Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold89
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: 5168001
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 33045 characters in sequence are not A, C, G, or T
File 22 of 27
Found at i:3686171 original size:19 final size:20
Alignment explanation
Indices: 3686133--3686172 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
3686123 AATTAGTTTG
3686133 ATATAAATTATTATTTATTA
1 ATATAAATTATTATTTATTA
3686153 ATATAAA-TA-TATGTTATTA
1 ATATAAATTATTAT-TTATTA
3686172 A
1 A
3686173 AATTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.16
19 9 0.47
20 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATAAATTATTATTTATTA
Found at i:3686653 original size:47 final size:47
Alignment explanation
Indices: 3686599--3686691 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
3686589 TAAAAACCAA
*
3686599 TTGTTGAAGTATTTATTCCAAGTTATGTGTACACATTATATATAATG
1 TTGTTGAAGTATTTATTCCAAGTCATGTGTACACATTATATATAATG
3686646 TTGTTGAAGTATTTATTCCAAGTCATGTGTACACATTATATATAAT
1 TTGTTGAAGTATTTATTCCAAGTCATGTGTACACATTATATATAAT
3686692 ATAATGTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (47 bp):
TTGTTGAAGTATTTATTCCAAGTCATGTGTACACATTATATATAATG
Found at i:3687940 original size:21 final size:23
Alignment explanation
Indices: 3687900--3687941 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3687890 AAAAAATTAA
*
3687900 AAATATTTATATCTTTGATATAT
1 AAATATTTATAGCTTTGATATAT
3687923 AAATATTTAT-GC-TTGATAT
1 AAATATTTATAGCTTTGATAT
3687942 TAACTCGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (23 bp):
AAATATTTATAGCTTTGATATAT
Found at i:3688836 original size:21 final size:22
Alignment explanation
Indices: 3688810--3688868 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
3688800 AAATTATTAT
3688810 TTAATAATAAAAAT-TTTAATA
1 TTAATAATAAAAATATTTAATA
3688831 TTAAT-ATAAAATTATAGTTTAATA
1 TTAATAATAAAA--ATA-TTTAATA
*
3688855 ATATATAATAAAAA
1 TTA-ATAATAAAAA
3688869 ATTAAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
20 6 0.19
21 5 0.16
22 2 0.06
24 10 0.32
25 2 0.06
26 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TTAATAATAAAAATATTTAATA
Found at i:3696240 original size:21 final size:22
Alignment explanation
Indices: 3696204--3696252 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
3696194 AAAATAAATT
*
3696204 TTTAAAAAATTTTA-TTT-TTA
1 TTTAAAAAATTATATTTTATTA
3696224 TTTAAAAAATTAATATTTTATTA
1 TTTAAAAAATT-ATATTTTATTA
3696247 TTTAAA
1 TTTAAA
3696253 TTAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 11 0.44
21 2 0.08
22 3 0.12
23 9 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAAAAAATTATATTTTATTA
Found at i:3700462 original size:17 final size:17
Alignment explanation
Indices: 3700431--3700464 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3700421 GCTCGTGCTT
*
3700431 TTTCTTTTTGGTTTTTG
1 TTTCTTTTTAGTTTTTG
*
3700448 TTTCTTTTTATTTTTTG
1 TTTCTTTTTAGTTTTTG
3700465 GGATTAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.06, G:0.12, T:0.79
Consensus pattern (17 bp):
TTTCTTTTTAGTTTTTG
Found at i:3706337 original size:11 final size:11
Alignment explanation
Indices: 3706321--3706364 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
3706311 CATTCGTATT
3706321 ATTATATTATA
1 ATTATATTATA
*
3706332 ATTATATTATT
1 ATTATATTATA
*
3706343 TTTATATTATA
1 ATTATATTATA
3706354 ATTATA-TATA
1 ATTATATTATA
3706364 A
1 A
3706365 AATAATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 5 0.17
11 24 0.83
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTATATTATA
Found at i:3706347 original size:22 final size:22
Alignment explanation
Indices: 3706317--3706360 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3706307 ATTTCATTCG
3706317 TATTATTATATTATAATTATAT
1 TATTATTATATTATAATTATAT
*
3706339 TATTTTTATATTATAATTATAT
1 TATTATTATATTATAATTATAT
3706361 ATAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTATTATATTATAATTATAT
Found at i:3706392 original size:20 final size:21
Alignment explanation
Indices: 3706369--3706409 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3706359 ATATAAAATA
*
3706369 ATATATTTAA-ATAAATTTTT
1 ATATATGTAACATAAATTTTT
*
3706389 ATATATGTAACATAGATTTTT
1 ATATATGTAACATAAATTTTT
3706410 TTATGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
ATATATGTAACATAAATTTTT
Found at i:3707032 original size:28 final size:28
Alignment explanation
Indices: 3706972--3707052 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
3706962 TTTATATAAA
**
3706972 ATAAGAATTTATTTAAAT-TAAATCCAATG
1 ATAA-AATTTATTTAAATAT-AATAAAATG
*
3707001 ATAAAATTTATTTAAATATAATAAAATT
1 ATAAAATTTATTTAAATATAATAAAATG
*
3707029 ATAAAATTTCATTAAAAATATAAT
1 ATAAAATTT-ATT-TAAATATAAT
3707053 TTCTTTTGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
28 28 0.62
29 8 0.18
30 9 0.20
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (28 bp):
ATAAAATTTATTTAAATATAATAAAATG
Found at i:3708960 original size:78 final size:78
Alignment explanation
Indices: 3708873--3709551 Score: 676
Period size: 78 Copynumber: 8.7 Consensus size: 78
3708863 ATTAATATCG
** * * * * *
3708873 TGGTGGCGATTGGGATCATGGTGCTATGGTGGCGAGCAGGGTCGGAGTGACTTGGTATCGCTGAC
1 TGGTGGCGATCAGGATCATGGTGCCATGGTGGCTAGCAGGATCGGAGTGACTTGGTGTCACTGAC
*
3708938 AGTATTGATGCCG
66 AGTATTGATGCCA
* * ** * * * * *
3708951 TGGTGGCGATCAAGATCGTAATGCCAGGGTGGCTAGCAAGATCGGAGTGCCATGGTGTCACTGAT
1 TGGTGGCGATCAGGATCATGGTGCCATGGTGGCTAGCAGGATCGGAGTGACTTGGTGTCACTGAC
*
3709016 AGTATTGATGCCT
66 AGTATTGATGCCA
* ** * * * * *
3709029 TGGTAGCGATCAGGATCATAATGACATGATGGCTAACAGGATCGAAGTG-CTATGGTGTCATTGA
1 TGGTGGCGATCAGGATCATGGTGCCATGGTGGCTAGCAGGATCGGAGTGACT-TGGTGTCACTGA
3709093 CAGTATTGATGCCA
65 CAGTATTGATGCCA
* * * * * * *
3709107 TGGTGACGATTAGGATCGTGGAGCCATGGTGGCGAGCAGGATTGGATTGACTTGGTGTCACTGAC
1 TGGTGGCGATCAGGATCATGGTGCCATGGTGGCTAGCAGGATCGGAGTGACTTGGTGTCACTGAC
* *
3709172 AATACTGATGCCA
66 AGTATTGATGCCA
* * *
3709185 TGGTGGCGATCAAGATCATGGTGACATGGTGGCTAGCAGGATCGGAAGTGACTTGGTATCACTGA
1 TGGTGGCGATCAGGATCATGGTGCCATGGTGGCTAGCAGGATCGG-AGTGACTTGGTGTCACTGA
3709250 CAGTATTGATGCCA
65 CAGTATTGATGCCA
* * * * *
3709264 TGGTGGCGATCATGATCATAGTGCCATGGTGACTAACAGGATCGGAGTGACTTGGTGCCACTGAC
1 TGGTGGCGATCAGGATCATGGTGCCATGGTGGCTAGCAGGATCGGAGTGACTTGGTGTCACTGAC
*
3709329 AGTATTGATGCCG
66 AGTATTGATGCCA
* * * * ** * * * *
3709342 TGGTGGCAATCAGGATGATAGTACCATGGTGGCTAATAGGATCGAAGTGCCATGGTGTCATTGAC
1 TGGTGGCGATCAGGATCATGGTGCCATGGTGGCTAGCAGGATCGGAGTGACTTGGTGTCACTGAC
* *
3709407 AGTAGTGATGCTA
66 AGTATTGATGCCA
* * * * * * * *
3709420 TGGTGGCGATCAGGATCGTGATGCCATAGTGGCGAGCAGGTTCAGAGTGCCATGGTGTCACTGAC
1 TGGTGGCGATCAGGATCATGGTGCCATGGTGGCTAGCAGGATCGGAGTGACTTGGTGTCACTGAC
* *
3709485 AGTAGTGATGCTA
66 AGTATTGATGCCA
** * * * * *
3709498 TGGTGGCGATCAGGATTGTGGTGCTATAGTGACGAGCAGGATCAGAGTGACTTG
1 TGGTGGCGATCAGGATCATGGTGCCATGGTGGCTAGCAGGATCGGAGTGACTTG
3709552 AATCGAGACA
Statistics
Matches: 496, Mismatches: 102, Indels: 6
0.82 0.17 0.01
Matches are distributed among these distances:
77 1 0.00
78 424 0.85
79 71 0.14
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.26
Consensus pattern (78 bp):
TGGTGGCGATCAGGATCATGGTGCCATGGTGGCTAGCAGGATCGGAGTGACTTGGTGTCACTGAC
AGTATTGATGCCA
Found at i:3709001 original size:26 final size:26
Alignment explanation
Indices: 3708952--3709007 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
3708942 TTGATGCCGT
* *
3708952 GGTGGCGATCAAGATCGTAATGCCAG
1 GGTGGCGAGCAAGATCGGAATGCCAG
* * *
3708978 GGTGGCTAGCAAGATCGGAGTGCCAT
1 GGTGGCGAGCAAGATCGGAATGCCAG
3709004 GGTG
1 GGTG
3709008 TCACTGATAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.18, G:0.39, T:0.20
Consensus pattern (26 bp):
GGTGGCGAGCAAGATCGGAATGCCAG
Found at i:3709312 original size:26 final size:25
Alignment explanation
Indices: 3709283--3709398 Score: 56
Period size: 26 Copynumber: 4.5 Consensus size: 25
3709273 TCATGATCAT
3709283 AGTGCCATGGTGACTAACAGGATCGG
1 AGTGCCATGGTGACTAACAGGAT-GG
* * * * *
3709309 AGTGACTTGGTGCCACTGACAGTATTG
1 AGTGCCATGGTG--ACTAACAGGATGG
* * *
3709336 A-TGCCGTGGTGGC-AATCAGGATGAT
1 AGTGCCATGGTGACTAA-CAGGATG-G
* * * *
3709361 AGTACCATGGTGGCTAATAGGATCGA
1 AGTGCCATGGTGACTAACAGGAT-GG
3709387 AGTGCCATGGTG
1 AGTGCCATGGTG
3709399 TCATTGACAG
Statistics
Matches: 66, Mismatches: 17, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
23 1 0.02
24 6 0.09
25 1 0.02
26 44 0.67
27 5 0.08
28 9 0.14
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.24
Consensus pattern (25 bp):
AGTGCCATGGTGACTAACAGGATGG
Found at i:3709440 original size:26 final size:26
Alignment explanation
Indices: 3709411--3709540 Score: 79
Period size: 26 Copynumber: 5.0 Consensus size: 26
3709401 ATTGACAGTA
3709411 GTGATGCTATGGTGGCGATCAGGATC
1 GTGATGCTATGGTGGCGATCAGGATC
* * * *
3709437 GTGATGCCATAGTGGCGAGCAGGTTC
1 GTGATGCTATGGTGGCGATCAGGATC
* * * *
3709463 -AGAGTGCCATGGTGTC-ACTGACA-G-TA
1 GTGA-TGCTATGGTGGCGA-T--CAGGATC
*
3709489 GTGATGCTATGGTGGCGATCAGGATT
1 GTGATGCTATGGTGGCGATCAGGATC
* * * *
3709515 GTGGTGCTATAGTGACGAGCAGGATC
1 GTGATGCTATGGTGGCGATCAGGATC
3709541 AGAGTGACTT
Statistics
Matches: 78, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
24 2 0.03
25 4 0.05
26 66 0.85
27 4 0.05
28 2 0.03
ACGTcount: A:0.22, C:0.16, G:0.37, T:0.25
Consensus pattern (26 bp):
GTGATGCTATGGTGGCGATCAGGATC
Found at i:3709503 original size:313 final size:312
Alignment explanation
Indices: 3708886--3709551 Score: 890
Period size: 313 Copynumber: 2.1 Consensus size: 312
3708876 TGGCGATTGG
* * *
3708886 GATCATGGTGCTATGGTGGCGAGCAGGGTCGGAGTGACTTGGTATCGCTGACAGTATTGATGCCG
1 GATCATGGTGCTATGGTGGCGAGCAGGATCGGAGTGACTTGGTATCACTGACAGTATTGATGCCA
* * * * * *
3708951 TGGTGGCGATCAAGATCGTAATGCCAGGGTGGCTAGCAAGATCGGAGTGCCATGGTGTCACTGAT
66 TGGTGGCGATCAAGATCATAATGCCAGGGTGACTAACAAGATCGGAGTGACATGGTGCCACTGAC
* * *
3709016 AGTATTGATGCCTTGGTAGCGATCAGGATCATAATGACATGATGGCTAACAGGATCGAAGTGCTA
131 AGTATTGATGCCGTGGTAGCAATCAGGATCATAATGACATGATGGCTAACAGGATCGAAGTGCCA
* * *
3709081 TGGTGTCATTGACAGTATTGATGCCATGGTGACGATTAGGATCGTGGAGCCATGGTGGCGAGCAG
196 TGGTGTCATTGACAGTAGTGATGCCATGGTGACGATCAGGATCGTGGAGCCATAGTGGCGAGCAG
* * *
3709146 GATTGGATTGACTTGGTGTCACTGACAATACTGATGCCATGGTGGCGATCAA
261 GATTAGAGTGACATGGTGTCACTGACAATACTGATGCCATGGTGGCGATCAA
*
3709198 GATCATGGTGAC-ATGGTGGCTAGCAGGATCGGAAGTGACTTGGTATCACTGACAGTATTGATGC
1 GATCATGGTG-CTATGGTGGCGAGCAGGATCGG-AGTGACTTGGTATCACTGACAGTATTGATGC
* * * * *
3709262 CATGGTGGCGATCATGATCATAGTGCCATGGTGACTAACAGGATCGGAGTGACTTGGTGCCACTG
64 CATGGTGGCGATCAAGATCATAATGCCAGGGTGACTAACAAGATCGGAGTGACATGGTGCCACTG
* * * * *
3709327 ACAGTATTGATGCCGTGGTGGCAATCAGGATGATAGT-ACCATGGTGGCTAATAGGATCGAAGTG
129 ACAGTATTGATGCCGTGGTAGCAATCAGGATCATAATGA-CATGATGGCTAACAGGATCGAAGTG
* *
3709391 CCATGGTGTCATTGACAGTAGTGATGCTATGGTGGCGATCAGGATCGT-GATGCCATAGTGGCGA
193 CCATGGTGTCATTGACAGTAGTGATGCCATGGTGACGATCAGGATCGTGGA-GCCATAGTGGCGA
* * * * *
3709455 GCAGG-TTCAGAGTGCCATGGTGTCACTGACAGTAGTGATGCTATGGTGGCGATCAG
257 GCAGGATT-AGAGTGACATGGTGTCACTGACAATACTGATGCCATGGTGGCGATCAA
** * * *
3709511 GATTGTGGTGCTATAGTGACGAGCAGGATCAGAGTGACTTG
1 GATCATGGTGCTATGGTGGCGAGCAGGATCGGAGTGACTTG
3709552 AATCGAGACA
Statistics
Matches: 306, Mismatches: 42, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
312 43 0.14
313 263 0.86
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.26
Consensus pattern (312 bp):
GATCATGGTGCTATGGTGGCGAGCAGGATCGGAGTGACTTGGTATCACTGACAGTATTGATGCCA
TGGTGGCGATCAAGATCATAATGCCAGGGTGACTAACAAGATCGGAGTGACATGGTGCCACTGAC
AGTATTGATGCCGTGGTAGCAATCAGGATCATAATGACATGATGGCTAACAGGATCGAAGTGCCA
TGGTGTCATTGACAGTAGTGATGCCATGGTGACGATCAGGATCGTGGAGCCATAGTGGCGAGCAG
GATTAGAGTGACATGGTGTCACTGACAATACTGATGCCATGGTGGCGATCAA
Found at i:3711715 original size:29 final size:30
Alignment explanation
Indices: 3711670--3711733 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
3711660 AATTAACGTT
3711670 ATTTTAAAAATTAATTATTAAAATAATATC
1 ATTTTAAAAATTAATTATTAAAATAATATC
* * *
3711700 ATTTT-AAAA-TATATTATTTAAATATTATT
1 ATTTTAAAAATTA-ATTATTAAAATAATATC
3711729 ATTTT
1 ATTTT
3711734 TGTTAAGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 2 0.07
29 23 0.77
30 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTTAAAAATTAATTATTAAAATAATATC
Found at i:3711721 original size:14 final size:14
Alignment explanation
Indices: 3711683--3711732 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
3711673 TTAAAAATTA
3711683 ATTA-TTAAAATAAT
1 ATTATTTAAAAT-AT
*
3711697 ATCATTTTAAAATAT
1 ATTA-TTTAAAATAT
3711712 ATTATTT-AAATATT
1 ATTATTTAAAATA-T
3711726 ATTATTT
1 ATTATTT
3711733 TTGTTAAGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 14 0.45
15 5 0.16
16 7 0.23
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTATTTAAAATAT
Found at i:3711845 original size:15 final size:14
Alignment explanation
Indices: 3711827--3711875 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
3711817 AAAAATTTTA
3711827 TTTTTATTTTTGAT
1 TTTTTATTTTTGAT
*
3711841 ATTTTT-TTGTT-AT
1 -TTTTTATTTTTGAT
3711854 TTTTTATTTTTTGAT
1 TTTTTA-TTTTTGAT
3711869 TTTTTAT
1 TTTTTAT
3711876 AATTTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 5 0.17
13 2 0.07
14 9 0.31
15 13 0.45
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (14 bp):
TTTTTATTTTTGAT
Found at i:3711853 original size:20 final size:17
Alignment explanation
Indices: 3711821--3711865 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 17
3711811 TGTACCAAAA
3711821 ATTTTATTTTTATTTTTGAT
1 ATTTT-TTTTTATTTTT--T
3711841 ATTTTTTTGTTATTTTTT
1 ATTTTTTT-TTATTTTTT
3711859 ATTTTTT
1 ATTTTTT
3711866 GATTTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
19 3 0.12
20 13 0.54
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (17 bp):
ATTTTTTTTTATTTTTT
Found at i:3711862 original size:7 final size:7
Alignment explanation
Indices: 3711822--3711875 Score: 58
Period size: 7 Copynumber: 7.9 Consensus size: 7
3711812 GTACCAAAAA
3711822 TTTTA-T
1 TTTTATT
3711828 TTTTATT
1 TTTTATT
* *
3711835 TTTGATA
1 TTTTATT
3711842 TTTT-TT
1 TTTTATT
*
3711848 TGTTATT
1 TTTTATT
3711855 TTTTATT
1 TTTTATT
3711862 TTTTGATT
1 TTTT-ATT
3711870 TTTTAT
1 TTTTAT
3711876 AATTTTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
6 9 0.23
7 23 0.59
8 7 0.18
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.80
Consensus pattern (7 bp):
TTTTATT
Found at i:3711880 original size:18 final size:18
Alignment explanation
Indices: 3711827--3711883 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
3711817 AAAAATTTTA
* *
3711827 TTTTT-ATTTTTGATATT
1 TTTTTGATTTTTTATAAT
*
3711844 TTTTTG-TTATTTT-TTAT
1 TTTTTGATT-TTTTATAAT
3711861 TTTTTGATTTTTTATAAT
1 TTTTTGATTTTTTATAAT
3711879 TTTTT
1 TTTTT
3711884 ATAAATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
17 19 0.59
18 13 0.41
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTTTGATTTTTTATAAT
Found at i:3712262 original size:42 final size:43
Alignment explanation
Indices: 3712190--3712271 Score: 107
Period size: 42 Copynumber: 1.9 Consensus size: 43
3712180 GCTGGGTTGT
*
3712190 AATATTTATAAAATTTTTAATTAAAAAAA-TTATAATTAATAA
1 AATATTTATAAAATTTTTAATTAAAAAAATTTAAAATTAATAA
*
3712232 AATATATT-TAAAATTATTTAA-TAAATAAATTTAAAATTAA
1 AATAT-TTATAAAATT-TTTAATTAAAAAAATTTAAAATTAA
3712272 AATTTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
42 19 0.54
43 16 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (43 bp):
AATATTTATAAAATTTTTAATTAAAAAAATTTAAAATTAATAA
Found at i:3712263 original size:23 final size:25
Alignment explanation
Indices: 3712215--3712270 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 25
3712205 TTTAATTAAA
*
3712215 AAAATTATAATTAATAAAATATATTT
1 AAAATTAT-ATTAATAAAATAAATTT
3712241 AAAATTAT-TTAAT-AAATAAATTT
1 AAAATTATATTAATAAAATAAATTT
3712264 AAAATTA
1 AAAATTA
3712271 AAATTTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 16 0.55
24 5 0.17
26 8 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAATTATATTAATAAAATAAATTT
Found at i:3712270 original size:43 final size:42
Alignment explanation
Indices: 3712190--3712271 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 42
3712180 GCTGGGTTGT
*
3712190 AATATTTATAAAATTTTTAATTAAAAAAATTATAATTAATAA
1 AATATTTATAAAATTTTTAATTAAAAAAATTAAAATTAATAA
*
3712232 AATATATT-TAAAATTATTTAA-TAAATAAATTTAAAATTAA
1 AATAT-TTATAAAATT-TTTAATTAAA-AAAATTAAAATTAA
3712272 AATTTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
42 16 0.46
43 19 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (42 bp):
AATATTTATAAAATTTTTAATTAAAAAAATTAAAATTAATAA
Found at i:3712655 original size:8 final size:8
Alignment explanation
Indices: 3712637--3712694 Score: 55
Period size: 8 Copynumber: 6.9 Consensus size: 8
3712627 AATACATAAA
3712637 TTTTTTCTC
1 TTTTTT-TC
3712646 TTTTTTTC
1 TTTTTTTC
3712654 TTTCTTTTTTC
1 --T-TTTTTTC
3712665 TTTTTTTC
1 TTTTTTTC
*
3712673 -TCTTTTC
1 TTTTTTTC
*
3712680 TTTCTTTC
1 TTTTTTTC
3712688 TTTTTTT
1 TTTTTTT
3712695 TTCAGCCTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
7 6 0.15
8 20 0.49
9 7 0.17
10 1 0.02
11 7 0.17
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:3712678 original size:26 final size:25
Alignment explanation
Indices: 3712649--3712697 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
3712639 TTTTCTCTTT
*
3712649 TTTTCTTTCTTTTTTCTTTTTTTCTC
1 TTTTCTTTCTTTCTT-TTTTTTTCTC
3712675 TTTTCTTTCTTTCTTTTTTTTTC
1 TTTTCTTTCTTTCTTTTTTTTTC
3712698 AGCCTTGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTCTTTCTTTCTTTTTTTTTCTC
Found at i:3712684 original size:30 final size:29
Alignment explanation
Indices: 3712637--3712693 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 29
3712627 AATACATAAA
3712637 TTTTTTCTCTTTTTTTCTTTCTTTTTTCT
1 TTTTTTCTCTTTTTTTCTTTCTTTTTTCT
3712666 TTTTTTCTCTTTTCTTTCTTTCTTTTTT
1 TTTTTTCTCTTTT-TTTCTTTCTTTTTT
3712694 TTTCAGCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (29 bp):
TTTTTTCTCTTTTTTTCTTTCTTTTTTCT
Found at i:3712832 original size:18 final size:19
Alignment explanation
Indices: 3712809--3712851 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
3712799 ATATAATATG
* *
3712809 AATTAAGATATA-ATACAA
1 AATTAACATATATATAAAA
3712827 AATTAACATATATATAAAA
1 AATTAACATATATATAAAA
3712846 AATTAA
1 AATTAA
3712852 AACATAACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (19 bp):
AATTAACATATATATAAAA
Found at i:3713175 original size:22 final size:21
Alignment explanation
Indices: 3713149--3713214 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
3713139 ACATAAATTT
3713149 TTTTTGTTTTCTTTCTTTTTTC
1 TTTTT-TTTTCTTTCTTTTTTC
* **
3713171 TTTTTTTCTCCTTTCTCCTTTC
1 TTTTTTT-TTCTTTCTTTTTTC
*
3713193 TTTATTTCTTTATTTCTTTTTT
1 TTT-TTT-TTTCTTTCTTTTTT
3713215 ATTGATGCAA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
21 2 0.06
22 19 0.56
23 12 0.35
24 1 0.03
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTTTTTTCTTTCTTTTTTC
Found at i:3715114 original size:13 final size:13
Alignment explanation
Indices: 3715096--3715143 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 13
3715086 GAAAATAACA
3715096 ATATTTTAATAAT
1 ATATTTTAATAAT
*
3715109 ATATTTAGATATAAT
1 ATATTT-TA-ATAAT
3715124 ATTATTTTAATAAT
1 A-TATTTTAATAAT
3715138 -TATTTT
1 ATATTTT
3715144 TAAATAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 6 0.20
13 6 0.20
14 6 0.20
15 7 0.23
16 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
ATATTTTAATAAT
Found at i:3715150 original size:28 final size:28
Alignment explanation
Indices: 3715088--3715192 Score: 104
Period size: 30 Copynumber: 3.6 Consensus size: 28
3715078 TAATATAAGA
* *
3715088 AAATAACAATATTTTAATAA-TATATTT
1 AAATAACATTATTTTAATAATTATTTTT
*
3715115 AGATATAATATTATTTTAATAATTATTTTT
1 A-A-ATAACATTATTTTAATAATTATTTTT
* *
3715145 AAATAACATTATTTAAATAATTAATTTCTA
1 AAATAACATTATTTTAATAATT-ATTT-TT
* *
3715175 AAACAACATTAGTTTAAT
1 AAATAACATTATTTTAAT
3715193 TAATCTCCCT
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.02
28 19 0.30
29 21 0.33
30 23 0.36
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (28 bp):
AAATAACATTATTTTAATAATTATTTTT
Found at i:3715960 original size:20 final size:20
Alignment explanation
Indices: 3715935--3715976 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3715925 ATCCGTTTAT
*
3715935 TGGTTAAGTTATTGTGTTTG
1 TGGTTAAGTTATTGTGTGTG
3715955 TGGTTAAGTTATTGTGTGTG
1 TGGTTAAGTTATTGTGTGTG
3715975 TG
1 TG
3715977 TGTGTGTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.33, T:0.52
Consensus pattern (20 bp):
TGGTTAAGTTATTGTGTGTG
Found at i:3715974 original size:2 final size:2
Alignment explanation
Indices: 3715967--3715993 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3715957 GTTAAGTTAT
3715967 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
3715994 ATTCAGTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3716439 original size:12 final size:12
Alignment explanation
Indices: 3716422--3716447 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3716412 GGAGAGCTGT
3716422 TTCCTTGGATGG
1 TTCCTTGGATGG
3716434 TTCCTTGGATGG
1 TTCCTTGGATGG
3716446 TT
1 TT
3716448 ATACATTTTA
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:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTCCTTGGATGG
Found at i:3717426 original size:2 final size:2
Alignment explanation
Indices: 3717419--3717454 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3717409 ATTTGTTGAA
*
3717419 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3717455 TATTCAACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3722835 original size:228 final size:233
Alignment explanation
Indices: 3722431--3722861 Score: 604
Period size: 228 Copynumber: 1.9 Consensus size: 233
3722421 AAGTACAAGC
**
3722431 GATATTAAGTCAATGCTTATGATGAATTCAATATTAATGGAATGGCAAATTAGGAAAAAAAATGT
1 GATATTAAGTCAATGCTTATGATGAATTCAATATTAATGGAATGAAAAATTAGGAAAAAAAATGT
*
3722496 CACTTCAAATACTTTTAAAACATAGATAGAATATTTCAATTTCGTCAAAAAAAAAAATCTTTGCA
66 CACTTCAAATACTTTTAAAACATAGATAGAATATTTCAATTTCGTC-AAAAAAAAAAGCTTTGCA
* * * * *
3722561 TATTTAACGTAGTTGACAATTGCTTGTTTTTGTTAATTAATTTGACGAGAAAAAAATAATAATCA
130 AATATAACGTACTTGACAATTGCTTGTATTTGCTAATTAATTTGACGAG-AAAAAATAATAATCA
3722626 CGTGATATAGGGAAATGTATTCAAAGATTGAGTTATCAAA
194 CGTGATATAGGGAAATGTATTCAAAGATTGAGTTATCAAA
* * * * * *
3722666 GATATTAAGTCAGTGGTTATTATGAATTCAATATTAATTGAATGAAAAATTAGGTACAAAAA-GT
1 GATATTAAGTCAATGCTTATGATGAATTCAATATTAATGGAATGAAAAATTAGGAAAAAAAATGT
* * * * *
3722730 CACTTCAAATGCTTTT-AAA-A-A-ATATATTTTTTCAATTTCGTC-CAAAAAAAAGCTTTGCAA
66 CACTTCAAATACTTTTAAAACATAGATAGAATATTTCAATTTCGTCAAAAAAAAAAGCTTTGCAA
* * *
3722790 ATATAATGTACTTGACAATTGCTTGTATTTGCTAATTAATTTGACGAGAAAAAATAATAATTATG
131 ATATAACGTACTTGACAATTGCTTGTATTTGCTAATTAATTTGACGAGAAAAAATAATAATCACG
3722855 TGATATA
196 TGATATA
3722862 AAAATATTTA
Statistics
Matches: 174, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
227 22 0.13
228 58 0.33
230 18 0.10
231 1 0.01
232 1 0.01
233 3 0.02
234 17 0.10
235 54 0.31
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (233 bp):
GATATTAAGTCAATGCTTATGATGAATTCAATATTAATGGAATGAAAAATTAGGAAAAAAAATGT
CACTTCAAATACTTTTAAAACATAGATAGAATATTTCAATTTCGTCAAAAAAAAAAGCTTTGCAA
ATATAACGTACTTGACAATTGCTTGTATTTGCTAATTAATTTGACGAGAAAAAATAATAATCACG
TGATATAGGGAAATGTATTCAAAGATTGAGTTATCAAA
Found at i:3722991 original size:20 final size:22
Alignment explanation
Indices: 3722958--3723000 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3722948 AAAATATTTT
3722958 TATATAAATTTATTTA-ATAAAA
1 TATATAAA-TTATTTATATAAAA
3722980 TATATAAA-TATTTATATAAAA
1 TATATAAATTATTTATATAAAA
3723001 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 6 0.30
22 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TATATAAATTATTTATATAAAA
Found at i:3724417 original size:17 final size:17
Alignment explanation
Indices: 3724397--3724446 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
3724387 TCATAATATT
* *
3724397 TATTAAATATATATTTC
1 TATTAAATATTTATTTA
3724414 TATT-AATGATTTA-TTA
1 TATTAAAT-ATTTATTTA
3724430 TATTAAATATTTATTTA
1 TATTAAATATTTATTTA
3724447 AAATTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTAAATATTTATTTA
Found at i:3724435 original size:16 final size:16
Alignment explanation
Indices: 3724393--3724472 Score: 55
Period size: 16 Copynumber: 5.1 Consensus size: 16
3724383 AAAATCATAA
*
3724393 TATT-TATTAAATATA
1 TATTATATTAAATATT
*
3724408 TATTTCTATT-AATGATT
1 TA-TTATATTAAAT-ATT
3724425 TATTATATTAAATATT
1 TATTATATTAAATATT
*
3724441 TATTTAAAATTAAA-A-T
1 TA-TT-ATATTAAATATT
3724457 TATT-T-TTAAATATT
1 TATTATATTAAATATT
3724471 TA
1 TA
3724473 ATATTTTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
12 5 0.09
13 1 0.02
14 3 0.06
15 4 0.08
16 19 0.36
17 14 0.26
18 7 0.13
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (16 bp):
TATTATATTAAATATT
Found at i:3724473 original size:20 final size:20
Alignment explanation
Indices: 3724434--3724488 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
3724424 TTATTATATT
3724434 AAATATTTATTTAAA-A-TTA
1 AAAT-TTTATTTAAATATTTA
3724453 AAATTATT-TTTAAATATTTA
1 AAATT-TTATTTAAATATTTA
*
3724473 ATATTTTATTTAAATA
1 AAATTTTATTTAAATA
3724489 AATTGATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 7 0.23
19 9 0.29
20 15 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTTTATTTAAATATTTA
Found at i:3731369 original size:27 final size:27
Alignment explanation
Indices: 3731301--3731361 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
3731291 AGGTGGCGAA
*
3731301 GGAGTTGATGAAGGGGGAGGAGTCATT
1 GGAGTTGATGAAGGGGGAGGAGCCATT
*
3731328 GGAGTTGATGAAGGGGTAGGAGCCATT
1 GGAGTTGATGAAGGGGGAGGAGCCATT
*
3731355 GGGGTTG
1 GGAGTTG
3731362 TTGGAGGGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.23, C:0.05, G:0.49, T:0.23
Consensus pattern (27 bp):
GGAGTTGATGAAGGGGGAGGAGCCATT
Found at i:3736398 original size:15 final size:16
Alignment explanation
Indices: 3736362--3736401 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
3736352 TCTAATTTTT
*
3736362 ATAAAATTTGTAATTAA
1 ATAAAA-TTATAATTAA
3736379 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
3736394 ATAAAATT
1 ATAAAATT
3736402 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:3736404 original size:16 final size:17
Alignment explanation
Indices: 3736362--3736404 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
3736352 TCTAATTTTT
*
3736362 ATAAAATTTGTAATTAA
1 ATAAAATTTATAATTAA
3736379 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
3736394 ATAAAATTTAT
1 ATAAAATTTAT
3736405 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:3736870 original size:13 final size:13
Alignment explanation
Indices: 3736851--3736882 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3736841 TGAATTATTA
3736851 ATATATAAAAAAT
1 ATATATAAAAAAT
*
3736864 TTATATAAAAAAT
1 ATATATAAAAAAT
3736877 ATATAT
1 ATATAT
3736883 TTTCAATACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATATAAAAAAT
Found at i:3737621 original size:11 final size:11
Alignment explanation
Indices: 3737592--3737629 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3737582 AAATATTTAA
*
3737592 AATATAACATG
1 AATATAATATG
3737603 AA-ATAATATG
1 AATATAATATG
*
3737613 TATATAATATG
1 AATATAATATG
3737624 AATATA
1 AATATA
3737630 TATACATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (11 bp):
AATATAATATG
Found at i:3737686 original size:30 final size:28
Alignment explanation
Indices: 3737635--3737729 Score: 68
Period size: 30 Copynumber: 3.2 Consensus size: 28
3737625 ATATATATAC
3737635 ATATAAAAATATACATAAAAAATTATCAAT
1 ATATAAAAATATACATAAAAAA-TAT-AAT
**
3737665 ATATAAAAA-ATTTATACAAAAATATAAT
1 ATATAAAAATATACATA-AAAAATATAAT
** * *
3737693 AT-TTTAAATAAAAATAACATAAATATAAAT
1 ATATAAAAATATACATAA-A-AAATAT-AAT
3737723 ATATAAA
1 ATATAAA
3737730 TTTTTTTCTT
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
27 5 0.10
28 10 0.20
29 14 0.28
30 19 0.38
31 2 0.04
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (28 bp):
ATATAAAAATATACATAAAAAATATAAT
Found at i:3737729 original size:29 final size:30
Alignment explanation
Indices: 3737618--3737730 Score: 79
Period size: 29 Copynumber: 3.6 Consensus size: 30
3737608 ATATGTATAT
3737618 AATATGAATATATATACATATAAAAATATACATAAAA
1 AATAT-AA-ATATATA-A-ATAAAAATATAC---AAA
* **
3737655 AATTATCAATATATAAA-AAATTTATACAAA
1 AA-TATAAATATATAAATAAAAATATACAAA
* *
3737685 AATAT-AATATTTTAAATAAAAATA-ACATA
1 AATATAAATA-TATAAATAAAAATATACAAA
3737714 AATATAAATATATAAAT
1 AATATAAATATATAAAT
3737731 TTTTTTCTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
28 4 0.06
29 23 0.36
30 14 0.22
33 8 0.12
34 1 0.02
35 1 0.02
36 7 0.11
37 3 0.05
38 3 0.05
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (30 bp):
AATATAAATATATAAATAAAAATATACAAA
Found at i:3737743 original size:4 final size:4
Alignment explanation
Indices: 3737734--3737788 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
3737724 TATAAATTTT
* * *
3737734 TTTC TTTC TTTC TTTTT TTTC TTT- TTT- TCTC TTTC TTTTT TTTC TTTC
1 TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC
3737782 TTTC TTT
1 TTTC TTT
3737789 TTCGGCTGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
3 5 0.12
4 31 0.74
5 6 0.14
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTC
Found at i:3737752 original size:17 final size:17
Alignment explanation
Indices: 3737730--3737791 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
3737720 AATATATAAA
3737730 TTTTTTTCTTTCTTTCT
1 TTTTTTTCTTTCTTTCT
*
3737747 TTTTTTTCTTTTTTTCT
1 TTTTTTTCTTTCTTTCT
*
3737764 CTTTCTTTTTTTTCTTTCT
1 -TTT-TTTTCTTTCTTTCT
3737783 TTCTTTTTC
1 TT-TTTTTC
3737792 GGCTGAACCC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
17 16 0.42
18 9 0.24
19 13 0.34
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTCTTTCTTTCT
Found at i:3737758 original size:23 final size:23
Alignment explanation
Indices: 3737732--3737788 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
3737722 TATATAAATT
3737732 TTTTTCTTTCTTTCTTTTTTTTC
1 TTTTTCTTTCTTTCTTTTTTTTC
3737755 TTTTT-TTCTCTTTCTTTTTTTTC
1 TTTTTCTT-TCTTTCTTTTTTTTC
3737778 --TTTCTTTCTTT
1 TTTTTCTTTCTTT
3737789 TTCGGCTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.25
22 4 0.12
23 20 0.62
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTCTTTCTTTCTTTTTTTTC
Found at i:3738164 original size:24 final size:24
Alignment explanation
Indices: 3738137--3738182 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3738127 AAGGAAAGCA
*
3738137 GAAGCTGAAGAGGAAGAGGAAGGG
1 GAAGCAGAAGAGGAAGAGGAAGGG
* *
3738161 GAAGCAGGAGAGGAAGGGGAAG
1 GAAGCAGAAGAGGAAGAGGAAG
3738183 ATAAAGTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.04, G:0.52, T:0.02
Consensus pattern (24 bp):
GAAGCAGAAGAGGAAGAGGAAGGG
Found at i:3740710 original size:3 final size:3
Alignment explanation
Indices: 3740702--3740731 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3740692 GCTTTAAGCT
3740702 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3740732 ATTCAAGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3741113 original size:28 final size:28
Alignment explanation
Indices: 3741082--3741137 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3741072 CGTATGAGTT
3741082 TTTAAAATTTTAATTAGTAATTCAATCC
1 TTTAAAATTTTAATTAGTAATTCAATCC
*
3741110 TTTAGAATTTTAATTAGTAATTCAATCC
1 TTTAAAATTTTAATTAGTAATTCAATCC
3741138 AGTAACAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (28 bp):
TTTAAAATTTTAATTAGTAATTCAATCC
Found at i:3749060 original size:124 final size:124
Alignment explanation
Indices: 3748840--3749088 Score: 498
Period size: 124 Copynumber: 2.0 Consensus size: 124
3748830 ATATGTAGCT
3748840 TGTCCTTCCACTTGATGGTGAGTTTGTTTCATTGTACAGGTGTTGAAAAAAGAAATTGATGTTTT
1 TGTCCTTCCACTTGATGGTGAGTTTGTTTCATTGTACAGGTGTTGAAAAAAGAAATTGATGTTTT
3748905 TCAGTTACAGTGGTATGCTTATTGATTGTTCAAAGCGCTTGCAAATCTTCATAAACAAG
66 TCAGTTACAGTGGTATGCTTATTGATTGTTCAAAGCGCTTGCAAATCTTCATAAACAAG
3748964 TGTCCTTCCACTTGATGGTGAGTTTGTTTCATTGTACAGGTGTTGAAAAAAGAAATTGATGTTTT
1 TGTCCTTCCACTTGATGGTGAGTTTGTTTCATTGTACAGGTGTTGAAAAAAGAAATTGATGTTTT
3749029 TCAGTTACAGTGGTATGCTTATTGATTGTTCAAAGCGCTTGCAAATCTTCATAAACAAG
66 TCAGTTACAGTGGTATGCTTATTGATTGTTCAAAGCGCTTGCAAATCTTCATAAACAAG
3749088 T
1 T
3749089 ATATGATTTT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 125 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (124 bp):
TGTCCTTCCACTTGATGGTGAGTTTGTTTCATTGTACAGGTGTTGAAAAAAGAAATTGATGTTTT
TCAGTTACAGTGGTATGCTTATTGATTGTTCAAAGCGCTTGCAAATCTTCATAAACAAG
Found at i:3757801 original size:26 final size:25
Alignment explanation
Indices: 3757749--3757809 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
3757739 ATCTATGTAG
*
3757749 TTTAATTTTATTTATTTATTAATTAT
1 TTTAATTTAATTTATTTA-TAATTAT
3757775 TTTAATTTAATATTATTTA-AATATAT
1 TTTAATTTAAT-TTATTTATAAT-TAT
*
3757801 TATAATTTA
1 TTTAATTTA
3757810 TTATGTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 3 0.10
26 21 0.68
27 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTAATTTAATTTATTTATAATTAT
Found at i:3757903 original size:42 final size:41
Alignment explanation
Indices: 3757820--3757903 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 41
3757810 TTATGTATAA
* *
3757820 ATTTTTAATATATATTATATATAAACTAAAAATAAAAAAAT
1 ATTTTTAATATATAATATAAATAAACTAAAAATAAAAAAAT
* * * *
3757861 ATTTTTATATATTTAATATAAATATATTAAAAATACAAAAAT
1 ATTTTTA-ATATATAATATAAATAAACTAAAAATAAAAAAAT
3757903 A
1 A
3757904 ATATATCATA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 7 0.19
42 29 0.81
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (41 bp):
ATTTTTAATATATAATATAAATAAACTAAAAATAAAAAAAT
Found at i:3758211 original size:16 final size:17
Alignment explanation
Indices: 3758184--3758216 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3758174 AACTGACGCG
3758184 CATCCAACAAATGTATA
1 CATCCAACAAATGTATA
*
3758201 CATCC-ACAAATTTATA
1 CATCCAACAAATGTATA
3758217 AAGAAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.24, G:0.03, T:0.27
Consensus pattern (17 bp):
CATCCAACAAATGTATA
Found at i:3763795 original size:16 final size:17
Alignment explanation
Indices: 3763751--3763796 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
3763741 TTGTTTAATT
*
3763751 TAAT-ATTTTTCAAAAA
1 TAATAATTTTTTAAAAA
* *
3763767 TAATCATTATTTAAAAA
1 TAATAATTTTTTAAAAA
3763784 T-ATAATTTTTTAA
1 TAATAATTTTTTAA
3763797 TTAATAAACG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATAATTTTTTAAAAA
Found at i:3765384 original size:17 final size:15
Alignment explanation
Indices: 3765350--3765382 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3765340 AAATTATAAA
3765350 TATTTTTTAAAATAT
1 TATTTTTTAAAATAT
3765365 TATTTTTTAAAA-AT
1 TATTTTTTAAAATAT
3765379 TATT
1 TATT
3765383 ATATATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTTTTAAAATAT
Found at i:3766359 original size:13 final size:14
Alignment explanation
Indices: 3766341--3766372 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
3766331 ATTTTTAATT
3766341 TTATTAAATTA-TA
1 TTATTAAATTATTA
3766354 TTATTAAATTATTA
1 TTATTAAATTATTA
3766368 TTATT
1 TTATT
3766373 TATAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTAAATTATTA
Found at i:3766362 original size:30 final size:30
Alignment explanation
Indices: 3766320--3766388 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
3766310 TAATTTTTAT
* *
3766320 TTAAGTTA-TAAATTTTTAAT-TTTATTAAA
1 TTAAATTATTAAATTATTAATATTTA-TAAA
* *
3766349 TTATATTATTAAATTATTATTATTTATAAA
1 TTAAATTATTAAATTATTAATATTTATAAA
3766379 TTAAATTATT
1 TTAAATTATT
3766389 TATGTTAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 6 0.18
30 23 0.70
31 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
TTAAATTATTAAATTATTAATATTTATAAA
Found at i:3767979 original size:32 final size:32
Alignment explanation
Indices: 3767941--3768005 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
3767931 GTTACTTTTT
3767941 TATAAATTTTAAAATATTAATAATTTATATTA
1 TATAAATTTTAAAATATTAATAATTTATATTA
* *
3767973 TATAAATTTTAATATTTTAATAATTTATATTA
1 TATAAATTTTAAAATATTAATAATTTATATTA
3768005 T
1 T
3768006 TTTTATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
TATAAATTTTAAAATATTAATAATTTATATTA
Found at i:3767997 original size:17 final size:17
Alignment explanation
Indices: 3767945--3768008 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
3767935 CTTTTTTATA
* *
3767945 AATTTTAAAATATTAAT
1 AATTTTAATATTTTAAT
*
3767962 AA-TTT-ATATTAT-AT
1 AATTTTAATATTTTAAT
3767976 AAATTTTAATATTTTAAT
1 -AATTTTAATATTTTAAT
*
3767994 AATTTATATTATTTT
1 AATTT-TAATATTTT
3768009 TATATTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
14 2 0.05
15 6 0.16
16 6 0.16
17 13 0.35
18 10 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTTAATATTTTAAT
Found at i:3768006 original size:18 final size:18
Alignment explanation
Indices: 3767957--3768047 Score: 68
Period size: 18 Copynumber: 5.3 Consensus size: 18
3767947 TTTTAAAATA
3767957 TTAATAATTTATATTA-T
1 TTAATAATTTATATTATT
* *
3767974 AT-A-AATTT-TAATATT
1 TTAATAATTTATATTATT
3767989 TTAATAATTTATATTATT
1 TTAATAATTTATATTATT
* *
3768007 TTTAT-ATTT-TTTTATAAT
1 TTAATAATTTATATTAT--T
**
3768025 TTAATTTTTTATATTATT
1 TTAATAATTTATATTATT
3768043 TTAAT
1 TTAAT
3768048 TTTTATTTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
14 4 0.07
15 7 0.12
16 7 0.12
17 10 0.18
18 21 0.37
19 3 0.05
20 5 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTAATAATTTATATTATT
Found at i:3768020 original size:10 final size:11
Alignment explanation
Indices: 3767996--3768044 Score: 55
Period size: 11 Copynumber: 4.2 Consensus size: 11
3767986 ATTTTAATAA
3767996 TTTATATTATT
1 TTTATATTATT
3768007 TTTATATT-TT
1 TTTATATTATT
3768017 TTTATAATTTAATTT
1 TTTAT-A-TT-A-TT
3768032 TTTATATTATT
1 TTTATATTATT
3768043 TT
1 TT
3768045 AATTTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
10 7 0.21
11 13 0.39
12 3 0.09
13 2 0.06
14 1 0.03
15 7 0.21
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTATATTATT
Found at i:3768048 original size:18 final size:18
Alignment explanation
Indices: 3767985--3768051 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
3767975 TAAATTTTAA
**
3767985 TATTTTAATAATTTATAT
1 TATTTTAATTTTTTATAT
3768003 TATTTTTATATTTTTT-TA-
1 TA-TTTTA-ATTTTTTATAT
*
3768021 TAATTTAATTTTTTATAT
1 TATTTTAATTTTTTATAT
3768039 TATTTTAATTTTT
1 TATTTTAATTTTT
3768052 ATTTAAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 7 0.17
17 6 0.15
18 16 0.39
19 7 0.17
20 5 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTTTAATTTTTTATAT
Found at i:3768052 original size:17 final size:17
Alignment explanation
Indices: 3767964--3768053 Score: 71
Period size: 17 Copynumber: 5.3 Consensus size: 17
3767954 ATATTAATAA
* *
3767964 TTTATATTA-TATAAAT
1 TTTATATTATTTTAATT
*
3767980 TTTA-A-TATTTTAATAA
1 TTTATATTATTTTAAT-T
3767996 TTTATATTATTTTTATATT
1 TTTATATTA-TTTTA-ATT
* *
3768015 TTTTTA-TAATTTAATTT
1 TTTATATTATTTTAA-TT
3768032 TTTATATTATTTTAATT
1 TTTATATTATTTTAATT
3768049 TTTAT
1 TTTAT
3768054 TTAAAATTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
14 2 0.03
15 5 0.09
16 9 0.16
17 19 0.33
18 11 0.19
19 10 0.17
20 2 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTATTTTAATT
Found at i:3768052 original size:25 final size:25
Alignment explanation
Indices: 3767979--3768047 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 25
3767969 ATTATATAAA
*
3767979 TTTTA-ATATTTTAATAATTTATATTAT
1 TTTTATATTTTTTAATAATTTA-A-T-T
*
3768006 TTTTATATTTTTTTATAATTTAATT
1 TTTTATATTTTTTAATAATTTAATT
3768031 TTTTATATTATTTTAAT
1 TTTTATATT-TTTTAAT
3768048 TTTTATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 10 0.27
26 7 0.19
27 6 0.16
28 14 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTTATATTTTTTAATAATTTAATT
Found at i:3768886 original size:20 final size:21
Alignment explanation
Indices: 3768858--3768898 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3768848 ATATTTTATA
3768858 ATTAATTTAA-ATAAAAATAT
1 ATTAATTTAATATAAAAATAT
*
3768878 ATTATTTTAATATAAAAATAT
1 ATTAATTTAATATAAAAATAT
3768899 TATTTCAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTAATTTAATATAAAAATAT
Found at i:3768889 original size:19 final size:19
Alignment explanation
Indices: 3768862--3768903 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3768852 TTTATAATTA
3768862 ATTTAAATA-AAAATATATT
1 ATTTAAATATAAAA-ATATT
*
3768881 ATTTTAATATAAAAATATT
1 ATTTAAATATAAAAATATT
3768900 ATTT
1 ATTT
3768904 CAAGTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTAAATATAAAAATATT
Found at i:3770624 original size:22 final size:20
Alignment explanation
Indices: 3770567--3770627 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 20
3770557 AATATATTAT
*
3770567 ATATTTATATAAATTTTAAAA
1 ATATTTATAT-TATTTTAAAA
*
3770588 GTATTTATAATTTATTTTATATAA
1 ATATTTAT-A-TTATTTTA-A-AA
3770612 ATATTTATATTATTTT
1 ATATTTATATTATTTT
3770628 TTAATTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 7 0.21
22 14 0.42
23 3 0.09
24 9 0.27
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATATTTATATTATTTTAAAA
Found at i:3771115 original size:18 final size:18
Alignment explanation
Indices: 3771088--3771128 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3771078 TTTTAATACA
* *
3771088 TTTAATTTTAAATTCTTT
1 TTTAACTTTAAATTATTT
*
3771106 TTTAACTTTAATTTATTT
1 TTTAACTTTAAATTATTT
3771124 TTTAA
1 TTTAA
3771129 AATTTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTAACTTTAAATTATTT
Found at i:3774020 original size:26 final size:26
Alignment explanation
Indices: 3773991--3774042 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3773981 TTGAATCACT
3773991 GAATTTAAGCTGTAGTTATAAGCAGA
1 GAATTTAAGCTGTAGTTATAAGCAGA
3774017 GAATTTAAGCTGTAGTTATAAGCAGA
1 GAATTTAAGCTGTAGTTATAAGCAGA
3774043 AACTGGTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (26 bp):
GAATTTAAGCTGTAGTTATAAGCAGA
Found at i:3775170 original size:82 final size:82
Alignment explanation
Indices: 3775033--3775194 Score: 315
Period size: 82 Copynumber: 2.0 Consensus size: 82
3775023 TGTAACATAT
3775033 ATTTGAATGTAAGTTCCCGTATTACTGTCTTCTTTCCTTATTTTTCTTAGGGACAAATCTTTAGA
1 ATTTGAATGTAAGTTCCCGTATTACTGTCTTCTTTCCTTATTTTTCTTAGGGACAAATCTTTAGA
3775098 ACTCAATTCTACTGCAG
66 ACTCAATTCTACTGCAG
*
3775115 ATTTGAATGTAAGTTCCCGTATTACTGTTTTCTTTCCTTATTTTTCTTAGGGACAAATCTTTAGA
1 ATTTGAATGTAAGTTCCCGTATTACTGTCTTCTTTCCTTATTTTTCTTAGGGACAAATCTTTAGA
3775180 ACTCAATTCTACTGC
66 ACTCAATTCTACTGC
3775195 TGCTATAGTG
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (82 bp):
ATTTGAATGTAAGTTCCCGTATTACTGTCTTCTTTCCTTATTTTTCTTAGGGACAAATCTTTAGA
ACTCAATTCTACTGCAG
Found at i:3775685 original size:67 final size:67
Alignment explanation
Indices: 3775577--3775712 Score: 254
Period size: 67 Copynumber: 2.0 Consensus size: 67
3775567 TGGAAACTAG
* *
3775577 ATAGTTGATGAAAAGAAAAAGGGCAAAACCCGTAATGACTATTAGTTATCTATAGTGATGGCTAA
1 ATAGTTGACGAAAAGAAAAAGGGCAAAACCCGAAATGACTATTAGTTATCTATAGTGATGGCTAA
3775642 TA
66 TA
3775644 ATAGTTGACGAAAAGAAAAAGGGCAAAACCCGAAATGACTATTAGTTATCTATAGTGATGGCTAA
1 ATAGTTGACGAAAAGAAAAAGGGCAAAACCCGAAATGACTATTAGTTATCTATAGTGATGGCTAA
3775709 TA
66 TA
3775711 AT
1 AT
3775713 TGTAACATTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.26
Consensus pattern (67 bp):
ATAGTTGACGAAAAGAAAAAGGGCAAAACCCGAAATGACTATTAGTTATCTATAGTGATGGCTAA
TA
Found at i:3777638 original size:15 final size:15
Alignment explanation
Indices: 3777620--3777648 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3777610 ATTTACATAT
3777620 GAATTTGAGTAATAC
1 GAATTTGAGTAATAC
3777635 GAATTTGAGTAATA
1 GAATTTGAGTAATA
3777649 GGCTCATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.34
Consensus pattern (15 bp):
GAATTTGAGTAATAC
Found at i:3779929 original size:198 final size:198
Alignment explanation
Indices: 3779591--3779982 Score: 554
Period size: 198 Copynumber: 2.0 Consensus size: 198
3779581 TCTTCACCAT
* * * *
3779591 TGTTATTTTCACGTTCCGTATTTCTTTCTTCACTCTCAGAATCAATAGTCTCAGTCGAAAAATCA
1 TGTTATTTTCACGTTCCATACTTCTTTCTTCACTCCCAGAATCAATAGCCTCAGTCGAAAAATCA
* * * *
3779656 AGCCTTCTTTTCCTATCACTTCCTTCACCAACTTCAAAATTGTATGCATGATTTTGTTGATTTTC
66 AGCCTTCTTTTCCAAACACTTCCTTCACCAACTTCAAAATTGTATGCATGATTTTGCTGATTTAC
* *
3779721 AAGCTCTAATTCTGAAGTAGCCCCAGGAGATGGACTAACATTCTTCAACGAATTCAATAATTTCT
131 AAGCTCTAATTCTGAAGTAGCCCCAGGAGACGGACGAACATTCTTCAACGAATTCAATAATTTCT
3779786 CGG
196 CGG
* *
3779789 TGTTATTTTCACTTTCCATACTTCTTTCTTCACTCCCAGAATCAATAGCCTGAGTCGAAAAATCA
1 TGTTATTTTCACGTTCCATACTTCTTTCTTCACTCCCAGAATCAATAGCCTCAGTCGAAAAATCA
*
3779854 AGCCTTCTTTTCCAAACACTTCCTTCACCAACTTCAAAA-TGATATTCATGGA-TTTGCTGATTT
66 AGCCTTCTTTTCCAAACACTTCCTTCACCAACTTCAAAATTG-TATGCAT-GATTTTGCTGATTT
* * * * * * * * *
3779917 AGAAGCTCTAATTCTGACGTATCTCCAGGAGCCGTACGAGCATTCTTTAACGATTTCAATAATTT
129 ACAAGCTCTAATTCTGAAGTAGCCCCAGGAGACGGACGAACATTCTTCAACGAATTCAATAATTT
3779982 C
194 C
3779983 CGGCAGTTCT
Statistics
Matches: 170, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
197 2 0.01
198 166 0.98
199 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.36
Consensus pattern (198 bp):
TGTTATTTTCACGTTCCATACTTCTTTCTTCACTCCCAGAATCAATAGCCTCAGTCGAAAAATCA
AGCCTTCTTTTCCAAACACTTCCTTCACCAACTTCAAAATTGTATGCATGATTTTGCTGATTTAC
AAGCTCTAATTCTGAAGTAGCCCCAGGAGACGGACGAACATTCTTCAACGAATTCAATAATTTCT
CGG
Found at i:3781362 original size:14 final size:14
Alignment explanation
Indices: 3781297--3781363 Score: 57
Period size: 14 Copynumber: 4.4 Consensus size: 14
3781287 TAAATACGTC
3781297 TAATTATATTATATT
1 TAATTATATTA-ATT
3781312 TAAATTATTTGATTGAATT
1 T-AATTA--T-ATT-AATT
3781331 TAA-TAT-TTAATAT
1 TAATTATATTAAT-T
3781344 TAATTATATTAATT
1 TAATTATATTAATT
3781358 TAATTA
1 TAATTA
3781364 AAAATATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 17
0.72 0.00 0.28
Matches are distributed among these distances:
12 3 0.07
13 6 0.14
14 10 0.23
15 7 0.16
16 5 0.11
17 2 0.05
18 3 0.07
19 7 0.16
20 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
TAATTATATTAATT
Found at i:3781411 original size:19 final size:20
Alignment explanation
Indices: 3781360--3781399 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
3781350 TATTAATTTA
3781360 ATTAAAA-ATATAATAAAAT
1 ATTAAAATATATAATAAAAT
3781379 ATTAAAAATATATAATAAAAT
1 ATT-AAAATATATAATAAAAT
3781400 GTTATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.16
20 4 0.21
21 12 0.63
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTAAAATATATAATAAAAT
Found at i:3782470 original size:8 final size:8
Alignment explanation
Indices: 3782453--3782486 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
3782443 GTTCAGGAAA
3782453 ATAT-TAT
1 ATATGTAT
3782460 ATATGTAT
1 ATATGTAT
*
3782468 ATACGTAT
1 ATATGTAT
3782476 ATATGTAT
1 ATATGTAT
3782484 ATA
1 ATA
3782487 AATATTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (8 bp):
ATATGTAT
Found at i:3785981 original size:18 final size:17
Alignment explanation
Indices: 3785953--3785987 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3785943 TGACATAGTG
3785953 TTGTAATATATAAGTAA
1 TTGTAATATATAAGTAA
*
3785970 TTGTATATATATATGTAA
1 TTGTA-ATATATAAGTAA
3785988 AGGATGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (17 bp):
TTGTAATATATAAGTAA
Found at i:3786903 original size:20 final size:21
Alignment explanation
Indices: 3786878--3786916 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3786868 TAATAAAATA
3786878 TGTTCAT-TTATTTGTTTCTC
1 TGTTCATATTATTTGTTTCTC
*
3786898 TGTTCATATTATTTTTTTC
1 TGTTCATATTATTTGTTTC
3786917 ATGCAGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TGTTCATATTATTTGTTTCTC
Found at i:3787918 original size:10 final size:10
Alignment explanation
Indices: 3787903--3787930 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3787893 AGAATTGTCT
3787903 AAACCCTATG
1 AAACCCTATG
3787913 AAACCCTATG
1 AAACCCTATG
3787923 AAACCCTA
1 AAACCCTA
3787931 ATTTGACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.32, G:0.07, T:0.18
Consensus pattern (10 bp):
AAACCCTATG
Found at i:3788465 original size:2 final size:2
Alignment explanation
Indices: 3788458--3788488 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3788448 AGATAATTAA
3788458 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
3788489 AACCCTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:3791808 original size:2 final size:2
Alignment explanation
Indices: 3791801--3791868 Score: 70
Period size: 2 Copynumber: 35.0 Consensus size: 2
3791791 TCACTAGTTT
* * *
3791801 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A AA CA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3791842 TCA -A T- TA TA TA TA TA TA TA TA TG TA TA
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
3791869 ATTTTCTTCC
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
1 3 0.05
2 54 0.93
3 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (2 bp):
TA
Found at i:3794767 original size:14 final size:15
Alignment explanation
Indices: 3794748--3794780 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3794738 TGAACATTTA
3794748 ATATTT-ATTTTTTT
1 ATATTTAATTTTTTT
3794762 ATATTTCAATTTTTTT
1 ATATTT-AATTTTTTT
3794778 ATA
1 ATA
3794781 AAGAATTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
16 11 0.65
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
ATATTTAATTTTTTT
Found at i:3799843 original size:22 final size:21
Alignment explanation
Indices: 3799811--3799921 Score: 77
Period size: 22 Copynumber: 5.1 Consensus size: 21
3799801 TAAAATTGAA
3799811 TAAA-TTAAAATTATTAAATT
1 TAAATTTAAAATTATTAAATT
*
3799831 TAATATTTAAAA-TATTTAAA-A
1 TAA-ATTTAAAATTA-TTAAATT
* *
3799852 TATATTTGATAAAATA-TAAATT
1 TAAATTT-A-AAATTATTAAATT
*
3799874 TAAATTTAAACTTATTTAAATT
1 TAAATTTAAAATTA-TTAAATT
* *
3799896 TAAATTAAAAACTTATCTAAACT
1 TAAATTTAAAA-TTAT-TAAATT
3799919 TAA
1 TAA
3799922 GGCTCAATTA
Statistics
Matches: 71, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
20 11 0.15
21 11 0.15
22 36 0.51
23 13 0.18
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (21 bp):
TAAATTTAAAATTATTAAATT
Found at i:3799852 original size:23 final size:24
Alignment explanation
Indices: 3799795--3799852 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
3799785 TTCCGTTATT
3799795 ATTATATAAAATTGAATAAATTAAA
1 ATTAT-TAAAATTGAATAAATTAAA
* *
3799820 ATTATT-AAATTTAAT-ATTTAAA
1 ATTATTAAAATTGAATAAATTAAA
3799842 A-TATTTAAAAT
1 ATTA-TTAAAAT
3799853 ATATTTGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 2 0.07
22 9 0.31
23 12 0.41
24 1 0.03
25 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTATTAAAATTGAATAAATTAAA
Found at i:3799911 original size:23 final size:22
Alignment explanation
Indices: 3799868--3799921 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
3799858 TGATAAAATA
* *
3799868 TAAATTTAAATTTAAACTTATT
1 TAAATTTAAATTAAAACTTATC
3799890 TAAATTTAAATTAAAAACTTATC
1 TAAATTTAAATT-AAAACTTATC
*
3799913 TAAACTTAA
1 TAAATTTAA
3799922 GGCTCAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATTTAAATTAAAACTTATC
Found at i:3811442 original size:18 final size:18
Alignment explanation
Indices: 3811419--3811456 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3811409 TATATATATA
3811419 TATATAAAAATTAAAATT
1 TATATAAAAATTAAAATT
* *
3811437 TATATAAATATTAAATTT
1 TATATAAAAATTAAAATT
3811455 TA
1 TA
3811457 ATGCGTCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATATAAAAATTAAAATT
Found at i:3812048 original size:17 final size:18
Alignment explanation
Indices: 3812014--3812060 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
3812004 ATGTTATAAT
*
3812014 TATATTAA-AAATATTTTA
1 TATATTAATAAAT-TTTAA
*
3812032 TATATTTATAAATTTTAA
1 TATATTAATAAATTTTAA
3812050 TATATTAATAA
1 TATATTAATAA
3812061 TTCATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATTAATAAATTTTAA
Found at i:3812109 original size:21 final size:20
Alignment explanation
Indices: 3812085--3812139 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 20
3812075 ATTTAATAAA
3812085 TTTATTTATTTATATTATATT
1 TTTATTT-TTTATATTATATT
3812106 TTTA-TTTTT-TATTATATT
1 TTTATTTTTTATATTATATT
*
3812124 TTAATTTTTTTATATT
1 TTTA-TTTTTTATATT
3812140 GTAACTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 12 0.40
19 3 0.10
20 7 0.23
21 8 0.27
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTATTTTTTATATTATATT
Found at i:3812130 original size:24 final size:25
Alignment explanation
Indices: 3812085--3812136 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
3812075 ATTTAATAAA
3812085 TTTATTTATTTATATTATATTTTTA
1 TTTATTTATTTATATTATATTTTTA
* *
3812110 TTT-TTTA-TTATATTTTAATTTT-
1 TTTATTTATTTATATTATATTTTTA
3812132 TTTAT
1 TTTAT
3812137 ATTGTAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 3 0.12
23 14 0.58
24 4 0.17
25 3 0.12
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTATTTATTTATATTATATTTTTA
Found at i:3812136 original size:16 final size:17
Alignment explanation
Indices: 3812092--3812139 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3812082 AAATTTATTT
*
3812092 ATTTATATTATATTTTTA
1 ATTTTTATTATA-TTTTA
*
3812110 TTTTTTATTATATTTTA
1 ATTTTTATTATATTTTA
3812127 ATTTTT-TTATATT
1 ATTTTTATTATATT
3812140 GTAACTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 7 0.26
17 10 0.37
18 10 0.37
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTTATTATATTTTA
Found at i:3812822 original size:11 final size:11
Alignment explanation
Indices: 3812806--3812831 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3812796 AAAAAATTAT
3812806 TTAAATTTAAA
1 TTAAATTTAAA
3812817 TTAAATTTAAA
1 TTAAATTTAAA
3812828 TTAA
1 TTAA
3812832 TTAATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:3819584 original size:18 final size:18
Alignment explanation
Indices: 3819561--3819596 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3819551 TATACAAATT
3819561 TAACATCAGTGAGATCAG
1 TAACATCAGTGAGATCAG
3819579 TAACATCAGTGAGATCAG
1 TAACATCAGTGAGATCAG
3819597 GGTTTTCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (18 bp):
TAACATCAGTGAGATCAG
Found at i:3820758 original size:23 final size:22
Alignment explanation
Indices: 3820713--3820760 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3820703 ACCTTTAAAA
** *
3820713 TTTTTAAAAATTATTTTTTATT
1 TTTTTAAAAATTATTAATCATT
3820735 TTTTTAAAAAATTATTAATCATT
1 TTTTT-AAAAATTATTAATCATT
3820758 TTT
1 TTT
3820761 AAATTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTAAAAATTATTAATCATT
Found at i:3821465 original size:2 final size:2
Alignment explanation
Indices: 3821458--3821487 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3821448 GGATGAAATG
3821458 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3821488 GGGATAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3821846 original size:27 final size:27
Alignment explanation
Indices: 3821792--3821846 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
3821782 TTAATTATAA
* **
3821792 AATATTTATATAAAATAAAATATTTTT
1 AATATTTATAAAAAATAAAATAAATTT
3821819 AATATTT-TAAAATAATAAAATAAATTT
1 AATATTTATAAAA-AATAAAATAAATTT
3821846 A
1 A
3821847 TAAATCGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATATTTATAAAAAATAAAATAAATTT
Found at i:3823269 original size:14 final size:13
Alignment explanation
Indices: 3823250--3823283 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
3823240 TAAAATAAAA
3823250 AAAATTTAAATATT
1 AAAATTTAAAT-TT
3823264 AAAATTTAAATTT
1 AAAATTTAAATTT
3823277 -AAATTTA
1 AAAATTTA
3823284 TTAAACATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 2 0.10
14 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATTTAAATTT
Found at i:3824660 original size:7 final size:7
Alignment explanation
Indices: 3824650--3824681 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
3824640 ACTAAAACCA
3824650 AAAAATT
1 AAAAATT
3824657 AAAAATT
1 AAAAATT
3824664 AAAAATT
1 AAAAATT
*
3824671 AAAAATC
1 AAAAATT
3824678 AAAA
1 AAAA
3824682 GGATCCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (7 bp):
AAAAATT
Found at i:3832301 original size:27 final size:28
Alignment explanation
Indices: 3832269--3832326 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
3832259 AAATTTTTTA
*
3832269 AATATTTATATATTTTA-TTTTTATA-TC
1 AATATTTATA-ATTATATTTTTTATATTC
3832296 AATATTTATAATTATATTTTTTATATTC
1 AATATTTATAATTATATTTTTTATATTC
3832324 AAT
1 AAT
3832327 TCAATTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 5 0.18
27 18 0.64
28 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (28 bp):
AATATTTATAATTATATTTTTTATATTC
Found at i:3833568 original size:2 final size:2
Alignment explanation
Indices: 3833561--3833600 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3833551 GTATCCTTTC
3833561 CT 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 CT
3833601 TAAATTGGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3835229 original size:2 final size:2
Alignment explanation
Indices: 3835222--3835253 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3835212 AAATCCTGAA
*
3835222 AT AT AT AT AC 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
3835254 GTCAAGTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3837321 original size:12 final size:12
Alignment explanation
Indices: 3837304--3837338 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3837294 AAAAGGAAAT
3837304 GTGAGAGAGAGA
1 GTGAGAGAGAGA
3837316 GTGAGAGAGAGA
1 GTGAGAGAGAGA
* *
3837328 GAGAGACAGAG
1 GTGAGAGAGAG
3837339 GCACTTCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.43, C:0.03, G:0.49, T:0.06
Consensus pattern (12 bp):
GTGAGAGAGAGA
Found at i:3840210 original size:31 final size:31
Alignment explanation
Indices: 3840167--3840322 Score: 213
Period size: 31 Copynumber: 5.0 Consensus size: 31
3840157 CGGTTCAAAA
3840167 TAAAAATAACTATTCTTATCCGGTGACACGG
1 TAAAAATAACTATTCTTATCCGGTGACACGG
* *
3840198 TAAAAATTACTATTCTTATCCGGTGATACGG
1 TAAAAATAACTATTCTTATCCGGTGACACGG
* * *
3840229 CAAAAATCACTATTCTTATCCGGTGGCACGG
1 TAAAAATAACTATTCTTATCCGGTGACACGG
* * *
3840260 CAAAAATCACTATTCTTATCCGGTGGCACGG
1 TAAAAATAACTATTCTTATCCGGTGACACGG
* * *
3840291 TAAAAACAACTATTCTTAACTGGTGACACGG
1 TAAAAATAACTATTCTTATCCGGTGACACGG
3840322 T
1 T
3840323 TTGAAATCAA
Statistics
Matches: 113, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 113 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (31 bp):
TAAAAATAACTATTCTTATCCGGTGACACGG
Found at i:3864669 original size:7 final size:7
Alignment explanation
Indices: 3864659--3864692 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
3864649 AAATAAATAA
3864659 ATATTTT
1 ATATTTT
3864666 ATATTTT
1 ATATTTT
3864673 ATATTATT
1 ATATT-TT
*
3864681 AAATTTT
1 ATATTTT
3864688 ATATT
1 ATATT
3864693 AATTTTTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
ATATTTT
Found at i:3864688 original size:15 final size:15
Alignment explanation
Indices: 3864659--3864693 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3864649 AAATAAATAA
*
3864659 ATATT-TTATATTTT
1 ATATTATTAAATTTT
3864673 ATATTATTAAATTTT
1 ATATTATTAAATTTT
3864688 ATATTA
1 ATATTA
3864694 ATTTTTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATTATTAAATTTT
Found at i:3864728 original size:23 final size:24
Alignment explanation
Indices: 3864691--3864766 Score: 77
Period size: 23 Copynumber: 3.1 Consensus size: 24
3864681 AAATTTTATA
*
3864691 TTAATTTTTACATAAATATTAAATTT
1 TTAATTATTA-ATAAA-ATTAAATTT
*
3864717 TTAATT-TT-ATAACATTATAATTT
1 TTAATTATTAATAAAATTA-AATTT
3864740 TT-ATTATTAATAAAATTAAATTAT
1 TTAATTATTAATAAAATTAAATT-T
3864764 TTA
1 TTA
3864767 TGTTAATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
22 7 0.16
23 17 0.40
24 11 0.26
25 2 0.05
26 6 0.14
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAATTATTAATAAAATTAAATTT
Found at i:3867091 original size:2 final size:2
Alignment explanation
Indices: 3867084--3867113 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3867074 ACAATTTTTC
3867084 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
3867114 TGCAGATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3868380 original size:30 final size:27
Alignment explanation
Indices: 3868332--3868387 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 27
3868322 TCTTAATTGT
3868332 TTTTTATTTTTATTATATTTAAATAAA
1 TTTTTATTTTTATTATATTTAAATAAA
3868359 TTTTTATCTTTTGATTTATATTTAAATAA
1 TTTTTAT-TTTT-A-TTATATTTAAATAA
3868388 GAATTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 1 0.04
30 14 0.54
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTTATTTTTATTATATTTAAATAAA
Found at i:3879413 original size:21 final size:20
Alignment explanation
Indices: 3879389--3879431 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
3879379 GCAATATTTT
*
3879389 ATATAAAAATAATTTTAAATA
1 ATATAAAAATAA-TATAAATA
*
3879410 ATATAATAATAATATAAATA
1 ATATAAAAATAATATAAATA
3879430 AT
1 AT
3879432 TTTTTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATAAAAATAATATAAATA
Found at i:3879415 original size:15 final size:15
Alignment explanation
Indices: 3879384--3879434 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3879374 AAAAAGCAAT
*
3879384 ATTTTATATAAAAATA
1 ATTTTA-ATATAAATA
3879400 ATTTTAA-ATAATATA
1 ATTTTAATATAA-ATA
**
3879415 ATAATAATATAAATA
1 ATTTTAATATAAATA
3879430 ATTTT
1 ATTTT
3879435 TTATAATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 3 0.11
15 15 0.54
16 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTTAATATAAATA
Found at i:3879442 original size:10 final size:10
Alignment explanation
Indices: 3879427--3879466 Score: 62
Period size: 11 Copynumber: 3.8 Consensus size: 10
3879417 AATAATATAA
3879427 ATAATTTTTT
1 ATAATTTTTT
3879437 ATAATTATTTT
1 ATAATT-TTTT
3879448 ATAATATTTTT
1 ATAAT-TTTTT
3879459 ATAATTTT
1 ATAATTTT
3879467 ATATTTGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.32
11 18 0.64
12 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:3879452 original size:30 final size:29
Alignment explanation
Indices: 3879381--3879454 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
3879371 ATAAAAAAGC
*
3879381 AATATTTTAT-ATAAAAATAATTTTAAAT
1 AATATTTTATAATATAAATAATTTTAAAT
* * **
3879409 AATATAATAATAATATAAATAATTTTTTAT
1 AATAT-TTTATAATATAAATAATTTTAAAT
3879439 AATTATTTTATAATAT
1 AA-TATTTTATAATAT
3879455 TTTTATAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
28 5 0.14
29 3 0.08
30 25 0.69
31 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AATATTTTATAATATAAATAATTTTAAAT
Found at i:3879616 original size:33 final size:32
Alignment explanation
Indices: 3879570--3879642 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
3879560 TAATCATATA
*
3879570 ATATAACACAAATTGACAAACATTTCAAAATTT
1 ATATAAAACAAATT-ACAAACATTTCAAAATTT
* ** *
3879603 ATATAAAATAAATTATTAACATTTTAAAATTT
1 ATATAAAACAAATTACAAACATTTCAAAATTT
*
3879635 ATACAAAA
1 ATATAAAA
3879643 ATAATAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 22 0.65
33 12 0.35
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.34
Consensus pattern (32 bp):
ATATAAAACAAATTACAAACATTTCAAAATTT
Found at i:3882306 original size:3 final size:3
Alignment explanation
Indices: 3882300--3882327 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3882290 TTATAATTCT
3882300 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3882328 TCTTTCGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3882905 original size:30 final size:30
Alignment explanation
Indices: 3882826--3882907 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
3882816 TTAAATCAGA
3882826 TTTATATTTTT-A-TTATA-TTAGAATAAGTG
1 TTTA-ATTTTTAATTTATATTTA-AATAAGTG
* * *
3882855 TTTAATTTTTATTTTATATTTAAATAATTT
1 TTTAATTTTTAATTTATATTTAAATAAGTG
3882885 TTTAATTTTTAATTTATATTTAA
1 TTTAATTTTTAATTTATATTTAA
3882908 TTAAAATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 6 0.13
29 4 0.09
30 33 0.72
31 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTAATTTTTAATTTATATTTAAATAAGTG
Found at i:3882918 original size:30 final size:30
Alignment explanation
Indices: 3882855--3882919 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
3882845 AGAATAAGTG
* **
3882855 TTTAATTTTTATTTTATATTTAAATAATTT
1 TTTAATTTTTAATTTATATTTAAATAAAAT
*
3882885 TTTAATTTTTAATTTATATTTAATTAAAAT
1 TTTAATTTTTAATTTATATTTAAATAAAAT
3882915 TTTAA
1 TTTAA
3882920 ATAAAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTAATTTTTAATTTATATTTAAATAAAAT
Found at i:3882954 original size:22 final size:22
Alignment explanation
Indices: 3882915--3882973 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
3882905 TAATTAAAAT
*
3882915 TTTAAATAAAATTATTATTTTA
1 TTTAAATAAAAATATTATTTTA
3882937 TTTAATATAAAAAT-TTATTTTA
1 TTTAA-ATAAAAATATTATTTTA
*
3882959 -GTATAATAAAAATAT
1 TTTA-AATAAAAATAT
3882974 AAAATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 10 0.31
22 15 0.47
23 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTAAATAAAAATATTATTTTA
Done.