Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 149 of 163
Found at i:40850547 original size:59 final size:57
Alignment explanation
Indices: 40850326--40850581 Score: 176
Period size: 59 Copynumber: 4.4 Consensus size: 57
40850316 TCGCGGGGGC
* * ** * *
40850326 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAAGGGAATTTTGGAAAATTCGAGGGT
1 AAAATGGTAATTTT-GG-AAAAGCGGGGGCAAAAATGGAATTTTGGAAAGTTCGAGGGT
** * * * ** * *
40850385 AAGGTAGTAATTTTTAGTG-AAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAA-TTTT-G-GAAAAGCGGGGGCAAAAATGGAATTTTGGAAAGTTCGAGGGT
* **
40850444 AAAATGGTAATTTTTGGCAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAA-TTTTGG-AAAAGCGGGGGCAAAAATGGAATTTTGGAAAGTTCGAGGGT
*** *
40850503 AAAATGGTAATTTTGGACTCGCGGGGGCAAAAATGGTAATTTTTGGTGAAA--TCGAGGTT
1 AAAATGGTAATTTTGGAAAAGCGGGGGCAAAAATGG-AA-TTTT-G-GAAAGTTCGAGGGT
* *
40850562 AAAAAGGGAATTTTGGAAAA
1 AAAATGGTAATTTTGGAAAA
40850582 TTCGAGGGTA
Statistics
Matches: 162, Mismatches: 27, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
57 15 0.09
58 9 0.06
59 127 0.78
60 6 0.04
61 5 0.03
ACGTcount: A:0.36, C:0.05, G:0.30, T:0.30
Consensus pattern (57 bp):
AAAATGGTAATTTTGGAAAAGCGGGGGCAAAAATGGAATTTTGGAAAGTTCGAGGGT
Found at i:40850595 original size:59 final size:59
Alignment explanation
Indices: 40850532--40850725 Score: 316
Period size: 59 Copynumber: 3.3 Consensus size: 59
40850522 CGCGGGGGCA
* *
40850532 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAGGGAATTTTGGAAAATTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * *
40850591 AAAATAGTAATTTTTGGTGAAATCGTGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * *
40850650 AAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
40850709 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
40850726 ACAGTCCAAG
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 125 1.00
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
Found at i:40850606 original size:118 final size:114
Alignment explanation
Indices: 40850484--40850726 Score: 283
Period size: 118 Copynumber: 2.1 Consensus size: 114
40850474 AAAAATGGAA
*
40850484 TTTTGGAAAGTTCGAGGGT-AAAATGGTAATTTTGG-ACTCGCGGGGGCAAAAATGGTAATTTTT
1 TTTTGGAAA--TCG-GGGTAAAAATGG-AATTTTGGAACT-GCGAGGG-AAAAATGGTAATTTTT
40850547 GGTGAAATCGAGGTTAAAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAGTAAT
60 GGTGAAATCGAGGTTAAAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAGTAAT
* * * *
40850602 TTTTGGTGAAATCGTGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGG
1 TTTT-G-GAAATCGGGGT-AAAAATGGAATTTTGG-AACTGCGAGGGAAAAATGGTAATTTTTGG
* * * * * *
40850667 TGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAAT
62 TGAAATCGAGGTTAAAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAGTAAT
40850720 TTTTGGA
1 TTTTGGA
40850727 CAGTCCAAGG
Statistics
Matches: 108, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
116 2 0.02
117 4 0.04
118 83 0.77
119 13 0.12
120 6 0.06
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (114 bp):
TTTTGGAAATCGGGGTAAAAATGGAATTTTGGAACTGCGAGGGAAAAATGGTAATTTTTGGTGAA
ATCGAGGTTAAAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAGTAAT
Found at i:40850613 original size:206 final size:205
Alignment explanation
Indices: 40850292--40850727 Score: 737
Period size: 206 Copynumber: 2.1 Consensus size: 205
40850282 TTGGATACCG
*
40850292 GAGGGTAAAATGGTAATTTTGGACTCGCGGGGGCAAAATGGTAATTTTCGGTGAAATCGGGGTTA
1 GAGGGTAAAATGGTAATTTTGGACTCGCGGGGGCAAAATGGTAATTTTCGGTGAAATCGAGGTTA
** *
40850357 AAAAGGGAATTTTGGAAAATTCGAGGGTAAGGTAGTAATTTTTAGTGAAATCGAGGTTAAAAATG
66 AAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAGTAATTTTTAGTGAAATCGAGGTCAAAAATG
* *
40850422 GAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGCAAAATCGGGGTTAAAAATGGAATTT
131 GAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGCAAAATCGGGGTTAAAAATGGAATTT
40850487 TGGAAAGTTC
196 TGGAAAGTTC
*
40850497 GAGGGTAAAATGGTAATTTTGGACTCGCGGGGGCAAAAATGGTAATTTTTGGTGAAATCGAGGTT
1 GAGGGTAAAATGGTAATTTTGGACTCGCGGGGGC-AAAATGGTAATTTTCGGTGAAATCGAGGTT
* *
40850562 AAAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAGTAATTTTTGGTGAAATCGTGGTCAAAAAT
65 AAAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAGTAATTTTTAGTGAAATCGAGGTCAAAAAT
** *
40850627 GGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATT
130 GGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGCAAAATCGGGGTTAAAAATGGAATT
40850692 TTGGAAAGTTC
195 TTGGAAAGTTC
*
40850703 GGGGGTAAAATGGTAATTTTTGGAC
1 GAGGGTAAAATGGTAA-TTTTGGAC
40850728 AGTCCAAGGA
Statistics
Matches: 216, Mismatches: 13, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
205 34 0.16
206 174 0.81
207 8 0.04
ACGTcount: A:0.34, C:0.05, G:0.31, T:0.31
Consensus pattern (205 bp):
GAGGGTAAAATGGTAATTTTGGACTCGCGGGGGCAAAATGGTAATTTTCGGTGAAATCGAGGTTA
AAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAGTAATTTTTAGTGAAATCGAGGTCAAAAATG
GAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGCAAAATCGGGGTTAAAAATGGAATTT
TGGAAAGTTC
Found at i:40852614 original size:17 final size:16
Alignment explanation
Indices: 40852592--40852647 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
40852582 GGTTTTGGAC
**
40852592 ATTTAATTTAATTTTAA
1 ATTTAATTTAA-AATAA
*
40852609 ATTTAAATTCAAAATAA
1 ATTT-AATTTAAAATAA
40852626 ATTTAATTTAAAACTAA
1 ATTTAATTTAAAA-TAA
40852643 ATTTA
1 ATTTA
40852648 TATCTTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 8 0.24
17 19 0.58
18 6 0.18
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTAATTTAAAATAA
Found at i:40856365 original size:9 final size:9
Alignment explanation
Indices: 40856329--40856376 Score: 51
Period size: 9 Copynumber: 4.9 Consensus size: 9
40856319 ATTTTGATTT
40856329 TTTAAAAAA
1 TTTAAAAAA
40856338 TATTAACAATAA
1 T-TTAA-AA-AA
40856350 TTCTAAAAAA
1 TT-TAAAAAA
40856360 TTTAAAAAA
1 TTTAAAAAA
*
40856369 ATTAAAAA
1 TTTAAAAA
40856377 TAAACATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
9 15 0.44
10 8 0.24
11 5 0.15
12 6 0.18
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:40858394 original size:21 final size:24
Alignment explanation
Indices: 40858351--40858396 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
40858341 TATGTAAGAA
*
40858351 AATAAAATATATATATATAATTAT
1 AATAAAATATAAATATATAATTAT
40858375 AATAAAA-ATAAATA-AT-ATTAT
1 AATAAAATATAAATATATAATTAT
40858396 A
1 A
40858397 TAATTATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 2 0.10
23 6 0.29
24 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AATAAAATATAAATATATAATTAT
Found at i:40858396 original size:29 final size:30
Alignment explanation
Indices: 40858349--40858419 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 30
40858339 TGTATGTAAG
40858349 AAAATAAA-ATATATATATATAATTATAATA
1 AAAATAAATA-ATATATATATAATTATAATA
* *
40858379 AAAATAAATAATAT-TATATAATTATCATT
1 AAAATAAATAATATATATATAATTATAATA
40858408 AAAATAAATAAT
1 AAAATAAATAAT
40858420 GTTTATATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 25 0.66
30 12 0.32
31 1 0.03
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (30 bp):
AAAATAAATAATATATATATAATTATAATA
Found at i:40858397 original size:35 final size:34
Alignment explanation
Indices: 40858350--40858415 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 34
40858340 GTATGTAAGA
*
40858350 AAATAAAATATAT-ATATATAATTATAATAAAAAT
1 AAATAAAATATATAAT-TATAATTAAAATAAAAAT
* *
40858384 AAATAATATTATATAATTATCATTAAAATAAA
1 AAATAA-AATATATAATTATAATTAAAATAAA
40858416 TAATGTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 6 0.22
35 19 0.70
36 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (34 bp):
AAATAAAATATATAATTATAATTAAAATAAAAAT
Found at i:40858577 original size:2 final size:2
Alignment explanation
Indices: 40858570--40858596 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40858560 TTAAGATAGC
40858570 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
40858597 TAATTTTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40859837 original size:2 final size:2
Alignment explanation
Indices: 40859830--40859863 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
40859820 TTAAAAAGAA
* *
40859830 AG AG AG AG AG AG AG AG AG AG AG AG GG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40859864 TAGCAAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40867092 original size:97 final size:97
Alignment explanation
Indices: 40866917--40867110 Score: 268
Period size: 97 Copynumber: 2.0 Consensus size: 97
40866907 AACCTTGGAA
* *
40866917 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTCGTGCCTAGTAAGTTAAGACACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTTCA
*
40866982 AAACCAGAGAT-AAAGAAACATTGCCTCGATTT
66 AAACCAGAAATAAAAG-AACATTGCCTCGATTT
* * *
40867014 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAAATTTT-
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACAC-AAATTTTC
* *
40867078 AAAACTC-GAAATAAAAGAATATTGTCTCGATTT
65 AAAAC-CAGAAATAAAAGAACATTGCCTCGATTT
40867111 TAAAGGTTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
97 74 0.86
98 12 0.14
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGACACAAATTTTCA
AAACCAGAAATAAAAGAACATTGCCTCGATTT
Found at i:40867384 original size:30 final size:27
Alignment explanation
Indices: 40867344--40867424 Score: 81
Period size: 30 Copynumber: 2.8 Consensus size: 27
40867334 TTTTGGATGC
40867344 TCGAGGGCAAAATGATAATTTTAGACACT
1 TCGAGGGCAAAATG-TAATTTTAGA-ACT
* *
40867373 TCGGGGGGCAAAAATGTAATATTTAGAAGT
1 TC-GAGGGC-AAAATGTAAT-TTTAGAACT
*
40867403 TCGAGGGTAAAATGGTAATTTT
1 TCGAGGGCAAAAT-GTAATTTT
40867425 TGGAAAGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 8 0.18
29 11 0.25
30 13 0.30
31 12 0.27
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.30
Consensus pattern (27 bp):
TCGAGGGCAAAATGTAATTTTAGAACT
Found at i:40867420 original size:29 final size:28
Alignment explanation
Indices: 40867383--40867714 Score: 184
Period size: 30 Copynumber: 11.2 Consensus size: 28
40867373 TCGGGGGGCA
* *
40867383 AAAATGTAATATTTAGAAGTTCGAGGGT
1 AAAATGTAATTTTTAGAAGTTTGAGGGT
* * *
40867411 AAAATGGTAATTTTTGGAAAGTTTGGGGGCA
1 AAAAT-GTAATTTTTAG-AAGTTTGAGGG-T
* * *
40867442 AAAATGTGATTTTTGGAA-TTTTAGGAGT
1 AAAATGTAATTTTTAGAAGTTTGAGG-GT
**
40867470 AAAATGGTAATTTTTAGAAGTTTGAGGACA
1 AAAAT-GTAATTTTTAGAAGTTTGAGG-GT
* *
40867500 AAAATGTGATTTTTCGAAAGTTT-AGGGGT
1 AAAATGTAATTTTTAG-AAGTTTGA-GGGT
* *
40867529 AAAATGGTAATTTTTGGAAAGTTTAGAGGTT
1 AAAAT-GTAATTTTTAG-AAGTTT-GAGGGT
* * *
40867560 AAAATATGATTTTTGAAAAGTTTGAGGGTT
1 AAAATGTAATTTTT-AGAAGTTTGAGGG-T
* *
40867590 AAAATATAATTTTTAAAAAGTTTGAGGGT
1 AAAATGTAATTTTT-AGAAGTTTGAGGGT
* * * *
40867619 CAAAATATGACTTTTGAAAAGTTT-AGGGGTT
1 -AAAATGT-AATTTTTAGAAGTTTGA-GGG-T
* * *
40867650 AAAATGTAGTTTTTGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTT-AGAAGTTTGAGGG-T
* * *
40867680 AAAATATAATTTTTAAAGAGTTTAAGGGT
1 AAAATGTAATTTTTAGA-AGTTTGAGGGT
40867709 CAAAAT
1 -AAAAT
40867715 ATGATTTCTA
Statistics
Matches: 248, Mismatches: 35, Indels: 40
0.77 0.11 0.12
Matches are distributed among these distances:
28 15 0.06
29 53 0.21
30 159 0.64
31 20 0.08
32 1 0.00
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (28 bp):
AAAATGTAATTTTTAGAAGTTTGAGGGT
Found at i:40867439 original size:59 final size:58
Alignment explanation
Indices: 40867376--40867672 Score: 251
Period size: 60 Copynumber: 5.0 Consensus size: 58
40867366 AGACACTTCG
* * *
40867376 GGGGGCAAAAATGTAATATTTAGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAGTTT
1 GGGGGCAAAAATGTGATTTTTAGAAGTT-TAGGGTAAAATGGTAATTTTTGGAAAGTTT
* * *
40867435 GGGGGCAAAAATGTGATTTTTGGAATTTTAGGAGTAAAATGGTAATTTTTAG-AAGTTT
1 GGGGGCAAAAATGTGATTTTTAGAAGTTTAGG-GTAAAATGGTAATTTTTGGAAAGTTT
* * *
40867493 GAGGACAAAAATGTGATTTTTCGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAGTTT
1 GGGGGCAAAAATGTGATTTTTAG-AAGTTTA-GGGTAAAATGGTAATTTTTGGAAAGTTT
* * ** * * * **
40867553 AGAGGTTAAAATATGATTTTTGAAAAGTTTGAGGGTTAAAAT-ATAATTTTTAAAAAGTTT
1 GGGGGCAAAAATGTGATTTTT-AGAAGTTT-AGGG-TAAAATGGTAATTTTTGGAAAGTTT
* * * * * *
40867613 GAGGGTC-AAAATATGACTTTTGAAAAGTTTAGGGGTTAAAAT-GTAGTTTTTGAAAAGTTT
1 G-GGGGCAAAAATGTGA-TTTTTAGAAGTTTA-GGG-TAAAATGGTAATTTTTGGAAAGTTT
40867673 AAGGGTTAAA
Statistics
Matches: 197, Mismatches: 31, Indels: 19
0.80 0.13 0.08
Matches are distributed among these distances:
58 29 0.15
59 67 0.34
60 88 0.45
61 13 0.07
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (58 bp):
GGGGGCAAAAATGTGATTTTTAGAAGTTTAGGGTAAAATGGTAATTTTTGGAAAGTTT
Found at i:40867580 original size:60 final size:59
Alignment explanation
Indices: 40867407--40867714 Score: 286
Period size: 60 Copynumber: 5.2 Consensus size: 59
40867397 AGAAGTTCGA
* * * * *
40867407 GGGTAAAATGGTAATTTTTGGAAAGTTTGGGGGCAAAAATGTGATTTTTG-GAATTTTAG
1 GGGTAAAATGGTAATTTTTGGAAAGTTT-GAGGTAAAAATATGATTTTTGAAAAGTTTAG
* * * *
40867466 GAGTAAAATGGTAATTTTTAG-AAGTTTGAGGACAAAAATGTGATTTTTCG-AAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAAGTTTGAGG-TAAAAATATGATTTTT-GAAAAGTTTAG
*
40867525 GGGTAAAATGGTAATTTTTGGAAAGTTTAGAGGTTAAAATATGATTTTTGAAAAGTTTGAG
1 GGGTAAAATGGTAATTTTTGGAAAGTTT-GAGGTAAAAATATGATTTTTGAAAAGTTT-AG
* * ** * *
40867586 GGTTAAAAT-ATAATTTTTAAAAAGTTTGAGGGTCAAAATATGACTTTTGAAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAAGTTTGA-GGTAAAAATATGATTTTTGAAAAGTTTAG
* * * * * *
40867645 GGGTTAAAAT-GTAGTTTTTGAAAAGTTTAAGGGTTAAAATATAATTTTT-AAAGAGTTTAA
1 GGG-TAAAATGGTAATTTTTGGAAAGTTTGA-GGTAAAAATATGATTTTTGAAA-AGTTTAG
40867705 GGGTCAAAAT
1 GGGT-AAAAT
40867715 ATGATTTCTA
Statistics
Matches: 214, Mismatches: 25, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
57 3 0.01
58 22 0.10
59 57 0.27
60 118 0.55
61 14 0.07
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTTGAGGTAAAAATATGATTTTTGAAAAGTTTAG
Found at i:40867602 original size:90 final size:86
Alignment explanation
Indices: 40867399--40867736 Score: 272
Period size: 90 Copynumber: 3.8 Consensus size: 86
40867389 TAATATTTAG
* * * * *
40867399 AAGTTCGAGGG-TAAAATGGTAATTTTTGGAAAGTTTGGGGGCAAAAATGTGATTTTTGG-AATT
1 AAGTTTGAGGGTTAAAAT-ATAATTTTTAGAAAGTTT-GGGG-TAAAATGTGATTTTTGGAAAGT
*
40867462 TTAGGAG-TAAAATGGTAATTTTT-AG
63 TTAGG-GTTAAAAT-GT-ATTTTTGAA
*** * * * *
40867487 AAGTTTGAGGACAAAAATGTGATTTTTCGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAGTT
1 AAGTTTGAGGGTTAAAATATAATTTTTAGAAAGTTT-GGGGTAAAAT-GTGATTTTTGGAAAGTT
*
40867552 TAGAGGTTAAAATATGATTTTTGAA
64 TAG-GGTTAAAATGT-ATTTTTGAA
* * * *
40867577 AAGTTTGAGGGTTAAAATATAATTTTTAAAAAGTTTGAGGGTCAAAATATGACTTTTGAAAAGTT
1 AAGTTTGAGGGTTAAAATATAATTTTTAGAAAGTTTG-GGGT-AAAATGTGATTTTTGGAAAGTT
40867642 TAGGGGTTAAAATGTAGTTTTTGAA
64 TA-GGGTTAAAATGTA-TTTTTGAA
* * * * **
40867667 AAGTTTAAGGGTTAAAATATAATTTTTA-AAGAGTTTAAGGGTCAAAATATGATTTCTAAAAAGT
1 AAGTTTGAGGGTTAAAATATAATTTTTAGAA-AGTTT-GGGGT-AAAATGTGATTTTTGGAAAGT
40867731 TTAGGG
63 TTAGGG
40867737 GCCTTCTGGG
Statistics
Matches: 209, Mismatches: 29, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
87 5 0.02
88 39 0.19
89 27 0.13
90 132 0.63
91 6 0.03
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (86 bp):
AAGTTTGAGGGTTAAAATATAATTTTTAGAAAGTTTGGGGTAAAATGTGATTTTTGGAAAGTTTA
GGGTTAAAATGTATTTTTGAA
Found at i:40867702 original size:30 final size:29
Alignment explanation
Indices: 40867516--40867733 Score: 206
Period size: 30 Copynumber: 7.3 Consensus size: 29
40867506 TGATTTTTCG
* * *
40867516 AAAGTTT-AGGGGTAAAATGGTAATTTTTGG
1 AAAGTTTAAGGGTTAAAAT-ATAATTTTT-A
*
40867546 AAAGTTT-AGAGGTTAAAATATGATTTTTGA
1 AAAGTTTAAG-GGTTAAAATATAATTTTT-A
*
40867576 AAAGTTTGAGGGTTAAAATATAATTTTTAA
1 AAAGTTTAAGGGTTAAAATATAATTTTT-A
* * * *
40867606 AAAGTTTGAGGGTCAAAATATGACTTTTGA
1 AAAGTTTAAGGGTTAAAATAT-AATTTTTA
* * *
40867636 AAAGTTTAGGGGTTAAAATGTAGTTTTTGA
1 AAAGTTTAAGGGTTAAAATATAATTTTT-A
40867666 AAAGTTTAAGGGTTAAAATATAATTTTTA
1 AAAGTTTAAGGGTTAAAATATAATTTTTA
* * *
40867695 AAGAGTTTAAGGGTCAAAATATGATTTCTAA
1 AA-AGTTTAAGGGTTAAAATATAATTT-TTA
40867726 AAAGTTTA
1 AAAGTTTA
40867734 GGGGCCTTCT
Statistics
Matches: 161, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.05
30 134 0.83
31 19 0.12
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.38
Consensus pattern (29 bp):
AAAGTTTAAGGGTTAAAATATAATTTTTA
Found at i:40867737 original size:90 final size:90
Alignment explanation
Indices: 40867546--40867737 Score: 298
Period size: 90 Copynumber: 2.1 Consensus size: 90
40867536 TAATTTTTGG
* *
40867546 AAAGTTTAGAGGTTAAAATATGATTTTTGAAAAGTTTGAGGGTTAAAATATAATTTTTAAAAAGT
1 AAAGTTTAGGGGTTAAAATATGATTTTTGAAAAGTTTAAGGGTTAAAATATAATTTTTAAAAAGT
* *
40867611 TTGAGGGTCAAAATATGACTTTTGA
66 TTAAGGGTCAAAATATGACTTTTAA
* *
40867636 AAAGTTTAGGGGTTAAAATGT-AGTTTTTGAAAAGTTTAAGGGTTAAAATATAATTTTTAAAGAG
1 AAAGTTTAGGGGTTAAAATATGA-TTTTTGAAAAGTTTAAGGGTTAAAATATAATTTTTAAAAAG
40867700 TTTAAGGGTCAAAATATGA-TTTCTAA
65 TTTAAGGGTCAAAATATGACTTT-TAA
40867726 AAAGTTTAGGGG
1 AAAGTTTAGGGG
40867738 CCTTCTGGGC
Statistics
Matches: 94, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
89 4 0.04
90 90 0.96
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (90 bp):
AAAGTTTAGGGGTTAAAATATGATTTTTGAAAAGTTTAAGGGTTAAAATATAATTTTTAAAAAGT
TTAAGGGTCAAAATATGACTTTTAA
Found at i:40868487 original size:50 final size:49
Alignment explanation
Indices: 40868376--40868489 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 49
40868366 TTTTGATGTT
** *
40868376 TTTTTCTTTTAAAAAACTTTTCTCTTTTAATTTCTTTAAAACGGTTTTGA
1 TTTTTCTTTT-AAAAACTTTTCTCTTTTAATTTCTTTAAAAAAGTTCTGA
*
40868426 TTTCTT-TTTTAAAAACTTTTCTCTTTTGA-TTCTTTAAAAAAAAGTTCTGA
1 TTT-TTCTTTTAAAAACTTTTCTCTTTTAATTTCTTT--AAAAAAGTTCTGA
*
40868476 TTTTTCCTTTAAAA
1 TTTTTCTTTTAAAA
40868490 CTCCCTTCTC
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
48 6 0.11
49 20 0.36
50 27 0.49
51 2 0.04
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.54
Consensus pattern (49 bp):
TTTTTCTTTTAAAAACTTTTCTCTTTTAATTTCTTTAAAAAAGTTCTGA
Found at i:40868491 original size:49 final size:49
Alignment explanation
Indices: 40868378--40868489 Score: 122
Period size: 49 Copynumber: 2.3 Consensus size: 49
40868368 TTGATGTTTT
* ** *
40868378 TTTCTT-TTAAAAAACTTTTCTCTTTTAATTTCTTTAAAACGGTTTTGA
1 TTTCTTCTTTAAAAACTTTTCTCTTTTAATTTCTTTAAAAAAGTTCTGA
* *
40868426 TTTCTTTTTTAAAAACTTTTCTCTTTTGA-TTCTTTAAAAAAAAGTTCTGA
1 TTTCTTCTTTAAAAACTTTTCTCTTTTAATTTCTTT--AAAAAAGTTCTGA
40868476 TTT-TTCCTTTAAAA
1 TTTCTT-CTTTAAAA
40868490 CTCCCTTCTC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
48 12 0.22
49 22 0.41
50 20 0.37
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.54
Consensus pattern (49 bp):
TTTCTTCTTTAAAAACTTTTCTCTTTTAATTTCTTTAAAAAAGTTCTGA
Found at i:40868722 original size:3 final size:3
Alignment explanation
Indices: 40868714--40868740 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40868704 ATTTATTTAT
40868714 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
40868741 ATCGTTTCAA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40869448 original size:17 final size:17
Alignment explanation
Indices: 40869418--40869527 Score: 103
Period size: 17 Copynumber: 6.4 Consensus size: 17
40869408 TATTTGGACT
*
40869418 TTTAAAATTAAATTTTAA
1 TTTAAAA-TAAATTTAAA
*
40869436 TTTAAAATAAATTTCAA
1 TTTAAAATAAATTTAAA
* *
40869453 TTTAAAGTAAACTTAAA
1 TTTAAAATAAATTTAAA
* * *
40869470 CTCAAAATGAATTTAAA
1 TTTAAAATAAATTTAAA
*
40869487 TTTAAAATAAAATTAAA
1 TTTAAAATAAATTTAAA
* * *
40869504 CTTAAAGTAAATTAAAA
1 TTTAAAATAAATTTAAA
*
40869521 ATTAAAA
1 TTTAAAA
40869528 ATTGGGACTC
Statistics
Matches: 73, Mismatches: 19, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
17 66 0.90
18 7 0.10
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:40870505 original size:209 final size:209
Alignment explanation
Indices: 40869840--40870529 Score: 897
Period size: 209 Copynumber: 3.3 Consensus size: 209
40869830 TCCTTGAGTC
* * * * * * **
40869840 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTTATCAGGAAGATGACCGCATCGCCTGTTTTG
1 TGGTTTCGTTGATTTGATCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTATTTCA
* * * * ** * *
40869905 ATCTACTTCTCTGTGTCTCATTAAGAAGACGAACCTGGTTCACTTCTCTG-TATCTCATCAAGAA
66 ATCTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTC-GATATCTCATCAGGAA
* *
40869969 GCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATCAGGTAGCT-AGAGTTCGAAGAT
130 GCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAG-GTTCGAAGAT
*
40870033 TCGCTCACTTTGAGTT
194 TCGCTCACTTTGAGCT
* * ** *
40870049 TGGTTTCGTTGATTTGATCTTCTTCTCAGT-TCCTCATCAAGAAGATGACCGCATTGCTTGTTTC
1 TGGTTTCGTTGATTTGATCTACTTCTCAGTAT-CTCATCAGGAAGATGACCGCATCACTTATTTC
* *
40870113 AAT-TCGCCTCTCTGTATCTCATCAGGAAGACGAATTTGATCCACTTCTC-AGTATCTCATCAGG
65 AATCT-GCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCGA-TATCTCATCAGG
* * * * *
40870176 AAGCTAACCATTTTATTGCTTCGATCTGCTTCTCAGTATCCCATCAGGAAGCTGGGGTTCAAAGG
128 AAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGA
*
40870241 TTCGCTCACTTTGAGCC
193 TTCGCTCACTTTGAGCT
* *
40870258 TGGTTTCGTTGATTTGATCTTCTTCTCAGTACCTCATCAGGAAGATGACCGCATCACTTATTTCA
1 TGGTTTCGTTGATTTGATCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTATTTCA
*
40870323 ATCTGCTTCTCTGTATCTCATCAGGAAGACGAGTTTGGTCCACTTCTCGATATCTCATCAGGAAG
66 ATCTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCGATATCTCATCAGGAAG
*
40870388 CTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTT
131 CTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTC
40870453 GCTCACTTTGAGCT
196 GCTCACTTTGAGCT
* * * * * * *
40870467 TGG-TTCTATTAAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTATTT
1 TGGTTTC-GTTGATTTGATCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTATTT
40870530 TGGATAATCG
Statistics
Matches: 420, Mismatches: 52, Indels: 18
0.86 0.11 0.04
Matches are distributed among these distances:
208 5 0.01
209 412 0.98
210 3 0.01
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (209 bp):
TGGTTTCGTTGATTTGATCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTATTTCA
ATCTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCGATATCTCATCAGGAAG
CTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTC
GCTCACTTTGAGCT
Found at i:40872994 original size:18 final size:18
Alignment explanation
Indices: 40872971--40873019 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 18
40872961 TATGATGATA
40872971 TATATGTGATGAACAATG
1 TATATGTGATGAACAATG
40872989 TATATGTGAAATATGAACAATG
1 TATATGTG----ATGAACAATG
40873011 TATATGTGA
1 TATATGTGA
40873020 AATATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 9 0.33
22 18 0.67
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (18 bp):
TATATGTGATGAACAATG
Found at i:40873004 original size:22 final size:22
Alignment explanation
Indices: 40872979--40873024 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
40872969 TATATATGTG
40872979 ATGAACAATGTATATGTGAAAT
1 ATGAACAATGTATATGTGAAAT
40873001 ATGAACAATGTATATGTGAAAT
1 ATGAACAATGTATATGTGAAAT
40873023 AT
1 AT
40873025 TATATGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (22 bp):
ATGAACAATGTATATGTGAAAT
Found at i:40873186 original size:6 final size:6
Alignment explanation
Indices: 40873175--40873207 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
40873165 TGATCAAAAT
*
40873175 TGAAAG TGAAAG TGAAAG TGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
40873208 TATGAATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.21
Consensus pattern (6 bp):
TGAAAG
Found at i:40879455 original size:12 final size:12
Alignment explanation
Indices: 40879440--40879474 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
40879430 CATTTCATAT
40879440 CACTTTCAATTC
1 CACTTTCAATTC
* *
40879452 CACTTTCACTTT
1 CACTTTCAATTC
40879464 CACTTTCAATT
1 CACTTTCAATT
40879475 TTGATCACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (12 bp):
CACTTTCAATTC
Found at i:40888179 original size:29 final size:29
Alignment explanation
Indices: 40888109--40888179 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
40888099 TAAACGGAGT
* * *
40888109 CAAAAATGCAATTTTCGGATACTCGGGGG
1 CAAAAATGCAATTATCGGACACTCGAGGG
*
40888138 C-AAAATGATAATTAT-GGACACTTCGAGGG
1 CAAAAATG-CAATTATCGGACAC-TCGAGGG
40888167 CAAAAATGCAATT
1 CAAAAATGCAATT
40888180 TTTAAAAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
28 11 0.32
29 17 0.50
30 6 0.18
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (29 bp):
CAAAAATGCAATTATCGGACACTCGAGGG
Found at i:40888191 original size:29 final size:30
Alignment explanation
Indices: 40888159--40888242 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 30
40888149 TTATGGACAC
40888159 TTCGAGGGCAAAAATGCAATTTTT-AAAAG
1 TTCGAGGGCAAAAATGCAATTTTTGAAAAG
* * *
40888188 TTCGAGAG-TAAAATGGTAATTTTTGAAAAG
1 TTCGAGGGCAAAAAT-GCAATTTTTGAAAAG
* **
40888218 TT-TAGGGGCAAAAATGTGATTTTTG
1 TTCGA-GGGCAAAAATGCAATTTTTG
40888243 GAATTTTAGG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
28 5 0.11
29 16 0.36
30 18 0.41
31 5 0.11
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (30 bp):
TTCGAGGGCAAAAATGCAATTTTTGAAAAG
Found at i:40888250 original size:29 final size:29
Alignment explanation
Indices: 40888196--40888597 Score: 310
Period size: 30 Copynumber: 13.5 Consensus size: 29
40888186 AGTTCGAGAG
* *
40888196 TAAAATGGTAATTTTTGAAAAGTTTAGGGGC
1 TAAAAT-GTAATTTTTG-GAAGTTTAGGGGT
* * * *
40888227 AAAAATGTGATTTTTGGAATTTTAGGGGG
1 TAAAATGTAATTTTTGGAAGTTTAGGGGT
* * *
40888256 TAAAATGGTAATTTTTAGAAG-TTCGGGAT
1 TAAAAT-GTAATTTTTGGAAGTTTAGGGGT
* * * * *
40888285 AAAAATGTGATTTTTTGGAAATTT-TGGGA
1 TAAAATGT-AATTTTTGGAAGTTTAGGGGT
*
40888314 TAAAATGGTAATTTTTAGAAGTTTAGGGGT
1 TAAAAT-GTAATTTTTGGAAGTTTAGGGGT
* *
40888344 AAAAATGGAATTTTTGGAAGTTT-GAGGGT
1 TAAAATGTAATTTTTGGAAGTTTAG-GGGT
40888373 TAAAATGTAATTTTTGGAAGTTT-GAGGGT
1 TAAAATGTAATTTTTGGAAGTTTAG-GGGT
*
40888402 TAAAATGTAATTTTTGGAAAGTTTAGTGGT
1 TAAAATGTAATTTTTGG-AAGTTTAGGGGT
* * * *
40888432 TAAAATATGATTTTTGAAAAGTTTAGGAGT
1 TAAAATGTAATTTTTG-GAAGTTTAGGGGT
* *
40888462 TAAAATGTAATTTTTGAAAAATTTAGGGGT
1 TAAAATGTAATTTTTG-GAAGTTTAGGGGT
* * *
40888492 CAAAATGTGATTTTTGAAAAGTTTAGGGGGT
1 TAAAATGTAATTTTTG-GAAGTTTA-GGGGT
* *** *
40888523 CAAAATGTAACTTTTAAAAAGTTT-GAAGGT
1 TAAAATGTAA-TTTTTGGAAGTTTAG-GGGT
* **
40888553 TAAAATGTAGTTTTTAAAAAGTTTAGGGGT
1 TAAAATGTAATTTTT-GGAAGTTTAGGGGT
*
40888583 CAAAATGTAATTTTT
1 TAAAATGTAATTTTT
40888598 AAAGAGTTAA
Statistics
Matches: 304, Mismatches: 53, Indels: 29
0.79 0.14 0.08
Matches are distributed among these distances:
28 3 0.01
29 121 0.40
30 148 0.49
31 28 0.09
32 4 0.01
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (29 bp):
TAAAATGTAATTTTTGGAAGTTTAGGGGT
Found at i:40889465 original size:49 final size:49
Alignment explanation
Indices: 40889362--40889478 Score: 141
Period size: 49 Copynumber: 2.3 Consensus size: 49
40889352 TTCTTTTAAA
** *
40889362 AAAAACTTTTCTCTTTTGATTTCTTTAAAACGGTTTTGATTTCTTTTTT
1 AAAAACTTTTCTCTTTTGATTTCTTTAAAAAAGTTTTGATTTCTTCTTT
40889411 AAAAACTTTTCTCTTTTGA-TTCTTTAAAAAAAAGTTTTGATTT-TTCCTTT
1 AAAAACTTTTCTCTTTTGATTTCTTT--AAAAAAGTTTTGATTTCTT-CTTT
40889461 -AAAACTCTCTTCTCTTTT
1 AAAAACT-T-TTCTCTTTT
40889479 CAGATTTGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
48 6 0.10
49 27 0.45
50 18 0.30
51 9 0.15
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.54
Consensus pattern (49 bp):
AAAAACTTTTCTCTTTTGATTTCTTTAAAAAAGTTTTGATTTCTTCTTT
Found at i:40889686 original size:9 final size:9
Alignment explanation
Indices: 40889669--40889716 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
40889659 GACCTTTTCG
*
40889669 TATTCTTTT
1 TATTATTTT
40889678 T-TTATTTT
1 TATTATTTT
*
40889686 TATTATTAT
1 TATTATTTT
*
40889695 TATTATTAT
1 TATTATTTT
*
40889704 TATTATTAT
1 TATTATTTT
40889713 TATT
1 TATT
40889717 CGTTTCAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
8 7 0.19
9 29 0.81
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (9 bp):
TATTATTTT
Found at i:40889691 original size:3 final size:3
Alignment explanation
Indices: 40889679--40889716 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
40889669 TATTCTTTTT
*
40889679 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40889717 CGTTTCAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:40890261 original size:13 final size:13
Alignment explanation
Indices: 40890243--40890268 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40890233 GTATAAGTTA
40890243 TGGCAGCAGATCT
1 TGGCAGCAGATCT
40890256 TGGCAGCAGATCT
1 TGGCAGCAGATCT
40890269 GGAAGGCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (13 bp):
TGGCAGCAGATCT
Found at i:40907770 original size:17 final size:17
Alignment explanation
Indices: 40907748--40907780 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
40907738 TCCATCTATG
40907748 CTGCCTCTCAAGCTTAC
1 CTGCCTCTCAAGCTTAC
40907765 CTGCCTCTCAAGCTTA
1 CTGCCTCTCAAGCTTA
40907781 AGCTGCCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.39, G:0.12, T:0.30
Consensus pattern (17 bp):
CTGCCTCTCAAGCTTAC
Found at i:40917219 original size:26 final size:25
Alignment explanation
Indices: 40917180--40917229 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
40917170 TTAAACAGCT
*
40917180 AATTGTCCATATTCAAATCTAGACAA
1 AATTGTCCAAATTC-AATCTAGACAA
* *
40917206 AATTGTCTAAATTCATTCTAGACA
1 AATTGTCCAAATTCAATCTAGACA
40917230 TTTTTTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (25 bp):
AATTGTCCAAATTCAATCTAGACAA
Found at i:40920679 original size:2 final size:2
Alignment explanation
Indices: 40920674--40920706 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40920664 TAAAAATAAT
40920674 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40920707 TTAAAAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40930347 original size:26 final size:26
Alignment explanation
Indices: 40930284--40930350 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
40930274 ATAATTGAAC
* * *
40930284 ATTAAAATATTTTAAAATGACTATAT
1 ATTAAAATAATATAAAATGACTAAAT
* *
40930310 A-TAAAACT-ATATAAAATTATTAAAT
1 ATTAAAA-TAATATAAAATGACTAAAT
40930335 ATTAAAATAATATAAA
1 ATTAAAATAATATAAA
40930351 TATAAACATA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
25 19 0.58
26 14 0.42
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (26 bp):
ATTAAAATAATATAAAATGACTAAAT
Found at i:40930350 original size:10 final size:9
Alignment explanation
Indices: 40930306--40930363 Score: 52
Period size: 8 Copynumber: 6.7 Consensus size: 9
40930296 TAAAATGACT
40930306 ATATATAAA
1 ATATATAAA
40930315 ACTATATAAA
1 A-TATATAAA
*
40930325 AT-TATTAA
1 ATATATAAA
40930333 ATAT-TAAA
1 ATATATAAA
40930341 ATA-ATATAA
1 ATATATA-AA
*
40930350 ATATA-AAC
1 ATATATAAA
40930358 ATATAT
1 ATATAT
40930364 TTTTAAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
8 21 0.52
9 9 0.22
10 10 0.25
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (9 bp):
ATATATAAA
Found at i:40940383 original size:30 final size:29
Alignment explanation
Indices: 40940301--40940396 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 29
40940291 ATTGAAGGTG
** * *
40940301 AAATTTATTAAATTTAATAGAATTTAAATT
1 AAATTTATTAAATTTTTTA-TATTAAAATT
* *
40940331 AAAATTA-TGAATTTTGTATATATTGAAAATT
1 AAATTTATTAAATTTT-T-TATATT-AAAATT
*
40940362 AAATTTATTAAATTTTTTATATCTAAGATT
1 AAATTTATTAAATTTTTTATAT-TAAAATT
40940392 AAATT
1 AAATT
40940397 AATAAAAATC
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
29 6 0.12
30 24 0.46
31 15 0.29
32 7 0.13
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (29 bp):
AAATTTATTAAATTTTTTATATTAAAATT
Found at i:40944465 original size:132 final size:132
Alignment explanation
Indices: 40944223--40944478 Score: 354
Period size: 132 Copynumber: 1.9 Consensus size: 132
40944213 GAAACCAAGA
* * *
40944223 AAGTGAAAGGATCTCTTCCTGATAACTTCTTTGATAGGGGTGAAACCAAGTTACCTATGAATCTT
1 AAGTGAAAGGATCTCTTCCTGATAACTTCTTTGATAAGGATGAAACCAAGTTACCTATGAATCTC
**
40944288 ATGAAGCCTCCTAGGGAGAATAAACTGGCAGCAAAGCAGGCTAGTGCTCCAGAAACCAAAACAAG
66 ATGAAGCCTCCTAGGGAGAATAAACAAGCAGCAAAGCAGGCTAGTGCTCCAGAAACCAAAACAAG
40944353 GC
131 GC
* * * **
40944355 AAGTTAAAGGATCTCTTCCTGGTGACTTCTTTGATAAGGATGATTCCAAGTTACCTATGAATGC-
1 AAGTGAAAGGATCTCTTCCTGATAACTTCTTTGATAAGGATGAAACCAAGTTACCTATGAAT-CT
* * **
40944419 CATGAAGCCTCCTAGGGAGAATATAGAAGCTTCAGAA-CAGGCTAGTGCTCCAGAAACCAA
65 CATGAAGCCTCCTAGGGAGAATAAACAAGCAGCA-AAGCAGGCTAGTGCTCCAGAAACCAA
40944479 GCAAGTAAAG
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
132 105 0.97
133 3 0.03
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (132 bp):
AAGTGAAAGGATCTCTTCCTGATAACTTCTTTGATAAGGATGAAACCAAGTTACCTATGAATCTC
ATGAAGCCTCCTAGGGAGAATAAACAAGCAGCAAAGCAGGCTAGTGCTCCAGAAACCAAAACAAG
GC
Found at i:40952299 original size:24 final size:24
Alignment explanation
Indices: 40952211--40952293 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
40952201 TAGAGTAATA
* *
40952211 AGAGTTTGATTCAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
* *
40952235 AGAGTTTAGTTGAAACAAATAAAT
1 AGAGTTTAATTGAAACAAATAAAC
* * *
40952259 AGAATTCAATTGAAATAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
40952283 AGAGTTTAATT
1 AGAGTTTAATT
40952294 AAAATATTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:40959184 original size:18 final size:18
Alignment explanation
Indices: 40959161--40959197 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40959151 TTAGTGATCA
40959161 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
40959179 AAATTGAAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
40959197 A
1 A
40959198 TATGAATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:40959186 original size:12 final size:12
Alignment explanation
Indices: 40959161--40959197 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
40959151 TTAGTGATCA
40959161 AAATTGAAAGTG
1 AAATTGAAAGTG
* *
40959173 AAAGTGAAATTG
1 AAATTGAAAGTG
40959185 AAATTGAAAGTG
1 AAATTGAAAGTG
40959197 A
1 A
40959198 TATGAATTGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:40959347 original size:41 final size:41
Alignment explanation
Indices: 40959300--40959398 Score: 107
Period size: 38 Copynumber: 2.5 Consensus size: 41
40959290 CGACCTTGAG
* * * *
40959300 TCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAAAT
1 TCGATGAGATACTGGGTGTCATCACTTTACTTCGGATAAAC
* * *
40959341 TCGATGAGGTACT-GG-GT-ATCACTTTACTTCGGCTAGAC
1 TCGATGAGATACTGGGTGTCATCACTTTACTTCGGATAAAC
40959379 T-GATGAGATACTGGGTGTCA
1 TCGATGAGATACTGGGTGTCA
40959399 CTTTATTGCT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
37 10 0.21
38 19 0.40
39 4 0.09
40 3 0.06
41 11 0.23
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.33
Consensus pattern (41 bp):
TCGATGAGATACTGGGTGTCATCACTTTACTTCGGATAAAC
Found at i:40959391 original size:37 final size:38
Alignment explanation
Indices: 40959325--40959403 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 38
40959315 GTGTCATTAT
* *
40959325 TTTACTTCGGATAAATTCGATGAGGTACTGGGTATCAC
1 TTTACTTCGGATAAACTCGATGAGATACTGGGTATCAC
* * *
40959363 TTTACTTCGGCTAGACT-GATGAGATACTGGGTGTCAC
1 TTTACTTCGGATAAACTCGATGAGATACTGGGTATCAC
40959400 TTTA
1 TTTA
40959404 TTGCTTCGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 22 0.61
38 14 0.39
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (38 bp):
TTTACTTCGGATAAACTCGATGAGATACTGGGTATCAC
Found at i:40965448 original size:16 final size:17
Alignment explanation
Indices: 40965429--40965469 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
40965419 TAATTTTTTA
40965429 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
40965445 AAAA-TATTAAAATAAT
1 AAAATTATAAAAATAAT
40965461 AAAATTATA
1 AAAATTATA
40965470 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 8 0.38
16 10 0.48
17 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:40965683 original size:5 final size:5
Alignment explanation
Indices: 40965673--40965697 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40965663 TTACTTGGGC
40965673 TCATG TCATG TCATG TCATG TCATG
1 TCATG TCATG TCATG TCATG TCATG
40965698 CGGCATGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
TCATG
Found at i:40981228 original size:17 final size:16
Alignment explanation
Indices: 40981208--40981241 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
40981198 TTTGATTTCG
*
40981208 ATTATTTAAATATTTTA
1 ATTAATTAAAT-TTTTA
40981225 ATTAATTAAATTTTTA
1 ATTAATTAAATTTTTA
40981241 A
1 A
40981242 ATATATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTAATTAAATTTTTA
Found at i:40982976 original size:21 final size:18
Alignment explanation
Indices: 40982930--40982977 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 18
40982920 TATATTAATT
40982930 TTTATTTTATTTTTTAAA
1 TTTATTTTATTTTTTAAA
*
40982948 TTTGTTTTATGGTTTTTAAA
1 TTTATTTTAT--TTTTTAAA
40982968 TATTATTTTA
1 T-TTATTTTA
40982978 CAAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.36
20 9 0.36
21 7 0.28
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTATTTTATTTTTTAAA
Found at i:40983101 original size:22 final size:23
Alignment explanation
Indices: 40983067--40983113 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
40983057 AAATATTTAT
40983067 TTTATATCATAAA-AATAAAATTAA
1 TTTATAT-ATAAATAA-AAAATTAA
40983091 TTTATAT-TAAATAAAAAATTAA
1 TTTATATATAAATAAAAAATTAA
40983113 T
1 T
40983114 ATAATAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 13 0.59
23 2 0.09
24 7 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTATATATAAATAAAAAATTAA
Found at i:40998296 original size:3 final size:3
Alignment explanation
Indices: 40998283--40998334 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
40998273 TACACTCGGG
40998283 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40998329 ATT ATT
1 ATT ATT
40998335 TCTTGGATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41000592 original size:91 final size:91
Alignment explanation
Indices: 41000490--41000665 Score: 352
Period size: 91 Copynumber: 1.9 Consensus size: 91
41000480 TACTAATTTA
41000490 AAATTTTAAATAACTTAAATACAAAATTTTACTTTTAAGATTTGTTTTCTTTATTTTAATTTGTT
1 AAATTTTAAATAACTTAAATACAAAATTTTACTTTTAAGATTTGTTTTCTTTATTTTAATTTGTT
41000555 AAATCAATACTTATATCCATATTAGT
66 AAATCAATACTTATATCCATATTAGT
41000581 AAATTTTAAATAACTTAAATACAAAATTTTACTTTTAAGATTTGTTTTCTTTATTTTAATTTGTT
1 AAATTTTAAATAACTTAAATACAAAATTTTACTTTTAAGATTTGTTTTCTTTATTTTAATTTGTT
41000646 AAATCAATACTTATATCCAT
66 AAATCAATACTTATATCCAT
41000666 TCTTCTCATG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (91 bp):
AAATTTTAAATAACTTAAATACAAAATTTTACTTTTAAGATTTGTTTTCTTTATTTTAATTTGTT
AAATCAATACTTATATCCATATTAGT
Found at i:41005032 original size:16 final size:16
Alignment explanation
Indices: 41005006--41005044 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41004996 ACTTTGAGTA
*
41005006 CCATTATTAATGGATG
1 CCATAATTAATGGATG
* *
41005022 CCTTAATTAATTGATG
1 CCATAATTAATGGATG
41005038 CCATAAT
1 CCATAAT
41005045 AAGAAAACAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (16 bp):
CCATAATTAATGGATG
Found at i:41022695 original size:6 final size:6
Alignment explanation
Indices: 41022677--41022709 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
41022667 AAAATTATGC
41022677 ATGAAA GATGAAA ATGAAA ATGAAA ATGAAA AT
1 ATGAAA -ATGAAA ATGAAA ATGAAA ATGAAA AT
41022710 TAAATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (6 bp):
ATGAAA
Found at i:41023972 original size:20 final size:18
Alignment explanation
Indices: 41023933--41023968 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41023923 CAACCAAAAA
41023933 TAAAATATATATTTAAAT
1 TAAAATATATATTTAAAT
*
41023951 TAAACTATATATTTAAAT
1 TAAAATATATATTTAAAT
41023969 ATTATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATATATATTTAAAT
Found at i:41026565 original size:14 final size:16
Alignment explanation
Indices: 41026532--41026568 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
41026522 ATTGTGAATG
*
41026532 AAAATATTTTATATTA
1 AAAATATATTATATTA
41026548 AAAATATATT-TA-TA
1 AAAATATATTATATTA
41026562 AAAATAT
1 AAAATAT
41026569 TTAAAGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 9 0.45
15 2 0.10
16 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATATATTATATTA
Found at i:41026804 original size:26 final size:26
Alignment explanation
Indices: 41026753--41026806 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
41026743 TCAAATATCG
* *
41026753 AATTAATTTATAATATTAATATAAGT
1 AATTAATATATAATATAAATATAAGT
*
41026779 AATTAATATAT-ATATAAATTTAAAGT
1 AATTAATATATAATATAAATAT-AAGT
41026805 AA
1 AA
41026807 AAATATTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (26 bp):
AATTAATATATAATATAAATATAAGT
Found at i:41028089 original size:5 final size:5
Alignment explanation
Indices: 41028079--41028103 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41028069 TATTTGTAGG
41028079 GTGAA GTGAA GTGAA GTGAA GTGAA
1 GTGAA GTGAA GTGAA GTGAA GTGAA
41028104 TGTTTCCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (5 bp):
GTGAA
Found at i:41031407 original size:251 final size:252
Alignment explanation
Indices: 41030964--41031470 Score: 874
Period size: 251 Copynumber: 2.0 Consensus size: 252
41030954 ACATAAAGGC
* *
41030964 TTTAATCTGAACTAAGGTGGCTAATATTAGAAGGTTTGTTTGCTATATGCGTGTCTAATGTCGTG
1 TTTAATCTGAACTAAGGTGGCTAATATTAGAAGGTTTGTTTGCTATATGCATGGCTAATGTCGTG
* *
41031029 TAGACTTCCATTATACTGTCAAAAGAAAGTCATTTTAAACCTTTGAACCAGAATTGATCAATTAG
66 TAGAATTCCATTATACTGTCAAAAGAAAGTCATTTTAAACCTTTGAACCAGAATTAATCAATTAG
41031094 TTTCTTAAATTTCCTGCTCATGTCTCCTTTTCTCTAATTCCTGATTTACTTACTATTAATATCTT
131 TTTCTTAAATTTCCTGCTCATGTCTCCTTTTCTCTAATTCCTGATTTACTTACTATTAATATCTT
41031159 AGA-ATTTTTTGCTAGTTGTGGTATATAATTTTGCC-TTGTGGAAACTGGATTTTTGT
196 AGATA-TTTTTGCTAGTTGTGGTATATAATTTTGCCTTTGTGGAAACTGGATTTTTGT
*
41031215 TTTAATCTGAACTAAGGTGGCTGATATTAGAAGGTTTGTTTGCTATATGCATGGCTAATGTCGTG
1 TTTAATCTGAACTAAGGTGGCTAATATTAGAAGGTTTGTTTGCTATATGCATGGCTAATGTCGTG
*
41031280 TAGAATTCCATTATACTGTCAAAAGAAAGTCATTTTAAACCTTTGAACCATAATTAATCAATTAG
66 TAGAATTCCATTATACTGTCAAAAGAAAGTCATTTTAAACCTTTGAACCAGAATTAATCAATTAG
* * * * * *
41031345 TTTTTTAAATTTTCTGCTTATGTCTTCTTTTCTCTAATTCTTGATTTACTTGCTATTAATATCTT
131 TTTCTTAAATTTCCTGCTCATGTCTCCTTTTCTCTAATTCCTGATTTACTTACTATTAATATCTT
*
41031410 AGATATTTTTGCTAGTTGTGGTATATAATTTTTCCTTTGTGGAAACTGGATTTTTGT
196 AGATATTTTTGCTAGTTGTGGTATATAATTTTGCCTTTGTGGAAACTGGATTTTTGT
41031467 TTTA
1 TTTA
41031471 GTTCATTTAA
Statistics
Matches: 241, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
251 215 0.89
252 26 0.11
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (252 bp):
TTTAATCTGAACTAAGGTGGCTAATATTAGAAGGTTTGTTTGCTATATGCATGGCTAATGTCGTG
TAGAATTCCATTATACTGTCAAAAGAAAGTCATTTTAAACCTTTGAACCAGAATTAATCAATTAG
TTTCTTAAATTTCCTGCTCATGTCTCCTTTTCTCTAATTCCTGATTTACTTACTATTAATATCTT
AGATATTTTTGCTAGTTGTGGTATATAATTTTGCCTTTGTGGAAACTGGATTTTTGT
Found at i:41035719 original size:16 final size:16
Alignment explanation
Indices: 41035698--41035730 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41035688 ACTTACGAAG
41035698 TATGATTAGCACTTAA
1 TATGATTAGCACTTAA
41035714 TATGATTAGCACTTAA
1 TATGATTAGCACTTAA
41035730 T
1 T
41035731 TTTGAATTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (16 bp):
TATGATTAGCACTTAA
Found at i:41038370 original size:30 final size:29
Alignment explanation
Indices: 41038336--41038393 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
41038326 GTTAGAAAAT
* *
41038336 TTTTTAGGGGTTAAAATTAAAATTTTATTA
1 TTTTTAGGGATT-AAAGTAAAATTTTATTA
* *
41038366 TTTTTATGGATTAAAGTATAATTTTATT
1 TTTTTAGGGATTAAAGTAAAATTTTATT
41038394 GTTACTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (29 bp):
TTTTTAGGGATTAAAGTAAAATTTTATTA
Found at i:41043629 original size:35 final size:35
Alignment explanation
Indices: 41043590--41043703 Score: 90
Period size: 35 Copynumber: 3.2 Consensus size: 35
41043580 AGACACAAAG
41043590 ATATAATCTATCTGCATATTGCAAGATAGACTGGT
1 ATATAATCTATCTGCATATTGCAAGATAGACTGGT
* * ** * * **
41043625 ATATAAT-TTTGCTTGCTTAAAGCATCA-AGACACAAAG-
1 ATATAATCTAT-C-TGCATATTGCA--AGATAGAC-TGGT
41043662 ATATAATCTATCTGCATATTGCAAGATAGACTGGT
1 ATATAATCTATCTGCATATTGCAAGATAGACTGGT
41043697 ATATAAT
1 ATATAAT
41043704 TTTGCTTGAA
Statistics
Matches: 55, Mismatches: 16, Indels: 16
0.63 0.18 0.18
Matches are distributed among these distances:
34 4 0.07
35 19 0.35
36 16 0.29
37 12 0.22
38 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (35 bp):
ATATAATCTATCTGCATATTGCAAGATAGACTGGT
Found at i:41043684 original size:72 final size:72
Alignment explanation
Indices: 41043567--41043711 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
41043557 TAAGCTTCAG
41043567 GCTTAAAGCATCAAGACACAAAGATATAATCTATCTGCATATTGCAAGATAGACTGGTATATAAT
1 GCTTAAAGCATCAAGACACAAAGATATAATCTATCTGCATATTGCAAGATAGACTGGTATATAAT
41043632 TTTGCTT
66 TTTGCTT
41043639 GCTTAAAGCATCAAGACACAAAGATATAATCTATCTGCATATTGCAAGATAGACTGGTATATAAT
1 GCTTAAAGCATCAAGACACAAAGATATAATCTATCTGCATATTGCAAGATAGACTGGTATATAAT
41043704 TTTGCTT
66 TTTGCTT
41043711 G
1 G
41043712 AAGTCATTAC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (72 bp):
GCTTAAAGCATCAAGACACAAAGATATAATCTATCTGCATATTGCAAGATAGACTGGTATATAAT
TTTGCTT
Found at i:41045948 original size:31 final size:31
Alignment explanation
Indices: 41045913--41045979 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
41045903 AAAAACATAT
*
41045913 TGACTTAAATAAAAACTTTCAAATAATTTAA
1 TGACTTAAATAAAAACTTTCAAATAATTCAA
* * * *
41045944 TGACTTGAATGAAAATTTTCTAATAATTCAA
1 TGACTTAAATAAAAACTTTCAAATAATTCAA
41045975 TGACT
1 TGACT
41045980 GTTTTATAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.37
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAATTCAA
Found at i:41048267 original size:60 final size:57
Alignment explanation
Indices: 41048137--41048334 Score: 274
Period size: 60 Copynumber: 3.4 Consensus size: 57
41048127 TTGACTTTCG
* *
41048137 GGGGTAAAAATGG-AA-TTTTGGTGAAACCGAGGTTAAAAATGGCATTTTGGAAAGTTT
1 GGGGT-AAAATGGTAATTTTTGGTGAAACCG-GGTCAAAAATGGAATTTTGGAAAGTTT
* *
41048194 GAGGGTAAAATGGTAATTTTTGGTGAAACCAGGGTCGAAAATGAAATTTTTGGAAAGTTT
1 G-GGGTAAAATGGTAATTTTTGGTGAAACC-GGGTCAAAAATGGAA-TTTTGGAAAGTTT
41048254 GGGAGTAAAATGGTAATTTTTGGTGAAACCGGGGTCAAAAATGGAATTTTGGAAAGTTT
1 GGG-GTAAAATGGTAATTTTTGGTGAAACC-GGGTCAAAAATGGAATTTTGGAAAGTTT
41048313 GGGGGTAAAATGGTAATTTTTG
1 -GGGGTAAAATGGTAATTTTTG
41048335 AGCAATTTAG
Statistics
Matches: 127, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
57 8 0.06
58 6 0.05
59 56 0.44
60 57 0.45
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.31
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTGGTGAAACCGGGTCAAAAATGGAATTTTGGAAAGTTT
Found at i:41048272 original size:30 final size:29
Alignment explanation
Indices: 41048181--41048334 Score: 106
Period size: 30 Copynumber: 5.2 Consensus size: 29
41048171 AAAAATGGCA
41048181 TTTTGGAAAGTTTGAGGGTAAAATGGTAAT
1 TTTTGGAAAGTTTG-GGGTAAAATGGTAAT
*** *
41048211 TTTTGGTGAAA--CCAGGGTCGAAAAT-GAAAT
1 TTTT-G-GAAAGTTTGGGGT--AAAATGGTAAT
41048241 TTTTGGAAAGTTTGGGAGTAAAATGGTAAT
1 TTTTGGAAAGTTTGGG-GTAAAATGGTAAT
**
41048271 TTTTGGTGAAA--CCGGGGTCAAAAATGG-AA-
1 TTTT-G-GAAAGTTTGGGGT--AAAATGGTAAT
41048300 TTTTGGAAAGTTTGGGGGTAAAATGGTAAT
1 TTTTGGAAAGTTT-GGGGTAAAATGGTAAT
41048330 TTTTG
1 TTTTG
41048335 AGCAATTTAG
Statistics
Matches: 95, Mismatches: 12, Indels: 34
0.67 0.09 0.24
Matches are distributed among these distances:
27 4 0.04
28 12 0.13
29 18 0.19
30 37 0.39
31 16 0.17
32 8 0.08
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (29 bp):
TTTTGGAAAGTTTGGGGTAAAATGGTAAT
Found at i:41049497 original size:21 final size:20
Alignment explanation
Indices: 41049471--41049509 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41049461 GTCATTATTA
*
41049471 TTATTAATTATTATTGTTATG
1 TTATTAA-TATTAATGTTATG
41049492 TTATTAATATTAATGTTA
1 TTATTAATATTAATGTTA
41049510 CTATTATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (20 bp):
TTATTAATATTAATGTTATG
Found at i:41049516 original size:21 final size:21
Alignment explanation
Indices: 41049469--41049517 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
41049459 AAGTCATTAT
*
41049469 TATTATTAATTATTATTGTTA
1 TATTATTAATTATTAATGTTA
*
41049490 TGTTATTAA-TATTAATGTTA
1 TATTATTAATTATTAATGTTA
41049510 CTATTATT
1 -TATTATT
41049518 TGCTAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (21 bp):
TATTATTAATTATTAATGTTA
Found at i:41050252 original size:18 final size:17
Alignment explanation
Indices: 41050181--41050260 Score: 72
Period size: 17 Copynumber: 4.5 Consensus size: 17
41050171 TTGGGTTTTT
* *
41050181 AATTTAAATTTTAATTA
1 AATTTAAATTTAAAATA
41050198 AATTTAAATTTATTTCAAAT-
1 AATTTAAATTTA----AAATA
*
41050218 ATTTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
41050235 AATTTATATTTAATAATA
1 AATTTAAATTTAA-AATA
41050253 AATTTAAA
1 AATTTAAA
41050261 CCCAAAAAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
16 4 0.08
17 22 0.43
18 11 0.22
20 11 0.22
21 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:41058732 original size:3 final size:3
Alignment explanation
Indices: 41058724--41058758 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
41058714 CGACATCAGT
41058724 TGC TGC TGC TGC TGC TGC TGC TGC TG- TGGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC T-GC TGC TG
41058759 GGATGTTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 28 0.93
4 1 0.03
ACGTcount: A:0.00, C:0.29, G:0.37, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:41065805 original size:20 final size:20
Alignment explanation
Indices: 41065768--41065814 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
41065758 ATCATTAAGC
*
41065768 CTTAATTAATCATTTTTA-A
1 CTTAATTAATCATATTTATA
41065787 TCTTAATTAAATC-TATTTATA
1 -CTTAATT-AATCATATTTATA
41065808 CTTAATT
1 CTTAATT
41065815 TAAACCATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (20 bp):
CTTAATTAATCATATTTATA
Found at i:41066399 original size:30 final size:30
Alignment explanation
Indices: 41066354--41066705 Score: 362
Period size: 30 Copynumber: 11.9 Consensus size: 30
41066344 TTTTAAAGAA
* *
41066354 TTTA-GGGTTAAAATGTGATTTTAGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
* *
41066383 TTTAGGGGTGAAAATGTGATTTT-GAAAAGG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAA-G
*
41066413 TTTAGGGGTTAAAATGTGATTTT-GAGAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGA-AAAG
*
41066443 TTTTGGGGTTAAAATGTAATTTTGGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
*
41066473 TTT--GGGTTAAAATGTAATTTTGGAGAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
*
41066501 TTTAGGGGTTAAAATGTAATTTTAGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
* * *
41066531 TTTAGGGCTTAAAATGTAATTTTAGATAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
** *
41066561 TTT-GTAGTCAAAAT-TCAATTTTGGAAAAG
1 TTTAGGGGTTAAAATGT-AATTTTGGAAAAG
* * *
41066590 TTT-GAGATCAAAATGTAATTTTGGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
* * * * *
41066619 TTTA-AGGTGAAAATGTGACTTTGAAAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
* * *
41066648 TTTAAGGGTGAAAATATAATTTTGGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
* * *
41066678 TTTAAGGGTGAAAATGTAATTTTAGAAA
1 TTTAGGGGTTAAAATGTAATTTTGGAAA
41066706 GATTTGAGGT
Statistics
Matches: 283, Mismatches: 30, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
28 28 0.10
29 78 0.28
30 172 0.61
31 5 0.02
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.36
Consensus pattern (30 bp):
TTTAGGGGTTAAAATGTAATTTTGGAAAAG
Found at i:41066506 original size:88 final size:89
Alignment explanation
Indices: 41066358--41066705 Score: 370
Period size: 88 Copynumber: 3.9 Consensus size: 89
41066348 AAAGAATTTA
* *
41066358 GGGTTAAAATGTGATTTTAGAAAAGTTTAGGGGTGAAAATGTGATTTT-GAAAAGGTTTAGGGGT
1 GGGTTAAAATGTAATTTTAGAAAAGTTTA-GGGTGAAAATGTAATTTTGGAAAA-GTTTAGGGGT
*
41066422 TAAAATGTGATTTT-GAGAAAGTTTTG
64 TAAAATGTAATTTTAGA-AAAGTTTTG
* * *
41066448 GGGTTAAAATGTAATTTTGGAAAAGTTT-GGGTTAAAATGTAATTTTGGAGAAGTTTAGGGGTTA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTGAAAATGTAATTTTGGAAAAGTTTAGGGGTTA
*
41066512 AAATGTAATTTTAGAAAAGTTTAG
66 AAATGTAATTTTAGAAAAGTTTTG
* * * * * *
41066536 GGCTTAAAATGTAATTTTAGATAAGTTT-GTAGTCAAAAT-TCAATTTTGGAAAAGTTT-GAGAT
1 GGGTTAAAATGTAATTTTAGAAAAGTTTAG-GGTGAAAATGT-AATTTTGGAAAAGTTTAGGGGT
* * *
41066598 CAAAATGTAATTTTGGAAAAG-TTTA
64 TAAAATGTAATTTTAGAAAAGTTTTG
* * * * * *
41066623 AGGTGAAAATGTGACTTT-GAAAAAGTTTAAGGGTGAAAATATAATTTTGGAAAAGTTTAAGGGT
1 GGGTTAAAATGTAATTTTAG-AAAAGTTT-AGGGTGAAAATGTAATTTTGGAAAAGTTTAGGGGT
*
41066687 GAAAATGTAATTTTAGAAA
64 TAAAATGTAATTTTAGAAA
41066706 GATTTGAGGT
Statistics
Matches: 217, Mismatches: 32, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
86 1 0.00
87 22 0.10
88 119 0.55
89 49 0.23
90 26 0.12
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.36
Consensus pattern (89 bp):
GGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTGAAAATGTAATTTTGGAAAAGTTTAGGGGTTA
AAATGTAATTTTAGAAAAGTTTTG
Found at i:41066543 original size:118 final size:116
Alignment explanation
Indices: 41066358--41066705 Score: 400
Period size: 118 Copynumber: 3.0 Consensus size: 116
41066348 AAAGAATTTA
* *
41066358 GGGTTAAAATGTGATTTTAGAAAAGTTTAGGGGTGAAAATGTGATTTTGAAAAGGTTTAGGGGTT
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGTGAAAATGTGATTTTGAAAA-GTTTA-GGGTT
* *
41066423 AAAATGTGATTTTGAGAAAGTTTTGGGGTTAAAATGTAATTTTGGAAAAGTTT
64 AAAATGTAATTTTGAGAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTT
* * *
41066476 GGGTTAAAATGTAATTTTGGAGAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGCTT
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGTGAAAATGTGATTTT-GAAAAGTTTAGGG-TT
**
41066541 AAAATGTAATTTT-AGATAAG-TTTGTAGTCAAAAT-TCAATTTTGGAAAAGTTT
64 AAAATGTAATTTTGAGA-AAGTTTTGGGGTCAAAATGT-AATTTTGGAAAAGTTT
* * * *
41066593 GAGATCAAAATGTAATTTTGGAAAAGTTTA-AGGTGAAAATGTGACTTTGAAAAAGTTTAAGGGT
1 G-GGTTAAAATGTAATTTTGGAAAAGTTTAGGGGTGAAAATGTGATTTTG-AAAAGTTT-AGGGT
* * ** * *
41066657 GAAAATATAATTTTG-GAAAAGTTTAAGGGTGAAAATGTAATTTTAGAAA
63 TAAAATGTAATTTTGAG-AAAGTTTTGGGGTCAAAATGTAATTTTGGAAA
41066706 GATTTGAGGT
Statistics
Matches: 195, Mismatches: 24, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
116 2 0.01
117 73 0.37
118 114 0.58
119 6 0.03
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.36
Consensus pattern (116 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGTGAAAATGTGATTTTGAAAAGTTTAGGGTTAA
AATGTAATTTTGAGAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTT
Found at i:41067739 original size:25 final size:25
Alignment explanation
Indices: 41067676--41067742 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
41067666 TGAATGCATG
*
41067676 TTTAGAAATAATAAATGTCATTAATAA
1 TTTA-AAAT-ATAAATATCATTAATAA
*
41067703 TATAATAA-ATAAATAT-ATTAATATA
1 TTTAA-AATATAAATATCATTAATA-A
41067728 TTTAAAATATAAATA
1 TTTAAAATATAAATA
41067743 GTTTTGAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
24 9 0.26
25 19 0.56
26 1 0.03
27 5 0.15
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (25 bp):
TTTAAAATATAAATATCATTAATAA
Found at i:41068241 original size:19 final size:19
Alignment explanation
Indices: 41068197--41068244 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
41068187 TAAATAAATT
*
41068197 TAAATTTAAAAATATATAG
1 TAAATTTAAAAATATAAAG
* * *
41068216 GACATTTAAAAATTTAAAG
1 TAAATTTAAAAATATAAAG
41068235 TAAATTTAAA
1 TAAATTTAAA
41068245 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (19 bp):
TAAATTTAAAAATATAAAG
Found at i:41068967 original size:85 final size:85
Alignment explanation
Indices: 41068831--41068987 Score: 233
Period size: 85 Copynumber: 1.8 Consensus size: 85
41068821 AATTGGTCTT
* * * * *
41068831 CTTCTCTATATCTCATTAGGAAGATGACCGCTTCATTGTTTTAATCTACTTCTCTGTATCTTATC
1 CTTCTCTATATCTCATTAGGAAGATGACCGCTTCATTGCTTTAACCCACTTCTCTATATCTCATC
41068896 AAGAAGACAGATTTGGTATA
66 AAGAAGACAGATTTGGTATA
* * * *
41068916 CTTCTCTGTATCTCATTAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATC
1 CTTCTCTATATCTCATTAGGAAGATGACCGCTTCATTGCTTTAACCCACTTCTCTATATCTCATC
41068981 AAGAAGA
66 AAGAAGA
41068988 TGAGGTTTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 63 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (85 bp):
CTTCTCTATATCTCATTAGGAAGATGACCGCTTCATTGCTTTAACCCACTTCTCTATATCTCATC
AAGAAGACAGATTTGGTATA
Found at i:41069034 original size:209 final size:208
Alignment explanation
Indices: 41068666--41069149 Score: 682
Period size: 209 Copynumber: 2.3 Consensus size: 208
41068656 CATATTTTTG
* * * *
41068666 TCCACTTCTCTATATCTCATCAGGAAGGCGGATTTGGTTCACTTCTCTGCATCTCGTCAGGAAGA
1 TCCACTTCTCTGTATCTCATCAGGAAGACGGATTTGGTT-ACTTCTCTGTATCTCATCAGGAAGA
* * * *
41068731 TGACCACTTTATTGCTTCGACATACTTCTCTGTATCTCATCAGGAAGATGGGGTTTAAAAGTTTC
65 TGACCACTTTATTGCTTCGACACACTTCTCTATATCTCATCAAGAAGATGAGGTTTAAAAGTTTC
* * * *
41068796 ACTCATATTGAGCTTCGCTTCATTGAATTGGTCTT-CTTCTCTATATCTCATTAGGAAGATGACC
130 ACTCATATTGAGCTTCACTTCACTGAATTGGT-TTACTTCTCTATATCTCATCAAGAAGATGACC
*
41068860 GCTTCATTGTTTTAA
194 ACTTCATTGTTTTAA
* * * * *
41068875 TCTACTTCTCTGTATCTTATCAAGAAGACAGATTTGGTATACTTCTCTGTATCTCATTAGGAAGA
1 TCCACTTCTCTGTATCTCATCAGGAAGACGGATTTGGT-TACTTCTCTGTATCTCATCAGGAAGA
* * * *
41068940 TGATCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGATGAGGTTTAAAAGTTTC
65 TGACCACTTTATTGCTTCGACACACTTCTCTATATCTCATCAAGAAGATGAGGTTTAAAAGTTTC
* *
41069005 ACTCATATTGAGCTTCACTTCACTGAATTGGTTTACTTCTTTATATCTCATCAAGAAGATGATCA
130 ACTCATATTGAGCTTCACTTCACTGAATTGGTTTACTTCTCTATATCTCATCAAGAAGATGACCA
*
41069070 TTTCATTGTTTTAA
195 CTTCATTGTTTTAA
* *
41069084 TCCACTTTTCTGTATCTCATCAGGAAGACGGATTTGATCTACTTCTCTGTATCTCATCAGGAAGA
1 TCCACTTCTCTGTATCTCATCAGGAAGACGGATTTGGT-TACTTCTCTGTATCTCATCAGGAAGA
41069149 T
65 T
41069150 AGGGTTTGAA
Statistics
Matches: 240, Mismatches: 33, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
208 2 0.01
209 237 0.99
210 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (208 bp):
TCCACTTCTCTGTATCTCATCAGGAAGACGGATTTGGTTACTTCTCTGTATCTCATCAGGAAGAT
GACCACTTTATTGCTTCGACACACTTCTCTATATCTCATCAAGAAGATGAGGTTTAAAAGTTTCA
CTCATATTGAGCTTCACTTCACTGAATTGGTTTACTTCTCTATATCTCATCAAGAAGATGACCAC
TTCATTGTTTTAA
Found at i:41069291 original size:161 final size:160
Alignment explanation
Indices: 41068962--41069312 Score: 436
Period size: 161 Copynumber: 2.2 Consensus size: 160
41068952 TGCTTTGACC
* * * *
41068962 CACTTCTCTATATCTCATCAAGAAGATGAGGTTTAAAAGTTTCACTCATATTGAGCTTCACTTCA
1 CACTTCTCTGTATCTCATCAGGAAGATGAGGTTTAAAAGTTTCACTCACATTAAGCTTCACTTCA
* * * * *
41069027 CTGAATTGGTTTACTTCTTTATATCTCATCAAGAAGATGATCATTTCATTGTTTTAATCCACTTT
66 CTGAATTGGTCTACTTCTTTATATCTCATCAAGAAGATGACCACTTCATTATTTTAATCCACTTC
* * *
41069092 TCTGTATCTCATCAGGAAGACGGATTTGAT
131 TCTGTATCTCATCAAGAAGACGAATTGGAT
* *
41069122 CTACTTCTCTGTATCTCATCAGGAAGAT-AGGGTTTGAAAGTTTCACTCACATTAAGCTTCGCTT
1 C-ACTTCTCTGTATCTCATCAGGAAGATGA-GGTTTAAAAGTTTCACTCACATTAAGCTTCACTT
* * * * *
41069186 CACTGAATTGGTCTACTTC-TTAGTATCTCATTAGGAGGATGACCGCTTCATTATTTTAATCTAC
64 CACTGAATTGGTCTACTTCTTTA-TATCTCATCAAGAAGATGACCACTTCATTATTTTAATCCAC
* *
41069250 TTCTCTGTATCTCATCAAGAAGATGAATTAGGTT
128 TTCTCTGTATCTCATCAAGAAGACGAATT-GGAT
* * *
41069284 CACTTCTCTGCATCTCGTTAGGAAGATGA
1 CACTTCTCTGTATCTCATCAGGAAGATGA
41069313 CACTTTATTG
Statistics
Matches: 162, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
160 5 0.03
161 153 0.94
162 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (160 bp):
CACTTCTCTGTATCTCATCAGGAAGATGAGGTTTAAAAGTTTCACTCACATTAAGCTTCACTTCA
CTGAATTGGTCTACTTCTTTATATCTCATCAAGAAGATGACCACTTCATTATTTTAATCCACTTC
TCTGTATCTCATCAAGAAGACGAATTGGAT
Found at i:41069616 original size:39 final size:41
Alignment explanation
Indices: 41069563--41069675 Score: 140
Period size: 40 Copynumber: 2.8 Consensus size: 41
41069553 TATTGAATGT
* * * * *
41069563 TTCAATCTACCCCTCTTGGTTAGGGGTAAAA-ACTGGAATC
1 TTCAATTTGCCCCTCTTGATTAGGGGTAAAAGACTAGAATA
*
41069603 TTCAATTTG-CCCTCTTGATTAGGGGTAAAAGATTAGAATA
1 TTCAATTTGCCCCTCTTGATTAGGGGTAAAAGACTAGAATA
* *
41069643 TTCAATTTGCCCCTCTTGACTAGAGGTAAAAGA
1 TTCAATTTGCCCCTCTTGATTAGGGGTAAAAGA
41069676 TTGGAATGAC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 20 0.32
40 22 0.35
41 21 0.33
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (41 bp):
TTCAATTTGCCCCTCTTGATTAGGGGTAAAAGACTAGAATA
Found at i:41069671 original size:41 final size:41
Alignment explanation
Indices: 41069563--41069682 Score: 154
Period size: 41 Copynumber: 3.0 Consensus size: 41
41069553 TATTGAATGT
* * * * *
41069563 TTCAATCTACCCCTCTTGGTTAGGGGTAAAA-ACTGGAATC
1 TTCAATTTGCCCCTCTTGATTAGGGGTAAAAGATTGGAATA
*
41069603 TTCAATTTG-CCCTCTTGATTAGGGGTAAAAGATTAGAATA
1 TTCAATTTGCCCCTCTTGATTAGGGGTAAAAGATTGGAATA
* *
41069643 TTCAATTTGCCCCTCTTGACTAGAGGTAAAAGATTGGAAT
1 TTCAATTTGCCCCTCTTGATTAGGGGTAAAAGATTGGAAT
41069683 GACTGCAGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 20 0.29
40 22 0.32
41 27 0.39
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (41 bp):
TTCAATTTGCCCCTCTTGATTAGGGGTAAAAGATTGGAATA
Found at i:41069971 original size:49 final size:50
Alignment explanation
Indices: 41069881--41070062 Score: 163
Period size: 49 Copynumber: 3.7 Consensus size: 50
41069871 TATAAGATTC
* * ** * *
41069881 ACCGTTGCGCCCTCAATTTTTCCCGTCATGT-TTCTAAGGTACCGGGTTT
1 ACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTACCGGGTTT
** * * **
41069930 GTCGTTGTGGCCTTAACCTTTCCCTTCATATCTTC-ATGGTACCGAATTT
1 ACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTACCGGGTTT
* * * * *
41069979 ACCGTTGCGGCGTCAATCC-TTCTCATCACATCTTCTAAGGTACCGGGTTT
1 ACCGTTGTGGCCTCAA-CCTTTCCCTTCATATCTTCTAAGGTACCGGGTTT
* *
41070029 ACCGTTGTGGCCTCAACCTTTTCCTTCATGTCTT
1 ACCGTTGTGGCCTCAACCTTTCCCTTCATATCTT
41070063 AATGTTTCCT
Statistics
Matches: 99, Mismatches: 30, Indels: 7
0.73 0.22 0.05
Matches are distributed among these distances:
49 59 0.60
50 40 0.40
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.37
Consensus pattern (50 bp):
ACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTACCGGGTTT
Found at i:41071005 original size:25 final size:25
Alignment explanation
Indices: 41070978--41071025 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
41070968 ACCTCTCATT
41070978 TTTTTCCTTTT-TTCTCTTTTTTTA
1 TTTTTCCTTTTCTTCTCTTTTTTTA
*
41071002 TTTTTCTTTTTCTTCTCTTTTTTT
1 TTTTTCCTTTTCTTCTCTTTTTTT
41071026 CTTTCTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTTCCTTTTCTTCTCTTTTTTTA
Found at i:41071025 original size:14 final size:12
Alignment explanation
Indices: 41070976--41071034 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
41070966 CGACCTCTCA
*
41070976 TTTT-TTTCCTT
1 TTTTCTTTCTTT
41070987 TTTTC--TCTTT
1 TTTTCTTTCTTT
*
41070997 TTTTATTT-TTCT
1 TTTTCTTTCTT-T
41071009 TTTTCTTCTCTTT
1 TTTTCTT-TCTTT
41071022 TTTTCTTTCTTT
1 TTTTCTTTCTTT
41071034 T
1 T
41071035 ATTTTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
10 8 0.21
11 6 0.15
12 14 0.36
13 9 0.23
14 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:41071029 original size:33 final size:33
Alignment explanation
Indices: 41070976--41071046 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 33
41070966 CGACCTCTCA
41070976 TTTTT-TTCCTTTTTTCTCTTT-TTTTATTTTT
1 TTTTTCTTCCTTTTTTCTCTTTCTTTTATTTTT
41071007 CTTTTTCTTCTCTTTTTT-TCTTTCTTTTATTTTT
1 -TTTTTCTTC-CTTTTTTCTCTTTCTTTTATTTTT
41071041 TTTTTC
1 TTTTTC
41071047 ATTGAATCCG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
32 5 0.14
33 14 0.39
34 17 0.47
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (33 bp):
TTTTTCTTCCTTTTTTCTCTTTCTTTTATTTTT
Found at i:41071030 original size:23 final size:22
Alignment explanation
Indices: 41070976--41071034 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 22
41070966 CGACCTCTCA
*
41070976 TTTTTTTCCTTTTTTCTCTTTTT
1 TTTTTTTCTTTTTTTCTC-TTTT
41070999 TTATTTTTCTTTTTCTTCTCTTTT
1 TT-TTTTTCTTTTT-TTCTCTTTT
*
41071023 TTTCTTTCTTTT
1 TTTTTTTCTTTT
41071035 ATTTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 11 0.34
24 16 0.50
25 5 0.16
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTTTCTTTTTTTCTCTTTT
Found at i:41076610 original size:30 final size:30
Alignment explanation
Indices: 41076540--41077020 Score: 343
Period size: 30 Copynumber: 16.4 Consensus size: 30
41076530 AAAATAAAAA
41076540 AGGGGTCAAAAATG-AAGTTTT-GAAGAA-TTT
1 AGGGGTC-AAAATGTAA-TTTTGGAA-AAGTTT
* *
41076570 -GGGGTCAAAATATGATTTTGGAAAAGTTT
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTT
* * *
41076599 AGGAGTGAAAATGTGATTGTT--AAAAGGTTT
1 AGGGGTCAAAATGTAATT-TTGGAAAA-GTTT
* * * * *
41076629 GGGGGTCAAAACGTGATTTTGAGGAAGGTTT
1 AGGGGTCAAAATGTAATTTTG-GAAAAGTTT
* * *
41076660 -GGGGTTAAAATGTGATTTTGAAAAAGTTT
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTT
* * *
41076689 AGAGGTC-AAATATAATTTTCGAAAAGTTT
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTT
*
41076718 AGGAGTCAAAATGTAATTTTGGAAAAGTTT
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTT
*
41076748 -GGGGATCAAAATGCAATTTTGGAAAAGTTT
1 AGGGG-TCAAAATGTAATTTTGGAAAAGTTT
* ** **
41076778 GGGGGTCAAAACATAATTTTTAAAAAGTTT
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTT
* *
41076808 A-TGGTCAAAATGTAATTTT-AAAGAAGTTT
1 AGGGGTCAAAATGTAATTTTGGAA-AAGTTT
*
41076837 --GGGTCAAAATGCAATTTTGGAAAAGTTT
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTT
**
41076865 --GGGTCAAAATGTAATTTTAAAAAAGTTT
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTT
* * * *
41076893 -GGGGTGAAAATGTGACTTTGGAAAAATTT
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTT
* * * * *
41076922 A-AGTTGAAAATGTGACTTTGG-AAAGTTT
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTT
* * *
41076950 A-GGGTTAAAATATAATTTTGGAAGAGTTT
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTT
* ** *
41076979 GGGGGAGAAAATGTAATTTTGGAAAGGTTT
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTT
* *
41077009 GGGGGTTAAAAT
1 AGGGGTCAAAAT
41077021 ATAGTTTTTA
Statistics
Matches: 365, Mismatches: 67, Indels: 38
0.78 0.14 0.08
Matches are distributed among these distances:
28 82 0.22
29 120 0.33
30 151 0.41
31 10 0.03
32 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (30 bp):
AGGGGTCAAAATGTAATTTTGGAAAAGTTT
Found at i:41078023 original size:21 final size:21
Alignment explanation
Indices: 41077982--41078026 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
41077972 ATGTTTAAAA
*
41077982 ATAATAAATGACATTAATAAT
1 ATAATAAATGAAATTAATAAT
*
41078003 ATAATAAAT-AAATATATTAAT
1 ATAATAAATGAAAT-TAATAAT
41078024 ATA
1 ATA
41078027 TTTAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
ATAATAAATGAAATTAATAAT
Found at i:41085632 original size:65 final size:65
Alignment explanation
Indices: 41085556--41085686 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
41085546 TTAAATACCT
41085556 TAATCATTGTTCAAAATCCTAAATATTAAAATTATTTTTGAAAACCCTAAATCCCCAAATATTGA
1 TAATCATTGTTCAAAATCCTAAATATTAAAATTATTTTTGAAAACCCTAAATCCCCAAATATTGA
* *
41085621 TAATCATTGTTCAAAATCCTAAATTTTAAAATTGTTTTTGAAAACCCTAAATCCCCAAATATTGA
1 TAATCATTGTTCAAAATCCTAAATATTAAAATTATTTTTGAAAACCCTAAATCCCCAAATATTGA
41085686 T
1 T
41085687 GGAAACTCCA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (65 bp):
TAATCATTGTTCAAAATCCTAAATATTAAAATTATTTTTGAAAACCCTAAATCCCCAAATATTGA
Found at i:41085773 original size:27 final size:28
Alignment explanation
Indices: 41085725--41085777 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
41085715 AAATTTATTC
* *
41085725 CAAACTCTCAAATTCAATTTTAAAACAT
1 CAAACTCTCAAATCCAAGTTTAAAACAT
*
41085753 CAAA-TCTCAAATCCCAGTTTAAAAC
1 CAAACTCTCAAATCCAAGTTTAAAAC
41085778 CCTAATTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.28
Consensus pattern (28 bp):
CAAACTCTCAAATCCAAGTTTAAAACAT
Found at i:41092618 original size:23 final size:23
Alignment explanation
Indices: 41092575--41092618 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
41092565 TTTATCAAAA
*
41092575 AAAAAAGAAATTATAATTATACC
1 AAAAAAGAAATTATAAATATACC
41092598 AAAAAAG-AATTATATAATATA
1 AAAAAAGAAATTATA-AATATA
41092619 TGAAAGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (23 bp):
AAAAAAGAAATTATAAATATACC
Found at i:41095450 original size:33 final size:33
Alignment explanation
Indices: 41095412--41095526 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
41095402 ATGCCTGGAA
*
41095412 TACCAGCCATGTCTGGCATTGACATTGGCAAAT
1 TACCAGCCATGTCTGGCATTGACGTTGGCAAAT
41095445 TACCAGCCATGTCTGGCATTGACGTTGGCAAAT
1 TACCAGCCATGTCTGGCATTGACGTTGGCAAAT
41095478 TACCAGCCATGTCTGGCATTGACGTTGGCAAAT
1 TACCAGCCATGTCTGGCATTGACGTTGGCAAAT
* *
41095511 TACCATCCATGCCTGG
1 TACCAGCCATGTCTGG
41095527 TATATTACCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (33 bp):
TACCAGCCATGTCTGGCATTGACGTTGGCAAAT
Found at i:41095577 original size:21 final size:21
Alignment explanation
Indices: 41095503--41095604 Score: 69
Period size: 27 Copynumber: 4.3 Consensus size: 21
41095493 GCATTGACGT
* *
41095503 TGGCAAATTACCATCCATGCC
1 TGGCATATTACCATCCTTGCC
*
41095524 TGGTATATTACCATCCTTGCC
1 TGGCATATTACCATCCTTGCC
41095545 TGGAATTGGCATATTACCATCCTTGCC
1 ------TGGCATATTACCATCCTTGCC
41095572 TGGCATTGGCATGTTACCATCCTTGCC
1 TGGCA-T---A--TTACCATCCTTGCC
41095599 TGGCAT
1 TGGCAT
41095605 TGGCATGTTA
Statistics
Matches: 65, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
21 23 0.35
22 1 0.02
25 1 0.02
26 1 0.02
27 39 0.60
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (21 bp):
TGGCATATTACCATCCTTGCC
Found at i:41095669 original size:27 final size:27
Alignment explanation
Indices: 41095528--41095672 Score: 193
Period size: 27 Copynumber: 5.4 Consensus size: 27
41095518 CATGCCTGGT
*
41095528 ATATTACCATCCTTGCCTGGAATTGGC
1 ATATTACCATCCTTGCCTGGCATTGGC
41095555 ATATTACCATCCTTGCCTGGCATTGGC
1 ATATTACCATCCTTGCCTGGCATTGGC
*
41095582 ATGTTACCATCCTTGCCTGGCATTGGC
1 ATATTACCATCCTTGCCTGGCATTGGC
* * *
41095609 ATGTTACCATCCATGCCTGGAATTGGC
1 ATATTACCATCCTTGCCTGGCATTGGC
* * * *
41095636 ACT-TTACCATCCTTGACTGCCGTTGGT
1 A-TATTACCATCCTTGCCTGGCATTGGC
41095663 ATATTACCAT
1 ATATTACCAT
41095673 TATTTGGCAC
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
26 1 0.01
27 104 0.98
28 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.34
Consensus pattern (27 bp):
ATATTACCATCCTTGCCTGGCATTGGC
Found at i:41099085 original size:87 final size:87
Alignment explanation
Indices: 41098957--41099128 Score: 267
Period size: 87 Copynumber: 2.0 Consensus size: 87
41098947 TCCTTTTCTT
* *
41098957 CTTCTCCAAGGTACTTGTGACATTTCATTTGGAAGAGACTTTTACTTTCAATATAATACATAGAA
1 CTTCTCCAAGGTACTTGTGAAATTTCATTTGGAAGAGACTTTTACTTTCAATATAATACATAAAA
*
41099022 AAGTGGTTGA-ATGAAACTGTTA
66 AAGTGATT-ATATGAAACTGTTA
* *
41099044 CTTCTCCAAGGTCCTTGTGAAATTTC-TTTCGGAAGAGACTTTTACTTTGAATATAATACATAAA
1 CTTCTCCAAGGTACTTGTGAAATTTCATTT-GGAAGAGACTTTTACTTTCAATATAATACATAAA
41099108 AAAGTGATTATATGAAACTGT
65 AAAGTGATTATATGAAACTGT
41099129 GATTCCATGT
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
86 4 0.05
87 74 0.95
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (87 bp):
CTTCTCCAAGGTACTTGTGAAATTTCATTTGGAAGAGACTTTTACTTTCAATATAATACATAAAA
AAGTGATTATATGAAACTGTTA
Found at i:41099682 original size:20 final size:20
Alignment explanation
Indices: 41099645--41099683 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
41099635 TTTTAAAAAA
*
41099645 TTAAATAAATATATAATATT
1 TTAAATAAATATACAATATT
41099665 TTAAATACAATAT-CAATAT
1 TTAAATA-AATATACAATAT
41099684 CAATATGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAATAAATATACAATATT
Found at i:41102995 original size:33 final size:32
Alignment explanation
Indices: 41102926--41102995 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
41102916 TCTCCCTCTG
* ** *
41102926 TTTTCCTATTTTCTCTATTTCTTTTAATGTGA
1 TTTTTCTATTTTCTCTATTTCTTTTAACATAA
41102958 TTTTTCTATGTTT-TCTATTTCTTTTAACATAA
1 TTTTTCTAT-TTTCTCTATTTCTTTTAACATAA
41102990 CTTTTT
1 -TTTTT
41102996 TATATTCCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 24 0.75
33 8 0.25
ACGTcount: A:0.17, C:0.14, G:0.04, T:0.64
Consensus pattern (32 bp):
TTTTTCTATTTTCTCTATTTCTTTTAACATAA
Found at i:41111355 original size:31 final size:31
Alignment explanation
Indices: 41111320--41111383 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
41111310 GTTACATATG
41111320 ATCATTAATGTTATTAATTTATTATATTTTA
1 ATCATTAATGTTATTAATTTATTATATTTTA
41111351 ATCATTAATGTTATTAATTTATTATATTTTA
1 ATCATTAATGTTATTAATTTATTATATTTTA
41111382 AT
1 AT
41111384 TACTAAATCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (31 bp):
ATCATTAATGTTATTAATTTATTATATTTTA
Found at i:41115856 original size:28 final size:29
Alignment explanation
Indices: 41115802--41115862 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
41115792 TAATTTTACA
41115802 AACCAATAGCACCCCCACATGAAAGCATTAG
1 AACCAATAGCA--CCCACATGAAAGCATTAG
41115833 AACCAATAGCA-CCACATGAAAGCATTAG
1 AACCAATAGCACCCACATGAAAGCATTAG
41115861 AA
1 AA
41115863 TCAAACACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 19 0.63
31 11 0.37
ACGTcount: A:0.46, C:0.28, G:0.13, T:0.13
Consensus pattern (29 bp):
AACCAATAGCACCCACATGAAAGCATTAG
Found at i:41158416 original size:24 final size:26
Alignment explanation
Indices: 41158366--41158416 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
41158356 CTATATGACA
*
41158366 TGTCATTTAATTATGAGTAATTTTTTT
1 TGTCATTCAATTAT-AGTAATTTTTTT
41158393 TGTCATTCAATTAT-G-AATTTTTTT
1 TGTCATTCAATTATAGTAATTTTTTT
41158417 AAATTGATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 1 0.04
27 13 0.57
ACGTcount: A:0.25, C:0.06, G:0.10, T:0.59
Consensus pattern (26 bp):
TGTCATTCAATTATAGTAATTTTTTT
Found at i:41161654 original size:16 final size:17
Alignment explanation
Indices: 41161633--41161669 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
41161623 AATATGAATA
41161633 TATACTA-TCATATA-AT
1 TATACTAGT-ATATATAT
41161649 TATACTAGTATATATAT
1 TATACTAGTATATATAT
41161666 TATA
1 TATA
41161670 AAAATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (17 bp):
TATACTAGTATATATAT
Found at i:41162080 original size:29 final size:27
Alignment explanation
Indices: 41162048--41162111 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
41162038 TTTTATACCT
* *
41162048 TTTAAAATAGTTTTAATGATTTTTTAAAA
1 TTTAAAATAATTTT--TGAATTTTTAAAA
41162077 TTTAAAAATAATTTTTGAATTTTTAAAA
1 TTT-AAAATAATTTTTGAATTTTTAAAA
41162105 TTTAAAA
1 TTTAAAA
41162112 AATATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 4 0.12
28 15 0.47
29 3 0.09
30 10 0.31
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (27 bp):
TTTAAAATAATTTTTGAATTTTTAAAA
Found at i:41166026 original size:2 final size:2
Alignment explanation
Indices: 41166019--41166046 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41166009 CAAATTAAAG
41166019 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
41166047 AATCTTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41167220 original size:41 final size:41
Alignment explanation
Indices: 41167149--41167240 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
41167139 ACTTATGGCA
* **
41167149 TATTTTATTATAATTTTTAACGGATAAAAGTTTAATTTTAT
1 TATTATATTATAATTTTTAACGGATAAAAGTACAATTTTAT
* * * *
41167190 TATTGTATTGTAATTTTTAA-GAGGTTAAAGTACAATTTTAT
1 TATTATATTATAATTTTTAACG-GATAAAAGTACAATTTTAT
41167231 TATTATATTA
1 TATTATATTA
41167241 ATTTATTATT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 1 0.02
41 41 0.98
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (41 bp):
TATTATATTATAATTTTTAACGGATAAAAGTACAATTTTAT
Found at i:41167400 original size:60 final size:59
Alignment explanation
Indices: 41167264--41167433 Score: 207
Period size: 59 Copynumber: 2.9 Consensus size: 59
41167254 ATAATATAAT
* * * * * **
41167264 ATTTGATACTTAAACTTGACACTTTTTCTTAATTTGGTATCT-AATTTTTTTTTGACCCA
1 ATTTGGTACTTGAACTTGACA-TTTTTCCTAATTTGGTACCTAAACTTTTTTGGGACCCA
* * *
41167323 ATGTGGTACCTGAACTTGACATTTTTTCCTAATTTGATACCTAAACTTTTTTGGGACCCA
1 ATTTGGTACTTGAACTTGACA-TTTTTCCTAATTTGGTACCTAAACTTTTTTGGGACCCA
* *
41167383 ATTTGGTACTTGAACTTGTCATTTTTCCTAATTTGGTACCTAAGCTTTTTT
1 ATTTGGTACTTGAACTTGACATTTTTCCTAATTTGGTACCTAAACTTTTTT
41167434 AGATTCAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 62 0.66
60 32 0.34
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (59 bp):
ATTTGGTACTTGAACTTGACATTTTTCCTAATTTGGTACCTAAACTTTTTTGGGACCCA
Found at i:41168378 original size:2 final size:2
Alignment explanation
Indices: 41168371--41168399 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41168361 TCATTTGCAA
41168371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41168400 ATTTTTGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41169749 original size:10 final size:9
Alignment explanation
Indices: 41169691--41169785 Score: 66
Period size: 10 Copynumber: 10.0 Consensus size: 9
41169681 TGTAATTTTA
*
41169691 AAAAATTGT
1 AAAAATTAT
41169700 AAAAATTAT
1 AAAAATTAT
*
41169709 -AAAACTATT
1 AAAAATTA-T
* *
41169718 AGAAATTTT
1 AAAAATTAT
*
41169727 AAAATATTGT
1 AAAA-ATTAT
41169737 AAAAATATAT
1 AAAAAT-TAT
41169747 AAAAATTATT
1 AAAAATTA-T
*
41169757 AAAAATCAT
1 AAAAATTAT
*
41169766 AAAAGATTGT
1 AAAA-ATTAT
41169776 GAAAAATTAT
1 -AAAAATTAT
41169786 TACAATTTTT
Statistics
Matches: 67, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
8 6 0.09
9 22 0.33
10 35 0.52
11 4 0.06
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:41169780 original size:20 final size:18
Alignment explanation
Indices: 41169650--41169782 Score: 63
Period size: 20 Copynumber: 6.9 Consensus size: 18
41169640 GAGAAAAACT
*
41169650 TAAAAAATCTTTAAAAATA
1 TAAAAAAT-TGTAAAAATA
** * *
41169669 TAAATAAAATTGTGTAATTT
1 T-AA-AAAATTGTAAAAATA
41169689 TAAAAAATTGTAAAAAT-
1 TAAAAAATTGTAAAAATA
* * *
41169706 TATAAAACTAT-TAGAAATTT
1 TA-AAAAAT-TGTA-AAAATA
*
41169726 TAAAATATTGTAAAAATA
1 TAAAAAATTGTAAAAATA
*
41169744 TATAAAAATTATTAAAAATCA
1 TA-AAAAATT-GTAAAAAT-A
*
41169765 TAAAAGATTGTGAAAAAT
1 TAAAAAATTGT-AAAAAT
41169783 TATTACAATT
Statistics
Matches: 85, Mismatches: 18, Indels: 21
0.69 0.15 0.17
Matches are distributed among these distances:
17 2 0.02
18 25 0.29
19 21 0.25
20 29 0.34
21 8 0.09
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (18 bp):
TAAAAAATTGTAAAAATA
Found at i:41169926 original size:14 final size:14
Alignment explanation
Indices: 41169907--41169936 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41169897 ATCAATTTTT
*
41169907 ATAAAAATTGTATA
1 ATAAAAATTGAATA
41169921 ATAAAAATTGAATA
1 ATAAAAATTGAATA
41169935 AT
1 AT
41169937 TTTTAGTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
ATAAAAATTGAATA
Found at i:41179943 original size:17 final size:17
Alignment explanation
Indices: 41179908--41179989 Score: 65
Period size: 17 Copynumber: 4.5 Consensus size: 17
41179898 GATCTTTAGG
*
41179908 TTTAAATTCATTATTAAA
1 TTTAAATTTATT-TTAAA
41179926 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
**
41179943 TTTAAAAATATTTGAAATAAA
1 TTTAAATTTATTT----TAAA
* *
41179964 TTTAAAATTTAATTAAAA
1 TTT-AAATTTATTTTAAA
41179982 TTTAAATT
1 TTTAAATT
41179990 AAAAGTCCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
17 21 0.40
18 17 0.33
21 7 0.13
22 7 0.13
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:41179989 original size:12 final size:12
Alignment explanation
Indices: 41179960--41179993 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
41179950 ATATTTGAAA
41179960 TAAATTTAAAATT
1 TAAA-TTAAAATT
41179973 T-AATTAAAATT
1 TAAATTAAAATT
41179984 TAAATTAAAA
1 TAAATTAAAA
41179994 GTCCAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 10 0.50
13 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATTAAAATT
Found at i:41180701 original size:18 final size:16
Alignment explanation
Indices: 41180678--41180720 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 16
41180668 GGCATTAATG
41180678 ATAATATTAATAATAA
1 ATAATATTAATAATAA
41180694 GTATAATATTAATAATAA
1 --ATAATATTAATAATAA
41180712 ATAATATTA
1 ATAATATTA
41180721 GTATTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 9 0.36
18 16 0.64
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
ATAATATTAATAATAA
Found at i:41181058 original size:9 final size:9
Alignment explanation
Indices: 41181041--41181097 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
41181031 TTGTTTTAAA
41181041 AAAAAGAAG
1 AAAAAGAAG
*
41181050 AAAATGAAG
1 AAAAAGAAG
41181059 AAAAAGAA-
1 AAAAAGAAG
*
41181067 ATAAAGAA-
1 AAAAAGAAG
* *
41181075 TAAAAGATG
1 AAAAAGAAG
41181084 AAAAAGAAAG
1 AAAAAG-AAG
41181094 AAAA
1 AAAA
41181098 GAGAGAAGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
8 12 0.32
9 20 0.53
10 6 0.16
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:41181092 original size:25 final size:26
Alignment explanation
Indices: 41181043--41181092 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
41181033 GTTTTAAAAA
41181043 AAAGAAGAAAATGAAGAAAAAGAAAT
1 AAAGAAGAAAATGAAGAAAAAGAAAT
* *
41181069 AAAGAATAAAA-GATGAAAAAGAAA
1 AAAGAAGAAAATGAAGAAAAAGAAA
41181093 GAAAAGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (26 bp):
AAAGAAGAAAATGAAGAAAAAGAAAT
Found at i:41181098 original size:26 final size:26
Alignment explanation
Indices: 41181039--41181104 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
41181029 TTTTGTTTTA
41181039 AAAAAAAGAAGAAAATGAAGAAAAAG
1 AAAAAAAGAAGAAAATGAAGAAAAAG
* * *
41181065 AAATAAAGAATAAAA-GATGAAAAAG
1 AAAAAAAGAAGAAAATGAAGAAAAAG
41181090 AAAGAAAAGAGAGAA
1 AAA-AAAAGA-AGAA
41181105 GAGACTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 12 0.36
26 18 0.55
27 3 0.09
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (26 bp):
AAAAAAAGAAGAAAATGAAGAAAAAG
Found at i:41181813 original size:29 final size:28
Alignment explanation
Indices: 41181776--41182034 Score: 163
Period size: 29 Copynumber: 8.9 Consensus size: 28
41181766 CCCTAGACTA
*
41181776 TCCAAAAATTATCATTTTACCCCCGAACT
1 TCCAAAAATT-CCATTTTACCCCCGAACT
* * * * *
41181805 TCCTAAAATTTCATTTTTAACCCTG-ATT
1 TCCAAAAATTCCA-TTTTACCCCCGAACT
41181833 TCATCAAAAATTACCATTTTACCCCCGAACT
1 TC--CAAAAATT-CCATTTTACCCCCGAACT
* * *
41181864 TCCCAAAATTCCATTTTAACCCCG-ATT
1 TCCAAAAATTCCATTTTACCCCCGAACT
41181891 TCATCAAAAATTACCATTTTACCCCCGAACTT
1 TC--CAAAAATT-CCATTTTACCCCCGAAC-T
*
41181923 TCC-AAAATTCCATTTTTA-CCCCG-ATT
1 TCCAAAAATTCCA-TTTTACCCCCGAACT
* *
41181949 TCACCAAAAATTACCATTTTACCTCTGAACTT
1 T--CCAAAAATT-CCATTTTACCCCCGAAC-T
* *
41181981 TCC-AAGATTCCATTTTTAACCCC-AATCT
1 TCCAAAAATTCCA-TTTTACCCCCGAA-CT
* *
41182009 CACCAAAAATTACCATTTTGCCCCCG
1 -TCCAAAAATT-CCATTTTACCCCCG
41182035 TGCGTCCAAA
Statistics
Matches: 179, Mismatches: 27, Indels: 46
0.71 0.11 0.18
Matches are distributed among these distances:
26 2 0.01
27 5 0.03
28 36 0.20
29 69 0.39
30 51 0.28
31 11 0.06
32 5 0.03
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.34
Consensus pattern (28 bp):
TCCAAAAATTCCATTTTACCCCCGAACT
Found at i:41181851 original size:59 final size:59
Alignment explanation
Indices: 41181777--41182034 Score: 378
Period size: 58 Copynumber: 4.4 Consensus size: 59
41181767 CCTAGACTAT
* * *
41181777 CCAAAAATTATCATTTTACCCCCGAAC-TTCCTAAAATTTCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCC-AAAATTCCATTTTTAACCCCGATTTCA
* *
41181836 TCAAAAATTACCATTTTACCCCCGAACTTCCCAAAATTCCA-TTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
41181894 TCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTT-ACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
41181952 CCAAAAATTACCATTTTACCTCTGAACTTTCCAAGATTCCATTTTTAACCCCAATCTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
41182011 CCAAAAATTACCATTTTGCCCCCG
1 CCAAAAATTACCATTTTACCCCCG
41182035 TGCGTCCAAA
Statistics
Matches: 181, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
58 110 0.61
59 68 0.38
60 3 0.02
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:41181998 original size:117 final size:117
Alignment explanation
Indices: 41181777--41182034 Score: 376
Period size: 117 Copynumber: 2.2 Consensus size: 117
41181767 CCTAGACTAT
* * * *
41181777 CCAAAAATTATCATTTTACCCCCGAACTTCCTAAAATTTCATTTTTAACCCTGATTTCATCAAAA
1 CCAAAAATTACCATTTTACCCCCGAACTTCCTAAAATTCCATTTTTAACCCCGATTTCACCAAAA
* *
41181842 ATTACCATTTTACCCCCGAACTTCCCAAAATTCCATTTTAACCCCGATTTCA
66 ATTACCATTTTACCCCCGAACTTCCCAAAATTCCATTTTAACCCCAATCTCA
*
41181894 TCAAAAATTACCATTTTACCCCCGAACTTTCC-AAAATTCCATTTTT-ACCCCGATTTCACCAAA
1 CCAAAAATTACCATTTTACCCCCGAAC-TTCCTAAAATTCCATTTTTAACCCCGATTTCACCAAA
* * * *
41181957 AATTACCATTTTACCTCTGAACTTTCCAAGATTCCATTTTTAACCCCAATCTCA
65 AATTACCATTTTACCCCCGAACTTCCCAAAATTCCA-TTTTAACCCCAATCTCA
*
41182011 CCAAAAATTACCATTTTGCCCCCG
1 CCAAAAATTACCATTTTACCCCCG
41182035 TGCGTCCAAA
Statistics
Matches: 126, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
116 47 0.37
117 75 0.60
118 4 0.03
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (117 bp):
CCAAAAATTACCATTTTACCCCCGAACTTCCTAAAATTCCATTTTTAACCCCGATTTCACCAAAA
ATTACCATTTTACCCCCGAACTTCCCAAAATTCCATTTTAACCCCAATCTCA
Done.