Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 3 of 208
Found at i:785559 original size:21 final size:22
Alignment explanation
Indices: 785534--785578 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
785524 TTTAAACATC
785534 TTAATTATT-ACTTAAATAATA
1 TTAATTATTAACTTAAATAATA
*
785555 TTAATTATTAATTTAAATAATA
1 TTAATTATTAACTTAAATAATA
785577 TT
1 TT
785579 GTTTAGCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAATTATTAACTTAAATAATA
Found at i:820064 original size:21 final size:19
Alignment explanation
Indices: 820034--820086 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
820024 CCGACCCATT
*
820034 TTTTAATAAATACCAAAAATTA
1 TTTT-ATAAATA--AAAAAGTA
820056 TTTTATAAATTAAAAAAGTA
1 TTTTATAAA-TAAAAAAGTA
*
820076 TTTTAAAAATA
1 TTTTATAAATA
820087 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
21 5 0.18
22 6 0.21
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
TTTTATAAATAAAAAAGTA
Found at i:820077 original size:20 final size:20
Alignment explanation
Indices: 820048--820085 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
820038 AATAAATACC
* *
820048 AAAAATTATTTTATAAATTA
1 AAAAAGTATTTTAAAAATTA
820068 AAAAAGTATTTTAAAAAT
1 AAAAAGTATTTTAAAAAT
820086 ATTTTAAAAA
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:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
AAAAAGTATTTTAAAAATTA
Found at i:820099 original size:10 final size:11
Alignment explanation
Indices: 820068--820104 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
820058 TTATAAATTA
820068 AAAAAGTATTTT
1 AAAAA-TATTTT
820080 AAAAATATTTT
1 AAAAATATTTT
820091 AAAAA-ATTTT
1 AAAAATATTTT
820101 AAAA
1 AAAA
820105 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 9 0.36
11 11 0.44
12 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:829124 original size:28 final size:28
Alignment explanation
Indices: 829042--829136 Score: 75
Period size: 31 Copynumber: 3.2 Consensus size: 28
829032 CTTTTTTATT
*
829042 AAATTATAAAATAGTGATTCAATTATTAA
1 AAATTATAAAATA-TCATTCAATTATTAA
**** * *
829071 TAAATTTATCTTTTCATTATTTAATTATTAA
1 -AAA-TTATAAAAT-ATCATTCAATTATTAA
829102 AAATTATAAAATATCATTCAATTAATT-A
1 AAATTATAAAATATCATTCAATT-ATTAA
829130 AAATTAT
1 AAATTAT
829137 TTTTTACCAC
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
28 17 0.34
29 8 0.16
30 6 0.12
31 18 0.36
32 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (28 bp):
AAATTATAAAATATCATTCAATTATTAA
Found at i:838830 original size:6 final size:6
Alignment explanation
Indices: 838819--838855 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
838809 AATGAAGGAG
838819 CCATAC CCATAC CCATAC CCATAC CCATAC CCATAC C
1 CCATAC CCATAC CCATAC CCATAC CCATAC CCATAC C
838856 AGATCCTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.51, G:0.00, T:0.16
Consensus pattern (6 bp):
CCATAC
Found at i:850045 original size:69 final size:69
Alignment explanation
Indices: 849934--850071 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
849924 ACTTAGTGCC
849934 CACCTTATACTCGCTTTAGGAGTTTGAATCACTGAAATTATTTGTTAATTCGTGAACTTGAAAAG
1 CACCTTATACTCGCTTTAGGAGTTTGAATCACTGAAATTATTTGTTAATTCGTGAACTTGAAAAG
849999 GCGA
66 GCGA
850003 CACCTTATACTCGCTTTAGGAGTTTGAATCACTGAAATTATTTGTTAATTCGTGAACTTGAAAAG
1 CACCTTATACTCGCTTTAGGAGTTTGAATCACTGAAATTATTTGTTAATTCGTGAACTTGAAAAG
850068 GCGA
66 GCGA
850072 TAAATTTATA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (69 bp):
CACCTTATACTCGCTTTAGGAGTTTGAATCACTGAAATTATTTGTTAATTCGTGAACTTGAAAAG
GCGA
Found at i:858438 original size:17 final size:18
Alignment explanation
Indices: 858397--858449 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 18
858387 CGTGCAATTG
858397 TATATATA-AATTTTGAT
1 TATATATATAATTTTGAT
*
858414 T-T-TGTATAATTTT-AT
1 TATATATATAATTTTGAT
858429 TATATATATAAAATTTTGAT
1 TATATATAT--AATTTTGAT
858449 T
1 T
858450 TGATTCACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
15 6 0.21
16 8 0.29
17 5 0.18
19 6 0.21
20 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
TATATATATAATTTTGAT
Found at i:858650 original size:31 final size:30
Alignment explanation
Indices: 858577--858664 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 30
858567 TTCTTTAAAT
*
858577 GTGTAT-ATTAAATCAAAATTAAAATTTTAA
1 GTGTATAATTAAATC-AAATTAAAATTTCAA
* * * * *
858607 ATATACATTTAAATCACAATTAAAATTTCAC
1 GTGTATAATTAAATCA-AATTAAAATTTCAA
858638 GTGTATAATTAAA-CTAAATTAAAATTT
1 GTGTATAATTAAATC-AAATTAAAATTT
858665 ATATACACAA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
30 16 0.36
31 29 0.64
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.39
Consensus pattern (30 bp):
GTGTATAATTAAATCAAATTAAAATTTCAA
Found at i:867706 original size:3 final size:3
Alignment explanation
Indices: 867698--867739 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
867688 ATTTTGAATA
867698 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAGG AA- AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG
867740 TTGAAACTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:867901 original size:16 final size:17
Alignment explanation
Indices: 867871--867904 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
867861 GGAAGTTGGA
867871 GGAGAGGGGAAGGGATG
1 GGAGAGGGGAAGGGATG
*
867888 GGAG-GGGGAGGGGATG
1 GGAGAGGGGAAGGGATG
867904 G
1 G
867905 CTTTTGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.71, T:0.06
Consensus pattern (17 bp):
GGAGAGGGGAAGGGATG
Found at i:897566 original size:4 final size:4
Alignment explanation
Indices: 897557--897587 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
897547 AATGAGAAGG
897557 CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CAT
897588 GTGGCGTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:902977 original size:18 final size:18
Alignment explanation
Indices: 902954--902993 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
902944 TATAATTTTA
*
902954 AAAAATA-TATAATACATC
1 AAAAATATTA-AAAACATC
902972 AAAAATATTAAAAACATC
1 AAAAATATTAAAAACATC
902990 AAAA
1 AAAA
902994 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATATTAAAAACATC
Found at i:909152 original size:21 final size:20
Alignment explanation
Indices: 909128--909170 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
909118 TATTAATATA
*
909128 AATAATATAATTTATTATTTC
1 AATAAT-TAATTTAATATTTC
*
909149 AATAATTTATTTAATATTTC
1 AATAATTAATTTAATATTTC
909169 AA
1 AA
909171 CTTTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTAATTTAATATTTC
Found at i:909193 original size:13 final size:14
Alignment explanation
Indices: 909175--909215 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
909165 TTTCAACTTT
909175 ATTTTAATAATA-A
1 ATTTTAATAATATA
909188 ATTTTAA-AATGATA
1 ATTTTAATAAT-ATA
909202 ATTTTAAATAATAT
1 ATTTT-AATAATAT
909216 TATTCACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.12
13 8 0.33
14 6 0.25
15 4 0.17
16 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:910398 original size:29 final size:30
Alignment explanation
Indices: 910328--910399 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
910318 AATAAGGCTT
*
910328 ATAGGTCGATTTTAAAATTTATTTAGACAT
1 ATAGGTCGATTTTAAAATTTATTTAGACAA
* * **
910358 TTAGG-CTAATTTTAAAA-TTATTTAGGGAA
1 ATAGGTC-GATTTTAAAATTTATTTAGACAA
910387 ATAGGTCGATTTT
1 ATAGGTCGATTTT
910400 GAGGAAAAGC
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.43
Consensus pattern (30 bp):
ATAGGTCGATTTTAAAATTTATTTAGACAA
Found at i:911932 original size:22 final size:21
Alignment explanation
Indices: 911879--911932 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
911869 AAATATTACG
911879 AAAATTAAAATTATTTGAAAA
1 AAAATTAAAATTATTTGAAAA
**
911900 ATAAAACAAAATTAAATTT-AAAA
1 A-AAATTAAAATT--ATTTGAAAA
911923 AAAATTAAAA
1 AAAATTAAAA
911933 AAAAACTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
21 1 0.04
22 16 0.62
23 5 0.19
24 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAATTAAAATTATTTGAAAA
Found at i:922871 original size:31 final size:31
Alignment explanation
Indices: 922836--922901 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
922826 ACAAATGATC
* *
922836 CACTAAACTATTTCA-AAATTTTCATTTAAGT
1 CACTAAACT-GTTCATAAATTTTAATTTAAGT
*
922867 CACTAAACTGTTCATAAGTTTTAATTTAAGT
1 CACTAAACTGTTCATAAATTTTAATTTAAGT
922898 CACT
1 CACT
922902 GAGCCACTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (31 bp):
CACTAAACTGTTCATAAATTTTAATTTAAGT
Found at i:933177 original size:4 final size:4
Alignment explanation
Indices: 933168--933197 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
933158 TGAAAGGAGG
933168 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GA
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GA
933198 GGAACAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:938653 original size:42 final size:42
Alignment explanation
Indices: 938606--938704 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
938596 TATACGAACA
* * *
938606 GCACTAAGTGCGCGAAACTAAAATGACAATGTTGAATAACGG
1 GCACTAAGTGTGCGAAACAAAAATGACAATGTCGAATAACGG
*
938648 GCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACGG
1 GCACTAAGTGTGCGAAACAAAAATGACAATGTCGAATAACGG
938690 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
938705 TATCAATATC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.18
Consensus pattern (42 bp):
GCACTAAGTGTGCGAAACAAAAATGACAATGTCGAATAACGG
Found at i:939236 original size:15 final size:15
Alignment explanation
Indices: 939216--939323 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
939206 TTTATGGAAA
939216 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
939231 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
939245 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
939261 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
939275 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
939291 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
939305 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
939321 ATC
1 ATC
939324 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:939245 original size:30 final size:30
Alignment explanation
Indices: 939209--939323 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
939199 ATCCATATTT
*
939209 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
939239 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
939269 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
939299 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
939324 GAGATATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:943930 original size:15 final size:15
Alignment explanation
Indices: 943910--944017 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
943900 TTTATGGAAA
943910 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
943925 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
*
943939 AGTCAATGATATGGGT
1 A-TCAAAGATATGGGT
* **
943955 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
943969 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
943985 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
943999 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
944015 ATC
1 ATC
944018 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 13 0.19
15 41 0.61
16 13 0.19
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:943939 original size:30 final size:30
Alignment explanation
Indices: 943903--944017 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
943893 ATCCATATTT
*
943903 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
943933 ATGGAAAGTCAATGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
943963 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
943993 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
944018 GAGATATTGG
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 81 1.00
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.26
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:948725 original size:16 final size:16
Alignment explanation
Indices: 948704--948739 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
948694 ATATCGACTC
948704 AAAAAAGAA-AAAAGA
1 AAAAAAGAAGAAAAGA
948719 GAAAAAAGAAGAAAAGA
1 -AAAAAAGAAGAAAAGA
948736 AAAA
1 AAAA
948740 CCCTTTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAGAAAAGA
Found at i:953764 original size:4 final size:4
Alignment explanation
Indices: 953755--953780 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
953745 ATCTGTCCGA
953755 CCAT CCAT CCAT CCAT CCAT CCAT CC
1 CCAT CCAT CCAT CCAT CCAT CCAT CC
953781 GTAGCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.54, G:0.00, T:0.23
Consensus pattern (4 bp):
CCAT
Found at i:959324 original size:40 final size:37
Alignment explanation
Indices: 959280--959387 Score: 119
Period size: 40 Copynumber: 2.8 Consensus size: 37
959270 TGTTTGATTA
*
959280 AAAATATATATATTTAATATATAATTCGAATTAAAAGTCT
1 AAAATATATATATTTAATATATAATTCG-ATTAAAA--AT
* *
959320 AAAATATATATATTTAATAAAAAGTATATTTGATTAAAAAT
1 AAAATATATATATTTAAT--ATA-TA-ATTCGATTAAAAAT
959361 AAAA-ATATATATTTAATATATAATTCG
1 AAAATATATATATTTAATATATAATTCG
959388 GGCCGAGCTC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
36 4 0.07
37 2 0.03
38 2 0.03
40 31 0.53
41 5 0.08
42 2 0.03
43 9 0.15
44 4 0.07
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (37 bp):
AAAATATATATATTTAATATATAATTCGATTAAAAAT
Found at i:960632 original size:3 final size:3
Alignment explanation
Indices: 960624--960648 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
960614 TTAAGGGTTC
960624 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
960649 TGCATTTGTT
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):
TAT
Found at i:971327 original size:20 final size:20
Alignment explanation
Indices: 971302--971339 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
971292 ATTTAACCAA
971302 AAAATT-AAGTATGAAAAAAC
1 AAAATTCAAG-ATGAAAAAAC
971322 AAAATTCAAGATGAAAAA
1 AAAATTCAAGATGAAAAA
971340 TATAAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (20 bp):
AAAATTCAAGATGAAAAAAC
Found at i:1000079 original size:106 final size:106
Alignment explanation
Indices: 999888--1000302 Score: 722
Period size: 106 Copynumber: 3.9 Consensus size: 106
999878 TGGATTGAGA
* * * *
999888 TTTAAGAGGATATTCGGCTATTTGGTCGAACGAGAACTCAAAACCCAGCACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
* * *
999953 CCTCGAATTTCTAAAAGCAAAATATTGCCTTACTTTGAAAT
66 CCTCAAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
999994 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
* *
1000059 TCTCAAATTTCCAAACGCAAAATATTGCCTAACTTTGAAAT
66 CCTCAAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
1000100 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
*
1000165 CCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
66 CCTCAAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
*
1000206 TTTAAAAGGATATTTGGCTATTTGGGCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
*
1000271 TCTCAAATTTCCAAACGCAAAATATTGCCTTA
66 CCTCAAATTTCCAAACGCAAAATATTGCCTTA
1000303 TTTTAAAACT
Statistics
Matches: 294, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 294 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
CCTCAAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
Found at i:1000783 original size:12 final size:12
Alignment explanation
Indices: 1000766--1000791 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1000756 ATAAGTAAGT
1000766 AATATTAAATAA
1 AATATTAAATAA
1000778 AATATTAAATAA
1 AATATTAAATAA
1000790 AA
1 AA
1000792 CTTATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATATTAAATAA
Found at i:1003757 original size:23 final size:23
Alignment explanation
Indices: 1003731--1003829 Score: 189
Period size: 23 Copynumber: 4.3 Consensus size: 23
1003721 AGTGTTATTG
1003731 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1003754 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
1003777 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1003800 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1003823 ATCAGTG
1 ATCAGTG
1003830 TGGCACTTAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:1007472 original size:46 final size:46
Alignment explanation
Indices: 1007410--1007595 Score: 309
Period size: 46 Copynumber: 4.0 Consensus size: 46
1007400 CCATGACAAA
* *
1007410 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATAATGAC
1 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
1007456 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
*
1007502 ATGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
* * * *
1007548 TCGTGAAAAGTAGGTATGGTATTTCAGTGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
1007594 TT
1 TT
1007596 ATAGCATTGT
Statistics
Matches: 131, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 131 1.00
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
Found at i:1009213 original size:20 final size:20
Alignment explanation
Indices: 1009170--1009213 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1009160 AAAAAAATTT
* ***
1009170 AAAAATAAAAAAATTATTTT
1 AAAAATAAAAAAATAATAAA
1009190 AAAAATAAAAAAATAATAAA
1 AAAAATAAAAAAATAATAAA
1009210 AAAA
1 AAAA
1009214 TATTTATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAATAAAAAAATAATAAA
Found at i:1010376 original size:73 final size:73
Alignment explanation
Indices: 1010294--1010479 Score: 363
Period size: 73 Copynumber: 2.5 Consensus size: 73
1010284 ACAACTTGAC
1010294 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1010359 CACTAACA
66 CACTAACA
*
1010367 AACTTAGTTGTAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1010432 CACTAACA
66 CACTAACA
1010440 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
1010480 AATAATAATA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.40, C:0.25, G:0.06, T:0.29
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:1010486 original size:3 final size:3
Alignment explanation
Indices: 1010480--1010508 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1010470 ATTACATCCA
1010480 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1010509 AACATGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1011577 original size:8 final size:8
Alignment explanation
Indices: 1011564--1011598 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1011554 AATAGATAAG
1011564 TATTATAT
1 TATTATAT
*
1011572 TATTATTT
1 TATTATAT
*
1011580 TATTATTT
1 TATTATAT
1011588 TATTATAT
1 TATTATAT
1011596 TAT
1 TAT
1011599 ATAAAGCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TATTATAT
Found at i:1011630 original size:13 final size:13
Alignment explanation
Indices: 1011612--1011636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1011602 AAGCATAAGA
1011612 AATAGAAACAGAG
1 AATAGAAACAGAG
1011625 AATAGAAACAGA
1 AATAGAAACAGA
1011637 ATAGGCAAAC
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:0.64, C:0.08, G:0.20, T:0.08
Consensus pattern (13 bp):
AATAGAAACAGAG
Found at i:1013589 original size:24 final size:24
Alignment explanation
Indices: 1013557--1013660 Score: 190
Period size: 24 Copynumber: 4.3 Consensus size: 24
1013547 ACTTTAGCGC
1013557 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
1013581 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
1013605 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
* *
1013629 GCTCTCTGATATTAGCACATTTGT
1 GCTCTCTGATATTAGCACGTTGGT
1013653 GCTCTCTG
1 GCTCTCTG
1013661 TGTTTGTTCC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 78 1.00
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.38
Consensus pattern (24 bp):
GCTCTCTGATATTAGCACGTTGGT
Found at i:1018017 original size:73 final size:73
Alignment explanation
Indices: 1017935--1018120 Score: 363
Period size: 73 Copynumber: 2.5 Consensus size: 73
1017925 ACAACTTGAC
1017935 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1018000 CACTAACA
66 CACTAACA
*
1018008 AACTTAGTTGTAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1018073 CACTAACA
66 CACTAACA
1018081 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
1018121 AATAATAATA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.40, C:0.25, G:0.06, T:0.29
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:1018127 original size:3 final size:3
Alignment explanation
Indices: 1018121--1018188 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
1018111 ATTACATCCA
1018121 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1018169 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
1018189 AACATGTGAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1021919 original size:21 final size:21
Alignment explanation
Indices: 1021893--1021933 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1021883 AGACGAGCAA
* *
1021893 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1021914 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1021934 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1029103 original size:55 final size:55
Alignment explanation
Indices: 1029044--1029168 Score: 130
Period size: 53 Copynumber: 2.3 Consensus size: 55
1029034 CCCACTACAT
** * **
1029044 CTGATTAAAAAAAAATTTTGGGTGTT-GATACACTGATGGTCGATACCCTTTTTAC
1 CTGATTAAAAAAAAATTTTGGACGTTAGA-ACACTGATGGTCGACACCCCCTTTAC
*** * *
1029099 CTGATT--AAAATTTTTTTGGACGTTAGAACACTGATGGTCGGCACCCCCTTTAT
1 CTGATTAAAAAAAAATTTTGGACGTTAGAACACTGATGGTCGACACCCCCTTTAC
1029152 CTGATTAAAAAAAAATT
1 CTGATTAAAAAAAAATT
1029169 GGGTGCTAGG
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
53 40 0.74
54 2 0.04
55 12 0.22
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (55 bp):
CTGATTAAAAAAAAATTTTGGACGTTAGAACACTGATGGTCGACACCCCCTTTAC
Found at i:1030106 original size:3 final size:3
Alignment explanation
Indices: 1030098--1030126 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1030088 ATTTCAATAG
1030098 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1030127 CATAAATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1031313 original size:20 final size:19
Alignment explanation
Indices: 1031270--1031313 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1031260 CATGCTTTCT
*
1031270 ATTCACATTTTCATATTCA
1 ATTCACATTTTCAAATTCA
1031289 ATTCACATTTTCAAAATTCA
1 ATTCACATTTTC-AAATTCA
*
1031309 GTTCA
1 ATTCA
1031314 ATACTAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.34, C:0.20, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTCACATTTTCAAATTCA
Found at i:1031903 original size:15 final size:15
Alignment explanation
Indices: 1031883--1031913 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1031873 TTTTTAGAAT
1031883 TTTTGACTTAGCCAA
1 TTTTGACTTAGCCAA
1031898 TTTTGACTTAGCCAA
1 TTTTGACTTAGCCAA
1031913 T
1 T
1031914 AAGTACAGTT
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:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (15 bp):
TTTTGACTTAGCCAA
Found at i:1032605 original size:45 final size:43
Alignment explanation
Indices: 1032518--1032606 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 43
1032508 AATAATAACA
* *
1032518 GATACACGGTGGATCAGCACATAGCACCACCCTTATAGTCAAT
1 GATACACGGTGGATCAACACATAGCACCACCCTTATAATCAAT
* *
1032561 GATACTCGGTGGAATCAACACATAGCAACCACCTTTATAATCAAT
1 GATACACGGTGG-ATCAACACATAGC-ACCACCCTTATAATCAAT
1032606 G
1 G
1032607 GTATGTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 11 0.28
44 12 0.30
45 17 0.43
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (43 bp):
GATACACGGTGGATCAACACATAGCACCACCCTTATAATCAAT
Found at i:1033757 original size:11 final size:11
Alignment explanation
Indices: 1033730--1033772 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
1033720 TGACCTTTCC
1033730 AAGGTATGGG-
1 AAGGTATGGGA
*
1033740 TAGGTATGGGA
1 AAGGTATGGGA
*
1033751 AAGGTATGGGC
1 AAGGTATGGGA
1033762 AAGGTATGGGA
1 AAGGTATGGGA
1033773 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:1033769 original size:22 final size:21
Alignment explanation
Indices: 1033730--1033772 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1033720 TGACCTTTCC
*
1033730 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
1033751 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
1033773 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:1037840 original size:18 final size:18
Alignment explanation
Indices: 1037817--1037909 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
1037807 CCCAACTACT
*
1037817 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
1037835 GTATACGTGAATAGTTCC
1 GTATACGTGAATAGTACC
*
1037853 GTATACGTGAATAGTATC
1 GTATACGTGAATAGTACC
* *
1037871 GTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACC
1037889 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
1037907 GTA
1 GTA
1037910 AACGGTCGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1038468 original size:11 final size:11
Alignment explanation
Indices: 1038441--1038483 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
1038431 TGACCTTTCC
1038441 AAGGTATGGG-
1 AAGGTATGGGA
*
1038451 TAGGTATGGGA
1 AAGGTATGGGA
*
1038462 AAGGTATGGGC
1 AAGGTATGGGA
1038473 AAGGTATGGGA
1 AAGGTATGGGA
1038484 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:1038480 original size:22 final size:21
Alignment explanation
Indices: 1038441--1038483 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1038431 TGACCTTTCC
*
1038441 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
1038462 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
1038484 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:1041531 original size:72 final size:72
Alignment explanation
Indices: 1041414--1041555 Score: 248
Period size: 72 Copynumber: 2.0 Consensus size: 72
1041404 CTTCCAAATA
* *
1041414 TGACATACTCCCCATCCACCTTGGTATGTCCCCAGAAAGCTCGTTATTGCTTAAATCCAATGTTG
1 TGACATACTCCCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCAATGTTG
1041479 ACAAACT
66 ACAAACT
* *
1041486 TGACATATTCTCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCAATGTTG
1 TGACATACTCCCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCAATGTTG
1041551 ACAAA
66 ACAAA
1041556 AAGGAGCAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (72 bp):
TGACATACTCCCCATCCACCTTGGTATCTCCCCAGAAAGCACGTTATTGCTTAAATCCAATGTTG
ACAAACT
Found at i:1042995 original size:17 final size:17
Alignment explanation
Indices: 1042973--1043006 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1042963 ATCCACTAAT
*
1042973 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1042990 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1043007 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1047634 original size:17 final size:17
Alignment explanation
Indices: 1047612--1047645 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1047602 ATCCACTAAT
*
1047612 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1047629 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1047646 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1053423 original size:21 final size:22
Alignment explanation
Indices: 1053393--1053433 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1053383 ATATCTAAAT
*
1053393 TACCACACACATATA-TATATA
1 TACCACACACACATACTATATA
*
1053414 TACCATACACACATACTATA
1 TACCACACACACATACTATA
1053434 AAACTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (22 bp):
TACCACACACACATACTATATA
Found at i:1055374 original size:15 final size:16
Alignment explanation
Indices: 1055354--1055383 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1055344 GTACTACTAG
1055354 ATTATTTT-TTTAAAA
1 ATTATTTTATTTAAAA
1055369 ATTATTTTATTTAAA
1 ATTATTTTATTTAAA
1055384 TGCCTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTATTTTATTTAAAA
Found at i:1055810 original size:25 final size:25
Alignment explanation
Indices: 1055728--1055797 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
1055718 GAATTTTAGC
1055728 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
*
1055753 GCTCTCTGATTATTAGCACATTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
1055778 GCTCTCTGA-TATTTAGCACG
1 GCTCTCTGATTA-TTAGCACG
1055798 CCAGTGCTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 2 0.05
25 40 0.95
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTGGT
Found at i:1055817 original size:22 final size:22
Alignment explanation
Indices: 1055751--1055856 Score: 77
Period size: 22 Copynumber: 4.5 Consensus size: 22
1055741 TAGCACGTTG
**
1055751 GTGCTCTCTGATTATTAGCACATTG
1 GTGCTCTCTG--T-TTAGCACATCA
**
1055776 GTGCTCTCTGATATTTAGCACGCCA
1 GTGCTCTCTG---TTTAGCACATCA
*
1055801 GTGCTCTCTGTTTAGCACATCT
1 GTGCTCTCTGTTTAGCACATCA
* * * *
1055823 GTGCTTTCTGTATAGCACTTTA
1 GTGCTCTCTGTTTAGCACATCA
1055845 GTGCTCTCTGTT
1 GTGCTCTCTGTT
1055857 CATTGGTGCA
Statistics
Matches: 64, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
22 36 0.56
25 27 0.42
26 1 0.02
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.41
Consensus pattern (22 bp):
GTGCTCTCTGTTTAGCACATCA
Found at i:1060565 original size:13 final size:13
Alignment explanation
Indices: 1060547--1060571 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1060537 GTTTTATTTT
1060547 TTATTTAAAATTG
1 TTATTTAAAATTG
1060560 TTATTTAAAATT
1 TTATTTAAAATT
1060572 ATGTTACATA
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTATTTAAAATTG
Found at i:1062994 original size:82 final size:82
Alignment explanation
Indices: 1062881--1063041 Score: 304
Period size: 82 Copynumber: 2.0 Consensus size: 82
1062871 ATTTGTTCCC
1062881 ATTAAAATTGATATTAAATTGATTTAATTTAGAGATAAATCTTTAAAATGTTTACATGAAATTTT
1 ATTAAAATTGATATTAAATTGATTTAATTTAGAGATAAATCTTTAAAATGTTTACATGAAATTTT
*
1062946 TACTGCTTTTTTTTTCT
66 TACTGCTTCTTTTTTCT
*
1062963 ATTAAAATTGATATTAAATTGATTTAATTTAGAGATAAATCTTTAAAATTTTTACATGAAATTTT
1 ATTAAAATTGATATTAAATTGATTTAATTTAGAGATAAATCTTTAAAATGTTTACATGAAATTTT
1063028 TACTGCTTCTTTTT
66 TACTGCTTCTTTTT
1063042 CTCCATTACT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (82 bp):
ATTAAAATTGATATTAAATTGATTTAATTTAGAGATAAATCTTTAAAATGTTTACATGAAATTTT
TACTGCTTCTTTTTTCT
Found at i:1073184 original size:13 final size:13
Alignment explanation
Indices: 1073166--1073195 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1073156 TCACTCTATC
1073166 ATATAAGTAAAGA
1 ATATAAGTAAAGA
1073179 ATATAAGTAAAGA
1 ATATAAGTAAAGA
1073192 ATAT
1 ATAT
1073196 TTGTTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (13 bp):
ATATAAGTAAAGA
Found at i:1082625 original size:23 final size:21
Alignment explanation
Indices: 1082573--1082660 Score: 70
Period size: 23 Copynumber: 4.0 Consensus size: 21
1082563 CCTGATCAGT
*
1082573 ATACGACACATAAGTGCCTGA
1 ATACGACACAGAAGTGCCTGA
*
1082594 A-ACGACACACGAGGTGCCTGA
1 ATACGACACA-GAAGTGCCTGA
*
1082615 GATACGACACATAAAGTGCCTGA
1 -ATACGACACA-GAAGTGCCTGA
* * *
1082638 TGTACAACACATAAAGTGCCTGA
1 -ATACGACACA-GAAGTGCCTGA
1082661 TCGGCAAAGC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
20 8 0.14
21 10 0.18
22 1 0.02
23 37 0.66
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.17
Consensus pattern (21 bp):
ATACGACACAGAAGTGCCTGA
Found at i:1082660 original size:46 final size:43
Alignment explanation
Indices: 1082573--1082660 Score: 104
Period size: 46 Copynumber: 2.0 Consensus size: 43
1082563 CCTGATCAGT
* * *
1082573 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTGAG
1 ATACGACACATAAGTGCCTGAAACAACACACAAAGTGCCTGAG
* *
1082616 ATACGACACATAAAGTGCCTGATGTACAACACATAAAGTGCCTGA
1 ATACGACACAT-AAGTGCCTGA--AACAACACACAAAGTGCCTGA
1082661 TCGGCAAAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 11 0.30
44 10 0.27
46 16 0.43
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.17
Consensus pattern (43 bp):
ATACGACACATAAGTGCCTGAAACAACACACAAAGTGCCTGAG
Found at i:1082661 original size:23 final size:24
Alignment explanation
Indices: 1082607--1082661 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 24
1082597 GACACACGAG
*
1082607 GTGCCTGA-GATACGACACATAAA
1 GTGCCTGATGATACAACACATAAA
1082630 GTGCCTGATG-TACAACACATAAA
1 GTGCCTGATGATACAACACATAAA
1082653 GTGCCTGAT
1 GTGCCTGAT
1082662 CGGCAAAGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (24 bp):
GTGCCTGATGATACAACACATAAA
Found at i:1083797 original size:18 final size:17
Alignment explanation
Indices: 1083755--1083809 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
1083745 GTCTGTTCTC
**
1083755 TGTTTCTTTTAAGCTATT
1 TGTTTCTTTTATTCT-TT
*
1083773 CTGTTTCTATTTCTTCTTT
1 -TGTTTCT-TTTATTCTTT
1083792 TGTTTCTTTTATTCTTT
1 TGTTTCTTTTATTCTTT
1083809 T
1 T
1083810 ATTTTATTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 10 0.32
18 7 0.23
19 9 0.29
20 5 0.16
ACGTcount: A:0.09, C:0.15, G:0.07, T:0.69
Consensus pattern (17 bp):
TGTTTCTTTTATTCTTT
Found at i:1083843 original size:3 final size:3
Alignment explanation
Indices: 1083835--1083880 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
1083825 ATGCATTAGT
* *
1083835 TAA TAA TAA TAA TAA TAA TAA TATA TTA TAA TAA TCA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
1083880 T
1 T
1083881 TTTTTTTCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.89
4 2 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1084016 original size:5 final size:5
Alignment explanation
Indices: 1084008--1084042 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1083998 TATTTAATTT
*
1084008 ATATA ATATA ATACA ATATA ATATA ATAT- ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
1084043 AAAATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:1086157 original size:24 final size:24
Alignment explanation
Indices: 1086130--1086176 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1086120 AGCCTATAAT
*
1086130 GGGTAGCTCCAAAGAGCAATTAAC
1 GGGTAGCTCCAAAGAACAATTAAC
* *
1086154 GGGTAGCTTCGAAGAACAATTAA
1 GGGTAGCTCCAAAGAACAATTAA
1086177 TGGGAAGTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (24 bp):
GGGTAGCTCCAAAGAACAATTAAC
Found at i:1086286 original size:26 final size:25
Alignment explanation
Indices: 1086222--1086287 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
1086212 ATGCGAGCAC
* * *
1086222 TAACGGGAAGCTTACGAAGAGCCTT
1 TAACGGGAAGCTCACAAAGAGCCTA
*
1086247 TAATCGGAAAGCTCACAAAGAGCCATA
1 TAA-CGGGAAGCTCACAAAGAGCC-TA
*
1086274 TAACGGGACGCTCA
1 TAACGGGAAGCTCA
1086288 TAAGAGCTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 3 0.09
26 26 0.79
27 4 0.12
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (25 bp):
TAACGGGAAGCTCACAAAGAGCCTA
Found at i:1099474 original size:109 final size:109
Alignment explanation
Indices: 1099336--1099603 Score: 466
Period size: 109 Copynumber: 2.4 Consensus size: 109
1099326 AGCTCAGTAA
1099336 GTTAGGGCACGATTTTCTCGAATTTTCTAAATACGAAATATTGCCTTTATTATTGAAAGTTTAAA
1 GTTAGGGCACG-TTTTCTCGAATTTTCTAAATACGAAATATTGCCTTTATTATTGAAAGTTTAAA
1099401 AGGGTATTTGGCCATTTGGTCGAACGAGGAATCGAAACCCAGCAC
65 AGGGTATTTGGCCATTTGGTCGAACGAGGAATCGAAACCCAGCAC
*
1099446 GTTAGGGCATGTTTTCTCGAATTTTCTAAATACGAAATATTGCCTTTATTATTGAAAGTTTAAAA
1 GTTAGGGCACGTTTTCTCGAATTTTCTAAATACGAAATATTGCCTTTATTATTGAAAGTTTAAAA
1099511 GGGTATTTGGCCATTTGGTCGAACGAGGAATCGAAACCCAGCAC
66 GGGTATTTGGCCATTTGGTCGAACGAGGAATCGAAACCCAGCAC
* ** *
1099555 GTTAGGGCACGTTTTCTCGAACTTTCCT-AACGCGAAATATTGCTTTTAT
1 GTTAGGGCACGTTTTCTCGAA-TTTTCTAAATACGAAATATTGCCTTTAT
1099604 GAAAGAATTA
Statistics
Matches: 151, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
109 136 0.90
110 15 0.10
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (109 bp):
GTTAGGGCACGTTTTCTCGAATTTTCTAAATACGAAATATTGCCTTTATTATTGAAAGTTTAAAA
GGGTATTTGGCCATTTGGTCGAACGAGGAATCGAAACCCAGCAC
Found at i:1099939 original size:15 final size:15
Alignment explanation
Indices: 1099919--1099949 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1099909 ATATATATTA
1099919 ATAATAGTAATAAAT
1 ATAATAGTAATAAAT
1099934 ATAATAGTAATAAAT
1 ATAATAGTAATAAAT
1099949 A
1 A
1099950 GAAAATAATA
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:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
ATAATAGTAATAAAT
Found at i:1100247 original size:3 final size:3
Alignment explanation
Indices: 1100241--1100377 Score: 109
Period size: 3 Copynumber: 45.7 Consensus size: 3
1100231 ATAGTTGTAG
* * * * * * *
1100241 TAA TAA TAA TAG TAA GAA AAA TAG TGA TAA T-A TAA CAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1100288 T-A TAA CAA -GA GAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1100334 TAG TAA TGGAGA TAA TAA TAA TAA TAA TGA TAC TAA TAA TAA TA
1 TAA TAA T--A-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1100378 TAAATAAAAA
Statistics
Matches: 105, Mismatches: 23, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
2 5 0.05
3 96 0.91
4 1 0.01
5 1 0.01
6 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:1100285 original size:20 final size:21
Alignment explanation
Indices: 1100246--1100285 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1100236 TGTAGTAATA
*
1100246 ATAATAGTAAGAAAAATAGTG
1 ATAATAGTAACAAAAATAGTG
*
1100267 ATAATA-TAACAATAATAGT
1 ATAATAGTAACAAAAATAGT
1100286 AATATAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.28
Consensus pattern (21 bp):
ATAATAGTAACAAAAATAGTG
Found at i:1100383 original size:12 final size:13
Alignment explanation
Indices: 1100300--1100391 Score: 86
Period size: 12 Copynumber: 7.1 Consensus size: 13
1100290 TAACAAGAGA
1100300 ATAATAATAATA-
1 ATAATAATAATAT
1100312 ATAATAATAATA-
1 ATAATAATAATAT
1100324 ATAATAATAATA-
1 ATAATAATAATAT
*
1100336 GTAATGGAGATAATA-
1 ATAAT--A-ATAATAT
1100351 ATAATAATAATGAT
1 ATAATAATAAT-AT
1100365 ACTAATAATAATAT
1 A-TAATAATAATAT
*
1100379 A-AATAAAAATAT
1 ATAATAATAATAT
1100391 A
1 A
1100392 AACAACAAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
12 44 0.62
13 2 0.03
14 5 0.07
15 20 0.28
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (13 bp):
ATAATAATAATAT
Found at i:1102277 original size:130 final size:130
Alignment explanation
Indices: 1102101--1102338 Score: 336
Period size: 130 Copynumber: 1.8 Consensus size: 130
1102091 ATTTCTAGCC
* * * *
1102101 TGTTACCCTACTACTTAGGGGGTTAAGGCTCATCGCATTTGATCTGTTTCCCTACTGCTTAGGGT
1 TGTTACCCTACTACTTAGGGGGTTAAAGCCCATCACATTCGATCTGTTTCCCTACTGCTTAGGGT
* *
1102166 -TATAAGATCTGTGAA-TTCAACCTATTACCCTATTGCTTAGGGGTTCAAGGTCTGTAAATTCGG
66 GT-TAAGATCTGTAAATTTC-ACCTATTACCCTACTGCTTAGGGGTTCAAGGTCTGTAAATTCGG
1102229 CT
129 CT
* * *
1102231 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCACCTTCGATCTGTTTCTCTACTGCTTAGGGT
1 TGTTACCCTACTACTTAGGGGGTTAAAGCCCATCACATTCGATCTGTTTCCCTACTGCTTAGGGT
* * *
1102296 GTTAAGATTTGTAAATTTCGCCTGTTACCCTACTGCTTAGGGG
66 GTTAAGATCTGTAAATTTCACCTATTACCCTACTGCTTAGGGG
1102339 GTTAAGGCCT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
130 90 0.96
131 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (130 bp):
TGTTACCCTACTACTTAGGGGGTTAAAGCCCATCACATTCGATCTGTTTCCCTACTGCTTAGGGT
GTTAAGATCTGTAAATTTCACCTATTACCCTACTGCTTAGGGGTTCAAGGTCTGTAAATTCGGCT
Found at i:1102310 original size:87 final size:86
Alignment explanation
Indices: 1102193--1102430 Score: 273
Period size: 87 Copynumber: 2.7 Consensus size: 86
1102183 CAACCTATTA
* * *
1102193 CCCTATTGCTTAGGG-GTTCAAGGTCTGTAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAA
1 CCCTACTGCTTAGGGTGTT-AAGATCTGTAAATTC-GCCTGTTACCCTACTGCTTAGGGGGTTAA
1102257 AGCCCATCACCTTCGATCTGTTT
64 AGCCCATCACCTTCGATCTGTTT
* * *
1102280 CTCTACTGCTTAGGGTGTTAAGATTTGTAAATTTCGCCTGTTACCCTACTGCTTAGGGGGTTAAG
1 CCCTACTGCTTAGGGTGTTAAGATCTGTAAA-TTCGCCTGTTACCCTACTGCTTAGGGGGTTAAA
** ** *
1102345 GCCTTTCGTCTTTGATCTGTTT
65 GCCCATCACCTTCGATCTGTTT
* * * * *
1102367 CCCTACTGCTTAGGGTGATAAGATCTATGAATTCAACCTGTT-CTCCTACTGCTTAGGGGTTTAA
1 CCCTACTGCTTAGGGTGTTAAGATCTGTAAATTC-GCCTGTTAC-CCTACTGCTTAGGGGGTTAA
1102431 GGTCTGTAAA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
86 4 0.03
87 119 0.92
88 6 0.05
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (86 bp):
CCCTACTGCTTAGGGTGTTAAGATCTGTAAATTCGCCTGTTACCCTACTGCTTAGGGGGTTAAAG
CCCATCACCTTCGATCTGTTT
Found at i:1102335 original size:43 final size:43
Alignment explanation
Indices: 1102144--1102467 Score: 180
Period size: 43 Copynumber: 7.5 Consensus size: 43
1102134 CGCATTTGAT
* * *
1102144 CTGTTTCCCTACTGCTTAGGGT-TATAAGATCTGTGAATTCAAC
1 CTGTTACCCTACTGCTTAGGGTGT-TAAGATCTGTAAATTCAGC
* * * *
1102187 CTATTACCCTATTGCTTAGGG-GTTCAAGGTCTGTAAATTCGGC
1 CTGTTACCCTACTGCTTAGGGTGTT-AAGATCTGTAAATTCAGC
* * ** * ** *
1102230 TTGTTACCCTACTGCTTAGGGGGTTAAAGCCCAT-CACCTTC-GAT
1 CTGTTACCCTACTGCTTAGGGTGTT-AAGATC-TGTAAATTCAG-C
* * *
1102274 CTGTTTCTCTACTGCTTAGGGTGTTAAGATTTGTAAATTTC-GC
1 CTGTTACCCTACTGCTTAGGGTGTTAAGATCTGTAAA-TTCAGC
* * * ** * *
1102317 CTGTTACCCTACTGCTTAGGGGGTTAAGGCCTTTCGT-CTTTGA-T
1 CTGTTACCCTACTGCTTAGGGTGTTAA-G-ATCT-GTAAATTCAGC
* * * * *
1102361 CTGTTTCCCTACTGCTTAGGGTGATAAGATCTATGAATTCAAC
1 CTGTTACCCTACTGCTTAGGGTGTTAAGATCTGTAAATTCAGC
* *
1102404 CTGTT-CTCCTACTGCTTAGGG-GTTTAAGGTCTGTAAATTCGGC
1 CTGTTAC-CCTACTGCTTAGGGTG-TTAAGATCTGTAAATTCAGC
* *
1102447 TTGCTACCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGG
1102468 GGTCAAGACC
Statistics
Matches: 211, Mismatches: 54, Indels: 32
0.71 0.18 0.11
Matches are distributed among these distances:
41 1 0.00
42 9 0.04
43 131 0.62
44 64 0.30
45 4 0.02
46 2 0.01
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGTGTTAAGATCTGTAAATTCAGC
Found at i:1102380 original size:44 final size:43
Alignment explanation
Indices: 1102231--1102381 Score: 128
Period size: 44 Copynumber: 3.5 Consensus size: 43
1102221 AAATTCGGCT
** ** *
1102231 TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCACCTTCGATC
1 TGTTACCCTACTGCTTAGGGGGTT-AAGCCTTTCGTCTTTGATC
* * * * * *
1102275 TGTTTCTCTACTGCTTAGGGTGTTAAG-ATTT-GTAAATTTCG-CC
1 TGTTACCCTACTGCTTAGGGGGTTAAGCCTTTCGT--CTTT-GATC
1102318 TGTTACCCTACTGCTTAGGGGGTTAAGGCCTTTCGTCTTTGATC
1 TGTTACCCTACTGCTTAGGGGGTTAA-GCCTTTCGTCTTTGATC
*
1102362 TGTTTCCCTACTGCTTAGGG
1 TGTTACCCTACTGCTTAGGG
1102382 TGATAAGATC
Statistics
Matches: 82, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
42 1 0.01
43 30 0.37
44 46 0.56
45 3 0.04
46 2 0.02
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (43 bp):
TGTTACCCTACTGCTTAGGGGGTTAAGCCTTTCGTCTTTGATC
Found at i:1102408 original size:130 final size:130
Alignment explanation
Indices: 1102278--1102566 Score: 358
Period size: 130 Copynumber: 2.2 Consensus size: 130
1102268 TTCGATCTGT
* *
1102278 TTCT-CTACTGCTTA-GGGTGTTAAGATTTGTAAATTTC-GCCTGTTACCCTACTGCTTAGGGGG
1 TTCTCCTACTGCTTAGGGGT-TTAAGATCTGTAAA-TTCGGCCTGCTACCCTACTGCTTAGGGGG
* * * * * *
1102340 TTAAGGCCTTTCGTCTTTGATCTGTTTCC-CTACTGCTTAGGGTGATAAGATCTATGAATTCAAC
64 TCAAGACCCTTCGTCTTCGATCTG-CTCCACTACTGCTTAGGGAGATAAGATCTATGAATTCAAC
1102404 CTG
128 CTG
* *
1102407 TTCTCCTACTGCTTAGGGGTTTAAGGTCTGTAAATTCGGCTTGCTACCCTACTGCTTAGGGGGTC
1 TTCTCCTACTGCTTAGGGGTTTAAGATCTGTAAATTCGGCCTGCTACCCTACTGCTTAGGGGGTC
***
1102472 AAGACCCTTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATC--TGCAATTCGGTCT
66 AAGACCCTTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATG-AATTCAACCT
1102535 G
130 G
*
1102536 TTAC-CCTACTGTTTAGGGGTTTAAGATCTGT
1 TT-CTCCTACTGCTTAGGGGTTTAAGATCTGT
1102567 GGTCTTCGAT
Statistics
Matches: 139, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
128 2 0.01
129 45 0.32
130 88 0.63
131 4 0.03
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (130 bp):
TTCTCCTACTGCTTAGGGGTTTAAGATCTGTAAATTCGGCCTGCTACCCTACTGCTTAGGGGGTC
AAGACCCTTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGAATTCAACCTG
Found at i:1102490 original size:217 final size:216
Alignment explanation
Indices: 1102098--1102560 Score: 639
Period size: 217 Copynumber: 2.1 Consensus size: 216
1102088 TTGATTTCTA
*
1102098 GCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCATCGCATTTGATCTGTTTCCCTACTGCTTAG
1 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGCATTTGATCTGTTTCCCTACTGCTTAG
* * *
1102163 GGTTATAAGATCTGTGAATTCAACCTATTACCCTATTGCTTAGGGGTTCAAGGTCTGTAAATTCG
66 GGTGATAAGATCTATGAATTCAACCTATTACCCTACTGCTTAGGGGTTCAAGGTCTGTAAATTCG
* * * * *
1102228 GCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCACCTTCGATCTGTTTCTCTACTGCTTAG
131 GCTTGCTACCCTACTGCTTAGGGGGTCAAAGCCCATCACCTTCGATCTGCTCCACTACTGCTTAG
* * *
1102293 GGTGTTAAGATTTGTAAATTTC-
196 GGAGATAAGATCTG-AAA-TTCG
*
1102315 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGC-CTTTCGTC-TTTGATCTGTTTCCCTACTGCTT
1 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTC-ATCG-CATTTGATCTGTTTCCCTACTGCTT
* *
1102378 AGGGTGATAAGATCTATGAATTCAACCTGTT-CTCCTACTGCTTAGGGGTTTAAGGTCTGTAAAT
64 AGGGTGATAAGATCTATGAATTCAACCTATTAC-CCTACTGCTTAGGGGTTCAAGGTCTGTAAAT
* **
1102442 TCGGCTTGCTACCCTACTGCTTAGGGGGTC-AAGACCCTTCGTCTTCGATCTGCTCCACTACTGC
128 TCGGCTTGCTACCCTACTGCTTAGGGGGTCAAAG-CCCATCACCTTCGATCTGCTCCACTACTGC
*
1102506 TTAGGGAGATAAGATCTGCAATTCG
192 TTAGGGAGATAAGATCTGAAATTCG
* * *
1102531 GTCTGTTACCCTACTGTTTAGGGGTTTAAG
1 GCCTGTTACCCTACTGCTTAGGGGGTTAAG
1102561 ATCTGTGGTC
Statistics
Matches: 219, Mismatches: 22, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
215 3 0.01
216 34 0.16
217 181 0.83
218 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (216 bp):
GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGCATTTGATCTGTTTCCCTACTGCTTAG
GGTGATAAGATCTATGAATTCAACCTATTACCCTACTGCTTAGGGGTTCAAGGTCTGTAAATTCG
GCTTGCTACCCTACTGCTTAGGGGGTCAAAGCCCATCACCTTCGATCTGCTCCACTACTGCTTAG
GGAGATAAGATCTGAAATTCG
Found at i:1102738 original size:97 final size:95
Alignment explanation
Indices: 1102581--1102757 Score: 273
Period size: 97 Copynumber: 1.8 Consensus size: 95
1102571 TTCGATCTAT
* * * * *
1102581 TCTATTCCACTGCTAACCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAGTCACAGG
1 TCTATTCCACTGCAAAACAGGGAGATAGAATTATCGGCTTCAATATACTCCACTGGAGTCACAGG
1102646 GAGGTAAAATCTGCCTTTTTTTATCTTCAA
66 GAGGTAAAATCTGCCTTTTTTTATCTTCAA
* *
1102676 TCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATATACTCCACTGGAGTCATA
1 TCTATTCCACTG-CAAA-ACAGGGAGATAGAATTATCGGCTTCAATATACTCCACTGGAGTCACA
1102741 GGGAGGTAAAATCTGCC
64 GGGAGGTAAAATCTGCC
1102758 ATCTTCGATC
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 12 0.16
96 3 0.04
97 58 0.79
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (95 bp):
TCTATTCCACTGCAAAACAGGGAGATAGAATTATCGGCTTCAATATACTCCACTGGAGTCACAGG
GAGGTAAAATCTGCCTTTTTTTATCTTCAA
Found at i:1102825 original size:46 final size:46
Alignment explanation
Indices: 1102668--1103950 Score: 444
Period size: 46 Copynumber: 28.2 Consensus size: 46
1102658 GCCTTTTTTT
* * *
1102668 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTAT-C-
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTA-AGATCTGCA
** * * * * * * *
1102713 GGCTTCAATATACTCCACTG--GAGTCATAGGGAGGTAAAATCTGCC
1 ATCTTCAATCTATTCCACTGCCAAAT-ACAGGGAGGTAAGATCTGCA
* * * * * *
1102758 ATCTTCGATCTGCTT-CGCTGCCAAATACAAGAAGGCAAGATCTGCA
1 ATCTTCAATCT-ATTCCACTGCCAAATACAGGGAGGTAAGATCTGCA
* * *
1102804 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTAT-C-
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTA-AGATCTGCA
** * * * * *
1102849 GGCTTCAATCTACTCCACTG--TAGTCACAGGGAGGTAAAATCTGCC
1 ATCTTCAATCTATTCCACTGCCAAAT-ACAGGGAGGTAAGATCTGCA
* * * *
1102894 ATCTTCGATCTGCTTCGCA--GCCAAATACAGGAAGGCAAGATCTGCA
1 ATCTTCAATCT-ATTC-CACTGCCAAATACAGGGAGGTAAGATCTGCA
* * *
1102940 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTAT-C-
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTA-AGATCTGCA
** * * * * *
1102985 GGCTTCAATCTACTCCACTG--TAGTCACAGGGAGGTAAAATCTGCC
1 ATCTTCAATCTATTCCACTGCCAAAT-ACAGGGAGGTAAGATCTGCA
* * * * * *
1103030 ATCTTCGATCTGCTT-CGCTGCCAAATACAAGAAGGCAAGATCTGCA
1 ATCTTCAATCT-ATTCCACTGCCAAATACAGGGAGGTAAGATCTGCA
* * *
1103076 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTAT-C-
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTA-AGATCTGCA
** * * * * * * *
1103121 GGCTTCAATGTACTCCACTG--TAGTCACATGGAGGTAAAATCTGCC
1 ATCTTCAATCTATTCCACTGCCAAAT-ACAGGGAGGTAAGATCTGCA
* * * * *
1103166 ATCTTCGATCTGCTT-CGCTGCCAAATACAGGAAGGCAAGATCTGCA
1 ATCTTCAATCT-ATTCCACTGCCAAATACAGGGAGGTAAGATCTGCA
* * *
1103212 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTAT-C-
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTA-AGATCTGCA
* * * * * * * *
1103257 AGCTTCAATGTACTCCACTG--TAGT-CAGGGAGGTAAAATCCGCC
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTAAGATCTGCA
* * * * *
1103300 ATCTTCGACCTGCTT-CGCTGCCAAATACAGGAAGGTAAGATCTGCA
1 ATCTTCAATCT-ATTCCACTGCCAAATACAGGGAGGTAAGATCTGCA
* * *
1103346 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTAT-C-
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTA-AGATCTGCA
** * * * * * *
1103391 GGCTTCAATGTACTCCACTG--TAGTCACATGGAGGTAAAATCTGCCA
1 ATCTTCAATCTATTCCACTGCCAAAT-ACAGGGAGGTAAGATCTG-CA
* * *
1103437 TCTTTGATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGC-
1 ------ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTA-AG--ATCTGCA
* * * * * *
1103491 -T-TT-AATGTACTCCACTG--TAGT-CAGGGAGGTAAAATCTGCC
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTAAGATCTGCA
* * * * *
1103531 ATCTTCGATCTGCTT-CGCTG-CAAATACAGGAAGGCAAGATCTGCA
1 ATCTTCAATCT-ATTCCACTGCCAAATACAGGGAGGTAAGATCTGCA
* * *
1103576 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTAT-C-
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTA-AGATCTGCA
* * * * * * * *
1103621 AGCTTCAATGTACTCCACTG--TAGT-CAGGGAGGTAAAATCCGCC
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTAAGATCTGCA
* * * * * * *
1103664 ATCTTCGACCTGCTT-CGCTGCCAAATATAGGAAGGCAAGATCTGCA
1 ATCTTCAATCT-ATTCCACTGCCAAATACAGGGAGGTAAGATCTGCA
* * *
1103710 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTAT-C-
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTA-AGATCTGCA
** * * * * * *
1103755 GGCTTCAATGTACTCCACTG--TAGTCACATGGAGGTAAAATCTGCCA
1 ATCTTCAATCTATTCCACTGCCAAAT-ACAGGGAGGTAAGATCTG-CA
* * * *
1103801 TCTTTGATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTAT-C-
1 ------ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTA-AGATCTGCA
** * * * * *
1103852 GGCTTCAATCTACTCCACTG--TAGTCACAGGGAGGTAAAATCTGCC
1 ATCTTCAATCTATTCCACTGCCAAAT-ACAGGGAGGTAAGATCTGCA
* * * * *
1103897 ATCTTCGATCTGCTT-CGCTGCCAAATACAGGAAGGCAAGATCTGCA
1 ATCTTCAATCT-ATTCCACTGCCAAATACAGGGAGGTAAGATCTGCA
1103943 ATCTTCAA
1 ATCTTCAA
1103951 CCAGCTCTGC
Statistics
Matches: 858, Mismatches: 286, Indels: 187
0.64 0.21 0.14
Matches are distributed among these distances:
39 5 0.01
41 6 0.01
42 31 0.04
43 70 0.08
44 79 0.09
45 264 0.31
46 300 0.35
47 41 0.05
52 33 0.04
53 16 0.02
54 8 0.01
55 1 0.00
56 4 0.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.27
Consensus pattern (46 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGGTAAGATCTGCA
Found at i:1102917 original size:136 final size:136
Alignment explanation
Indices: 1102668--1103446 Score: 1409
Period size: 136 Copynumber: 5.7 Consensus size: 136
1102658 GCCTTTTTTT
*
1102668 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATATACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
* * *
1102733 GAGTCATAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAAGAAGGCAAGA
66 TAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
1102798 TCTGCA
131 TCTGCA
*
1102804 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
1102869 TAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCAGCCAAATACAGGAAGGCAAGA
66 TAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
1102934 TCTGCA
131 TCTGCA
*
1102940 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
1103005 TAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAAGAAGGCAAGA
66 TAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
1103070 TCTGCA
131 TCTGCA
1103076 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
1103141 TAGTCACATGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
66 TAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
1103206 TCTGCA
131 TCTGCA
*
1103212 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCAGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
* * *
1103277 TAGT--CAGGGAGGTAAAATCCGCCATCTTCGACCTGCTTCGCTGCCAAATACAGGAAGGTAAGA
66 TAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
1103340 TCTGCA
131 TCTGCA
1103346 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
* *
1103411 TAGTCACATGGAGGTAAAATCTGCCATCTTTGATCT
66 TAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCT
1103447 TCAATCTATT
Statistics
Matches: 621, Mismatches: 20, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
134 129 0.21
136 492 0.79
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (136 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
TCTGCA
Found at i:1103035 original size:90 final size:89
Alignment explanation
Indices: 1102668--1103305 Score: 256
Period size: 90 Copynumber: 7.1 Consensus size: 89
1102658 GCCTTTTTTT
* *
1102668 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATATACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCAGCTTCAATCTACTCCACTG
* * *
1102733 GAGTCATAGGGAGGTAAAATCTGCC
66 AAAT-ACAGGGAGGTAAAATCTGCC
* * * * * ** * * * *
1102758 ATCTTCGATCTGCTT-CGCTGCCAAATACAAGAAGGCA-AGATCTGCAATCTTCAATCTATTCCA
1 ATCTTCAATCT-ATTCCACTGCCAAATACAGGGAGATAGAGTTAT-C-AGCTTCAATCTACTCCA
* * * **
1102821 CTGCCAAATACAGGGAGATAGAGT-TATC
63 CTG--AAATACAGGGAGGTAAAATCTGCC
** * * * * * * ** * * *
1102849 GGCTTCAATCTACTCCACTG--TAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGC
1 ATCTTCAATCTATTCCACTGCCAAAT-ACAGGGAGATAGAGT-TATCAGCTTCAATCTAC-TC-C
* * * * *
1102912 AGC-CAAATACAGGAAGGCAAGATCTGCA
62 A-CTGAAATACAGGGAGGTAAAATCTGCC
*
1102940 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCAGCTTCAATCTACTCCACTG
* *
1103005 TAGTCACAGGGAGGTAAAATCTGCC
66 AAAT-ACAGGGAGGTAAAATCTGCC
* * * * * ** * * * *
1103030 ATCTTCGATCTGCTT-CGCTGCCAAATACAAGAAGGCA-AGATCTGCAATCTTCAATCTATTCCA
1 ATCTTCAATCT-ATTCCACTGCCAAATACAGGGAGATAGAGTTAT-C-AGCTTCAATCTACTCCA
* * * **
1103093 CTGCCAAATACAGGGAGATAGAGT-TATC
63 CTG--AAATACAGGGAGGTAAAATCTGCC
** * * * * * * * * ** * * * * *
1103121 GGCTTCAATGTACTCCACTG--TAGTCACATGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGC
1 ATCTTCAATCTATTCCACTGCCAAAT-ACAGGGAGATAGAGT-TATCAGCTTCAATCTACTCCAC
* * * *
1103184 TGCCAAATACAGGAAGGCAAGATCTGCA
64 TG--AAATACAGGGAGGTAAAATCTGCC
*
1103212 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCAGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCAGCTTCAATCTACTCCACTG
* * *
1103277 TAGT-CAGGGAGGTAAAATCCGCC
66 AAATACAGGGAGGTAAAATCTGCC
1103300 ATCTTC
1 ATCTTC
1103306 GACCTGCTTC
Statistics
Matches: 375, Mismatches: 144, Indels: 60
0.65 0.25 0.10
Matches are distributed among these distances:
88 21 0.06
89 18 0.05
90 145 0.39
91 132 0.35
92 50 0.13
93 9 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (89 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCAGCTTCAATCTACTCCACTG
AAATACAGGGAGGTAAAATCTGCC
Found at i:1103459 original size:97 final size:96
Alignment explanation
Indices: 1103346--1103907 Score: 399
Period size: 97 Copynumber: 6.0 Consensus size: 96
1103336 AAGATCTGCA
*
1103346 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
*
1103411 TAGTCACATGGAGGTAAAATCTGCCATCTTTG
66 TAGTCACAGGGAGGTAAAATCTGCCATC-TTG
* * *
1103443 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTTAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
1103508 TAGT--CAGGGAGGTAAAATCTGCCATCTTCG
66 TAGTCACAGGGAGGTAAAATCTGCCATCTT-G
* * * ** * * ** *
1103538 ATC-T---GC--TT-CGCTG-CAAATACAGGAAGGCA-AGATCTGCAATCTTCAATCTATTCCAC
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTAT-C-GGCTTCAATCTACTCCAC
* * * * *
1103594 TGCCAAAT-ACAGGGAGATAGAGT-T---ATC---
64 TG--TAGTCACAGGGAGGTAAAATCTGCCATCTTG
* * * * * * * * *** ** * * * * *
1103621 AGCTTCAATGTACTCCACTG--TAGT-CAGGGAGGTAAAATCCGCCATCTTCGACCTGCTTCGCT
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGT-TATCGGCTTCAATCTACTCCACT
* * * * * *
1103683 GCCAAAT-ATAGGAAGGCAAGATCTG-CA-----
65 G--TAGTCACAGGGAGGTAAAATCTGCCATCTTG
*
1103710 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
*
1103775 TAGTCACATGGAGGTAAAATCTGCCATCTTTG
66 TAGTCACAGGGAGGTAAAATCTGCCATC-TTG
*
1103807 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
1103872 TAGTCACAGGGAGGTAAAATCTGCCATCTTCG
66 TAGTCACAGGGAGGTAAAATCTGCCATCTT-G
1103904 ATCT
1 ATCT
1103908 GCTTCGCTGC
Statistics
Matches: 358, Mismatches: 77, Indels: 60
0.72 0.16 0.12
Matches are distributed among these distances:
83 2 0.01
84 1 0.00
86 4 0.01
87 16 0.04
88 55 0.15
89 27 0.08
90 20 0.06
91 30 0.08
92 11 0.03
94 3 0.01
95 25 0.07
96 2 0.01
97 162 0.45
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (96 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
TAGTCACAGGGAGGTAAAATCTGCCATCTTG
Found at i:1103681 original size:133 final size:134
Alignment explanation
Indices: 1103443--1103804 Score: 636
Period size: 133 Copynumber: 2.7 Consensus size: 134
1103433 GCCATCTTTG
* *
1103443 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTTAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
1103508 TAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTG-CAAATACAGGAAGGCAAGATC
66 TAGTCAGGGAGGTAAAATCTGCCATCTTCGACCTGCTTCGCTGCCAAATACAGGAAGGCAAGATC
1103572 TGCA
131 TGCA
*
1103576 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCAGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
* *
1103641 TAGTCAGGGAGGTAAAATCCGCCATCTTCGACCTGCTTCGCTGCCAAATATAGGAAGGCAAGATC
66 TAGTCAGGGAGGTAAAATCTGCCATCTTCGACCTGCTTCGCTGCCAAATACAGGAAGGCAAGATC
1103706 TGCA
131 TGCA
1103710 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
1103775 TAGTCACATGGAGGTAAAATCTGCCATCTT
66 TAGT--CAGGGAGGTAAAATCTGCCATCTT
1103805 TGATCTTCAA
Statistics
Matches: 217, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
133 103 0.47
134 92 0.42
136 22 0.10
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.27
Consensus pattern (134 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TAGTCAGGGAGGTAAAATCTGCCATCTTCGACCTGCTTCGCTGCCAAATACAGGAAGGCAAGATC
TGCA
Found at i:1103748 original size:364 final size:366
Alignment explanation
Indices: 1103076--1103950 Score: 1664
Period size: 364 Copynumber: 2.4 Consensus size: 366
1103066 AAGATCTGCA
*
1103076 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
1103141 TAGTCACATGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
66 TAGT-ACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
1103206 TCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCAGCTTCAATGTACT
130 TCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCAGCTTCAATGTACT
*
1103271 CCACTGTAGTCAGGGAGGTAAAATCCGCCATCTTCGACCTGCTTCGCTGCCAAATACAGGAAGGT
195 CCACTGTAGTCAGGGAGGTAAAATCCGCCATCTTCGACCTGCTTCGCTGCCAAATACAGGAAGGC
1103336 AAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATG
260 AAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATG
1103401 TACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTTG
325 TACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTTG
*
1103443 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTTAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1103508 TAGT-CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTG-CAAATACAGGAAGGCAAGAT
66 TAGTACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
1103571 CTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCAGCTTCAATGTACTC
131 CTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCAGCTTCAATGTACTC
*
1103636 CACTGTAGTCAGGGAGGTAAAATCCGCCATCTTCGACCTGCTTCGCTGCCAAATATAGGAAGGCA
196 CACTGTAGTCAGGGAGGTAAAATCCGCCATCTTCGACCTGCTTCGCTGCCAAATACAGGAAGGCA
1103701 AGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGT
261 AGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGT
1103766 ACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTTG
326 ACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTTG
*
1103807 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1103872 TAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
66 TAGT-ACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
1103937 TCTGCAATCTTCAA
130 TCTGCAATCTTCAA
1103951 CCAGCTCTGC
Statistics
Matches: 498, Mismatches: 7, Indels: 6
0.97 0.01 0.01
Matches are distributed among these distances:
364 321 0.64
365 38 0.08
366 39 0.08
367 100 0.20
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (366 bp):
ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TAGTACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
CTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCAGCTTCAATGTACTC
CACTGTAGTCAGGGAGGTAAAATCCGCCATCTTCGACCTGCTTCGCTGCCAAATACAGGAAGGCA
AGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGT
ACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTTG
Found at i:1108132 original size:19 final size:20
Alignment explanation
Indices: 1108108--1108151 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1108098 CGTGAAAGTC
* *
1108108 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
1108127 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
1108147 -AATGC
1 TAATGC
1108152 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:1109878 original size:109 final size:109
Alignment explanation
Indices: 1109742--1110009 Score: 457
Period size: 109 Copynumber: 2.4 Consensus size: 109
1109732 AGCTCAGTAA
1109742 GTTAGGGCACGATTTTCTCGAATTTTCTAAATACGAAATATTGCCTTTATTATTGAAAGTTTAAA
1 GTTAGGGCACG-TTTTCTCGAATTTTCTAAATACGAAATATTGCCTTTATTATTGAAAGTTTAAA
*
1109807 AGGGTATTTGGCCATTTGGTCGAACGGGGAATCGAAACCCAGCAC
65 AGGGTATTTGGCCATTTGGTCGAACGAGGAATCGAAACCCAGCAC
1109852 GTTAGGGCACGTTTTCTCGAATTTTCTAAATACGAAATATTGCCTTTATTATTGAAAGTTTAAAA
1 GTTAGGGCACGTTTTCTCGAATTTTCTAAATACGAAATATTGCCTTTATTATTGAAAGTTTAAAA
1109917 GGGTATTTGGCCATTTGGTCGAACGAGGAATCGAAACCCAGCAC
66 GGGTATTTGGCCATTTGGTCGAACGAGGAATCGAAACCCAGCAC
* * ** *
1109961 GTTAAGGCACGTTTTCTCGAACTTTCCT-AACGCGAAATATTGCTTTTAT
1 GTTAGGGCACGTTTTCTCGAA-TTTTCTAAATACGAAATATTGCCTTTAT
1110010 GAAAGAATTA
Statistics
Matches: 151, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
109 135 0.89
110 16 0.11
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (109 bp):
GTTAGGGCACGTTTTCTCGAATTTTCTAAATACGAAATATTGCCTTTATTATTGAAAGTTTAAAA
GGGTATTTGGCCATTTGGTCGAACGAGGAATCGAAACCCAGCAC
Found at i:1110345 original size:15 final size:15
Alignment explanation
Indices: 1110325--1110355 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1110315 ATATATATTA
1110325 ATAATAGTAATAAAT
1 ATAATAGTAATAAAT
1110340 ATAATAGTAATAAAT
1 ATAATAGTAATAAAT
1110355 A
1 A
1110356 GAAAATAATA
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:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
ATAATAGTAATAAAT
Found at i:1110655 original size:3 final size:3
Alignment explanation
Indices: 1110649--1110782 Score: 103
Period size: 3 Copynumber: 44.7 Consensus size: 3
1110639 ATAGTTGTAG
* * * * * * *
1110649 TAA TAA TAA TAG TAA GAA AAA TAG TGA TAA T-A TAA CAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
1110696 T-A TAA CAA -GA GAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1110742 TGGAGA TAA TAA TAA TAA TAA TAA TGA TAC TAA TAA TAA TA
1 T--A-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1110783 TAAATAAAAA
Statistics
Matches: 102, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
2 5 0.05
3 93 0.91
4 1 0.01
5 1 0.01
6 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:1110693 original size:20 final size:21
Alignment explanation
Indices: 1110654--1110693 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1110644 TGTAGTAATA
*
1110654 ATAATAGTAAGAAAAATAGTG
1 ATAATAGTAACAAAAATAGTG
*
1110675 ATAATA-TAACAATAATAGT
1 ATAATAGTAACAAAAATAGT
1110694 AATATAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.28
Consensus pattern (21 bp):
ATAATAGTAACAAAAATAGTG
Found at i:1119860 original size:19 final size:20
Alignment explanation
Indices: 1119836--1119873 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1119826 ATCTCATATC
*
1119836 TCAATTTTCAA-TTCACATA
1 TCAATTCTCAATTTCACATA
1119855 TCAATTCTCAATTTCACAT
1 TCAATTCTCAATTTCACAT
1119874 TCTCATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (20 bp):
TCAATTCTCAATTTCACATA
Found at i:1121125 original size:8 final size:8
Alignment explanation
Indices: 1121108--1121149 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
1121098 CTTTTCTTTT
1121108 ATATATATA
1 ATATA-ATA
1121117 ATA-ATATA
1 ATATA-ATA
1121125 ATATAATA
1 ATATAATA
1121133 ATATAATTA
1 ATATAA-TA
1121142 ATATAATA
1 ATATAATA
1121150 CTTATTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 19 0.61
9 12 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAATA
Found at i:1121130 original size:13 final size:13
Alignment explanation
Indices: 1121107--1121144 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
1121097 TCTTTTCTTT
1121107 TATATATATAATAA
1 TATA-ATATAATAA
1121121 TATAATATAATAA
1 TATAATATAATAA
1121134 TATAAT-TAATA
1 TATAATATAATA
1121145 TAATACTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.21
13 15 0.62
14 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATAATATAATAA
Found at i:1134034 original size:46 final size:44
Alignment explanation
Indices: 1133930--1134037 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
1133920 TGTCTTTAAC
** * * *
1133930 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
1133974 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
1134020 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
1134038 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:1134929 original size:9 final size:9
Alignment explanation
Indices: 1134915--1134949 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1134905 TTCTATTCTG
1134915 TTTCTTTTC
1 TTTCTTTTC
*
1134924 TTTCTTTTT
1 TTTCTTTTC
*
1134933 TTTCTATTC
1 TTTCTTTTC
1134942 TTTCTTTT
1 TTTCTTTT
1134950 GTTTTATGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:1134942 original size:18 final size:19
Alignment explanation
Indices: 1134915--1134954 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1134905 TTCTATTCTG
*
1134915 TTTCTTTTCTTTCTTTT-T
1 TTTCTATTCTTTCTTTTGT
1134933 TTTCTATTCTTTCTTTTGT
1 TTTCTATTCTTTCTTTTGT
1134952 TTT
1 TTT
1134955 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTCTATTCTTTCTTTTGT
Found at i:1134971 original size:5 final size:5
Alignment explanation
Indices: 1134958--1135030 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
1134948 TTGTTTTATG
1134958 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
1135006 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
1135031 TTTTTAACAC
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:1134983 original size:19 final size:19
Alignment explanation
Indices: 1134959--1135001 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1134949 TGTTTTATGT
1134959 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
1134978 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
1134997 ATATA
1 ATATA
1135002 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:1135011 original size:24 final size:25
Alignment explanation
Indices: 1134965--1135029 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
1134955 ATGTATATAT
* *
1134965 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
1134989 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
1135014 TTACTATAATATAATA
1 ATAATATAATATAATA
1135030 TTTTTTAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 13 0.38
26 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:1141052 original size:44 final size:43
Alignment explanation
Indices: 1140985--1141074 Score: 153
Period size: 44 Copynumber: 2.1 Consensus size: 43
1140975 TTAAATTTTA
* *
1140985 GGATTCAAAATTAAATTATTTAAATCTTACTTTTTAAGAATAT
1 GGATTCAAAATTAAATTACTTAAATCTTACTTTTTAAAAATAT
1141028 GGATTCAAAAATTAAATTACTTAAATCTTACTTTTTAAAAATAT
1 GGATTC-AAAATTAAATTACTTAAATCTTACTTTTTAAAAATAT
1141072 GGA
1 GGA
1141075 ATTAAATACA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
43 6 0.14
44 38 0.86
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (43 bp):
GGATTCAAAATTAAATTACTTAAATCTTACTTTTTAAAAATAT
Found at i:1145972 original size:22 final size:24
Alignment explanation
Indices: 1145947--1146002 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
1145937 GAGCACAGAT
* *
1145947 GTGCTAA-A-CAAAGAGCACTAAC
1 GTGCTAATATCAAAAAGCACCAAC
1145969 GTGCTAAATATCAAAAAGCACCAAC
1 GTGCT-AATATCAAAAAGCACCAAC
1145994 GTGCTAATA
1 GTGCTAATA
1146003 ATCAGAGAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 5 0.17
23 2 0.07
24 5 0.17
25 17 0.59
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (24 bp):
GTGCTAATATCAAAAAGCACCAAC
Found at i:1147036 original size:15 final size:14
Alignment explanation
Indices: 1147016--1147045 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1147006 AAACCCTAAA
1147016 TTTCTTTCTTTACTT
1 TTTCTTTCTTT-CTT
1147031 TTTCTTTCTTTCTT
1 TTTCTTTCTTTCTT
1147045 T
1 T
1147046 CTCCCCTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCTTTCTTTCTT
Found at i:1147133 original size:10 final size:10
Alignment explanation
Indices: 1147111--1147147 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1147101 TTGTTTTATA
1147111 TATATAATA-
1 TATATAATAT
1147120 -ATATAATAT
1 TATATAATAT
*
1147129 TATATTATAT
1 TATATAATAT
1147139 TATATAATA
1 TATATAATA
1147148 AAATAACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 8 0.33
10 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TATATAATAT
Found at i:1150476 original size:26 final size:26
Alignment explanation
Indices: 1150447--1150541 Score: 102
Period size: 26 Copynumber: 3.5 Consensus size: 26
1150437 TTATATTAAG
1150447 AATTTTATTAAATTATATTTAATAAT
1 AATTTTATTAAATTATATTTAATAAT
* * *
1150473 AATTTTGTTAAAATATAGTTAAATTATTTAT
1 AATTTTATTAAATTATA-TTTAA-TA---AT
1150504 AATTTTTATTAAATTAT-TTTAATAAT
1 AA-TTTTATTAAATTATATTTAATAAT
1150530 AATTTTATTAAA
1 AATTTTATTAAA
1150542 ATTTATTAAC
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
25 10 0.18
26 19 0.33
27 4 0.07
28 2 0.04
29 2 0.04
30 4 0.07
31 4 0.07
32 12 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
AATTTTATTAAATTATATTTAATAAT
Found at i:1150544 original size:26 final size:25
Alignment explanation
Indices: 1150491--1150541 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1150481 TAAAATATAG
1150491 TTAAATTA-TTT-ATAAT--TTTTA
1 TTAAATTATTTTAATAATAATTTTA
1150512 TTAAATTATTTTAATAATAATTTTA
1 TTAAATTATTTTAATAATAATTTTA
1150537 TTAAA
1 TTAAA
1150542 ATTTATTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.31
22 3 0.12
23 5 0.19
25 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTAAATTATTTTAATAATAATTTTA
Found at i:1150550 original size:25 final size:26
Alignment explanation
Indices: 1150449--1150556 Score: 69
Period size: 26 Copynumber: 4.0 Consensus size: 26
1150439 ATATTAAGAA
*
1150449 TTTTATTAAATTATATTTAATAATAA-
1 TTTTATTAAATTATA-TTAACAATAAT
* * *
1150475 TTTTGTTAAAATATAGTTAAATTATTTATAAT
1 TTTTATTAAATTATA-TT-AA-CA---ATAAT
* *
1150507 TTTTATTAAATTATTTTAATAATAA-
1 TTTTATTAAATTATATTAACAATAAT
1150532 TTTTATTAAAATT-TATTAACAATAA
1 TTTTATT-AAATTATATTAACAATAA
1150557 CAATAATCAT
Statistics
Matches: 67, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
25 17 0.25
26 24 0.36
27 2 0.03
28 2 0.03
29 2 0.03
30 2 0.03
31 6 0.09
32 12 0.18
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (26 bp):
TTTTATTAAATTATATTAACAATAAT
Found at i:1150563 original size:57 final size:58
Alignment explanation
Indices: 1150449--1150563 Score: 153
Period size: 57 Copynumber: 2.0 Consensus size: 58
1150439 ATATTAAGAA
* * ***
1150449 TTTTATTAAATTATATTTAATAATAATTTTGTTAAAATATAGTTAAATTATTTATAAT
1 TTTTATTAAATTATATTTAATAATAATTTTATTAAAATATAGTTAAAATAACAATAAT
*
1150507 TTTTATTAAATTAT-TTTAATAATAATTTTATTAAAATTTA-TTAACAATAACAATAAT
1 TTTTATTAAATTATATTTAATAATAATTTTATTAAAATATAGTTAA-AATAACAATAAT
1150564 CATTTACGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
56 4 0.08
57 32 0.64
58 14 0.28
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (58 bp):
TTTTATTAAATTATATTTAATAATAATTTTATTAAAATATAGTTAAAATAACAATAAT
Found at i:1151795 original size:150 final size:150
Alignment explanation
Indices: 1151524--1151822 Score: 598
Period size: 150 Copynumber: 2.0 Consensus size: 150
1151514 GAGTGGAATA
1151524 GTAATACACCTTTTAAGAGAAAATGTATGTTTGAATATTAGAGATTATGTTATTGAAAAGGACAA
1 GTAATACACCTTTTAAGAGAAAATGTATGTTTGAATATTAGAGATTATGTTATTGAAAAGGACAA
1151589 TTTCAAATCCTGAACATGAACTATAAAATAGACATGAAAAAAAATTGAATGAGATAATTGTATTA
66 TTTCAAATCCTGAACATGAACTATAAAATAGACATGAAAAAAAATTGAATGAGATAATTGTATTA
1151654 ATCTAATCCAATATGTAATG
131 ATCTAATCCAATATGTAATG
1151674 GTAATACACCTTTTAAGAGAAAATGTATGTTTGAATATTAGAGATTATGTTATTGAAAAGGACAA
1 GTAATACACCTTTTAAGAGAAAATGTATGTTTGAATATTAGAGATTATGTTATTGAAAAGGACAA
1151739 TTTCAAATCCTGAACATGAACTATAAAATAGACATGAAAAAAAATTGAATGAGATAATTGTATTA
66 TTTCAAATCCTGAACATGAACTATAAAATAGACATGAAAAAAAATTGAATGAGATAATTGTATTA
1151804 ATCTAATCCAATATGTAAT
131 ATCTAATCCAATATGTAAT
1151823 TACTTAAAAA
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 149 1.00
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (150 bp):
GTAATACACCTTTTAAGAGAAAATGTATGTTTGAATATTAGAGATTATGTTATTGAAAAGGACAA
TTTCAAATCCTGAACATGAACTATAAAATAGACATGAAAAAAAATTGAATGAGATAATTGTATTA
ATCTAATCCAATATGTAATG
Found at i:1151970 original size:125 final size:123
Alignment explanation
Indices: 1151749--1152400 Score: 822
Period size: 125 Copynumber: 5.3 Consensus size: 123
1151739 TTTCAAATCC
* * *
1151749 TGAACATGAACTATAAAATAGACAT---G-A-AAAAAAATTGAATGAGATAATTGTATTAATCTA
1 TGAATATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAA
* *
1151809 ATCCAATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAAATTGACTTAAAACCT
66 ATCCGATATGTAATTACTTAAAAAAGAAAATGCCTTTT-AAAAAATTGACTTGAAACCT
* * * *
1151868 TGAATATGAACTATAAAATAGACCTGAAGAATAAAAAAAATTGAATGAGATAATTCTATTAATCG
1 TGAATATGAACTATAAAATAGACATGAAGAAT-AAAAAAATTGAATGAGTTAATTGTATTAATCA
* * * *
1151933 GATCCAATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAAATTGAATTGAAACAT
65 AATCCGATATGTAATTACTTAAAAAAGAAAATGCCTTTT-AAAAAATTGACTTGAAACCT
* ** *
1151993 TGAATATGAACTATAAAATAGGC-TGAAGAATGTAAAAATTGAATGAGTTAATTGTATTAATCAT
1 TGAATATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAA
* *
1152057 ATCCGATATGTAATTACTTAAAAAAGAAGATGCCTTTTAAAAAATTGAATTGAAACCT
66 ATCCGATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTGACTTGAAACCT
*
1152115 TGAATATGAACTAGAACTATAAAATAGACATGAATAAT-AAAAAATTGAATGAGTTAATTGTATT
1 TG-A-AT--A-T-GAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATT
** * *
1152179 AATCGGATCCGATATGTAATTACTT-AAAAAGAAAATGCCTTTT-AAAAGTTGGCTTGAAACCT
60 AATCAAATCCGATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTGACTTGAAACCT
* * *
1152241 TGAACATAAACTATAAAACAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAA
1 TGAATATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAA
* * *
1152306 ATCCGATATGTAATTACTT-AAAAAGAAAATGTCTTTTAAAAAATTGACTTAAAAACTT
66 ATCCGATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTGACTT-GAAACCT
* * * * *
1152364 TAAAAAT-AACTTTAAAATAAATATGAAGAATAAAAAA
1 TGAATATGAACTATAAAATAGACATGAAGAATAAAAAA
1152401 TTAGTTAATT
Statistics
Matches: 473, Mismatches: 44, Indels: 29
0.87 0.08 0.05
Matches are distributed among these distances:
119 23 0.05
120 22 0.05
121 67 0.14
122 59 0.12
123 75 0.16
124 11 0.02
125 109 0.23
126 19 0.04
127 18 0.04
128 63 0.13
129 7 0.01
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (123 bp):
TGAATATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAA
ATCCGATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTGACTTGAAACCT
Found at i:1152238 original size:248 final size:246
Alignment explanation
Indices: 1151749--1152400 Score: 842
Period size: 248 Copynumber: 2.7 Consensus size: 246
1151739 TTTCAAATCC
* * *
1151749 TGAACATGAACTATAAAATAGACAT---G-A-AAAAAAATTGAATGAGATAATTGTATTAATC-T
1 TGAACATAAACTATAAAACAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAT
* *
1151808 AATCCAATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAAATTGACTTAAAACCTTGAAT
66 -ATCCGATATGTAATTACTTAAAAAAGAAAATGCCTTTT-AAAAAATTGAATTAAAACCTTGAAT
*
1151873 ATGAACTATAAAATAGACCTGAAGAATAAAAAAAATTGAATGAGATAATTCTATTAATCGGATCC
129 ATGAACTATAAAATAGACATGAAGAAT-AAAAAAATTGAATGAGATAATTCTATTAATCGGATCC
1151938 AATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAAATTGAATTGAAACAT
193 AATATGTAATTACTTAAAAAAGAAAATGCCTTTT-AAAAAATTGAATTGAAACAT
* * * * **
1151993 TGAATATGAACTATAAAATAGGC-TGAAGAATGTAAAAATTGAATGAGTTAATTGTATTAATCAT
1 TGAACATAAACTATAAAACAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAT
* *
1152057 ATCCGATATGTAATTACTTAAAAAAGAAGATGCCTTTTAAAAAATTGAATTGAAACCTTGAATAT
66 ATCCGATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTGAATTAAAACCTTG-A-AT
* * *
1152122 GAACTAGAACTATAAAATAGACATGAATAAT-AAAAAATTGAATGAGTTAATTGTATTAATCGGA
129 --A-T-GAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGATAATTCTATTAATCGGA
* * ** *
1152186 TCCGATATGTAATTACTT-AAAAAGAAAATGCCTTTT-AAAAGTTGGCTTGAAACCT
190 TCCAATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTGAATTGAAACAT
*
1152241 TGAACATAAACTATAAAACAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAA
1 TGAACATAAACTATAAAACAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAT
* * * * *
1152306 ATCCGATATGTAATTACTT-AAAAAGAAAATGTCTTTTAAAAAATTGACTTAAAAACTTTAAAAA
66 ATCCGATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTGAATT-AAAACCTTGAATA
* * *
1152370 T-AACTTTAAAATAAATATGAAGAATAAAAAA
130 TGAACTATAAAATAGACATGAAGAATAAAAAA
1152401 TTAGTTAATT
Statistics
Matches: 357, Mismatches: 36, Indels: 31
0.84 0.08 0.07
Matches are distributed among these distances:
242 20 0.06
243 6 0.02
244 22 0.06
245 1 0.00
246 1 0.00
247 22 0.06
248 128 0.36
249 66 0.18
250 18 0.05
251 49 0.14
252 1 0.00
253 23 0.06
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (246 bp):
TGAACATAAACTATAAAACAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAT
ATCCGATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTGAATTAAAACCTTGAATAT
GAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGATAATTCTATTAATCGGATCCAAT
ATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTGAATTGAAACAT
Found at i:1166648 original size:75 final size:75
Alignment explanation
Indices: 1166568--1166722 Score: 301
Period size: 75 Copynumber: 2.1 Consensus size: 75
1166558 AGCTTTAAAT
*
1166568 TTTTATAAAATTGTTTGATATATTACTTAAAATAAATTAATTACGAAACATAATCAGTTTTTTGA
1 TTTTATAAAATTGTTTGATATATTACTTAAAAAAAATTAATTACGAAACATAATCAGTTTTTTGA
1166633 TAAATAAAGA
66 TAAATAAAGA
1166643 TTTTATAAAATTGTTTGATATATTACTTAAAAAAAATTAATTACGAAACATAATCAGTTTTTTGA
1 TTTTATAAAATTGTTTGATATATTACTTAAAAAAAATTAATTACGAAACATAATCAGTTTTTTGA
1166708 TAAATAAAGA
66 TAAATAAAGA
1166718 TTTTA
1 TTTTA
1166723 AATTATAAAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 79 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (75 bp):
TTTTATAAAATTGTTTGATATATTACTTAAAAAAAATTAATTACGAAACATAATCAGTTTTTTGA
TAAATAAAGA
Found at i:1168721 original size:51 final size:51
Alignment explanation
Indices: 1168642--1168896 Score: 343
Period size: 51 Copynumber: 5.0 Consensus size: 51
1168632 GATGCCGAAC
* * *
1168642 CAGCAAGGTGGAAACATCGAAT-CTCAAACATACACTCAGCTACCACTACAG
1 CAGCAAGGTGGAAACATTGAATAC-CAAACATATACTCAGCTACCACAACAG
* ** *
1168693 CAGCAAGGTGGTAACATCAAATACCAAACATATACTCAACTACCACAACAG
1 CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAGCTACCACAACAG
* * *
1168744 CAGCAAGGTGGAAACGTTGAATACCAAACATATACTCAGCTGCCACAACAA
1 CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAGCTACCACAACAG
* * * *
1168795 CAGCAAGGTGGAAGCATTGAATCCCAAACTTATACTCAGCTACAACAACAG
1 CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAGCTACCACAACAG
*
1168846 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCCT-CCACAACAG
1 CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAG-CTACCACAACAG
1168897 TACTTAATGG
Statistics
Matches: 180, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
51 177 0.98
52 3 0.02
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (51 bp):
CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAGCTACCACAACAG
Found at i:1177548 original size:24 final size:24
Alignment explanation
Indices: 1177521--1177572 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1177511 TTAGTAAGTC
*
1177521 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1177545 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1177569 AAAT
1 AAAT
1177573 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1198191 original size:20 final size:21
Alignment explanation
Indices: 1198159--1198197 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1198149 ACTAAAGATA
1198159 TTTAAAAATTTTAC-TATTAT
1 TTTAAAAATTTTACATATTAT
1198179 TTTAATAAA-TTTACATATT
1 TTTAA-AAATTTTACATATT
1198198 TAAATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAAAAATTTTACATATTAT
Found at i:1199337 original size:26 final size:26
Alignment explanation
Indices: 1199305--1199361 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
1199295 TTGACTAAGT
1199305 GTATATGGATTATTTCAAGGATTGTA
1 GTATATGGATTATTTCAAGGATTGTA
1199331 GTATATGGATTATTTCAAGGATTGTA
1 GTATATGGATTATTTCAAGGATTGTA
*
1199357 CTATA
1 GTATA
1199362 AAAGTGAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (26 bp):
GTATATGGATTATTTCAAGGATTGTA
Found at i:1199691 original size:33 final size:33
Alignment explanation
Indices: 1199653--1199754 Score: 154
Period size: 33 Copynumber: 3.2 Consensus size: 33
1199643 AGATTAATTT
* *
1199653 ATATTTGATGTATCATTATATTAAATTATTTAA
1 ATATTTCATGTATCATTCTATTAAATTATTTAA
1199686 ATATTTCATGTATCATTCTATTAAATTATTTAA
1 ATATTTCATGTATCATTCTATTAAATTATTTAA
* *
1199719 ATA--TCATTTACCATTCTATTAAATTATTTAA
1 ATATTTCATGTATCATTCTATTAAATTATTTAA
1199750 ATATT
1 ATATT
1199755 ATATAACTTA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
31 29 0.46
33 34 0.54
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (33 bp):
ATATTTCATGTATCATTCTATTAAATTATTTAA
Found at i:1199737 original size:31 final size:31
Alignment explanation
Indices: 1199660--1199753 Score: 134
Period size: 31 Copynumber: 3.0 Consensus size: 31
1199650 TTTATATTTG
* *
1199660 ATGTATCATTATATTAAATTATTTAAATATTTC
1 ATGTACCATTCTATTAAATTATTTAAATA--TC
*
1199693 ATGTATCATTCTATTAAATTATTTAAATATC
1 ATGTACCATTCTATTAAATTATTTAAATATC
*
1199724 ATTTACCATTCTATTAAATTATTTAAATAT
1 ATGTACCATTCTATTAAATTATTTAAATAT
1199754 TATATAACTT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 30 0.52
33 28 0.48
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (31 bp):
ATGTACCATTCTATTAAATTATTTAAATATC
Done.