Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 7 of 318
Found at i:2319859 original size:2 final size:2
Alignment explanation
Indices: 2319854--2319878 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2319844 TATATATATA
2319854 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2319879 TTATTAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2320318 original size:14 final size:14
Alignment explanation
Indices: 2320299--2320327 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2320289 GAGCTCTAAG
2320299 TAAGTCCTTTTTTC
1 TAAGTCCTTTTTTC
2320313 TAAGTCCTTTTTTC
1 TAAGTCCTTTTTTC
2320327 T
1 T
2320328 TTTTAATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.59
Consensus pattern (14 bp):
TAAGTCCTTTTTTC
Found at i:2337881 original size:47 final size:47
Alignment explanation
Indices: 2337809--2337935 Score: 245
Period size: 47 Copynumber: 2.7 Consensus size: 47
2337799 GGGATATTTG
*
2337809 GGCATCCGAACTCGTTGAGTGGAGTCCGAGTTCGTGAGATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTA
2337856 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTA
2337903 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
2337936 ACTCATGGAT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 79 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (47 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:2339812 original size:53 final size:53
Alignment explanation
Indices: 2339731--2339881 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
2339721 TCTTACAGGT
* *
2339731 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
2339786 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
2339839 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
2339882 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:2346946 original size:53 final size:53
Alignment explanation
Indices: 2346889--2347008 Score: 204
Period size: 53 Copynumber: 2.3 Consensus size: 53
2346879 TATCCCAGAC
*
2346889 ATGGTCTTATACGGAATCACATTATCACATTATACCGATGCCATAGCCCAGCT
1 ATGGTCTTATACGGAATCACATTATCACATTACACCGATGCCATAGCCCAGCT
* *
2346942 ATGGTCTTATACGGAGTCACATTATCACATTGCACCGATGCCATAGCCCAGCT
1 ATGGTCTTATACGGAATCACATTATCACATTACACCGATGCCATAGCCCAGCT
*
2346995 ATGGTCTTAAACGG
1 ATGGTCTTATACGG
2347009 GCACACTTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 63 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (53 bp):
ATGGTCTTATACGGAATCACATTATCACATTACACCGATGCCATAGCCCAGCT
Found at i:2362913 original size:3 final size:3
Alignment explanation
Indices: 2362907--2362938 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2362897 TTTGCTTTTT
2362907 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2362939 GTTCTCACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2385592 original size:125 final size:125
Alignment explanation
Indices: 2385370--2385598 Score: 390
Period size: 125 Copynumber: 1.8 Consensus size: 125
2385360 TAGCTTTAAG
* *
2385370 AGGATATTCGAATATTCGAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATCATTT
1 AGGATATTCGAATATTCAAAACAAACAAAGAAAACGAAACCCAGTACGTTAGGGCACGATCATTT
*
2385435 GAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAATTTTGAGAGTAAACCGGTAAA
66 GAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAATTTTGAGAGTAAACCGGTAAA
2385495 AGGATATTCTG-ATATTCAAAACAAACAAAGAAAACGAAACCCAGTACGTTAGGGCACGATCATT
1 AGGATATTC-GAATATTCAAAACAAACAAAGAAAACGAAACCCAGTACGTTAGGGCACGATCATT
*
2385559 TGAATTCTTTAAATACCGAACATT-TCTATTATTTTAAAAA
65 TGAATTCTTTAAATACCGAACATTGCCT-TTATTTTAAAAA
2385599 CAATTGAGAA
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
124 2 0.02
125 95 0.97
126 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (125 bp):
AGGATATTCGAATATTCAAAACAAACAAAGAAAACGAAACCCAGTACGTTAGGGCACGATCATTT
GAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAATTTTGAGAGTAAACCGGTAAA
Found at i:2386260 original size:16 final size:17
Alignment explanation
Indices: 2386239--2386270 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2386229 TAGTAGAATA
2386239 TAAT-AAATAATATTAG
1 TAATAAAATAATATTAG
2386255 TAATAAAATAATATTA
1 TAATAAAATAATATTA
2386271 ACTATTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATAAAATAATATTAG
Found at i:2386307 original size:14 final size:14
Alignment explanation
Indices: 2386288--2386329 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
2386278 ACAGTAAAGT
*
2386288 ATAATAAAATAGTA
1 ATAATAAAATAATA
2386302 ATAATAAAATAATA
1 ATAATAAAATAATA
*
2386316 ATACTAAAAATAAT
1 ATAAT-AAAATAAT
2386330 CAATTTTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (14 bp):
ATAATAAAATAATA
Found at i:2414880 original size:126 final size:126
Alignment explanation
Indices: 2414643--2414886 Score: 384
Period size: 126 Copynumber: 1.9 Consensus size: 126
2414633 TAGCTTTAAG
* *
2414643 AGGATATTCGAATATTCGAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATCATTT
1 AGGATATTCGAATATTCAAAACAAACAAAGAAAACGAAACCCAGTACGTTAGGGCACGATCATTT
* *** *
2414708 GAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAATTTTTGAGAGTAAACCGGTAAA
66 GAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAACAATTGAGAATAAACCGGTAAA
2414769 AGGATATTCTG-ATATTCAAAACAAACAAAGAAAACGAAACCCAGTACGTTAGGGCACGATCATT
1 AGGATATTC-GAATATTCAAAACAAACAAAGAAAACGAAACCCAGTACGTTAGGGCACGATCATT
*
2414833 TGAATTCTTTAAATACCGAACATT-TCTATTATTTTAAAAACAATTGAGAATAAA
65 TGAATTCTTTAAATACCGAACATTGCCT-TTATTTTAAAAACAATTGAGAATAAA
2414887 TCTGTGAATA
Statistics
Matches: 108, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
125 2 0.02
126 105 0.97
127 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (126 bp):
AGGATATTCGAATATTCAAAACAAACAAAGAAAACGAAACCCAGTACGTTAGGGCACGATCATTT
GAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAACAATTGAGAATAAACCGGTAAA
Found at i:2415537 original size:16 final size:17
Alignment explanation
Indices: 2415516--2415547 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2415506 TAGTAGAATA
2415516 TAAT-AAATAATATTAG
1 TAATAAAATAATATTAG
2415532 TAATAAAATAATATTA
1 TAATAAAATAATATTA
2415548 ACTATTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATAAAATAATATTAG
Found at i:2415590 original size:15 final size:15
Alignment explanation
Indices: 2415565--2415607 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2415555 ACAGTAAAGT
*
2415565 ATAAT-AAAATAGTA
1 ATAATAAAAATAATA
2415579 ATAATAAAAATAATA
1 ATAATAAAAATAATA
*
2415594 ATACTAAAAATAAT
1 ATAATAAAAATAAT
2415608 CAATTTTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
ATAATAAAAATAATA
Found at i:2416646 original size:17 final size:15
Alignment explanation
Indices: 2416613--2416648 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
2416603 TAGGTTTAGG
2416613 TGGGTTTTGGGGTAT
1 TGGGTTTTGGGGTAT
2416628 TGGGTTATTGGGTGTAT
1 TGGGTT-TTGGG-GTAT
2416645 TGGG
1 TGGG
2416649 CTTAGAGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 8 0.42
ACGTcount: A:0.08, C:0.00, G:0.47, T:0.44
Consensus pattern (15 bp):
TGGGTTTTGGGGTAT
Found at i:2450405 original size:6 final size:6
Alignment explanation
Indices: 2450394--2450429 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
2450384 GATGAGTCCA
2450394 TGTAGG TGTAGG TGTAGG TGTAGG TGTAGG TGTAGG
1 TGTAGG TGTAGG TGTAGG TGTAGG TGTAGG TGTAGG
2450430 GTCTTCGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
TGTAGG
Found at i:2456923 original size:22 final size:23
Alignment explanation
Indices: 2456898--2456950 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
2456888 ATTGATGAAG
2456898 ATAATAAAT-TGT-ACATATTAAA
1 ATAA-AAATGTGTAACATATTAAA
2456920 ATAAAAATGTGTAAAACATATTAAA
1 ATAAAAATGTGT--AACATATTAAA
2456945 ATAAAA
1 ATAAAA
2456951 CTTTAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.15
22 7 0.26
25 16 0.59
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (23 bp):
ATAAAAATGTGTAACATATTAAA
Found at i:2457290 original size:59 final size:60
Alignment explanation
Indices: 2457198--2457369 Score: 179
Period size: 59 Copynumber: 2.9 Consensus size: 60
2457188 TTAATATAAC
* * * * * * *
2457198 ATTTGCTACCTGAACTTCACACTTTTTCCTAATTTTGTACCTTAA-CTTTTTTTGGCCCA
1 ATTTGATACCTAAACTTGACAATTTTTCCTAATTTAGTACCTAAACCATTTTTTGGCCCA
* * * *
2457257 ATTTGGTACCTCAACTTGACAATTTTTCCTAATTTGGCACCTAAACCATTTTTTGGCCCA
1 ATTTGATACCTAAACTTGACAATTTTTCCTAATTTAGTACCTAAACCATTTTTTGGCCCA
* * * *
2457317 ATTTTATACGC-AAACTTGCCATTTTTTCCTAATTTAGTACCT-AAGCATTTTTT
1 ATTTGATAC-CTAAACTTGACAATTTTTCCTAATTTAGTACCTAAACCATTTTTT
2457370 TAGGTTCATT
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
59 48 0.51
60 46 0.48
61 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (60 bp):
ATTTGATACCTAAACTTGACAATTTTTCCTAATTTAGTACCTAAACCATTTTTTGGCCCA
Found at i:2457370 original size:60 final size:59
Alignment explanation
Indices: 2457198--2457370 Score: 172
Period size: 60 Copynumber: 2.9 Consensus size: 59
2457188 TTAATATAAC
* * * * *
2457198 ATTTGCTACCTGAACTTCACACTTTTTCCTAATTTTGTACCTTAAC-TTTTTTTGGCCCA
1 ATTTGATACCTAAACTTGACAATTTTTCCTAATTTAGTACC-TAACATTTTTTTGGCCCA
* * * *
2457257 ATTTGGTACCTCAACTTGACAATTTTTCCTAATTTGGCACCTAAACCA-TTTTTTGGCCCA
1 ATTTGATACCTAAACTTGACAATTTTTCCTAATTTAGTACCT-AA-CATTTTTTTGGCCCA
* * *
2457317 ATTTTATACGC-AAACTTGCCATTTTTTCCTAATTTAGTACCTAAGCATTTTTTT
1 ATTTGATAC-CTAAACTTGACAATTTTTCCTAATTTAGTACCTAA-CATTTTTTT
2457371 AGGTTCATTT
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
58 1 0.01
59 41 0.43
60 52 0.55
61 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (59 bp):
ATTTGATACCTAAACTTGACAATTTTTCCTAATTTAGTACCTAACATTTTTTTGGCCCA
Found at i:2458425 original size:28 final size:28
Alignment explanation
Indices: 2458368--2458426 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
2458358 TGTTTATATC
* *
2458368 TTTTTTATCAAATTTATTCCTTATTCCT
1 TTTTTTATCAAATTTATTCCCTAATCCT
* *
2458396 TTTTTTAGTTAAATTTGTTCCCTAAT-CT
1 TTTTTTA-TCAAATTTATTCCCTAATCCT
2458424 TTT
1 TTT
2458427 CAAAAACAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.20, C:0.15, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTTTTATCAAATTTATTCCCTAATCCT
Found at i:2471463 original size:14 final size:14
Alignment explanation
Indices: 2471444--2471472 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2471434 ATGTTGAGAT
2471444 AAGGTTATACCAAG
1 AAGGTTATACCAAG
2471458 AAGGTTATACCAAG
1 AAGGTTATACCAAG
2471472 A
1 A
2471473 CAGCAAGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AAGGTTATACCAAG
Found at i:2480217 original size:20 final size:21
Alignment explanation
Indices: 2480183--2480223 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2480173 GCAGGGGAAG
2480183 GAAAGAAAGAAAAAGAGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
*
2480204 GAAAGAAA-AAAAAGGGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
2480224 TCCAAGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAAAGAGAAAA
Found at i:2482236 original size:45 final size:46
Alignment explanation
Indices: 2482158--2482338 Score: 240
Period size: 46 Copynumber: 4.0 Consensus size: 46
2482148 GCTCTCTCAT
* * *
2482158 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACTTGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
2482204 ATGAAATGTGTAAGA-CATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
**
2482249 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
2482295 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
2482339 TCAAAGATAA
Statistics
Matches: 121, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
45 41 0.34
46 80 0.66
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:2497067 original size:38 final size:37
Alignment explanation
Indices: 2497012--2497090 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 37
2497002 GATGTGTATT
* *
2497012 CGGGTAAATCCCGCAGGCTTCA-TGTTGGTATTATATC
1 CGGGTAAATCCCGCAGGCCT-AGTGCTGGTATTATATC
*
2497049 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATT
1 CGGG-TAAATCCCGCAGGCCTAGTGCTGGTATTATATC
2497087 CGGG
1 CGGG
2497091 CCTTCGTGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 5 0.14
38 32 0.86
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (37 bp):
CGGGTAAATCCCGCAGGCCTAGTGCTGGTATTATATC
Found at i:2497138 original size:43 final size:43
Alignment explanation
Indices: 2497062--2497336 Score: 374
Period size: 43 Copynumber: 6.4 Consensus size: 43
2497052 GATAAATCCC
* * *
2497062 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
2497103 GCAGGCTTAGTGCCGGTGATGTGTATTCAGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
2497146 GCAGGCTTAGTGCCGGTGATGTGTATTCCGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * * *
2497189 GCAGACTTCGTGCCGATGATGTGTATTCGGGCCATCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
2497232 GCAGGCTTCGTGCCGATGATGTGTATTCGGGTCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
2497275 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
** * *
2497318 ATAGGCGTAATGCCGGTGA
1 GCAGGCTTAGTGCCGGTGA
2497337 AATGATATGT
Statistics
Matches: 210, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 15 0.07
42 2 0.01
43 193 0.92
ACGTcount: A:0.14, C:0.24, G:0.32, T:0.30
Consensus pattern (43 bp):
GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:2502374 original size:22 final size:23
Alignment explanation
Indices: 2502348--2502392 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
2502338 ACCTGATCAG
2502348 AATACGACACAT-AAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
2502370 AATACGACACATAAAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
2502393 TCAGTAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTGA
Found at i:2502627 original size:28 final size:28
Alignment explanation
Indices: 2502595--2502674 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
2502585 AAAACACCAG
* * **
2502595 TATAATCCTCCAAAATACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGCAAAA
*
2502623 TATAATCCTCCCAAACACACCAGCAAAA
1 TATAATCCTCCAAAACACACCAGCAAAA
2502651 TATAATCCATCCAAAACACACCAG
1 TATAATCC-TCCAAAACACACCAG
2502675 AATAGCACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
28 31 0.69
29 14 0.31
ACGTcount: A:0.45, C:0.33, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGCAAAA
Found at i:2517979 original size:44 final size:45
Alignment explanation
Indices: 2517884--2517998 Score: 144
Period size: 44 Copynumber: 2.6 Consensus size: 45
2517874 ACAGGACAGA
*
2517884 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGATTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGATTTGGAG
* *
2517930 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCA-TTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGG-ATTTGGAG
* **
2517974 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
2517999 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
44 34 0.56
45 1 0.02
46 26 0.43
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGATTTGGAG
Found at i:2520733 original size:53 final size:53
Alignment explanation
Indices: 2520652--2520802 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
2520642 CTTACACGGT
* *
2520652 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
* *
2520707 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCATATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
2520760 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
2520803 GCACACTTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:2522531 original size:42 final size:42
Alignment explanation
Indices: 2522467--2522593 Score: 136
Period size: 42 Copynumber: 3.0 Consensus size: 42
2522457 CTTCGTTTTC
** *
2522467 TCGATGCCATAGTTCAACTATGGTCTTACACATC-TTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACA-CATTCACAT-A
* * *
2522510 T-GATGCTATAGCCCGGCTATGGTCTTACACACATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACACATTCACATA
*
2522551 TCGATGCCATAGCCTAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ACATTCACATA
2522592 TC
1 TC
2522594 TCACTGATGC
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
41 11 0.15
42 58 0.82
43 2 0.03
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACACATTCACATA
Found at i:2522653 original size:47 final size:46
Alignment explanation
Indices: 2522552--2522675 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 46
2522542 ATTCATATAT
* * * * * *
2522552 CGATGCCATAGCCTAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
2522598 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
2522645 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
2522676 GAAATCACTT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
46 26 0.39
47 41 0.61
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:2522728 original size:31 final size:31
Alignment explanation
Indices: 2522693--2522872 Score: 265
Period size: 31 Copynumber: 5.8 Consensus size: 31
2522683 CTTGTCACTT
*
2522693 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
**
2522724 GTAGCC-AGAGCTACCGTTTTTCACTGATCAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
2522755 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
2522786 GTAGCCAGAA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
* *
2522817 GTAGCAGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
2522848 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
2522873 TGTCATTTGT
Statistics
Matches: 135, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
30 4 0.03
31 129 0.96
32 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:2526448 original size:37 final size:37
Alignment explanation
Indices: 2526384--2526540 Score: 199
Period size: 37 Copynumber: 4.0 Consensus size: 37
2526374 TACGTATGAT
*
2526384 CACTTATCAC-TTGTCCCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
2526420 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
2526457 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AGC
*
2526500 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 ---CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
2526540 C
1 C
2526541 GAAGCTATCA
Statistics
Matches: 107, Mismatches: 4, Indels: 19
0.82 0.03 0.15
Matches are distributed among these distances:
36 10 0.09
37 54 0.50
39 2 0.02
40 4 0.04
41 1 0.01
42 1 0.01
43 3 0.03
44 2 0.02
46 30 0.28
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:2526510 original size:46 final size:46
Alignment explanation
Indices: 2526457--2526823 Score: 437
Period size: 46 Copynumber: 7.6 Consensus size: 46
2526447 TAAGTGTAGC
* **
2526457 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
2526503 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
2526549 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
2526601 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
2526653 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * *
2526699 AACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
2526745 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
2526797 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
2526824 AGTACTCAAA
Statistics
Matches: 290, Mismatches: 18, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
46 154 0.53
48 1 0.00
49 1 0.00
50 2 0.01
51 3 0.01
52 129 0.44
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:2526576 original size:52 final size:52
Alignment explanation
Indices: 2526500--2526817 Score: 417
Period size: 52 Copynumber: 6.3 Consensus size: 52
2526490 TAGCTAAAGC
* *
2526500 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
2526553 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * *
2526605 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
2526657 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
2526703 TATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
2526749 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
2526801 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
2526818 ATCAGAAGTA
Statistics
Matches: 238, Mismatches: 17, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
46 83 0.35
47 2 0.01
48 2 0.01
52 133 0.56
53 18 0.08
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:2526765 original size:196 final size:196
Alignment explanation
Indices: 2526457--2526809 Score: 598
Period size: 196 Copynumber: 1.8 Consensus size: 196
2526447 TAAGTGTAGC
* * * * * *
2526457 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCACT
*
2526522 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGT
66 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
* *
2526587 GTAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
131 GTAGCCAAAGCTACCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
2526652 T
196 T
*
2526653 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACTTATCACTTTATCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCACT
*
2526718 TGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
66 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
*
2526783 GTAGCTAAAGCTACCACTTATCACTTT
131 GTAGCCAAAGCTACCACTTATCACTTT
2526810 ATCACTTGAT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
196 145 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (196 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCACT
TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
GTAGCCAAAGCTACCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
T
Found at i:2526813 original size:98 final size:97
Alignment explanation
Indices: 2526457--2526823 Score: 492
Period size: 98 Copynumber: 3.7 Consensus size: 97
2526447 TAAGTGTAGC
* * * *
2526457 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTT-TCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACT
2526522 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
64 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
2526556 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTG
1 CAC-TTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTT--A----
* *
2526621 TCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
59 TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * *
2526660 CAC--T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACTTATCACTTTATCACTTG
1 CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTG
*
2526720 ATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 ATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
2526752 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTT
1 CACTTT-CACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTT
2526817 GATCAGA
65 GATCAGA
2526824 AGTACTCAAA
Statistics
Matches: 238, Mismatches: 17, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
92 39 0.16
94 1 0.00
96 1 0.00
98 148 0.62
99 7 0.03
100 2 0.01
101 1 0.00
104 39 0.16
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (97 bp):
CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTG
ATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:2529999 original size:49 final size:49
Alignment explanation
Indices: 2529944--2530138 Score: 309
Period size: 49 Copynumber: 4.0 Consensus size: 49
2529934 TTCGTTTTCT
* * *
2529944 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
* * *
2529993 CGATGCCATAGCCCAGCTATGGTCTTACACGGAGTCACATATCACTTAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
* *
2530042 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACTTAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
2530091 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACA-AATCACAT
2530139 GTTCACATGT
Statistics
Matches: 136, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 130 0.96
50 6 0.04
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (49 bp):
CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
Found at i:2531460 original size:37 final size:37
Alignment explanation
Indices: 2531396--2531552 Score: 199
Period size: 37 Copynumber: 4.0 Consensus size: 37
2531386 TACGTATGAT
*
2531396 CACTTATCAC-TTGTCCCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
2531432 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
2531469 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AGC
*
2531512 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 ---CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
2531552 C
1 C
2531553 GAAGCTATCA
Statistics
Matches: 107, Mismatches: 4, Indels: 19
0.82 0.03 0.15
Matches are distributed among these distances:
36 10 0.09
37 54 0.50
39 2 0.02
40 4 0.04
41 1 0.01
42 1 0.01
43 3 0.03
44 2 0.02
46 30 0.28
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:2531522 original size:46 final size:46
Alignment explanation
Indices: 2531469--2531835 Score: 437
Period size: 46 Copynumber: 7.6 Consensus size: 46
2531459 TAAGTGTAGC
* **
2531469 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
2531515 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
2531561 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
2531613 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
2531665 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * *
2531711 AACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
2531757 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
2531809 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
2531836 AGTACTCAAA
Statistics
Matches: 290, Mismatches: 18, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
46 154 0.53
48 1 0.00
49 1 0.00
50 2 0.01
51 3 0.01
52 129 0.44
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:2531588 original size:52 final size:52
Alignment explanation
Indices: 2531512--2531829 Score: 417
Period size: 52 Copynumber: 6.3 Consensus size: 52
2531502 TAGCTAAAGC
* *
2531512 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
2531565 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * *
2531617 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
2531669 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
2531715 TATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
2531761 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
2531813 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
2531830 ATCAGAAGTA
Statistics
Matches: 238, Mismatches: 17, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
46 83 0.35
47 2 0.01
48 2 0.01
52 133 0.56
53 18 0.08
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:2531777 original size:196 final size:196
Alignment explanation
Indices: 2531469--2531821 Score: 598
Period size: 196 Copynumber: 1.8 Consensus size: 196
2531459 TAAGTGTAGC
* * * * * *
2531469 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCACT
*
2531534 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGT
66 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
* *
2531599 GTAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
131 GTAGCCAAAGCTACCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
2531664 T
196 T
*
2531665 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACTTATCACTTTATCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCACT
*
2531730 TGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
66 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
*
2531795 GTAGCTAAAGCTACCACTTATCACTTT
131 GTAGCCAAAGCTACCACTTATCACTTT
2531822 ATCACTTGAT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
196 145 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (196 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCACT
TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
GTAGCCAAAGCTACCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
T
Found at i:2531825 original size:98 final size:97
Alignment explanation
Indices: 2531469--2531835 Score: 492
Period size: 98 Copynumber: 3.7 Consensus size: 97
2531459 TAAGTGTAGC
* * * *
2531469 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTT-TCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACT
2531534 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
64 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
2531568 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTG
1 CAC-TTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTT--A----
* *
2531633 TCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
59 TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * *
2531672 CAC--T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACTTATCACTTTATCACTTG
1 CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTG
*
2531732 ATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 ATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
2531764 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTT
1 CACTTT-CACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTT
2531829 GATCAGA
65 GATCAGA
2531836 AGTACTCAAA
Statistics
Matches: 238, Mismatches: 17, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
92 39 0.16
94 1 0.00
96 1 0.00
98 148 0.62
99 7 0.03
100 2 0.01
101 1 0.00
104 39 0.16
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (97 bp):
CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTG
ATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:2542439 original size:9 final size:9
Alignment explanation
Indices: 2542425--2542466 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
2542415 AGAGATTTAA
2542425 TTAAAATAT
1 TTAAAATAT
2542434 TTAAAAT-T
1 TTAAAATAT
*
2542442 TAAGAAATAAT
1 TTA-AAAT-AT
2542453 TTAAAATAT
1 TTAAAATAT
2542462 TTAAA
1 TTAAA
2542467 TTATGTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 3 0.11
9 18 0.64
10 4 0.14
11 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
TTAAAATAT
Found at i:2543997 original size:24 final size:24
Alignment explanation
Indices: 2543969--2544028 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
2543959 TTAATATATT
*
2543969 TATTT-AGTTTGAATATTAATTTGG
1 TATTTAAGTTT-AATATTAATTTAG
*
2543993 TATTTAAGTTTAATTTTAATTTAG
1 TATTTAAGTTTAATATTAATTTAG
*
2544017 TATTTGAGTTTA
1 TATTTAAGTTTA
2544029 GTATCTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 27 0.84
25 5 0.16
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (24 bp):
TATTTAAGTTTAATATTAATTTAG
Found at i:2560421 original size:10 final size:10
Alignment explanation
Indices: 2560406--2560433 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2560396 GTCTCTTTCT
2560406 TCTCTCTCCC
1 TCTCTCTCCC
2560416 TCTCTCTCCC
1 TCTCTCTCCC
2560426 TCTCTCTC
1 TCTCTCTC
2560434 TCTCCCCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (10 bp):
TCTCTCTCCC
Found at i:2561637 original size:24 final size:24
Alignment explanation
Indices: 2561592--2561638 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2561582 TTTGTTTGTT
*
2561592 TAATTTTAAAATTCAGATATCAAA
1 TAATTTTAAAATTCAGAAATCAAA
*
2561616 TAATTTTAACAATT-TGAAATCAA
1 TAATTTTAA-AATTCAGAAATCAA
2561639 TCTATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (24 bp):
TAATTTTAAAATTCAGAAATCAAA
Found at i:2561748 original size:21 final size:22
Alignment explanation
Indices: 2561713--2561755 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
2561703 ATAACTACCT
*
2561713 AATAATTTGAATAATTTTTTTA
1 AATAATTTGAATAATTATTTTA
2561735 AATAATTT-AATAATTATTTTA
1 AATAATTTGAATAATTATTTTA
2561756 TAACTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
AATAATTTGAATAATTATTTTA
Found at i:2561764 original size:22 final size:22
Alignment explanation
Indices: 2561713--2561771 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
2561703 ATAACTACCT
2561713 AATAATTTGAATAATT-TTTTTA
1 AATAATTT-AATAATTATTTTTA
2561735 AATAATTTAATAATTATTTTATA
1 AATAATTTAATAATTATTTT-TA
*
2561758 ACT-ATTTAA-AATTA
1 AATAATTTAATAATTA
2561772 AATTAATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
21 12 0.35
22 18 0.53
23 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
AATAATTTAATAATTATTTTTA
Found at i:2562231 original size:28 final size:28
Alignment explanation
Indices: 2562173--2562231 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
2562163 ACATTAATCG
* *
2562173 ATTATTTAATTAGTAAACGAAGTATAAA
1 ATTATTTAACTAATAAACGAAGTATAAA
2562201 ATTATTTAACTACATAAAC-AA-TATAATA
1 ATTATTTAACTA-ATAAACGAAGTATAA-A
2562229 ATT
1 ATT
2562232 TTACCTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 17 0.63
29 5 0.19
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (28 bp):
ATTATTTAACTAATAAACGAAGTATAAA
Found at i:2562637 original size:27 final size:27
Alignment explanation
Indices: 2562607--2562660 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2562597 ATTAACTGTT
2562607 TTTTAACAATTTTATTATAA-ATTTAAA
1 TTTTAACAATTTTA-TATAATATTTAAA
* **
2562634 TTTTATCTTTTTTATATAATATTTAAA
1 TTTTAACAATTTTATATAATATTTAAA
2562661 ACTATTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTAACAATTTTATATAATATTTAAA
Found at i:2564964 original size:9 final size:9
Alignment explanation
Indices: 2564939--2564968 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2564929 ATCATTAGCC
2564939 TAAGTTAAT
1 TAAGTTAAT
2564948 TAAGGTTAAT
1 TAA-GTTAAT
2564958 TAAGTTAAT
1 TAAGTTAAT
2564967 TA
1 TA
2564969 TGATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (9 bp):
TAAGTTAAT
Found at i:2564978 original size:19 final size:19
Alignment explanation
Indices: 2564939--2564978 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2564929 ATCATTAGCC
*
2564939 TAAGTTAATTAAGGTTAAT
1 TAAGTTAATTAAGATTAAT
* *
2564958 TAAGTTAATTATGATTTAT
1 TAAGTTAATTAAGATTAAT
2564977 TA
1 TA
2564979 TATATTAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (19 bp):
TAAGTTAATTAAGATTAAT
Found at i:2565517 original size:24 final size:24
Alignment explanation
Indices: 2565488--2565535 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2565478 AATGAAAAAG
2565488 TTTAAGGAACATTTGAAAATTGAA
1 TTTAAGGAACATTTGAAAATTGAA
2565512 TTTAAGGAACATTTGAAAATTGAA
1 TTTAAGGAACATTTGAAAATTGAA
2565536 ATTGAACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (24 bp):
TTTAAGGAACATTTGAAAATTGAA
Found at i:2568576 original size:19 final size:17
Alignment explanation
Indices: 2568541--2568582 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
2568531 CTTATTTTAA
2568541 TATTTATATTAGAGTAG
1 TATTTATATTAGAGTAG
*
2568558 TATTATATATTTAGTGTAG
1 TATT-TATA-TTAGAGTAG
2568577 -ATTTAT
1 TATTTAT
2568583 TTTATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 7 0.32
19 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (17 bp):
TATTTATATTAGAGTAG
Found at i:2572441 original size:6 final size:6
Alignment explanation
Indices: 2572430--2572457 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2572420 TCCCAATATC
2572430 AGCCTT AGCCTT AGCCTT AGCCTT AGCC
1 AGCCTT AGCCTT AGCCTT AGCCTT AGCC
2572458 ATTTCACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.18, T:0.29
Consensus pattern (6 bp):
AGCCTT
Found at i:2574080 original size:38 final size:38
Alignment explanation
Indices: 2574029--2574105 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
2574019 CAATTCGACA
* *
2574029 ATCAATATAGTAGATTAATAGTCATTGATAAGTAGAAG
1 ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
2574067 ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
1 ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
2574105 A
1 A
2574106 ACATACCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (38 bp):
ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
Found at i:2581158 original size:25 final size:26
Alignment explanation
Indices: 2581120--2581178 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
2581110 TTAGAATCTA
*
2581120 TTTTTAA-AATAATTAAA-T-TTAAAT
1 TTTTTAATAAAAATTAAACTATT-AAT
2581144 TTTTTAATAAAAATTAAACTATTAAT
1 TTTTTAATAAAAATTAAACTATTAAT
*
2581170 TTTGTAATA
1 TTTTTAATA
2581179 CATATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 7 0.23
25 9 0.30
26 12 0.40
27 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TTTTTAATAAAAATTAAACTATTAAT
Found at i:2584577 original size:2 final size:2
Alignment explanation
Indices: 2584570--2584603 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2584560 CTTATCTAAA
2584570 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2584604 ATGCCATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2587718 original size:15 final size:16
Alignment explanation
Indices: 2587689--2587734 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
2587679 TAATAAAGTC
2587689 TCATTCTTTTCATTTTA
1 TCATT-TTTTCATTTTA
2587706 TCATTTTTT-ATTTTA
1 TCATTTTTTCATTTTA
*
2587721 TTATTTTATTCATT
1 TCATTTT-TTCATT
2587735 CAAAAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 12 0.46
16 6 0.23
17 8 0.31
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (16 bp):
TCATTTTTTCATTTTA
Found at i:2590628 original size:17 final size:17
Alignment explanation
Indices: 2590606--2590664 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 17
2590596 AAAAAATATA
2590606 AAATTAATAATGTTAAC
1 AAATTAATAATGTTAAC
2590623 AAATTAATAATG--AATC
1 AAATTAATAATGTTAA-C
* *
2590639 TAATTAA-AAT-TTAAA
1 AAATTAATAATGTTAAC
2590654 AAATTAATAAT
1 AAATTAATAAT
2590665 ATTTTTCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 11 0.31
16 12 0.34
17 12 0.34
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
AAATTAATAATGTTAAC
Found at i:2591755 original size:48 final size:48
Alignment explanation
Indices: 2591694--2591813 Score: 231
Period size: 48 Copynumber: 2.5 Consensus size: 48
2591684 ATTACAAACA
2591694 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
*
2591742 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAATTTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
2591790 TCAATTATTTACCCTATTAACAAA
1 TCAATTATTTACCCTATTAACAAA
2591814 GCTCGGACTA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.43
Consensus pattern (48 bp):
TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
Found at i:2593421 original size:5 final size:5
Alignment explanation
Indices: 2593411--2593438 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2593401 TATATATATA
2593411 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
2593439 CTTAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:2596100 original size:31 final size:31
Alignment explanation
Indices: 2596065--2596125 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2596055 GTTAACACTC
2596065 TTAAAATTACTTTATCAAATTCAGGTTCATA
1 TTAAAATTACTTTATCAAATTCAGGTTCATA
* **
2596096 TTAAATTTTTTTTATCAAATTCAGGTTCAT
1 TTAAAATTACTTTATCAAATTCAGGTTCAT
2596126 TATAGCATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (31 bp):
TTAAAATTACTTTATCAAATTCAGGTTCATA
Found at i:2611379 original size:15 final size:15
Alignment explanation
Indices: 2611336--2611368 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2611326 TAATAAATTG
2611336 AAAAATAAATATTAA
1 AAAAATAAATATTAA
2611351 AAAAATAAATATTAA
1 AAAAATAAATATTAA
2611366 AAA
1 AAA
2611369 TTTAAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAAATATTAA
Found at i:2629276 original size:39 final size:39
Alignment explanation
Indices: 2629222--2629412 Score: 208
Period size: 39 Copynumber: 4.9 Consensus size: 39
2629212 TTCAGTGATG
* *
2629222 TATATCCGGACTTAGGGTCCGCAGGCTATGTGTTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
2629261 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* *
2629300 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * * * *
2629339 TATGTCCGGGCTAAAGTTCCGCAGGCT-TCGAGCTGGTAT
1 TATATCCGGACTTAAGGTCCGCAGGCTAT-GTGCTGGAAT
** **
2629378 TATA-CCGGGTTTAAATTCCCGCAGGCT-TGTGCTGG
1 TATATCCGGACTTAAGGT-CCGCAGGCTATGTGCTGG
2629413 TATCTGGATT
Statistics
Matches: 133, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
38 16 0.12
39 117 0.88
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:2632051 original size:21 final size:21
Alignment explanation
Indices: 2632025--2632152 Score: 114
Period size: 21 Copynumber: 6.0 Consensus size: 21
2632015 ATAAAAATAT
2632025 TCAGGCACCTCGTGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
* *
2632046 TCAGGCACTTCGTGTGTCGTT
1 TCAGGCACCTCGTGTGTCGTA
* ** **
2632067 TTAGGCATTTTATGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
* *
2632088 TTTCAGGCACCTTGTGTGTTGTA
1 --TCAGGCACCTCGTGTGTCGTA
*
2632111 TCAGGCACCTCGTGTGTCGTT
1 TCAGGCACCTCGTGTGTCGTA
* **
2632132 TCAAGCA-CTTATGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
2632152 T
1 T
2632153 ACTGATCAGG
Statistics
Matches: 86, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
20 11 0.13
21 59 0.69
23 16 0.19
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (21 bp):
TCAGGCACCTCGTGTGTCGTA
Found at i:2632114 original size:65 final size:64
Alignment explanation
Indices: 2632024--2632152 Score: 195
Period size: 65 Copynumber: 2.0 Consensus size: 64
2632014 TATAAAAATA
* * * *
2632024 TTCAGGCACCTCGTGTGTCGTATCAGGCACTTCGTGTGTCGTTTTAGGCATTTTATGTGTCGTAT
1 TTCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGTTTCAAGCA-CTTATGTGTCGTAT
* *
2632089 TTCAGGCACCTTGTGTGTTGTATCAGGCACCTCGTGTGTCGTTTCAAGCACTTATGTGTCGTAT
1 TTCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGTTTCAAGCACTTATGTGTCGTAT
2632153 ACTGATCAGG
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
64 13 0.22
65 45 0.78
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.39
Consensus pattern (64 bp):
TTCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGTTTCAAGCACTTATGTGTCGTAT
Found at i:2632127 original size:44 final size:42
Alignment explanation
Indices: 2632025--2632152 Score: 125
Period size: 44 Copynumber: 3.0 Consensus size: 42
2632015 ATAAAAATAT
*
2632025 TCAGGCACCTCGTGTGTCGTATCAGGCACTTCGTGTGTCGTT
1 TCAGGCACCTCGTGTGTCGTATCAGGCACTTCGTGTGTCGTA
* ** ** *
2632067 TTAGGCATTTTATGTGTCGTATTTCAGGCACCTT-GTGTGTTGTA
1 TCAGGCACCTCGTGTGTCGTA--TCAGGCA-CTTCGTGTGTCGTA
* * *
2632111 TCAGGCACCTCGTGTGTCGTTTCAAGCACTT-ATGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTATCAGGCACTTCGTGTGTCGTA
2632152 T
1 T
2632153 ACTGATCAGG
Statistics
Matches: 67, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
41 12 0.18
42 22 0.33
44 30 0.45
45 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (42 bp):
TCAGGCACCTCGTGTGTCGTATCAGGCACTTCGTGTGTCGTA
Found at i:2634754 original size:7 final size:7
Alignment explanation
Indices: 2634742--2634820 Score: 54
Period size: 7 Copynumber: 10.6 Consensus size: 7
2634732 TATATAAAAA
2634742 TATATAT
1 TATATAT
2634749 TATATAT
1 TATATAT
2634756 TATATTAACT
1 TATA-T-A-T
2634766 TA-ATAT
1 TATATAT
2634772 T-TAAGTAT
1 TAT-A-TAT
2634780 TAATATAT
1 T-ATATAT
*
2634788 AATATAT
1 TATATAT
2634795 TATATTAT
1 TATA-TAT
2634803 TATATAT
1 TATATAT
* *
2634810 AATATAA
1 TATATAT
2634817 TATA
1 TATA
2634821 ATATATAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
6 2 0.03
7 33 0.57
8 16 0.28
9 3 0.05
10 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (7 bp):
TATATAT
Found at i:2634814 original size:20 final size:20
Alignment explanation
Indices: 2634743--2634828 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 20
2634733 ATATAAAAAT
* *
2634743 ATATATTATATATTATATTA
1 ATATATAATATATAATATTA
* *
2634763 A-CT-TAATATTTAAGTATTA
1 ATATATAATATATAA-TATTA
*
2634782 ATATATAATATATTATATTA
1 ATATATAATATATAATATTA
*
2634802 TTATAT-ATAATATAATA-TA
1 ATATATAAT-ATATAATATTA
2634821 ATATATAA
1 ATATATAA
2634829 AACATAAGTA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
18 7 0.14
19 16 0.31
20 20 0.39
21 8 0.16
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (20 bp):
ATATATAATATATAATATTA
Found at i:2634815 original size:17 final size:17
Alignment explanation
Indices: 2634784--2634828 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
2634774 AAGTATTAAT
2634784 ATATAATATAT--TATA
1 ATATAATATATAATATA
* *
2634799 TTATTATATATAATATA
1 ATATAATATATAATATA
2634816 ATATAATATATAA
1 ATATAATATATAA
2634829 AACATAAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 9 0.38
17 15 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAATATATAATATA
Found at i:2635983 original size:29 final size:31
Alignment explanation
Indices: 2635946--2636003 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
2635936 CTAGCGCGCT
2635946 TTCTGATTATTAGCACATT-AGTGCTCTCCG
1 TTCTGATTATTAGCACATTAAGTGCTCTCCG
*
2635976 TTCT-ATTATTAGCACGTTAAGTGCTCTC
1 TTCTGATTATTAGCACATTAAGTGCTCTC
2636004 TGTTTAGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (31 bp):
TTCTGATTATTAGCACATTAAGTGCTCTCCG
Found at i:2638525 original size:47 final size:47
Alignment explanation
Indices: 2638415--2638547 Score: 162
Period size: 46 Copynumber: 2.9 Consensus size: 47
2638405 ATAATCTCAC
* * *
2638415 CCATAATGAACTCGGAACGCAACTCAATGAGCTCGGGTG-TTCGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
* * * *
2638461 TCATAATGAACTTGGAACACAACTCAACGAGTTTGGATGCTT-GCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
* *
2638507 CCATAGGTGAACTCGGAACGCAACTCAACGTGTTCGGATGC
1 CCATA-ATGAACTCGGAACGCAACTCAACGAGTTCGGATGC
2638548 CTCATAATTC
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
46 40 0.56
47 32 0.44
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.23
Consensus pattern (47 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
Found at i:2654449 original size:18 final size:18
Alignment explanation
Indices: 2654428--2654469 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2654418 CATACATGAC
2654428 ATGCAAAACATAATAAAA
1 ATGCAAAACATAATAAAA
* *
2654446 ATGCAGAACATAATAGAA
1 ATGCAAAACATAATAAAA
2654464 ATGCAA
1 ATGCAA
2654470 CAATTGAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.17
Consensus pattern (18 bp):
ATGCAAAACATAATAAAA
Found at i:2660020 original size:11 final size:11
Alignment explanation
Indices: 2660004--2660034 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2659994 AAGTATGGGT
2660004 AGGTATGGGAA
1 AGGTATGGGAA
*
2660015 AGGTATGGGCA
1 AGGTATGGGAA
2660026 AGGTATGGG
1 AGGTATGGG
2660035 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:2669726 original size:12 final size:11
Alignment explanation
Indices: 2669704--2669737 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2669694 TCCCCCACAC
*
2669704 TTTTTCTTTTT
1 TTTTTCCTTTT
2669715 TTTTTCCCTTTT
1 TTTTT-CCTTTT
2669727 TTTTTCCTTTT
1 TTTTTCCTTTT
2669738 CTCTCTCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCCTTTT
Found at i:2669976 original size:29 final size:29
Alignment explanation
Indices: 2669911--2669983 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
2669901 AAAGTATTTG
2669911 AAATTTTTTATTTAAATAATTGAACTATT
1 AAATTTTTTATTTAAATAATTGAACTATT
* * *
2669940 AAAGTTTTTATTTAAGTCATT-AAGCTATT
1 AAATTTTTTATTTAAATAATTGAA-CTATT
*
2669969 -AATTTTTTTTTTAAA
1 AAATTTTTTATTTAAA
2669984 ATCTAGCTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 14 0.38
29 23 0.62
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.53
Consensus pattern (29 bp):
AAATTTTTTATTTAAATAATTGAACTATT
Found at i:2670299 original size:29 final size:29
Alignment explanation
Indices: 2670228--2670292 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
2670218 ACAAATAGAG
*
2670228 AATGTCATAAAATATCGATTTTTACAATT
1 AATGACATAAAATATCGATTTTTACAATT
* *
2670257 AATGTCATAAAATATCGATTTTTACAGTT
1 AATGACATAAAATATCGATTTTTACAATT
2670286 CAATGAC
1 -AATGAC
2670293 TTGAATAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 28 0.85
30 5 0.15
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (29 bp):
AATGACATAAAATATCGATTTTTACAATT
Found at i:2683117 original size:8 final size:9
Alignment explanation
Indices: 2683084--2683116 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
2683074 ATAGAAGATA
2683084 TTTTTTTAT
1 TTTTTTTAT
2683093 TTTTTTTAT
1 TTTTTTTAT
2683102 TTTTTTTAT
1 TTTTTTTAT
2683111 TATTTT
1 T-TTTT
2683117 AGGATTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:2692338 original size:14 final size:14
Alignment explanation
Indices: 2692319--2692348 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2692309 GTCATTTAGG
2692319 CCAACCAAACTGGC
1 CCAACCAAACTGGC
2692333 CCAACCAAACTGGC
1 CCAACCAAACTGGC
2692347 CC
1 CC
2692349 GGTGATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.47, G:0.13, T:0.07
Consensus pattern (14 bp):
CCAACCAAACTGGC
Found at i:2702931 original size:59 final size:59
Alignment explanation
Indices: 2702862--2702980 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
2702852 AAACGCAACA
*
2702862 TATACTTATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTATAGT
1 TATACATATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTATAGT
*
2702921 TATACATATTCCATTACTTCAATTCCTTTATTTTATCTGCCTTTCAATTTTTCTATAGT
1 TATACATATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTATAGT
2702980 T
1 T
2702981 TTACTCTCAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.24, C:0.20, G:0.03, T:0.54
Consensus pattern (59 bp):
TATACATATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTATAGT
Found at i:2706875 original size:21 final size:22
Alignment explanation
Indices: 2706851--2706897 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
2706841 CTTTGCTCAA
*
2706851 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
2706872 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
2706894 ACTC
1 ACTC
2706898 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:2715013 original size:16 final size:16
Alignment explanation
Indices: 2714992--2715043 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
2714982 TTTGGTTCGC
2714992 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
2715008 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
2715024 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
2715040 TGTA
1 TGTA
2715044 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:2715301 original size:18 final size:17
Alignment explanation
Indices: 2715280--2715314 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2715270 TTATTATTTA
*
2715280 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
2715298 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
2715315 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:2715308 original size:28 final size:27
Alignment explanation
Indices: 2715238--2715310 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
2715228 TTTATTATCA
*
2715238 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
2715266 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
2715293 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
2715311 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:2715448 original size:18 final size:17
Alignment explanation
Indices: 2715427--2715461 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2715417 TTATTATTAA
*
2715427 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
2715445 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
2715462 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:2715473 original size:147 final size:149
Alignment explanation
Indices: 2715199--2715473 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 149
2715189 ATGATTATTG
*
2715199 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
2715264 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
2715329 AGAAATTTATTTTGGTAAA
131 AGAAATTTATTTTGGTAAA
* *
2715348 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATTAATAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
2715411 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
2715474 ATATTCTTAT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
147 94 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTATTTTGGTAAA
Found at i:2715505 original size:54 final size:54
Alignment explanation
Indices: 2715447--2715625 Score: 128
Period size: 55 Copynumber: 3.1 Consensus size: 54
2715437 ATTAAAATAT
*
2715447 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
** * * * * *
2715501 ATAATATATGATACTGTAAAATAT-AAAATAACATAATTATTATTAAATAT-AATATAATTAAAA
1 ATAAT-T-T-A-A---TAAAAT-TCTTAATAA-TTAA-TATTCTT--ATATGAAT-TTACTCAAA
*
2715564 TAT
53 -AC
*
2715567 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
2715621 ATAAT
1 ATAAT
2715626 ATATGATACT
Statistics
Matches: 91, Mismatches: 18, Indels: 32
0.65 0.13 0.23
Matches are distributed among these distances:
54 10 0.11
55 11 0.12
56 4 0.04
57 7 0.08
58 5 0.05
59 11 0.12
61 11 0.12
62 5 0.05
63 7 0.08
64 4 0.04
65 11 0.12
66 5 0.05
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
Found at i:2715568 original size:18 final size:17
Alignment explanation
Indices: 2715547--2715581 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2715537 TTATTATTAA
2715547 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
2715565 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
2715582 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:2715696 original size:18 final size:17
Alignment explanation
Indices: 2715657--2715688 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2715647 TTTTAAATAA
2715657 TTAATATTAAATATATT
1 TTAATATTAAATATATT
2715674 TTAAT-TTAAATATAT
1 TTAATATTAAATATAT
2715689 GATTTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATATTAAATATATT
Found at i:2715713 original size:120 final size:120
Alignment explanation
Indices: 2715410--2715702 Score: 482
Period size: 120 Copynumber: 2.4 Consensus size: 120
2715400 ATCATATTTA
2715410 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
2715475 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATATAAAAT
* *
2715530 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
2715595 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATA-AAATTTT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATATAAA--AT
* * *
2715651 AA-ATAATTAATATTAAATATATTTTAATTTAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
2715703 TAAAATAATT
Statistics
Matches: 161, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
119 3 0.02
120 155 0.96
121 3 0.02
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATATAAAAT
Found at i:2717518 original size:20 final size:19
Alignment explanation
Indices: 2717459--2717505 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 19
2717449 CAACTACACA
2717459 AATTCACAATGTAACCTACT
1 AATT-ACAATGTAACCTACT
2717479 AATTACAATGTAACCTACT
1 AATTACAATGTAACCTACT
2717498 AATTACAA
1 AATTACAA
2717506 CTTCGACCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (19 bp):
AATTACAATGTAACCTACT
Found at i:2718222 original size:14 final size:14
Alignment explanation
Indices: 2718197--2718231 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
2718187 AAGAAGAAGC
2718197 AGAAATATGGAGAAA
1 AGAAA-ATGGAGAAA
2718212 AGAAAATGGAGAAA
1 AGAAAATGGAGAAA
2718226 AGAAAA
1 AGAAAA
2718232 GAAATGTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.66, C:0.00, G:0.26, T:0.09
Consensus pattern (14 bp):
AGAAAATGGAGAAA
Found at i:2718229 original size:19 final size:18
Alignment explanation
Indices: 2718207--2718251 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
2718197 AGAAATATGG
2718207 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
2718226 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
2718243 AGAAAAGAA
1 AGAAAAGAA
2718252 GCGTACCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Found at i:2722502 original size:48 final size:48
Alignment explanation
Indices: 2722446--2722543 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
2722436 CACAGGCGAT
2722446 GAAGAACAATCAAATCAATTGTTGGCGAATGGACATTGTGGCGAAGAG
1 GAAGAACAATCAAATCAATTGTTGGCGAATGGACATTGTGGCGAAGAG
2722494 GAAGAACAATCAAATCAATTGTTGGCGAATGGACATTGTGGCGAAGAG
1 GAAGAACAATCAAATCAATTGTTGGCGAATGGACATTGTGGCGAAGAG
2722542 GA
1 GA
2722544 TTCTCTCATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (48 bp):
GAAGAACAATCAAATCAATTGTTGGCGAATGGACATTGTGGCGAAGAG
Found at i:2726704 original size:39 final size:39
Alignment explanation
Indices: 2726650--2726724 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
2726640 GGCATGTTCA
2726650 TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAATAT
1 TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAATAT
*
2726689 TTCAAGGTCAACATTTTTACTCTCTTCTCAATTTAA
1 TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAA
2726725 CATTCTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (39 bp):
TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAATAT
Found at i:2735863 original size:20 final size:20
Alignment explanation
Indices: 2735838--2735877 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2735828 CGTAAAATGA
*
2735838 TTTCTGTAAAATGTTTTACT
1 TTTCTGTAAAATGATTTACT
2735858 TTTCTGTAAAATGATTTACT
1 TTTCTGTAAAATGATTTACT
2735878 GAAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53
Consensus pattern (20 bp):
TTTCTGTAAAATGATTTACT
Found at i:2735867 original size:34 final size:35
Alignment explanation
Indices: 2735823--2735889 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
2735813 CAGTAAAATA
* *
2735823 TTTTCCGTAAAATGATTT-CTGTAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
2735857 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
2735890 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:2736108 original size:25 final size:25
Alignment explanation
Indices: 2736080--2736173 Score: 66
Period size: 26 Copynumber: 3.7 Consensus size: 25
2736070 ATATTAATCG
2736080 TTATAAATTGAAAAAAAATACATTC
1 TTATAAATTGAAAAAAAATACATTC
* * * * *
2736105 TTAT-TATT-AAACTACAATATTAATC
1 TTATAAATTGAAA-AAAAATA-CATTC
*
2736130 GTTATAAATTGAAAAAAAATGCATTC
1 -TTATAAATTGAAAAAAAATACATTC
* *
2736156 TTATTAGTTAGAAAAAAA
1 TTATAAATT-GAAAAAAA
2736174 GTGAAGAGAA
Statistics
Matches: 50, Mismatches: 13, Indels: 11
0.68 0.18 0.15
Matches are distributed among these distances:
23 3 0.06
24 8 0.16
25 14 0.28
26 15 0.30
27 7 0.14
28 3 0.06
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.35
Consensus pattern (25 bp):
TTATAAATTGAAAAAAAATACATTC
Found at i:2736117 original size:51 final size:51
Alignment explanation
Indices: 2736056--2736161 Score: 203
Period size: 51 Copynumber: 2.1 Consensus size: 51
2736046 ATAATACTCA
2736056 ATTATTAAACTACAATATTAATCGTTATAAATTGAAAAAAAATACATTCTT
1 ATTATTAAACTACAATATTAATCGTTATAAATTGAAAAAAAATACATTCTT
*
2736107 ATTATTAAACTACAATATTAATCGTTATAAATTGAAAAAAAATGCATTCTT
1 ATTATTAAACTACAATATTAATCGTTATAAATTGAAAAAAAATACATTCTT
2736158 ATTA
1 ATTA
2736162 GTTAGAAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (51 bp):
ATTATTAAACTACAATATTAATCGTTATAAATTGAAAAAAAATACATTCTT
Found at i:2736660 original size:111 final size:111
Alignment explanation
Indices: 2736466--2736687 Score: 444
Period size: 111 Copynumber: 2.0 Consensus size: 111
2736456 TGATGAAGTA
2736466 TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
1 TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
2736531 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
66 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
2736577 TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
1 TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
2736642 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
66 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
2736688 CATGGTATTG
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (111 bp):
TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
Found at i:2746784 original size:68 final size:68
Alignment explanation
Indices: 2746675--2746810 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
2746665 CCTTAAAGTT
2746675 GAAAATTTCAAACCCTTCACTCCTAATTCGATTTCCATTATTAAAGTGAAAAACAAATTTGAAGT
1 GAAAATTTCAAACCCTTCACTCCTAATTCGATTTCCATTATTAAAGTGAAAAACAAATTTGAAGT
2746740 TGC
66 TGC
2746743 GAAAATTTCAAACCCTTCACTCCTAATTCGATTTCCATTATTAAAGTGAAAAACAAATTTGAAGT
1 GAAAATTTCAAACCCTTCACTCCTAATTCGATTTCCATTATTAAAGTGAAAAACAAATTTGAAGT
2746808 TGC
66 TGC
2746811 TCCTGAAATT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (68 bp):
GAAAATTTCAAACCCTTCACTCCTAATTCGATTTCCATTATTAAAGTGAAAAACAAATTTGAAGT
TGC
Found at i:2753408 original size:10 final size:10
Alignment explanation
Indices: 2753395--2753419 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2753385 CAAAATTTTT
2753395 TAAAAAAATA
1 TAAAAAAATA
2753405 TAAAAAAATA
1 TAAAAAAATA
2753415 TAAAA
1 TAAAA
2753420 CTATACAGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:2753539 original size:23 final size:22
Alignment explanation
Indices: 2753498--2753541 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2753488 TACTCAATTA
2753498 AATAAAGAATAATTATTTAAAT
1 AATAAAGAATAATTATTTAAAT
2753520 AATAAA-AATATATATATTTAAA
1 AATAAAGAATA-AT-TATTTAAA
2753542 AGTTGAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AATAAAGAATAATTATTTAAAT
Found at i:2757686 original size:52 final size:53
Alignment explanation
Indices: 2757593--2757742 Score: 187
Period size: 52 Copynumber: 2.8 Consensus size: 53
2757583 CTTACACGGT
* * *
2757593 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTTTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
2757648 TCACATTATACCGATGCCATA-CCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** * *
2757700 TCACATTGCACCGATGCCATAGCCAAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
2757743 GCACACTTAT
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
51 1 0.01
52 46 0.53
53 32 0.37
54 1 0.01
55 6 0.07
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:2757753 original size:52 final size:52
Alignment explanation
Indices: 2757624--2757757 Score: 173
Period size: 52 Copynumber: 2.6 Consensus size: 52
2757614 TATCCCAGAC
* * * * *
2757624 ATGGTTTTATACGGAATCACATTATCACATTATACCGATGCCATACCCAGCT
1 ATGGTCTTAAACGGAGTCACATTATCACATTACACCGATGCCATACCAAGCT
* *
2757676 ATGGTCTTATACGGAGTCACATTATCACATTGCACCGATGCCATAGCCAAGCT
1 ATGGTCTTAAACGGAGTCACATTATCACATTACACCGATGCCATA-CCAAGCT
2757729 ATGGTCTTAAACGG-G-CACACTTATCACAT
1 ATGGTCTTAAACGGAGTCACA-TTATCACAT
2757758 ATTTTTCGTC
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
51 4 0.05
52 51 0.69
53 19 0.26
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (52 bp):
ATGGTCTTAAACGGAGTCACATTATCACATTACACCGATGCCATACCAAGCT
Found at i:2758219 original size:20 final size:20
Alignment explanation
Indices: 2758182--2758220 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2758172 TTGAACTAAT
*
2758182 TTTTATCAATTAACACTTTA
1 TTTTATCAATTAAAACTTTA
2758202 TTTTATC-ATTATAAACTTT
1 TTTTATCAATTA-AAACTTT
2758221 TTCAAAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTATCAATTAAAACTTTA
Found at i:2765158 original size:46 final size:47
Alignment explanation
Indices: 2765073--2765257 Score: 142
Period size: 53 Copynumber: 3.7 Consensus size: 47
2765063 CGCATCACAC
** * *
2765073 ACCGAAGCCATAGCCTTGCCATGGTCTTACACGG-TTCACA-TATCAT
1 ACCGAAGCCATAGCCCAG-CATGGTCTTATACGGAATCACATTATCAT
*
2765119 ACCGAAGCCATATCCCAGACATGGT-TTATACGGAATCACATTATCACATTAT
1 ACCGAAGCCATAGCCCAG-CATGGTCTTATACGGAATCACATTAT--C---AT
* *
2765171 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATT
1 ACCGAAGCCATAGCCCAGC-ATGGTCTTATACGGAATCACATTAT--CA-T
* *
2765222 GCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 --ACCGAAGCCATAGCCCAGC-ATGGTCTTATACGG
2765258 GCACACTTAT
Statistics
Matches: 117, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
45 7 0.06
46 26 0.22
47 3 0.03
49 1 0.01
50 1 0.01
51 2 0.02
52 23 0.20
53 54 0.46
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (47 bp):
ACCGAAGCCATAGCCCAGCATGGTCTTATACGGAATCACATTATCAT
Found at i:2765220 original size:53 final size:53
Alignment explanation
Indices: 2765108--2765272 Score: 212
Period size: 53 Copynumber: 3.1 Consensus size: 53
2765098 CTTACACGGT
* * *
2765108 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGT-TTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAGTCACATTA
2765162 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
** *
2765215 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG-G-CACACTTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACA-TTA
2765267 TCACAT
1 TCACAT
2765273 ATTTTTCGTC
Statistics
Matches: 102, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
51 5 0.05
52 33 0.32
53 58 0.57
54 6 0.06
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
Found at i:2771105 original size:56 final size:56
Alignment explanation
Indices: 2771019--2771194 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
2771009 ACAAGGGATG
*
2771019 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
2771075 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
2771131 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
2771187 ATGGGCAA
1 ATGGGCAA
2771195 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:2772560 original size:40 final size:40
Alignment explanation
Indices: 2772322--2772546 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
2772312 TCGAATGATG
* * * * *
2772322 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAATGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
2772362 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2772402 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2772441 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2772481 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
2772522 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2772547 AACGAGTAGC
Statistics
Matches: 164, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 120 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:2774003 original size:4 final size:4
Alignment explanation
Indices: 2773994--2774034 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
2773984 AGCAAACGTG
2773994 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
2774035 TAGAAAAGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2774751 original size:17 final size:17
Alignment explanation
Indices: 2774711--2774754 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2774701 ATTATGAGCC
*
2774711 TAAAAAAAACTAAATAG
1 TAAAAAATACTAAATAG
* *
2774728 TATAAAAATACTTATTAG
1 TA-AAAAATACTAAATAG
2774746 TAAAAAATA
1 TAAAAAATA
2774755 ATAATATAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (17 bp):
TAAAAAATACTAAATAG
Found at i:2779996 original size:46 final size:46
Alignment explanation
Indices: 2779946--2780121 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
2779936 TGGTTGAGCA
2779946 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2779992 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
2780037 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
2780085 CCCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2780122 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.56
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:2780102 original size:93 final size:93
Alignment explanation
Indices: 2779943--2780114 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
2779933 GGATGGTTGA
* * *
2779943 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
2780008 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
2780036 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
2780101 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
2780115 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2781797 original size:30 final size:29
Alignment explanation
Indices: 2781763--2781819 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
2781753 TTAACTCAAA
2781763 TTTTGGAAAAATTACAATTTTGCCCCTAAC
1 TTTT-GAAAAATTACAATTTTGCCCCTAAC
* * * *
2781793 TTTTGCATATTTACACTTTTGCCCCTA
1 TTTTGAAAAATTACAATTTTGCCCCTA
2781820 GGCTCGGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (29 bp):
TTTTGAAAAATTACAATTTTGCCCCTAAC
Found at i:2782880 original size:135 final size:135
Alignment explanation
Indices: 2782694--2783345 Score: 968
Period size: 135 Copynumber: 4.8 Consensus size: 135
2782684 TTTCAATCCA
* * * * * ** *
2782694 TGGAGATAAGATTCACCGAAATTTGGTCTGC-TCTGCTCCTACTCAGCGAAGATAAGACCTGGTA
1 TGGAGATAAGATTCTCCAAAATTTGATCTGCTTC-ACTCCTGCTCAATGAAGATAAGATCTGGTA
* * * * * **
2782758 TATTTATCCTGCTCCACTCCTACTCAGTGAAGATAAAGCTGATGATTGGAATCTGTTTAATCGCC
65 TATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCCATCGCC
2782823 GGTACG
130 GGTACG
*
2782829 TGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCTTGCTCAATGAAGATAAGATCTGGTAT
1 TGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
* *
2782894 ATTTAGCCTACTCCACTCCTGCTCAGTTGAAGATAAGGTTGATGATTGGAATCTGCTCCATCGCT
66 ATTTAGCCTGCTCCACTCCTGCTCAG-TGAAGATAAGGTTGATGATTGGAATCTGCTCCATCGCC
2782959 GGTACG
130 GGTACG
* *
2782965 TGGAGATAAGATTCTCCAAAAATTCGATCTACTTCACTCCCTGCTCAATGAAGATAAGATCTGGT
1 TGGAGATAAGATTCTCC-AAAATTTGATCTGCTTCACT-CCTGCTCAATGAAGATAAGATCTGGT
*
2783030 ATATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCCATCGT
64 ATATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCCATCGC
2783095 CGGTACG
129 CGGTACG
* * *
2783102 TGGAGACAAGATTCTCCAAAATTCGATCTGCTTCACTCTTGCTCAATGAAGATAAGATCTGGTAT
1 TGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
*
2783167 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCCATCGCTG
66 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCCATCGCCG
2783232 GTACG
131 GTACG
* *
2783237 TAGAGAT-AGATTCTCCAAAACTTGATCTGCTTCACTCCTGCTCAATGAAGATAAGATC-GAGTA
1 TGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTG-GTA
* * *
2783300 TGTTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGAT
65 TATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGAT
2783346 ATCTGTCTTT
Statistics
Matches: 475, Mismatches: 37, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
133 1 0.00
134 94 0.20
135 176 0.37
136 76 0.16
137 76 0.16
138 52 0.11
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (135 bp):
TGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCCATCGCCG
GTACG
Found at i:2782917 original size:45 final size:45
Alignment explanation
Indices: 2782862--2783067 Score: 125
Period size: 45 Copynumber: 4.5 Consensus size: 45
2782852 TGATCTGCTT
*
2782862 CACTCTTGCTCAATGAAGATAAGATCTGGTATATTTAGCCTACTC
1 CACTCCTGCTCAATGAAGATAAGATCTGGTATATTTAGCCTACTC
* * * ** *
2782907 CACTCCTGCTCAGTTGAAGATAAGGT-T-G-ATGATTGGAATCTGCTC
1 CACTCCTGCTCA-ATGAAGATAAGATCTGGTAT-ATT-TAGCCTACTC
* * * *** * * * * *
2782952 CA-TCGCTGGT-ACGTGGAGATAAGATTCTCCAAAAATTCGATCTACTT
1 CACTC-CTGCTCA-ATGAAGATAAGA-TCTGGTATATTTAG-CCTACTC
*
2782999 CACTCCCTGCTCAATGAAGATAAGATCTGGTATATTTAGCCTGCTC
1 CACT-CCTGCTCAATGAAGATAAGATCTGGTATATTTAGCCTACTC
*
2783045 CACTCCTGCTCAGTGAAGATAAG
1 CACTCCTGCTCAATGAAGATAAG
2783068 GTTGATGATT
Statistics
Matches: 116, Mismatches: 33, Indels: 24
0.67 0.19 0.14
Matches are distributed among these distances:
43 2 0.02
44 16 0.14
45 43 0.37
46 20 0.17
47 17 0.15
48 16 0.14
49 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (45 bp):
CACTCCTGCTCAATGAAGATAAGATCTGGTATATTTAGCCTACTC
Found at i:2783135 original size:273 final size:269
Alignment explanation
Indices: 2782741--2783345 Score: 1005
Period size: 273 Copynumber: 2.2 Consensus size: 269
2782731 CCTACTCAGC
* * * *
2782741 GAAGATAAGACCTGGTATATTTATCCTGCTCCACTCCTACTCAGTGAAGATAAAGCTGATGATTG
1 GAAGATAAGATCTGGTATATTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTG
* * * *
2782806 GAATCTGTTTAATCGCCGGTACGTGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCTTGC
66 GAATCTGCTCAATCGCCGGTACGTGGAGACAAGATTCTCCAAAATTCGATCTGCTTCACTCTTGC
2782871 TCAATGAAGATAAGATCTGGTATATTTAGCCTACTCCACTCCTGCTCAGTTGAAGATAAGGTTGA
131 TCAATGAAGATAAGATCTGGTATATTTAGCCTACTCCACTCCTGCTCAG-TGAAGATAAGGTTGA
*
2782936 TGATTGGAATCTGCTCCATCGCTGGTACGTGGAGATAAGATTCTCCAAAAATTCGATCTACTTCA
195 TGATTGGAATCTGCTCCATCGCTGGTACGTAGAGAT-AGATTCTCCAAAAATT-GATCTACTTCA
2783001 CTCCCTGCTCAAT
258 CT-CCTGCTCAAT
* *
2783014 GAAGATAAGATCTGGTATATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTG
1 GAAGATAAGATCTGGTATATTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTG
* *
2783079 GAATCTGCTCCATCGTCGGTACGTGGAGACAAGATTCTCCAAAATTCGATCTGCTTCACTCTTGC
66 GAATCTGCTCAATCGCCGGTACGTGGAGACAAGATTCTCCAAAATTCGATCTGCTTCACTCTTGC
*
2783144 TCAATGAAGATAAGATCTGGTATATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGTTGAT
131 TCAATGAAGATAAGATCTGGTATATTTAGCCTACTCCACTCCTGCTCAGTGAAGATAAGGTTGAT
* *
2783209 GATTGGAATCTGCTCCATCGCTGGTACGTAGAGATAGATTCTCCAAAACTTGATCTGCTTCACTC
196 GATTGGAATCTGCTCCATCGCTGGTACGTAGAGATAGATTCTCCAAAAATTGATCTACTTCACTC
2783274 CTGCTCAAT
261 CTGCTCAAT
*
2783283 GAAGATAAGATC-GAGTATGTTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGAT
1 GAAGATAAGATCTG-GTATATTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGAT
2783346 ATCTGTCTTT
Statistics
Matches: 313, Mismatches: 18, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
268 1 0.00
269 68 0.22
270 12 0.04
271 15 0.05
272 50 0.16
273 167 0.53
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (269 bp):
GAAGATAAGATCTGGTATATTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGATTG
GAATCTGCTCAATCGCCGGTACGTGGAGACAAGATTCTCCAAAATTCGATCTGCTTCACTCTTGC
TCAATGAAGATAAGATCTGGTATATTTAGCCTACTCCACTCCTGCTCAGTGAAGATAAGGTTGAT
GATTGGAATCTGCTCCATCGCTGGTACGTAGAGATAGATTCTCCAAAAATTGATCTACTTCACTC
CTGCTCAAT
Found at i:2798739 original size:52 final size:53
Alignment explanation
Indices: 2798643--2798806 Score: 280
Period size: 52 Copynumber: 3.1 Consensus size: 53
2798633 ACAAGGGATG
*
2798643 ATGGCAAAACAT-TCATGAAACAT-TGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGCAAAACATGTCATGAAACATGT-TGTTAATGGAAGAATAAAATAAGAAGC
2798695 ATGGCAAAACATGTCATGAAACATGTTGTTAATGGAAGAA-AAAATAAGAAGC
1 ATGGCAAAACATGTCATGAAACATGTTGTTAATGGAAGAATAAAATAAGAAGC
*
2798747 AGGGCAAAACATGTCATGAAACATGTTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGCAAAACATGTCATGAAACATGTTGTTAATGGAAGAATAAAATAAGAAGC
2798800 ATGGCAA
1 ATGGCAA
2798807 TAAACTAATA
Statistics
Matches: 106, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
52 63 0.59
53 42 0.40
54 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (53 bp):
ATGGCAAAACATGTCATGAAACATGTTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:2800064 original size:40 final size:40
Alignment explanation
Indices: 2799926--2800146 Score: 251
Period size: 40 Copynumber: 5.7 Consensus size: 40
2799916 TCGAATGATG
* * * * *
2799926 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAATGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
2799966 TCCGGACTAAGAT-CCGAAGGCATTTG-GC-AGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2800004 TCC-GGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2800042 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2800082 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
2800123 -CCGGGCTATGT-CCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2800147 AACGAGTAGC
Statistics
Matches: 158, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
36 12 0.08
37 8 0.05
38 18 0.11
39 19 0.12
40 94 0.59
41 7 0.04
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Done.