Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 15 of 20
Found at i:2493042 original size:26 final size:26
Alignment explanation
Indices: 2493006--2493058 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
2492996 AGACGTCAGC
*
2493006 ACGAGTCCAGCATCCTAAATTTTACT
1 ACGAGTCCAGCATCCTAAATTTAACT
*
2493032 ACGAGTTCAGCATCCTAAATTTAACT
1 ACGAGTCCAGCATCCTAAATTTAACT
2493058 A
1 A
2493059 ACAAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (26 bp):
ACGAGTCCAGCATCCTAAATTTAACT
Found at i:2494616 original size:22 final size:21
Alignment explanation
Indices: 2494593--2494649 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
2494583 TTAATTCAAT
2494593 TTTATTTTATTTTTTATTAAA
1 TTTATTTTATTTTTTATTAAA
*
2494614 TTTAATTTACTTTTTTATTTAAA
1 TTTATTTTA-TTTTTTA-TTAAA
* *
2494637 ATAATTTTATTTT
1 TTTATTTTATTTT
2494650 ATTTTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 8 0.27
22 11 0.37
23 11 0.37
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATTTTATTTTTTATTAAA
Found at i:2494650 original size:5 final size:5
Alignment explanation
Indices: 2494640--2494664 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2494630 ATTTAAAATA
2494640 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
2494665 TAATTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:2495124 original size:3 final size:3
Alignment explanation
Indices: 2495116--2495147 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2495106 ATTATATTTG
2495116 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2495148 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2495216 original size:28 final size:28
Alignment explanation
Indices: 2495169--2495222 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
2495159 TACACGATAT
2495169 AATTATATAATATAAAAAATA-ATTAAA
1 AATTATATAATATAAAAAATATATTAAA
*
2495196 AATTAATATAAGTAT-ACAAATATATTA
1 AATT-ATATAA-TATAAAAAATATATTA
2495223 CTTATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 4 0.17
28 12 0.52
29 7 0.30
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (28 bp):
AATTATATAATATAAAAAATATATTAAA
Found at i:2495945 original size:23 final size:23
Alignment explanation
Indices: 2495915--2495963 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2495905 TGCTTAATTC
2495915 TTAATTTTATTTTAATATAAACT
1 TTAATTTTATTTTAATATAAACT
2495938 TTAATTTTATTTTAATATAAACT
1 TTAATTTTATTTTAATATAAACT
2495961 TTA
1 TTA
2495964 TTAATCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
TTAATTTTATTTTAATATAAACT
Found at i:2501813 original size:4 final size:4
Alignment explanation
Indices: 2501804--2501828 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2501794 TTAATATCAG
2501804 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
2501829 TAAGAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:2502971 original size:2 final size:2
Alignment explanation
Indices: 2502964--2502994 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2502954 ATCAAGTACC
*
2502964 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2502995 CCAAAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2503924 original size:48 final size:48
Alignment explanation
Indices: 2503868--2503963 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
2503858 AGAAAATAAC
* *
2503868 TTCTTCACGACCCACTATGTGATTCAATGGAACTAACTATGCGTGTCA
1 TTCTTCACGACCCACTATGTGAATCAATGGAACTAACTATGCATGTCA
2503916 TTCTTCACGACCCACTATGTGAATCAATGGAACTAACTATGCATGTCA
1 TTCTTCACGACCCACTATGTGAATCAATGGAACTAACTATGCATGTCA
2503964 GCCTTTAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (48 bp):
TTCTTCACGACCCACTATGTGAATCAATGGAACTAACTATGCATGTCA
Found at i:2507167 original size:2 final size:2
Alignment explanation
Indices: 2507162--2507198 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2507152 GCAAAAAACA
*
2507162 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2507199 AATTGTTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2507570 original size:10 final size:12
Alignment explanation
Indices: 2507543--2507590 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
2507533 TTAAAAATTT
2507543 ATATAAAATATA
1 ATATAAAATATA
2507555 ATATAAAATA-A
1 ATATAAAATATA
2507566 A-ATAAAA-A-A
1 ATATAAAATATA
*
2507575 ATA-CAAATATA
1 ATATAAAATATA
2507586 ATATA
1 ATATA
2507591 CATATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
9 6 0.20
10 8 0.27
11 6 0.20
12 10 0.33
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (12 bp):
ATATAAAATATA
Found at i:2507624 original size:7 final size:7
Alignment explanation
Indices: 2507612--2507636 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2507602 ATTTTCAAAT
2507612 TTATAAA
1 TTATAAA
2507619 TTATAAA
1 TTATAAA
2507626 TTATAAA
1 TTATAAA
2507633 TTAT
1 TTAT
2507637 TAAAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTATAAA
Found at i:2508325 original size:24 final size:25
Alignment explanation
Indices: 2508285--2508374 Score: 78
Period size: 24 Copynumber: 3.6 Consensus size: 25
2508275 AATTTTAGAT
2508285 ATAATATAAATATAATAT-TAAAAA
1 ATAATATAAATATAATATGTAAAAA
*
2508309 ATAATAT-TATATAAATATGTAAAAA
1 ATAATATAAATAT-AATATGTAAAAA
* * * * *
2508334 TTTATATAAATATATGATATTTTAAAT
1 ATAATATAAATATA--ATATGTAAAAA
2508361 ATAATAT-AATATAA
1 ATAATATAAATATAA
2508375 AAAAATAATT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
23 4 0.08
24 13 0.25
25 12 0.23
26 10 0.19
27 13 0.25
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
ATAATATAAATATAATATGTAAAAA
Found at i:2508375 original size:16 final size:16
Alignment explanation
Indices: 2508283--2508375 Score: 59
Period size: 16 Copynumber: 5.8 Consensus size: 16
2508273 ATAATTTTAG
2508283 ATATAATATAAATATA
1 ATATAATATAAATATA
*
2508299 ATAT--TA-AAAAATA
1 ATATAATATAAATATA
*
2508312 ATATTATATAAATATGTAA
1 ATATAATATAAATA--T-A
* *
2508331 AAATTTATATAAATAT-
1 ATA-TAATATAAATATA
* *
2508347 ATGATATTTTAAATATA
1 AT-ATAATATAAATATA
2508364 ATATAATATAAA
1 ATATAATATAAA
2508376 AAAATAATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
13 10 0.17
14 2 0.03
15 2 0.03
16 26 0.44
17 3 0.05
18 2 0.03
19 3 0.05
20 11 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
ATATAATATAAATATA
Found at i:2509042 original size:14 final size:14
Alignment explanation
Indices: 2509025--2509076 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
2509015 AAATATAAAA
2509025 ATATATTAAAATTT
1 ATATATTAAAATTT
*
2509039 ATATAATATAAATTATTA
1 ATAT-AT-TAAA--ATTT
2509057 ATATATTAAAATTT
1 ATATATTAAAATTT
2509071 ATATAT
1 ATATAT
2509077 ATTAAATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 13 0.41
15 2 0.06
16 8 0.25
17 2 0.06
18 7 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATTAAAATTT
Found at i:2509064 original size:32 final size:33
Alignment explanation
Indices: 2509010--2509084 Score: 109
Period size: 32 Copynumber: 2.3 Consensus size: 33
2509000 ATATAAATAA
2509010 AATATAAATATAAAAATATATTAAAATTTATAT
1 AATATAAATATAAAAATATATTAAAATTTATAT
**
2509043 AATATAAAT-TATTAATATATTAAAATTTATAT
1 AATATAAATATAAAAATATATTAAAATTTATAT
2509075 -ATATTAAATA
1 AATA-TAAATA
2509085 CAATTATTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 3 0.08
32 26 0.68
33 9 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
AATATAAATATAAAAATATATTAAAATTTATAT
Found at i:2509066 original size:16 final size:16
Alignment explanation
Indices: 2509024--2509083 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
2509014 TAAATATAAA
2509024 AATATATTAAA--ATT
1 AATATATTAAATTATT
*
2509038 TATATAATATAAATTATT
1 AATAT-AT-TAAATTATT
*
2509056 AATATATTAAAAT-TT
1 AATATATTAAATTATT
2509071 ATATATATTAAAT
1 A-ATATATTAAAT
2509084 ACAATTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 4 0.11
15 5 0.14
16 19 0.51
17 2 0.05
18 7 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATATTAAATTATT
Found at i:2510072 original size:8 final size:8
Alignment explanation
Indices: 2510057--2510098 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
2510047 AATAAAAAAG
2510057 AAGACAGA
1 AAGACAGA
*
2510065 AAGCCAGA
1 AAGACAGA
*
2510073 AAGAAAGA
1 AAGACAGA
2510081 AAGACAGA
1 AAGACAGA
2510089 AAGACAGA
1 AAGACAGA
2510097 AA
1 AA
2510099 CCAAGAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.64, C:0.12, G:0.24, T:0.00
Consensus pattern (8 bp):
AAGACAGA
Found at i:2510104 original size:24 final size:24
Alignment explanation
Indices: 2510053--2510105 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2510043 AAAGAATAAA
* *
2510053 AAAG-AAGACAGAAAGCCAGAAAG
1 AAAGAAAGACAGAAAGACAGAAAC
2510076 AAAGAAAGACAGAAAGACAGAAAC
1 AAAGAAAGACAGAAAGACAGAAAC
*
2510100 CAAGAA
1 AAAGAA
2510106 GATTTGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.64, C:0.13, G:0.23, T:0.00
Consensus pattern (24 bp):
AAAGAAAGACAGAAAGACAGAAAC
Found at i:2511328 original size:22 final size:22
Alignment explanation
Indices: 2511297--2511341 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2511287 ATTACAAATC
2511297 TATATATGGATATATATATATA
1 TATATATGGATATATATATATA
*
2511319 TATATGTGGATATATATATATA
1 TATATATGGATATATATATATA
2511341 T
1 T
2511342 GTGTATATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
TATATATGGATATATATATATA
Found at i:2511356 original size:18 final size:18
Alignment explanation
Indices: 2511310--2511349 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2511300 ATATGGATAT
2511310 ATATATATATATATGTGG
1 ATATATATATATATGTGG
*
2511328 ATATATATATATATGTGT
1 ATATATATATATATGTGG
2511346 ATAT
1 ATAT
2511350 TCGTATACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (18 bp):
ATATATATATATATGTGG
Found at i:2511722 original size:2 final size:2
Alignment explanation
Indices: 2511689--2511714 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2511679 AGCTAAAAGC
2511689 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2511715 GTTATATACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2516309 original size:2 final size:2
Alignment explanation
Indices: 2516304--2516342 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2516294 TAAAAAAGGC
*
2516304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2516343 AGAGAAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2517498 original size:23 final size:23
Alignment explanation
Indices: 2517472--2517532 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
2517462 AAAAAATTAT
*
2517472 ATATTATTTAAATTTAATTATAA
1 ATATTATTTAAATATAATTATAA
* * *
2517495 ATATTAATATAAA-ATAATTTTTA
1 ATATT-ATTTAAATATAATTATAA
2517518 ATATTATTTTAAATA
1 ATATTA-TTTAAATA
2517533 ATAAAATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
22 1 0.03
23 22 0.73
24 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATTATTTAAATATAATTATAA
Found at i:2517867 original size:24 final size:24
Alignment explanation
Indices: 2517808--2517867 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
2517798 ATATTTTAGA
2517808 TTATTAAATT-T-AATAATAATTT
1 TTATTAAATTATAAATAATAATTT
*
2517830 TTATGTAAATTATAAATATTTAA-TT
1 TTAT-TAAATTATAAATA-ATAATTT
2517855 TTATTAAATTATA
1 TTATTAAATTATA
2517868 TTGATAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.12
23 6 0.18
24 10 0.30
25 10 0.30
26 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTATTAAATTATAAATAATAATTT
Found at i:2521392 original size:11 final size:11
Alignment explanation
Indices: 2521368--2521435 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
2521358 TAATTTTTTT
2521368 AAAATTAT-TAC
1 AAAATTATAT-C
2521379 AAAATTATATC
1 AAAATTATATC
*
2521390 AAAAGT-TATC
1 AAAATTATATC
* *
2521400 ATATTTATATC
1 AAAATTATATC
*
2521411 -AAATTTTATC
1 AAAATTATATC
*
2521421 AAAATTATATT
1 AAAATTATATC
2521432 AAAA
1 AAAA
2521436 GTATTGTTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
10 14 0.31
11 30 0.67
12 1 0.02
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.40
Consensus pattern (11 bp):
AAAATTATATC
Found at i:2521407 original size:21 final size:21
Alignment explanation
Indices: 2521378--2521437 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
2521368 AAAATTATTA
2521378 CAAAATTATATCAAAAGTTAT
1 CAAAATTATATCAAAAGTTAT
* * **
2521399 CATATTTATATCAAATTTTAT
1 CAAAATTATATCAAAAGTTAT
*
2521420 CAAAATTATATTAAAAGT
1 CAAAATTATATCAAAAGT
2521438 ATTGTTAAAG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.40
Consensus pattern (21 bp):
CAAAATTATATCAAAAGTTAT
Found at i:2525120 original size:2 final size:2
Alignment explanation
Indices: 2525113--2525147 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2525103 CATCACATGC
2525113 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2525148 AAGAAAGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2529522 original size:6 final size:6
Alignment explanation
Indices: 2529515--2529554 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
2529505 AAGAAAGTTA
*
2529515 AAGCTA AAGCTC AAGCTC AAGCTC AAGCTC AAGCTC AAGC
1 AAGCTC AAGCTC AAGCTC AAGCTC AAGCTC AAGCTC AAGC
2529555 ATCTTCAGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.38, C:0.30, G:0.17, T:0.15
Consensus pattern (6 bp):
AAGCTC
Found at i:2531317 original size:3 final size:3
Alignment explanation
Indices: 2531309--2531357 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
2531299 TCCAAACTAC
2531309 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2531357 A
1 A
2531358 AACGTATTCG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2533504 original size:6 final size:6
Alignment explanation
Indices: 2533493--2533531 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
2533483 TAAATTCATG
2533493 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TAT
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TAT
2533532 ACTCGAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (6 bp):
TATGTA
Found at i:2535382 original size:2 final size:2
Alignment explanation
Indices: 2535375--2535412 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2535365 AATTGGCTAC
2535375 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2535413 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2541401 original size:4 final size:4
Alignment explanation
Indices: 2541392--2541507 Score: 142
Period size: 4 Copynumber: 29.0 Consensus size: 4
2541382 CAGCATGGTG
* * * *
2541392 TATA TATA TATA TGTA TGTA TATA TATA TATA TATG TATG TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
2541440 TATA TATA TGTA TGTA TATA TATA TATA TATA TATG TATG TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
2541488 TATA TGTA TGTA TATA TATA
1 TATA TATA TATA TATA TATA
2541508 ATTCATCTGA
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 102 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:2541413 original size:18 final size:18
Alignment explanation
Indices: 2541390--2541507 Score: 159
Period size: 18 Copynumber: 6.7 Consensus size: 18
2541380 TGCAGCATGG
2541390 TGTATATATATATATGTA
1 TGTATATATATATATGTA
*
2541408 TGTATATATATATATATA
1 TGTATATATATATATGTA
*
2541426 TGTATGTATATATA--TA
1 TGTATATATATATATGTA
* * * *
2541442 TATATATGTATGTATATA
1 TGTATATATATATATGTA
*
2541460 TATATATATATATATGTA
1 TGTATATATATATATGTA
2541478 TGTATATATATATATGTA
1 TGTATATATATATATGTA
2541496 TGTATATATATA
1 TGTATATATATA
2541508 ATTCATCTGA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
16 12 0.14
18 76 0.86
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (18 bp):
TGTATATATATATATGTA
Found at i:2541420 original size:22 final size:22
Alignment explanation
Indices: 2541392--2541507 Score: 214
Period size: 22 Copynumber: 5.3 Consensus size: 22
2541382 CAGCATGGTG
2541392 TATATATATATATGTATGTATA
1 TATATATATATATGTATGTATA
2541414 TATATATATATATGTATGTATA
1 TATATATATATATGTATGTATA
2541436 TATATATATATATGTATGTATA
1 TATATATATATATGTATGTATA
* *
2541458 TATATATATATATATATGTATG
1 TATATATATATATGTATGTATA
2541480 TATATATATATATGTATGTATA
1 TATATATATATATGTATGTATA
2541502 TATATA
1 TATATA
2541508 ATTCATCTGA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 90 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (22 bp):
TATATATATATATGTATGTATA
Found at i:2541431 original size:26 final size:26
Alignment explanation
Indices: 2541393--2541492 Score: 154
Period size: 26 Copynumber: 4.0 Consensus size: 26
2541383 AGCATGGTGT
* *
2541393 ATATATATATATGTATGTATATATAT
1 ATATATATGTATGTATATATATATAT
2541419 ATATATATGTATG----TATATATAT
1 ATATATATGTATGTATATATATATAT
2541441 ATATATATGTATGTATATATATATAT
1 ATATATATGTATGTATATATATATAT
2541467 ATATATATGTATGTATATATATATAT
1 ATATATATGTATGTATATATATATAT
2541493 GTATGTATAT
Statistics
Matches: 69, Mismatches: 1, Indels: 8
0.88 0.01 0.10
Matches are distributed among these distances:
22 22 0.32
26 47 0.68
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (26 bp):
ATATATATGTATGTATATATATATAT
Found at i:2544954 original size:15 final size:15
Alignment explanation
Indices: 2544934--2544974 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 15
2544924 ATTGTTATAA
2544934 ATAAAATTTTAATTT
1 ATAAAATTTTAATTT
2544949 ATAAAA--TT-ATTT
1 ATAAAATTTTAATTT
*
2544961 AAAAAATTTTAATT
1 ATAAAATTTTAATT
2544975 ATATTAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 2 0.09
15 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATAAAATTTTAATTT
Found at i:2545136 original size:26 final size:28
Alignment explanation
Indices: 2545098--2545154 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
2545088 ATATATATAT
2545098 ATATATACTTAATCCTTA-TTTCAAAAAA
1 ATATATAC-TAATCCTTATTTTCAAAAAA
** *
2545126 ATATATA-TAATTTTTATTTTTAAAAAA
1 ATATATACTAATCCTTATTTTCAAAAAA
2545153 AT
1 AT
2545155 GGGCCACGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 7 0.28
27 11 0.44
28 7 0.28
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (28 bp):
ATATATACTAATCCTTATTTTCAAAAAA
Found at i:2547021 original size:14 final size:13
Alignment explanation
Indices: 2546994--2547051 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
2546984 TAAGAAAAAA
*
2546994 ATATTTTAATTTT
1 ATATTTTAAATTT
2547007 ATATTATTAAATTT
1 ATATT-TTAAATTT
2547021 AATATTTT-AATTAT
1 -ATATTTTAAATT-T
*
2547035 ATATTTTTAAAATT
1 ATA-TTTTAAATTT
2547049 ATA
1 ATA
2547052 ATAAATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 12 0.32
14 18 0.47
15 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTTTAAATTT
Found at i:2547025 original size:15 final size:14
Alignment explanation
Indices: 2546993--2547030 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
2546983 ATAAGAAAAA
2546993 AATATTTT-AATTT
1 AATATTTTAAATTT
*
2547006 TATATTATTAAATTT
1 AATATT-TTAAATTT
2547021 AATATTTTAA
1 AATATTTTAA
2547031 TTATATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 5 0.24
14 6 0.29
15 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATATTTTAAATTT
Found at i:2547031 original size:28 final size:30
Alignment explanation
Indices: 2546993--2547054 Score: 92
Period size: 28 Copynumber: 2.1 Consensus size: 30
2546983 ATAAGAAAAA
*
2546993 AATATTTTAATTTTATATTATT-AAATT-T
1 AATATTTTAATTATATATTATTAAAATTAT
*
2547021 AATATTTTAATTATATATTTTTAAAATTAT
1 AATATTTTAATTATATATTATTAAAATTAT
2547051 AATA
1 AATA
2547055 AATAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 20 0.67
29 5 0.17
30 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
AATATTTTAATTATATATTATTAAAATTAT
Found at i:2547038 original size:13 final size:12
Alignment explanation
Indices: 2546994--2547041 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 12
2546984 TAAGAAAAAA
2546994 ATATTTTAATTTT
1 ATATTTTAA-TTT
2547007 ATATTATTAAATTT
1 ATATT-TT-AATTT
2547021 AATATTTTAATTAT
1 -ATATTTTAATT-T
2547035 ATATTTT
1 ATATTTT
2547042 TAAAATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 16 0.52
14 8 0.26
15 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATTTTAATTT
Found at i:2547087 original size:18 final size:17
Alignment explanation
Indices: 2547041--2547087 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
2547031 TTATATATTT
*
2547041 TTAAAATTA-TAATAAA
1 TTAAAAATATTAATAAA
*
2547057 TAAAAAATAATTAATAAA
1 TTAAAAAT-ATTAATAAA
2547075 GTTAAAAATATTA
1 -TTAAAAATATTA
2547088 TTTAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 6 0.24
17 1 0.04
18 11 0.44
19 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
TTAAAAATATTAATAAA
Found at i:2547171 original size:22 final size:20
Alignment explanation
Indices: 2547146--2547191 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2547136 ATATTAATAA
2547146 TTTAATAATATTTAAATAATTT
1 TTTAATAATA-TT-AATAATTT
* *
2547168 TTTACTAATATTAATTATTT
1 TTTAATAATATTAATAATTT
2547188 TTTA
1 TTTA
2547192 TTTATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 2 0.09
22 9 0.41
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATAATATTAATAATTT
Found at i:2557296 original size:20 final size:21
Alignment explanation
Indices: 2557246--2557309 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 21
2557236 ATTGATGATA
2557246 ATAAATATATTTATTTA-TATT
1 ATAAA-ATATTTATTTATTATT
**
2557267 ATAATCTA-TTATTTATTATT
1 ATAAAATATTTATTTATTATT
2557287 ATAAAATATTTAATTTATT-TT
1 ATAAAATATTT-ATTTATTATT
2557308 AT
1 AT
2557310 TTAATTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 7 0.19
20 12 0.33
21 10 0.28
22 7 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATAAAATATTTATTTATTATT
Found at i:2557336 original size:27 final size:30
Alignment explanation
Indices: 2557274--2557336 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 30
2557264 ATTATAATCT
*
2557274 ATTATTTATTATTATAAAATATTTAATTTAT
1 ATTATTTA-TATTATAAAATATTTAATTTAA
*
2557305 TTTATTTA-ATT-TAAAAT-TTTAATTTAA
1 ATTATTTATATTATAAAATATTTAATTTAA
2557332 ATTAT
1 ATTAT
2557337 AATCATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 13 0.45
28 6 0.21
29 3 0.10
31 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
ATTATTTATATTATAAAATATTTAATTTAA
Found at i:2557611 original size:39 final size:40
Alignment explanation
Indices: 2557555--2557653 Score: 109
Period size: 37 Copynumber: 2.6 Consensus size: 40
2557545 TCTAAAATTT
*
2557555 AAATAATTAAACT-ATTACAATTTTTAATTTAAAT-TCTAA
1 AAATAATTAAA-TGATTACAATTTTTAAATTAAATATCTAA
* * *
2557594 AAATAATTAGATGATTAC---TTTTAAATTAAATATTTTA
1 AAATAATTAAATGATTACAATTTTTAAATTAAATATCTAA
*
2557631 AAATAATTACATGATTACAATTT
1 AAATAATTAAATGATTACAATTT
2557654 AAATAAATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
36 12 0.24
37 20 0.40
38 1 0.02
39 15 0.30
40 2 0.04
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (40 bp):
AAATAATTAAATGATTACAATTTTTAAATTAAATATCTAA
Found at i:2557645 original size:37 final size:38
Alignment explanation
Indices: 2557576--2557662 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 38
2557566 CTATTACAAT
* *
2557576 TTTTAATTTAAAT-TCTAAAAATAATTAGATGATTAC-
1 TTTTAAATTAAATATCTAAAAATAATTACATGATTACA
* *
2557612 TTTTAAATTAAATATTTTAAAATAATTACATGATTACA
1 TTTTAAATTAAATATCTAAAAATAATTACATGATTACA
*
2557650 ATTTAAA-TAAATA
1 TTTTAAATTAAATA
2557663 AATTTATTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
36 12 0.27
37 26 0.59
38 6 0.14
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (38 bp):
TTTTAAATTAAATATCTAAAAATAATTACATGATTACA
Found at i:2557695 original size:29 final size:28
Alignment explanation
Indices: 2557649--2557720 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 28
2557639 ACATGATTAC
2557649 AATTTAAATAAATAAATTTATTATTATT
1 AATTTAAATAAATAAATTTATTATTATT
*
2557677 AATTATAAATAAAATAATTTTTTATTATTATT
1 AATT-TAAAT-AAATAA--ATTTATTATTATT
*
2557709 AATCTAAA-AAAT
1 AATTTAAATAAAT
2557721 GTCAACATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 4 0.11
29 9 0.24
30 6 0.16
31 4 0.11
32 15 0.39
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTTAAATAAATAAATTTATTATTATT
Found at i:2557866 original size:23 final size:24
Alignment explanation
Indices: 2557839--2557896 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
2557829 TGAATATGTT
*
2557839 AATTAATTTAATAAT-TTTTTATA
1 AATTAATTTAATAATATTTTAATA
**
2557862 AATTAAAATAATAATATTTTAATA
1 AATTAATTTAATAATATTTTAATA
* *
2557886 ATTTATTTTAA
1 AATTAATTTAA
2557897 ATTTATATTA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AATTAATTTAATAATATTTTAATA
Found at i:2557883 original size:34 final size:33
Alignment explanation
Indices: 2557845--2557932 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 33
2557835 TGTTAATTAA
2557845 TTTAATAATTT-TTTATAAATTAAAATAATAATAT
1 TTTAATAATTTATTTATAAATT-AAAT-ATAATAT
*
2557879 TTTAATAATTTATTT-TAAATT---TATATTAT
1 TTTAATAATTTATTTATAAATTAAATATAATAT
*
2557908 TTTAATAATTTATTTAAAAATTAAA
1 TTTAATAATTTATTTATAAATTAAA
2557933 GATATTTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
29 21 0.45
30 6 0.13
34 17 0.36
35 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TTTAATAATTTATTTATAAATTAAATATAATAT
Found at i:2557892 original size:13 final size:13
Alignment explanation
Indices: 2557876--2557922 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
2557866 AAAATAATAA
2557876 TATTTTAATAATT
1 TATTTTAATAATT
*
2557889 TATTTTAAATTTATAT
1 TATTTT-AA-TAAT-T
2557905 TATTTTAATAATT
1 TATTTTAATAATT
2557918 TATTT
1 TATTT
2557923 AAAAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 12 0.41
14 5 0.17
15 5 0.17
16 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTAATAATT
Found at i:2557897 original size:29 final size:29
Alignment explanation
Indices: 2557864--2557943 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
2557854 TTTTTATAAA
2557864 TTAAAATAATAATATTTTAATAATTTATT
1 TTAAAATAATAATATTTTAATAATTTATT
* * *
2557893 TTAAATTTATATTATTTTAATAATTTATT
1 TTAAAATAATAATATTTTAATAATTTATT
*
2557922 TAAAAATTAA-AGATATTTTAAT
1 TTAAAA-TAATA-ATATTTTAAT
2557944 CAATCTGTGC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 31 0.74
30 11 0.26
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
TTAAAATAATAATATTTTAATAATTTATT
Found at i:2558331 original size:7 final size:7
Alignment explanation
Indices: 2558319--2558348 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2558309 TACCAAGCAG
2558319 GCGGGAA
1 GCGGGAA
2558326 GCGGGAA
1 GCGGGAA
*
2558333 GCGGGCA
1 GCGGGAA
2558340 GCGGGAA
1 GCGGGAA
2558347 GC
1 GC
2558349 AACCGAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.57, T:0.00
Consensus pattern (7 bp):
GCGGGAA
Found at i:2558990 original size:41 final size:42
Alignment explanation
Indices: 2558938--2559071 Score: 145
Period size: 43 Copynumber: 3.2 Consensus size: 42
2558928 TATTATTTAT
*
2558938 TTTTATTTAAGTTTAATTT-GATTTA-AAAT-ATTAATTTTAAA
1 TTTTATTTAAG-TTAATTTAGATTTATAAATAAATAA-TTTAAA
*
2558979 TTTTATTTAAGTTAATTTATATTTATAAATAAATAATTTAAA
1 TTTTATTTAAGTTAATTTAGATTTATAAATAAATAATTTAAA
* *
2559021 -TTTATTT-AGATTCATTTTTATATTTATAAATAAATAATTTAAA
1 TTTTATTTAAG-TT-A-ATTTAGATTTATAAATAAATAATTTAAA
2559064 -TTTATTTA
1 TTTTATTTA
2559072 GATTCATTAT
Statistics
Matches: 83, Mismatches: 3, Indels: 11
0.86 0.03 0.11
Matches are distributed among these distances:
40 9 0.11
41 25 0.30
42 11 0.13
43 38 0.46
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (42 bp):
TTTTATTTAAGTTAATTTAGATTTATAAATAAATAATTTAAA
Found at i:2558997 original size:21 final size:20
Alignment explanation
Indices: 2558967--2559028 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
2558957 GATTTAAAAT
2558967 ATTAATTTTAAATTTTATTTA
1 ATTAA-TTTAAATTTTATTTA
* **
2558988 AGTTAATTTATATTTATAAATA
1 A-TTAATTTAAATTT-TATTTA
*
2559010 AATAATTTAAA-TTTATTTA
1 ATTAATTTAAATTTTATTTA
2559029 GATTCATTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 17 0.53
22 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
ATTAATTTAAATTTTATTTA
Found at i:2559086 original size:47 final size:43
Alignment explanation
Indices: 2558994--2559079 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
2558984 TTTAAGTTAA
2558994 TTTATATTTATAAATAAATAATTTAAATTTATTTAGATTCATT
1 TTTATATTTATAAATAAATAATTTAAATTTATTTAGATTCATT
2559037 TTTATATTTATAAATAAATAATTTAAATTTATTTAGATTCATT
1 TTTATATTTATAAATAAATAATTTAAATTTATTTAGATTCATT
2559080 ATTTTTTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (43 bp):
TTTATATTTATAAATAAATAATTTAAATTTATTTAGATTCATT
Found at i:2559093 original size:47 final size:44
Alignment explanation
Indices: 2558994--2559094 Score: 150
Period size: 43 Copynumber: 2.2 Consensus size: 44
2558984 TTTAAGTTAA
2558994 TTTATATTTATAAATAAATAATTTAAATTTATTTAGATTCATTTT
1 TTTA-ATTTATAAATAAATAATTTAAATTTATTTAGATTCATTTT
*
2559039 TAT-ATTTATAAATAAATAATTTAAATTTATTTAGATTCATTATTTT
1 TTTAATTTATAAATAAATAATTTAAATTTATTTAGATTC---ATTTT
2559085 TTTAATTTAT
1 TTTAATTTAT
2559095 TTTTAAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
43 35 0.70
45 2 0.04
46 7 0.14
47 6 0.12
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (44 bp):
TTTAATTTATAAATAAATAATTTAAATTTATTTAGATTCATTTT
Found at i:2564052 original size:5 final size:5
Alignment explanation
Indices: 2564042--2564066 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2564032 ACTTGCAGAC
2564042 GCAGG GCAGG GCAGG GCAGG GCAGG
1 GCAGG GCAGG GCAGG GCAGG GCAGG
2564067 CCAACCTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.60, T:0.00
Consensus pattern (5 bp):
GCAGG
Found at i:2565994 original size:3 final size:3
Alignment explanation
Indices: 2565986--2566017 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2565976 CTTGAGAGCT
2565986 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2566018 GACATCAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2567017 original size:20 final size:21
Alignment explanation
Indices: 2566988--2567027 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2566978 AATTTATAAA
*
2566988 TTTTAAATTT-ATTTCACGTC
1 TTTTAAATTTCATGTCACGTC
*
2567008 TTTTATATTTCATGTCACGT
1 TTTTAAATTTCATGTCACGT
2567028 AACATCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTAAATTTCATGTCACGTC
Found at i:2570079 original size:5 final size:5
Alignment explanation
Indices: 2570064--2570131 Score: 50
Period size: 5 Copynumber: 13.6 Consensus size: 5
2570054 AAATTAGATT
* * * *
2570064 TAATA TGATA TAATA TAAATA TAATA TAAAAA TAAT- TAAAA T-ATA TTATA
1 TAATA TAATA TAATA T-AATA TAATA T-AATA TAATA TAATA TAATA TAATA
* *
2570114 AAATA TTATA TAATA TAA
1 TAATA TAATA TAATA TAA
2570132 AAATAAAAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
4 6 0.12
5 33 0.69
6 9 0.19
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:2570124 original size:17 final size:18
Alignment explanation
Indices: 2570104--2570173 Score: 65
Period size: 17 Copynumber: 4.1 Consensus size: 18
2570094 AATAATTAAA
2570104 ATATATTATAAAATAT-T
1 ATATATTATAAAATATAT
* *
2570121 ATATAATATAAAA-ATAA
1 ATATATTATAAAATATAT
*
2570138 AAATATTA-AAAATATAT
1 ATATATTATAAAATATAT
* * *
2570155 AAATATTTTAAAATTTAT
1 ATATATTATAAAATATAT
2570173 A
1 A
2570174 ATGGGTTTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
16 6 0.14
17 28 0.65
18 9 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATTATAAAATATAT
Found at i:2570138 original size:45 final size:41
Alignment explanation
Indices: 2570071--2570161 Score: 112
Period size: 45 Copynumber: 2.1 Consensus size: 41
2570061 ATTTAATATG
* *
2570071 ATATAATATAAATATAATATAAAAATAATTAAAATATATTATAAA
1 ATATTATATAAATATAAAATAAAAAT-ATTAAAA-ATA-TAT-AA
2570116 ATATTATAT-AATATAAAAATAAAAATATTAAAAATATATAA
1 ATATTATATAAATAT-AAAATAAAAATATTAAAAATATATAA
2570157 ATATT
1 ATATT
2570162 TTAAAATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
41 7 0.16
42 3 0.07
43 3 0.07
44 12 0.28
45 18 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (41 bp):
ATATTATATAAATATAAAATAAAAATATTAAAAATATATAA
Found at i:2571172 original size:18 final size:18
Alignment explanation
Indices: 2571140--2571216 Score: 61
Period size: 18 Copynumber: 4.2 Consensus size: 18
2571130 GATGCTTAAT
*
2571140 ATAATTAAAATATAATAAA
1 ATAATTAAAAGATAA-AAA
2571159 ATAA-TAAAAGATAAAAA
1 ATAATTAAAAGATAAAAA
* *
2571176 A-AATTTAATA-ATTAAAA
1 ATAA-TTAAAAGATAAAAA
*
2571193 ATAATTTAAAAAATAAATAA
1 ATAA-TTAAAAGATAAA-AA
2571213 ATAA
1 ATAA
2571217 ATTGAATGCG
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
16 2 0.04
17 11 0.23
18 21 0.44
19 8 0.17
20 6 0.12
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (18 bp):
ATAATTAAAAGATAAAAA
Found at i:2574804 original size:15 final size:15
Alignment explanation
Indices: 2574772--2574828 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
2574762 AATATTAGAT
*
2574772 TATAAAAAATTTTAAA
1 TATAAAAAATTAT-AA
2574788 TATAAAAAATTATAA
1 TATAAAAAATTATAA
*
2574803 TATAATATAA-TATAA
1 TATAA-AAAATTATAA
2574818 TATTAAAAAAT
1 TA-TAAAAAAT
2574829 AATATTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 17 0.49
16 18 0.51
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAAAAATTATAA
Found at i:2574808 original size:5 final size:5
Alignment explanation
Indices: 2574798--2574919 Score: 62
Period size: 5 Copynumber: 25.0 Consensus size: 5
2574788 TATAAAAAAT
2574798 TATAA TATAA TATAA TATAA TATTAA -A-AA -ATAA TATTAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TA-TAA TATAA TATAA TA-TAA TATAA TATAA
* * * * * *
2574847 -AT-A TATAA -ATAT TTTAAA AATTA TATAA TAT-A TATTAT TATAA TAAAA
1 TATAA TATAA TATAA TAT-AA TATAA TATAA TATAA TA-TAA TATAA TATAA
* * *
2574895 TTTAT TA-AA TATAA TTATAA CATAA
1 TATAA TATAA TATAA -TATAA TATAA
2574920 ATATTATATC
Statistics
Matches: 88, Mismatches: 17, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
3 4 0.05
4 15 0.17
5 52 0.59
6 17 0.19
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:2574839 original size:19 final size:18
Alignment explanation
Indices: 2574809--2574877 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 18
2574799 ATAATATAAT
2574809 ATAATATAATATTAAAAA
1 ATAATATAATATTAAAAA
2574827 ATAATATTAATA-TAATATAA
1 ATAATA-TAATATTAA-A-AA
*
2574847 AT-ATATAAATATTTTAAAA
1 ATAATAT-AATA-TTAAAAA
*
2574866 ATTATATAATAT
1 ATAATATAATAT
2574878 ATATTATTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
18 11 0.26
19 21 0.49
20 9 0.21
21 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATATAATATTAAAAA
Found at i:2574890 original size:15 final size:14
Alignment explanation
Indices: 2574798--2574912 Score: 61
Period size: 13 Copynumber: 8.6 Consensus size: 14
2574788 TATAAAAAAT
*
2574798 TATAATATAATATAA
1 TATAAT-TATTATAA
*
2574813 TATAA-TATTAAAA
1 TATAATTATTATAA
*
2574826 AATAA-TA-T-TAA
1 TATAATTATTATAA
*
2574837 TATAA-TA-TAAATA
1 TATAATTATTATA-A
* *
2574850 TATAAATATTTTAA
1 TATAATTATTATAA
2574864 -A-AATTA-TATAA
1 TATAATTATTATAA
2574875 TATATATTATTATAA
1 TATA-ATTATTATAA
*
2574890 TAAAATTTATTA-AA
1 TATAA-TTATTATAA
2574904 TATAATTAT
1 TATAATTAT
2574913 AACATAAATA
Statistics
Matches: 79, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
11 13 0.16
12 7 0.09
13 24 0.30
14 14 0.18
15 21 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TATAATTATTATAA
Found at i:2574893 original size:38 final size:40
Alignment explanation
Indices: 2574798--2574898 Score: 115
Period size: 39 Copynumber: 2.6 Consensus size: 40
2574788 TATAAAAAAT
2574798 TATAATAT-AATATAATATAATA-TTAAAAAATAATATTAA
1 TATAATATAAATATAATA-AATATTTAAAAAATAATATTAA
* *
2574837 TATAATATAAATAT-ATAAATATTTTAAAAATTATA-TAA
1 TATAATATAAATATAATAAATATTTAAAAAATAATATTAA
* *
2574875 TAT-ATATTATTATAATAAA-ATTTA
1 TATAATATAAATATAATAAATATTTA
2574899 TTAAATATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
37 12 0.22
38 15 0.28
39 22 0.41
40 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (40 bp):
TATAATATAAATATAATAAATATTTAAAAAATAATATTAA
Found at i:2575946 original size:24 final size:26
Alignment explanation
Indices: 2575922--2576018 Score: 81
Period size: 28 Copynumber: 3.5 Consensus size: 26
2575912 ATAAAAATTA
* *
2575922 AATATAATATACATAAAAAAATTAAAATTT
1 AATATAATAT--AT-AAAATATT-AAATAT
2575952 A-TATAA-ATATAAAATATTTTAAATAT
1 AATATAATATATAAAATA--TTAAATAT
2575978 AATTATAATATATAAAATATATAAATAT
1 AA-TATAATATATAAAATAT-TAAATAT
2576006 AATATAAATATAT
1 AATAT-AATATAT
2576019 TACCTTATTT
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
25 5 0.09
26 8 0.14
27 6 0.10
28 23 0.40
29 15 0.26
30 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (26 bp):
AATATAATATATAAAATATTAAATAT
Found at i:2575989 original size:11 final size:11
Alignment explanation
Indices: 2575891--2576017 Score: 58
Period size: 11 Copynumber: 11.8 Consensus size: 11
2575881 TTGTATTTCA
2575891 ATAACATATAAT
1 ATAA-ATATAAT
2575903 -TAAAATATAAT
1 AT-AAATATAAT
*
2575914 AAAAAT-TAA-
1 ATAAATATAAT
2575923 ATATAATATACAT
1 ATA-AATATA-AT
2575936 A-AAA-A-AAT
1 ATAAATATAAT
*
2575944 -TAAA-ATTTAT
1 ATAAATA-TAAT
*
2575954 ATAAATATAAA
1 ATAAATATAAT
* *
2575965 AT-ATTTTAAAT
1 ATAAATAT-AAT
*
2575976 ATAATTATAAT
1 ATAAATATAAT
*
2575987 ATATAAAAT-AT
1 ATA-AATATAAT
2575998 ATAAATATAAT
1 ATAAATATAAT
2576009 ATAAATATA
1 ATAAATATA
2576018 TTACCTTATT
Statistics
Matches: 88, Mismatches: 12, Indels: 31
0.67 0.09 0.24
Matches are distributed among these distances:
8 6 0.07
9 3 0.03
10 16 0.18
11 50 0.57
12 12 0.14
13 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:2577289 original size:2 final size:2
Alignment explanation
Indices: 2577282--2577314 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2577272 TGTGCTAATC
2577282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2577315 CACATTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2582453 original size:19 final size:19
Alignment explanation
Indices: 2582429--2582467 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2582419 CACCGCTGAC
2582429 TTCATTTTATTTCACCTTT
1 TTCATTTTATTTCACCTTT
2582448 TTCATTTTATTTCACCTTT
1 TTCATTTTATTTCACCTTT
2582467 T
1 T
2582468 CTTATTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (19 bp):
TTCATTTTATTTCACCTTT
Found at i:2588463 original size:13 final size:14
Alignment explanation
Indices: 2588430--2588490 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
2588420 TGTTGAGTTA
*
2588430 TAAAAAATTTAAGTT
1 TAAAAAATATAA-TT
2588445 TAAAAAA-ATATATT
1 TAAAAAATATA-ATT
*
2588459 TAAAAAATATGA-T
1 TAAAAAATATAATT
*
2588472 GAAAAATATATAATT
1 TAAAAA-ATATAATT
2588487 TAAA
1 TAAA
2588491 TTTTTTAAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 6 0.16
14 17 0.46
15 14 0.38
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (14 bp):
TAAAAAATATAATT
Found at i:2590748 original size:2 final size:2
Alignment explanation
Indices: 2590686--2590736 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2590676 GCAACCCAAC
*
2590686 GA GA GA GA GC GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2590728 GA GA GA GA G
1 GA GA GA GA G
2590737 GGGGGAAGAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.02, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2596303 original size:2 final size:2
Alignment explanation
Indices: 2596296--2596321 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2596286 AACTGTAGTA
2596296 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2596322 TAAACATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2611278 original size:3 final size:3
Alignment explanation
Indices: 2611270--2611301 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2611260 AAAGGTTGTT
2611270 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2611302 TTTCTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2611712 original size:16 final size:16
Alignment explanation
Indices: 2611673--2611715 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2611663 TTATATTTTG
2611673 AAATTATTATTATAAAT
1 AAATT-TTATTATAAAT
** *
2611690 ATTTTTTATTATTAAT
1 AAATTTTATTATAAAT
2611706 AAATTTTATT
1 AAATTTTATT
2611716 TAATTTATAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATTTTATTATAAAT
Found at i:2611723 original size:22 final size:20
Alignment explanation
Indices: 2611676--2611717 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
2611666 TATTTTGAAA
2611676 TTATTATT-ATAAATATTT-T
1 TTATTATTAATAAAT-TTTAT
2611695 TTATTATTAATAAATTTTAT
1 TTATTATTAATAAATTTTAT
2611715 TTA
1 TTA
2611718 ATTTATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTATTAATAAATTTTAT
Found at i:2611736 original size:18 final size:18
Alignment explanation
Indices: 2611682--2611736 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
2611672 GAAATTATTA
2611682 TTATAAATATTTTTTATTAT
1 TTATAAATATTTTTTA--AT
*
2611702 TAATAAAT-TTTATTTAAT
1 TTATAAATATTT-TTTAAT
*
2611720 TTATAAATAATTTTTAA
1 TTATAAATATTTTTTAA
2611737 AGTAATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 14 0.47
19 5 0.17
20 11 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATAAATATTTTTTAAT
Found at i:2611998 original size:18 final size:18
Alignment explanation
Indices: 2611952--2611999 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
2611942 AATTTTGTAA
2611952 AAAAAAAGTATT--AAAAT
1 AAAAAAA-TATTAAAAAAT
*
2611969 AAAAAACT-TTAAAAAAT
1 AAAAAAATATTAAAAAAT
2611986 AAAAAAATATTAAA
1 AAAAAAATATTAAA
2612000 TACCCATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.08
16 1 0.04
17 18 0.69
18 5 0.19
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
AAAAAAATATTAAAAAAT
Found at i:2612268 original size:29 final size:28
Alignment explanation
Indices: 2612228--2612288 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
2612218 GAAGTATTAT
2612228 TATT-ATTTAAATAAATTACGAAAATAA
1 TATTAATTTAAATAAATTACGAAAATAA
** *
2612255 TATTAATTTAAAATAAATTATTAAAATAT
1 TATTAATTT-AAATAAATTACGAAAATAA
2612284 TATTA
1 TATTA
2612289 TTTTGATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 4 0.14
28 4 0.14
29 21 0.72
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
TATTAATTTAAATAAATTACGAAAATAA
Found at i:2612278 original size:13 final size:13
Alignment explanation
Indices: 2612229--2612282 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
2612219 AAGTATTATT
*
2612229 ATTATTTAAATAA
1 ATTATTAAAATAA
**
2612242 ATTACGAAAATAA
1 ATTATTAAAATAA
2612255 TATTAATTTAAAATAA
1 -ATT-A-TTAAAATAA
2612271 ATTATTAAAATA
1 ATTATTAAAATA
2612283 TTATTATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
13 18 0.55
14 4 0.12
15 4 0.12
16 7 0.21
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
ATTATTAAAATAA
Found at i:2612435 original size:26 final size:24
Alignment explanation
Indices: 2612409--2612457 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
2612399 AATATTATTA
*
2612409 AATT-TATTATTTTATTTGAATTTTT
1 AATTATATTATTATA-TT-AATTTTT
2612434 AATTATATTATTATATTAATTTTT
1 AATTATATTATTATATTAATTTTT
2612458 TCAGTCAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
AATTATATTATTATATTAATTTTT
Found at i:2616775 original size:16 final size:16
Alignment explanation
Indices: 2616754--2616787 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2616744 TTTCGGCCAA
2616754 CTCTATCTCATTCTTG
1 CTCTATCTCATTCTTG
*
2616770 CTCTATCTCGTTCTTG
1 CTCTATCTCATTCTTG
2616786 CT
1 CT
2616788 TTGTTATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.32, G:0.09, T:0.50
Consensus pattern (16 bp):
CTCTATCTCATTCTTG
Found at i:2622012 original size:22 final size:22
Alignment explanation
Indices: 2621993--2622048 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
2621983 AAAAATTATT
2621993 ATATTTTTAAATTATTATTATAA
1 ATATTTTT-AATTATTATTATAA
*
2622016 ATATTTTTTATTATTA--ATAA
1 ATATTTTTAATTATTATTATAA
*
2622036 ATTTTATTTAATT
1 ATATT-TTTAATT
2622049 TATAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 8 0.28
21 6 0.21
22 7 0.24
23 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTTTTAATTATTATTATAA
Found at i:2622026 original size:19 final size:20
Alignment explanation
Indices: 2622004--2622056 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2621994 TATTTTTAAA
2622004 TTATTATTATAAATATTT-T
1 TTATTATTATAAATATTTAT
2622023 TTATTATTAATAAAT-TTTAT
1 TTATTATT-ATAAATATTTAT
*
2622043 TTAAT-TTATAAATA
1 TTATTATTATAAATA
2622057 AATTTAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.20
19 13 0.43
20 11 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTATTATAAATATTTAT
Found at i:2622040 original size:16 final size:16
Alignment explanation
Indices: 2622000--2622043 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2621990 ATTATATTTT
2622000 TAAATTATTATTATAAA
1 TAAATT-TTATTATAAA
** *
2622017 TATTTTTTATTATTAA
1 TAAATTTTATTATAAA
2622033 TAAATTTTATT
1 TAAATTTTATT
2622044 TAATTTATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAAATTTTATTATAAA
Found at i:2622051 original size:22 final size:19
Alignment explanation
Indices: 2622004--2622061 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 19
2621994 TATTTTTAAA
2622004 TTATTATT-ATAAATATTTT
1 TTATTATTAATAAAT-TTTT
2622023 TTATTATTAATAAATTTTAT
1 TTATTATTAATAAATTTT-T
*
2622043 TTAATTTATAAATAAATTT
1 TT-A-TTATTAATAAATTT
2622062 AAAAAGTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 11 0.32
20 9 0.26
21 1 0.03
22 13 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTATTAATAAATTTTT
Found at i:2622053 original size:18 final size:19
Alignment explanation
Indices: 2622010--2622056 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2622000 TAAATTATTA
2622010 TTATAAATATTTTTTATTAT
1 TTATAAATATTTTTTA-TAT
*
2622030 TAATAAAT-TTTATTTA-AT
1 TTATAAATATTT-TTTATAT
2622048 TTATAAATA
1 TTATAAATA
2622057 AATTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 9 0.39
19 3 0.13
20 11 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATAAATATTTTTTATAT
Found at i:2622573 original size:13 final size:13
Alignment explanation
Indices: 2622550--2622603 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
2622540 AAGCATTATT
*
2622550 ATTATTTAAATAA
1 ATTATTAAAATAA
*
2622563 ATTATGAAAATAA
1 ATTATTAAAATAA
*
2622576 TGTTAATTTAAAATAA
1 -ATT-A-TTAAAATAA
2622592 ATTATTAAAATA
1 ATTATTAAAATA
2622604 TTATTATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
13 19 0.58
14 3 0.09
15 3 0.09
16 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (13 bp):
ATTATTAAAATAA
Found at i:2622850 original size:22 final size:22
Alignment explanation
Indices: 2622825--2622885 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
2622815 TAAATGGGTC
2622825 AATTAATTTAATAATTTTTTAA
1 AATTAATTTAATAATTTTTTAA
** **
2622847 AATTAAAATAATAATATTTTTTT
1 AATTAATTTAATAAT-TTTTTAA
* *
2622870 AATTTATTTAAAAATT
1 AATTAATTTAATAATT
2622886 AAAGATATTT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTAATTTAATAATTTTTTAA
Found at i:2627104 original size:16 final size:16
Alignment explanation
Indices: 2627083--2627116 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2627073 TTTCGGCCAA
2627083 CTCTATCTCATTCTTG
1 CTCTATCTCATTCTTG
*
2627099 CTCTATCTCGTTCTTG
1 CTCTATCTCATTCTTG
2627115 CT
1 CT
2627117 TTGTTATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.32, G:0.09, T:0.50
Consensus pattern (16 bp):
CTCTATCTCATTCTTG
Found at i:2631985 original size:3 final size:3
Alignment explanation
Indices: 2631977--2632008 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2631967 AAAGGTTGTT
2631977 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2632009 TTTCTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2632419 original size:16 final size:16
Alignment explanation
Indices: 2632380--2632422 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2632370 TTATATTTTG
2632380 AAATTATTATTATAAAT
1 AAATT-TTATTATAAAT
** *
2632397 ATTTTTTATTATTAAT
1 AAATTTTATTATAAAT
2632413 AAATTTTATT
1 AAATTTTATT
2632423 TAATTTATAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATTTTATTATAAAT
Found at i:2632430 original size:22 final size:20
Alignment explanation
Indices: 2632383--2632424 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
2632373 TATTTTGAAA
2632383 TTATTATT-ATAAATATTT-T
1 TTATTATTAATAAAT-TTTAT
2632402 TTATTATTAATAAATTTTAT
1 TTATTATTAATAAATTTTAT
2632422 TTA
1 TTA
2632425 ATTTATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTATTAATAAATTTTAT
Found at i:2632443 original size:18 final size:18
Alignment explanation
Indices: 2632389--2632443 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
2632379 GAAATTATTA
2632389 TTATAAATATTTTTTATTAT
1 TTATAAATATTTTTTA--AT
*
2632409 TAATAAAT-TTTATTTAAT
1 TTATAAATATTT-TTTAAT
*
2632427 TTATAAATAATTTTTAA
1 TTATAAATATTTTTTAA
2632444 AGTAATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 14 0.47
19 5 0.17
20 11 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATAAATATTTTTTAAT
Found at i:2632705 original size:18 final size:18
Alignment explanation
Indices: 2632659--2632706 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
2632649 AATTTTGTAA
2632659 AAAAAAAGTATT--AAAAT
1 AAAAAAA-TATTAAAAAAT
*
2632676 AAAAAACT-TTAAAAAAT
1 AAAAAAATATTAAAAAAT
2632693 AAAAAAATATTAAA
1 AAAAAAATATTAAA
2632707 TACCCATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.08
16 1 0.04
17 18 0.69
18 5 0.19
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
AAAAAAATATTAAAAAAT
Found at i:2632975 original size:29 final size:28
Alignment explanation
Indices: 2632935--2632995 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
2632925 GAAGTATTAT
2632935 TATT-ATTTAAATAAATTACGAAAATAA
1 TATTAATTTAAATAAATTACGAAAATAA
** *
2632962 TATTAATTTAAAATAAATTATTAAAATAT
1 TATTAATTT-AAATAAATTACGAAAATAA
2632991 TATTA
1 TATTA
2632996 TTTTGATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 4 0.14
28 4 0.14
29 21 0.72
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
TATTAATTTAAATAAATTACGAAAATAA
Found at i:2632985 original size:13 final size:13
Alignment explanation
Indices: 2632936--2632989 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
2632926 AAGTATTATT
*
2632936 ATTATTTAAATAA
1 ATTATTAAAATAA
**
2632949 ATTACGAAAATAA
1 ATTATTAAAATAA
2632962 TATTAATTTAAAATAA
1 -ATT-A-TTAAAATAA
2632978 ATTATTAAAATA
1 ATTATTAAAATA
2632990 TTATTATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
13 18 0.55
14 4 0.12
15 4 0.12
16 7 0.21
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
ATTATTAAAATAA
Found at i:2633142 original size:26 final size:24
Alignment explanation
Indices: 2633116--2633164 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
2633106 AATATTATTA
*
2633116 AATT-TATTATTTTATTTGAATTTTT
1 AATTATATTATTATA-TT-AATTTTT
2633141 AATTATATTATTATATTAATTTTT
1 AATTATATTATTATATTAATTTTT
2633165 TCAGTCAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
AATTATATTATTATATTAATTTTT
Found at i:2642896 original size:30 final size:30
Alignment explanation
Indices: 2642855--2642920 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 30
2642845 TAATTATTTT
2642855 TTTTTTGTCAAACT-TTAATGAGGTAAGTA-A
1 TTTTTTGTCAAA-TGTT-ATGAGGTAAGTATA
2642885 TTATTTT-TCAAATGTTATGAGGTAAGTATA
1 TT-TTTTGTCAAATGTTATGAGGTAAGTATA
2642915 TTTTTT
1 TTTTTT
2642921 ATAAAGATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
29 17 0.52
30 12 0.36
31 4 0.12
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (30 bp):
TTTTTTGTCAAATGTTATGAGGTAAGTATA
Found at i:2642920 original size:62 final size:61
Alignment explanation
Indices: 2642783--2642920 Score: 163
Period size: 61 Copynumber: 2.3 Consensus size: 61
2642773 TAGCTTAAGG
* * *
2642783 GATAAGTGTA-TTTTTTTGTCAAACTTTAAAAGAGTAAGTGATTATTTTGAAATGTTAAAA
1 GATAAGTATATTTTTTTTGTCAAACTTTAAAAGAGTAAGTAATTATTTTCAAATGTTAAAA
* * * **
2642843 GATAATTATTTTTTTTTTGTCAAACTTT-AATGAGGTAAGTAATTATTTTTCAAATGTTATGA
1 GATAAGTATATTTTTTTTGTCAAACTTTAAAAGA-GTAAGTAATTA-TTTTCAAATGTTAAAA
*
2642905 GGTAAGTATATTTTTT
1 GATAAGTATATTTTTT
2642921 ATAAAGATTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
60 11 0.17
61 27 0.42
62 26 0.41
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (61 bp):
GATAAGTATATTTTTTTTGTCAAACTTTAAAAGAGTAAGTAATTATTTTCAAATGTTAAAA
Found at i:2643905 original size:20 final size:21
Alignment explanation
Indices: 2643866--2643906 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2643856 TAGTTTATTT
* *
2643866 ATTATATTTTCATGTATTATA
1 ATTATATTTTAATATATTATA
2643887 ATTATA-TTTAATATATTATA
1 ATTATATTTTAATATATTATA
2643907 TTTTAATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTATATTTTAATATATTATA
Found at i:2643906 original size:14 final size:16
Alignment explanation
Indices: 2643887--2643922 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2643877 ATGTATTATA
2643887 ATTATA-TTTAATAT-
1 ATTATATTTTAATATG
2643901 ATTATATTTTAATATG
1 ATTATATTTTAATATG
2643917 ATTATA
1 ATTATA
2643923 CAATTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 8 0.40
16 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
ATTATATTTTAATATG
Found at i:2651676 original size:2 final size:2
Alignment explanation
Indices: 2651669--2651706 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2651659 CCATTTCCCC
2651669 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2651707 GTATATATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2652493 original size:2 final size:2
Alignment explanation
Indices: 2652477--2652516 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2652467 TGTAAGAAAA
*
2652477 AT AT AT AC AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2652517 CTGAAATCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2652672 original size:23 final size:23
Alignment explanation
Indices: 2652645--2652688 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2652635 ATATTTTATA
*
2652645 TTAAATA-TAATAATTAAAATTTT
1 TTAAATATTAA-AAATAAAATTTT
2652668 TTAAATATTAAAAATAAAATT
1 TTAAATATTAAAAATAAAATT
2652689 AATTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAAATATTAAAAATAAAATTTT
Found at i:2652692 original size:27 final size:29
Alignment explanation
Indices: 2652642--2652703 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
2652632 AGTATATTTT
* *
2652642 ATATTAAATATAATAATTAAAATTTTTTAA
1 ATATTAAAAATAATAATT-AAATTATTTAA
*
2652672 ATATTAAAAATAA-AATT-AATTATTTAT
1 ATATTAAAAATAATAATTAAATTATTTAA
2652699 ATATT
1 ATATT
2652704 TATATTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 13 0.45
29 4 0.14
30 12 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATATTAAAAATAATAATTAAATTATTTAA
Found at i:2652796 original size:18 final size:18
Alignment explanation
Indices: 2652773--2652812 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2652763 AATATTATTA
*
2652773 AATTTAATTAA-AAATCAT
1 AATTT-ATTAATAAATAAT
2652791 AATTTATTAATAAATAAT
1 AATTTATTAATAAATAAT
2652809 AATT
1 AATT
2652813 AATAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTTATTAATAAATAAT
Found at i:2653199 original size:3 final size:3
Alignment explanation
Indices: 2653191--2653216 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2653181 ATCTTAACAA
2653191 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2653217 ATTGCTTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2653331 original size:16 final size:16
Alignment explanation
Indices: 2653312--2653342 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2653302 TATCTTTACT
*
2653312 AATAATTTAATTTAAA
1 AATAATTAAATTTAAA
2653328 AATAATTAAATTTAA
1 AATAATTAAATTTAA
2653343 TAATTTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTAAATTTAAA
Found at i:2653633 original size:2 final size:2
Alignment explanation
Indices: 2653626--2653654 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2653616 TTTAAGCAAC
2653626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2653655 CATGTGTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2661369 original size:17 final size:16
Alignment explanation
Indices: 2661343--2661382 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
2661333 TTTTTTTAAA
2661343 ATTAATTAAAAATAAT
1 ATTAATTAAAAATAAT
*
2661359 ATTATATTAAATATAAT
1 ATTA-ATTAAAAATAAT
2661376 AATTAAT
1 -ATTAAT
2661383 AATTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 13 0.62
18 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTAATTAAAAATAAT
Found at i:2661743 original size:20 final size:20
Alignment explanation
Indices: 2661704--2661743 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2661694 TTTTTTATTT
*
2661704 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
2661724 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
2661744 TATAAATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:2661785 original size:15 final size:14
Alignment explanation
Indices: 2661754--2661789 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
2661744 TATAAATGAT
2661754 TTTATATTATATTTA
1 TTTA-ATTATATTTA
2661769 TTTAATTATATTATA
1 TTTAATTATATT-TA
2661784 TTTAAT
1 TTTAAT
2661790 ATTATTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTAATTATATTTA
Found at i:2661792 original size:31 final size:31
Alignment explanation
Indices: 2661697--2661794 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 31
2661687 AATAAATTTT
2661697 TTTATTTATATTATAATTATATTTAAAATATTATATA
1 TTTATTTA-ATTAT-ATTATATTT--AATA-T-TATA
* * * *
2661734 TTTATATAAATATA-AATGATTTTATATTATA
1 TTTATTTAATTATATTAT-ATTTAATATTATA
2661765 TTTATTTAATTATATTATATTTAATATTAT
1 TTTATTTAATTATATTATATTTAATATTAT
2661795 TAAGTTTATT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
31 27 0.53
32 3 0.06
33 3 0.06
34 2 0.04
35 5 0.10
36 4 0.08
37 7 0.14
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (31 bp):
TTTATTTAATTATATTATATTTAATATTATA
Found at i:2662145 original size:3 final size:3
Alignment explanation
Indices: 2662137--2662168 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2662127 ATATTAATAT
*
2662137 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2662169 GGGATGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2669189 original size:22 final size:22
Alignment explanation
Indices: 2669164--2669207 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2669154 TTTATATGTA
2669164 TGTTGATATTGTATCTTTTACT
1 TGTTGATATTGTATCTTTTACT
2669186 TGTTGATATTGTATCTTTTACT
1 TGTTGATATTGTATCTTTTACT
2669208 ACGAAACAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.14, T:0.59
Consensus pattern (22 bp):
TGTTGATATTGTATCTTTTACT
Done.