Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold21
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: 2821038
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 98422 characters in sequence are not A, C, G, or T
File 8 of 15
Found at i:1076754 original size:19 final size:20
Alignment explanation
Indices: 1076703--1076754 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
1076693 ATAATTATAC
*
1076703 TTAAATTTAATTATAAATTTT
1 TTAAATTTAA-AATAAATTTT
* *
1076724 TTTAATAATAAAATAAA-TTT
1 TTAAAT-TTAAAATAAATTTT
1076744 TTAAATTTAAA
1 TTAAATTTAAA
1076755 TCAAATCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
19 4 0.16
20 8 0.32
21 10 0.40
22 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAATTTAAAATAAATTTT
Found at i:1080020 original size:38 final size:38
Alignment explanation
Indices: 1079978--1080053 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
1079968 CTGGTCCCGT
1079978 GCTCTACTCCTTTTGAGCAGTAGCTCTGATGCTGATGA
1 GCTCTACTCCTTTTGAGCAGTAGCTCTGATGCTGATGA
*
1080016 GCTCTACTCCTTTTGAGCAGTGGCTCTGATGCTGATGA
1 GCTCTACTCCTTTTGAGCAGTAGCTCTGATGCTGATGA
1080054 CACTGAAGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (38 bp):
GCTCTACTCCTTTTGAGCAGTAGCTCTGATGCTGATGA
Found at i:1081598 original size:2 final size:2
Alignment explanation
Indices: 1081591--1081627 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1081581 AGGGGGAAAA
1081591 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1081628 CAAAAGTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1082184 original size:30 final size:31
Alignment explanation
Indices: 1082149--1082206 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1082139 TTGATGATTC
1082149 ATTTAA-CATTTATT-TATTAATTTATTTATA
1 ATTTAATCA-TTATTATATTAATTTATTTATA
* *
1082179 ATTTAATCATTATTATTTTATTTTATTT
1 ATTTAATCATTATTATATTAATTTATTT
1082207 CATTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (31 bp):
ATTTAATCATTATTATATTAATTTATTTATA
Found at i:1082199 original size:5 final size:5
Alignment explanation
Indices: 1082191--1082252 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
1082181 TTAATCATTA
* *
1082191 TTATT TTATT TTATT TCA-T TTA-T TTATT TATATT AATATT TTATT TTA--
1 TTATT TTATT TTATT TTATT TTATT TTATT T-TATT -TTATT TTATT TTATT
1082239 TTATT TTATAT TTA
1 TTATT TTAT-T TTA
1082253 AAATAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
3 3 0.06
4 7 0.15
5 25 0.53
6 12 0.26
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (5 bp):
TTATT
Found at i:1082220 original size:48 final size:48
Alignment explanation
Indices: 1082156--1082252 Score: 119
Period size: 48 Copynumber: 2.0 Consensus size: 48
1082146 TTCATTTAAC
1082156 ATTTATTTATTAATTTAT-TT-ATAATTTAATCATTATTATTTTAT-TTT
1 ATTTATTTATTAATTTATATTAAT-ATTTAAT-ATTATTATTTTATATTT
* * *
1082203 ATTTCATTTATTTATTTATATTAATATTTTATTTTATTATTTTATATTT
1 ATTT-ATTTATTAATTTATATTAATATTTAATATTATTATTTTATATTT
1082252 A
1 A
1082253 AAATAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
47 4 0.09
48 25 0.58
49 12 0.28
50 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (48 bp):
ATTTATTTATTAATTTATATTAATATTTAATATTATTATTTTATATTT
Found at i:1082233 original size:13 final size:13
Alignment explanation
Indices: 1082217--1082250 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1082207 CATTTATTTA
1082217 TTTATATTAATAT
1 TTTATATTAATAT
* *
1082230 TTTATTTTATTAT
1 TTTATATTAATAT
1082243 TTTATATT
1 TTTATATT
1082251 TAAAATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATATTAATAT
Found at i:1084381 original size:18 final size:19
Alignment explanation
Indices: 1084358--1084400 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1084348 ATTAAAATAT
*
1084358 TATATTAAAA-TATATTAA
1 TATATTAAAATTATATAAA
1084376 TATATTAAAATTTATATAAA
1 TATATTAAAA-TTATATAAA
1084396 TATAT
1 TATAT
1084401 AATATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATTAAAATTATATAAA
Found at i:1084409 original size:20 final size:20
Alignment explanation
Indices: 1084368--1084425 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
1084358 TATATTAAAA
*
1084368 TATATTAATATATTAA-AATT
1 TATATAAATATA-TAATAATT
*
1084388 TATATAAATATATAATATTT
1 TATATAAATATATAATAATT
1084408 TAAATATAAATATA-AATA
1 T--ATATAAATATATAATA
1084426 CATAAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 3 0.09
20 15 0.45
21 4 0.12
22 11 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATATAAATATATAATAATT
Found at i:1085151 original size:15 final size:16
Alignment explanation
Indices: 1085126--1085162 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1085116 ATGAACTCGA
1085126 AATTATTTTATATAAT
1 AATTATTTTATATAAT
*
1085142 AATT-TTTTATTTAAT
1 AATTATTTTATATAAT
1085157 -ATTATT
1 AATTATT
1085163 AAATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 3 0.16
15 12 0.63
16 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTATTTTATATAAT
Found at i:1085748 original size:13 final size:13
Alignment explanation
Indices: 1085732--1085777 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 13
1085722 AATATTTTAT
1085732 TTAAATAAATTAA
1 TTAAATAAATTAA
1085745 TTAAATAAA--AA
1 TTAAATAAATTAA
1085756 TT--ATAAATTAA
1 TTAAATAAATTAA
1085767 --AAATAAATTAA
1 TTAAATAAATTAA
1085778 AAATATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
9 5 0.17
11 15 0.52
13 9 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TTAAATAAATTAA
Found at i:1085766 original size:18 final size:18
Alignment explanation
Indices: 1085743--1085787 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1085733 TAAATAAATT
*
1085743 AATTAAATAA-AAATTATA
1 AATTAAA-AATAAATTAAA
1085761 AATTAAAAATAAATTAAA
1 AATTAAAAATAAATTAAA
1085779 AATATAAAA
1 AAT-TAAAA
1085788 CAAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 17 0.71
19 5 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATTAAAAATAAATTAAA
Found at i:1085772 original size:11 final size:11
Alignment explanation
Indices: 1085758--1085782 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1085748 AATAAAAATT
1085758 ATAAATTAAAA
1 ATAAATTAAAA
1085769 ATAAATTAAAA
1 ATAAATTAAAA
1085780 ATA
1 ATA
1085783 TAAAACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAATTAAAA
Found at i:1085792 original size:24 final size:24
Alignment explanation
Indices: 1085746--1085794 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1085736 ATAAATTAAT
**
1085746 TAAATAAAAATTATAAATTAAAAA
1 TAAATAAAAATTATAAAACAAAAA
1085770 TAAATTAAAAA-TATAAAACAAAAA
1 TAAA-TAAAAATTATAAAACAAAAA
1085794 T
1 T
1085795 TTATTTACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (24 bp):
TAAATAAAAATTATAAAACAAAAA
Found at i:1087593 original size:16 final size:18
Alignment explanation
Indices: 1087572--1087606 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1087562 AACAACCACA
1087572 TCAATT-AATGA-AAAAT
1 TCAATTAAATGAGAAAAT
1087588 TCAATTAAATGAGAAAAT
1 TCAATTAAATGAGAAAAT
1087606 T
1 T
1087607 TCGAACAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (18 bp):
TCAATTAAATGAGAAAAT
Found at i:1089566 original size:2 final size:2
Alignment explanation
Indices: 1089559--1089657 Score: 90
Period size: 2 Copynumber: 48.5 Consensus size: 2
1089549 TTCATATGCT
* * * * *
1089559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TG TG TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
1089601 TG TG TG TCA GTG TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1089645 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1089658 TAAATCCTAA
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
2 88 0.99
4 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1090337 original size:25 final size:25
Alignment explanation
Indices: 1090286--1090358 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
1090276 CTCCAAGTTT
* **
1090286 TTTATAAATATTTAATTTCTAAAATA
1 TTTAT-AATATTTAATTTTTAGGATA
1090312 TTTATAATATTTAATTTTTAGGATA
1 TTTATAATATTTAATTTTTAGGATA
* *
1090337 TTTAATAA-GTTTAATCTTTAGG
1 TTT-ATAATATTTAATTTTTAGG
1090359 TAACCCATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 32 0.78
26 9 0.22
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (25 bp):
TTTATAATATTTAATTTTTAGGATA
Found at i:1092561 original size:20 final size:20
Alignment explanation
Indices: 1092510--1092563 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
1092500 TTATATTTAT
*
1092510 AAATTATTTAAATTTAATTAA
1 AAATTA-TTAAATTAAATTAA
*
1092531 AAATATTTTAAATTAAATTAA
1 AAAT-TATTAAATTAAATTAA
1092552 AAATTATTAAAT
1 AAATTATTAAAT
1092564 CGAGTTCAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.24
21 21 0.72
22 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTATTAAATTAAATTAA
Found at i:1092967 original size:11 final size:11
Alignment explanation
Indices: 1092925--1092969 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
1092915 TAAATTTTAA
*
1092925 AAATAAAATTT
1 AAATTAAATTT
*
1092936 -AATTAAATTC
1 AAATTAAATTT
1092946 AAATTAAATTT
1 AAATTAAATTT
*
1092957 AAATTGAATTT
1 AAATTAAATTT
1092968 AA
1 AA
1092970 GCTCGAACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:1093167 original size:30 final size:31
Alignment explanation
Indices: 1093128--1093187 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1093118 TAATATGATG
*
1093128 TTATAATTATTATTTAATA-ATTTAATTTTT
1 TTATAATTATTATTTAATATAATTAATTTTT
*
1093158 TTATTATTATTATTTAATATAATTAATTTT
1 TTATAATTATTATTTAATATAATTAATTTT
1093188 AATAATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (31 bp):
TTATAATTATTATTTAATATAATTAATTTTT
Found at i:1096698 original size:80 final size:81
Alignment explanation
Indices: 1096565--1096720 Score: 235
Period size: 80 Copynumber: 1.9 Consensus size: 81
1096555 TGCTGGTAAG
* * **
1096565 GGTAAGTTTCAATTTAGATATCAATAGAATTATCGCATCAGTTGATGGCCTTTCTGG-AAAAGTA
1 GGTAAGCTTCAATTTAGATATCAATAGAATTATCGAATCAGTTGATGGCCTTTCTGGAAAAACAA
1096629 TAGCAATGATTGTACT
66 TAGCAATGATTGTACT
* *
1096645 GGTAAGCTTCGATTTAGATGTCAATAGAATTATCGAATTCA-TTGATGGCCTTTCTGGAAAAACA
1 GGTAAGCTTCAATTTAGATATCAATAGAATTATCGAA-TCAGTTGATGGCCTTTCTGGAAAAACA
1096709 ATAGCAATGATT
65 ATAGCAATGATT
1096721 CATTCTAGTC
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 49 0.72
81 19 0.28
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (81 bp):
GGTAAGCTTCAATTTAGATATCAATAGAATTATCGAATCAGTTGATGGCCTTTCTGGAAAAACAA
TAGCAATGATTGTACT
Found at i:1097728 original size:20 final size:20
Alignment explanation
Indices: 1097697--1097742 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
1097687 TTTATCAATG
*
1097697 TATTATACTTTTTCAAGAATT
1 TATT-TACTTTTTTAAGAATT
1097718 T-TTTACTTTTTTAAGAATT
1 TATTTACTTTTTTAAGAATT
1097737 TATTTA
1 TATTTA
1097743 TTTATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 16 0.70
20 6 0.26
21 1 0.04
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (20 bp):
TATTTACTTTTTTAAGAATT
Found at i:1101945 original size:131 final size:132
Alignment explanation
Indices: 1101750--1102000 Score: 441
Period size: 131 Copynumber: 1.9 Consensus size: 132
1101740 AACAGAATGT
* * * *
1101750 ACAAAACCAACTCTAGCCCATGAAATGTGTGACATGCAAAATAATTACAGGATGGATGGAGCATC
1 ACAAAACCAACTCTAGCCCATGAAATGTGGGACATGAAAAATAAGTACAGGACGGATGGAGCATC
*
1101815 AAGCATGCATAATGTGTTTATGTCCATGAAACATCCTCAAATAAAGCTAAGAGGTTTTTCAATGT
66 AAGCATGCATAATGTGTTCATGTCCATGAAACATCCTCAAATAAAGCTAAGAGGTTTTTCAATGT
1101880 TG
131 TG
*
1101882 ACAAAACCAACTCTAGCCCATG-AATGTGGGACATGAAAAATAAGTACATGACGGATGGAGCATC
1 ACAAAACCAACTCTAGCCCATGAAATGTGGGACATGAAAAATAAGTACAGGACGGATGGAGCATC
1101946 AAGCATGCATAATGTGTTCATGTCCATGAAACATCCTCAAATAAAGCTAAGAGGT
66 AAGCATGCATAATGTGTTCATGTCCATGAAACATCCTCAAATAAAGCTAAGAGGT
1102001 CCTTCACTGT
Statistics
Matches: 113, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
131 91 0.81
132 22 0.19
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (132 bp):
ACAAAACCAACTCTAGCCCATGAAATGTGGGACATGAAAAATAAGTACAGGACGGATGGAGCATC
AAGCATGCATAATGTGTTCATGTCCATGAAACATCCTCAAATAAAGCTAAGAGGTTTTTCAATGT
TG
Found at i:1105203 original size:19 final size:21
Alignment explanation
Indices: 1105153--1105208 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 21
1105143 TTTTGGACAC
*
1105153 AATTAATTTTATATATATTAA
1 AATTAATATTATATATATTAA
*
1105174 AATTTAA-ATTA-ATA-ATTAT
1 AA-TTAATATTATATATATTAA
1105193 AATTAATATTAT-TATA
1 AATTAATATTATATATA
1105209 CTTTTAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 4 0.14
19 12 0.41
20 4 0.14
21 5 0.17
22 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTAATATTATATATATTAA
Found at i:1105577 original size:223 final size:224
Alignment explanation
Indices: 1105321--1105765 Score: 750
Period size: 224 Copynumber: 2.0 Consensus size: 224
1105311 ATTTAGTTAT
*
1105321 ATTTTTATATACAGTTATCACTATAATTAAAATTT-TTTATATTAAAATATATTAATTTTAGAAT
1 ATTTTTATATAAAGTTATCACTATAATTAAAATTTCTTTATATTAAAATATATTAATTTTAGAAT
*
1105385 TATTAAATATATCAAAAGAATAATAATTTAATATTAAATTAATATATTTTTATTTAAGAAGTAAA
66 TATTAAATATATCAAAAGAATAATAATTTAATATTAAATTAATATATTTTTATTTAA-AAATAAA
*
1105450 ACTACAATAATTTAATAATAAATTATGTTCAATAAT-AAAAAAGATCATATGATTTAAATTTAAA
130 AATACAATAATTTAATAATAAATTATGTTCAATAATAAAAAAAGATCATATGATTTAAATTTAAA
** * *
1105514 AATTGAGTAAATTACTTAAATATCAAGATG
195 AACGGAGTAAATTACTCAAATATAAAGATG
* *
1105544 ATTTTTATATAAAGTTATCACTGTAATTAAAATTTCTTTATATTAAATTATATTAATTTTAGAAT
1 ATTTTTATATAAAGTTATCACTATAATTAAAATTTCTTTATATTAAAATATATTAATTTTAGAAT
1105609 TATTAAATATATCAAAAGAATAATAATTTAATATTAAATTAATATATTTTTATTTAAAAATAAAA
66 TATTAAATATATCAAAAGAATAATAATTTAATATTAAATTAATATATTTTTATTTAAAAATAAAA
* * * *
1105674 ATACGATAATTTAATAATAAATTGTGTTCAATAATAAAAAAATATCATATGATTTGAATTTAAAA
131 ATACAATAATTTAATAATAAATTATGTTCAATAATAAAAAAAGATCATATGATTTAAATTTAAAA
1105739 ACGGAGTAAATTACTCAAATATAAAGA
196 ACGGAGTAAATTACTCAAATATAAAGA
1105766 GAGGGAGAAG
Statistics
Matches: 207, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
223 72 0.35
224 135 0.65
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (224 bp):
ATTTTTATATAAAGTTATCACTATAATTAAAATTTCTTTATATTAAAATATATTAATTTTAGAAT
TATTAAATATATCAAAAGAATAATAATTTAATATTAAATTAATATATTTTTATTTAAAAATAAAA
ATACAATAATTTAATAATAAATTATGTTCAATAATAAAAAAAGATCATATGATTTAAATTTAAAA
ACGGAGTAAATTACTCAAATATAAAGATG
Found at i:1106622 original size:3 final size:3
Alignment explanation
Indices: 1106607--1106642 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1106597 TTATTTGATT
*
1106607 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1106643 AAAATAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1108939 original size:23 final size:22
Alignment explanation
Indices: 1108913--1108964 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
1108903 TTAAACATTT
1108913 TTTAATATTAAATATAAAAT-AAA
1 TTTAATATT-AAT-TAAAATCAAA
*
1108936 TTTATATATTAATTTAAATCAAA
1 TTTA-ATATTAATTAAAATCAAA
1108959 TTTAAT
1 TTTAAT
1108965 TAAAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 7 0.27
23 14 0.54
24 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTAATATTAATTAAAATCAAA
Found at i:1109759 original size:21 final size:21
Alignment explanation
Indices: 1109730--1109773 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1109720 AATTAACAGG
* * *
1109730 TTAACATTTAATTTATTATTT
1 TTAAAATTTAATATATAATTT
*
1109751 TTAAAATTTTATATATAATTT
1 TTAAAATTTAATATATAATTT
1109772 TT
1 TT
1109774 TGATGGTTGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAAAATTTAATATATAATTT
Found at i:1110398 original size:21 final size:21
Alignment explanation
Indices: 1110369--1110409 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1110359 TATCAAAAAA
*
1110369 TTTACATTAATATTATTATATT
1 TTTACATTAAAATT-TTATATT
1110391 TTTA-ATTAAAATTTTATAT
1 TTTACATTAAAATTTTATAT
1110410 ATTTCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTACATTAAAATTTTATATT
Found at i:1111010 original size:16 final size:17
Alignment explanation
Indices: 1110958--1111013 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
1110948 TAAATTTATT
*
1110958 TTTTTATTTATTTAAATA
1 TTTTTAATTATTT-AATA
**
1110976 TTTTT-A-TATAAAATA
1 TTTTTAATTATTTAATA
1110991 TTTTTAATTATTTAAT-
1 TTTTTAATTATTTAATA
1111007 TTTTTAA
1 TTTTTAA
1111014 AAAATTTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 9 0.29
16 11 0.35
17 6 0.19
18 5 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTAATTATTTAATA
Found at i:1111025 original size:33 final size:36
Alignment explanation
Indices: 1110949--1111026 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 36
1110939 TATAAAAAAT
* * *
1110949 AAATTTATTTTTTTATTTATTTAAATATTTTTATAT
1 AAATTTATATTTTTAATTATTTAAATATTTTTATAA
1110985 AAA---ATATTTTTAATTATTT-AAT-TTTTTA-AA
1 AAATTTATATTTTTAATTATTTAAATATTTTTATAA
1111015 AAATTTATATTT
1 AAATTTATATTT
1111027 ATATAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
30 4 0.11
31 6 0.17
32 3 0.08
33 20 0.56
36 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (36 bp):
AAATTTATATTTTTAATTATTTAAATATTTTTATAA
Found at i:1113856 original size:25 final size:26
Alignment explanation
Indices: 1113804--1113882 Score: 67
Period size: 25 Copynumber: 3.1 Consensus size: 26
1113794 TAATATTTTT
* * *
1113804 ATTTATATAATATATAAATTAAT-TTA
1 ATTTA-ATAATATATAAAATGATAATA
*
1113830 ATTTAA-AATTATATATAAT-ATAATA
1 ATTTAATAA-TATATAAAATGATAATA
*
1113855 ATATAATAATATATAAAATGATAA-A
1 ATTTAATAATATATAAAATGATAATA
1113880 ATT
1 ATT
1113883 AATTAATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
24 4 0.09
25 28 0.65
26 11 0.26
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (26 bp):
ATTTAATAATATATAAAATGATAATA
Found at i:1114396 original size:16 final size:15
Alignment explanation
Indices: 1114371--1114400 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1114361 TAAAACAAAA
1114371 AAAATATATATATAT
1 AAAATATATATATAT
1114386 AAAATACTATATATA
1 AAAATA-TATATATA
1114401 ATAATAAAAA
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:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATATATATATAT
Found at i:1114417 original size:20 final size:19
Alignment explanation
Indices: 1114367--1114419 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
1114357 CTACTAAAAC
1114367 AAAAAAAATATATATATAT
1 AAAAAAAATATATATATAT
* *
1114386 -AAAATACTATATATAATAAT
1 AAAAAAAATATATAT-AT-AT
1114406 AAAAAAAGATATAT
1 AAAAAAA-ATATAT
1114420 TACTACTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 12 0.46
19 2 0.08
20 2 0.08
21 5 0.19
22 5 0.19
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAAAAATATATATATAT
Found at i:1119022 original size:37 final size:37
Alignment explanation
Indices: 1118981--1119052 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
1118971 TATTATAAGT
* *
1118981 TTTAGATAATAAATCATAAAAATTATAGTTCGAGACC
1 TTTAGATAATAAATCATAAAAAGTATAGCTCGAGACC
1119018 TTTAGATAATAAATCATAAAAAGTATAGCTCGAGA
1 TTTAGATAATAAATCATAAAAAGTATAGCTCGAGA
1119053 TCGATTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (37 bp):
TTTAGATAATAAATCATAAAAAGTATAGCTCGAGACC
Found at i:1121269 original size:2 final size:2
Alignment explanation
Indices: 1121223--1121252 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1121213 ACAATGTGAG
1121223 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1121253 CGATCATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1122367 original size:8 final size:8
Alignment explanation
Indices: 1122356--1122402 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
1122346 TTTATATATT
*
1122356 TATTTTGA
1 TATTTTAA
*
1122364 TA-TTTAT
1 TATTTTAA
1122371 TAATTTTAA
1 TA-TTTTAA
1122380 -ATTTTAA
1 TATTTTAA
1122387 TATTTTAA
1 TATTTTAA
1122395 TATTTTAA
1 TATTTTAA
1122403 AGTTTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 11 0.33
8 18 0.55
9 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TATTTTAA
Found at i:1122385 original size:16 final size:16
Alignment explanation
Indices: 1122373--1122402 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1122363 ATATTTATTA
1122373 ATTTTAA-ATTTTAAT
1 ATTTTAATATTTTAAT
1122388 ATTTTAATATTTTAA
1 ATTTTAATATTTTAA
1122403 AGTTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTAATATTTTAAT
Found at i:1122408 original size:16 final size:15
Alignment explanation
Indices: 1122357--1122431 Score: 55
Period size: 16 Copynumber: 4.9 Consensus size: 15
1122347 TTATATATTT
* *
1122357 ATTTTGATATTTATTA
1 ATTTTAATATTT-TAA
1122373 ATTTTAA-ATTTTAA
1 ATTTTAATATTTTAA
1122387 TATTTTAATATTTTAA
1 -ATTTTAATATTTTAA
**
1122403 AGTTTTTTTATTTTTAA
1 A-TTTTAATA-TTTTAA
*
1122420 ATTATAAT-TTTT
1 ATTTTAATATTTT
1122432 TTATAAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
14 6 0.12
15 12 0.25
16 23 0.48
17 7 0.15
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
ATTTTAATATTTTAA
Found at i:1123513 original size:21 final size:22
Alignment explanation
Indices: 1123469--1123516 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1123459 AAAGTAACTG
* *
1123469 TTAAAAATAATTTTTTTATATT
1 TTAAAAATAATTTATTAATATT
*
1123491 TTAAAAATAA-TTATTAATTTT
1 TTAAAAATAATTTATTAATATT
1123512 TTAAA
1 TTAAA
1123517 TTTTATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAAAAATAATTTATTAATATT
Found at i:1124540 original size:16 final size:15
Alignment explanation
Indices: 1124519--1124552 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1124509 ATCATTATTT
1124519 AATTAATTTAAATTAA
1 AATTAA-TTAAATTAA
*
1124535 AATTAATTAAATTTA
1 AATTAATTAAATTAA
1124550 AAT
1 AAT
1124553 ATATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAATTAAATTAA
Found at i:1125332 original size:2 final size:2
Alignment explanation
Indices: 1125325--1125352 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1125315 CTATAGCATA
1125325 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1125353 TAATAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1130852 original size:44 final size:44
Alignment explanation
Indices: 1130771--1130859 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 44
1130761 TTATATAAAT
* *
1130771 TTTAATATATTTATATATTATATTATATTTTATTAATTTTTTAA
1 TTTAATATATTTATATATTATATTATATCTTATTAATTTTATAA
1130815 TTTATATATATTT-TA-ATTTATATTCATATCTTA-TAATTTTATAA
1 TTTA-ATATATTTATATA-TTATATT-ATATCTTATTAATTTTATAA
1130859 T
1 T
1130860 GTACAAGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
43 1 0.03
44 24 0.60
45 15 0.38
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (44 bp):
TTTAATATATTTATATATTATATTATATCTTATTAATTTTATAA
Found at i:1131263 original size:5 final size:5
Alignment explanation
Indices: 1131253--1131280 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1131243 ATATGGGGCC
1131253 GATGG GATGG GATGG GATGG GATGG GAT
1 GATGG GATGG GATGG GATGG GATGG GAT
1131281 TTTCAAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.57, T:0.21
Consensus pattern (5 bp):
GATGG
Found at i:1131782 original size:2 final size:2
Alignment explanation
Indices: 1131775--1131810 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1131765 GGTGCTTCCT
1131775 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
1131811 AACTTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1132279 original size:2 final size:2
Alignment explanation
Indices: 1132272--1132306 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1132262 TCATATAATC
1132272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1132307 AAACAAATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1137268 original size:16 final size:16
Alignment explanation
Indices: 1137249--1137296 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1137239 ATATATAAAC
1137249 ATATCAAATTTATATA
1 ATATCAAATTTATATA
*
1137265 ATATC-AA-TTATTAAA
1 ATATCAAATTTA-TATA
*
1137280 ATATTAAATTTATATA
1 ATATCAAATTTATATA
1137296 A
1 A
1137297 ACATATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
14 3 0.12
15 9 0.35
16 11 0.42
17 3 0.12
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATCAAATTTATATA
Found at i:1137291 original size:31 final size:32
Alignment explanation
Indices: 1137230--1137296 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
1137220 ATTTTAAAAA
*
1137230 ATAATATGAATATATAAACATATCAAATTTAT
1 ATAATATCAATATATAAACATATCAAATTTAT
*
1137262 ATAATATCAAT-TATTAAA-ATATTAAATTTAT
1 ATAATATCAATATA-TAAACATATCAAATTTAT
1137293 ATAA
1 ATAA
1137297 ACATATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 18 0.56
32 14 0.44
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (32 bp):
ATAATATCAATATATAAACATATCAAATTTAT
Found at i:1137309 original size:19 final size:17
Alignment explanation
Indices: 1137240--1137314 Score: 59
Period size: 19 Copynumber: 4.4 Consensus size: 17
1137230 ATAATATGAA
1137240 TATATAAACATATCAAATT
1 TATATAAA-ATAT-AAATT
*
1137259 TATAT--AATATCAA-T
1 TATATAAAATATAAATT
1137273 TAT-TAAAATATTAAATT
1 TATATAAAATA-TAAATT
1137290 TATATAAACATATAATATT
1 TATATAAA-ATATAA-ATT
*
1137309 TTTATA
1 TATATA
1137315 CATGATAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
13 1 0.02
14 4 0.09
15 6 0.13
16 7 0.15
17 5 0.11
18 7 0.15
19 16 0.35
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TATATAAAATATAAATT
Found at i:1151243 original size:3 final size:3
Alignment explanation
Indices: 1151235--1151259 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1151225 ATTCATTCTC
1151235 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1151260 ATTTTGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1153135 original size:20 final size:21
Alignment explanation
Indices: 1153096--1153136 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1153086 ATTCGTAAAA
1153096 ATTTTTTAAAAAATTGATTTT
1 ATTTTTTAAAAAATTGATTTT
* *
1153117 ATTTTTTTAAAAGTT-ATTTT
1 ATTTTTTAAAAAATTGATTTT
1153137 GAAATATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
ATTTTTTAAAAAATTGATTTT
Found at i:1155108 original size:29 final size:29
Alignment explanation
Indices: 1155076--1155133 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1155066 ATTATTTTCA
* *
1155076 TATATTTTA-TTATATTATAATTACATATT
1 TATATTATATTTATATCATAATTA-ATATT
*
1155105 TATATTATATTTATATCATATTTAATATT
1 TATATTATATTTATATCATAATTAATATT
1155134 ATTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (29 bp):
TATATTATATTTATATCATAATTAATATT
Found at i:1155114 original size:11 final size:11
Alignment explanation
Indices: 1155057--1155135 Score: 69
Period size: 11 Copynumber: 7.3 Consensus size: 11
1155047 TAACAATTTA
1155057 TATATTTATAT
1 TATATTTATAT
*
1155068 TAT-TTT-CA-
1 TATATTTATAT
1155076 TATATTT-TAT
1 TATATTTATAT
1155086 TATA-TTATAAT
1 TATATTTAT-AT
1155097 TACATATTTATAT
1 T--ATATTTATAT
1155110 TATATTTATAT
1 TATATTTATAT
*
1155121 CATATTTAATAT
1 TATATTT-ATAT
1155133 TAT
1 TAT
1155136 TATGTCTACT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
8 3 0.05
9 7 0.12
10 8 0.14
11 22 0.39
12 6 0.11
13 6 0.11
14 4 0.07
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1157811 original size:27 final size:27
Alignment explanation
Indices: 1157753--1157805 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1157743 TTCTTTATGG
* *
1157753 TATTTGAATGCATAATTTTTTTTAATA
1 TATTTGAATGCAAAATTTTTTTCAATA
1157780 TATTTGAATG-AAAATTTTATTTCAAT
1 TATTTGAATGCAAAATTTT-TTTCAAT
1157806 TAATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.53
Consensus pattern (27 bp):
TATTTGAATGCAAAATTTTTTTCAATA
Found at i:1158310 original size:32 final size:31
Alignment explanation
Indices: 1158273--1158343 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 31
1158263 TTGAATATAA
*
1158273 ATATAATACAAATATATTGAT-ATATTAAAATT
1 ATATAATACAAAT-TATTAATAATATTAAAA-T
* *
1158305 TTATAATATAAATTATTAATAATATTAAAAT
1 ATATAATACAAATTATTAATAATATTAAAAT
1158336 ATATAATA
1 ATATAATA
1158344 TTTTAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.41
32 20 0.59
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (31 bp):
ATATAATACAAATTATTAATAATATTAAAAT
Found at i:1158330 original size:40 final size:39
Alignment explanation
Indices: 1158270--1158395 Score: 113
Period size: 37 Copynumber: 3.3 Consensus size: 39
1158260 AAATTGAATA
* * *
1158270 TAAATATAA-TACAA-ATATATTGATATAT-TAAAATTT
1 TAAATATAATTATAATATATATTAAAATATATAAAATTT
*
1158306 TATAATATAAATTATTAATA-ATATTAAAATATATAATATTT
1 TA-AATAT-AATTA-TAATATATATTAAAATATATAAAATTT
1158347 TAAATATAATTATAATATATA-T-AAATATA-AAAATTAT
1 TAAATATAATTATAATATATATTAAAATATATAAAATT-T
* *
1158384 TTAATTTAATTA
1 TAAATATAATTA
1158396 GATTTGTACC
Statistics
Matches: 75, Mismatches: 7, Indels: 15
0.77 0.07 0.15
Matches are distributed among these distances:
36 7 0.09
37 23 0.31
38 8 0.11
39 10 0.13
40 17 0.23
41 10 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (39 bp):
TAAATATAATTATAATATATATTAAAATATATAAAATTT
Found at i:1158343 original size:15 final size:15
Alignment explanation
Indices: 1158294--1158380 Score: 54
Period size: 15 Copynumber: 5.7 Consensus size: 15
1158284 ATATATTGAT
*
1158294 ATATTAAAATTTTATA
1 ATATTAAAA-TATATA
*
1158310 ATA-TAAATTATTAATA
1 ATATTAAAATA-T-ATA
1158326 ATATTAAAATATATA
1 ATATTAAAATATATA
**
1158341 ATATTTTAA-ATATA
1 ATATTAAAATATATA
*
1158355 AT-TATAATATATATAA
1 ATAT-TAAAATATAT-A
*
1158371 ATATAAAAAT
1 ATATTAAAAT
1158381 TATTTAATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
13 1 0.02
14 10 0.19
15 19 0.35
16 17 0.31
17 7 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATTAAAATATATA
Found at i:1158345 original size:24 final size:22
Alignment explanation
Indices: 1158294--1158345 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 22
1158284 ATATATTGAT
* *
1158294 ATATTAAAATTTTATAATATAA
1 ATATTAAAATATTAAAATATAA
1158316 ATTATTAATAATATTAAAATATATA
1 A-TATTAA-AATATTAAAATATA-A
1158341 ATATT
1 ATATT
1158346 TTAAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 1 0.04
23 6 0.24
24 16 0.64
25 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTAAAATATTAAAATATAA
Found at i:1158439 original size:7 final size:7
Alignment explanation
Indices: 1158427--1158458 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
1158417 TCACTTAAGT
1158427 TTTTTTA
1 TTTTTTA
1158434 TTTTTTA
1 TTTTTTA
1158441 TTTTTTA
1 TTTTTTA
1158448 TTTTTTA
1 TTTTTTA
1158455 TTTT
1 TTTT
1158459 CAGTAACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:1159454 original size:6 final size:7
Alignment explanation
Indices: 1159424--1159468 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
1159414 AAAAATATTA
1159424 TAAATAT
1 TAAATAT
1159431 TAAATAT
1 TAAATAT
*
1159438 TAAATTT
1 TAAATAT
1159445 TAAAT-T
1 TAAATAT
1159451 TAAATATAT
1 T-AA-ATAT
1159460 TAAATAT
1 TAAATAT
1159467 TA
1 TA
1159469 TTTTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
6 2 0.06
7 26 0.76
8 4 0.12
9 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAAATAT
Found at i:1160086 original size:24 final size:25
Alignment explanation
Indices: 1160032--1160087 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1160022 ATTTATAAAT
* * * *
1160032 AATAAAAGTTATATTTATAATATTG
1 AATAAAAGTTATATTAAAAATAATA
*
1160057 ATTAAAA-TTATATTAAAAATAATA
1 AATAAAAGTTATATTAAAAATAATA
1160081 AATAAAA
1 AATAAAA
1160088 AATATAACAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
AATAAAAGTTATATTAAAAATAATA
Found at i:1160962 original size:2 final size:2
Alignment explanation
Indices: 1160955--1160980 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1160945 TTTTTATTTA
1160955 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
1160981 GTTATCTCAC
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:1161107 original size:14 final size:14
Alignment explanation
Indices: 1161090--1161165 Score: 52
Period size: 15 Copynumber: 5.4 Consensus size: 14
1161080 AATTATTAAA
1161090 TATAAATTTAAATT
1 TATAAATTTAAATT
*
1161104 TATATAA-TT-ATTT
1 TATA-AATTTAAATT
*
1161117 TA-AAATTTTATATT
1 TATAAA-TTTAAATT
*
1161131 TAATAATTTTAAATT
1 T-ATAAATTTAAATT
1161146 T-TAAATTTTAAAATT
1 TATAAA-TTT-AAATT
1161161 TATAA
1 TATAA
1161166 TTTCATATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
11 2 0.04
12 1 0.02
13 10 0.21
14 12 0.26
15 17 0.36
16 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATAAATTTAAATT
Found at i:1161145 original size:7 final size:7
Alignment explanation
Indices: 1161113--1161168 Score: 58
Period size: 7 Copynumber: 7.6 Consensus size: 7
1161103 TTATATAATT
1161113 ATTTTAAA
1 ATTTT-AA
*
1161121 ATTTTAT
1 ATTTTAA
*
1161128 ATTTAATA
1 ATTTTA-A
1161136 ATTTTAA
1 ATTTTAA
1161143 ATTTTAA
1 ATTTTAA
1161150 ATTTTAA
1 ATTTTAA
*
1161157 AATTTATA
1 ATTTTA-A
1161165 ATTT
1 ATTT
1161169 CATATTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
7 26 0.65
8 14 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTTAA
Found at i:1161176 original size:22 final size:23
Alignment explanation
Indices: 1161115--1161177 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
1161105 ATATAATTAT
*
1161115 TTTAAAATTTTATA-TTTAATAA
1 TTTATAATTTTATATTTTAATAA
*
1161137 TTT-TAAATTTTAAATTTTAA-AA
1 TTTAT-AATTTTATATTTTAATAA
*
1161159 TTTATAATTTCATATTTTA
1 TTTATAATTTTATATTTTA
1161178 TGTTTAGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 28 0.82
23 6 0.18
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTATAATTTTATATTTTAATAA
Found at i:1161178 original size:15 final size:15
Alignment explanation
Indices: 1161112--1161178 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
1161102 TTTATATAAT
*
1161112 TATTTTAAAATTTTA
1 TATTTTATAATTTTA
*
1161127 TATTTAATAATTTTA
1 TATTTTATAATTTTA
*
1161142 AATTTTA-AATTTTA
1 TATTTTATAATTTTA
* * *
1161156 AAATTTATAATTTCA
1 TATTTTATAATTTTA
1161171 TATTTTAT
1 TATTTTAT
1161179 GTTTAGGATG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 13 0.30
15 30 0.70
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTTTATAATTTTA
Found at i:1162775 original size:22 final size:21
Alignment explanation
Indices: 1162748--1162790 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1162738 TACCTAAAAT
*
1162748 TTAAATTGAATAAATTAATTTA
1 TTAAATTAAATAAA-TAATTTA
1162770 TTAAATTAAATAAATAATTTA
1 TTAAATTAAATAAATAATTTA
1162791 ATTCATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTAAATTAAATAAATAATTTA
Found at i:1163130 original size:2 final size:2
Alignment explanation
Indices: 1163123--1163150 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1163113 TAATCCTTCA
1163123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1163151 TGTAATTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1163541 original size:22 final size:22
Alignment explanation
Indices: 1163506--1163547 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1163496 TATGAATTTA
* *
1163506 TTTTAATATATTAATAATAATT
1 TTTTAAAATATTAAAAATAATT
*
1163528 TTTTAAAATTTTAAAAATAA
1 TTTTAAAATATTAAAAATAA
1163548 GGTTATCAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAAAATATTAAAAATAATT
Found at i:1164344 original size:20 final size:21
Alignment explanation
Indices: 1164307--1164345 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1164297 TTTTATATCA
*
1164307 TAAATTTTATTTATAAAATTT
1 TAAATTTTATTGATAAAATTT
1164328 TAAATTTTA-TGATAAAAT
1 TAAATTTTATTGATAAAAT
1164346 ATTTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
TAAATTTTATTGATAAAATTT
Found at i:1165217 original size:21 final size:19
Alignment explanation
Indices: 1165179--1165217 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
1165169 TTTTTTATAA
1165179 TTTAAAAATTTATTAATTT
1 TTTAAAAATTTATTAATTT
*
1165198 TTTAATAATATTATTTAATT
1 TTTAAAAAT-TTA-TTAATT
1165218 AATAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTAAAAATTTATTAATTT
Found at i:1171948 original size:2 final size:2
Alignment explanation
Indices: 1171943--1171975 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1171933 TATATATATA
1171943 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1171976 ATATATGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1173071 original size:15 final size:16
Alignment explanation
Indices: 1173045--1173074 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1173035 ATTAATATAT
1173045 TATAATTATAATTTTA
1 TATAATTATAATTTTA
1173061 TATAA-TATAATTTT
1 TATAATTATAATTTT
1173075 CAACCCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATAATTATAATTTTA
Found at i:1173605 original size:11 final size:11
Alignment explanation
Indices: 1173589--1173618 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1173579 TAAAAGTAAC
1173589 ATATAATATAA
1 ATATAATATAA
1173600 ATATAATATAA
1 ATATAATATAA
1173611 ATATAATA
1 ATATAATA
1173619 ATATATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1173610 original size:16 final size:16
Alignment explanation
Indices: 1173589--1173645 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 16
1173579 TAAAAGTAAC
1173589 ATATAATATAAATATA
1 ATATAATATAAATATA
*
1173605 ATATAA-ATATA-ATA
1 ATATAATATAAATATA
* *
1173619 ATATATTA-AAAT-TT
1 ATATAATATAAATATA
*
1173633 ATATAACATAAAT
1 ATATAATATAAAT
1173646 TATTATTGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
14 17 0.53
15 9 0.28
16 6 0.19
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAATATAAATATA
Found at i:1173638 original size:19 final size:20
Alignment explanation
Indices: 1173594--1173643 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
1173584 GTAACATATA
1173594 ATATA-AATATAATATAAAT
1 ATATATAATATAATATAAAT
*
1173613 ATA-ATAATATATTA-AAAT
1 ATATATAATATAATATAAAT
* *
1173631 TTATATAACATAA
1 ATATATAATATAA
1173644 ATTATTATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATATAATATAATATAAAT
Found at i:1173748 original size:17 final size:17
Alignment explanation
Indices: 1173728--1173761 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1173718 AATACGAATA
* *
1173728 TAAATATAATATTATAT
1 TAAAAATAATATGATAT
1173745 TAAAAATAATATGATAT
1 TAAAAATAATATGATAT
1173762 GATATAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAAAATAATATGATAT
Found at i:1173751 original size:19 final size:19
Alignment explanation
Indices: 1173729--1173801 Score: 53
Period size: 20 Copynumber: 3.7 Consensus size: 19
1173719 ATACGAATAT
1173729 AAATATAATATTATATTAA
1 AAATATAATATTATATTAA
*
1173748 AAATAATATGATATGATA-TAA
1 AAAT-ATA--ATATTATATTAA
*
1173769 ATATATAA-A-TATATTAA
1 AAATATAATATTATATTAA
1173786 AATTTATATAATATTA
1 AA---ATATAATATTA
1173802 ATTGTTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 15
0.68 0.07 0.25
Matches are distributed among these distances:
16 3 0.07
17 5 0.12
18 1 0.02
19 4 0.10
20 12 0.29
21 7 0.17
22 9 0.22
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AAATATAATATTATATTAA
Found at i:1173799 original size:17 final size:17
Alignment explanation
Indices: 1173779--1173849 Score: 55
Period size: 16 Copynumber: 4.4 Consensus size: 17
1173769 ATATATAAAT
1173779 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
*
1173796 ATATT-AATTGTTA-AT-
1 ATATTAAAAT-TTATATA
*
1173811 ATATTAAATTTTATATA
1 ATATTAAAATTTATATA
1173828 A-ATATAAATATTT-TA-A
1 ATAT-TAAA-ATTTATATA
1173844 ATATTA
1 ATATTA
1173850 TTATGATAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
15 8 0.18
16 17 0.38
17 17 0.38
18 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:1173831 original size:20 final size:18
Alignment explanation
Indices: 1173766--1173836 Score: 50
Period size: 18 Copynumber: 4.3 Consensus size: 18
1173756 TGATATGATA
*
1173766 TAAATATATA-AATATAT
1 TAAATTTATATAATATAT
1173783 TAAAATTTATAT-A-ATAT
1 T-AAATTTATATAATATAT
*
1173800 T-AA-TTGT-TAATATAT
1 TAAATTTATATAATATAT
1173815 TAAATTTTATATAA-ATA-
1 TAAA-TTTATATAATATAT
1173832 TAAAT
1 TAAAT
1173837 ATTTTAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 17
0.68 0.05 0.27
Matches are distributed among these distances:
13 1 0.02
14 4 0.09
15 7 0.16
16 3 0.07
17 10 0.23
18 15 0.35
19 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (18 bp):
TAAATTTATATAATATAT
Found at i:1173848 original size:33 final size:33
Alignment explanation
Indices: 1173724--1173849 Score: 112
Period size: 33 Copynumber: 3.7 Consensus size: 33
1173714 ATACAATACG
* *
1173724 AATATAAATATAATATTATATTAAAAATAATATGATAT
1 AATATAAATATATTAATATATT-AAAAT--T-T-ATAT
* *
1173762 GATATAAATATATAAATATATTAAAATTTATAT
1 AATATAAATATATTAATATATTAAAATTTATAT
* * *
1173795 AATATTAAT-TGTTAATATATTAAATTTTATAT
1 AATATAAATATATTAATATATTAAAATTTATAT
*
1173827 AAATATAAATATTTTAA-ATATTA
1 -AATATAAATATATTAATATATTA
1173850 TTATGATAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
32 20 0.27
33 25 0.33
34 6 0.08
35 1 0.01
37 5 0.07
38 18 0.24
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (33 bp):
AATATAAATATATTAATATATTAAAATTTATAT
Found at i:1177212 original size:2 final size:2
Alignment explanation
Indices: 1177205--1177235 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1177195 ATTTATTTAT
1177205 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 T
1177236 TATTGTGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1180276 original size:24 final size:24
Alignment explanation
Indices: 1180244--1180294 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
1180234 AGTTAAAAAC
*
1180244 TTAATAAAATTTATATAATATAAATA
1 TTAA-AAAATATATA-AATATAAATA
*
1180270 TTAAAAAATATATAAATATATATA
1 TTAAAAAATATATAAATATAAATA
1180294 T
1 T
1180295 AATATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
25 9 0.39
26 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TTAAAAAATATATAAATATAAATA
Found at i:1180305 original size:20 final size:20
Alignment explanation
Indices: 1180282--1180319 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1180272 AAAAAATATA
1180282 TAAATAT-ATATATAATATTT
1 TAAATATAAT-TATAATATTT
1180302 TAAATATAATTATAATAT
1 TAAATATAATTATAATAT
1180320 AAAAATACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATATAATTATAATATTT
Found at i:1182273 original size:17 final size:17
Alignment explanation
Indices: 1182253--1182289 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1182243 ATTTTGATTT
*
1182253 TATATTTTTTTTAAATA
1 TATATTTTTATTAAATA
1182270 TATATTTTTATTAAATA
1 TATATTTTTATTAAATA
1182287 TAT
1 TAT
1182290 TTAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTTTTATTAAATA
Found at i:1183376 original size:37 final size:38
Alignment explanation
Indices: 1183323--1183419 Score: 98
Period size: 37 Copynumber: 2.6 Consensus size: 38
1183313 AAAATTTAAT
** *
1183323 ATTTTAATAATTTATATTAATAAATT-T-TTATTATATT-T
1 ATTTTAATTTTTTATATTAAT--ATTATATT-TTATATTAC
1183361 ATTTT-ATTTTTTATATT-ATATTATATTTTATATTAC
1 ATTTTAATTTTTTATATTAATATTATATTTTATATTAC
1183397 ATTTTAATTTTTTATATT-ATATT
1 ATTTTAATTTTTTATATTAATATT
1183420 TATAAAATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
34 3 0.06
35 8 0.15
36 9 0.17
37 27 0.52
38 5 0.10
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (38 bp):
ATTTTAATTTTTTATATTAATATTATATTTTATATTAC
Found at i:1183377 original size:23 final size:23
Alignment explanation
Indices: 1183347--1183391 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1183337 TATTAATAAA
1183347 TTTTTATTATATT-TATTTTATT
1 TTTTTATTATATTATATTTTATT
1183369 TTTTATATTATATTATATTTTAT
1 TTTT-TATTATATTATATTTTAT
1183392 ATTACATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.19
23 9 0.43
24 8 0.38
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTATTATATTATATTTTATT
Found at i:1183379 original size:12 final size:12
Alignment explanation
Indices: 1183353--1183420 Score: 57
Period size: 12 Copynumber: 5.7 Consensus size: 12
1183343 TAAATTTTTA
1183353 TTATA-TTTATT
1 TTATATTTTATT
* *
1183364 TTATTTTTTATA
1 TTATATTTTATT
*
1183376 TTATATTATATT
1 TTATATTTTATT
**
1183388 TTATATTACATT
1 TTATATTTTATT
* *
1183400 TTAATTTTTTATA
1 TT-ATATTTTATT
1183413 TTATATTT
1 TTATATTT
1183421 ATAAAATATA
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
11 4 0.09
12 32 0.73
13 8 0.18
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATATTTTATT
Found at i:1183418 original size:5 final size:5
Alignment explanation
Indices: 1183351--1183443 Score: 52
Period size: 5 Copynumber: 18.8 Consensus size: 5
1183341 AATAAATTTT
* * * *
1183351 TATTA TATT- TATTT TATT- TTTTA TATTA TATTA TATTTTA TATTA CATTT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA--TTA TATTA TATTA
* * *
1183401 TAATT- TTTTA TATTA TATT- TA-TA AAATA TAATTA TATTA TATT
1 T-ATTA TATTA TATTA TATTA TATTA TATTA T-ATTA TATTA TATT
1183444 TAAAATTATC
Statistics
Matches: 69, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
3 1 0.01
4 12 0.17
5 44 0.64
6 7 0.10
7 5 0.07
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (5 bp):
TATTA
Found at i:1183442 original size:13 final size:11
Alignment explanation
Indices: 1183332--1183445 Score: 73
Period size: 11 Copynumber: 10.5 Consensus size: 11
1183322 TATTTTAATA
1183332 ATTTATATTAAT
1 ATTTATATT-AT
*
1183344 AAATTTTTATTAT
1 --ATTTATATTAT
1183357 ATTTAT-TT-T
1 ATTTATATTAT
1183366 ATTT-T-TTAT
1 ATTTATATTAT
1183375 A-TTATATTAT
1 ATTTATATTAT
*
1183385 ATTTTATATTAC
1 A-TTTATATTAT
1183397 ATTT-TAATT-T
1 ATTTAT-ATTAT
1183407 -TTTATATTAT
1 ATTTATATTAT
*
1183417 ATTTATAAAATAT
1 ATTTAT--ATTAT
*
1183430 AATTATATTAT
1 ATTTATATTAT
1183441 ATTTA
1 ATTTA
1183446 AAATTATCTT
Statistics
Matches: 81, Mismatches: 8, Indels: 25
0.71 0.07 0.22
Matches are distributed among these distances:
8 5 0.06
9 14 0.17
10 10 0.12
11 24 0.30
12 9 0.11
13 11 0.14
14 8 0.10
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:1184724 original size:22 final size:24
Alignment explanation
Indices: 1184698--1184744 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1184688 TTATTTAAAA
*
1184698 TTTTAAAGT-T-TTTTTTTTCGTT
1 TTTTAAAGTATATTTGTTTTCGTT
1184720 TTTTAAAGTATATTTGTTTTCGTT
1 TTTTAAAGTATATTTGTTTTCGTT
1184744 T
1 T
1184745 CAAATAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.41
23 1 0.05
24 12 0.55
ACGTcount: A:0.17, C:0.04, G:0.11, T:0.68
Consensus pattern (24 bp):
TTTTAAAGTATATTTGTTTTCGTT
Found at i:1187401 original size:5 final size:5
Alignment explanation
Indices: 1187393--1187421 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1187383 GGGAAGGATA
1187393 GATGG GATGG GATGG GATGG GATGG GATG
1 GATGG GATGG GATGG GATGG GATGG GATG
1187422 AGATTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.59, T:0.21
Consensus pattern (5 bp):
GATGG
Found at i:1187465 original size:18 final size:18
Alignment explanation
Indices: 1187442--1187508 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
1187432 TTGTAATTTG
1187442 AATATAAAATAATTATAA
1 AATATAAAATAATTATAA
* *
1187460 AATATAAATAAAATATAAAA
1 AATATAAA-ATAAT-TATAA
* *
1187480 AATAATAAAA-ATTTATAT
1 AAT-ATAAAATAATTATAA
1187498 AATATAAAATA
1 AATATAAAATA
1187509 TTAATTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
17 6 0.15
18 15 0.38
19 6 0.15
20 8 0.20
21 5 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATATAAAATAATTATAA
Found at i:1187474 original size:29 final size:28
Alignment explanation
Indices: 1187442--1187513 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
1187432 TTGTAATTTG
*
1187442 AATATAAAATAATTATAAAATATAAATAA
1 AATATAAAATAATAATAAAA-ATAAATAA
** *
1187471 AATATAAAA-AATAATAAAAATTTATAT
1 AATATAAAATAATAATAAAAATAAATAA
*
1187498 AATATAAAATATTAAT
1 AATATAAAATAATAAT
1187514 TTATTAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 14 0.38
28 14 0.38
29 9 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
AATATAAAATAATAATAAAAATAAATAA
Found at i:1187545 original size:15 final size:15
Alignment explanation
Indices: 1187526--1187556 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1187516 ATTAAATTTT
1187526 TAAAAAT-TATAATA
1 TAAAAATATATAATA
1187540 TAAAAATATATAATA
1 TAAAAATATATAATA
1187555 TA
1 TA
1187557 TATTTATTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAAATATATAATA
Found at i:1188112 original size:13 final size:13
Alignment explanation
Indices: 1188094--1188127 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
1188084 AAAATAAATA
1188094 AAATTTTATTTAT
1 AAATTTTATTTAT
1188107 AAATTTTATTTAT
1 AAATTTTATTTAT
1188120 AAATTTTA
1 AAATTTTA
1188128 AGTTAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AAATTTTATTTAT
Found at i:1189566 original size:3 final size:3
Alignment explanation
Indices: 1189560--1189591 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1189550 AAACAACAGC
1189560 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1189592 AGAAAGTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1197899 original size:2 final size:2
Alignment explanation
Indices: 1197892--1197917 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1197882 TATATTTACC
1197892 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
1197918 GTTTATTATA
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:1197944 original size:15 final size:15
Alignment explanation
Indices: 1197926--1197972 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1197916 ATGTTTATTA
1197926 TAATTATATTAAATT
1 TAATTATATTAAATT
1197941 TAA-TATATTAATAATT
1 TAATTATATT-A-AATT
1197957 TATATTATA-TAAATT
1 TA-ATTATATTAAATT
1197972 T
1 T
1197973 TGATACGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 6 0.21
15 9 0.32
16 7 0.25
17 2 0.07
18 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTATATTAAATT
Found at i:1198142 original size:29 final size:29
Alignment explanation
Indices: 1198100--1198161 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1198090 TATACTATAA
*
1198100 TAAATGTAACATTTTAATTTTTATATTAT
1 TAAATGTAACATTTTAATATTTATATTAT
* * * *
1198129 TAAATTTAATATTTTAGTATTTATATTTT
1 TAAATGTAACATTTTAATATTTATATTAT
1198158 TAAA
1 TAAA
1198162 ATTATAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (29 bp):
TAAATGTAACATTTTAATATTTATATTAT
Found at i:1198616 original size:24 final size:24
Alignment explanation
Indices: 1198589--1198636 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1198579 TATTTACTTT
*
1198589 AATGTATTAAAAGTAACAAAATAA
1 AATGTATTAAAAATAACAAAATAA
*
1198613 AATGTATTAAAAATAATAAAATAA
1 AATGTATTAAAAATAACAAAATAA
1198637 CATAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (24 bp):
AATGTATTAAAAATAACAAAATAA
Found at i:1198895 original size:17 final size:18
Alignment explanation
Indices: 1198870--1198907 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1198860 TTCAATACTC
*
1198870 AAAAGATAAT-TTTAAAT
1 AAAAAATAATATTTAAAT
1198887 AAAAAATAATACTTTAAAT
1 AAAAAATAATA-TTTAAAT
1198906 AA
1 AA
1198908 TATATATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
AAAAAATAATATTTAAAT
Found at i:1198914 original size:2 final size:2
Alignment explanation
Indices: 1198907--1198943 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1198897 ACTTTAAATA
* *
1198907 AT AT AT AT GT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1198944 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1198948 original size:2 final size:2
Alignment explanation
Indices: 1198943--1198967 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1198933 ATATATATAT
1198943 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1198968 ATAATGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1203939 original size:18 final size:19
Alignment explanation
Indices: 1203912--1203971 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
1203902 ATAATCTATA
1203912 TAATATATTTTATTTATATT
1 TAATA-ATTTTATTTATATT
*
1203932 TAA-AATTTTA-ATATATT
1 TAATAATTTTATTTATATT
1203949 TAATAATTTATATTT-TA-T
1 TAATAATTT-TATTTATATT
1203967 TAATA
1 TAATA
1203972 TTTATATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 9 0.26
18 17 0.49
19 5 0.14
20 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TAATAATTTTATTTATATT
Found at i:1203958 original size:17 final size:16
Alignment explanation
Indices: 1203926--1203986 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
1203916 ATATTTTATT
1203926 TATATTTAA-AATTTTAA
1 TATATTTAATAA-TTT-A
1203943 TATATTTAATAATTTA
1 TATATTTAATAATTTA
*
1203959 TAT-TTTATTAATATTTA
1 TATATTTAAT-A-ATTTA
*
1203976 TATAATTAATA
1 TATATTTAATA
1203987 TAAAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 5 0.14
16 5 0.14
17 21 0.57
18 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATTTAATAATTTA
Found at i:1204148 original size:18 final size:21
Alignment explanation
Indices: 1204127--1204170 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 21
1204117 AGATTAAGTT
1204127 ATTTATTTAA-A-TT-AAAAA
1 ATTTATTTAATAGTTAAAAAA
1204145 ATTTATTTAATAGTTAAAAAA
1 ATTTATTTAATAGTTAAAAAA
1204166 ATTTA
1 ATTTA
1204171 AATAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
19 1 0.04
20 2 0.09
21 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTTATTTAATAGTTAAAAAA
Found at i:1204613 original size:12 final size:13
Alignment explanation
Indices: 1204573--1204613 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
1204563 AATTTAAATA
1204573 AATATTAATATTT
1 AATATTAATATTT
1204586 -ATATTAATAATATT
1 AATATTAAT-AT-TT
1204600 AATATT-ATATTT
1 AATATTAATATTT
1204612 AA
1 AA
1204614 ACTCGATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 12 0.48
13 4 0.16
14 4 0.16
15 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AATATTAATATTT
Found at i:1204613 original size:21 final size:21
Alignment explanation
Indices: 1204564--1204613 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
1204554 ATCAAATCAA
1204564 ATTTAAATAAATATTAATATTT
1 ATTT-AATAAATATTAATATTT
1204586 ATATTAAT-AATATTAATATTAT
1 AT-TTAATAAATATTAATATT-T
1204608 ATTTAA
1 ATTTAA
1204614 ACTCGATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 16 0.62
22 8 0.31
23 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTAATAAATATTAATATTT
Found at i:1211300 original size:2 final size:2
Alignment explanation
Indices: 1211293--1211324 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1211283 GTTTGTACAC
1211293 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
1211325 CACACACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1211975 original size:16 final size:16
Alignment explanation
Indices: 1211896--1211992 Score: 70
Period size: 17 Copynumber: 5.7 Consensus size: 16
1211886 CAGTTTAAAA
* *
1211896 TTTAAATTTATGATTGT
1 TTTAAATTTA-AATTAT
1211913 TTTAAAATTTAAATTAT
1 TTT-AAATTTAAATTAT
* * *
1211930 TTTAATTTTGATCAATAAAA
1 TTTAAATTT-A--AAT-TAT
1211950 TTTAATATTTAAATTAT
1 TTTAA-ATTTAAATTAT
1211967 TTTAAATTTAAATTA-
1 TTTAAATTTAAATTAT
*
1211982 ATTAAATTTAA
1 TTTAAATTTAA
1211993 TACTTAAATT
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
15 10 0.15
16 15 0.23
17 17 0.26
18 10 0.15
19 3 0.05
20 7 0.11
21 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Found at i:1211989 original size:38 final size:37
Alignment explanation
Indices: 1211913--1212002 Score: 117
Period size: 38 Copynumber: 2.4 Consensus size: 37
1211903 TTATGATTGT
* **
1211913 TTTAAAATTTAAATTATTTTAATTTTGATCAATAAAA
1 TTTAATATTTAAATTATTTTAATTTAAATCAATAAAA
* *
1211950 TTTAATATTTAAATTATTTTAAATTTAAATTAATTAAA
1 TTTAATATTTAAATTATTTT-AATTTAAATCAATAAAA
*
1211988 TTTAATACTTAAATT
1 TTTAATATTTAAATT
1212003 TAATCAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 19 0.41
38 27 0.59
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (37 bp):
TTTAATATTTAAATTATTTTAATTTAAATCAATAAAA
Found at i:1212019 original size:14 final size:13
Alignment explanation
Indices: 1211947--1212031 Score: 70
Period size: 13 Copynumber: 6.5 Consensus size: 13
1211937 TTGATCAATA
*
1211947 AAATTTAATATTT
1 AAATTTAATAATT
*
1211960 AAA-TT-AT-TTT
1 AAATTTAATAATT
1211970 AAATTTAAATTAATT
1 AAATTT-AA-TAATT
*
1211985 AAATTTAATACTT
1 AAATTTAATAATT
1211998 AAATTTAATCAATT
1 AAATTTAAT-AATT
*
1212012 AAACTTAAT-ATT
1 AAATTTAATAATT
1212024 AAAATTTA
1 -AAATTTA
1212032 TCAAATTTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.10
11 4 0.07
12 5 0.08
13 23 0.38
14 14 0.23
15 8 0.13
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTTAATAATT
Found at i:1212019 original size:27 final size:26
Alignment explanation
Indices: 1211947--1212035 Score: 87
Period size: 27 Copynumber: 3.5 Consensus size: 26
1211937 TTGATCAATA
* *
1211947 AAATTTAAT-ATTTAAA-TT-ATTTT
1 AAATTTAATCAATTAAACTTAATATT
* *
1211970 AAATTTAAATTAATTAAATTTAATACTT
1 AAATTT-AATCAATTAAACTTAATA-TT
1211998 AAATTTAATCAATTAAACTTAATATT
1 AAATTTAATCAATTAAACTTAATATT
1212024 AAAATTT-ATCAA
1 -AAATTTAATCAA
1212036 ATTTAAATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
23 6 0.11
24 3 0.05
25 6 0.11
26 9 0.16
27 24 0.43
28 8 0.14
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATTTAATCAATTAAACTTAATATT
Found at i:1222953 original size:3 final size:3
Alignment explanation
Indices: 1222940--1222972 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
1222930 ATGTTCTTTT
1222940 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
1222973 TTTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1228535 original size:3 final size:3
Alignment explanation
Indices: 1228527--1228559 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1228517 TAAAGGTACC
1228527 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1228560 TCTTTCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1229141 original size:2 final size:2
Alignment explanation
Indices: 1229129--1229176 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1229119 ACAAAAATTA
*
1229129 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1229171 AT AT AT
1 AT AT AT
1229177 GCTAGTCGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1231728 original size:2 final size:2
Alignment explanation
Indices: 1231721--1231759 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1231711 GTGAGTTCTT
1231721 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 T
1231760 GCCATTGCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1232327 original size:42 final size:39
Alignment explanation
Indices: 1232248--1232337 Score: 92
Period size: 42 Copynumber: 2.2 Consensus size: 39
1232238 CATTTTTTTA
* *
1232248 TAATAAAAAAATAATTTTATTTAATTTAATTATAAATAT
1 TAATATAAAAATAATTTTATTTAATTTAATTATAAATAG
* *
1232287 TAATATAAAAATATTTTTTATACTTAATATT-ATTTTAAATAG
1 TAATATAAAAATA-ATTTTAT--TTAAT-TTAATTATAAATAG
*
1232329 TAAAATAAA
1 TAATATAAA
1232338 CTTTTGAACC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
39 12 0.29
40 6 0.14
42 22 0.52
43 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (39 bp):
TAATATAAAAATAATTTTATTTAATTTAATTATAAATAG
Found at i:1234211 original size:2 final size:2
Alignment explanation
Indices: 1234204--1234240 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1234194 TTCTTGAGAC
*
1234204 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1234241 TCAAGTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Done.