 final size:2
Alignment explanation
Indices: 2175926--2175950 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2175916 CCAACCCCCG
2175926 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 A
2175951 AAGAAGCAAC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2176575 original size:119 final size:120
Alignment explanation
Indices: 2176329--2176583 Score: 376
Period size: 119 Copynumber: 2.1 Consensus size: 120
2176319 ATTATTAATT
* *
2176329 TTTTAATGATTTAGTTTAAAAGATACTTGAATTTGAATTTTATTGAATTTATAACTAAACAATTA
1 TTTTAAT--TTTAATTTAAAAGATACTTGAATATGAATTTTATTGAATTTATAACTAAACAATTA
*
2176394 TTTATAATAAAAAAATAATAAAAAATTTTAATTATATAATTGAATCAATTAAACTAA
64 TTTATAATAAAAAAATAATAAAAAATTTTAATTATATAATTAAATCAATTAAACTAA
* * * *
2176451 -ATTAATTTTAATTTAAAAGATACTTGAATATGAGTTTTATTGAATTTATAA-TAAAATAATTGT
1 TTTTAATTTTAATTTAAAAGATACTTGAATATGAATTTTATTGAATTTATAACT-AAACAATTAT
*
2176514 TTATAATAAAAAAATAAT-AAAAATTTTAATTATATAATTAAATCAATTAAATTAA
65 TTATAATAAAAAAATAATAAAAAATTTTAATTATATAATTAAATCAATTAAACTAA
2176569 TTTTAA--TTAATTTAA
1 TTTTAATTTTAATTTAA
2176584 TTATAATTAA
Statistics
Matches: 122, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
117 9 0.07
118 36 0.30
119 72 0.59
121 5 0.04
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (120 bp):
TTTTAATTTTAATTTAAAAGATACTTGAATATGAATTTTATTGAATTTATAACTAAACAATTATT
TATAATAAAAAAATAATAAAAAATTTTAATTATATAATTAAATCAATTAAACTAA
Found at i:2176594 original size:15 final size:15
Alignment explanation
Indices: 2176558--2176595 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2176548 TAATTAAATC
* *
2176558 AATTAAATTAATTTT
1 AATTAATTTAATTAT
2176573 AATTAATTTAATTAT
1 AATTAATTTAATTAT
2176588 AATTAATT
1 AATTAATT
2176596 ATTTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTAATTTAATTAT
Found at i:2177410 original size:19 final size:19
Alignment explanation
Indices: 2177386--2177424 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2177376 AAATATCATA
*
2177386 ATTAAATTATATATTTTTT
1 ATTAAATTATATATATTTT
*
2177405 ATTAAATTTTATATATTTT
1 ATTAAATTATATATATTTT
2177424 A
1 A
2177425 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTAAATTATATATATTTT
Found at i:2189333 original size:14 final size:12
Alignment explanation
Indices: 2189299--2189324 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2189289 TTAAACTGGA
2189299 AAAAATAAAAAC
1 AAAAATAAAAAC
2189311 AAAAATAAAAAC
1 AAAAATAAAAAC
2189323 AA
1 AA
2189325 GAAACTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAATAAAAAC
Found at i:2193677 original size:27 final size:26
Alignment explanation
Indices: 2193647--2193703 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
2193637 TAAGACGATA
*
2193647 TTATTTAATATAATCTTATTCATAATT
1 TTATTTAATATAATCTTATT-ATAATC
* * *
2193674 TTATTTTATCTTATCTTATTATAATC
1 TTATTTAATATAATCTTATTATAATC
2193700 TTAT
1 TTAT
2193704 ATGCCAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATTTAATATAATCTTATTATAATC
Found at i:2198225 original size:2 final size:2
Alignment explanation
Indices: 2198218--2198268 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
2198208 TGATTTGAGG
* * *
2198218 AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT AT AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2198260 AT AT AT AT A
1 AT AT AT AT A
2198269 AAGGGAAAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2201871 original size:17 final size:17
Alignment explanation
Indices: 2201849--2201917 Score: 88
Period size: 17 Copynumber: 4.0 Consensus size: 17
2201839 TATTTAATAA
2201849 TTTCATAATATATTTAT
1 TTTCATAATATATTTAT
2201866 TTTCATAATATATTTTAT
1 TTTCATAATATA-TTTAT
*
2201884 TTAT-ACCAATATATTTAT
1 TT-TCA-TAATATATTTAT
2201902 TTTCATAATAT-TTTAT
1 TTTCATAATATATTTAT
2201918 ATTATTTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
16 5 0.11
17 18 0.39
18 16 0.35
19 7 0.15
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTCATAATATATTTAT
Found at i:2204834 original size:90 final size:83
Alignment explanation
Indices: 2204692--2204897 Score: 254
Period size: 90 Copynumber: 2.4 Consensus size: 83
2204682 TAGTGCCAAT
* *
2204692 CTTTAGGTATATTGATATTTAA-GGTGAGCTTAAGGTTTGTTATTTAATATCAGAG-GACACAAA
1 CTTTAGGGATATTGATA-TTAAGGGTGAGCTTAAGGTTTGTGATTTAATATCAGAGAG-CA-AAA
2204755 GGTAGAGGATACAAGGTTAGTACCAGA
63 GG-AGAGGAT---A--TTAGTACCAGA
* **
2204782 CTTTAGGGATATTGATATTAAGGGAGAGCTTAAGGTTTGTGATTTAATATCAGAGAGCAGTAGGA
1 CTTTAGGGATATTGATATTAAGGGTGAGCTTAAGGTTTGTGATTTAATATCAGAGAGCAAAAGGA
*
2204847 TAGGATATTAGTACCAGA
66 GAGGATATTAGTACCAGA
*
2204865 CTTTAGGGATATTGATATTGAGGGTGAGCTTAA
1 CTTTAGGGATATTGATATTAAGGGTGAGCTTAA
2204898 AATTTATGAT
Statistics
Matches: 106, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
83 42 0.40
85 1 0.01
88 6 0.06
89 7 0.07
90 49 0.46
91 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.33
Consensus pattern (83 bp):
CTTTAGGGATATTGATATTAAGGGTGAGCTTAAGGTTTGTGATTTAATATCAGAGAGCAAAAGGA
GAGGATATTAGTACCAGA
Found at i:2209589 original size:49 final size:49
Alignment explanation
Indices: 2209408--2209628 Score: 230
Period size: 51 Copynumber: 4.4 Consensus size: 49
2209398 AAAGACATCA
* * * *
2209408 AAACTTTAAAAGTTCTTATTTAAAAATGGCTCCGCCTAAACAGAGGCTTTA
1 AAACTTTAAAA-ATCTTGTTTGAAAATGGCTCC-CCTAAACAGAGGCTTTG
* * *
2209459 AAACTTTAAAAAATCTTATTTGAAAATTGCTTGCCCTAAACAGAGGCTTTG
1 AAACTTT-AAAAATCTTGTTTGAAAATGGC-TCCCCTAAACAGAGGCTTTG
* * * *
2209510 AAACTTTAAAAATCTTTTTTTGAAAATGGCTCCCCTTAAATAGAAGTTTTG
1 AAACTTTAAAAATC-TTGTTTGAAAATGGCTCCCC-TAAACAGAGGCTTTG
* * * *
2209561 AAACTTTAAGAA-CTTGTTTGAAAATGGCTTCTCTAAAACAGAGGCTTTT
1 AAACTTTAAAAATCTTGTTTGAAAATGGCTCCCCT-AAACAGAGGCTTTG
2209610 AAACTTT-AAAATCTTGTTT
1 AAACTTTAAAAATCTTGTTT
2209629 TATCTAGTGG
Statistics
Matches: 144, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
48 4 0.03
49 41 0.28
50 12 0.08
51 81 0.56
52 6 0.04
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (49 bp):
AAACTTTAAAAATCTTGTTTGAAAATGGCTCCCCTAAACAGAGGCTTTG
Found at i:2210992 original size:10 final size:10
Alignment explanation
Indices: 2210960--2210993 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2210950 CAATTATGAG
2210960 TTTTTCATTT
1 TTTTTCATTT
*
2210970 TTATTCATTT
1 TTTTTCATTT
*
2210980 TTTTTAATTT
1 TTTTTCATTT
2210990 TTTT
1 TTTT
2210994 GTTTTTGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:2211016 original size:25 final size:26
Alignment explanation
Indices: 2210987--2211044 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
2210977 TTTTTTTTAA
*
2210987 TTTTTTTGTT-TTTGTTTTGTTTTCT
1 TTTTTTTATTCTTTGTTTTGTTTTCT
* *
2211012 CTTTTTTTATTCTTTTTTTTTTTTTCT
1 -TTTTTTTATTCTTTGTTTTGTTTTCT
2211039 TTTTTT
1 TTTTTT
2211045 CAAGCAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.02, C:0.07, G:0.05, T:0.86
Consensus pattern (26 bp):
TTTTTTTATTCTTTGTTTTGTTTTCT
Found at i:2211018 original size:14 final size:13
Alignment explanation
Indices: 2211001--2211044 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
2210991 TTTGTTTTTG
*
2211001 TTTTGTTTTCTCT
1 TTTTTTTTTCTCT
*
2211014 TTTTTTATTCT-T
1 TTTTTTTTTCTCT
*
2211026 TTTTTTTTTTTCT
1 TTTTTTTTTCTCT
2211039 TTTTTT
1 TTTTTT
2211045 CAAGCAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.02, C:0.09, G:0.02, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTCTCT
Found at i:2211041 original size:11 final size:11
Alignment explanation
Indices: 2210967--2211045 Score: 54
Period size: 11 Copynumber: 6.8 Consensus size: 11
2210957 GAGTTTTTCA
*
2210967 TTTTTATTCATT
1 TTTTTTTTC-TT
2210979 TTTTTTAATT-TT
1 TTTTTT--TTCTT
*
2210991 TTTGTTTTTGTT
1 TTT-TTTTTCTT
*
2211003 TTGTTTTCTCTT
1 TT-TTTTTTCTT
*
2211015 TTTTTATTCTT
1 TTTTTTTTCTT
2211026 TTTTTTTT-TT
1 TTTTTTTTCTT
2211036 TCTTTTTTTC
1 T-TTTTTTTC
2211046 AAGCAAAGTA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
10 3 0.06
11 23 0.43
12 22 0.41
13 4 0.07
14 2 0.04
ACGTcount: A:0.06, C:0.08, G:0.04, T:0.82
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:2212552 original size:23 final size:23
Alignment explanation
Indices: 2212521--2212571 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
2212511 CTCCTATTAA
*
2212521 GAATATTTAGACTCATATACAGT
1 GAATGTTTAGACTCATATACAGT
2212544 GAATGTTTAGACTCATATACAGT
1 GAATGTTTAGACTCATATACAGT
2212567 GAATG
1 GAATG
2212572 ATTAATAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (23 bp):
GAATGTTTAGACTCATATACAGT
Found at i:2221145 original size:3 final size:3
Alignment explanation
Indices: 2221137--2221210 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
2221127 TTTTCATTTT
* * * * * *
2221137 TTA TTA TTA TTA TTA TTG TTG TTG TTA TTA TTA CTA TCA TT- TTT TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* *
2221185 TT- TTA TTA TTA TTA TAA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2221211 CTACTACTAT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
2 4 0.07
3 51 0.89
4 2 0.04
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2242519 original size:19 final size:19
Alignment explanation
Indices: 2242477--2242524 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2242467 TATTTAATAT
*
2242477 ATTTTATTTATAATTTTGTC
1 ATTTTATTT-TAATTTTGTA
* *
2242497 ATTTTATTTTAGTTTTTTA
1 ATTTTATTTTAATTTTGTA
2242516 A-TTTATTTT
1 ATTTTATTTT
2242525 TAAAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.32
19 8 0.32
20 9 0.36
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (19 bp):
ATTTTATTTTAATTTTGTA
Found at i:2242568 original size:13 final size:13
Alignment explanation
Indices: 2242545--2242581 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2242535 ACATGAATAC
2242545 TAAATATAAATAAA
1 TAAATA-AAATAAA
2242559 TAAATAAAATAAA
1 TAAATAAAATAAA
*
2242572 TAAACAAAAT
1 TAAATAAAAT
2242582 GCTTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:2243898 original size:21 final size:23
Alignment explanation
Indices: 2243874--2243915 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2243864 AAAATTTATT
*
2243874 TTTTCTCATT-TT-TTATTTTTA
1 TTTTATCATTATTATTATTTTTA
2243895 TTTTATCATTATTATTATTTT
1 TTTTATCATTATTATTATTTT
2243916 AAATATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 2 0.11
23 7 0.39
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTATCATTATTATTATTTTTA
Found at i:2243991 original size:11 final size:11
Alignment explanation
Indices: 2243955--2243992 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2243945 AAAATATTCA
2243955 TTTTTATATTT
1 TTTTTATATTT
* *
2243966 ATTTTATATTA
1 TTTTTATATTT
2243977 TTTTTAT-TTT
1 TTTTTATATTT
2243987 TTTTTA
1 TTTTTA
2243993 AAACCTTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATATTT
Found at i:2244137 original size:9 final size:9
Alignment explanation
Indices: 2244125--2244174 Score: 52
Period size: 8 Copynumber: 5.7 Consensus size: 9
2244115 ATTTTCATTA
2244125 TTTATATTT
1 TTTATATTT
2244134 TTTA-ATCATT
1 TTTATAT--TT
2244144 TTT-TATTT
1 TTTATATTT
2244152 TTT-TATTT
1 TTTATATTT
*
2244160 TTTATGTTT
1 TTTATATTT
2244169 TTTATA
1 TTTATA
2244175 CACATGTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 15 0.43
9 13 0.37
10 7 0.20
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTATATTT
Found at i:2244148 original size:20 final size:19
Alignment explanation
Indices: 2244119--2244156 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2244109 TCAGAGATTT
2244119 TCATTATTTATATTTTTTAA
1 TCATTATTTAT-TTTTTTAA
*
2244139 TCATTTTTTATTTTTTTA
1 TCATTATTTATTTTTTTA
2244157 TTTTTTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
TCATTATTTATTTTTTTAA
Found at i:2244161 original size:16 final size:16
Alignment explanation
Indices: 2244141--2244173 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2244131 TTTTTTAATC
2244141 ATTTTTTAT-TTTTTT
1 ATTTTTTATGTTTTTT
2244156 ATTTTTTATGTTTTTT
1 ATTTTTTATGTTTTTT
2244172 AT
1 AT
2244174 ACACATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (16 bp):
ATTTTTTATGTTTTTT
Found at i:2245937 original size:19 final size:19
Alignment explanation
Indices: 2245910--2245950 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2245900 TTAATTCTAT
*
2245910 AAAATAAAAATAAAAAAGG
1 AAAAGAAAAATAAAAAAGG
*
2245929 AAAAGAAAAATAAAAAATG
1 AAAAGAAAAATAAAAAAGG
2245948 AAA
1 AAA
2245951 TTGGGCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (19 bp):
AAAAGAAAAATAAAAAAGG
Found at i:2246036 original size:14 final size:15
Alignment explanation
Indices: 2246003--2246033 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2245993 GCCTTTGCCA
*
2246003 TTAAATTTGGGCTTT
1 TTAAAATTGGGCTTT
2246018 TTAAAATTGGGCTTT
1 TTAAAATTGGGCTTT
2246033 T
1 T
2246034 AAAGTTTGAT
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:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (15 bp):
TTAAAATTGGGCTTT
Found at i:2246376 original size:8 final size:8
Alignment explanation
Indices: 2246365--2246480 Score: 64
Period size: 8 Copynumber: 14.4 Consensus size: 8
2246355 TTTGATTTTA
2246365 TTGTTGTT
1 TTGTTGTT
2246373 TTGTTGTT
1 TTGTTGTT
2246381 TTGTTGCTT
1 TTGTTG-TT
* *
2246390 TTATGGTT
1 TTGTTGTT
*
2246398 TT-TATGGT
1 TTGT-TGTT
2246406 TT-TT-TT
1 TTGTTGTT
*
2246412 TTGTTATT
1 TTGTTGTT
*
2246420 TTTTTGTT
1 TTGTTGTT
* *
2246428 ATTTTTCTT
1 -TTGTTGTT
2246437 TTGGCCTT-TT
1 TT-G--TTGTT
2246447 TT-TTGGTT
1 TTGTT-GTT
2246455 TT-TTGTT
1 TTGTTGTT
2246462 TTGTTGTT
1 TTGTTGTT
2246470 TTGTTGTT
1 TTGTTGTT
2246478 TTG
1 TTG
2246481 CTTTTGCTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
6 5 0.06
7 9 0.10
8 55 0.62
9 13 0.15
10 4 0.05
11 2 0.02
ACGTcount: A:0.03, C:0.03, G:0.19, T:0.74
Consensus pattern (8 bp):
TTGTTGTT
Found at i:2246421 original size:11 final size:11
Alignment explanation
Indices: 2246407--2246433 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2246397 TTTTATGGTT
2246407 TTTTTTTGTTA
1 TTTTTTTGTTA
2246418 TTTTTTTGTTA
1 TTTTTTTGTTA
2246429 TTTTT
1 TTTTT
2246434 CTTTTGGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (11 bp):
TTTTTTTGTTA
Found at i:2246438 original size:14 final size:13
Alignment explanation
Indices: 2246405--2246471 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 13
2246395 GTTTTTATGG
2246405 TTTTTTTTTGTTA
1 TTTTTTTTTGTTA
2246418 --TTTTTTTGTTA
1 TTTTTTTTTGTTA
***
2246429 TTTTTCTTTTGGCC
1 TTTTT-TTTTGTTA
*
2246443 TTTTTTTTGGTT-
1 TTTTTTTTTGTTA
* *
2246455 TTTTGTTTTGTTG
1 TTTTTTTTTGTTA
2246468 TTTT
1 TTTT
2246472 GTTGTTTTGC
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
11 11 0.26
12 10 0.24
13 11 0.26
14 10 0.24
ACGTcount: A:0.03, C:0.04, G:0.13, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTGTTA
Found at i:2246458 original size:12 final size:12
Alignment explanation
Indices: 2246396--2246512 Score: 55
Period size: 12 Copynumber: 9.8 Consensus size: 12
2246386 GCTTTTATGG
*
2246396 TTTTTATGG-TT
1 TTTTTTTGGTTT
*
2246407 TTTTTTT-GTTA
1 TTTTTTTGGTTT
*
2246418 TTTTTTTGTTATT
1 TTTTTTTGGT-TT
**
2246431 TTTCTTTTGGCCT
1 TTT-TTTTGGTTT
2246444 TTTTTTTGGTTT
1 TTTTTTTGGTTT
*
2246456 TTTGTTTT-GTTG
1 TTT-TTTTGGTTT
*
2246468 TTTTGTT-GTTT
1 TTTTTTTGGTTT
** *
2246479 TGCTTTTGCTTT
1 TTTTTTTGGTTT
*
2246491 TGTTTTT-GTCTT
1 TTTTTTTGGT-TT
2246503 TGTTTTTTGG
1 T-TTTTTTGG
2246513 AAAAATTTAA
Statistics
Matches: 78, Mismatches: 19, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
10 1 0.01
11 25 0.32
12 29 0.37
13 17 0.22
14 6 0.08
ACGTcount: A:0.03, C:0.05, G:0.17, T:0.75
Consensus pattern (12 bp):
TTTTTTTGGTTT
Found at i:2246471 original size:25 final size:25
Alignment explanation
Indices: 2246352--2246471 Score: 61
Period size: 25 Copynumber: 4.8 Consensus size: 25
2246342 AGATTTTAAT
*
2246352 TTTTTTGATTTTATTGTTGTTTTGTT-G
1 TTTTTTG-TTTTGTTGTT-TTTT-TTGG
* * *
2246379 TTTTGTTGCTTTT-ATGGTTTTTATGG
1 TTTT-TTG-TTTTGTTGTTTTTTTTGG
* *
2246405 -TTTTT-TTTTGTT-ATTTTTTTGT
1 TTTTTTGTTTTGTTGTTTTTTTTGG
* ***
2246427 TATTTTTCTTTTGGCCTTTTTTTTGG
1 T-TTTTTGTTTTGTTGTTTTTTTTGG
2246453 TTTTTTGTTTTGTTGTTTT
1 TTTTTTGTTTTGTTGTTTT
2246472 GTTGTTTTGC
Statistics
Matches: 70, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
22 11 0.16
23 1 0.01
24 7 0.10
25 23 0.33
26 14 0.20
27 7 0.10
28 7 0.10
ACGTcount: A:0.05, C:0.03, G:0.17, T:0.75
Consensus pattern (25 bp):
TTTTTTGTTTTGTTGTTTTTTTTGG
Found at i:2246497 original size:47 final size:48
Alignment explanation
Indices: 2246365--2246498 Score: 125
Period size: 47 Copynumber: 2.8 Consensus size: 48
2246355 TTTGATTTTA
*
2246365 TTGTTGTTTTGTTGTTTTG---TTGCTTTTATGGTTTTTATGGTTTTTTTTTG
1 TTGTTGTTTTGTTGTTTTGCTTTTGC-TTT-T-G-TTTT-TGGTTTTTTGTTG
* * * * *
2246415 TTATTTTTTTGTTATTTTTCTTTTGGCCTTT-TTTTTGGTTTTTTGTT-
1 TTGTTGTTTTGTTGTTTTGCTTTT-GCTTTTGTTTTTGGTTTTTTGTTG
2246462 TTGTTGTTTTGTTGTTTTGCTTTTGCTTTTGTTTTTG
1 TTGTTGTTTTGTTGTTTTGCTTTTGCTTTTGTTTTTG
2246499 TCTTTGTTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
46 5 0.07
47 26 0.38
48 11 0.16
49 4 0.06
50 15 0.22
52 1 0.01
53 4 0.06
54 2 0.03
ACGTcount: A:0.03, C:0.04, G:0.19, T:0.74
Consensus pattern (48 bp):
TTGTTGTTTTGTTGTTTTGCTTTTGCTTTTGTTTTTGGTTTTTTGTTG
Found at i:2246965 original size:207 final size:207
Alignment explanation
Indices: 2246610--2246990 Score: 516
Period size: 207 Copynumber: 1.8 Consensus size: 207
2246600 GATCATGTCC
* * * *
2246610 AGAGGTCTTACAAATCTTAACATTTGCAAAAGCTCCTCTAATCAAAGGCATTGAAACTTTAAAAA
1 AGAGGTCTTACAAATCTCAAAATTTACAAAAGCTACTCTAATCAAAGGCATTGAAACTTTAAAAA
* * * * * * ** *
2246675 TTAAAAATATTTTATCCAAAGGACTTATAGATTATATCTGGAGGTCTTACAAATGTTGACGTCTA
66 TTAAAAATATTTTAGCCAAAGGACTTAGAAATTATATCTAGAGATCTTACAAATCTCAACATCTA
*
2246740 TGAAAACTCCTCTAATAAGAGGCATTGGAACTTTAAAGATTTAAAATGTTTACTTTGAACTCTTA
131 TGAAAACTCCTCTAATAAGAGGCATTGAAACTTTAAAGATTTAAAATGTTTACTTTGAACTCTTA
2246805 GAGATTATTTTT
196 GAGATTATTTTT
*
2246817 AGAGGTCTTACAAATCTCAAAATTTACAAAAGCTACTCTAATCAGAA-GTATTGAAACTTTAAAA
1 AGAGGTCTTACAAATCTCAAAATTTACAAAAGCTACTCTAATCA-AAGGCATTGAAACTTTAAAA
* * *
2246881 TTTTAAAATATTTT-GCCAAGAGGGCTTAGAAATTATA-CTTAGAGATCTTACAAATCTCAACAT
65 ATTAAAAATATTTTAGCCAA-AGGACTTAGAAATTATATC-TAGAGATCTTACAAATCTCAACAT
* ** *
2246944 TTATGAATGCTCCTTTAATAAGAGGCATTGAAACTTTAAAGATTTAA
128 CTATGAAAACTCCTCTAATAAGAGGCATTGAAACTTTAAAGATTTAA
2246991 CCTAGTGGTC
Statistics
Matches: 149, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
206 5 0.03
207 142 0.95
208 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (207 bp):
AGAGGTCTTACAAATCTCAAAATTTACAAAAGCTACTCTAATCAAAGGCATTGAAACTTTAAAAA
TTAAAAATATTTTAGCCAAAGGACTTAGAAATTATATCTAGAGATCTTACAAATCTCAACATCTA
TGAAAACTCCTCTAATAAGAGGCATTGAAACTTTAAAGATTTAAAATGTTTACTTTGAACTCTTA
GAGATTATTTTT
Found at i:2246990 original size:104 final size:103
Alignment explanation
Indices: 2246610--2246990 Score: 358
Period size: 104 Copynumber: 3.7 Consensus size: 103
2246600 GATCATGTCC
* * *
2246610 AGAGGTCTTACAAATCTTAACATTTGCAAAAGCTCCTCTAATCAA-AGGCATTGAAACTTTAAAA
1 AGAGGTCTTACAAATCTCAACATTTACAAAAGCTCCTCTAAT-AAGAGGCATTGAAACTTTAAAG
* *
2246674 ATTAAAAATATTTTATCCAA-AGGACTTATAGATTATATCT
65 ATTTAAAATATTTTA-CCAAGAGGACTTAGAGATTATAT-T
* * ** * * * *
2246714 GGAGGTCTTACAAATGTTGACGTCTATGAAAA-CTCCTCTAATAAGAGGCATTGGAACTTTAAAG
1 AGAGGTCTTACAAATCTCAACATTTA-CAAAAGCTCCTCTAATAAGAGGCATTGAAACTTTAAAG
* *** *** *
2246778 ATTTAAAAT-GTTTACTTTGAACTCTTAGAGATTATTTTT
65 ATTTAAAATATTTTACCAAGAGGACTTAGAGATTA-TATT
* * * * *
2246817 AGAGGTCTTACAAATCTCAAAATTTACAAAAGCTACTCTAATCAGAAGTATTGAAACTTTAAA-A
1 AGAGGTCTTACAAATCTCAACATTTACAAAAGCTCCTCTAATAAGAGGCATTGAAACTTTAAAGA
* * *
2246881 TTTTAAAATATTTTGCCAAGAGGGCTTAGAAATTATACTT
66 -TTTAAAATATTTTACCAAGAGGACTTAGAGATTATA-TT
* ** * *
2246921 AGAGATCTTACAAATCTCAACATTTATGAATGCTCCTTTAATAAGAGGCATTGAAACTTTAAAGA
1 AGAGGTCTTACAAATCTCAACATTTACAAAAGCTCCTCTAATAAGAGGCATTGAAACTTTAAAGA
2246986 TTTAA
66 TTTAA
2246991 CCTAGTGGTC
Statistics
Matches: 216, Mismatches: 52, Indels: 18
0.76 0.18 0.06
Matches are distributed among these distances:
102 6 0.03
103 72 0.33
104 133 0.62
105 5 0.02
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (103 bp):
AGAGGTCTTACAAATCTCAACATTTACAAAAGCTCCTCTAATAAGAGGCATTGAAACTTTAAAGA
TTTAAAATATTTTACCAAGAGGACTTAGAGATTATATT
Found at i:2247063 original size:73 final size:73
Alignment explanation
Indices: 2246926--2247060 Score: 200
Period size: 73 Copynumber: 1.9 Consensus size: 73
2246916 TACTTAGAGA
* * * *
2246926 TCTTACAAATCTCAACATTTATGAATGCTCCTTTAATAAGAGGCATTGAAACTTTAAAGATTTAA
1 TCTTACAAATCTCAACATCTATAAAAGCTCCTCTAATAAGAGGCATTGAAACTTTAAAGATTTAA
2246991 CCTAGTGG
66 CCTAGTGG
* * *
2246999 TCTTATAAATCTCGACATCTATAAAAGCTCCTCTAATCAGAGGCATTGAAACTTTAAA-ATTT
1 TCTTACAAATCTCAACATCTATAAAAGCTCCTCTAATAAGAGGCATTGAAACTTTAAAGATTT
2247061 TAAAATGTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
72 4 0.07
73 51 0.93
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (73 bp):
TCTTACAAATCTCAACATCTATAAAAGCTCCTCTAATAAGAGGCATTGAAACTTTAAAGATTTAA
CCTAGTGG
Found at i:2247228 original size:41 final size:41
Alignment explanation
Indices: 2247145--2247246 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 41
2247135 CCCAGCGGTC
2247145 TTAGAAATCATTTAGAAATTTAAGATTTTGCCTAGAAATCT
1 TTAGAAATCATTTAGAAATTTAAGATTTTGCCTAGAAATCT
* *
2247186 TTAGAATTCATTT-GAAGATTTGAA-ATTTTGCTCTA-AAGTCT
1 TTAGAAATCATTTAGAA-ATTT-AAGATTTTGC-CTAGAAATCT
*
2247227 TT-GAAAATCTTTTA-AAATTT
1 TTAG-AAATCATTTAGAAATTT
2247247 TGAGCTTTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
40 8 0.15
41 39 0.75
42 5 0.10
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (41 bp):
TTAGAAATCATTTAGAAATTTAAGATTTTGCCTAGAAATCT
Found at i:2247433 original size:21 final size:23
Alignment explanation
Indices: 2247404--2247459 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
2247394 TTGAATTCTA
*
2247404 TTCACTTCAAAA-TTTTCACT-T
1 TTCATTTCAAAAGTTTTCACTGT
2247425 TTCATTTCAAAAGTTTTTCACTGT
1 TTCATTTCAAAAG-TTTTCACTGT
*
2247449 TT-GTTTCAAAA
1 TTCATTTCAAAA
2247460 AATCTTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 11 0.37
23 16 0.53
24 3 0.10
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (23 bp):
TTCATTTCAAAAGTTTTCACTGT
Found at i:2247719 original size:25 final size:25
Alignment explanation
Indices: 2247691--2247739 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2247681 GCGAACATAC
** *
2247691 AAATATCTTTTTCTGATGCAAATGT
1 AAATATCTTTCCCTAATGCAAATGT
*
2247716 AAATGTCTTTCCCTAATGCAAATG
1 AAATATCTTTCCCTAATGCAAATG
2247740 ATCCATGCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (25 bp):
AAATATCTTTCCCTAATGCAAATGT
Found at i:2248218 original size:20 final size:20
Alignment explanation
Indices: 2248177--2248218 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2248167 CCTTTTCAAC
*
2248177 AACATTAATCCTGCATTAAA
1 AACATTAATCCTGCAATAAA
*
2248197 AACATTAATCCTTCAATGAAA
1 AACATTAATCCTGCAAT-AAA
2248218 A
1 A
2248219 GTATTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.29
Consensus pattern (20 bp):
AACATTAATCCTGCAATAAA
Found at i:2249379 original size:6 final size:6
Alignment explanation
Indices: 2249368--2249476 Score: 62
Period size: 6 Copynumber: 17.3 Consensus size: 6
2249358 TTTTCCTTTC
* * *
2249368 TTTCTT TTTCTT TACTCTA TTTCTT TTTCATTT TTTCATT TTT-TG TTT-TT
1 TTTCTT TTTCTT T-TTCTT TTTCTT TTTC--TT TTTC-TT TTTCTT TTTCTT
* * * *
2249418 TTCCTT TTTCTT GTTCTCTT TTTTTT TTTATT TTTACTTT TTTCAT TTTCTT
1 TTTCTT TTTCTT -TT-TCTT TTTCTT TTTCTT TTT-C-TT TTTCTT TTTCTT
2249470 TTT-TT TT
1 TTTCTT TT
2249477 CTTATTTTCT
Statistics
Matches: 81, Mismatches: 14, Indels: 17
0.72 0.12 0.15
Matches are distributed among these distances:
5 11 0.14
6 41 0.51
7 14 0.17
8 15 0.19
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:2249407 original size:58 final size:57
Alignment explanation
Indices: 2249339--2249486 Score: 151
Period size: 57 Copynumber: 2.5 Consensus size: 57
2249329 TTCTTCCCTT
* *
2249339 TTTTTCTCATTTTCCTTTTTTTTCCTTTCTTTCTT-TT-TCTTTACTCTATTTCTTTTT-C
1 TTTTT-TCATTTTCTTTTTTTTTCC-TT-TTTCTTGTTCTCTTT-CTCTATTTATTTTTAC
* * *
2249397 ATTTTTTCATTTT-TTGTTTTTTTCCTTTTTCTTGTTCTCTTTTTTTTTTTATTTTTAC
1 -TTTTTTCATTTTCTT-TTTTTTTCCTTTTTCTTGTTCTCTTTCTCTATTTATTTTTAC
*
2249455 TTTTTTCATTTTCTTTTTTTTTCTTATTTTCT
1 TTTTTTCATTTTCTTTTTTTTTCCT-TTTTCT
2249487 CCTTCTTTCA
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
56 6 0.08
57 36 0.47
58 30 0.39
59 5 0.06
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.76
Consensus pattern (57 bp):
TTTTTTCATTTTCTTTTTTTTTCCTTTTTCTTGTTCTCTTTCTCTATTTATTTTTAC
Found at i:2249408 original size:19 final size:18
Alignment explanation
Indices: 2249364--2249476 Score: 63
Period size: 19 Copynumber: 6.1 Consensus size: 18
2249354 TTTTTTTTCC
2249364 TTTC-TTTCTTTTTCTTT
1 TTTCATTTCTTTTTCTTT
**
2249381 ACTCTATTTCTTTTTCATTT
1 TTTC-ATTTCTTTTTC-TTT
2249401 TTTCATTT-TTTGTT-TTT
1 TTTCATTTCTTT-TTCTTT
* *
2249418 TTCCTTTTTCTTGTTCTCTTT
1 TTTC-ATTTCTT-TT-TCTTT
** *
2249439 TTTTTTTTATTTTTACTTT
1 TTTCATTTCTTTTT-CTTT
2249458 TTTCATTTTCTTTTT-TTT
1 TTTCA-TTTCTTTTTCTTT
2249476 T
1 T
2249477 CTTATTTTCT
Statistics
Matches: 73, Mismatches: 12, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
17 8 0.11
18 11 0.15
19 28 0.38
20 21 0.29
21 5 0.07
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTCATTTCTTTTTCTTT
Found at i:2249452 original size:27 final size:28
Alignment explanation
Indices: 2249408--2249474 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
2249398 TTTTTTCATT
* * *
2249408 TTTTGTTTTTTTCCTTTTTCTTGTTCTC-
1 TTTTCTTTTTTTACTTTTACTT-TTCTCA
* *
2249436 TTTT-TTTTTTTATTTTTACTTTTTTCA
1 TTTTCTTTTTTTACTTTTACTTTTCTCA
2249463 TTTTCTTTTTTT
1 TTTTCTTTTTTT
2249475 TTCTTATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 4 0.12
27 18 0.55
28 11 0.33
ACGTcount: A:0.04, C:0.12, G:0.03, T:0.81
Consensus pattern (28 bp):
TTTTCTTTTTTTACTTTTACTTTTCTCA
Found at i:2249452 original size:33 final size:32
Alignment explanation
Indices: 2249337--2249514 Score: 105
Period size: 33 Copynumber: 5.2 Consensus size: 32
2249327 TGTTCTTCCC
* **
2249337 TTTTTTTCTCA-TTTTCCTTTTTTTTCCTTTCTT
1 TTTTTTTCTTATTTTTCCTTTTTCAT--TTTCTT
*
2249370 TCTTTTTCTTTACTCTATTT-CTTTTTCATTTT-TT
1 TTTTTTTC-TTA-T-T-TTTCCTTTTTCATTTTCTT
* *
2249404 CATTTTTTGTT-TTTTTCCTTTTTC-TTGTTCTCT
1 -TTTTTTTCTTATTTTTCCTTTTTCATT-TTCT-T
* *
2249437 TTTTTTTTTTATTTTTACTTTTTTCATTTTCTT
1 TTTTTTTCTTATTTTT-CCTTTTTCATTTTCTT
*
2249470 TTTTTTTCTTATTTTCTCCTTCTTTCACCTTTTATT
1 TTTTTTTCTTATTTT-TCCTT-TTTCA--TTTTCTT
2249506 TTTCTTTTC
1 TTT-TTTTC
2249515 CTTCAAGTGG
Statistics
Matches: 114, Mismatches: 13, Indels: 32
0.72 0.08 0.20
Matches are distributed among these distances:
30 5 0.04
31 10 0.09
32 10 0.09
33 31 0.27
34 23 0.20
35 10 0.09
36 9 0.08
37 13 0.11
38 3 0.03
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.75
Consensus pattern (32 bp):
TTTTTTTCTTATTTTTCCTTTTTCATTTTCTT
Found at i:2249476 original size:50 final size:50
Alignment explanation
Indices: 2249356--2249479 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 50
2249346 CATTTTCCTT
* *
2249356 TTTTTTCCTTTCTTTCTTTTTCTTTACTCTATTTCTTTTTCATTTTTTCA
1 TTTTTTCTTTTCTTTCTTTTTCTTTACTCTATTTCTTTTTCATTTTTACA
* * * *
2249406 TTTTTTGTTTT-TTTCCTTTTTCTTGTTCTCT-TTTTTTTTTTATTTTTAC-
1 TTTTTTCTTTTCTTT-CTTTTTCTT-TACTCTATTTCTTTTTCATTTTTACA
*
2249455 TTTTTTCATTTTCTTTTTTTTTCTT
1 TTTTTTC-TTTTCTTTCTTTTTCTT
2249480 ATTTTCTCCT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
49 9 0.15
50 45 0.73
51 8 0.13
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (50 bp):
TTTTTTCTTTTCTTTCTTTTTCTTTACTCTATTTCTTTTTCATTTTTACA
Found at i:2250011 original size:4 final size:5
Alignment explanation
Indices: 2249958--2250016 Score: 59
Period size: 5 Copynumber: 11.8 Consensus size: 5
2249948 ATCAAATAAT
* *
2249958 TTTTC TTTTC ATTATTC TCTTC -TTGC TTTTC TTTT- TTTTC TTTTC TTTTC
1 TTTTC TTTTC -TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
*
2250008 TTTCC TTTT
1 TTTTC TTTT
2250017 TTCCTTTTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 6 0.14
5 32 0.73
6 3 0.07
7 3 0.07
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:2250011 original size:14 final size:14
Alignment explanation
Indices: 2249958--2250016 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
2249948 ATCAAATAAT
2249958 TTTTCTTTTCATTATTC
1 TTTTC-TTTC-TT-TTC
* *
2249975 TCTTCTTGCTTTTC
1 TTTTCTTTCTTTTC
*
2249989 TTTTTTTTCTTTTC
1 TTTTCTTTCTTTTC
2250003 TTTTCTTTCCTTTT
1 TTTTCTTT-CTTTT
2250017 TTCCTTTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 21 0.60
15 7 0.20
16 3 0.09
17 4 0.11
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTTCTTTCTTTTC
Found at i:2254782 original size:4 final size:4
Alignment explanation
Indices: 2254773--2254807 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
2254763 AGGATAAAAA
2254773 TTAT TTAT TTAT TTAT TTA- TTAT TTA- TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
2254808 ATTATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:2254797 original size:7 final size:7
Alignment explanation
Indices: 2254777--2254816 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
2254767 TAAAAATTAT
2254777 TTATTTA
1 TTATTTA
2254784 TTTATTTA
1 -TTATTTA
2254792 TTATTTA
1 TTATTTA
2254799 TTATTTA
1 TTATTTA
2254806 TTA-TTA
1 TTATTTA
2254812 TTATT
1 TTATT
2254817 ATTTAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.19
7 18 0.58
8 7 0.23
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATTTA
Found at i:2256101 original size:46 final size:45
Alignment explanation
Indices: 2256048--2256184 Score: 159
Period size: 45 Copynumber: 3.0 Consensus size: 45
2256038 GCATGTGAAT
* * * *
2256048 TAATTGCATAAATCAAACACTGAATTTTCCTACAAAATCTTCAATG
1 TAATTGCATGAATCAAGCACT-AAATTTACTACAAAATCTTCAATG
* * * *
2256094 TAATTGCATGAATCAAGCACTAAAATTACTGCAAAATCTTTAACG
1 TAATTGCATGAATCAAGCACTAAATTTACTACAAAATCTTCAATG
* *
2256139 TAATTGCATGAAT-AAGCACCAAAATTTACTTCAAAATCTTCAATG
1 TAATTGCATGAATCAAGCA-CTAAATTTACTACAAAATCTTCAATG
2256184 T
1 T
2256185 TTTTTTCAAT
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
44 5 0.06
45 53 0.69
46 19 0.25
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (45 bp):
TAATTGCATGAATCAAGCACTAAATTTACTACAAAATCTTCAATG
Found at i:2256898 original size:51 final size:51
Alignment explanation
Indices: 2256813--2256915 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 51
2256803 AAATCAAAAG
*
2256813 GATTCAAGATTTGCAAAGGTTTTCAGAATCACAAAAATGGAAGATTCACAA
1 GATTCAAGATTTGCAAAGGTTCTCAGAATCACAAAAATGGAAGATTCACAA
* * * *
2256864 GATTCCAAGTTTTGCAAAGGTTCT-AGATTCACAAAGATGGAAGATTCGCAA
1 GATT-CAAGATTTGCAAAGGTTCTCAGAATCACAAAAATGGAAGATTCACAA
2256915 G
1 G
2256916 GATTTTCAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 29 0.63
52 17 0.37
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (51 bp):
GATTCAAGATTTGCAAAGGTTCTCAGAATCACAAAAATGGAAGATTCACAA
Found at i:2256994 original size:51 final size:51
Alignment explanation
Indices: 2256939--2257051 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 51
2256929 ACAAGAAAGA
* * ** *
2256939 AAGATTTGCAAAAGTCCAAGTTTTGTAAAGGTTATAGATTCACAAAGACGC
1 AAGATTCGCAAAACTCCAAGTTTCATAAAGGTTATAGATTCACAAAGACAC
* * * * * *
2256990 AAGATTCGTAAGACTCTAAGTTTCATAAAGGTTCTAGATTCATAAAGATAC
1 AAGATTCGCAAAACTCCAAGTTTCATAAAGGTTATAGATTCACAAAGACAC
2257041 AAGATTCGCAA
1 AAGATTCGCAA
2257052 GGAATTTTAG
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (51 bp):
AAGATTCGCAAAACTCCAAGTTTCATAAAGGTTATAGATTCACAAAGACAC
Found at i:2257753 original size:33 final size:33
Alignment explanation
Indices: 2257712--2257848 Score: 111
Period size: 33 Copynumber: 4.1 Consensus size: 33
2257702 CAAGATCGGA
2257712 TGACTAGGATGAAATCATGAGTCAAAAATAAAG
1 TGACTAGGATGAAATCATGAGTCAAAAATAAAG
* * *
2257745 CGACTAGGATCG-AGT--TGAGGTAAAAAATAAA-
1 TGACTAGGAT-GAAATCATGA-GTCAAAAATAAAG
* *
2257776 TGATTAGGATGAAACCATGAGTCATAAGAAATAAAG
1 TGACTAGGATGAAATCATGAGTC--AA-AAATAAAG
** ***
2257812 TGACTAGGACAAAATCGCAAGTCAAAAATAAAG
1 TGACTAGGATGAAATCATGAGTCAAAAATAAAG
2257845 TGAC
1 TGAC
2257849 CAAGATCGAG
Statistics
Matches: 80, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
30 1 0.01
31 12 0.15
32 13 0.16
33 26 0.32
34 5 0.06
35 7 0.09
36 16 0.20
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.20
Consensus pattern (33 bp):
TGACTAGGATGAAATCATGAGTCAAAAATAAAG
Found at i:2262990 original size:36 final size:36
Alignment explanation
Indices: 2262920--2262992 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
2262910 TAGCAAAAGT
* * *
2262920 AAATAAAATAATAAAATACATGAAATATATAAATAA
1 AAATAAAATAATAAAATAAATAAAACATATAAATAA
2262956 AAATAAAATAAATAAAA-AAATCAAAACATA-AAATAA
1 AAATAAAAT-AATAAAATAAAT-AAAACATATAAATAA
2262992 A
1 A
2262993 TAAAAAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 19 0.59
37 13 0.41
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (36 bp):
AAATAAAATAATAAAATAAATAAAACATATAAATAA
Found at i:2263014 original size:25 final size:25
Alignment explanation
Indices: 2262950--2263000 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
2262940 TGAAATATAT
2262950 AAAT-AAAA-ATAAAATAAATAAAA
1 AAATCAAAACATAAAATAAATAAAA
2262973 AAATCAAAACATAAAATAAATAAAA
1 AAATCAAAACATAAAATAAATAAAA
2262998 AAA
1 AAA
2263001 GATACCTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 4 0.15
24 4 0.15
25 18 0.69
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (25 bp):
AAATCAAAACATAAAATAAATAAAA
Found at i:2265157 original size:16 final size:14
Alignment explanation
Indices: 2265138--2265176 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
2265128 AAAAAATTTA
2265138 TTTTGTTTGAATTTTT
1 TTTTGTTTG--TTTTT
2265154 TTTTGTTTGTTTTT
1 TTTTGTTTGTTTTT
2265168 TGTTTGTTT
1 T-TTTGTTT
2265177 TTCAGATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.27
15 7 0.32
16 9 0.41
ACGTcount: A:0.05, C:0.00, G:0.15, T:0.79
Consensus pattern (14 bp):
TTTTGTTTGTTTTT
Found at i:2265177 original size:10 final size:11
Alignment explanation
Indices: 2265152--2265178 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2265142 GTTTGAATTT
2265152 TTTTTTGTTTG
1 TTTTTTGTTTG
2265163 TTTTTTGTTTG
1 TTTTTTGTTTG
2265174 TTTTT
1 TTTTT
2265179 CAGATAATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (11 bp):
TTTTTTGTTTG
Found at i:2266722 original size:17 final size:16
Alignment explanation
Indices: 2266700--2266745 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
2266690 TAGATAAAAA
2266700 TTTTATTTTTTATTTAT
1 TTTTATTTTTTATTT-T
*
2266717 TTTTATTTTGATATTTT
1 TTTTATTTT-TTATTTT
*
2266734 TATTATTTTTTA
1 TTTTATTTTTTA
2266746 AATATTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 18 0.72
18 5 0.20
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTATTTTTTATTTT
Found at i:2266745 original size:24 final size:22
Alignment explanation
Indices: 2266699--2266743 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
2266689 TTAGATAAAA
2266699 ATTTTATTTTTTATTTATTTTT
1 ATTTTATTTTTTATTTATTTTT
2266721 ATTTTGATATTTTTA-TTATTTTT
1 ATTTT-AT-TTTTTATTTATTTTT
2266744 TAAATATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 10 0.48
24 6 0.29
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (22 bp):
ATTTTATTTTTTATTTATTTTT
Found at i:2266855 original size:25 final size:24
Alignment explanation
Indices: 2266827--2266882 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 24
2266817 TCTTATTAAA
* *
2266827 TTTATTTATATTTTTTATAAAAACC
1 TTTATTTAAATATTTTATAAAAA-C
* *
2266852 TTTATATTAAATATTTTGTAAACAC
1 TTTAT-TTAAATATTTTATAAAAAC
2266877 TTTATT
1 TTTATT
2266883 ACTTTGGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 11 0.42
26 14 0.54
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTATTTAAATATTTTATAAAAAC
Found at i:2267126 original size:21 final size:21
Alignment explanation
Indices: 2267094--2267134 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2267084 AAATTATGCA
2267094 TTAATAAATAAA-ATAAATAAT
1 TTAATAAATAAAGA-AAATAAT
2267115 TTAA-AAATTAAAGAAAATAA
1 TTAATAAA-TAAAGAAAATAA
2267135 AAAATACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.17
21 14 0.78
22 1 0.06
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
TTAATAAATAAAGAAAATAAT
Found at i:2267145 original size:25 final size:25
Alignment explanation
Indices: 2267098--2267146 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2267088 TATGCATTAA
* * **
2267098 TAAATAAAATAAATAATTTAAAAAT
1 TAAAGAAAATAAAAAATACAAAAAT
2267123 TAAAGAAAATAAAAAATACAAAAA
1 TAAAGAAAATAAAAAATACAAAAA
2267147 ACTAAAAAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (25 bp):
TAAAGAAAATAAAAAATACAAAAAT
Found at i:2268776 original size:19 final size:19
Alignment explanation
Indices: 2268754--2268802 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
2268744 TTAAAAGCTT
2268754 AATTTGGGCTTTA-AATTGA
1 AATTTGGGCTTTATAATT-A
* *
2268773 AATTTAGGACTTTATCATTA
1 AATTT-GGGCTTTATAATTA
2268793 AATTTGGGCT
1 AATTTGGGCT
2268803 CTCAAAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 9 0.36
20 13 0.52
21 3 0.12
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (19 bp):
AATTTGGGCTTTATAATTA
Found at i:2275369 original size:25 final size:26
Alignment explanation
Indices: 2275320--2275370 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
2275310 TAATAAAATT
* *
2275320 AATTTAATAATATTATATATTTAAAA
1 AATTTAAAAATATTATATATATAAAA
2275346 AATTTAAAAATA-TATATATATAAAA
1 AATTTAAAAATATTATATATATAAAA
2275371 TAAAAAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AATTTAAAAATATTATATATATAAAA
Found at i:2276901 original size:76 final size:76
Alignment explanation
Indices: 2276815--2276997 Score: 194
Period size: 76 Copynumber: 2.4 Consensus size: 76
2276805 GTAAACTAAA
* *
2276815 AAATTTTGAAAAATAATTTTTTTCATATTTTT-AACAAAAACCACG-TTTTTCATCTTAAAAACG
1 AAATTTTGAAAAATAAATTTTTTCATATTTTTAAACAAAAACCACGTTTTTTCATCTTAAAAACA
2276878 TCATTTTTTTGTT
66 TCA--TTTTTGTT
* * * ** * * *
2276891 AAATTATGAAAAATAAGTTTTTTC-T-TTTTTACAACAAAGACCGTGTTTTTTTTATTTTAGAAA
1 AAATTTTGAAAAATAAATTTTTTCATATTTTTA-AACAAAAACCACG-TTTTTTCATCTTAAAAA
*
2276954 TATCATTTTTGTT
64 CATCATTTTTGTT
*
2276967 AAATTTTGAAAAATAAATTTTTACATATTTT
1 AAATTTTGAAAAATAAATTTTTTCATATTTT
2276998 CAATAAAGAT
Statistics
Matches: 88, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
74 5 0.06
75 1 0.01
76 61 0.69
77 1 0.01
78 20 0.23
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.49
Consensus pattern (76 bp):
AAATTTTGAAAAATAAATTTTTTCATATTTTTAAACAAAAACCACGTTTTTTCATCTTAAAAACA
TCATTTTTGTT
Found at i:2277385 original size:9 final size:10
Alignment explanation
Indices: 2277364--2277407 Score: 54
Period size: 9 Copynumber: 4.3 Consensus size: 10
2277354 TCTTAATTTT
2277364 ATATAATAAA
1 ATATAATAAA
2277374 ATATAA-AAA
1 ATATAATAAA
2277383 ATATAATTAACA
1 ATATAA-TAA-A
*
2277395 AAATAATAAA
1 ATATAATAAA
2277405 ATA
1 ATA
2277408 ATTTGTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 9 0.31
10 9 0.31
11 5 0.17
12 6 0.21
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (10 bp):
ATATAATAAA
Done.