Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold19
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: 2266706
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17655 characters in sequence are not A, C, G, or T
File 9 of 15
Found at i:1149130 original size:13 final size:13
Alignment explanation
Indices: 1149112--1149137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1149102 GCATAAGTTT
1149112 TGTATCGATACAA
1 TGTATCGATACAA
1149125 TGTATCGATACAA
1 TGTATCGATACAA
1149138 AGCTACCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1149204 original size:19 final size:19
Alignment explanation
Indices: 1149162--1149214 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
1149152 CTACCAAGGA
* *
1149162 AATGTATTGATACGTTAAT
1 AATGTATCGATACATTAAT
*
1149181 AATGTATCGATACATTATT
1 AATGTATCGATACATTAAT
* *
1149200 CATGTATCAATACAT
1 AATGTATCGATACAT
1149215 GCGGGCAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (19 bp):
AATGTATCGATACATTAAT
Found at i:1151971 original size:13 final size:13
Alignment explanation
Indices: 1151953--1151978 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1151943 CAATTTTTTG
1151953 TGTATCGATACAT
1 TGTATCGATACAT
1151966 TGTATCGATACAT
1 TGTATCGATACAT
1151979 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1151990 original size:32 final size:33
Alignment explanation
Indices: 1151933--1151996 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1151923 TACAAGCCAA
**
1151933 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1151966 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1151997 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1152739 original size:21 final size:21
Alignment explanation
Indices: 1152698--1152741 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1152688 CTCCCCTTTA
* *
1152698 TCTCCCCCTTTTATTAATAAT
1 TCTCCCCCTTTAATCAATAAT
1152719 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCTTTAATCAA-TAAT
1152740 TC
1 TC
1152742 ATGTCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (21 bp):
TCTCCCCCTTTAATCAATAAT
Found at i:1154557 original size:13 final size:13
Alignment explanation
Indices: 1154539--1154577 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1154529 ATAATCCCCC
*
1154539 TGTATCGATACAG
1 TGTATCGATACAA
1154552 TGTATCGATACAA
1 TGTATCGATACAA
1154565 TGTATCGATACAA
1 TGTATCGATACAA
1154578 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1156666 original size:15 final size:15
Alignment explanation
Indices: 1156646--1156676 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1156636 ATTTCGTTTG
*
1156646 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1156661 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1156676 G
1 G
1156677 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1160770 original size:13 final size:13
Alignment explanation
Indices: 1160752--1160777 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1160742 CAATTTTTTG
1160752 TGTATCGATACAT
1 TGTATCGATACAT
1160765 TGTATCGATACAT
1 TGTATCGATACAT
1160778 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1163643 original size:19 final size:19
Alignment explanation
Indices: 1163619--1163657 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1163609 TGATCATTTG
1163619 CTTGTTCCTTACAGATATA
1 CTTGTTCCTTACAGATATA
1163638 CTTGTTCCTTACAGATATA
1 CTTGTTCCTTACAGATATA
1163657 C
1 C
1163658 ATTCGATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (19 bp):
CTTGTTCCTTACAGATATA
Found at i:1164648 original size:7 final size:8
Alignment explanation
Indices: 1164631--1164693 Score: 54
Period size: 8 Copynumber: 6.9 Consensus size: 8
1164621 AGAAATATAT
1164631 AAAAATAA
1 AAAAATAA
1164639 AAAAATAA
1 AAAAATAA
1164647 AATCAACATCATA
1 AA--AA-AT-A-A
1164660 AAAAATATA
1 AAAAATA-A
1164669 AAAAATTAAA
1 AAAAA-T-AA
1164679 AAAAATAA
1 AAAAATAA
1164687 AAAAATA
1 AAAAATA
1164694 GTTATAAACG
Statistics
Matches: 48, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
8 19 0.40
9 9 0.19
10 11 0.23
11 5 0.10
12 1 0.02
13 3 0.06
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:1164681 original size:10 final size:9
Alignment explanation
Indices: 1164631--1164691 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
1164621 AGAAATATAT
1164631 AAAAAT-AA
1 AAAAATAAA
1164639 AAAAATAAA
1 AAAAATAAA
* *
1164648 ATCAACATCATA
1 A--AAAAT-AAA
1164660 AAAAATATAA
1 AAAAATA-AA
*
1164670 AAAATTAAA
1 AAAAATAAA
1164679 AAAAATAAA
1 AAAAATAAA
1164688 AAAA
1 AAAA
1164692 TAGTTATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
8 6 0.14
9 18 0.43
10 11 0.26
11 4 0.10
12 3 0.07
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAATAAA
Found at i:1169570 original size:29 final size:29
Alignment explanation
Indices: 1169528--1169586 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1169518 AAATGCATAC
1169528 TTGAATCAACTATGAAAACATTTACCTGA
1 TTGAATCAACTATGAAAACATTTACCTGA
1169557 TTGAATCAACTATGAAAACATTTACCTGA
1 TTGAATCAACTATGAAAACATTTACCTGA
1169586 T
1 T
1169587 CATATCCTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (29 bp):
TTGAATCAACTATGAAAACATTTACCTGA
Found at i:1171657 original size:19 final size:17
Alignment explanation
Indices: 1171633--1171671 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
1171623 AAATTAAATA
1171633 ATTTATATATTTATATTAT
1 ATTTATATATTT-T-TTAT
1171652 ATTTATATATTTTTTAT
1 ATTTATATATTTTTTAT
1171669 ATT
1 ATT
1171672 AAAATTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
19 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTATATATTTTTTAT
Found at i:1171781 original size:19 final size:18
Alignment explanation
Indices: 1171747--1171814 Score: 77
Period size: 16 Copynumber: 3.7 Consensus size: 18
1171737 TTTTGATATA
*
1171747 TTTATATATTTATATCATT
1 TTTAT-TATTTTTATCATT
1171766 TCTTATTATTTTTATCA--
1 T-TTATTATTTTTATCATT
1171783 TTTATTATTTTTATCATGT
1 TTTATTATTTTTATCAT-T
1171802 TTTAATTATTTTT
1 TTT-ATTATTTTT
1171815 TATGTTTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
16 15 0.35
17 1 0.02
19 14 0.33
20 13 0.30
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTATTATTTTTATCATT
Found at i:1171814 original size:10 final size:9
Alignment explanation
Indices: 1171747--1171814 Score: 50
Period size: 10 Copynumber: 7.3 Consensus size: 9
1171737 TTTTGATATA
1171747 TTTATATATT
1 TTTAT-TATT
* *
1171757 TATATCATT
1 TTTATTATT
1171766 TCTTATTATT
1 T-TTATTATT
*
1171776 TTTATCA--
1 TTTATTATT
1171783 TTTATTATT
1 TTTATTATT
*
1171792 TTTATCATGT
1 TTTATTAT-T
1171802 TTTAATTATT
1 TTT-ATTATT
1171812 TTT
1 TTT
1171815 TATGTTTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
7 6 0.13
9 16 0.36
10 19 0.42
11 4 0.09
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (9 bp):
TTTATTATT
Found at i:1171824 original size:37 final size:36
Alignment explanation
Indices: 1171746--1171814 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
1171736 ATTTTGATAT
1171746 ATTTATATATTTATATCATTTCTTATTATTTTTATC
1 ATTTATATATTTATATCATTTCTTATTATTTTTATC
*
1171782 ATTTAT-TATTTTTATCATGTT-TTAATTATTTTT
1 ATTTATATATTTATATCAT-TTCTT-ATTATTTTT
1171815 TATGTTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 13 0.43
36 17 0.57
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (36 bp):
ATTTATATATTTATATCATTTCTTATTATTTTTATC
Found at i:1171827 original size:20 final size:20
Alignment explanation
Indices: 1171753--1171823 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 20
1171743 TATATTTATA
*
1171753 TATTTATATCAT-TTCTT-AT
1 TATTTTTATCATGTT-TTAAT
1171772 TATTTTTATCA---TTT-AT
1 TATTTTTATCATGTTTTAAT
1171788 TATTTTTATCATGTTTTAAT
1 TATTTTTATCATGTTTTAAT
1171808 TATTTTT-T-ATGTTTTA
1 TATTTTTATCATGTTTTA
1171824 TAATATTATT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
16 15 0.32
17 1 0.02
18 8 0.17
19 14 0.30
20 9 0.19
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.68
Consensus pattern (20 bp):
TATTTTTATCATGTTTTAAT
Found at i:1173488 original size:25 final size:26
Alignment explanation
Indices: 1173432--1173488 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
1173422 TCATTTTTTA
* *
1173432 TTTTTCTTTTCGGCCTTTTTTCTTCT
1 TTTTTCTTTTCGACCTTTTTCCTTCT
*
1173458 TATTTCTTTT-GACCTTTTTCCCTT-T
1 TTTTTCTTTTCGACCTTTTT-CCTTCT
1173483 TTTTTC
1 TTTTTC
1173489 CCCTCCCGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.04, C:0.23, G:0.05, T:0.68
Consensus pattern (26 bp):
TTTTTCTTTTCGACCTTTTTCCTTCT
Found at i:1176159 original size:6 final size:6
Alignment explanation
Indices: 1176150--1176179 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1176140 TTAGATTAAT
1176150 GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG
1 GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG
1176180 CACCGTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.83, T:0.00
Consensus pattern (6 bp):
GGAGGG
Found at i:1177209 original size:43 final size:42
Alignment explanation
Indices: 1177156--1177385 Score: 161
Period size: 43 Copynumber: 5.3 Consensus size: 42
1177146 TGATCACTTA
1177156 ATTTAATATAAAATTATTTAAAGTTAAATATATTAGTTGGACC
1 ATTTAATATAAAATTATTTAAAGTTAAATATATTAGTT-GACC
* * * *
1177199 ATTT-AT-TATAATTAAGTTTAAAGTTTTAAA-ATAATT-GATCACTTA
1 ATTTAATATAAAATT-A-TTTAAAG--TTAAATAT-ATTAGTTGAC--C
1177244 ATTTAATATAAAATTATTTAAAGTTAAATATATTAGTTAGACC
1 ATTTAATATAAAATTATTTAAAGTTAAATATATTAGTT-GACC
* * * *
1177287 ATTT-AT-TATAATTAAATTTAAAGTTTTAAGATA-ATT-GATCACTTA
1 ATTTAATATAAAATT--ATTTAAAG--TTAA-ATATATTAGTTGAC--C
*
1177332 ATTTAATATAAAATTATTTAAAGTTAAATATATTAGTTGGATC
1 ATTTAATATAAAATTATTTAAAGTTAAATATATTAGTT-GACC
*
1177375 ATTTATTATAA
1 ATTTAATATAA
1177386 TTAAGTTTAA
Statistics
Matches: 145, Mismatches: 18, Indels: 48
0.69 0.09 0.23
Matches are distributed among these distances:
41 12 0.08
42 8 0.06
43 52 0.36
44 12 0.08
45 41 0.28
46 8 0.06
47 12 0.08
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (42 bp):
ATTTAATATAAAATTATTTAAAGTTAAATATATTAGTTGACC
Found at i:1177251 original size:88 final size:88
Alignment explanation
Indices: 1177081--1177427 Score: 517
Period size: 88 Copynumber: 4.0 Consensus size: 88
1177071 ATGATGTATC
* * * *
1177081 AAAATTATTTAAATTTAAATATAATAGTTAG-CTCATTTA-T-T-A-CAAGTTT-AAGATTTTAT
1 AAAATTATTTAAAGTTAAATATATTAGTTAGAC-CATTTATTATAATTAAGTTTAAAG-TTTTAA
1177140 GATAATTGATCACTTAATTTAATAT
64 GATAATTGATCACTTAATTTAATAT
* *
1177165 AAAATTATTTAAAGTTAAATATATTAGTTGGACCATTTATTATAATTAAGTTTAAAGTTTTAAAA
1 AAAATTATTTAAAGTTAAATATATTAGTTAGACCATTTATTATAATTAAGTTTAAAGTTTTAAGA
1177230 TAATTGATCACTTAATTTAATAT
66 TAATTGATCACTTAATTTAATAT
*
1177253 AAAATTATTTAAAGTTAAATATATTAGTTAGACCATTTATTATAATTAAATTTAAAGTTTTAAGA
1 AAAATTATTTAAAGTTAAATATATTAGTTAGACCATTTATTATAATTAAGTTTAAAGTTTTAAGA
1177318 TAATTGATCACTTAATTTAATAT
66 TAATTGATCACTTAATTTAATAT
* * *
1177341 AAAATTATTTAAAGTTAAATATATTAGTTGGATCATTTATTATAATTAAGTTTAAAATTTTAAGA
1 AAAATTATTTAAAGTTAAATATATTAGTTAGACCATTTATTATAATTAAGTTTAAAGTTTTAAGA
* * *
1177406 TAATTAATCATTTGATTTAATA
66 TAATTGATCACTTAATTTAATA
1177428 CAGTATTAGA
Statistics
Matches: 241, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
84 34 0.14
85 2 0.01
86 1 0.00
87 1 0.00
88 200 0.83
89 3 0.01
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (88 bp):
AAAATTATTTAAAGTTAAATATATTAGTTAGACCATTTATTATAATTAAGTTTAAAGTTTTAAGA
TAATTGATCACTTAATTTAATAT
Found at i:1177254 original size:45 final size:44
Alignment explanation
Indices: 1177141--1177356 Score: 134
Period size: 45 Copynumber: 4.9 Consensus size: 44
1177131 AGATTTTATG
1177141 ATAATTGATCACTTAATTTAATATAAAATT-ATTTAAAG--TT-AA
1 ATAATTGATCACTTAATTTAATAT--AATTAATTTAAAGTTTTAAA
* * * *
1177183 ATATATTAGTTGGAC--CATTTATTATAATTAAGTTTAAAGTTTTAAA
1 ATA-ATT-GAT-CACTTAATTTAATATAATTAA-TTTAAAGTTTTAAA
1177229 ATAATTGATCACTTAATTTAATATAAAATT-ATTTAAAG--TT-AA
1 ATAATTGATCACTTAATTTAATAT--AATTAATTTAAAGTTTTAAA
* * * * *
1177271 ATATATTAGTTAGAC--CATTTATTATAATTAAATTTAAAGTTTTAAG
1 ATA-ATT-GAT-CACTTAATTTAATATAATT-AATTTAAAGTTTTAAA
1177317 ATAATTGATCACTTAATTTAATATAAAATT-ATTTAAAGTT
1 ATAATTGATCACTTAATTTAATAT--AATTAATTTAAAGTT
1177357 AAATATATTA
Statistics
Matches: 133, Mismatches: 17, Indels: 45
0.68 0.09 0.23
Matches are distributed among these distances:
41 8 0.06
42 9 0.07
43 43 0.32
44 8 0.06
45 47 0.35
46 10 0.08
47 8 0.06
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (44 bp):
ATAATTGATCACTTAATTTAATATAATTAATTTAAAGTTTTAAA
Found at i:1178750 original size:10 final size:11
Alignment explanation
Indices: 1178719--1178765 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
1178709 TAAATTAATA
*
1178719 TAATTAAAAAT
1 TAATAAAAAAT
1178730 TAATAAAAAAT
1 TAATAAAAAAT
*
1178741 T-ATATAAAAT
1 TAATAAAAAAT
**
1178751 CGATAAAAAAT
1 TAATAAAAAAT
1178762 TAAT
1 TAAT
1178766 TATATATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (11 bp):
TAATAAAAAAT
Found at i:1179147 original size:16 final size:17
Alignment explanation
Indices: 1179126--1179160 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1179116 TCAAGTAATA
*
1179126 TATTTTAATA-AAAAAT
1 TATTTTAAAATAAAAAT
1179142 TATTTTAAAATAAAAAT
1 TATTTTAAAATAAAAAT
1179159 TA
1 TA
1179161 AAATATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TATTTTAAAATAAAAAT
Found at i:1179188 original size:17 final size:18
Alignment explanation
Indices: 1179122--1179188 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 18
1179112 TATATCAAGT
1179122 AATATATTTTAATA-AAA
1 AATATATTTTAATATAAA
*
1179139 AAT-TATTTTAAAATAAA
1 AATATATTTTAATATAAA
* *
1179156 AATTAAAATATTAATATAAA
1 AA-T-ATATTTTAATATAAA
1179176 AATAT-TTTTAATA
1 AATATATTTTAATA
1179189 ATTAAATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 9 0.22
17 15 0.38
18 2 0.05
19 1 0.03
20 13 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATATTTTAATATAAA
Found at i:1180032 original size:21 final size:22
Alignment explanation
Indices: 1179981--1180033 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
1179971 AATAAAATAA
1179981 TAAATTTAAATTTAGATAAATT
1 TAAATTTAAATTTAGATAAATT
*
1180003 TAACA-TTAATTTTTA-AT-AATT
1 TAA-ATTTAA-ATTTAGATAAATT
1180024 TAAATTTAAA
1 TAAATTTAAA
1180034 ATTAATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
20 1 0.04
21 11 0.42
22 9 0.35
23 5 0.19
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TAAATTTAAATTTAGATAAATT
Found at i:1180847 original size:33 final size:32
Alignment explanation
Indices: 1180786--1180847 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
1180776 TTTGCTTTTC
* * *
1180786 ATTTTTATTTTATTTTCTTTATTCATTTTCTA
1 ATTTTTATTATATTTTCTTTAATAATTTTCTA
1180818 ATTTTTATTATATTTTTCTTTAATAATTTT
1 ATTTTTATTATA-TTTTCTTTAATAATTTT
1180848 TTTATTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 11 0.42
33 15 0.58
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (32 bp):
ATTTTTATTATATTTTCTTTAATAATTTTCTA
Found at i:1180855 original size:33 final size:32
Alignment explanation
Indices: 1180781--1180855 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 32
1180771 TTCATTTTGC
* * * *
1180781 TTTTCATTTTTATTTTATTTTCTTTATTCATT
1 TTTTAATTTTTATTATATTTTCTTTAATAATT
*
1180813 TTCTAATTTTTATTATATTTTTCTTTAATAATT
1 TTTTAATTTTTATTATA-TTTTCTTTAATAATT
*
1180846 TTTTTATTTT
1 TTTTAATTTT
1180856 CAAAAACTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
32 14 0.40
33 21 0.60
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (32 bp):
TTTTAATTTTTATTATATTTTCTTTAATAATT
Found at i:1181211 original size:15 final size:15
Alignment explanation
Indices: 1181193--1181223 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1181183 ATTAATTTCG
1181193 AGTTAGATTATTTTA
1 AGTTAGATTATTTTA
1181208 AGTTAGATTATTTTA
1 AGTTAGATTATTTTA
1181223 A
1 A
1181224 ATTTTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (15 bp):
AGTTAGATTATTTTA
Found at i:1181309 original size:16 final size:16
Alignment explanation
Indices: 1181267--1181324 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
1181257 ATCATTTTGG
*
1181267 ATTTGAGTCATTTCGA
1 ATTTGAGTTATTTCGA
* ** * *
1181283 GTTCAAATTATTTTGA
1 ATTTGAGTTATTTCGA
1181299 ATTTGAGTTATTTCGA
1 ATTTGAGTTATTTCGA
*
1181315 ATTTGGGTTA
1 ATTTGAGTTA
1181325 ATCGGGTTTA
Statistics
Matches: 30, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.48
Consensus pattern (16 bp):
ATTTGAGTTATTTCGA
Found at i:1182900 original size:39 final size:40
Alignment explanation
Indices: 1182843--1182935 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
1182833 AAAATAAGAG
* * *
1182843 AAAATTTTGTGTAGATTTAT-ATTCGTATTATGTAGATTT
1 AAAATTTTATATAAATTTATAATTCGTATTATGTAGATTT
*
1182882 AAAATTTTATATAAATTTATAATTCGTTTTATGTAGATTT
1 AAAATTTTATATAAATTTATAATTCGTATTATGTAGATTT
* *
1182922 GACATATTTATATA
1 AAAAT-TTTATATA
1182936 TTCATATTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 17 0.37
40 21 0.46
41 8 0.17
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (40 bp):
AAAATTTTATATAAATTTATAATTCGTATTATGTAGATTT
Found at i:1182921 original size:22 final size:22
Alignment explanation
Indices: 1182847--1182921 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 22
1182837 TAAGAGAAAA
*
1182847 TTTTGTGTAGATTTAT-ATTCG
1 TTTTATGTAGATTTATAATTCG
* *
1182868 TATTATGTAGATTTA-AA---A
1 TTTTATGTAGATTTATAATTCG
* *
1182886 TTTTATATAAATTTATAATTCG
1 TTTTATGTAGATTTATAATTCG
1182908 TTTTATGTAGATTT
1 TTTTATGTAGATTT
1182922 GACATATTTA
Statistics
Matches: 40, Mismatches: 9, Indels: 9
0.69 0.16 0.16
Matches are distributed among these distances:
18 12 0.30
19 2 0.05
21 14 0.35
22 12 0.30
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.55
Consensus pattern (22 bp):
TTTTATGTAGATTTATAATTCG
Found at i:1183524 original size:13 final size:13
Alignment explanation
Indices: 1183506--1183531 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1183496 ACACCAAAGT
1183506 ATGTATCGATACA
1 ATGTATCGATACA
1183519 ATGTATCGATACA
1 ATGTATCGATACA
1183532 CAAAAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1183548 original size:32 final size:33
Alignment explanation
Indices: 1183487--1183550 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1183477 TAGCCAAACT
* *
1183487 TGTATCGATACACCAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
1183520 TGTATCGATACACAAAAAT-TGTATCGATACA
1 TGTATCGATACACAAAAATATGTATCGATACA
1183551 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:1189734 original size:12 final size:13
Alignment explanation
Indices: 1189717--1189753 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
1189707 TACATTTTCT
1189717 TGTATCGATACA-
1 TGTATCGATACAC
1189729 TGTATCGATACAC
1 TGTATCGATACAC
*
1189742 TGTATTGATACA
1 TGTATCGATACA
1189754 GGGGGATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1191338 original size:22 final size:20
Alignment explanation
Indices: 1191296--1191338 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
1191286 GTGTTTAATA
*
1191296 TATTTGCTTGACTTTGTATT
1 TATTTGCTTGACTTTGAATT
1191316 TATTTGCATTGTACTTTGAATT
1 TATTTGC-TTG-ACTTTGAATT
1191338 T
1 T
1191339 TAATCTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 3 0.15
22 10 0.50
ACGTcount: A:0.19, C:0.09, G:0.14, T:0.58
Consensus pattern (20 bp):
TATTTGCTTGACTTTGAATT
Found at i:1192239 original size:13 final size:13
Alignment explanation
Indices: 1192221--1192246 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1192211 ACACCAAAGT
1192221 ATGTATCGATACA
1 ATGTATCGATACA
1192234 ATGTATCGATACA
1 ATGTATCGATACA
1192247 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1192244 original size:33 final size:33
Alignment explanation
Indices: 1192202--1192266 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1192192 TAGCCAAACT
* *
1192202 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
1192235 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1192267 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1194499 original size:19 final size:19
Alignment explanation
Indices: 1194447--1194499 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
1194437 ACTTATATCG
*
1194447 ATATAAAATTAAATTAATTTT
1 ATATATAATT-AA-TAATTTT
* *
1194468 ATACAT-TTTAATAATTTT
1 ATATATAATTAATAATTTT
1194486 ATATATAATTAATA
1 ATATATAATTAATA
1194500 TATTAACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 12 0.46
19 8 0.31
20 2 0.08
21 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATAATTAATAATTTT
Found at i:1195144 original size:2 final size:2
Alignment explanation
Indices: 1195137--1195177 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1195127 TCCTCCTTTT
1195137 TA TA TA TA 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 TA TA TA TA T
1195178 GCATTTTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1195945 original size:20 final size:19
Alignment explanation
Indices: 1195922--1195959 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1195912 ATATTTTTCG
*
1195922 ATGTATTGATACATGTATGA
1 ATGTATCGATACAT-TATGA
1195942 ATGTATCGATACATTATG
1 ATGTATCGATACATTATG
1195960 TCTTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATTATGA
Found at i:1196049 original size:51 final size:54
Alignment explanation
Indices: 1195921--1196059 Score: 189
Period size: 51 Copynumber: 2.7 Consensus size: 54
1195911 TATATTTTTC
* * *
1195921 GATGTATTGATACA-TGTATGAATGTATCGATACATTATGTCTTTTTTAACCCA
1 GATGTATTGATACATTGAATCAATGTATCGATACATTATATCTTTTTTAACCCA
* **
1195974 GATGTATCGATACATT-CTTCAATGTATCGATACATTATATC-TTTTT-ACCCA
1 GATGTATTGATACATTGAATCAATGTATCGATACATTATATCTTTTTTAACCCA
1196025 GATGTATTGATACATTGAAT-AATGTATCGATACAT
1 GATGTATTGATACATTGAATCAATGTATCGATACAT
1196060 CTAGTTAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
51 35 0.46
52 6 0.08
53 34 0.45
54 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (54 bp):
GATGTATTGATACATTGAATCAATGTATCGATACATTATATCTTTTTTAACCCA
Found at i:1209984 original size:12 final size:11
Alignment explanation
Indices: 1209963--1210040 Score: 70
Period size: 11 Copynumber: 6.9 Consensus size: 11
1209953 CATCCTTCAT
1209963 ACAAAAAAAAA
1 ACAAAAAAAAA
*
1209974 CCAAGAAAAAAA
1 ACAA-AAAAAAA
1209986 ACAAAAAAATAA
1 ACAAAAAAA-AA
1209998 A-AAATAGAAAAA
1 ACAAA-A-AAAAA
* **
1210010 ACTAAAAGCAA
1 ACAAAAAAAAA
1210021 A-AAAAAAAAA
1 ACAAAAAAAAA
1210031 ACAAAAAAAA
1 ACAAAAAAAA
1210041 GGGTCCAGAT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
10 7 0.13
11 23 0.43
12 18 0.34
13 5 0.09
ACGTcount: A:0.83, C:0.09, G:0.04, T:0.04
Consensus pattern (11 bp):
ACAAAAAAAAA
Found at i:1210009 original size:37 final size:36
Alignment explanation
Indices: 1209968--1210038 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
1209958 TTCATACAAA
*
1209968 AAAAAACCAAGAA-AAAAAACAAAAAAATAAAAAATAG
1 AAAAAACCAA-AACAAAAAA-AAAAAAACAAAAAATAG
*
1210005 AAAAAACTAAAAGCAAAAAAAAAAAAACAAAAAA
1 AAAAAACCAAAA-CAAAAAAAAAAAAACAAAAAA
1210039 AAGGGTCCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 2 0.07
37 22 0.73
38 6 0.20
ACGTcount: A:0.83, C:0.08, G:0.04, T:0.04
Consensus pattern (36 bp):
AAAAAACCAAAACAAAAAAAAAAAAACAAAAAATAG
Found at i:1210040 original size:14 final size:14
Alignment explanation
Indices: 1209965--1210040 Score: 73
Period size: 14 Copynumber: 5.3 Consensus size: 14
1209955 TCCTTCATAC
*
1209965 AAAAAAAAAC-CAA
1 AAAAAAAAACAAAA
*
1209978 GAAAAAAAACAAAA
1 AAAAAAAAACAAAA
*
1209992 AAATAAAAAATAGAAA
1 AAA-AAAAAACA-AAA
* *
1210008 AAACTAAAAGCAAAA
1 AAA-AAAAAACAAAA
1210023 AAAAAAAAACAAAA
1 AAAAAAAAACAAAA
1210037 AAAA
1 AAAA
1210041 GGGTCCAGAT
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
13 9 0.18
14 17 0.34
15 13 0.26
16 11 0.22
ACGTcount: A:0.84, C:0.08, G:0.04, T:0.04
Consensus pattern (14 bp):
AAAAAAAAACAAAA
Found at i:1211151 original size:28 final size:28
Alignment explanation
Indices: 1211119--1211464 Score: 361
Period size: 28 Copynumber: 12.1 Consensus size: 28
1211109 CGTTCATCTC
* * *
1211119 TTCAAAGCCCACAGGTTAGTGGTATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1211147 TTCAAAGCTCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1211175 TTCAAAGGCCACAAGTTAGTGGAATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1211203 TTCAAAGCCCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* ** *
1211231 TTCAAAACCCTTAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1211259 TTCAAAGCCCACAAGTGAGTGGCATCAT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1211287 TTCAAAGCCCACAAGTCAGTGGTACCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1211315 TTCAAAGGCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1211343 TTCTAAGCCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* *
1211373 TTCAAAGCCCACAAGTCGGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1211401 TTCAAAGCCCACACAAGT-AGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCA-GTGGC-A-TCCT
* *
1211433 TTCAAAGCCCACACAAGTTAGTGGCACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
1211463 TT
1 TT
1211465 TTTTTTCTAA
Statistics
Matches: 267, Mismatches: 43, Indels: 14
0.82 0.13 0.04
Matches are distributed among these distances:
28 196 0.73
29 2 0.01
30 41 0.15
31 2 0.01
32 25 0.09
33 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:1212387 original size:20 final size:20
Alignment explanation
Indices: 1212362--1212415 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1212352 TTTTACCTAG
*
1212362 ATGTATCGATACA-GTTTTCA
1 ATGTATCGATACATG-TATCA
*
1212382 ATGTATCGATACATGTATGA
1 ATGTATCGATACATGTATCA
1212402 ATGTATCGATACAT
1 ATGTATCGATACAT
1212416 TCTATCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:1212407 original size:40 final size:39
Alignment explanation
Indices: 1212362--1212503 Score: 127
Period size: 40 Copynumber: 3.7 Consensus size: 39
1212352 TTTTACCTAG
1212362 ATGTATCGATACAGTTTTCAATGTATCGATACATGTATGA
1 ATGTATCGATACA-TTTTCAATGTATCGATACATGTATGA
* * *** *
1212402 ATGTATCGATACA--TTCTATCT-TTTTTAC--CTA-G-
1 ATGTATCGATACATTTTCAATGTATCGATACATGTATGA
* *
1212434 ATGTGTCGATACATTTTTCAATGTATCGATACATGGATGA
1 ATGTATCGATACA-TTTTCAATGTATCGATACATGTATGA
*
1212474 ATGCATCGATACATTCTTCAATGTATCGAT
1 ATGTATCGATACATT-TTCAATGTATCGAT
1212504 GCATTCTATC
Statistics
Matches: 77, Mismatches: 16, Indels: 18
0.69 0.14 0.16
Matches are distributed among these distances:
32 12 0.16
33 1 0.01
34 2 0.03
35 6 0.08
36 8 0.10
37 6 0.08
38 1 0.01
39 3 0.04
40 38 0.49
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (39 bp):
ATGTATCGATACATTTTCAATGTATCGATACATGTATGA
Found at i:1212462 original size:20 final size:20
Alignment explanation
Indices: 1212434--1212510 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
1212424 TTTTACCTAG
* *
1212434 ATGTGTCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
*** *
1212454 ATGTATCGATACATGGATGA
1 ATGTATCGATACATTCTTCA
*
1212474 ATGCATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
1212494 ATGTATCGATGCATTCT
1 ATGTATCGATACATTCT
1212511 ATCTTTTTAC
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1212474 original size:72 final size:72
Alignment explanation
Indices: 1212352--1212490 Score: 242
Period size: 72 Copynumber: 1.9 Consensus size: 72
1212342 AAAGTCACAG
* *
1212352 TTTTACCTAGATGTATCGATACAGTTTTCAATGTATCGATACATGTATGAATGTATCGATACATT
1 TTTTACCTAGATGTATCGATACAGTTTTCAATGTATCGATACATGGATGAATGCATCGATACATT
1212417 CTATCTT
66 CTATCTT
* *
1212424 TTTTACCTAGATGTGTCGATACATTTTTCAATGTATCGATACATGGATGAATGCATCGATACATT
1 TTTTACCTAGATGTATCGATACAGTTTTCAATGTATCGATACATGGATGAATGCATCGATACATT
1212489 CT
66 CT
1212491 TCAATGTATC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (72 bp):
TTTTACCTAGATGTATCGATACAGTTTTCAATGTATCGATACATGGATGAATGCATCGATACATT
CTATCTT
Found at i:1215995 original size:2 final size:2
Alignment explanation
Indices: 1215988--1216017 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1215978 TCTTTACATA
*
1215988 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1216018 CTTAGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1216904 original size:20 final size:20
Alignment explanation
Indices: 1216879--1216916 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1216869 TTATGTTCAA
1216879 ATTTAAAATAAATTTAAAAT
1 ATTTAAAATAAATTTAAAAT
* *
1216899 ATTTAATATATATTTAAA
1 ATTTAAAATAAATTTAAA
1216917 TAAGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTAAAATAAATTTAAAAT
Found at i:1220531 original size:20 final size:20
Alignment explanation
Indices: 1220506--1220580 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
1220496 AAAAGGATAG
*
1220506 AATGTATCGATATATTGAAA
1 AATGTATCGATACATTGAAA
* *
1220526 AATGTATCGATACATTCATA
1 AATGTATCGATACATTGAAA
*
1220546 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
1220566 AATGTATCGATACAT
1 AATGTATCGATACAT
1220581 CTGGGTACTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:1221540 original size:28 final size:28
Alignment explanation
Indices: 1221462--1222511 Score: 1321
Period size: 28 Copynumber: 37.4 Consensus size: 28
1221452 ACTAGCTTGG
* *
1221462 GTGGGCTTTGAAAAGAGTGCCACTGACTTGT
1 GTGGGCTTTG-AAAGGGTGCCACTGAC-T-C
* *
1221493 GTGGGCTTTGAAAGAGTGCCACTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* * * * *
1221521 GTAGGCATTGAAAAGATGCCACTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* * *
1221549 GTGGGCTTTGAAAGGATACCACTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
** *
1221577 GTGATCTTTGAAAGGGTGCCACTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* *
1221605 GTGGACTTTGAAAGGGTGCCACTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
*
1221633 GTGGGCTTTGAAAGGGTGCCATTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* *
1221661 GTAGGCTTTGAAAGGGTGCCATTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* * *
1221689 GTAGGCTTTGAAAGGGTGCCGCTAACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
*
1221717 GTGGGCTTTGAAAGGGTGCCGCTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* *
1221745 GTGGGCTTTGAAAGGATACCACTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* *
1221773 GTGGGCTTTGAAAGGATGCCGCTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* * * *
1221801 ATGGACTTTGAAAGGATGCCGCTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
*
1221829 GTGGGCTTTGAAAGGATGCCACTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* * *
1221857 GTGAGCTTTGAAAGGGTGCCATTGACTG
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* *
1221885 GTGGGCTTTAAAAGGGTGCCACTGACTA
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
*
1221913 GTGGGCTTT-AGAA-GGTGCCACTAACTC
1 GTGGGCTTTGA-AAGGGTGCCACTGACTC
*
1221940 GTGGGCTTTGAAAGGGTGCCACTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* *
1221968 GTAGGCTTTGAAAGCGTGCCACTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* *
1221996 GTGGGCTTTAAAAGGGTGCCACTAACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
** * * *
1222024 GTAAGCTTTAAAAGGGTGCCATTCACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
*
1222052 GTGGGCTTTGAAAGGGTGCCACTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
*
1222080 GTGGGCTTCGAAAGGGTGCCACTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* * *
1222108 GTGAGCTTTGAAAGGGTTCCACTAACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* *
1222136 ATGGGCTTTGAAAGGGTGCCATTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* *
1222164 ATGGGCTTTAAAAGGGTGCCACTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* *
1222192 GTGGGCTTTAAAAGGGTGCCACTAACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* * *
1222220 ATGGGCTTTGAAAGGGTGCCATTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* *
1222248 ATGGGCTTTGAAAGGATGCCACTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* *
1222276 GTGGGCTTTGAAAGGATGCCACTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* * *
1222304 GTGGGCTTTGAAAGGGTGCCATTAACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
*
1222332 ATGGGCTTTGAAAGGGTGCCACTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* * * *
1222360 ATGGGCTTTAAAAGGATGCCACTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
*
1222388 GTGGGCTTTGAAAGGGTGTCACTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
*
1222416 GTGGGCTTTAAAAGGGTGCCACTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* * *
1222444 GTGGGCTTTGGAAGGATGCCACTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
*
1222472 GTGGGCTTTGAAAGGGTGCCACTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
1222500 GTGGGCTTTGAA
1 GTGGGCTTTGAA
1222512 GAGATGAACG
Statistics
Matches: 905, Mismatches: 111, Indels: 9
0.88 0.11 0.01
Matches are distributed among these distances:
27 24 0.03
28 854 0.94
29 1 0.00
30 16 0.02
31 10 0.01
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (28 bp):
GTGGGCTTTGAAAGGGTGCCACTGACTC
Found at i:1223745 original size:14 final size:12
Alignment explanation
Indices: 1223726--1223805 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 12
1223716 CCTTTTTCTG
1223726 TTTTTTTTTGCTAT
1 TTTTTTTTTG--AT
*
1223740 TTTTTTCTTGAT
1 TTTTTTTTTGAT
1223752 TTTTTTTGTT--T
1 TTTTTTT-TTGAT
1223763 TTTGTTTTTTG-T
1 TTT-TTTTTTGAT
*
1223775 TTTTTGTTTT-TT
1 TTTTT-TTTTGAT
*
1223787 TGTTTTTTTTGGT
1 T-TTTTTTTTGAT
1223800 TTTTTT
1 TTTTTT
1223806 GTATAAAGGA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
11 8 0.14
12 31 0.55
13 8 0.14
14 9 0.16
ACGTcount: A:0.03, C:0.03, G:0.11, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTGAT
Found at i:1223745 original size:24 final size:22
Alignment explanation
Indices: 1223718--1223787 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
1223708 CACCTGGACC
1223718 TTTTTCTGTTTTTTTTTGCTATT
1 TTTTTCTGTTTTTTTTTG-TATT
*
1223741 TTTTTCTTGATTTTTTTTGT-TT
1 TTTTTC-TGTTTTTTTTTGTATT
1223763 TTTGTT-T-TTTGTTTTTTGT-TT
1 TTT-TTCTGTTT-TTTTTTGTATT
1223784 TTTT
1 TTTT
1223788 GTTTTTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 3 0.07
21 14 0.33
22 5 0.12
23 9 0.21
24 11 0.26
ACGTcount: A:0.03, C:0.04, G:0.10, T:0.83
Consensus pattern (22 bp):
TTTTTCTGTTTTTTTTTGTATT
Found at i:1223765 original size:8 final size:8
Alignment explanation
Indices: 1223752--1223807 Score: 73
Period size: 7 Copynumber: 7.1 Consensus size: 8
1223742 TTTTCTTGAT
1223752 TTTTTTTG
1 TTTTTTTG
1223760 -TTTTTTG
1 TTTTTTTG
1223767 -TTTTTTG
1 TTTTTTTG
1223774 -TTTTTTG
1 TTTTTTTG
1223781 TTTTTTTG
1 TTTTTTTG
1223789 TTTTTTTTGG
1 -TTTTTTT-G
1223799 TTTTTTTG
1 TTTTTTTG
1223807 T
1 T
1223808 ATAAAGGACG
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
7 21 0.47
8 9 0.20
9 14 0.31
10 1 0.02
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1223803 original size:7 final size:7
Alignment explanation
Indices: 1223753--1223794 Score: 75
Period size: 7 Copynumber: 5.9 Consensus size: 7
1223743 TTTCTTGATT
1223753 TTTTTTG
1 TTTTTTG
1223760 TTTTTTG
1 TTTTTTG
1223767 TTTTTTG
1 TTTTTTG
1223774 TTTTTTG
1 TTTTTTG
1223781 TTTTTTTG
1 -TTTTTTG
1223789 TTTTTT
1 TTTTTT
1223795 TTGGTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 27 0.79
8 7 0.21
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTTG
Found at i:1227585 original size:20 final size:20
Alignment explanation
Indices: 1227559--1227614 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1227549 GTTTACCCAG
1227559 ATGTATCGATACATTGCT-CA
1 ATGTATCGATACATT-CTACA
* *
1227579 TTGTATCGATACATTTTACA
1 ATGTATCGATACATTCTACA
1227599 ATGTATCGATACATTC
1 ATGTATCGATACATTC
1227615 AGGCATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTACA
Found at i:1230093 original size:51 final size:51
Alignment explanation
Indices: 1230017--1230238 Score: 164
Period size: 51 Copynumber: 4.4 Consensus size: 51
1230007 TATTTTCGAG
*
1230017 GGGGATACTCCAACCCCGGCTTTA-TTCCTAAAATATTGATTTCTCACAAAC
1 GGGGATACTCCAACCCCGGCTTTATTTCC-AAAATATTAATTTCTCACAAAC
* * *
1230068 GGGGATACTACTAA-CCCGGCTTTATTTCCAAAATATTAATTTTTCACAATC
1 GGGGATACT-CCAACCCCGGCTTTATTTCCAAAATATTAATTTCTCACAAAC
** * * * ** * *
1230119 GGGGATACTTTAACCCCGACCTTATTT-CTAAATCATCGATTTCTTACAATC
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAAT-ATTAATTTCTCACAAAC
* ** ** * * * * *
1230170 GGGAATACTTTAACCCTTGCGTTATTT-CTAAATGATCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAAT-ATTAATTTCTCACAAAC
*
1230221 GGGGATACTCCAATCCCG
1 GGGGATACTCCAACCCCG
1230239 TTATTTCGAG
Statistics
Matches: 140, Mismatches: 27, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
50 8 0.06
51 125 0.89
52 7 0.05
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTAATTTCTCACAAAC
Found at i:1230144 original size:102 final size:102
Alignment explanation
Indices: 1230017--1230238 Score: 261
Period size: 102 Copynumber: 2.2 Consensus size: 102
1230007 TATTTTCGAG
* * * *
1230017 GGGGATACTCCAACCCCGGCTTTATTCCTAAAAT-ATTGATTTCTCACAAACGGGGATACTACTA
1 GGGGATACTCCAACCCCGACCTTATTCCT-AAATCATCGATTTCTCACAAACGGGAATACT-CTA
* *
1230081 ACCC-GGCTTTATTTCCAAAAT-ATTAATTTTTCACAATC
64 ACCCTGGCGTTATTT-CAAAATGATCAATTTTTCACAATC
** * * * *
1230119 GGGGATACTTTAACCCCGACCTTATTTCTAAATCATCGATTTCTTACAATCGGGAATACTTTAAC
1 GGGGATACTCCAACCCCGACCTTATTCCTAAATCATCGATTTCTCACAAACGGGAATACTCTAAC
* *
1230184 CCTTGCGTTATTTCTAAATGATCAATTTTTCACAATC
66 CCTGGCGTTATTTCAAAATGATCAATTTTTCACAATC
*
1230221 GGGGATACTCCAATCCCG
1 GGGGATACTCCAACCCCG
1230239 TTATTTCGAG
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
101 15 0.15
102 85 0.85
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (102 bp):
GGGGATACTCCAACCCCGACCTTATTCCTAAATCATCGATTTCTCACAAACGGGAATACTCTAAC
CCTGGCGTTATTTCAAAATGATCAATTTTTCACAATC
Found at i:1238412 original size:13 final size:13
Alignment explanation
Indices: 1238394--1238418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1238384 ACATAAATGT
1238394 TGTATCGATACAA
1 TGTATCGATACAA
1238407 TGTATCGATACA
1 TGTATCGATACA
1238419 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1238419 original size:32 final size:32
Alignment explanation
Indices: 1238375--1238445 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
1238365 AAACCGTAAC
*
1238375 TGTATCGCTACATAAATGTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
* *
1238407 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
1238439 TGTATCG
1 TGTATCG
1238446 CTACGAAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAATGTTGTATCGATACAA
Found at i:1240657 original size:27 final size:27
Alignment explanation
Indices: 1240627--1240695 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
1240617 TATTCATCGG
1240627 GGACACTCCAACCCCATTCCTCCGAGA
1 GGACACTCCAACCCCATTCCTCCGAGA
*
1240654 GGACACTCCAACCCCATTCCTCCGAGG
1 GGACACTCCAACCCCATTCCTCCGAGA
1240681 GGACACTCCAACCCC
1 GGACACTCCAACCCC
1240696 GTTTTCGACC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.25, C:0.46, G:0.16, T:0.13
Consensus pattern (27 bp):
GGACACTCCAACCCCATTCCTCCGAGA
Found at i:1244106 original size:18 final size:18
Alignment explanation
Indices: 1244083--1244120 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1244073 TGGAATAGAT
* *
1244083 AAAAATCATTTTTGTTTG
1 AAAAATCATGTGTGTTTG
1244101 AAAAATCATGTGTGTTTG
1 AAAAATCATGTGTGTTTG
1244119 AA
1 AA
1244121 CTCATTTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (18 bp):
AAAAATCATGTGTGTTTG
Found at i:1245326 original size:20 final size:21
Alignment explanation
Indices: 1245294--1245358 Score: 89
Period size: 20 Copynumber: 3.2 Consensus size: 21
1245284 TAGGTTAAAA
*
1245294 GATAGAATATATCGATACATT
1 GATAGAATGTATCGATACATT
1245315 GA-AGAATGTATCGATACATT
1 GATAGAATGTATCGATACATT
* *
1245335 CATA-CATGTATCGATACATT
1 GATAGAATGTATCGATACATT
1245355 GATA
1 GATA
1245359 TCGATACATC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
20 36 0.92
21 3 0.08
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (21 bp):
GATAGAATGTATCGATACATT
Found at i:1249369 original size:38 final size:38
Alignment explanation
Indices: 1249309--1249408 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 38
1249299 TCACCAGCCA
* * * *
1249309 TCAGTCAATTTTTAATTGAATTCTCTAATCATTAATCAT
1 TCAGACAATTTTAAATTAAATTCTCTAATCATTAA-CAG
* * *
1249348 TGA-ACAATTTTAAATTAAATTCTCTAATCGTTAACCG
1 TCAGACAATTTTAAATTAAATTCTCTAATCATTAACAG
*
1249385 TCAGTCAATTTTAAATTAAATTCT
1 TCAGACAATTTTAAATTAAATTCT
1249409 TTAACCGTCA
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
37 3 0.06
38 46 0.90
39 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (38 bp):
TCAGACAATTTTAAATTAAATTCTCTAATCATTAACAG
Found at i:1249415 original size:31 final size:31
Alignment explanation
Indices: 1249378--1249462 Score: 89
Period size: 38 Copynumber: 2.5 Consensus size: 31
1249368 TCTCTAATCG
*
1249378 TTAACCGTCAGTCAATTTTAAATTAAATTCT
1 TTAACCGTCAGTCAATTTAAAATTAAATTCT
*
1249409 TTAACCGTCAATTATAAACTAATTTAAAATTAAATTCT
1 TTAACCGTC-A--GT---C-AATTTAAAATTAAATTCT
1249447 TTAACCGTCAGTCAAT
1 TTAACCGTCAGTCAAT
1249463 ACAATTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
31 12 0.27
32 2 0.05
34 1 0.02
35 1 0.02
37 2 0.05
38 26 0.59
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (31 bp):
TTAACCGTCAGTCAATTTAAAATTAAATTCT
Found at i:1249530 original size:2 final size:2
Alignment explanation
Indices: 1249488--1249512 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1249478 TTTGATTCAC
1249488 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
1249513 CTAACATATT
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:1250389 original size:31 final size:32
Alignment explanation
Indices: 1250357--1250417 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
1250347 ATTTATCTAT
1250357 TTTAA-AATTAAATT-TAAATAAAAATAAATA
1 TTTAATAATTAAATTATAAATAAAAATAAATA
* *
1250387 TTTAATAATTAAATTATAAATTAAATTAAAT
1 TTTAATAATTAAATTATAAATAAAAATAAAT
1250418 TAATTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 5 0.19
31 9 0.33
32 13 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
TTTAATAATTAAATTATAAATAAAAATAAATA
Found at i:1250441 original size:21 final size:21
Alignment explanation
Indices: 1250359--1250441 Score: 60
Period size: 21 Copynumber: 3.7 Consensus size: 21
1250349 TTATCTATTT
* *
1250359 TAAAATTAAATTTAAATAAAAA
1 TAAAATTAAA-TTAATTATAAA
1250381 TAAATATTTAATAATTAAATTATAAA
1 TAAA-A-TT-A-AATT-AATTATAAA
*
1250407 TTAAATTAAATTAATTATAAA
1 TAAAATTAAATTAATTATAAA
*
1250428 -AAAATATAAGTTAA
1 TAAAAT-TAAATTAA
1250442 GCTCGAACTC
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
20 4 0.08
21 16 0.32
22 8 0.16
23 2 0.04
24 4 0.08
25 4 0.08
26 12 0.24
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (21 bp):
TAAAATTAAATTAATTATAAA
Found at i:1251051 original size:10 final size:9
Alignment explanation
Indices: 1251017--1251060 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
1251007 AAAAAATTTA
1251017 AAATTTAAT
1 AAATTTAAT
*
1251026 TAA-TTAAT
1 AAATTTAAT
*
1251034 TAATTTAAT
1 AAATTTAAT
1251043 AATATTTAAT
1 AA-ATTTAAT
1251053 AAATTTAA
1 AAATTTAA
1251061 ATTTTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 8 0.26
9 14 0.45
10 9 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AAATTTAAT
Found at i:1251314 original size:30 final size:30
Alignment explanation
Indices: 1251275--1251351 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
1251265 TTTATCTAAT
* *
1251275 TAAATTAAATTCATAATCTTTAAATTATATC
1 TAAA-TAAATTCTTAATCTTTAAATTATACC
* *
1251306 TAAATAAA-TCTTTAATTTTTAATTTATACC
1 TAAATAAATTC-TTAATCTTTAAATTATACC
1251336 TAAATAAATTCTTAAT
1 TAAATAAATTCTTAAT
1251352 ATAAATTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 32 0.80
31 6 0.15
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (30 bp):
TAAATAAATTCTTAATCTTTAAATTATACC
Found at i:1251390 original size:16 final size:16
Alignment explanation
Indices: 1251353--1251391 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1251343 ATTCTTAATA
* *
1251353 TAAATTAATTTTTATT
1 TAAATAAATATTTATT
1251369 TAAAATAAATATTTATT
1 T-AAATAAATATTTATT
1251386 TAAATA
1 TAAATA
1251392 TAAAAAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAATAAATATTTATT
Found at i:1254351 original size:20 final size:20
Alignment explanation
Indices: 1254334--1254372 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1254324 TATGTTTAGT
1254334 TTTAAATTTAATTATTTATA
1 TTTAAATTTAATTATTTATA
*
1254354 TTTAAATTTAATTTTTTAT
1 TTTAAATTTAATTATTTAT
1254373 TGATAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTAAATTTAATTATTTATA
Found at i:1254367 original size:25 final size:25
Alignment explanation
Indices: 1254311--1254364 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
1254301 TAGTGAAAAA
* **
1254311 TAAATTTAATTTTTATGTTTAGTTT
1 TAAATTTAATTTTTATATTTAAATT
1254336 TAAATTTAATTATTTATATTTAAATT
1 TAAATTTAATT-TTTATATTTAAATT
1254362 TAA
1 TAA
1254365 TTTTTTATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
TAAATTTAATTTTTATATTTAAATT
Found at i:1258455 original size:16 final size:17
Alignment explanation
Indices: 1258428--1258459 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1258418 TGAATAACGT
1258428 TTTAATAAAAGTATCAC
1 TTTAATAAAAGTATCAC
1258445 TTTAA-AAAAGTATCA
1 TTTAATAAAAGTATCA
1258460 ATACTTCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (17 bp):
TTTAATAAAAGTATCAC
Found at i:1260067 original size:6 final size:6
Alignment explanation
Indices: 1260056--1260081 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1260046 TAGTTTTACT
1260056 TCCTAA TCCTAA TCCTAA TCCTAA TC
1 TCCTAA TCCTAA TCCTAA TCCTAA TC
1260082 ATTATCATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (6 bp):
TCCTAA
Found at i:1260094 original size:12 final size:12
Alignment explanation
Indices: 1260079--1260128 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
1260069 CCTAATCCTA
1260079 ATCATTATCATC
1 ATCATTATCATC
*
1260091 ATCATTATCGTC
1 ATCATTATCATC
*
1260103 ATCATTCTCATC
1 ATCATTATCATC
*
1260115 CTCATTATCATC
1 ATCATTATCATC
1260127 AT
1 AT
1260129 TGTCTTTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.02, T:0.42
Consensus pattern (12 bp):
ATCATTATCATC
Found at i:1261246 original size:16 final size:16
Alignment explanation
Indices: 1261225--1261262 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1261215 TGATCAAAAA
1261225 TTGAAACAACCAGAAT
1 TTGAAACAACCAGAAT
*
1261241 TTGAAACAACTAGAAT
1 TTGAAACAACCAGAAT
1261257 TTGAAA
1 TTGAAA
1261263 ATAATCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (16 bp):
TTGAAACAACCAGAAT
Found at i:1262982 original size:13 final size:13
Alignment explanation
Indices: 1262964--1262988 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1262954 ATAATGTATA
1262964 GTATCGATACATT
1 GTATCGATACATT
1262977 GTATCGATACAT
1 GTATCGATACAT
1262989 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1263001 original size:20 final size:21
Alignment explanation
Indices: 1262976--1263028 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1262966 ATCGATACAT
*
1262976 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
*
1262996 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
1263017 TGTATCGATACA
1 TGTATCGATACA
1263029 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:1263107 original size:13 final size:13
Alignment explanation
Indices: 1263089--1263113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1263079 ACATACAAGA
1263089 TGTATCGATACAG
1 TGTATCGATACAG
1263102 TGTATCGATACA
1 TGTATCGATACA
1263114 TGACCAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1263132 original size:34 final size:32
Alignment explanation
Indices: 1263070--1263134 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 32
1263060 CTTAACTGTT
1263070 TGTATCGATACATACAAGATGTATCGATACAG
1 TGTATCGATACATACAAGATGTATCGATACAG
1263102 TGTATCGATACATGACCAA-ATTGTATCGATACA
1 TGTATCGATACAT-A-CAAGA-TGTATCGATACA
1263135 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 13 0.43
33 2 0.07
34 15 0.50
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (32 bp):
TGTATCGATACATACAAGATGTATCGATACAG
Found at i:1269732 original size:20 final size:22
Alignment explanation
Indices: 1269699--1269743 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 22
1269689 GCAGCACTCA
1269699 CCAGGTCGCGACC-GGCA-CCC
1 CCAGGTCGCGACCGGGCAGCCC
1269719 CCAGGTCG-GAACCGGGCAGCCC
1 CCAGGTCGCG-ACCGGGCAGCCC
1269741 CCA
1 CCA
1269744 CACTCACAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.05
20 11 0.50
21 4 0.18
22 6 0.27
ACGTcount: A:0.18, C:0.47, G:0.31, T:0.04
Consensus pattern (22 bp):
CCAGGTCGCGACCGGGCAGCCC
Found at i:1271154 original size:20 final size:21
Alignment explanation
Indices: 1271117--1271180 Score: 103
Period size: 20 Copynumber: 3.0 Consensus size: 21
1271107 TGATTAAAGA
1271117 AAATTATTTTATTAAGGGGGAG
1 AAATT-TTTTATTAAGGGGGAG
*
1271139 AAATTTTTTATT-AGGGGGAA
1 AAATTTTTTATTAAGGGGGAG
1271159 AAATTTTTTATTAAGGGGGAG
1 AAATTTTTTATTAAGGGGGAG
1271180 A
1 A
1271181 GAAAAGGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
20 19 0.49
21 15 0.38
22 5 0.13
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.38
Consensus pattern (21 bp):
AAATTTTTTATTAAGGGGGAG
Found at i:1271866 original size:19 final size:19
Alignment explanation
Indices: 1271842--1271887 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 19
1271832 CTTAACTGTT
1271842 TGTATCGATACATACAAGA
1 TGTATCGATACATACAAGA
1271861 TGTATCG----ATACAAGA
1 TGTATCGATACATACAAGA
1271876 TGTATCGATACA
1 TGTATCGATACA
1271888 GTGTATCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
15 15 0.65
19 8 0.35
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (19 bp):
TGTATCGATACATACAAGA
Found at i:1271873 original size:15 final size:15
Alignment explanation
Indices: 1271853--1271900 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
1271843 GTATCGATAC
1271853 ATACAAGATGTATCG
1 ATACAAGATGTATCG
1271868 ATACAAGATGTATCG
1 ATACAAGATGTATCG
*
1271883 ATAC-AG-TGTATCA
1 ATACAAGATGTATCG
1271896 ATACA
1 ATACA
1271901 TGACCAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
13 10 0.32
14 2 0.06
15 19 0.61
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (15 bp):
ATACAAGATGTATCG
Found at i:1277470 original size:20 final size:19
Alignment explanation
Indices: 1277445--1277517 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
1277435 ATTTAACTAG
1277445 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATT-AAAA
****
1277465 ATGTATCGATACAATTCCTT
1 ATGTATCGATAC-ATTAAAA
*
1277485 ATGTATCAATACATTTAAAA
1 ATGTATCGATACA-TTAAAA
*
1277505 ATGTATTGATACA
1 ATGTATCGATACA
1277518 ATTTCCTTCC
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 1 0.03
20 36 0.90
21 3 0.08
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (19 bp):
ATGTATCGATACATTAAAA
Found at i:1277491 original size:40 final size:41
Alignment explanation
Indices: 1277445--1277525 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 41
1277435 ATTTAACTAG
*
1277445 ATGTATCGATACATTGAAAAATGTATCGATACAA-TTCCTT
1 ATGTATCAATACATTGAAAAATGTATCGATACAATTTCCTT
* *
1277485 ATGTATCAATACATTTAAAAATGTATTGATACAATTTCCTT
1 ATGTATCAATACATTGAAAAATGTATCGATACAATTTCCTT
1277526 CCAAAATGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
40 31 0.84
41 6 0.16
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (41 bp):
ATGTATCAATACATTGAAAAATGTATCGATACAATTTCCTT
Found at i:1277591 original size:20 final size:20
Alignment explanation
Indices: 1277545--1277618 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
1277535 CATATGGTTC
***
1277545 TGTATCGATACATTTTAGGCA
1 TGTATCGATACA-TTTACTAA
* *
1277566 TATATCGATACATTTACTTA
1 TGTATCGATACATTTACTAA
*
1277586 TGTATCGATACATTCACTAA
1 TGTATCGATACATTTACTAA
*
1277606 TTGTATTGATACA
1 -TGTATCGATACA
1277619 AATCGTAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 22 0.50
21 22 0.50
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTTACTAA
Found at i:1288389 original size:16 final size:16
Alignment explanation
Indices: 1288365--1288407 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1288355 TTTTTAGTTT
1288365 GAATCATTTTAAATTC
1 GAATCATTTTAAATTC
* *
1288381 GGATTATTTTAAATTC
1 GAATCATTTTAAATTC
1288397 GAATCATTTTA
1 GAATCATTTTA
1288408 GATTTAAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (16 bp):
GAATCATTTTAAATTC
Found at i:1294613 original size:71 final size:69
Alignment explanation
Indices: 1294535--1294833 Score: 237
Period size: 71 Copynumber: 4.1 Consensus size: 69
1294525 AAAAACGAAA
1294535 AAGCATGAATAATAAAATGAAGCATGATGGAATGAAATAAAAAAAAAAGAAAAAGCATGAATAAT
1 AAGCATGAATAATAAAATGAAGCATGATGGAATGAAAT--AAAAAAAAGAAAAAGCATGAATAAT
1294600 AAAATG
64 AAAATG
* * ** * ** * * * * *
1294606 TAGCATG-ATGGAATGTAATAATAAAAAAAGAAAAAGCATG-AATAATAAAATGAAGCATG-ATG
1 AAGCATGAAT--AA--TAA-AATGAAGCATG--ATGGAATGAAATAAAAAAAAGAA-AAAGCAT-
*
1294668 GAATAAAATAAAAAATAA
57 GAAT--AAT--AAAAT-G
*
1294686 AAGCATGAATAATAAAATGTAGCATGATGGAATGAAAT-AAAAAAAGAAAAAGCATGAATAATAA
1 AAGCATGAATAATAAAATGAAGCATGATGGAATGAAATAAAAAAAAGAAAAAGCATGAATAATAA
*
1294750 AAAG
66 AATG
* *
1294754 AAAAAGCATGAATAATAAAATGTAGCATGATGGAATGAAATAATAAAAAGAAAAAGCATGAATAA
1 ---AAGCATGAATAATAAAATGAAGCATGATGGAATGAAATAAAAAAAAGAAAAAGCATGAATAA
1294819 TAAAATG
63 TAAAATG
*
1294826 TAGCATGA
1 AAGCATGA
1294834 TGGAATGAAA
Statistics
Matches: 176, Mismatches: 31, Indels: 44
0.70 0.12 0.18
Matches are distributed among these distances:
69 11 0.06
70 2 0.01
71 47 0.27
72 30 0.17
73 6 0.03
74 29 0.16
75 16 0.09
76 9 0.05
77 11 0.06
79 7 0.04
80 6 0.03
81 2 0.01
ACGTcount: A:0.60, C:0.04, G:0.17, T:0.19
Consensus pattern (69 bp):
AAGCATGAATAATAAAATGAAGCATGATGGAATGAAATAAAAAAAAGAAAAAGCATGAATAATAA
AATG
Found at i:1294702 original size:22 final size:22
Alignment explanation
Indices: 1294674--1294773 Score: 78
Period size: 22 Copynumber: 4.3 Consensus size: 22
1294664 GATGGAATAA
1294674 AATAAAAAATAAAAGCATGAAT
1 AATAAAAAATAAAAGCATGAAT
** * *
1294696 AATAAAATGTAGCATG-ATGGAAT
1 AATAAAAAATA-AAAGCAT-GAAT
*
1294719 GAAATAAAAAAAGAAAAAGCATGAAT
1 --AAT-AAAAAA-TAAAAGCATGAAT
1294745 AATAAAAAGA-AAAAGCATGAAT
1 AATAAAAA-ATAAAAGCATGAAT
1294767 AATAAAA
1 AATAAAA
1294774 TGTAGCATGA
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
22 30 0.49
23 11 0.18
24 4 0.07
25 3 0.05
26 10 0.16
27 3 0.05
ACGTcount: A:0.65, C:0.04, G:0.14, T:0.17
Consensus pattern (22 bp):
AATAAAAAATAAAAGCATGAAT
Found at i:1294764 original size:52 final size:49
Alignment explanation
Indices: 1294413--1294751 Score: 520
Period size: 52 Copynumber: 6.7 Consensus size: 49
1294403 AAATCAATCA
1294413 AATGAAATAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1 AATGAAATAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
*
1294462 AATGAAATAAAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATAATGG
1 AATGAAAT--AAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
*
1294513 AATGAAATAATAAAAAACGAAAAAGCATGAATAATAAAATGAAGCATGATGG
1 AATGAAAT-A-AAAAAA-GAAAAAGCATGAATAATAAAATGTAGCATGATGG
1294565 AATGAAATAAAAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1 AATGAAAT---AAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
*
1294617 AATGTAATAATAAAAAAAGAAAAAGCATGAATAATAAAATGAAGCATGATGG
1 AATG--A-AATAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
* *
1294669 AATAAAAT-AAAAAA-TAAAAGCATGAATAATAAAATGTAGCATGATGG
1 AATGAAATAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1294716 AATGAAATAAAAAAAGAAAAAGCATGAATAATAAAA
1 AATGAAATAAAAAAAGAAAAAGCATGAATAATAAAA
1294752 AGAAAAAGCA
Statistics
Matches: 269, Mismatches: 10, Indels: 22
0.89 0.03 0.07
Matches are distributed among these distances:
47 38 0.14
48 12 0.04
49 30 0.11
50 3 0.01
51 54 0.20
52 120 0.45
53 6 0.02
54 3 0.01
55 3 0.01
ACGTcount: A:0.62, C:0.04, G:0.16, T:0.18
Consensus pattern (49 bp):
AATGAAATAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
Found at i:1294800 original size:28 final size:28
Alignment explanation
Indices: 1294764--1294851 Score: 98
Period size: 28 Copynumber: 3.4 Consensus size: 28
1294754 AAAAAGCATG
1294764 AATAATAAAATGTAGCATGATGGAATGA
1 AATAATAAAATGTAGCATGATGGAATGA
* ** *
1294792 AATAATAAAA---AG-A-AAAAGCATG-
1 AATAATAAAATGTAGCATGATGGAATGA
1294814 AATAATAAAATGTAGCATGATGGAATGA
1 AATAATAAAATGTAGCATGATGGAATGA
1294842 AATAATAAAA
1 AATAATAAAA
1294852 AGAAAAAGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
22 10 0.22
23 5 0.11
24 1 0.02
25 4 0.09
26 1 0.02
27 5 0.11
28 20 0.43
ACGTcount: A:0.58, C:0.03, G:0.17, T:0.22
Consensus pattern (28 bp):
AATAATAAAATGTAGCATGATGGAATGA
Found at i:1294801 original size:50 final size:50
Alignment explanation
Indices: 1294742--1294895 Score: 274
Period size: 50 Copynumber: 3.1 Consensus size: 50
1294732 AAAAAGCATG
1294742 AATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGGAATGA
1 AATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGGAATGA
1294792 AATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGGAATGA
1 AATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGGAATGA
* * *
1294842 AATAATAAAAAGAAAAAGCATGAATAATAAAAGGGAGCATGATAGAAT-A
1 AATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGGAATGA
1294891 AATAA
1 AATAA
1294896 AGGAAAAAGA
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
49 6 0.06
50 95 0.94
ACGTcount: A:0.60, C:0.04, G:0.18, T:0.19
Consensus pattern (50 bp):
AATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGGAATGA
Found at i:1294818 original size:22 final size:22
Alignment explanation
Indices: 1294792--1294873 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 22
1294782 GATGGAATGA
1294792 AATAATAAAAAGAAAAAGCATG
1 AATAATAAAAAGAAAAAGCATG
* ** *
1294814 AATAATAAAATGTAGCATGATGGAATG
1 AATAATAAAA---AG-A-AAAAGCATG
1294841 AAATAATAAAAAGAAAAAGCATG
1 -AATAATAAAAAGAAAAAGCATG
1294864 AATAATAAAA
1 AATAATAAAA
1294874 GGGAGCATGA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
22 20 0.43
23 5 0.11
24 1 0.02
25 4 0.09
26 1 0.02
27 5 0.11
28 10 0.22
ACGTcount: A:0.63, C:0.04, G:0.15, T:0.18
Consensus pattern (22 bp):
AATAATAAAAAGAAAAAGCATG
Found at i:1294843 original size:121 final size:119
Alignment explanation
Indices: 1294625--1294873 Score: 432
Period size: 121 Copynumber: 2.1 Consensus size: 119
1294615 GGAATGTAAT
1294625 AATAA-AAAAAGAAAAAGCATGAATAATAAAATGAAGCATGATGGAATAAAATAAAAAATAAAAG
1 AATAATAAAAAGAAAAAGCATGAATAATAAAATGAAGCATGATGGAATAAAATAAAAAATAAAAG
1294689 CATGAATAATAAAATGTAGCATGATGGAATGAAATAA-AAAAAGAAAAAGCATG
66 CATGAATAATAAAATGTAGCATGATGGAATGAAATAATAAAAAGAAAAAGCATG
*
1294742 AATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGGAATGAAATAATAAAAAGA-A
1 AATAATAAAAAGAAAAAGCATGAATAATAAAATGAAGCATGATGGAAT--AA-AATAAAAA-ATA
1294806 AAAGCATGAATAATAAAATGTAGCATGATGGAATGAAATAATAAAAAGAAAAAGCATG
62 AAAGCATGAATAATAAAATGTAGCATGATGGAATGAAATAATAAAAAGAAAAAGCATG
1294864 AATAATAAAA
1 AATAATAAAA
1294874 GGGAGCATGA
Statistics
Matches: 125, Mismatches: 1, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
117 5 0.04
118 41 0.33
120 2 0.02
121 50 0.40
122 27 0.22
ACGTcount: A:0.62, C:0.04, G:0.16, T:0.18
Consensus pattern (119 bp):
AATAATAAAAAGAAAAAGCATGAATAATAAAATGAAGCATGATGGAATAAAATAAAAAATAAAAG
CATGAATAATAAAATGTAGCATGATGGAATGAAATAATAAAAAGAAAAAGCATG
Found at i:1299799 original size:52 final size:51
Alignment explanation
Indices: 1299763--1300253 Score: 590
Period size: 52 Copynumber: 9.7 Consensus size: 51
1299753 AAATCAATCA
*
1299763 AATGAAATAAAAAAAGAAAAAGCATGAATAATAAAATGT--AGCATGATGG
1 AATGAAATAAAAAAAGAAAAAGCATGAATAATAAAATGTACAGCATAATGG
1299812 AATGAAATAAAAAAAAAAGAAAAAGCATGAATAATAAAATGT--AGCATAATGG
1 AATGAAAT---AAAAAAAGAAAAAGCATGAATAATAAAATGTACAGCATAATGG
*
1299864 AATGAAATAATAAAAAACGAAAAAGCATGAATAATAAAATG-A-AGCATGATGG
1 AATGAAAT-A-AAAAAA-GAAAAAGCATGAATAATAAAATGTACAGCATAATGG
*
1299916 AATGAAATAAAAAAAAAAAGAAAAAGCATGAATAATAAAATGT--AGCATGATGG
1 AATGAAAT----AAAAAAAGAAAAAGCATGAATAATAAAATGTACAGCATAATGG
*
1299969 AATGTAATAATAAAAAAAGAAAAAGCATGAATAATAAAATG-A-AGCATGATGG
1 AATG--A-AATAAAAAAAGAAAAAGCATGAATAATAAAATGTACAGCATAATGG
* * *
1300021 AATAAAAT-AAAAAA-TAAAAGCATGAATAATAAAATGT--AGCATGATGG
1 AATGAAATAAAAAAAGAAAAAGCATGAATAATAAAATGTACAGCATAATGG
* * *
1300068 AATGAAATAAAAAAAGGAAAAGCATGAATAATAAAATG-A-AGTATGATGG
1 AATGAAATAAAAAAAGAAAAAGCATGAATAATAAAATGTACAGCATAATGG
*
1300117 AATGAAATAATAAAAAGAAAAAGCATGAATAATAAAATGT--AGCATGATGG
1 AATGAAATAA-AAAAAGAAAAAGCATGAATAATAAAATGTACAGCATAATGG
*
1300167 AATGAAATAATAAAAAGAAAAAGCATGAATAATAAAATGT--AGCATGATGG
1 AATGAAATAA-AAAAAGAAAAAGCATGAATAATAAAATGTACAGCATAATGG
1300217 AATGAAATAATAAAAAGAAAAAGCATGAATAATAAAA
1 AATGAAATAA-AAAAAGAAAAAGCATGAATAATAAAA
1300254 GGGAGCATGA
Statistics
Matches: 413, Mismatches: 9, Indels: 39
0.90 0.02 0.08
Matches are distributed among these distances:
47 38 0.09
48 12 0.03
49 51 0.12
50 126 0.31
51 6 0.01
52 131 0.32
53 37 0.09
54 6 0.01
55 3 0.01
56 3 0.01
ACGTcount: A:0.61, C:0.04, G:0.17, T:0.19
Consensus pattern (51 bp):
AATGAAATAAAAAAAGAAAAAGCATGAATAATAAAATGTACAGCATAATGG
Found at i:1300062 original size:99 final size:99
Alignment explanation
Indices: 1299768--1300275 Score: 697
Period size: 99 Copynumber: 5.0 Consensus size: 99
1299758 AATCAAATGA
* *
1299768 AATAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGGAATGAAATAAAAAAAAAAGAA
1 AATAAAAAAAGAAAAAGCATGAATAATAAAATGAAGCATGATGGAAT---A-AAAATAAAAA-AA
*
1299833 AAAGCATGAATAATAAAATGTAGCATAATGGAATGAAAT
61 AAAGCATGAATAATAAAATGTAGCATGATGGAATGAAAT
* *
1299872 AATAAAAAACGAAAAAGCATGAATAATAAAATGAAGCATGATGGAATGAAATAAAAAAAAAAAGA
1 AATAAAAAAAGAAAAAGCATGAATAATAAAATGAAGCATGAT-G---G-AATAAAAATAAAAA-A
*
1299937 AAAAGCATGAATAATAAAATGTAGCATGATGGAATGTAAT
60 AAAAGCATGAATAATAAAATGTAGCATGATGGAATGAAAT
1299977 AATAAAAAAAGAAAAAGCATGAATAATAAAATGAAGCATGATGGAAT-AAAATAAAAAATAAAAG
1 AATAAAAAAAGAAAAAGCATGAATAATAAAATGAAGCATGATGGAATAAAAATAAAAAA-AAAAG
1300041 CATGAATAATAAAATGTAGCATGATGGAATG--A-
65 CATGAATAATAAAATGTAGCATGATGGAATGAAAT
* *
1300073 AATAAAAAAAGGAAAAGCATGAATAATAAAATGAAGTATGATGGAATGAAATAATAAAAAGAAAA
1 AATAAAAAAAGAAAAAGCATGAATAATAAAATGAAGCATGATGGAAT-AAA-AATAAAAA-AAAA
1300138 AGCATGAATAATAAAATGTAGCATGATGGAATGAAAT
63 AGCATGAATAATAAAATGTAGCATGATGGAATGAAAT
*
1300175 AAT--AAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGGAATGAAATAATAAAAAGAAAA
1 AATAAAAAAAGAAAAAGCATGAATAATAAAATGAAGCATGATGGAAT-AAA-AATAAAAA-AAAA
* * *
1300238 AGCATGAATAATAAAAGGGAGCATGATAGAAT-AAAT
63 AGCATGAATAATAAAATGTAGCATGATGGAATGAAAT
1300274 AA
1 AA
1300276 AGGAAAAAAG
Statistics
Matches: 377, Mismatches: 14, Indels: 31
0.89 0.03 0.07
Matches are distributed among these distances:
96 45 0.12
97 1 0.00
98 3 0.01
99 95 0.25
100 90 0.24
101 2 0.01
102 3 0.01
104 41 0.11
105 92 0.24
106 1 0.00
108 1 0.00
109 3 0.01
ACGTcount: A:0.60, C:0.04, G:0.17, T:0.19
Consensus pattern (99 bp):
AATAAAAAAAGAAAAAGCATGAATAATAAAATGAAGCATGATGGAATAAAAATAAAAAAAAAAGC
ATGAATAATAAAATGTAGCATGATGGAATGAAAT
Found at i:1300133 original size:50 final size:50
Alignment explanation
Indices: 1299763--1300275 Score: 779
Period size: 50 Copynumber: 10.2 Consensus size: 50
1299753 AAATCAATCA
1299763 AATGAAATAA-AAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1 AATGAAATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
* *
1299812 AATGAAATAAAAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATAATGG
1 AATGAAAT--AATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
*
1299864 AATGAAATAATAAAAAACGAAAAAGCATGAATAATAAAATGAAGCATGATGG
1 AATGAAATAAT-AAAAA-GAAAAAGCATGAATAATAAAATGTAGCATGATGG
*
1299916 AATGAAATAAAAAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1 AATGAAAT---AATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
* *
1299969 AATGTAATAATAAAAAAAGAAAAAGCATGAATAATAAAATGAAGCATGATGG
1 AATGAAATAAT--AAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1300021 AAT--AA-AATAAAAA-ATAAAAGCATGAATAATAAAATGTAGCATGATGG
1 AATGAAATAATAAAAAGA-AAAAGCATGAATAATAAAATGTAGCATGATGG
* * *
1300068 AATGAAATAA-AAAAAGGAAAAGCATGAATAATAAAATGAAGTATGATGG
1 AATGAAATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1300117 AATGAAATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1 AATGAAATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1300167 AATGAAATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1 AATGAAATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
* * *
1300217 AATGAAATAATAAAAAGAAAAAGCATGAATAATAAAAGGGAGCATGATAG
1 AATGAAATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1300267 AAT-AAATAA
1 AATGAAATAA
1300276 AGGAAAAAAG
Statistics
Matches: 429, Mismatches: 19, Indels: 32
0.89 0.04 0.07
Matches are distributed among these distances:
46 1 0.00
47 39 0.09
49 64 0.15
50 144 0.34
51 7 0.02
52 127 0.30
53 40 0.09
54 5 0.01
55 2 0.00
ACGTcount: A:0.60, C:0.04, G:0.17, T:0.19
Consensus pattern (50 bp):
AATGAAATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
Found at i:1305666 original size:22 final size:19
Alignment explanation
Indices: 1305636--1305684 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
1305626 TTAATGGCAT
1305636 TCATATTCATGACATTCATTCA
1 TCATATTCAT-A-A-TCATTCA
*
1305658 TCATTTTCATAATCATTCA
1 TCATATTCATAATCATTCA
1305677 TCAGTATT
1 TCA-TATT
1305685 TGCTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 4 0.17
21 1 0.04
22 9 0.38
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (19 bp):
TCATATTCATAATCATTCA
Found at i:1311736 original size:20 final size:17
Alignment explanation
Indices: 1311711--1311751 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 17
1311701 TTGGCACTAA
1311711 ATTTTATACTAAATAGAGAG
1 ATTTTATAC-AAA-A-AGAG
1311731 ATTTTATACAAAAAGAG
1 ATTTTATACAAAAAGAG
1311748 ATTT
1 ATTT
1311752 GATCAAACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 1 0.05
19 3 0.14
20 9 0.43
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (17 bp):
ATTTTATACAAAAAGAG
Found at i:1314063 original size:42 final size:42
Alignment explanation
Indices: 1313883--1315864 Score: 1380
Period size: 42 Copynumber: 47.1 Consensus size: 42
1313873 CTTTTCTATT
* * * * *
1313883 TTCCCTCAGTCTGCCTGTCAG-TTTAACCTTGGAGAC-ATTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
1313923 TTTCCCTTAATCTGCCTGTCGGTTTTGACCCTAGAGACTTTCC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * * *
1313966 TTTCCTTTCAGCCTACCTGTCGGCTTCGTCCCTGGAGAC--TGC
1 -TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* ** * * *
1314008 CTCATTTAAAGTCTACCTGTTGGCTTTGACCCTAGAGACTTTTC
1 TTCCCTT--AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
1314052 TTCCCTTAGTCTGCCTGTCGGCTTTGACCATTGAGATTTTTT
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
1314094 TTCCCTTAGTCTACCTGTCGGCTTTGACCCTGAAGAC--TAC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
1314134 TTCATCTAAAGTCTGCCTGTCGGC-TTCATCCCTGGAGACTTTTC
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTTC
** * * * * * *
1314178 AACCCTCAATCTTCCTGTCGGCTTTGACCATGAAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
1314220 TTCCCTCAGTCTGCCTGTCGGCTTTGA-CCTCCGAGACTTTT-
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCT-GGAGACTTTTC
** *
1314261 TATCCCTTAGTCTGCCTGTCAACTTTGACCCTGAAGACTTTTC
1 T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* **
1314304 AAT-CCTTAGTCTGCCTGTCAACTTTGACCCTGGAGACTTTTC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
1314346 TT-CCTTCAGTCTACCTATTGGCTTTGTCCCTGGAGACTTTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** * * ** * **
1314388 AACCCTCAGTCTTCCTGTCGGCTTTGACCCTAAAGACCTCCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * * * *
1314430 TTCCCTCAGTTTGCTTTTCAGCTTTGACCCTAGAAAC-TTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
1314471 TT-CCTTCAGTCTACCTGTCGGCTTCGTCCCTGGAGACTTTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** * * * * *
1314513 AACCCTCAGTCTTCCTGTAGGTTTTGACCCTGAAGACTTTT-
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
*
1314554 TATCCCTTAGTCTGCCTGTCGGCTTTGACCCCGGAGACTTTTC
1 T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * ** *
1314597 AAT-CCTTAGTCTGCCTATCATCTTTAACCCTGGAGACTTTTC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * * *
1314639 TT-CCTTCAGTTTGCTTTTCGGCTTCGTCCCTGGAGACTTTTT
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** * * *
1314681 TTCCCACAGTCTACCTGTCAGCTTTGTCCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * *
1314723 TTCCCTTAGTCTACCTGTCGGCTTTAACCCTAGAGAC--TAC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
1314763 TTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
1314807 TT-CCTTCAGTCTACCTGTTGGCTTTGACCCTGAAGA-TTTTCC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTT-C
*
1314849 TTCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * * * * *
1314891 TT-CTTTCAATCTGCCTGTTGACTTCGTCCTTAGAGACTTTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
** * * * *
1314933 -AACCTTCAGTCTTCCTGTTGGCTTTGACCCTGAAGACTTTCC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
1314975 TT-CCTTCAGTCTGCCTGTCAGCTTTTACCCTAGAGACTTTT-
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
1315016 TATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
1 T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
1315059 AAT-CCTTAGTCTGCCTGTTGGCTTTGACTCTGGAGACTTTTC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
*
1315101 TT-CCTTCAGTCTGCCTGTCGG-TTTCATCCCTGGAGAC-TTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTTC
** * * * * *
1315142 TTTCCCACAGTCTGCATGTCAGCTTCGTCCCTGGAGACTTTTTT
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTTC
* * * *
1315186 TTCCCTTAGTCTACCTGTCGGCTTT-AACCTAAGAGAC--TGC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCT-GGAGACTTTTC
* * * * * *
1315226 TTCATCTAAAGTTTGCCTGTCGGCTTTGACCTTAGAGACTTTCC
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* **
1315270 TT-ACTTCAGTCTGCCTGTCGGCTTTGACCCCAGAGAC-TTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * *
1315311 TTTCCTTCAGTCTGCCTGTCGACTTTAACCCTAGAGAC--TGC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * *
1315352 TTCATCTAAAGTCTACCTGTCGGCTTTGACCCTGAAGACTTTCC
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
1315396 TT-CATTCAGTCTGCCTGTCGGCTTTGACCCCGAAGAC-TTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
1315437 TTTCCCTCAGTCTGCCTGTCAGCTTTGACCCTAGAGA-TTTTCC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTT-C
* * * * * * **
1315480 TACCTTTCAGTCTACCTATCAGCTTTGTCCCTGGAGACTGCCTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACT-TTTC
* * * *
1315524 TT--CTAAAGTCTACCTGTCGGCTTTGACCCTGAAGACTTTCC
1 TTCCCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * **
1315565 TT-CCTTCAGTCTACCTATCGGCTTTGACCCCCGAGAC-TTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * * * * *
1315606 TTTCCTTCAGACTGTCTGTCAGCTTTAACCCTGGAGA--TTGC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* * *
1315647 TTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTAGGAGACTTTCC
1 TTC-CCT-TAGTCTGCCTGTCGGCTTTGACCCT-GGAGACTTTTC
* ** *
1315692 TT-CCTTCAGTCTGCCTTTTAGCTTTGACCTTGGAGAC-TTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
1315733 TTTCCCTCAGTCTGCCTGTCGACTTTGACCCTGGAGAC-TTTC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
* *
1315775 TTTCCTTCAGTCTGCCTGTCGGCTTTGATCCC-GAAGAC-TTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTTC
* *
1315817 TTTCCCTCAGTCTGCCTGTCGGCTTTGTCCCTGGAGACTTTTC
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
1315860 TTCCC
1 TTCCC
1315865 GTTGGTTTTG
Statistics
Matches: 1518, Mismatches: 337, Indels: 171
0.75 0.17 0.08
Matches are distributed among these distances:
40 16 0.01
41 125 0.08
42 1181 0.78
43 140 0.09
44 50 0.03
45 6 0.00
ACGTcount: A:0.15, C:0.30, G:0.18, T:0.37
Consensus pattern (42 bp):
TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
Found at i:1316409 original size:27 final size:28
Alignment explanation
Indices: 1316356--1316415 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
1316346 ATATAATAAT
* *
1316356 AAAAATCAAGAAATTAAAAAAATAAAA-
1 AAAAATCAACAAATGAAAAAAATAAAAG
*
1316383 AAAAATCAATCAAATGAAATAAA-AAAAG
1 AAAAATCAA-CAAATGAAAAAAATAAAAG
1316411 AAAAA
1 AAAAA
1316416 GCATGAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (28 bp):
AAAAATCAACAAATGAAAAAAATAAAAG
Found at i:1316454 original size:25 final size:25
Alignment explanation
Indices: 1316424--1316503 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
1316414 AAGCATGAAT
1316424 AATAAAATGTAGCATGATGGAATGA
1 AATAAAATGTAGCATGATGGAATGA
*** * *
1316449 AATAAAAAAAAGAAAAAGCAT-GAAT--
1 AATAAAATGTAG--CATG-ATGGAATGA
1316474 AATAAAATGTAGCATGATGGAATGA
1 AATAAAATGTAGCATGATGGAATGA
1316499 AATAA
1 AATAA
1316504 TAAAAAAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 12
0.64 0.16 0.20
Matches are distributed among these distances:
22 2 0.05
23 6 0.15
25 23 0.59
27 6 0.15
28 2 0.05
ACGTcount: A:0.57, C:0.04, G:0.19, T:0.20
Consensus pattern (25 bp):
AATAAAATGTAGCATGATGGAATGA
Found at i:1316467 original size:50 final size:50
Alignment explanation
Indices: 1316395--1316805 Score: 600
Period size: 50 Copynumber: 8.2 Consensus size: 50
1316385 AAATCAATCA
1316395 AATGAAAT-AAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1 AATGAAATAAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1316444 AATGAAATAAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1 AATGAAATAAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
* * *
1316494 AATGAAAT-AATAAAA-AAAAAGCATGAATAATAAAATGAAGTATGATGG
1 AATGAAATAAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
* *
1316542 AATGAAATAAAAAAAAAGAAAAAGCATAAATAACAAAATGTAGCATGATGG
1 AATGAAAT-AAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
* * *
1316593 AATGAAATAAAAAAAGGAAAAA-CGTGAATAATAAAATGAAGCATGATGG
1 AATGAAATAAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
*
1316642 AATGAAATAAAAAAAAAAAAGAAATAGCATGAATAATAAAATGTAGCATGATGG
1 AATGAAAT----AAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
*
1316696 AATGAAATAATAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
1 AATGAAATAAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
* * * *
1316746 AATAAAATAATAAAAAGAAAAAGCATGAATAATAAAAAAG-AGCATGATAG
1 AATGAAATAAAAAAAAGAAAAAGCATGAATAAT-AAAATGTAGCATGATGG
1316796 AAT-AAATAAA
1 AATGAAATAAA
1316806 GGAAAAAAGA
Statistics
Matches: 329, Mismatches: 23, Indels: 20
0.88 0.06 0.05
Matches are distributed among these distances:
48 39 0.12
49 51 0.16
50 152 0.46
51 42 0.13
53 12 0.04
54 33 0.10
ACGTcount: A:0.61, C:0.04, G:0.17, T:0.18
Consensus pattern (50 bp):
AATGAAATAAAAAAAAGAAAAAGCATGAATAATAAAATGTAGCATGATGG
Found at i:1316727 original size:22 final size:22
Alignment explanation
Indices: 1316701--1316783 Score: 67
Period size: 22 Copynumber: 3.5 Consensus size: 22
1316691 GATGGAATGA
1316701 AATAATAAAAAGAAAAAGCATG
1 AATAATAAAAAGAAAAAGCATG
* ** * *
1316723 AATAATAAAATGTAGCATGATGGAATAA
1 AATAATAAAA---AG-A-AAAAGCAT-G
1316751 AATAATAAAAAGAAAAAGCATG
1 AATAATAAAAAGAAAAAGCATG
1316773 AATAATAAAAA
1 AATAATAAAAA
1316784 AGAGCATGAT
Statistics
Matches: 45, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
22 21 0.47
23 4 0.09
24 1 0.02
25 4 0.09
26 1 0.02
27 4 0.09
28 10 0.22
ACGTcount: A:0.65, C:0.04, G:0.13, T:0.18
Consensus pattern (22 bp):
AATAATAAAAAGAAAAAGCATG
Found at i:1316789 original size:19 final size:20
Alignment explanation
Indices: 1316754--1316806 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
1316744 GGAATAAAAT
*
1316754 AATAA-AAAGAAAAAGCATG
1 AATAATAAAGAAAGAGCATG
1316773 AATAATAAA-AAAGAGCATG
1 AATAATAAAGAAAGAGCATG
* *
1316792 ATAGAATAAATAAAG
1 A-ATAATAAAGAAAG
1316807 GAAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 15 0.52
20 10 0.34
21 4 0.14
ACGTcount: A:0.66, C:0.04, G:0.15, T:0.15
Consensus pattern (20 bp):
AATAATAAAGAAAGAGCATG
Found at i:1319557 original size:20 final size:20
Alignment explanation
Indices: 1319515--1319568 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 20
1319505 TTCTATAATT
1319515 TGTATCGATACAATAAGGTAA
1 TGTATCGATAC-ATAAGGTAA
1319536 TGTATCGATACATAA-GTGAA
1 TGTATCGATACATAAGGT-AA
1319556 TGTATCGATACAT
1 TGTATCGATACAT
1319569 GCTTTAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.06
20 19 0.59
21 11 0.34
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATAAGGTAA
Found at i:1319686 original size:20 final size:20
Alignment explanation
Indices: 1319625--1319679 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
1319615 CTGAAAAGAA
** *
1319625 AATATATCGATACATTTTTT
1 AATATATCGATACATAATTG
* * *
1319645 ATTGTATCGATACATAAGTG
1 AATATATCGATACATAATTG
1319665 AATATATCGATACAT
1 AATATATCGATACAT
1319680 GCTTGAAATG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (20 bp):
AATATATCGATACATAATTG
Found at i:1319730 original size:111 final size:111
Alignment explanation
Indices: 1319536--1319770 Score: 407
Period size: 111 Copynumber: 2.1 Consensus size: 111
1319526 AATAAGGTAA
* *
1319536 TGTATCGATACATAAGTGAATGTATCGATACATGCTTTAAATGTATCGATATAGGACCATGCAAG
1 TGTATCGATACATAAGTGAATATATCGATACATGCTTGAAATGTATCGATATAGGACCATGCAAG
* * *
1319601 CAAAATTTTATATTCTGAAAAGAAAATATATCGATACATTTTTTAT
66 CAAAATTTTACATTCTGAAAAGAAAATATATCAATACATTTTTAAT
1319647 TGTATCGATACATAAGTGAATATATCGATACATGCTTGAAATGTATCGATATAGGACCATGCAAG
1 TGTATCGATACATAAGTGAATATATCGATACATGCTTGAAATGTATCGATATAGGACCATGCAAG
* *
1319712 CAAAATTTTGCATTCTGAAAAGAACATATATCAATACATTTTTAAT
66 CAAAATTTTACATTCTGAAAAGAAAATATATCAATACATTTTTAAT
1319758 TGTATCGATACAT
1 TGTATCGATACAT
1319771 TCTGGGTTTT
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 117 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (111 bp):
TGTATCGATACATAAGTGAATATATCGATACATGCTTGAAATGTATCGATATAGGACCATGCAAG
CAAAATTTTACATTCTGAAAAGAAAATATATCAATACATTTTTAAT
Found at i:1319824 original size:19 final size:19
Alignment explanation
Indices: 1319787--1319824 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1319777 TTTTGACCCA
1319787 TATTTATCGATACATTTTT
1 TATTTATCGATACATTTTT
1319806 TATTGTATCGATACATTTT
1 TATT-TATCGATACATTTT
1319825 GGGTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (19 bp):
TATTTATCGATACATTTTT
Found at i:1320170 original size:13 final size:13
Alignment explanation
Indices: 1320152--1320187 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1320142 CATTTATTCT
1320152 CAGCCACCTTACC
1 CAGCCACCTTACC
*
1320165 CAGCCACCTTACT
1 CAGCCACCTTACC
1320178 CAGCCACCTT
1 CAGCCACCTT
1320188 TGCCAGCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.22, C:0.50, G:0.08, T:0.19
Consensus pattern (13 bp):
CAGCCACCTTACC
Found at i:1324639 original size:15 final size:16
Alignment explanation
Indices: 1324613--1324646 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1324603 TATAAATTAG
1324613 ATAAATATTATTGATA
1 ATAAATATTATTGATA
*
1324629 ATAAA-ATTATTTATA
1 ATAAATATTATTGATA
1324644 ATA
1 ATA
1324647 GCAATTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
ATAAATATTATTGATA
Found at i:1327114 original size:2 final size:2
Alignment explanation
Indices: 1327107--1327161 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1327097 TCAGAAAAGT
1327107 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1327149 TA TA TA TA CA TA T
1 TA TA TA TA TA TA T
1327162 CTTTTAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1328098 original size:22 final size:22
Alignment explanation
Indices: 1328063--1328108 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1328053 TAATTGTGTT
*
1328063 TTAAATAGTATTTTTATTATTA
1 TTAAATAGTATTTTAATTATTA
* * *
1328085 TTAAATTGTTTTTTAATTTTTA
1 TTAAATAGTATTTTAATTATTA
1328107 TT
1 TT
1328109 TATTATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TTAAATAGTATTTTAATTATTA
Found at i:1329195 original size:2 final size:2
Alignment explanation
Indices: 1329188--1329213 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1329178 AGTATCTAAC
1329188 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1329214 TGAACTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1329968 original size:21 final size:21
Alignment explanation
Indices: 1329927--1329968 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1329917 TTTGTGAAAG
* *
1329927 GAGAGAAAGAAGGAAATGAGA
1 GAGAGAAAGAAGAAAAAGAGA
1329948 GAGAGAAAGAA-AACAAAGAGA
1 GAGAGAAAGAAGAA-AAAGAGA
1329969 AAAAAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.62, C:0.02, G:0.33, T:0.02
Consensus pattern (21 bp):
GAGAGAAAGAAGAAAAAGAGA
Done.