Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 84 of 144
Found at i:25568173 original size:25 final size:24
Alignment explanation
Indices: 25568120--25568167 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
25568110 CATTTAAATA
25568120 AATAAATAAATTTATGTTTATATTG
1 AATAAATAAATTTATG-TTATATTG
25568145 AATAAATATAATTATATG-TATAT
1 AATAAATA-AATT-TATGTTATAT
25568168 GCAATATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
25 13 0.62
26 4 0.19
27 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (24 bp):
AATAAATAAATTTATGTTATATTG
Found at i:25570300 original size:5 final size:5
Alignment explanation
Indices: 25570290--25570360 Score: 62
Period size: 5 Copynumber: 14.6 Consensus size: 5
25570280 GTAAAAATAT
* *
25570290 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TCATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA T-ATTA
25570336 -A-TA TATTA TATTA TATTA TA-TA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT
25570361 ACATAAAACA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
3 4 0.07
4 8 0.15
5 32 0.58
6 10 0.18
7 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (5 bp):
TATTA
Found at i:25570342 original size:19 final size:19
Alignment explanation
Indices: 25570318--25570360 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
25570308 ATTATGTTTT
25570318 TATATTATATTATCATTA-A
1 TATATTATATTAT-ATTATA
25570337 TATATTATATTATATTATA
1 TATATTATATTATATTATA
25570356 TATAT
1 TATAT
25570361 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:25570392 original size:17 final size:17
Alignment explanation
Indices: 25570370--25570403 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25570360 TACATAAAAC
*
25570370 AAAAGAAAGAATAGAAA
1 AAAAGAAAGAAAAGAAA
25570387 AAAAGAAAGAAAAGAAA
1 AAAAGAAAGAAAAGAAA
25570404 CAGAATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAAGAAAGAAAAGAAA
Found at i:25570399 original size:9 final size:9
Alignment explanation
Indices: 25570370--25570403 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
25570360 TACATAAAAC
25570370 AAAAGAAAG
1 AAAAGAAAG
*
25570379 AATAGAAA-
1 AAAAGAAAG
25570387 AAAAGAAAG
1 AAAAGAAAG
25570396 AAAAGAAA
1 AAAAGAAA
25570404 CAGAATAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:25571424 original size:46 final size:44
Alignment explanation
Indices: 25571372--25571457 Score: 136
Period size: 46 Copynumber: 1.9 Consensus size: 44
25571362 AGAACAGAAA
*
25571372 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGAT
1 TGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAGACAGGAT
*
25571418 TGAGCCATGTAAGTCCATATTATATATGGCATTGGAGACA
1 TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACA
25571458 TGAATAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 17 0.45
46 21 0.55
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (44 bp):
TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGGAT
Found at i:25571471 original size:44 final size:45
Alignment explanation
Indices: 25571365--25571498 Score: 135
Period size: 46 Copynumber: 3.0 Consensus size: 45
25571355 ACAGGACAGA
* * *
25571365 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* * *
25571411 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
25571455 ACATGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
25571499 CAGGATATTG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
44 35 0.48
45 1 0.01
46 37 0.51
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:25572796 original size:250 final size:250
Alignment explanation
Indices: 25572355--25572855 Score: 966
Period size: 250 Copynumber: 2.0 Consensus size: 250
25572345 AGTCTATTTT
25572355 CTATAGAAACAAGTAAGAACTTCATATGAAAATCCTATAGCGAGAAAACTTATTTTTAGTGACTA
1 CTATAGAAACAAGTAAGAACTTCATATGAAAATCCTATAGCGAGAAAACTTATTTTTAGTGACTA
25572420 GAGGTCAGGGCAGTCTGGTGGTGACACAGGGGAGACTTTAACTAATAAACTGTACTAATTTGCTA
66 GAGGTCAGGGCAGTCTGGTGGTGACACAGGGGAGACTTTAACTAATAAACTGTACTAATTTGCTA
25572485 AACCAAAAATTCTAAAAATTTTATGGTGAGTAGATATATGAGTCTAGTTTCAGGGAAAATTTACG
131 AACCAAAAATTCTAAAAATTTTATGGTGAGTAGATATATGAGTCTAGTTTCAGGGAAAATTTACG
25572550 GGATTAAATTTCGAGTTCTTTAGCTCAAGTTATAATTAATTTAGTAACTGCTGCG
196 GGATTAAATTTCGAGTTCTTTAGCTCAAGTTATAATTAATTTAGTAACTGCTGCG
*
25572605 CTATAGAAACAAGTAAGAACTTCATATGAAAATCCTATAGCGATAAAACTTATTTTTAGTGACTA
1 CTATAGAAACAAGTAAGAACTTCATATGAAAATCCTATAGCGAGAAAACTTATTTTTAGTGACTA
*
25572670 GAGGTCAGGGCAGTCTGGTGGTGACACAGGGGAGACTTTAACTAATAAGCTGTACTAATTTGCTA
66 GAGGTCAGGGCAGTCTGGTGGTGACACAGGGGAGACTTTAACTAATAAACTGTACTAATTTGCTA
*
25572735 AACCAAAAATTCTAAAAATTTTATGGTGAGTAGATATATGAGTCTAGTTTCAGGTAAAATTTACG
131 AACCAAAAATTCTAAAAATTTTATGGTGAGTAGATATATGAGTCTAGTTTCAGGGAAAATTTACG
*
25572800 GGATTAAATTTTGAGTTCTTTAGCTCAAGTTATAATTAATTTAGTAACTGCTGCG
196 GGATTAAATTTCGAGTTCTTTAGCTCAAGTTATAATTAATTTAGTAACTGCTGCG
25572855 C
1 C
25572856 GATTAGACAG
Statistics
Matches: 247, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
250 247 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (250 bp):
CTATAGAAACAAGTAAGAACTTCATATGAAAATCCTATAGCGAGAAAACTTATTTTTAGTGACTA
GAGGTCAGGGCAGTCTGGTGGTGACACAGGGGAGACTTTAACTAATAAACTGTACTAATTTGCTA
AACCAAAAATTCTAAAAATTTTATGGTGAGTAGATATATGAGTCTAGTTTCAGGGAAAATTTACG
GGATTAAATTTCGAGTTCTTTAGCTCAAGTTATAATTAATTTAGTAACTGCTGCG
Found at i:25577367 original size:5 final size:5
Alignment explanation
Indices: 25577357--25577428 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
25577347 TGTTAAAAAA
* *
25577357 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATCATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT AT-ATT
25577403 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
25577429 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 33 0.59
6 10 0.18
7 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:25577410 original size:19 final size:19
Alignment explanation
Indices: 25577386--25577428 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
25577376 ATTATGTTTT
25577386 TATATTATATTATCATTA-A
1 TATATTATATTAT-ATTATA
25577405 TATATTATATTATATTATA
1 TATATTATATTATATTATA
25577424 TATAT
1 TATAT
25577429 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:25577460 original size:17 final size:17
Alignment explanation
Indices: 25577438--25577471 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25577428 TACATAAAAC
*
25577438 AAAAGAAAGAATAGAAA
1 AAAAGAAAGAAAAGAAA
25577455 AAAAGAAAGAAAAGAAA
1 AAAAGAAAGAAAAGAAA
25577472 CAGAATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAAGAAAGAAAAGAAA
Found at i:25577467 original size:9 final size:9
Alignment explanation
Indices: 25577438--25577471 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
25577428 TACATAAAAC
25577438 AAAAGAAAG
1 AAAAGAAAG
*
25577447 AATAGAAA-
1 AAAAGAAAG
25577455 AAAAGAAAG
1 AAAAGAAAG
25577464 AAAAGAAA
1 AAAAGAAA
25577472 CAGAATAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:25577538 original size:4 final size:4
Alignment explanation
Indices: 25577531--25577558 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
25577521 GAGAAGGAAG
25577531 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
25577559 AAGAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:25578493 original size:46 final size:44
Alignment explanation
Indices: 25578434--25578548 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
25578424 ACAGGACAGA
* *
25578434 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
25578480 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
25578524 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
25578549 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:25578529 original size:44 final size:45
Alignment explanation
Indices: 25578434--25578567 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
25578424 ACAGGACAGA
* *
25578434 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
25578480 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
25578524 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
25578568 CAGGGTATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:25580176 original size:2 final size:2
Alignment explanation
Indices: 25580171--25580197 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25580161 TATATATATA
25580171 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
25580198 CAAGAAATAA
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:25584106 original size:63 final size:63
Alignment explanation
Indices: 25584034--25584157 Score: 239
Period size: 63 Copynumber: 2.0 Consensus size: 63
25584024 CAAACAACCC
*
25584034 TTGAAAGTTTGTGGCAATGGAGCAACTAAGCAAAACTTTCTTTCTTCTATTTTTTTGTACTCT
1 TTGAAAGTTTGTGGCAATGGAGCAACTAAGCAAAACTTTCTTTCTTCTATTTCTTTGTACTCT
25584097 TTGAAAGTTTGTGGCAATGGAGCAACTAAGCAAAACTTTCTTTCTTCTATTTCTTTGTACT
1 TTGAAAGTTTGTGGCAATGGAGCAACTAAGCAAAACTTTCTTTCTTCTATTTCTTTGTACT
25584158 TTTTCCCACT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (63 bp):
TTGAAAGTTTGTGGCAATGGAGCAACTAAGCAAAACTTTCTTTCTTCTATTTCTTTGTACTCT
Found at i:25587575 original size:51 final size:51
Alignment explanation
Indices: 25587520--25587658 Score: 122
Period size: 51 Copynumber: 2.7 Consensus size: 51
25587510 TATAGCCTGG
* * * *
25587520 TGGTGCCGACAACGAGAACA-CCAACA-CAAAAGAAAATTGCATTAACAACAC
1 TGGTGCCGACAACAAGAA-AGCCAACACCAAAA-AAAATTGCAATAAAAAAAC
* * *
25587571 TGGTGCTGGCAACAAGAAAGCCAACACCAAAAAAAATTTCAATAAAAAAAC
1 TGGTGCCGACAACAAGAAAGCCAACACCAAAAAAAATTGCAATAAAAAAAC
* ** *
25587622 TGGTGCTGGA-TTCAGGAAAGCCAACACCAAATAAAAA
1 TGGTGC-CGACAACAAGAAAGCCAACACCAAA-AAAAA
25587659 ATATTTTTTA
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
50 1 0.01
51 60 0.83
52 11 0.15
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.14
Consensus pattern (51 bp):
TGGTGCCGACAACAAGAAAGCCAACACCAAAAAAAATTGCAATAAAAAAAC
Found at i:25591577 original size:30 final size:30
Alignment explanation
Indices: 25591543--25591601 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
25591533 TGTTAAGCTA
25591543 TATGTATGGAACTTGAATGGCATATTTGGT
1 TATGTATGGAACTTGAATGGCATATTTGGT
*
25591573 TATGTATGGCACTTGAATGGCATATTTGG
1 TATGTATGGAACTTGAATGGCATATTTGG
25591602 GGTATGAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.39
Consensus pattern (30 bp):
TATGTATGGAACTTGAATGGCATATTTGGT
Found at i:25602450 original size:209 final size:208
Alignment explanation
Indices: 25602086--25602481 Score: 559
Period size: 209 Copynumber: 1.9 Consensus size: 208
25602076 CGTTCGAAGA
* * * *
25602086 TCCATCATCCGTCTTATTTTCGTTTTCTTCCAATCAATATTTTTATTTTCATCTCACCCCCAATA
1 TCCATCATCCATCTTATTTTCATTTTCTTCCAATCAATAATTGTATTTTCATCTCACCCCCAATA
* * * *
25602151 TTTATTTTTTGATTTTATGTTTTGTTTTTCTGTTTATTTCTATTATTTCTAATCTGTTTTGTTTT
66 TTTATTTTTTGATTTTATGTTTTGTTTTTCTCTTTATTTCCATTATTTCTAATCTATTTTGTTTC
* *
25602216 TTCTTTCAGGTCAAATCCAAATCTTTCACGAGTCAAACAACTTGAATATGATCTTCTGCTACCCT
131 TTCTTTCAAGTCAAATCCAAATCTTTCACGAGTCAAACAACTTGAATACGATCTTCTGCTACCCT
25602281 ATTAGACTATCTT
196 ATTAGACTATCTT
*
25602294 TCCATCATCCATCTTATTTTCATTTTCTTCCATTCAA-AATTGT-TTTTCATCTCA-CCCCAATA
1 TCCATCATCCATCTTATTTTCATTTTCTTCCAATCAATAATTGTATTTTCATCTCACCCCCAATA
25602356 TTTATTATTTTCTTGATTTTATGTTTTGTTTTTCTCTTTATTTCCATTATTTCTAAT-TCATTTT
66 --T-TTATTTT-TTGATTTTATGTTTTGTTTTTCTCTTTATTTCCATTATTTCTAATCT-ATTTT
* * ** *
25602420 GTTTCTTCTTTTAAGTCAGAT-CAGAATCTTTCTTGAGTCGAACAACTTGAATACGATCTTCT
126 GTTTCTTCTTTCAAGTCAAATCCA-AATCTTTCACGAGTCAAACAACTTGAATACGATCTTCT
25602482 TCCACTGCCC
Statistics
Matches: 166, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
205 8 0.05
206 11 0.07
207 5 0.03
208 44 0.27
209 98 0.59
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.51
Consensus pattern (208 bp):
TCCATCATCCATCTTATTTTCATTTTCTTCCAATCAATAATTGTATTTTCATCTCACCCCCAATA
TTTATTTTTTGATTTTATGTTTTGTTTTTCTCTTTATTTCCATTATTTCTAATCTATTTTGTTTC
TTCTTTCAAGTCAAATCCAAATCTTTCACGAGTCAAACAACTTGAATACGATCTTCTGCTACCCT
ATTAGACTATCTT
Found at i:25605869 original size:8 final size:8
Alignment explanation
Indices: 25605855--25605890 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
25605845 AGTTCTTTGC
25605855 CAAAAAAA
1 CAAAAAAA
*
25605863 AAAAAAAA
1 CAAAAAAA
25605871 CAAAAAAA
1 CAAAAAAA
*
25605879 CAAAAAAC
1 CAAAAAAA
25605887 CAAA
1 CAAA
25605891 GCAAATGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:25605877 original size:15 final size:15
Alignment explanation
Indices: 25605857--25605886 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25605847 TTCTTTGCCA
25605857 AAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
*
25605872 AAAAAAACAAAAAAC
1 AAAAAAAAAAAAAAC
25605887 CAAAGCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:25610399 original size:27 final size:28
Alignment explanation
Indices: 25610354--25610410 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
25610344 CTCTAATATT
* *
25610354 TATTAAAAGTATAGTTTTATATTATGTA
1 TATTAAAAGTAGAGCTTTATATTATGTA
*
25610382 TATT-AAAGTAGAGCTTTATATTATTTA
1 TATTAAAAGTAGAGCTTTATATTATGTA
25610409 TA
1 TA
25610411 CTTTTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.49
Consensus pattern (28 bp):
TATTAAAAGTAGAGCTTTATATTATGTA
Found at i:25613674 original size:20 final size:18
Alignment explanation
Indices: 25613638--25613682 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
25613628 AAACCTTAAA
25613638 TTTTCCCTTTCTTCTTTC
1 TTTTCCCTTTCTTCTTTC
25613656 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTTC-TTCTTTC
25613676 -TTTCCCT
1 TTTTCCCT
25613683 GCTTTTCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTC
Found at i:25614347 original size:10 final size:10
Alignment explanation
Indices: 25614332--25614356 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25614322 CCATAATTTA
25614332 TGATACAAAT
1 TGATACAAAT
25614342 TGATACAAAT
1 TGATACAAAT
25614352 TGATA
1 TGATA
25614357 ATAGGTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (10 bp):
TGATACAAAT
Found at i:25614388 original size:26 final size:26
Alignment explanation
Indices: 25614352--25614461 Score: 170
Period size: 26 Copynumber: 4.2 Consensus size: 26
25614342 TGATACAAAT
25614352 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
25614378 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
25614404 TGATAAT-GAGTTAGGTAAATGTTTCA
1 TGATAATAG-GTTAGGTAAATGTTTCA
*
25614430 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
25614456 TGATAA
1 TGATAA
25614462 GAATTTCATG
Statistics
Matches: 79, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
25 1 0.01
26 75 0.95
27 3 0.04
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:25616104 original size:27 final size:27
Alignment explanation
Indices: 25616072--25616182 Score: 116
Period size: 27 Copynumber: 4.1 Consensus size: 27
25616062 GGAAGTGTTT
* *
25616072 TGGTGGTTATGCCACAAATATCTGATC
1 TGGTGGCTCTGCCACAAATATCTGATC
* *
25616099 TGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTCTGCCACAAATATCTGATC
*
25616126 TGGTGGCTCTGCCACAATTATCTGTATC
1 TGGTGGCTCTGCCACAAATATCTG-ATC
* * * * *
25616154 TGATGACTCTGTCAC-ATTATCTGTTC
1 TGGTGGCTCTGCCACAAATATCTGATC
25616180 TGG
1 TGG
25616183 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 4 0.06
27 53 0.75
28 14 0.20
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.37
Consensus pattern (27 bp):
TGGTGGCTCTGCCACAAATATCTGATC
Found at i:25616175 original size:54 final size:54
Alignment explanation
Indices: 25616067--25616182 Score: 153
Period size: 54 Copynumber: 2.1 Consensus size: 54
25616057 ATGGAGGAAG
* * * *
25616067 TGTTTTGGTGGTTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATC
1 TGTTCTGGTGGCTATGCCACAAATATCTGATCTGATGACTCTGCCACATATATC
* * *
25616121 TGTTCTGGTGGCTCTGCCACAATTATCTGTATCTGATGACTCTGTCACAT-TATC
1 TGTTCTGGTGGCTATGCCACAAATATCTG-ATCTGATGACTCTGCCACATATATC
25616175 TGTTCTGG
1 TGTTCTGG
25616183 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 37 0.69
55 17 0.31
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.39
Consensus pattern (54 bp):
TGTTCTGGTGGCTATGCCACAAATATCTGATCTGATGACTCTGCCACATATATC
Found at i:25621042 original size:29 final size:30
Alignment explanation
Indices: 25620995--25621063 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
25620985 TGGCCCAAGA
* * *
25620995 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TGAAAAGTTGAAGGACTAATAGT
25621025 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATGAAAAGTTGAAGGACTAATAGT
*
25621055 GCAAATATG
1 GTAAATATG
25621064 TTAAGGGTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.47
30 18 0.53
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (30 bp):
GTAAATATGAAAAGTTGAAGGACTAATAGT
Found at i:25621063 original size:30 final size:29
Alignment explanation
Indices: 25621005--25621063 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
25620995 GTAAATACTC
* * *
25621005 AAAATTTGAAGGATTAAAGTGTAAATATG
1 AAAAGTTGAAGGACTAAAGTGCAAATATG
25621034 AAAAGTTGAAGGACTAATAGTGCAAATATG
1 AAAAGTTGAAGGACTAA-AGTGCAAATATG
25621064 TTAAGGGTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.47, C:0.03, G:0.22, T:0.27
Consensus pattern (29 bp):
AAAAGTTGAAGGACTAAAGTGCAAATATG
Found at i:25623280 original size:46 final size:46
Alignment explanation
Indices: 25623221--25623392 Score: 245
Period size: 46 Copynumber: 3.7 Consensus size: 46
25623211 ATGAAATGTG
*
25623221 TAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAA
* * * *
25623267 TAAGACCATGGTTGGAAGATACCATGGCAACGTGATATGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAA
* *
25623313 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAA
* * * *
25623359 TAAGACCATAGTTGAAAGACACTATGGCATCATG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATG
25623393 TCAAAGATAA
Statistics
Matches: 111, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 111 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAA
Found at i:25623364 original size:92 final size:92
Alignment explanation
Indices: 25623207--25623387 Score: 281
Period size: 92 Copynumber: 2.0 Consensus size: 92
25623197 GTGTGTTCTC
** * *
25623207 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATGAATAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGA
* * *
25623272 CCATGGTTGGAAGATACCATGGCAACG
66 CCATAGTTGAAAGACACCATGGCAACG
*
25623299 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGA
*
25623364 CCATAGTTGAAAGACACTATGGCA
66 CCATAGTTGAAAGACACCATGGCA
25623388 TCATGTCAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 80 1.00
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (92 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGA
CCATAGTTGAAAGACACCATGGCAACG
Found at i:25623694 original size:16 final size:17
Alignment explanation
Indices: 25623673--25623705 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25623663 ATGATAGAGC
25623673 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
25623689 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
25623706 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:25627917 original size:44 final size:45
Alignment explanation
Indices: 25627851--25627944 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 45
25627841 TATTAATGCA
* * *
25627851 ATATTTGGTACTACAAATTTAGTTTAAAGCTCCAAAAGAGCTAAT
1 ATATTGGGTACTACAAAATTAGTTGAAAGCTCCAAAAGAGCTAAT
* *
25627896 -TATTGGGTAGTACAAAATTAGTTGAAAGCTCCAAAAGAGTTAAT
1 ATATTGGGTACTACAAAATTAGTTGAAAGCTCCAAAAGAGCTAAT
25627940 ATATT
1 ATATT
25627945 AATATTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 39 0.91
45 4 0.09
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (45 bp):
ATATTGGGTACTACAAAATTAGTTGAAAGCTCCAAAAGAGCTAAT
Found at i:25629327 original size:96 final size:95
Alignment explanation
Indices: 25629217--25629405 Score: 288
Period size: 96 Copynumber: 2.0 Consensus size: 95
25629207 AAGACACTTA
* *
25629217 TCAATTTATATCATGCTTATTTCTATTTTATTCATTTCAATCCAATTCTCAACATTTAATATCAA
1 TCAATTTATATCATGCTTATTTATATTTTATTCATTTCAATCCAATTCTCAACATTCAATATCAA
25629282 CAATCACGAATCAAGTCATGAGACATTTTT
66 CAATCACGAATCAAGTCATGAGACATTTTT
* * * *
25629312 TCAATTTGTTATCATGCTTATTTATATTTTATTCATTTCAGTCCAATTCTCGATATTCAATATCA
1 TCAATTT-ATATCATGCTTATTTATATTTTATTCATTTCAATCCAATTCTCAACATTCAATATCA
** *
25629377 ACAATTGCGAATCAAGTCATGAGATATTT
65 ACAATCACGAATCAAGTCATGAGACATTT
25629406 AATCATCTTA
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 7 0.08
96 77 0.92
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.43
Consensus pattern (95 bp):
TCAATTTATATCATGCTTATTTATATTTTATTCATTTCAATCCAATTCTCAACATTCAATATCAA
CAATCACGAATCAAGTCATGAGACATTTTT
Found at i:25630209 original size:21 final size:20
Alignment explanation
Indices: 25630184--25630222 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
25630174 GAGTATTTTG
25630184 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
25630205 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
25630223 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:25630845 original size:52 final size:48
Alignment explanation
Indices: 25630773--25630961 Score: 204
Period size: 48 Copynumber: 3.9 Consensus size: 48
25630763 ATTAGGGATA
*
25630773 TATTGAGTTGGCTTCAGGCCATGATATTGGCACTTCAGGTGCGA-GATATAT
1 TATTGAGTTGGCTTCGGGCCATGATATTGGCACTTCAGGTGC-ATG--AT-T
* * **
25630824 ATATTGAGTTAGCTAT-GGGCCATGATATTTGCACTTTGGGTGCATGATT
1 -TATTGAGTTGGCT-TCGGGCCATGATATTGGCACTTCAGGTGCATGATT
* * *
25630873 TATTGAGTTGGCTACGAGCCATGATATTTGCACTTC-GAGTGCATGATT
1 TATTGAGTTGGCTTCGGGCCATGATATTGGCACTTCAG-GTGCATGATT
* *
25630921 TATTGAGTTGGCTTCGGGCTATGATATTGGCACTTAAGGTG
1 TATTGAGTTGGCTTCGGGCCATGATATTGGCACTTCAGGTG
25630962 AAAAACTCTC
Statistics
Matches: 118, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
47 1 0.01
48 75 0.64
49 2 0.02
50 2 0.02
51 1 0.01
52 36 0.31
53 1 0.01
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (48 bp):
TATTGAGTTGGCTTCGGGCCATGATATTGGCACTTCAGGTGCATGATT
Found at i:25632980 original size:11 final size:11
Alignment explanation
Indices: 25632964--25632996 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
25632954 CTCAACAACA
25632964 TTTTTCTTTTC
1 TTTTTCTTTTC
*
25632975 TTTTTCTCTTC
1 TTTTTCTTTTC
25632986 TTTTTCTTTTC
1 TTTTTCTTTTC
25632997 AATTTTGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:25650613 original size:15 final size:14
Alignment explanation
Indices: 25650580--25650618 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
25650570 AAAATTTATA
*
25650580 ATATTATAT-ATAT
1 ATATAATATGATAT
25650593 ATATAATATGATAT
1 ATATAATATGATAT
25650607 GATATAATATGA
1 -ATATAATATGA
25650619 AAGAGCAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.35
14 4 0.17
15 11 0.48
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (14 bp):
ATATAATATGATAT
Found at i:25652902 original size:17 final size:17
Alignment explanation
Indices: 25652867--25652904 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
25652857 AGATAAAAAG
*
25652867 TAAATTATTTATGAGAA
1 TAAATTATTTATGACAA
25652884 TAAATTATTT-TGAACAA
1 TAAATTATTTATG-ACAA
25652901 TAAA
1 TAAA
25652905 AATTGGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (17 bp):
TAAATTATTTATGACAA
Found at i:25652982 original size:15 final size:15
Alignment explanation
Indices: 25652962--25652990 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25652952 AAAATAAACA
25652962 AAATAAAATAATAAT
1 AAATAAAATAATAAT
25652977 AAATAAAATAATAA
1 AAATAAAATAATAA
25652991 AATTTTAATT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAAATAATAAT
Found at i:25654507 original size:3 final size:3
Alignment explanation
Indices: 25654499--25654525 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
25654489 TTTTGATGCA
25654499 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
25654526 TATTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:25663083 original size:33 final size:33
Alignment explanation
Indices: 25663046--25663115 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
25663036 TATTATCAAC
* *
25663046 CATACCAAAACATTCCCAAAAATATGTTCAAAT
1 CATACCAAAACATACCCAAAAACATGTTCAAAT
* * * *
25663079 CATACCTAAACATACTCAAAAGCATTTTCAAAT
1 CATACCAAAACATACCCAAAAACATGTTCAAAT
25663112 CATA
1 CATA
25663116 TTTAAATAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (33 bp):
CATACCAAAACATACCCAAAAACATGTTCAAAT
Found at i:25668723 original size:80 final size:79
Alignment explanation
Indices: 25668639--25668810 Score: 211
Period size: 79 Copynumber: 2.2 Consensus size: 79
25668629 GGACTAAGAT
*
25668639 CCGAAGGCATTTGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATGACAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
25668703 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * ** * * * *
25668719 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
25668784 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
25668798 CCGAAGGCATTTG
1 CCGAAGGCATTTG
25668811 AACGAGGAGC
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 38 0.49
80 37 0.47
81 3 0.04
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:25668790 original size:39 final size:39
Alignment explanation
Indices: 25668586--25668808 Score: 200
Period size: 40 Copynumber: 5.6 Consensus size: 39
25668576 TTGAATGCTG
* * * * *
25668586 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
25668626 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
25668665 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* **
25668706 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
25668746 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
25668785 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
25668809 TGAACGAGGA
Statistics
Matches: 155, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
39 39 0.25
40 102 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:25668828 original size:79 final size:80
Alignment explanation
Indices: 25668666--25668843 Score: 198
Period size: 79 Copynumber: 2.2 Consensus size: 80
25668656 AGATACAAAT
* * * *
25668666 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** ** *
25668731 GTGCGAGTTGTTAAA
66 GAACGAGGAGCTAAA
* * * * *
25668746 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
25668810 GAACGAGGAGCTATA
66 GAACGAGGAGCTAAA
*
25668825 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
25668844 TACGTGATTT
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 14 0.17
79 49 0.60
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGGAGCTAAA
Found at i:25676579 original size:40 final size:39
Alignment explanation
Indices: 25676548--25676757 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
25676538 GGACTAAGAT
* *
25676548 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
25676588 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
25676628 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
25676668 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
25676708 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
25676747 CCGAAGGCATT
1 CCGAAGGCATT
25676758 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:25676711 original size:120 final size:120
Alignment explanation
Indices: 25676495--25676757 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
25676485 TTGAATGCTG
* *
25676495 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
25676559 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
25676615 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
25676678 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
25676734 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
25676758 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:25676777 original size:79 final size:80
Alignment explanation
Indices: 25676496--25676792 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
25676486 TGAATGCTGT
* ** * * * **
25676496 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
25676559 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
25676576 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
25676640 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
25676656 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
25676720 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
25676735 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
25676793 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:25678340 original size:17 final size:18
Alignment explanation
Indices: 25678318--25678351 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25678308 CAATTCAAGG
25678318 TCAATTT-CACAATTTTA
1 TCAATTTACACAATTTTA
*
25678335 TCAATTTACACCATTTT
1 TCAATTTACACAATTTT
25678352 TAATTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (18 bp):
TCAATTTACACAATTTTA
Found at i:25679311 original size:66 final size:66
Alignment explanation
Indices: 25679205--25679331 Score: 211
Period size: 66 Copynumber: 1.9 Consensus size: 66
25679195 CAATTTAGCA
*
25679205 GATCCCTAGCAGTTAAATTAGAGTCAGCCCTGTATGCATAATACACCAGACCTGGCTTAGTCAGT
1 GATCCCTAGCAGTTAAATTAGAGTCAGCCCTGTATGCATAATACACCAGACCTAGCTTAGTCAGT
25679270 C
66 C
* *
25679271 GATCCCT-GACAGTTAAATTAGAGTTAGCCCTGTATGCATAATACACTAGACCTAGCTTAGT
1 GATCCCTAG-CAGTTAAATTAGAGTCAGCCCTGTATGCATAATACACCAGACCTAGCTTAGT
25679332 ATCTTAGGTA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 1 0.02
66 56 0.98
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (66 bp):
GATCCCTAGCAGTTAAATTAGAGTCAGCCCTGTATGCATAATACACCAGACCTAGCTTAGTCAGT
C
Found at i:25682054 original size:25 final size:23
Alignment explanation
Indices: 25682026--25682072 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
25682016 TTTCCCAATT
*
25682026 TAATTTTATTTCCAATTTATTTAAA
1 TAATGTTATTT-CAA-TTATTTAAA
*
25682051 TAATGTTGTTTCAATTATTTAA
1 TAATGTTATTTCAATTATTTAA
25682073 TTTCTAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 3 0.15
25 9 0.45
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.55
Consensus pattern (23 bp):
TAATGTTATTTCAATTATTTAAA
Found at i:25683305 original size:38 final size:37
Alignment explanation
Indices: 25683263--25683380 Score: 107
Period size: 38 Copynumber: 3.1 Consensus size: 37
25683253 ACACCCAATG
* *
25683263 CCTCATCAGAACATCTGAAGTATAATTTGTGCTTCACA
1 CCTCATCGGAACATCTGAAGT-TAATATGTGCTTCACA
* *
25683301 CCTCATCGGTATAAATC-GAAG-TAATATGTG-TTACGCA
1 CCTCATCGG-A-ACATCTGAAGTTAATATGTGCTT-CACA
* * *
25683338 CCTCATTGGAACATCTGAAGTGTAATATGTGCTCCACG
1 CCTCATCGGAACATCTGAAGT-TAATATGTGCTTCACA
25683376 CCTCA
1 CCTCA
25683381 ACGGCATAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
35 4 0.06
36 7 0.11
37 19 0.30
38 24 0.38
39 6 0.09
40 4 0.06
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (37 bp):
CCTCATCGGAACATCTGAAGTTAATATGTGCTTCACA
Found at i:25694765 original size:17 final size:16
Alignment explanation
Indices: 25694723--25694765 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
25694713 ATGAATTAGC
25694723 TTGAATTAAGGTTAAT
1 TTGAATTAAGGTTAAT
*
25694739 TT-AGTGTAAGGATTAAT
1 TTGAAT-TAAGG-TTAAT
25694756 TTGAATTAAG
1 TTGAATTAAG
25694766 TGTGAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
15 2 0.09
16 7 0.32
17 11 0.50
18 2 0.09
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (16 bp):
TTGAATTAAGGTTAAT
Found at i:25694937 original size:17 final size:18
Alignment explanation
Indices: 25694910--25694948 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
25694900 ATTTACTTAT
25694910 TATATAAGTAAATAATAA
1 TATATAAGTAAATAATAA
*
25694928 TATA-AAGTAAATTATAA
1 TATATAAGTAAATAATAA
25694945 TATA
1 TATA
25694949 GTATATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
TATATAAGTAAATAATAA
Found at i:25694956 original size:15 final size:15
Alignment explanation
Indices: 25694906--25694958 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 15
25694896 ATGTATTTAC
*
25694906 TTATTATATAAGTAAA
1 TTATAATAT-AGTAAA
*
25694922 TAATAATATAAAGTAAA
1 TTATAATAT--AGTAAA
*
25694939 TTATAATATAGTATA
1 TTATAATATAGTAAA
25694954 TTATA
1 TTATA
25694959 TAATTATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 10 0.31
16 7 0.22
17 15 0.47
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
TTATAATATAGTAAA
Found at i:25705373 original size:21 final size:22
Alignment explanation
Indices: 25705336--25705384 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
25705326 ATTCCTTCCA
*
25705336 CCCTTTCATCTCCTTTT-CTTT
1 CCCTTTCATCTCCTTTTCCCTT
*
25705357 CCCTTTC-TCTACTTTTTCCCTT
1 CCCTTTCATCT-CCTTTTCCCTT
25705379 CCCTTT
1 CCCTTT
25705385 TTCTTTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 12 0.50
22 9 0.38
ACGTcount: A:0.04, C:0.41, G:0.00, T:0.55
Consensus pattern (22 bp):
CCCTTTCATCTCCTTTTCCCTT
Found at i:25708663 original size:2 final size:2
Alignment explanation
Indices: 25708658--25708694 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25708648 TCCTCCCATT
25708658 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
25708695 TTTTGCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:25711556 original size:18 final size:17
Alignment explanation
Indices: 25711533--25711567 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
25711523 ATATTTAAAG
25711533 TTATTTCATAAAAAAAAT
1 TTATTT-ATAAAAAAAAT
*
25711551 TTATTTGTAAAAAAAAT
1 TTATTTATAAAAAAAAT
25711568 GAATAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (17 bp):
TTATTTATAAAAAAAAT
Found at i:25722322 original size:54 final size:53
Alignment explanation
Indices: 25722261--25722450 Score: 210
Period size: 54 Copynumber: 3.6 Consensus size: 53
25722251 CCATGGCAAC
*
25722261 AAGTGATAAGTGATATCCGTATAAGACCATAACTGGGCTATGGCATTGGAAAA
1 AAGTGATAAGTGATATCCGTATAAGACCATAGCTGGGCTATGGCATTGGAAAA
* * * *
25722314 CAAGTGATAAGTGATTTCCATATAATACCATAGCTGGGCTATGGC-TTCGGATTAA
1 -AAGTGATAAGTGATATCCGTATAAGACCATAGCTGGGCTATGGCATT-GGA-AAA
* *
25722369 AA-TGATACAAGTG--ATCCGTATAAGACCATAGCTGGGCTATGGCATCGGAGAA
1 AAGTGAT--AAGTGATATCCGTATAAGACCATAGCTGGGCTATGGCATTGGAAAA
* * *
25722421 AAGTGATAAGTGCT-CCCGTGTAAGACCATA
1 AAGTGATAAGTGATATCCGTATAAGACCATA
25722451 TTCAGGATAT
Statistics
Matches: 116, Mismatches: 12, Indels: 18
0.79 0.08 0.12
Matches are distributed among these distances:
51 5 0.04
52 18 0.16
53 40 0.34
54 46 0.40
55 7 0.06
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.25
Consensus pattern (53 bp):
AAGTGATAAGTGATATCCGTATAAGACCATAGCTGGGCTATGGCATTGGAAAA
Found at i:25729931 original size:54 final size:53
Alignment explanation
Indices: 25729871--25730042 Score: 190
Period size: 53 Copynumber: 3.2 Consensus size: 53
25729861 CCATGGAAAC
* *
25729871 AAGTGATAAGTGATATTCGTACAAGACCATAGCTGGGCTATAGCATCGAAAAA
1 AAGTGATAAGTGATATTCGTATAAGACCATAGCTAGGCTATAGCATCGAAAAA
* * **
25729924 CAAGTGATAAGTGAT-TTCTGTATAAGACCATAGCTAGGCTATAGCTTCGGATTA
1 -AAGTGATAAGTGATATTC-GTATAAGACCATAGCTAGGCTATAGCATCGAAAAA
* * *
25729978 AAGTGATACAAGTG--ATCCGTATAAGACCATAGCTAGGCTATGGCATC-AGAGAA
1 AAGTGAT--AAGTGATATTCGTATAAGACCATAGCTAGGCTATAGCATCGA-AAAA
25730031 AAGTGATAAGTG
1 AAGTGATAAGTG
25730043 CTCCCGTGTA
Statistics
Matches: 101, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
51 5 0.05
53 46 0.46
54 45 0.45
55 5 0.05
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.25
Consensus pattern (53 bp):
AAGTGATAAGTGATATTCGTATAAGACCATAGCTAGGCTATAGCATCGAAAAA
Found at i:25730005 original size:53 final size:53
Alignment explanation
Indices: 25729867--25730060 Score: 198
Period size: 54 Copynumber: 3.6 Consensus size: 53
25729857 TGGACCATGG
* * *
25729867 AAACAAGTGATAAGTGATATTCGTACAAGACCATAGCTGGGCTATAGCATCGAA
1 AAACAAGTGATAAGTGAT-TCCGTATAAGACCATAGCTAGGCTATAGCATCGAA
* * *
25729921 AAACAAGTGATAAGTGATTTCTGTATAAGACCATAGCTAGGCTATAGCTTCGGA
1 AAACAAGTGATAAGTGA-TTCCGTATAAGACCATAGCTAGGCTATAGCATCGAA
** *
25729975 TTA-AAGTGATACAAGTGA-TCCGTATAAGACCATAGCTAGGCTATGGCATC-AGA
1 AAACAAGTGAT--AAGTGATTCCGTATAAGACCATAGCTAGGCTATAGCATCGA-A
* * * *
25730028 GAA-AAGTGATAAGTGCTCCCGTGTAAGACCATA
1 AAACAAGTGATAAGTGATTCCGTATAAGACCATA
25730061 TCTGGGATAT
Statistics
Matches: 118, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
51 5 0.04
52 14 0.12
53 45 0.38
54 47 0.40
55 7 0.06
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (53 bp):
AAACAAGTGATAAGTGATTCCGTATAAGACCATAGCTAGGCTATAGCATCGAA
Found at i:25730072 original size:52 final size:52
Alignment explanation
Indices: 25729871--25730076 Score: 150
Period size: 53 Copynumber: 3.9 Consensus size: 52
25729861 CCATGGAAAC
* * * * * *
25729871 AAGTGAT-AAGTGATATTCGTACAAGACCATAGCTGGGCTATAGCATC-GAAAAA
1 AAGTGATAAAGTG--ATCCGTATAAGACCATAGCTAGGATATGGCATCAG-AGAA
* * * * * **
25729924 CAAGTGAT-AAGTGATTTCTGTATAAGACCATAGCTAGGCTATAGCTTCGGATTA
1 -AAGTGATAAAGTGA--TCCGTATAAGACCATAGCTAGGATATGGCATCAGAGAA
*
25729978 AAGTGATACAAGTGATCCGTATAAGACCATAGCTAGGCTATGGCATCAGAGAA
1 AAGTGATA-AAGTGATCCGTATAAGACCATAGCTAGGATATGGCATCAGAGAA
* * * *
25730031 AAGTGAT-AAGTGCTCCCGTGTAAGACCATATCTGGGATATGGCATC
1 AAGTGATAAAGTGAT-CCGTATAAGACCATAGCTAGGATATGGCATC
25730077 GGTATGATAT
Statistics
Matches: 128, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
51 6 0.05
52 28 0.22
53 46 0.36
54 41 0.32
55 7 0.05
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (52 bp):
AAGTGATAAAGTGATCCGTATAAGACCATAGCTAGGATATGGCATCAGAGAA
Found at i:25731847 original size:3 final size:3
Alignment explanation
Indices: 25731798--25731833 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
25731788 AAATGTAAAC
25731798 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
25731834 CATGGACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25732249 original size:60 final size:60
Alignment explanation
Indices: 25732156--25732279 Score: 230
Period size: 60 Copynumber: 2.1 Consensus size: 60
25732146 AAATAAACCA
25732156 ATATTAATGCAATATCTGGGTGTACAAATTTAGTTTAAAGCTCTAGAAGAGCTAATATTG
1 ATATTAATGCAATATCTGGGTGTACAAATTTAGTTTAAAGCTCTAGAAGAGCTAATATTG
* *
25732216 ATATTAATGCAATATTTGGGTGTACAGATTTAGTTTAAAGCTCTAGAAGAGCTAATATTG
1 ATATTAATGCAATATCTGGGTGTACAAATTTAGTTTAAAGCTCTAGAAGAGCTAATATTG
25732276 ATAT
1 ATAT
25732280 ATCTAAAAGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (60 bp):
ATATTAATGCAATATCTGGGTGTACAAATTTAGTTTAAAGCTCTAGAAGAGCTAATATTG
Found at i:25732655 original size:21 final size:21
Alignment explanation
Indices: 25732631--25732672 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25732621 TACATAAACA
* **
25732631 ATAATAGTTTTGCCTTTTAAC
1 ATAATAATTTTGAATTTTAAC
25732652 ATAATAATTTTGAATTTTAAC
1 ATAATAATTTTGAATTTTAAC
25732673 TTTAGAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (21 bp):
ATAATAATTTTGAATTTTAAC
Found at i:25736352 original size:28 final size:28
Alignment explanation
Indices: 25736302--25736360 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
25736292 TAGCAAGAAA
*
25736302 AAAATTTGAAATTTTGGTGAAATAAGAGT
1 AAAATTTGAAATTTTGGTAAAATAA-AGT
*
25736331 AAAA-TTGAAAATTTT-GTAAAATTAAGT
1 AAAATTTG-AAATTTTGGTAAAATAAAGT
25736358 AAA
1 AAA
25736361 TAAAATAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.22
28 10 0.37
29 11 0.41
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (28 bp):
AAAATTTGAAATTTTGGTAAAATAAAGT
Found at i:25736909 original size:105 final size:101
Alignment explanation
Indices: 25736730--25736927 Score: 254
Period size: 105 Copynumber: 1.9 Consensus size: 101
25736720 GAATTGATGG
* * *
25736730 ATAAGACAATGGTTAGACCATGGTAATGTTTAAATGTAAGACCATAACTGGGCTATGGCATTTTA
1 ATAAGACAATGGTTAGACCATGGTAATGTATAAATGTAAGACCATAACTGGGCTATGGCATCTGA
* *
25736795 GTGAAAAGACTATAACTGGGTTATGACACCATGAAC
66 GTGAAAAGACCATAAATGGGTTATGACACCATGAAC
* * * *
25736831 ATAAGACCATGGTTAGACCATGGTAGTATATGTATAAGTGTAAGACCATAATTGGGTTATGGCAT
1 ATAAGACAATGGTTAGACCAT-G--GTA-ATGTATAAATGTAAGACCATAACTGGGCTATGGCAT
*
25736896 CCTGA-TGATAAGACCATAAATGGGTTATGACA
62 -CTGAGTGAAAAGACCATAAATGGGTTATGACA
25736928 TTACGAGTGT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
101 20 0.24
102 1 0.01
104 3 0.04
105 56 0.68
106 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (101 bp):
ATAAGACAATGGTTAGACCATGGTAATGTATAAATGTAAGACCATAACTGGGCTATGGCATCTGA
GTGAAAAGACCATAAATGGGTTATGACACCATGAAC
Found at i:25736941 original size:33 final size:33
Alignment explanation
Indices: 25736867--25736945 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
25736857 TATATGTATA
* * *
25736867 AGTGTAAGACCATAATTGGGTTATGGCATCCTG
1 AGTGTAAGACCATAAATGGGTTATGACATACTG
25736900 A-TGATAAGACCATAAATGGGTTATGACATTAC-G
1 AGTG-TAAGACCATAAATGGGTTATGACA-TACTG
25736933 AGTGTAAGACCAT
1 AGTGTAAGACCAT
25736946 GGCAAGGCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 2 0.05
33 34 0.85
34 4 0.10
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (33 bp):
AGTGTAAGACCATAAATGGGTTATGACATACTG
Found at i:25741118 original size:13 final size:13
Alignment explanation
Indices: 25741081--25741122 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
25741071 ACGTCACATT
25741081 AATGAACCAAAAA
1 AATGAACCAAAAA
* *
25741094 AAGTGCA-TAAAAA
1 AA-TGAACCAAAAA
25741107 AATGAACCAAAAA
1 AATGAACCAAAAA
25741120 AAT
1 AAT
25741123 CACGTCATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 3 0.13
13 17 0.74
14 3 0.13
ACGTcount: A:0.67, C:0.12, G:0.10, T:0.12
Consensus pattern (13 bp):
AATGAACCAAAAA
Found at i:25750206 original size:45 final size:45
Alignment explanation
Indices: 25750156--25750343 Score: 243
Period size: 45 Copynumber: 4.2 Consensus size: 45
25750146 TGCTGGAGGT
* * * * *
25750156 GCTGGAGGTGCCGGAGGAGGCTGGAAGGGGTTCGGGATAAATGGA
1 GCTGGAGGTGCGGGAGGAGGCTGAAAAGGGTTTGGAATAAATGGA
* *
25750201 GCTGGAGGTGCGGGAGGAGGCTGGAAAGGGTTTGGAATAAGTGGA
1 GCTGGAGGTGCGGGAGGAGGCTGAAAAGGGTTTGGAATAAATGGA
* * *
25750246 GCCGGTGGTGCGGGAGGAGGCTGAAAAGGGTTTGGAATAAGTGGA
1 GCTGGAGGTGCGGGAGGAGGCTGAAAAGGGTTTGGAATAAATGGA
* * *
25750291 GCCGGTGGTGCTGGAGGAGGCTGAAAAGGGTTTGGAATAAGA-GGA
1 GCTGGAGGTGCGGGAGGAGGCTGAAAAGGGTTTGGAATAA-ATGGA
25750336 GCTGGAGG
1 GCTGGAGG
25750344 AGGCTGAAAG
Statistics
Matches: 130, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
45 130 1.00
ACGTcount: A:0.24, C:0.09, G:0.50, T:0.17
Consensus pattern (45 bp):
GCTGGAGGTGCGGGAGGAGGCTGAAAAGGGTTTGGAATAAATGGA
Found at i:25750347 original size:36 final size:36
Alignment explanation
Indices: 25750295--25750412 Score: 200
Period size: 36 Copynumber: 3.3 Consensus size: 36
25750285 AGTGGAGCCG
*
25750295 GTGGTGCTGGAGGAGGCTGAAAAGGGTTTGGAATAA
1 GTGGAGCTGGAGGAGGCTGAAAAGGGTTTGGAATAA
* *
25750331 GAGGAGCTGGAGGAGGCTGAAAGGGGTTTGGAATAA
1 GTGGAGCTGGAGGAGGCTGAAAAGGGTTTGGAATAA
*
25750367 GTGGAGCTGGAGGAGGCTGAAATGGGTTTGGAATAA
1 GTGGAGCTGGAGGAGGCTGAAAAGGGTTTGGAATAA
25750403 GTGGAGCTGG
1 GTGGAGCTGG
25750413 TGGTGGCAGT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 77 1.00
ACGTcount: A:0.27, C:0.06, G:0.47, T:0.20
Consensus pattern (36 bp):
GTGGAGCTGGAGGAGGCTGAAAAGGGTTTGGAATAA
Found at i:25754839 original size:55 final size:53
Alignment explanation
Indices: 25754770--25754954 Score: 246
Period size: 54 Copynumber: 3.4 Consensus size: 53
25754760 TAAAAAAAAA
*
25754770 TTGGTGCTTGCCTGTCAATGGCGGCACCAGTATTTAAAAAAAATTTGAAATTTTT
1 TTGGTGCTGGCCTGTCAATGGCGGCACCAGTA-TTAAAAAAAA-TTGAAATTTTT
* *
25754825 TTAGTGCTGGCCTGTCAATGGTCGGCACCAGTATTAAAAAAAATTGAATTTTTT
1 TTGGTGCTGGCCTGTCAATGG-CGGCACCAGTATTAAAAAAAATTGAAATTTTT
* * *
25754879 TTGGTGGTAGCTTGTCAATGGCAGGCACCAGTATTAAAAAAAAATT-AAATTTTT
1 TTGGTGCTGGCCTGTCAATGGC-GGCACCAGTATT-AAAAAAAATTGAAATTTTT
* *
25754933 TTGGTGTTGGCCTATCAATGGC
1 TTGGTGCTGGCCTGTCAATGGC
25754955 CAGCACTAAA
Statistics
Matches: 115, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
53 1 0.01
54 64 0.56
55 39 0.34
56 11 0.10
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (53 bp):
TTGGTGCTGGCCTGTCAATGGCGGCACCAGTATTAAAAAAAATTGAAATTTTT
Found at i:25756751 original size:3 final size:3
Alignment explanation
Indices: 25756743--25756786 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
25756733 ATATATTTAC
25756743 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TT- TTA TCTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
25756787 ATTGAGATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:25758953 original size:20 final size:19
Alignment explanation
Indices: 25758928--25758982 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 19
25758918 CTGCCTACGG
25758928 CCAGGCCACACGGGCATGTT
1 CCAGGCCACACGGGCATG-T
25758948 CCAGGCCACACGGGCATGT
1 CCAGGCCACACGGGCATGT
25758967 CCTAGGCCACACGGGC
1 CC-AGGCCACACGGGC
25758983 GTGTGCCCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 3 0.09
20 31 0.91
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (19 bp):
CCAGGCCACACGGGCATGT
Found at i:25760884 original size:27 final size:27
Alignment explanation
Indices: 25760854--25760905 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
25760844 AAGAAAGATA
*
25760854 AATTCAAAAGAAATGAGGAAAAAATTT
1 AATTCAAAAGAAATGAGAAAAAAATTT
* *
25760881 AATTGAAATGAAATGAGAAAAAAAT
1 AATTCAAAAGAAATGAGAAAAAAAT
25760906 GAAATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.62, C:0.02, G:0.15, T:0.21
Consensus pattern (27 bp):
AATTCAAAAGAAATGAGAAAAAAATTT
Found at i:25760916 original size:75 final size:70
Alignment explanation
Indices: 25760837--25761026 Score: 181
Period size: 75 Copynumber: 2.7 Consensus size: 70
25760827 ATTTAAATGA
*
25760837 AAATTGAAAGAAAGATAAATTCAAAAGAAATGAGGAAAAAATTTAATTGAAATGAA-ATGAGAAA
1 AAATTGAAAGAAAGATAAATTTAAAAGAAATGAGGAAAAAATTTAATTGAAAT-AAGATGAG--A
25760901 AAAATGAAATT
63 AAAA--AAA-T
* * * ** *
25760912 AAATTTGAAAGAAATACAAATTTAAATG-AATG-GGAGAAACTTTTAATTTAAATAAGATGAGAA
1 AAA-TTGAAAGAAAGATAAATTTAAAAGAAATGAGGA-AAAAATTTAATTGAAATAAGATGAGAA
25760975 AAAAAAT
64 AAAAAAT
* * **
25760982 AAATGGAAAGATAGAT-AATTTAAAAGAAATGACAAAAAAATTTAA
1 AAATTGAAAGAAAGATAAATTTAAAAGAAATGAGGAAAAAATTTAA
25761027 AATTGCATTG
Statistics
Matches: 94, Mismatches: 16, Indels: 16
0.75 0.13 0.13
Matches are distributed among these distances:
68 9 0.10
69 21 0.22
70 5 0.05
71 3 0.03
73 5 0.05
74 5 0.05
75 26 0.28
76 20 0.21
ACGTcount: A:0.59, C:0.02, G:0.15, T:0.24
Consensus pattern (70 bp):
AAATTGAAAGAAAGATAAATTTAAAAGAAATGAGGAAAAAATTTAATTGAAATAAGATGAGAAAA
AAAAT
Found at i:25760920 original size:76 final size:73
Alignment explanation
Indices: 25760779--25761026 Score: 190
Period size: 76 Copynumber: 3.4 Consensus size: 73
25760769 AAAAATTGAT
* * * ** * *
25760779 AATTTAAATGAAATGA-GAAAAAAATAAATTGAAATGAAGCG-GTACAAAATTTAAATGAAAATT
1 AATTTAAAAGAAATGAGGAAAAAATTTAATTGAAATGAAATGAG-A-AAAA-ATAAAT-TAAATT
25760842 GAAAGAAAGATA
62 GAAAGAAAGATA
*
25760854 AATTCAAAAGAAATGAGGAAAAAATTTAATTGAAATGAAATGAGAAAAAAATGAAATTAAATTTG
1 AATTTAAAAGAAATGAGGAAAAAATTTAATTGAAATGAAATGAG-AAAAAAT-AAATTAAA-TTG
* *
25760919 AAAGAAATACA
63 AAAGAAAGATA
* ** * *
25760930 AATTTAAATG-AATG-GGAGAAACTTTTAATTTAAAT-AAGATGAG-AAAAA-AAA-TAAATGGA
1 AATTTAAAAGAAATGAGGA-AAAAATTTAATTGAAATGAA-ATGAGAAAAAATAAATTAAATTGA
*
25760989 AAGATAGAT-
64 AAGAAAGATA
**
25760998 AATTTAAAAGAAATGACAAAAAAATTTAA
1 AATTTAAAAGAAATGAGGAAAAAATTTAA
25761027 AATTGCATTG
Statistics
Matches: 140, Mismatches: 25, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
68 9 0.06
69 21 0.15
70 5 0.04
71 3 0.02
73 5 0.04
74 5 0.04
75 41 0.29
76 49 0.35
77 2 0.01
ACGTcount: A:0.59, C:0.02, G:0.15, T:0.24
Consensus pattern (73 bp):
AATTTAAAAGAAATGAGGAAAAAATTTAATTGAAATGAAATGAGAAAAAATAAATTAAATTGAAA
GAAAGATA
Found at i:25761058 original size:20 final size:20
Alignment explanation
Indices: 25761035--25761099 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
25761025 AAAATTGCAT
25761035 TGAAAAATAAAAAATTTAAA
1 TGAAAAATAAAAAATTTAAA
** *
25761055 TGAAATAAGGAAAAATTAAAA
1 TGAAA-AATAAAAAATTTAAA
* * *
25761076 TTAAAATTAAAAAATATAAA
1 TGAAAAATAAAAAATTTAAA
25761096 TGAA
1 TGAA
25761100 TTGAGAAAAA
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.25
Consensus pattern (20 bp):
TGAAAAATAAAAAATTTAAA
Found at i:25761130 original size:41 final size:41
Alignment explanation
Indices: 25761037--25761129 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
25761027 AATTGCATTG
* * *
25761037 AAAAATAAAAAATTTAAATGAAATAAGGAAAAATTAAAATT
1 AAAATTAAAAAATATAAATGAAATAAGGAAAAAATAAAATT
* *
25761078 AAAATTAAAAAATATAAATGAATTGA-GAAAAAAT-AAATT
1 AAAATTAAAAAATATAAATGAAATAAGGAAAAAATAAAATT
*
25761117 TAAATTGAAAAAA
1 AAAATT-AAAAAA
25761130 AATTTTAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 10 0.22
40 13 0.29
41 22 0.49
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.25
Consensus pattern (41 bp):
AAAATTAAAAAATATAAATGAAATAAGGAAAAAATAAAATT
Found at i:25761136 original size:18 final size:18
Alignment explanation
Indices: 25761104--25761143 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
25761094 AATGAATTGA
25761104 GAAAAAATAAATTTAAATT
1 GAAAAAATAAATTTAAA-T
*
25761123 GAAAAAA-AATTTTAAAT
1 GAAAAAATAAATTTAAAT
25761140 GAAA
1 GAAA
25761144 TGAAATTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 8 0.40
19 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (18 bp):
GAAAAAATAAATTTAAAT
Found at i:25761146 original size:5 final size:5
Alignment explanation
Indices: 25761136--25761212 Score: 82
Period size: 5 Copynumber: 14.6 Consensus size: 5
25761126 AAAAAATTTT
* * *
25761136 AAATG AAATG AAATT AGAATG AAATG AAGTTG AAATG AAATA AAATG AAGATG
1 AAATG AAATG AAATG A-AATG AAATG AA-ATG AAATG AAATG AAATG AA-ATG
*
25761189 AAATG AAAATG AAAAG AAATG AAA
1 AAATG -AAATG AAATG AAATG AAA
25761213 AAAAAAGAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
5 42 0.70
6 18 0.30
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.19
Consensus pattern (5 bp):
AAATG
Found at i:25761169 original size:11 final size:11
Alignment explanation
Indices: 25761136--25761212 Score: 72
Period size: 11 Copynumber: 7.3 Consensus size: 11
25761126 AAAAAATTTT
25761136 AAATGAA-ATG
1 AAATGAAGATG
*
25761146 AAAT-TAGAATG
1 AAATGAAG-ATG
*
25761157 AAATGAAGTTG
1 AAATGAAGATG
*
25761168 AAATGAA-ATA
1 AAATGAAGATG
25761178 AAATGAAGATG
1 AAATGAAGATG
*
25761189 AAATGAAAATG
1 AAATGAAGATG
*
25761200 AAAAGAA-ATG
1 AAATGAAGATG
25761210 AAA
1 AAA
25761213 AAAAAAGAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
9 1 0.02
10 18 0.33
11 34 0.62
12 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.19
Consensus pattern (11 bp):
AAATGAAGATG
Found at i:25761207 original size:16 final size:16
Alignment explanation
Indices: 25761136--25761213 Score: 88
Period size: 16 Copynumber: 4.9 Consensus size: 16
25761126 AAAAAATTTT
*
25761136 AAATGAAATG-AAATT
1 AAATGAAATGAAAATG
**
25761151 AGAATGAAATGAAGTTG
1 A-AATGAAATGAAAATG
25761168 AAATGAAAT-AAAATG
1 AAATGAAATGAAAATG
25761183 AAGATGAAATGAAAATG
1 AA-ATGAAATGAAAATG
*
25761200 AAAAGAAATGAAAA
1 AAATGAAATGAAAA
25761214 AAAAAGAGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
15 7 0.13
16 35 0.66
17 11 0.21
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (16 bp):
AAATGAAATGAAAATG
Found at i:25761443 original size:21 final size:21
Alignment explanation
Indices: 25761404--25761448 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
25761394 ATATGAAAAA
* *
25761404 AAATTACAAAATTTTAAATTT
1 AAATTACAAAATTTAAAATAT
25761425 AAATTGACAAAA-TTAAAATAT
1 AAATT-ACAAAATTTAAAATAT
25761446 AAA
1 AAA
25761449 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (21 bp):
AAATTACAAAATTTAAAATAT
Found at i:25761555 original size:15 final size:15
Alignment explanation
Indices: 25761528--25761580 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 15
25761518 AAAATAATAT
25761528 AAAATGAAT-TGAAAA
1 AAAAT-AATATGAAAA
25761543 AAAATAATATG---A
1 AAAATAATATGAAAA
25761555 AAAATAATATGAAAAA
1 AAAATAATATG-AAAA
25761571 GAAAATAATA
1 -AAAATAATA
25761581 ATATGAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 12 0.38
14 3 0.09
15 7 0.22
16 1 0.03
17 9 0.28
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (15 bp):
AAAATAATATGAAAA
Found at i:25761557 original size:12 final size:12
Alignment explanation
Indices: 25761542--25761570 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
25761532 TGAATTGAAA
25761542 AAAAATAATATG
1 AAAAATAATATG
25761554 AAAAATAATATG
1 AAAAATAATATG
25761566 AAAAA
1 AAAAA
25761571 GAAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (12 bp):
AAAAATAATATG
Found at i:25761581 original size:57 final size:55
Alignment explanation
Indices: 25761514--25761630 Score: 162
Period size: 57 Copynumber: 2.1 Consensus size: 55
25761504 TAATTAATTT
* *
25761514 GAAAAAAATAATATAAAATGAATTGAAAAAAAATAATATGAAAAATAATATGAAAAA
1 GAAAAAAATAATATAAAATGAATTG-AAAAAAATAAAAT-AAAAATAAAATGAAAAA
* * *
25761571 GAAAATAATAATATGAAATGAATTGAAAAAAATAAAATAAAATTAAAATGAAAAA
1 GAAAAAAATAATATAAAATGAATTGAAAAAAATAAAATAAAAATAAAATGAAAAA
*
25761626 TAAAA
1 GAAAA
25761631 GGGTTGATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 19 0.35
56 12 0.22
57 23 0.43
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (55 bp):
GAAAAAAATAATATAAAATGAATTGAAAAAAATAAAATAAAAATAAAATGAAAAA
Found at i:25763667 original size:54 final size:54
Alignment explanation
Indices: 25763607--25763745 Score: 233
Period size: 54 Copynumber: 2.6 Consensus size: 54
25763597 TTTTTAATAT
* * *
25763607 TGGTGCCAGCCATTGATAGGCCAACACCAAATTTTTTTTTGAAAACTTGTATTC
1 TGGTGCCAGCCATTGATAGGCCAGCACCAAATTTTTTTTTAAAAACTCGTATTC
*
25763661 TGGTGCCAGCCATTGACAGGCCAGCACCAAATTTTTTTTTAAAAACTCGTATTC
1 TGGTGCCAGCCATTGATAGGCCAGCACCAAATTTTTTTTTAAAAACTCGTATTC
*
25763715 TGGTGCCGGCCATTGATAGGCCAGCACCAAA
1 TGGTGCCAGCCATTGATAGGCCAGCACCAAA
25763746 AAAATTTAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (54 bp):
TGGTGCCAGCCATTGATAGGCCAGCACCAAATTTTTTTTTAAAAACTCGTATTC
Found at i:25763785 original size:55 final size:55
Alignment explanation
Indices: 25763714--25763870 Score: 201
Period size: 55 Copynumber: 2.9 Consensus size: 55
25763704 AACTCGTATT
*
25763714 CTGGTGCCGGCCATTGATAGGCCAGCACCAAAAAAATTTAAATTTTTTT-AAATTA
1 CTGGTGCCGGCCATTGATAGGCCAGCACCAAAAAAAATT-AATTTTTTTAAAATTA
* *
25763769 CTGGTGCCGACTATTGATAGGCCAGCA-CAAAAAAAATTAATTTTTTTAAAATTA
1 CTGGTGCCGGCCATTGATAGGCCAGCACCAAAAAAAATTAATTTTTTTAAAATTA
* * * * * **
25763823 TTGGTGCCGGCCATTGACAGACCAGTACAAAAAAAAATTCTTTTTTTT
1 CTGGTGCCGGCCATTGATAGGCCAGCACCAAAAAAAATTAATTTTTTT
25763871 TGAAAACTTG
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
53 9 0.10
54 37 0.42
55 42 0.48
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (55 bp):
CTGGTGCCGGCCATTGATAGGCCAGCACCAAAAAAAATTAATTTTTTTAAAATTA
Found at i:25763828 original size:54 final size:54
Alignment explanation
Indices: 25763714--25763858 Score: 202
Period size: 54 Copynumber: 2.7 Consensus size: 54
25763704 AACTCGTATT
*
25763714 CTGGTGCCGGCCATTGATAGGCCAGCACCAAAAAAATTTAAATTTTTTTAAATTA
1 CTGGTGCCGGCCATTGATAGGCCAGCA-CAAAAAAAATTAAATTTTTTTAAATTA
* *
25763769 CTGGTGCCGACTATTGATAGGCCAGCACAAAAAAAATT-AATTTTTTTAAAATTA
1 CTGGTGCCGGCCATTGATAGGCCAGCACAAAAAAAATTAAATTTTTTT-AAATTA
* * * *
25763823 TTGGTGCCGGCCATTGACAGACCAGTACAAAAAAAA
1 CTGGTGCCGGCCATTGATAGGCCAGCACAAAAAAAA
25763859 ATTCTTTTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
53 9 0.11
54 46 0.57
55 25 0.31
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (54 bp):
CTGGTGCCGGCCATTGATAGGCCAGCACAAAAAAAATTAAATTTTTTTAAATTA
Found at i:25770384 original size:19 final size:20
Alignment explanation
Indices: 25770360--25770412 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
25770350 AATAAAAAAA
25770360 TAAAATTTAAAATTATTT-T
1 TAAAATTTAAAATTATTTAT
25770379 TAAAATTTAAAA-TATTTAT
1 TAAAATTTAAAATTATTTAT
*
25770398 AAAAATTTCAAAATT
1 TAAAATTT-AAAATT
25770413 TATATCTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 5 0.17
19 20 0.67
20 4 0.13
21 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAATTTAAAATTATTTAT
Found at i:25770436 original size:26 final size:26
Alignment explanation
Indices: 25770393--25770442 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
25770383 ATTTAAAATA
* *
25770393 TTTATAAAAATTTCAAAATTTATATC
1 TTTATAAAAATTTAAAAAATTATATC
25770419 TTTA-AAAAATTATAAAAAATTATA
1 TTTATAAAAATT-TAAAAAATTATA
25770443 AAAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (26 bp):
TTTATAAAAATTTAAAAAATTATATC
Found at i:25770445 original size:9 final size:10
Alignment explanation
Indices: 25770421--25770452 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
25770411 TTTATATCTT
25770421 TAAAAAATTA
1 TAAAAAATTA
25770431 TAAAAAATTA
1 TAAAAAATTA
*
25770441 TAAAAAAATA
1 TAAAAAATTA
25770451 TA
1 TA
25770453 TAAAGAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:25770454 original size:12 final size:11
Alignment explanation
Indices: 25770422--25770456 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
25770412 TTATATCTTT
25770422 AAAAAATTAT-
1 AAAAAATTATA
25770432 AAAAAATTATA
1 AAAAAATTATA
25770443 AAAAAATATATA
1 AAAAAAT-TATA
25770455 AA
1 AA
25770457 GAAAGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.43
11 7 0.30
12 6 0.26
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:25770466 original size:22 final size:21
Alignment explanation
Indices: 25770422--25770468 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
25770412 TTATATCTTT
*
25770422 AAAAAATTATAAAAAATTATA
1 AAAAAATTATAAAAAAGTATA
25770443 AAAAAATATATAAAGAAAGT-TA
1 AAAAAAT-TATAAA-AAAGTATA
25770465 AAAA
1 AAAA
25770469 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 12 0.52
23 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (21 bp):
AAAAAATTATAAAAAAGTATA
Found at i:25770532 original size:16 final size:16
Alignment explanation
Indices: 25770511--25770541 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25770501 CTAAATAAGT
25770511 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
25770527 TTTCAAATTTATATG
1 TTTCAAATATATATG
25770542 CTCTAATATG
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:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:25770993 original size:11 final size:11
Alignment explanation
Indices: 25770960--25771013 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
25770950 AAAGATCAAC
* *
25770960 AAATTAAATTA
1 AAATAAAATAA
* *
25770971 AATTAAATTAA
1 AAATAAAATAA
*
25770982 ACATAAAATAA
1 AAATAAAATAA
*
25770993 AAATAAAAGAA
1 AAATAAAATAA
25771004 AAATAAAATA
1 AAATAAAATA
25771014 GGGTTTCCGG
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:25776523 original size:20 final size:20
Alignment explanation
Indices: 25776498--25776539 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
25776488 GTAAAAGTTA
25776498 AATGGAAGAACTGCTAATTC
1 AATGGAAGAACTGCTAATTC
25776518 AATGGAAGAACTGCTAATTC
1 AATGGAAGAACTGCTAATTC
25776538 AA
1 AA
25776540 CTAACACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (20 bp):
AATGGAAGAACTGCTAATTC
Found at i:25779057 original size:14 final size:14
Alignment explanation
Indices: 25779038--25779065 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25779028 GCTATAAGAG
25779038 TAGATTGAAATTCC
1 TAGATTGAAATTCC
25779052 TAGATTGAAATTCC
1 TAGATTGAAATTCC
25779066 ATTTGTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
TAGATTGAAATTCC
Found at i:25801233 original size:31 final size:31
Alignment explanation
Indices: 25801198--25801267 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
25801188 AATTTGACAC
*
25801198 TTTTTTATAATTT-GATATTTGAACTTAA-AA
1 TTTTTTTTAATTTAG-TATTTGAACTTAACAA
*
25801228 TTTTTTCTTAATTTAGTATTTGAACTTAACAC
1 TTTTTT-TTAATTTAGTATTTGAACTTAACAA
25801260 TTTTTTTT
1 TTTTTTTT
25801268 TAAAAAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 6 0.17
31 21 0.60
32 8 0.23
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.59
Consensus pattern (31 bp):
TTTTTTTTAATTTAGTATTTGAACTTAACAA
Found at i:25809113 original size:23 final size:23
Alignment explanation
Indices: 25809083--25809169 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
25809073 GCTTTACTGA
* *
25809083 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
25809106 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
25809127 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
25809149 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
25809170 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:25811378 original size:20 final size:20
Alignment explanation
Indices: 25811342--25811381 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
25811332 AATTTTTTTT
*
25811342 ATAATTTTTATACTTTTTAA
1 ATAATTTTAATACTTTTTAA
25811362 ATAATTTTAATGA-TTTTTAA
1 ATAATTTTAAT-ACTTTTTAA
25811382 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (20 bp):
ATAATTTTAATACTTTTTAA
Found at i:25811572 original size:23 final size:25
Alignment explanation
Indices: 25811532--25811583 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
25811522 GTAATTTAAA
* *
25811532 AAAAAAACTTAAATAT-AA-AAACT
1 AAAAAAACTGAAAAATAAATAAACT
*
25811555 AAAAAAAGTGAAAAATAAATAAACT
1 AAAAAAACTGAAAAATAAATAAACT
25811580 AAAA
1 AAAA
25811584 TTACTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 13 0.54
24 2 0.08
25 9 0.38
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (25 bp):
AAAAAAACTGAAAAATAAATAAACT
Found at i:25813375 original size:9 final size:9
Alignment explanation
Indices: 25813361--25813397 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
25813351 TATAGTTTAA
25813361 TATTCGAAT
1 TATTCGAAT
25813370 TATTCGAAT
1 TATTCGAAT
*
25813379 TATTCGAGT
1 TATTCGAAT
25813388 TATTCGAAT
1 TATTCGAAT
25813397 T
1 T
25813398 CAAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:25814283 original size:58 final size:58
Alignment explanation
Indices: 25814193--25814308 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 58
25814183 CCTCTTCATC
** *
25814193 ATGAATCTTTAATTTTGAAAGATTGATCTGCAATATCACAGGTAGTCTTTAGACCATT
1 ATGAATCTCCAATTTTGAAAGATTGATCTGCAATATCACAGGTAGTCTTTAAACCATT
*
25814251 ATGAATCTCCAATTTTTAAAGATTGATCTGCAATATCACAGGTAGTCTTTAAACCATT
1 ATGAATCTCCAATTTTGAAAGATTGATCTGCAATATCACAGGTAGTCTTTAAACCATT
25814309 TTGATAGGTC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Consensus pattern (58 bp):
ATGAATCTCCAATTTTGAAAGATTGATCTGCAATATCACAGGTAGTCTTTAAACCATT
Found at i:25815176 original size:22 final size:20
Alignment explanation
Indices: 25815127--25815178 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
25815117 ATTAATAAAT
*
25815127 ATATTTTAATTAAA-AATAA
1 ATATTTTAATAAAATAATAA
*
25815146 ACATTTTAATAAACATAATAA
1 ATATTTTAATAAA-ATAATAA
25815167 ATACTTTTAATA
1 ATA-TTTTAATA
25815179 CTTTATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.41
20 1 0.04
21 7 0.26
22 8 0.30
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATTTTAATAAAATAATAA
Found at i:25815349 original size:21 final size:21
Alignment explanation
Indices: 25815323--25815380 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
25815313 ACACCTGTTT
*
25815323 TTAATCACATCATTACGAT-A
1 TTAATCTCATCATTACGATAA
25815343 TTCAATCTCATCATTACGATAA
1 TT-AATCTCATCATTACGATAA
*
25815365 TTAATCTTATCATTAC
1 TTAATCTCATCATTAC
25815381 CGTTGTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 2 0.06
21 29 0.85
22 3 0.09
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (21 bp):
TTAATCTCATCATTACGATAA
Found at i:25815547 original size:21 final size:21
Alignment explanation
Indices: 25815521--25815563 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
25815511 GGTTCGCTGT
*
25815521 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
25815542 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
25815563 A
1 A
25815564 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:25815563 original size:16 final size:16
Alignment explanation
Indices: 25815544--25815576 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
25815534 TGTATTGGAT
*
25815544 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
25815560 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
25815576 T
1 T
25815577 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:25815621 original size:45 final size:44
Alignment explanation
Indices: 25815555--25815649 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
25815545 GGATTAGAGG
* *
25815555 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
25815600 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
25815644 TGTAAT
1 TGTAAT
25815650 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:25815832 original size:18 final size:17
Alignment explanation
Indices: 25815811--25815845 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25815801 TTATTATTTA
*
25815811 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
25815829 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
25815846 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:25815839 original size:28 final size:27
Alignment explanation
Indices: 25815769--25815841 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
25815759 TTTATTATCA
*
25815769 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
25815797 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
25815824 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
25815842 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:25815976 original size:18 final size:17
Alignment explanation
Indices: 25815955--25815989 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25815945 TTATTATTAA
*
25815955 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
25815973 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
25815990 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:25816000 original size:144 final size:147
Alignment explanation
Indices: 25815730--25816001 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
25815720 ATGATTATTG
25815730 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
25815795 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
25815860 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
25815879 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
25815941 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
25816002 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:25820676 original size:26 final size:26
Alignment explanation
Indices: 25820594--25820676 Score: 78
Period size: 28 Copynumber: 3.1 Consensus size: 26
25820584 ATATAAATAA
* ** *
25820594 TAAAAATAAATAAATTTATATCATAT
1 TAAAAATATATAAATAAATATTATAT
* *
25820620 TATAAAA-ATATATATAAATATTAATTTT
1 TA-AAAATATATAAATAAATATT-A-TAT
25820648 TAAAAATATATAAATAAATATTATAT
1 TAAAAATATATAAATAAATATTATAT
25820674 TAA
1 TAA
25820677 TTTGAATAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
26 17 0.38
27 10 0.22
28 18 0.40
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (26 bp):
TAAAAATATATAAATAAATATTATAT
Found at i:25834830 original size:16 final size:16
Alignment explanation
Indices: 25834811--25834841 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25834801 ATTTAAGTAA
*
25834811 ATATTATTTTATTATT
1 ATATTATATTATTATT
25834827 ATATTATATTATTAT
1 ATATTATATTATTAT
25834842 AGTTAAAACA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATTATATTATTATT
Found at i:25841824 original size:16 final size:16
Alignment explanation
Indices: 25841803--25841841 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
25841793 TAGAATGGAA
25841803 AGAAAATT-GAAAGAAT
1 AGAAAATTAG-AAGAAT
*
25841819 AGAAAAATAGAAGAAT
1 AGAAAATTAGAAGAAT
25841835 AGAAAAT
1 AGAAAAT
25841842 ATAAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (16 bp):
AGAAAATTAGAAGAAT
Found at i:25842863 original size:22 final size:24
Alignment explanation
Indices: 25842818--25842869 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
25842808 AGATAAGTCT
* *
25842818 CCTTTTTTTTTTTCAATTTATTTC
1 CCTTCTTTTTTTTCAATGTATTTC
25842842 CCTTCTTTTTTTT-AATGT-TTTC
1 CCTTCTTTTTTTTCAATGTATTTC
*
25842864 TCTTCT
1 CCTTCT
25842870 CTGCTTGTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.36
23 4 0.16
24 12 0.48
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (24 bp):
CCTTCTTTTTTTTCAATGTATTTC
Found at i:25843358 original size:17 final size:20
Alignment explanation
Indices: 25843331--25843369 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
25843321 AATTTAGTTA
25843331 TTAATATTTAC-ATT-TTTT
1 TTAATATTTACTATTATTTT
25843349 TTAA-ATTTACTATTATTTT
1 TTAATATTTACTATTATTTT
25843368 TT
1 TT
25843370 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTAATATTTACTATTATTTT
Done.