Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 101 of 313
Found at i:33504164 original size:3 final size:3
Alignment explanation
Indices: 33504156--33504215 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
33504146 ATTCCCACTC
* *
33504156 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
33504204 CTA ATA TTA ATA
1 ATA ATA ATA ATA
33504216 CTTACCTCAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:33504978 original size:3 final size:3
Alignment explanation
Indices: 33504970--33504995 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
33504960 ATTCATTAGT
33504970 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
33504996 TATTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:33505145 original size:17 final size:17
Alignment explanation
Indices: 33505123--33505157 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
33505113 TATTTAAAAT
*
33505123 ATAATACTAATTTAATA
1 ATAATAATAATTTAATA
33505140 ATAATAATAATTTAATA
1 ATAATAATAATTTAATA
33505157 A
1 A
33505158 CATTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAATAATAATTTAATA
Found at i:33505550 original size:5 final size:5
Alignment explanation
Indices: 33505542--33505570 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
33505532 ATTTATTTTA
33505542 ATTTG ATTTG ATTTG ATTTG ATTTG ATTT
1 ATTTG ATTTG ATTTG ATTTG ATTTG ATTT
33505571 TTCTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.17, T:0.62
Consensus pattern (5 bp):
ATTTG
Found at i:33509635 original size:24 final size:24
Alignment explanation
Indices: 33509604--33509690 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 24
33509594 CATTTAATTT
*
33509604 TTATTAATTATAAAAAAATTAAAA
1 TTATTAATTATAAAAAAATTATAA
* **
33509628 TTATTAATTAT-TAATTATTATAA
1 TTATTAATTATAAAAAAATTATAA
* *
33509651 -TATTTA-TATATAAAAAATTATAT
1 TTATTAATTATA-AAAAAATTATAA
33509674 TTATTTAATTATAAAAA
1 TTA-TTAATTATAAAAA
33509691 TTTGGATTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
21 3 0.06
22 5 0.10
23 16 0.33
24 13 0.27
25 7 0.15
26 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATTAATTATAAAAAAATTATAA
Found at i:33510743 original size:17 final size:17
Alignment explanation
Indices: 33510717--33510752 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
33510707 ATAGAACTAA
33510717 ATAAAAATAAATAAAAT
1 ATAAAAATAAATAAAAT
*
33510734 ATAAATATAAATAAAAT
1 ATAAAAATAAATAAAAT
33510751 AT
1 AT
33510753 GATATGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAATAAATAAAAT
Found at i:33511797 original size:50 final size:48
Alignment explanation
Indices: 33511700--33511798 Score: 110
Period size: 50 Copynumber: 2.0 Consensus size: 48
33511690 TCAAAATTGT
* *
33511700 TTTTTTTTATTCTTTGTTTTTTTATTTTCAATATTCTCTTCAATACAATC
1 TTTTTTTGATTCTTAGTTTTTTTATTTTCAATATTCTCTT--ATACAATC
* *
33511750 TTTTTTTGATTCTTAGTTTTTGTTTTTTCTTCAATATTTTCTT-TACAAT
1 TTTTTTTGATTCTTAG-TTTT-TTTATT-TTCAATATTCTCTTATACAAT
33511799 ATTTGTCTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
50 20 0.48
51 4 0.10
52 5 0.12
53 13 0.31
ACGTcount: A:0.18, C:0.12, G:0.04, T:0.66
Consensus pattern (48 bp):
TTTTTTTGATTCTTAGTTTTTTTATTTTCAATATTCTCTTATACAATC
Found at i:33513671 original size:18 final size:18
Alignment explanation
Indices: 33513648--33513688 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
33513638 ATTAGCTCCC
33513648 TCCAAGATTCC-TCCAAAA
1 TCCAAGATTCCAT-CAAAA
33513666 TCCAAGATTCCATCAAAA
1 TCCAAGATTCCATCAAAA
33513684 TCCAA
1 TCCAA
33513689 CACATAGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22
Consensus pattern (18 bp):
TCCAAGATTCCATCAAAA
Found at i:33516549 original size:19 final size:21
Alignment explanation
Indices: 33516510--33516549 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
33516500 TAAAATATAA
33516510 TTAATATATTTTATATGAAAT
1 TTAATATATTTTATATGAAAT
33516531 TTAA-ATATTTTAT-TGAAAT
1 TTAATATATTTTATATGAAAT
33516550 AATATCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTAATATATTTTATATGAAAT
Found at i:33518044 original size:18 final size:18
Alignment explanation
Indices: 33517981--33518045 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
33517971 ATTTAATTTT
33517981 TTAAATAAATTTTAAAAAA
1 TTAAATAAATTTT-AAAAA
* *
33518000 TAAAAAAAATATTTAAAAA
1 TTAAATAAAT-TTTAAAAA
* **
33518019 GTACTTAAATTTTAAAAA
1 TTAAATAAATTTTAAAAA
*
33518037 TTAATTAAA
1 TTAAATAAA
33518046 CGTTGATATG
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
18 15 0.42
19 18 0.50
20 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (18 bp):
TTAAATAAATTTTAAAAA
Found at i:33527218 original size:31 final size:30
Alignment explanation
Indices: 33527183--33527242 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
33527173 AGAGGTGGGA
*
33527183 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
33527214 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
33527243 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:33527471 original size:9 final size:9
Alignment explanation
Indices: 33527457--33527493 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
33527447 TATAGTTTGA
33527457 TATTCGAAT
1 TATTCGAAT
33527466 TATTCGAAT
1 TATTCGAAT
*
33527475 TATTCGAGT
1 TATTCGAAT
33527484 TATTCGAAT
1 TATTCGAAT
33527493 T
1 T
33527494 CAAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:33527564 original size:9 final size:9
Alignment explanation
Indices: 33527547--33527577 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
33527537 TCGAGTTGAT
33527547 TCGAATAAC
1 TCGAATAAC
*
33527556 TCGATTAAC
1 TCGAATAAC
33527565 TCGAATAAC
1 TCGAATAAC
33527574 TCGA
1 TCGA
33527578 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:33528737 original size:17 final size:17
Alignment explanation
Indices: 33528715--33528749 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
33528705 AATGGCATAG
33528715 AAATAATAT-AAACAAAT
1 AAATAA-ATGAAACAAAT
33528732 AAATAAATGAAACAAAT
1 AAATAAATGAAACAAAT
33528749 A
1 A
33528750 TACATAAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (17 bp):
AAATAAATGAAACAAAT
Found at i:33529140 original size:30 final size:30
Alignment explanation
Indices: 33529104--33529174 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
33529094 GAATATTCAT
33529104 TAAAAATAAATATATGTATACATGCACATA
1 TAAAAATAAATATATGTATACATGCACATA
33529134 TAAAAATAAATATATGTATACATGCACATA
1 TAAAAATAAATATATGTATACATGCACATA
33529164 T-AAAATAAATA
1 TAAAAATAAATA
33529175 CGCATTTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 10 0.24
30 31 0.76
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.30
Consensus pattern (30 bp):
TAAAAATAAATATATGTATACATGCACATA
Found at i:33529575 original size:19 final size:19
Alignment explanation
Indices: 33529548--33529586 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
33529538 TGTGCAATTG
* *
33529548 TATATATGAACTTTGATTT
1 TATACATGAAATTTGATTT
*
33529567 TATACATGAAATTTTATTT
1 TATACATGAAATTTGATTT
33529586 T
1 T
33529587 GATCAAATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (19 bp):
TATACATGAAATTTGATTT
Found at i:33530240 original size:27 final size:27
Alignment explanation
Indices: 33530210--33530272 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
33530200 CCACCTTGGC
* *
33530210 GGTGCCAAAGAGATTGGTGGCACCAAT
1 GGTGCCAAAGAGATTAGCGGCACCAAT
*
33530237 GGTGCCAAAGTGATTAGCGGCACCAAT
1 GGTGCCAAAGAGATTAGCGGCACCAAT
*
33530264 GGTGTCAAA
1 GGTGCCAAA
33530273 AGACTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.30, C:0.19, G:0.32, T:0.19
Consensus pattern (27 bp):
GGTGCCAAAGAGATTAGCGGCACCAAT
Found at i:33530382 original size:18 final size:19
Alignment explanation
Indices: 33530345--33530383 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33530335 TTAACTCATT
* *
33530345 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACACTA
33530364 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACACTA
33530382 TT
1 TT
33530384 ACCATTTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATTTAATAACACTA
Found at i:33530575 original size:18 final size:19
Alignment explanation
Indices: 33530538--33530607 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
33530528 TCAACTCATT
*
33530538 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
33530557 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
33530575 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
33530594 TTTTAATTTAATAA
1 TTTTAATTTAATAA
33530608 TATATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:33530860 original size:18 final size:19
Alignment explanation
Indices: 33530823--33530861 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
33530813 TTCAACTCAT
*
33530823 TTTTTATTTAATAAATCTA
1 TTTTAATTTAATAAATCTA
33530842 TTTTAATTTAATAAA-CTA
1 TTTTAATTTAATAAATCTA
33530860 TT
1 TT
33530862 CTCATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATTTAATAAATCTA
Found at i:33530868 original size:18 final size:19
Alignment explanation
Indices: 33530828--33530870 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
33530818 CTCATTTTTT
*
33530828 ATTTAATAAATCTATTTTA
1 ATTTAATAAATCTATTCTA
*
33530847 ATTTAATAAA-CTATTCTC
1 ATTTAATAAATCTATTCTA
33530865 ATTTAA
1 ATTTAA
33530871 ATTAAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAATAAATCTATTCTA
Found at i:33537037 original size:24 final size:24
Alignment explanation
Indices: 33537010--33537070 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
33537000 TGTATTTGTT
33537010 TATTTTTTAATTTACTAA-ATA-ATA
1 TATTTTTTAATTT--TAATATATATA
33537034 TATTTTTATAATTTTAATATATATA
1 TATTTTT-TAATTTTAATATATATA
*
33537059 AATTTTTTAATT
1 TATTTTTTAATT
33537071 AAATGACAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.09
24 15 0.45
25 15 0.45
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTTTTAATTTTAATATATATA
Found at i:33537063 original size:25 final size:23
Alignment explanation
Indices: 33537011--33537070 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 23
33537001 GTATTTGTTT
*
33537011 ATTTTTTAATTTACTAAATAATAT
1 ATTTTTTAATTTA-TAAATAATAA
33537035 ATTTTTATAATTT-TAATATATATAA
1 ATTTTT-TAATTTATAA-ATA-ATAA
33537060 ATTTTTTAATT
1 ATTTTTTAATT
33537071 AAATGACAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.09
24 14 0.44
25 15 0.47
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTTTTAATTTATAAATAATAA
Found at i:33537318 original size:22 final size:22
Alignment explanation
Indices: 33537288--33537330 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
33537278 ACACCAAAAC
* *
33537288 AGGCTTTTAGCAGTGCTTTTTT
1 AGGCCTTTAGCAGCGCTTTTTT
*
33537310 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCAGCGCTTTTT
33537331 AGCGCGGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCAGCGCTTTTTT
Found at i:33537478 original size:43 final size:43
Alignment explanation
Indices: 33537424--33537564 Score: 151
Period size: 43 Copynumber: 3.3 Consensus size: 43
33537414 TTATTTCTAA
* * * *
33537424 AAACGCCGCTAAAGGTTATGGTCTTTAGCGGCGCTTACGAAAC
1 AAACGCCGCTAAAGGTCATGGACTTTAACGGCGCTTACCAAAC
*
33537467 AAACGCTGCTAAAGGTCATGGACTTTAACGGCGCTTACCAAAC
1 AAACGCCGCTAAAGGTCATGGACTTTAACGGCGCTTACCAAAC
* * ** * **
33537510 AAATGCCGCTAAA-GACAACGACCTTTAGCGGCGCTT-CCTTAC
1 AAACGCCGCTAAAGGTCATGGA-CTTTAACGGCGCTTACCAAAC
33537552 AAACGCCGCTAAA
1 AAACGCCGCTAAA
33537565 TACCCTGATC
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
42 21 0.25
43 62 0.75
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGGACTTTAACGGCGCTTACCAAAC
Found at i:33537621 original size:43 final size:44
Alignment explanation
Indices: 33537402--33537632 Score: 143
Period size: 43 Copynumber: 5.4 Consensus size: 44
33537392 GCGTCGCTAA
* * * *** **
33537402 CTTTAGCGGCGTTTATTTC-TAAAAACGCCGCTAAAGGTTATGGT
1 CTTTAGCGGCGCTT-TTCCATACAAACGCCGCTAAAGACCATGAC
* * * * **
33537446 CTTTAGCGGCGC-TTACGAAACAAACGCTGCTAAAGGTCATGGA-
1 CTTTAGCGGCGCTTTTCCATACAAACGCCGCTAAAGACCAT-GAC
* * * * * *
33537489 CTTTAACGGCGC-TTACCAAACAAATGCCGCTAAAGACAACGAC
1 CTTTAGCGGCGCTTTTCCATACAAACGCCGCTAAAGACCATGAC
* * * *
33537532 CTTTAGCGGCGC--TTCCTTACAAACGCCGCTAAATACCCTGAT
1 CTTTAGCGGCGCTTTTCCATACAAACGCCGCTAAAGACCATGAC
* *
33537574 CTTTAGCGGCGCTTTTGCATA-AAACGCCGCTAAAGACCATTAC
1 CTTTAGCGGCGCTTTTCCATACAAACGCCGCTAAAGACCATGAC
* *
33537617 CTTTAACGGCGTTTTT
1 CTTTAGCGGCGCTTTT
33537633 TTAAAAACGC
Statistics
Matches: 147, Mismatches: 35, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
42 36 0.24
43 94 0.64
44 17 0.12
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (44 bp):
CTTTAGCGGCGCTTTTCCATACAAACGCCGCTAAAGACCATGAC
Found at i:33537971 original size:21 final size:21
Alignment explanation
Indices: 33537945--33537994 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
33537935 TTTTACGCTG
33537945 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
33537966 CTCTGCTTCTCTCGTTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
33537987 ATCTGCTT
1 CTCTGCTT
33537995 TAAGCTACTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.04, C:0.42, G:0.18, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:33538076 original size:66 final size:64
Alignment explanation
Indices: 33537965--33538131 Score: 199
Period size: 66 Copynumber: 2.6 Consensus size: 64
33537955 CTCGCTGCAG
* * * *
33537965 CCTCTGCTTCTCTCGTTGCCGCATCTGCTTTAAGCTACTGCTGGAGTTCTTCATACTTTCGTTGA
1 CCTCAGCTTCTCTCGATGCTGCATCTGCTTTAAG-TTCTGCTGGAGTTCTTCAT-CTTTCGTTGA
33538030 A
64 A
* * * **
33538031 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATTTTTTTTTGAA
1 CCTCAGCTTCTCTCGATGCTGCATCTGCTTTAAGTTCT-GCTGGAGTTCTTCATCTTTCGTTGAA
* * *
33538096 CCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTT
1 CCTCAGCTTCTCTCGATGCTGCATCTGCTTTAAGTT
33538132 TTGTAATTTG
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
65 42 0.48
66 46 0.52
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.41
Consensus pattern (64 bp):
CCTCAGCTTCTCTCGATGCTGCATCTGCTTTAAGTTCTGCTGGAGTTCTTCATCTTTCGTTGAA
Found at i:33540468 original size:187 final size:187
Alignment explanation
Indices: 33540153--33540526 Score: 748
Period size: 187 Copynumber: 2.0 Consensus size: 187
33540143 ATACATTCCT
33540153 TTGCCAAGTAGCTTTCAGCAATCGATCCTTCTGGATAACGCTTGTTGCGGCAGTAAGACTTTAAT
1 TTGCCAAGTAGCTTTCAGCAATCGATCCTTCTGGATAACGCTTGTTGCGGCAGTAAGACTTTAAT
33540218 TTGGATAGGAACCTAAACACGATATGCAACATTATAAAAAGTTGTACTTAAAGGCATAAATGGAA
66 TTGGATAGGAACCTAAACACGATATGCAACATTATAAAAAGTTGTACTTAAAGGCATAAATGGAA
33540283 TGGAATGAAGGAAAATTTTAAAAATAAAATAACACCTTTCTATGGGATACATCCATC
131 TGGAATGAAGGAAAATTTTAAAAATAAAATAACACCTTTCTATGGGATACATCCATC
33540340 TTGCCAAGTAGCTTTCAGCAATCGATCCTTCTGGATAACGCTTGTTGCGGCAGTAAGACTTTAAT
1 TTGCCAAGTAGCTTTCAGCAATCGATCCTTCTGGATAACGCTTGTTGCGGCAGTAAGACTTTAAT
33540405 TTGGATAGGAACCTAAACACGATATGCAACATTATAAAAAGTTGTACTTAAAGGCATAAATGGAA
66 TTGGATAGGAACCTAAACACGATATGCAACATTATAAAAAGTTGTACTTAAAGGCATAAATGGAA
33540470 TGGAATGAAGGAAAATTTTAAAAATAAAATAACACCTTTCTATGGGATACATCCATC
131 TGGAATGAAGGAAAATTTTAAAAATAAAATAACACCTTTCTATGGGATACATCCATC
33540527 GGTAGAAAAC
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
187 187 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (187 bp):
TTGCCAAGTAGCTTTCAGCAATCGATCCTTCTGGATAACGCTTGTTGCGGCAGTAAGACTTTAAT
TTGGATAGGAACCTAAACACGATATGCAACATTATAAAAAGTTGTACTTAAAGGCATAAATGGAA
TGGAATGAAGGAAAATTTTAAAAATAAAATAACACCTTTCTATGGGATACATCCATC
Found at i:33543020 original size:15 final size:16
Alignment explanation
Indices: 33542977--33543026 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
33542967 TTATTATGTC
*
33542977 GTATTATGTAAGTTAT
1 GTATTATATAAGTTAT
33542993 GTATTATATAAGTTAT
1 GTATTATATAAGTTAT
33543009 GTATTA-ATAAGTTAT
1 GTATTATATAAGTTAT
33543024 GTA
1 GTA
33543027 AGTTATGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 12 0.36
16 21 0.64
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (16 bp):
GTATTATATAAGTTAT
Found at i:33543033 original size:9 final size:9
Alignment explanation
Indices: 33542980--33543035 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
33542970 TTATGTCGTA
33542980 TTATGTAAG
1 TTATGTAAG
33542989 TTATGT-A-
1 TTATGTAAG
*
33542996 TTATATAAG
1 TTATGTAAG
33543005 TTATGT-A-
1 TTATGTAAG
*
33543012 TTA-ATAAG
1 TTATGTAAG
33543020 TTATGTAAG
1 TTATGTAAG
33543029 TTATGTA
1 TTATGTA
33543036 TCATTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 1 0.03
7 9 0.24
8 6 0.16
9 22 0.58
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:33543069 original size:43 final size:40
Alignment explanation
Indices: 33542980--33543086 Score: 121
Period size: 43 Copynumber: 2.6 Consensus size: 40
33542970 TTATGTCGTA
* * *
33542980 TTATGTAAGTTATGTATTATATAAGTTATGTATTAATAAG
1 TTATGTAAGTTATGTATCATATAAATTATATATTAATAAG
*
33543020 TTATGTAAGTTATGTATCATTTTAAAATATATATATTAATAAG
1 TTATGTAAGTTATGTATCA-TAT-AAAT-TATATATTAATAAG
33543063 TTATGTAA-TGTATGTAT--TATAAAT
1 TTATGTAAGT-TATGTATCATATAAAT
33543087 GGGTAATTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
39 4 0.07
40 20 0.34
41 2 0.03
42 4 0.07
43 28 0.48
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.48
Consensus pattern (40 bp):
TTATGTAAGTTATGTATCATATAAATTATATATTAATAAG
Found at i:33543711 original size:15 final size:15
Alignment explanation
Indices: 33543683--33543718 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
33543673 TTAATAAAAG
*
33543683 GAAAA-AGTAGAAAT
1 GAAAACAGTACAAAT
33543697 GAAAACAGTACAAAT
1 GAAAACAGTACAAAT
33543712 GAAAACA
1 GAAAACA
33543719 AATTGGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (15 bp):
GAAAACAGTACAAAT
Found at i:33546292 original size:7 final size:7
Alignment explanation
Indices: 33546280--33546305 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
33546270 TCAATAAGGC
33546280 TAAACCA
1 TAAACCA
33546287 TAAACCA
1 TAAACCA
33546294 TAAACCA
1 TAAACCA
33546301 TAAAC
1 TAAAC
33546306 ATCAAGCCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCA
Found at i:33548084 original size:41 final size:41
Alignment explanation
Indices: 33548019--33548130 Score: 111
Period size: 41 Copynumber: 2.7 Consensus size: 41
33548009 GATTTTATTA
* * *
33548019 TTAGCGGCGTTTCTCAGAAAGCGCCACTAATGCTCCGGTCT
1 TTAGCGGCGTTTCTAAGAAAGCGCCACTAATGCTCAGGTAT
* *
33548060 TTAGCGGCGTTTTCTAAG-ATGCGCCGCTAATGCTCAGGTAT
1 TTAGCGGCG-TTTCTAAGAAAGCGCCACTAATGCTCAGGTAT
* * * *
33548101 TTACCAGCGCTTTTTAAGAAA-CGCCGCTAA
1 TTAGCGGCG-TTTCTAAGAAAGCGCCACTAA
33548131 AGACCGAAGC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 51 0.86
42 8 0.14
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (41 bp):
TTAGCGGCGTTTCTAAGAAAGCGCCACTAATGCTCAGGTAT
Found at i:33548152 original size:41 final size:40
Alignment explanation
Indices: 33548107--33548338 Score: 218
Period size: 41 Copynumber: 5.7 Consensus size: 40
33548097 GTATTTACCA
33548107 GCGCTTTTTAAGAAACGCCGCTAAAGACCGAAGCATTAGCG
1 GCGCTTTTTAAGAAACGCCGCTAAAGACCG-AGCATTAGCG
* * * **
33548148 GCGCTTTCTGAGAAACGCCGATAAAGATTGTAGCATTAGCG
1 GCGCTTTTTAAGAAACGCCGCTAAAGACCG-AGCATTAGCG
* * *
33548189 GCGCTTTGTAAAAAATGCCGCTAAAGACCTGAGCATTAGCG
1 GCGCTTTTTAAGAAACGCCGCTAAAGACC-GAGCATTAGCG
* * * * *
33548230 ACGCCTCTTACA-AAGCGCCGCTAAAGGCCTGAGCATTAGCG
1 GCGCTTTTTA-AGAAACGCCGCTAAAGACC-GAGCATTAGCG
* *
33548271 GCGCATCTT-AGAAAACGCCGCTAAAGACCGCAGCATTAGCG
1 GCGCTTTTTAAG-AAACGCCGCTAAAGACCG-AGCATTAGCG
* *
33548312 GCGATTATTCAAG-AACGCCGCTAAAGA
1 GCGCTT-TTTAAGAAACGCCGCTAAAGA
33548339 TAGGAGAATT
Statistics
Matches: 156, Mismatches: 28, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 149 0.96
42 3 0.02
43 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (40 bp):
GCGCTTTTTAAGAAACGCCGCTAAAGACCGAGCATTAGCG
Found at i:33548370 original size:123 final size:123
Alignment explanation
Indices: 33548122--33548352 Score: 279
Period size: 123 Copynumber: 1.9 Consensus size: 123
33548112 TTTTAAGAAA
* * ** *
33548122 CGCCGCTAAAGACCGAAGCATTAGCGGCGCTTTCTGAGAAACGCCGATAAAGATTGTAGCATTAG
1 CGCCGCTAAAGGCCGAAGCATTAGCGGCGCTATCTGAGAAACGCCGATAAAGACCGCAGCATTAG
* * ** *
33548187 CGGCGCTTTGTAAAAAATGCCGCTAAAGACCTGAGCATTAGCGACGCCTCTTACAAAG
66 CGGCGATTTGTAAAAAACGCCGCTAAAGACAGGAGAATTAGCGACGCCTCTTACAAAG
* *
33548245 CGCCGCTAAAGGCCTG-AGCATTAGCGGCGC-ATCTTAGAAAACGCCGCTAAAGACCGCAGCATT
1 CGCCGCTAAAGGCC-GAAGCATTAGCGGCGCTATCTGAG-AAACGCCGATAAAGACCGCAGCATT
* * *
33548308 AGCGGCGATTAT-TCAAGAACGCCGCTAAAGATAGGAGAATTAGCG
64 AGCGGCGATT-TGTAAAAAACGCCGCTAAAGACAGGAGAATTAGCG
33548353 GCGTGTTTTG
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
122 5 0.06
123 83 0.92
124 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.19
Consensus pattern (123 bp):
CGCCGCTAAAGGCCGAAGCATTAGCGGCGCTATCTGAGAAACGCCGATAAAGACCGCAGCATTAG
CGGCGATTTGTAAAAAACGCCGCTAAAGACAGGAGAATTAGCGACGCCTCTTACAAAG
Found at i:33548624 original size:39 final size:39
Alignment explanation
Indices: 33548570--33548648 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
33548560 CCTAACAGAT
33548570 TAGCAGCAGGTCAGCAGCCGAACCATCCAGGCGCTACCA
1 TAGCAGCAGGTCAGCAGCCGAACCATCCAGGCGCTACCA
*
33548609 TAGCAGCAGGTCAGCAGCTGAACCATCCAGGCGCTACCA
1 TAGCAGCAGGTCAGCAGCCGAACCATCCAGGCGCTACCA
33548648 T
1 T
33548649 CGCCCCCACG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.34, G:0.25, T:0.13
Consensus pattern (39 bp):
TAGCAGCAGGTCAGCAGCCGAACCATCCAGGCGCTACCA
Found at i:33549502 original size:14 final size:13
Alignment explanation
Indices: 33549475--33549512 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
33549465 TTATTTTTGT
33549475 TATTATATTA-TA
1 TATTATATTATTA
33549487 TATTACTATTATTA
1 TATTA-TATTATTA
33549501 TATTATTATTAT
1 TATTA-TATTAT
33549513 ACTTATACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 5 0.22
13 5 0.22
14 13 0.57
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTATATTATTA
Found at i:33549682 original size:26 final size:26
Alignment explanation
Indices: 33549646--33549709 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
33549636 TTATATATAG
*
33549646 TTTAT-ATACATATATACATTTACAT
1 TTTATAATACATATACACATTTACAT
** *
33549671 TTTATAATACATATACATTTTTCCAT
1 TTTATAATACATATACACATTTACAT
*
33549697 TTTATAATTCATA
1 TTTATAATACATA
33549710 CATATTTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 5 0.15
26 28 0.85
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTATAATACATATACACATTTACAT
Found at i:33549716 original size:26 final size:26
Alignment explanation
Indices: 33549668--33549717 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
33549658 TATACATTTA
*
33549668 CATTTTATAATACATATACATTTTTC
1 CATTTTATAATACATACACATTTTTC
* *
33549694 CATTTTATAATTCATACATATTTT
1 CATTTTATAATACATACACATTTT
33549718 CACATACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (26 bp):
CATTTTATAATACATACACATTTTTC
Found at i:33549852 original size:14 final size:14
Alignment explanation
Indices: 33549833--33549865 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
33549823 ATCTTATTTT
33549833 CATATATATACATA
1 CATATATATACATA
33549847 CATATATATACATA
1 CATATATATACATA
33549861 CATAT
1 CATAT
33549866 TTTCTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (14 bp):
CATATATATACATA
Found at i:33550777 original size:39 final size:40
Alignment explanation
Indices: 33550733--33550825 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 40
33550723 GGTTTCGACA
* * ** *
33550733 GCCGCTAATGCT-TTTTTTTAGCGGCGTTTTACATATAGC
1 GCCGCTAATGCTCTATCTTTAGCAACGTTTTACATAAAGC
* *
33550772 GCCGCTAATGCTCGTATCTTTGGCAACGTTTTACGTAAAGC
1 GCCGCTAATGCTC-TATCTTTAGCAACGTTTTACATAAAGC
33550813 GCCGCTAATGCTC
1 GCCGCTAATGCTC
33550826 AATTTTTTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 12 0.27
41 33 0.73
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (40 bp):
GCCGCTAATGCTCTATCTTTAGCAACGTTTTACATAAAGC
Found at i:33553529 original size:34 final size:34
Alignment explanation
Indices: 33553486--33553553 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
33553476 GCATTTTTGA
* *
33553486 CACTGTACTGAGATGGGCTAAGGCCCAA-ACTGT
1 CACTGTACTGAAAAGGGCTAAGGCCCAAGACTGT
*
33553519 CACTGATACTGAAAAGGGCTTAGGCCCAAGACTGT
1 CACTG-TACTGAAAAGGGCTAAGGCCCAAGACTGT
33553554 TCAACTGTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (34 bp):
CACTGTACTGAAAAGGGCTAAGGCCCAAGACTGT
Found at i:33554517 original size:126 final size:126
Alignment explanation
Indices: 33554340--33554568 Score: 372
Period size: 126 Copynumber: 1.8 Consensus size: 126
33554330 AGCTAATAAG
*
33554340 TAGACTTGCCGACATACGCTTTGGTCAACTCTTTGTATAAGGTTTGAGATATGCATGCCTAAGGC
1 TAGACTTGCCGACATACGCTTTGGCCAACTCTTTGTATAAGGTTTGAGATATGCATGCCTAAGGC
* *
33554405 AACACTTAAATAAGATTCGAG-TTTGTCCAACACTATGCTGACACTTTCCTAAGTGTTAGGA
66 AACACTTAAATAAGAATC-AGTTTTATCCAACACTATGCTGACACTTTCCTAAGTGTTAGGA
* *
33554466 TAGACTTGTCGACATACGCTTTGGCCAACTCTTTGTATAAAGG-TTGGGATATGCATGCCTAAGG
1 TAGACTTGCCGACATACGCTTTGGCCAACTCTTTGTAT-AAGGTTTGAGATATGCATGCCTAAGG
*
33554530 CAACGCTTAAATAAGAATCAGTTTTATCCAACACTATGC
65 CAACACTTAAATAAGAATCAGTTTTATCCAACACTATGC
33554569 CGACTTTTGT
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
125 2 0.02
126 89 0.94
127 4 0.04
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (126 bp):
TAGACTTGCCGACATACGCTTTGGCCAACTCTTTGTATAAGGTTTGAGATATGCATGCCTAAGGC
AACACTTAAATAAGAATCAGTTTTATCCAACACTATGCTGACACTTTCCTAAGTGTTAGGA
Found at i:33557264 original size:28 final size:28
Alignment explanation
Indices: 33557233--33557290 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
33557223 TTTTGTTCAT
33557233 TTTAAAAAATTAAA-ATATATTTATATCA
1 TTTAAAAAATTAAAGA-ATATTTATATCA
** *
33557261 TTTAAAACTTTAAAGACTATTTATATCA
1 TTTAAAAAATTAAAGAATATTTATATCA
33557289 TT
1 TT
33557291 CATGTTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (28 bp):
TTTAAAAAATTAAAGAATATTTATATCA
Found at i:33561308 original size:16 final size:17
Alignment explanation
Indices: 33561278--33561311 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
33561268 TTAGGTCATA
*
33561278 TTTAAATTTATAAAAAT
1 TTTAAATTTAAAAAAAT
33561295 TTTAAA-TTAAAAAAAT
1 TTTAAATTTAAAAAAAT
33561311 T
1 T
33561312 AATAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAAAAAT
Found at i:33564647 original size:16 final size:17
Alignment explanation
Indices: 33564621--33564654 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
33564611 TTTGTTATTT
*
33564621 ATATCATATTTTTATAA
1 ATATCATATTTATATAA
33564638 ATAT-ATATTTATATAA
1 ATATCATATTTATATAA
33564654 A
1 A
33564655 ATTTCACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATCATATTTATATAA
Found at i:33584276 original size:108 final size:108
Alignment explanation
Indices: 33584146--33584359 Score: 401
Period size: 108 Copynumber: 2.0 Consensus size: 108
33584136 ATATCTAATT
33584146 TGTGTTTCTCTTGTGTCTAGATTCGGGTTTCCGCATCAGTTGGTATCAGTTTCAGGCCATTCGGT
1 TGTGTTTCTCTTGTGTCTAGATTCGGGTTTCCGCATCAGTTGGTATCAGTTTCAGGCCATTCGGT
*
33584211 GTTATTTTTGAAGCTAAAATCAAATCCGAAACGAGTCAAAATA
66 GTTATTTTTGAAGCTAAAATCAAATCCGAAACGAGTAAAAATA
33584254 TGTGTTTCTCTTGTGTCTAGATTCGGGTTTCCGCATCAGTTGGTATCAGTTTCAGGCCATTCGGT
1 TGTGTTTCTCTTGTGTCTAGATTCGGGTTTCCGCATCAGTTGGTATCAGTTTCAGGCCATTCGGT
* *
33584319 GTTATTTTTGAAGCTAAAGTCATATCCGAAACGAGTAAAAA
66 GTTATTTTTGAAGCTAAAATCAAATCCGAAACGAGTAAAAA
33584360 AAACAGCAAA
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 103 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (108 bp):
TGTGTTTCTCTTGTGTCTAGATTCGGGTTTCCGCATCAGTTGGTATCAGTTTCAGGCCATTCGGT
GTTATTTTTGAAGCTAAAATCAAATCCGAAACGAGTAAAAATA
Found at i:33584382 original size:12 final size:13
Alignment explanation
Indices: 33584367--33584396 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
33584357 AAAAAACAGC
*
33584367 AAAAAGCGCAAAA
1 AAAAACCGCAAAA
33584380 AAAAACCGCAAAA
1 AAAAACCGCAAAA
33584393 AAAA
1 AAAA
33584397 TTTGCCTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.17, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAACCGCAAAA
Found at i:33589843 original size:285 final size:285
Alignment explanation
Indices: 33589333--33589902 Score: 1140
Period size: 285 Copynumber: 2.0 Consensus size: 285
33589323 TTAGGGTTCA
33589333 ATTACTCTTGTATTTTGCCTATAAATAGGCTTGCTTTCTATACATTGGGGCACATAAGAAAAAAG
1 ATTACTCTTGTATTTTGCCTATAAATAGGCTTGCTTTCTATACATTGGGGCACATAAGAAAAAAG
33589398 AGTATTGGTTTTCTTCCAAATTTGTGTGAGGCAATTTTTTTAGAGTAGAGTGATTCTTCTCTTGC
66 AGTATTGGTTTTCTTCCAAATTTGTGTGAGGCAATTTTTTTAGAGTAGAGTGATTCTTCTCTTGC
33589463 TATTTAGTTTGAAGTTTGTTACTTCGAGGGTTTTTCGGAGTTACAAATATTCAAATTTCCTTCCC
131 TATTTAGTTTGAAGTTTGTTACTTCGAGGGTTTTTCGGAGTTACAAATATTCAAATTTCCTTCCC
33589528 GTTCATCGGTGTTTCTAGAGGTTCTTCTTCTAGGGGTTTCGTAGGGAGCCGCTCAATCATTGGCG
196 GTTCATCGGTGTTTCTAGAGGTTCTTCTTCTAGGGGTTTCGTAGGGAGCCGCTCAATCATTGGCG
33589593 TTTTTGGTTGCAAGTTAACCAAGGG
261 TTTTTGGTTGCAAGTTAACCAAGGG
33589618 ATTACTCTTGTATTTTGCCTATAAATAGGCTTGCTTTCTATACATTGGGGCACATAAGAAAAAAG
1 ATTACTCTTGTATTTTGCCTATAAATAGGCTTGCTTTCTATACATTGGGGCACATAAGAAAAAAG
33589683 AGTATTGGTTTTCTTCCAAATTTGTGTGAGGCAATTTTTTTAGAGTAGAGTGATTCTTCTCTTGC
66 AGTATTGGTTTTCTTCCAAATTTGTGTGAGGCAATTTTTTTAGAGTAGAGTGATTCTTCTCTTGC
33589748 TATTTAGTTTGAAGTTTGTTACTTCGAGGGTTTTTCGGAGTTACAAATATTCAAATTTCCTTCCC
131 TATTTAGTTTGAAGTTTGTTACTTCGAGGGTTTTTCGGAGTTACAAATATTCAAATTTCCTTCCC
33589813 GTTCATCGGTGTTTCTAGAGGTTCTTCTTCTAGGGGTTTCGTAGGGAGCCGCTCAATCATTGGCG
196 GTTCATCGGTGTTTCTAGAGGTTCTTCTTCTAGGGGTTTCGTAGGGAGCCGCTCAATCATTGGCG
33589878 TTTTTGGTTGCAAGTTAACCAAGGG
261 TTTTTGGTTGCAAGTTAACCAAGGG
33589903 TTCCATAGGG
Statistics
Matches: 285, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
285 285 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.40
Consensus pattern (285 bp):
ATTACTCTTGTATTTTGCCTATAAATAGGCTTGCTTTCTATACATTGGGGCACATAAGAAAAAAG
AGTATTGGTTTTCTTCCAAATTTGTGTGAGGCAATTTTTTTAGAGTAGAGTGATTCTTCTCTTGC
TATTTAGTTTGAAGTTTGTTACTTCGAGGGTTTTTCGGAGTTACAAATATTCAAATTTCCTTCCC
GTTCATCGGTGTTTCTAGAGGTTCTTCTTCTAGGGGTTTCGTAGGGAGCCGCTCAATCATTGGCG
TTTTTGGTTGCAAGTTAACCAAGGG
Found at i:33591497 original size:21 final size:21
Alignment explanation
Indices: 33591473--33591516 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
33591463 TTAATATTGC
33591473 TATTATTATTATAACAT-TATA
1 TATTATTATTAT-ACATATATA
33591494 TATTATTATTATACATATATA
1 TATTATTATTATACATATATA
33591515 TA
1 TA
33591517 CACGTGCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTATTATTATACATATATA
Found at i:33591745 original size:12 final size:12
Alignment explanation
Indices: 33591728--33591753 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33591718 CACATTTTTA
33591728 ATATATATATAC
1 ATATATATATAC
33591740 ATATATATATAC
1 ATATATATATAC
33591752 AT
1 AT
33591754 GCACTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATATATATAC
Found at i:33595586 original size:45 final size:45
Alignment explanation
Indices: 33595531--33595620 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
33595521 AAAAAGGTGG
* * * *
33595531 GACCAAGGTGAAAGCCTACAAAGGGTGCTTTGAGTCAAAAAAAAA
1 GACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAAAA
*
33595576 GACCAGGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAAAA
1 GACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAAAA
33595621 AAGAGGCTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (45 bp):
GACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAAAA
Found at i:33596972 original size:44 final size:44
Alignment explanation
Indices: 33596892--33597106 Score: 128
Period size: 44 Copynumber: 4.9 Consensus size: 44
33596882 TCCCTCGGAG
* * ** * * *
33596892 GCAGTGGAGCAGGTTGAAGATTTCAGATCTTGCCTCCCTAAGCA
1 GCAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTAAGCA
* **
33596936 GTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTT
1 GCAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCT-AAGCA
* * * *** ** * * * **
33596981 GCAGTGGAGTACATTGAAGCCAG-TAATTCTACTTCCATGGGCA
1 GCAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTAAGCA
** * ** *
33597024 GCAGTGGAATAGATTGAAGATTTCAGATCTTT-CCTCCCTAAGCA
1 GCAGTGGAGCAGATCGAAGATGGCGGAT-TTTACCTCCCTAAGCA
*
33597068 GTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCT
1 GCAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCT
33597107 GAAGTTGAAT
Statistics
Matches: 121, Mismatches: 46, Indels: 8
0.69 0.26 0.05
Matches are distributed among these distances:
43 21 0.17
44 79 0.65
45 21 0.17
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (44 bp):
GCAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTAAGCA
Found at i:33597160 original size:132 final size:132
Alignment explanation
Indices: 33596892--33597174 Score: 444
Period size: 132 Copynumber: 2.1 Consensus size: 132
33596882 TCCCTCGGAG
* *
33596892 GCAGTGGAGCAGGTTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT
1 GCAGTGGAACAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT
* * *
33596957 GGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCATGGG
66 GGCGGATTTTACCTCCCTGAAGTTGCAATGAAGTACATTGAAGCCAGTAATTCTACTTCCATGAG
33597022 CA
131 CA
* *
33597024 GCAGTGGAATAGATTGAAGATTTCAGATCTTTCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT
1 GCAGTGGAACAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT
* *
33597089 GGCGGATTTTACCTCCCTGAAGTTG-AATGAAGTACATTGAAGCCAGTAATTTTACTTCC-TTAG
66 GGCGGATTTTACCTCCCTGAAGTTGCAATGAAGTACATTGAAGCCAGTAATTCTACTTCCATGAG
33597152 CA
131 CA
*
33597154 GTGCAGTGGAACATATTGAAG
1 --GCAGTGGAACAGATTGAAG
33597175 CTACGACGGC
Statistics
Matches: 138, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
130 4 0.03
131 31 0.22
132 103 0.75
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (132 bp):
GCAGTGGAACAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT
GGCGGATTTTACCTCCCTGAAGTTGCAATGAAGTACATTGAAGCCAGTAATTCTACTTCCATGAG
CA
Found at i:33597444 original size:100 final size:100
Alignment explanation
Indices: 33597140--33597525 Score: 603
Period size: 100 Copynumber: 3.9 Consensus size: 100
33597130 GCCAGTAATT
* *
33597140 TTACTTCCTTAGCAGTGCAGTGGAACATATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
*
33597205 TGCAATTAAAAAGATTGAAGCAACAACGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* * * * *
33597240 TTATTTCGTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGGTCTGGGTTTCCTTGATG
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCT-GGTTTCCCTGATA
33597305 TTGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
65 TTGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
*
33597341 TTACTTCCTTAGCAGTGTAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
33597406 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* * * * *
33597441 TTACTTCCCT-GACGGTGCGGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGACA
1 TTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATA
* *
33597505 TTGCAATTGAATAGATTGAAG
65 TTGCAATTAAAAAGATTGAAG
33597526 ATTTCAGACC
Statistics
Matches: 262, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
99 1 0.00
100 168 0.64
101 93 0.35
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (100 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
Found at i:33597485 original size:201 final size:200
Alignment explanation
Indices: 33597140--33597525 Score: 603
Period size: 201 Copynumber: 1.9 Consensus size: 200
33597130 GCCAGTAATT
*
33597140 TTACTTCCTTAGCAGTGCAGTGGAACATATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATAT
* * *
33597205 TGCAATTAAAAAGATTGAAGCAACAACGGCGGATCTTATTTCGTTAGCAGTGCAGTGGAACAGAT
66 TGCAATTAAAAAGATTGAAGCAACAACGGCGGATCTTATTCCCTGAGCAGTGCAGTGGAACAGAT
* ** **
33597270 TGAAGCTACGACGGCGGGTCTGGGTTTCCTTGATGTTGCAATTAAAAAGATTGAAGCCACAACGG
131 TGAAGCTACGACGGCGGATCT-GGTTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACGG
33597335 CGGATC
195 CGGATC
* *
33597341 TTACTTCCTTAGCAGTGTAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATAT
* * *
33597406 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGA-CGGTGCGGTGGAACAGA
66 TGCAATTAAAAAGATTGAAGCAACAACGGCGGATCTTA-TTCCCTGAGCAGTGCAGTGGAACAGA
* *
33597470 TTGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTGCAATTGAATAGATTGAAG
130 TTGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTGCAATTAAAAAGATTGAAG
33597526 ATTTCAGACC
Statistics
Matches: 168, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
200 28 0.17
201 135 0.80
202 5 0.03
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (200 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATAT
TGCAATTAAAAAGATTGAAGCAACAACGGCGGATCTTATTCCCTGAGCAGTGCAGTGGAACAGAT
TGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACGGC
GGATC
Found at i:33597499 original size:50 final size:50
Alignment explanation
Indices: 33597152--33597525 Score: 277
Period size: 50 Copynumber: 7.5 Consensus size: 50
33597142 ACTTCCTTAG
* *
33597152 CAGTGCAGTGGAACATATTGAAGCTACGACGGCAGATCTGGTTTCCCTGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
* * * ** * * * ** * *
33597202 TATTGCAATTAAAAAGATTGAAGCAACAACGGCGGATCTTATTT-CGTTA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
* *
33597251 GCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGGTCTGGGTTTCCTTGA
1 -CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCT-GGTTTCCCTGA
* * ** * * * *** *
33597303 -TGTTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTA
1 CAG-TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
*
33597352 GCAGTGTAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
1 -CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
* * * ** * * * ***
33597403 TATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
* * *
33597453 CGGTGCGGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
* * * *
33597503 CATTGCAATTGAATAGATTGAAG
1 CAGTGCAGTGGAACAGATTGAAG
33597526 ATTTCAGACC
Statistics
Matches: 233, Mismatches: 84, Indels: 14
0.70 0.25 0.04
Matches are distributed among these distances:
49 6 0.03
50 187 0.80
51 37 0.16
52 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (50 bp):
CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
Found at i:33599333 original size:21 final size:21
Alignment explanation
Indices: 33599309--33599352 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
33599299 TTAATATTGC
33599309 TATTATTATTATA-ATATTATA
1 TATTATTATTATACATA-TATA
33599330 TATTATTATTATACATATATA
1 TATTATTATTATACATATATA
33599351 TA
1 TA
33599353 CACGTGCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTATTATTATACATATATA
Found at i:33603924 original size:21 final size:21
Alignment explanation
Indices: 33603873--33603925 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
33603863 ACCATTGTTT
* *
33603873 CTAATCTCACCGCTACAGTAT
1 CTAATCTCACCACTACAGTAA
* *
33603894 CCAATTTCACCACTACAGTAA
1 CTAATCTCACCACTACAGTAA
33603915 CTAATCTCACC
1 CTAATCTCACC
33603926 GCCACCGCTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.36, G:0.06, T:0.26
Consensus pattern (21 bp):
CTAATCTCACCACTACAGTAA
Found at i:33607319 original size:20 final size:20
Alignment explanation
Indices: 33607294--33607333 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
33607284 CATGACGGAA
33607294 GCAGC-AACAGAAACAGAAAC
1 GCAGCAAACAGAAACA-AAAC
*
33607314 GCAGCAAACAGTAACAAAAC
1 GCAGCAAACAGAAACAAAAC
33607334 AACAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.25, G:0.17, T:0.03
Consensus pattern (20 bp):
GCAGCAAACAGAAACAAAAC
Found at i:33608229 original size:3 final size:3
Alignment explanation
Indices: 33608223--33608339 Score: 155
Period size: 3 Copynumber: 38.7 Consensus size: 3
33608213 TTTAGCAATT
*
33608223 TTA TTA TTA TTA TCA TCTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
33608269 TTA TTA TTA TTA TTA TTA TTA TCT- TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
* * **
33608314 TTA TTA TCA ATA TTA TGG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
33608340 GTGATGTTTT
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.01
3 95 0.96
4 3 0.03
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:33610651 original size:19 final size:20
Alignment explanation
Indices: 33610611--33610654 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
33610601 GTCTCTTTAG
* *
33610611 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
33610630 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
33610649 GCATTA
1 GCATTA
33610655 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:33617051 original size:20 final size:21
Alignment explanation
Indices: 33617019--33617079 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
33617009 TTATTAATAT
*
33617019 TATAT-TTAGTTATATATCTA
1 TATATCTTAGTTATATATCCA
*
33617039 TATATCTTATTATATATATCCA
1 TATATCTTAGT-TATATATCCA
*
33617061 TATATCTTAATATATATAT
1 TATATCTTAGT-TATATAT
33617080 GTGCATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 5 0.14
21 4 0.11
22 27 0.75
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (21 bp):
TATATCTTAGTTATATATCCA
Found at i:33617057 original size:22 final size:22
Alignment explanation
Indices: 33617029--33617079 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
33617019 TATATTTAGT
* *
33617029 TATATATCTATATATCTTATTA
1 TATATATCCATATATCTTAATA
33617051 TATATATCCATATATCTTAATA
1 TATATATCCATATATCTTAATA
33617073 TATATAT
1 TATATAT
33617080 GTGCATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATATCCATATATCTTAATA
Found at i:33617858 original size:109 final size:109
Alignment explanation
Indices: 33617661--33617868 Score: 355
Period size: 109 Copynumber: 1.9 Consensus size: 109
33617651 AAATGTTTCC
33617661 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* *
33617726 CTCGTTCGACCAAATAGCTAAATATCCTTTTGAAAACTTTTCAA
66 CTCGTTCAACCAAATAGCTAAATATCCTATTGAAAACTTTTCAA
*
33617770 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* *
33617835 CTCGTTTAACCAAATTG-TCAAATATCCTATTGAA
66 CTCGTTCAACCAAATAGCT-AAATATCCTATTGAA
33617869 TTTAAACTCA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 1 0.01
109 92 0.99
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (109 bp):
AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
CTCGTTCAACCAAATAGCTAAATATCCTATTGAAAACTTTTCAA
Found at i:33619641 original size:24 final size:25
Alignment explanation
Indices: 33619609--33619660 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
33619599 AATACTTTTA
33619609 TTTATTTTTAAATTTTAAAAT-ATT
1 TTTATTTTTAAATTTTAAAATAATT
* *
33619633 TTTATTTTTTATTTTTAAAATAATT
1 TTTATTTTTAAATTTTAAAATAATT
33619658 TTT
1 TTT
33619661 TGGTATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTATTTTTAAATTTTAAAATAATT
Found at i:33620358 original size:3 final size:3
Alignment explanation
Indices: 33620352--33620421 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
33620342 AAAGGAGGAG
33620352 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
33620400 GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA G
33620422 GAGAGAGATG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:33623566 original size:7 final size:7
Alignment explanation
Indices: 33623554--33623592 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
33623544 ACCCAAATCC
33623554 TAAACCT
1 TAAACCT
33623561 TAAACCT
1 TAAACCT
33623568 TAAA-CT
1 TAAACCT
*
33623574 TGAACCT
1 TAAACCT
*
33623581 TAAACCC
1 TAAACCT
33623588 TAAAC
1 TAAAC
33623593 TATGAAAGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.44, C:0.28, G:0.03, T:0.26
Consensus pattern (7 bp):
TAAACCT
Found at i:33623579 original size:20 final size:21
Alignment explanation
Indices: 33623556--33623598 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
33623546 CCAAATCCTA
*
33623556 AACCTTAAACCTTAAACT-TG
1 AACCTTAAACCCTAAACTATG
33623576 AACCTTAAACCCTAAACTATG
1 AACCTTAAACCCTAAACTATG
33623597 AA
1 AA
33623599 AGGTTTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (21 bp):
AACCTTAAACCCTAAACTATG
Found at i:33623659 original size:20 final size:21
Alignment explanation
Indices: 33623612--33623668 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
33623602 TTTAAGATTT
33623612 AAGGTTTAGTGTTTAGTATTC
1 AAGGTTTAGTGTTTAGTATTC
* *
33623633 AAAGTTTAGTGTTTTG-ATTC
1 AAGGTTTAGTGTTTAGTATTC
* *
33623653 ATGGTTTAGGGTTTAG
1 AAGGTTTAGTGTTTAG
33623669 GGTTTAGGGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.23, C:0.04, G:0.26, T:0.47
Consensus pattern (21 bp):
AAGGTTTAGTGTTTAGTATTC
Found at i:33623665 original size:7 final size:7
Alignment explanation
Indices: 33623655--33623679 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
33623645 TTTGATTCAT
33623655 GGTTTAG
1 GGTTTAG
33623662 GGTTTAG
1 GGTTTAG
33623669 GGTTTAG
1 GGTTTAG
33623676 GGTT
1 GGTT
33623680 CGGGGTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:33624983 original size:7 final size:7
Alignment explanation
Indices: 33624971--33625027 Score: 114
Period size: 7 Copynumber: 8.1 Consensus size: 7
33624961 TTGCTACTTT
33624971 TATAATA
1 TATAATA
33624978 TATAATA
1 TATAATA
33624985 TATAATA
1 TATAATA
33624992 TATAATA
1 TATAATA
33624999 TATAATA
1 TATAATA
33625006 TATAATA
1 TATAATA
33625013 TATAATA
1 TATAATA
33625020 TATAATA
1 TATAATA
33625027 T
1 T
33625028 GTGAATGTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATAATA
Found at i:33626751 original size:25 final size:25
Alignment explanation
Indices: 33626691--33626819 Score: 81
Period size: 25 Copynumber: 5.2 Consensus size: 25
33626681 ATTCGAAAAT
*
33626691 GCTCATACGAGCACATA-AATGGGAA
1 GCTCATACGAGC-CATATAACGGGAA
* * *
33626716 ACTCTTTCGAGCCATATAACGGGAA
1 GCTCATACGAGCCATATAACGGGAA
** *
33626741 GCTCATACGAGCCA-ATATTGAGAA
1 GCTCATACGAGCCATATAACGGGAA
* *
33626765 GGTTCA-AGCGAGCCA-ATATCGGGAA
1 -GCTCATA-CGAGCCATATAACGGGAA
* *
33626790 GCTCCAGA-GAGCCAT-TAACAGGAA
1 GCT-CATACGAGCCATATAACGGGAA
33626814 GCTCAT
1 GCTCAT
33626820 GGAAGAGCCT
Statistics
Matches: 81, Mismatches: 17, Indels: 14
0.72 0.15 0.12
Matches are distributed among these distances:
23 2 0.02
24 30 0.37
25 48 0.59
26 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (25 bp):
GCTCATACGAGCCATATAACGGGAA
Found at i:33628098 original size:29 final size:33
Alignment explanation
Indices: 33628056--33628123 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 33
33628046 TTGGATTTAA
33628056 TTAT-ATATAAATATA-C-ATA-CATACAT-TT
1 TTATAATATAAATATACCTATACCATACATATT
*
33628084 TTATAATATATATATACCTATACCCATACATATT
1 TTATAATATAAATATACCTATA-CCATACATATT
33628118 TTATAA
1 TTATAA
33628124 CTTATTTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 4 0.12
29 10 0.30
30 1 0.03
31 3 0.09
33 7 0.21
34 8 0.24
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (33 bp):
TTATAATATAAATATACCTATACCATACATATT
Found at i:33629193 original size:21 final size:20
Alignment explanation
Indices: 33629159--33629197 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
33629149 TCATGGACAA
33629159 AAATCGTGTTTTAATAAAATC
1 AAATCGTGTTTTAA-AAAATC
33629180 AAATCGT-TTATTAAAAAA
1 AAATCGTGTT-TTAAAAAA
33629198 CTTTTCGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (20 bp):
AAATCGTGTTTTAAAAAATC
Found at i:33631686 original size:22 final size:24
Alignment explanation
Indices: 33631658--33631707 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
33631648 GAAAATATTT
*
33631658 TTTTTCATT-TTTT-AATCTAATA
1 TTTTTCATTATTTTCAATATAATA
*
33631680 TTTTTCATTATTTTCAATATAATG
1 TTTTTCATTATTTTCAATATAATA
33631704 TTTT
1 TTTT
33631708 AATTTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.38
23 4 0.17
24 11 0.46
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTTTCATTATTTTCAATATAATA
Found at i:33632534 original size:30 final size:30
Alignment explanation
Indices: 33632498--33632646 Score: 178
Period size: 30 Copynumber: 5.0 Consensus size: 30
33632488 AATTTTTTTG
* *
33632498 CATTTTAACCCTTAAACTTTTTTAAAATTT
1 CATTTTAACCCTTAAACTTTCTTAAAATTA
*
33632528 CATTTTAACCCTTAAACTTTCTCAAAATTA
1 CATTTTAACCCTTAAACTTTCTTAAAATTA
* *
33632558 CAATTCAACACC-TAAACTTT-TCT-AAATTA
1 CATTTTAAC-CCTTAAACTTTCT-TAAAATTA
* *
33632587 CATTTTGACCCCTAAACTTTCTTAAAATTA
1 CATTTTAACCCTTAAACTTTCTTAAAATTA
* *
33632617 CATTTGAACCCTTAAACTTTCTCAAAATTA
1 CATTTTAACCCTTAAACTTTCTTAAAATTA
33632647 TGATTCGGCC
Statistics
Matches: 101, Mismatches: 13, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
28 2 0.02
29 22 0.22
30 75 0.74
31 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.01, T:0.40
Consensus pattern (30 bp):
CATTTTAACCCTTAAACTTTCTTAAAATTA
Found at i:33632591 original size:59 final size:59
Alignment explanation
Indices: 33632504--33632646 Score: 180
Period size: 59 Copynumber: 2.4 Consensus size: 59
33632494 TTTGCATTTT
* * *
33632504 AACCCTTAAACTTTTTTAAAATTTCATTTTAACCCTTAAACTTTCTCAAAATTACAATTC
1 AACCCTTAAACTTTTCT-AAATTACATTTTAACCCCTAAACTTTCTCAAAATTACAATTC
* * * *
33632564 AACACC-TAAACTTTTCTAAATTACATTTTGACCCCTAAACTTTCTTAAAATTACATTTG
1 AAC-CCTTAAACTTTTCTAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACAATTC
*
33632623 AACCCTTAAACTTTCTCAAAATTA
1 AACCCTTAAACTTT-TCTAAATTA
33632647 TGATTCGGCC
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
58 2 0.03
59 47 0.65
60 21 0.29
61 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.39
Consensus pattern (59 bp):
AACCCTTAAACTTTTCTAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACAATTC
Found at i:33632821 original size:20 final size:19
Alignment explanation
Indices: 33632798--33632835 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
33632788 GGGACTTTCT
*
33632798 CCCCAAAAAAATAAAAAAA
1 CCCCCAAAAAATAAAAAAA
*
33632817 CCCCCACAAAATAAAAAAA
1 CCCCCAAAAAATAAAAAAA
33632836 AAAGAAGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.26, G:0.00, T:0.05
Consensus pattern (19 bp):
CCCCCAAAAAATAAAAAAA
Found at i:33633041 original size:17 final size:17
Alignment explanation
Indices: 33632986--33633052 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
33632976 AAGCAAAAAT
*
33632986 AAAAAAGAAAGAAAGAAA
1 AAAAAACAAAG-AAGAAA
* * *
33633004 AAACAAC-AACAAGCAAG
1 AAAAAACAAAGAAG-AAA
33633021 AAAAAACAAAGAAGAAA
1 AAAAAACAAAGAAGAAA
33633038 AAAAAGA-AAAGAAGA
1 AAAAA-ACAAAGAAGA
33633053 GAAAGAAAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
16 3 0.08
17 25 0.64
18 11 0.28
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAACAAAGAAGAAA
Found at i:33633061 original size:20 final size:18
Alignment explanation
Indices: 33632986--33633061 Score: 68
Period size: 20 Copynumber: 4.1 Consensus size: 18
33632976 AAGCAAAAAT
33632986 AAAAAAGAAAGAAAGAAA
1 AAAAAAGAAAGAAAGAAA
*
33633004 AAACAACA-ACAAGCAAGAAA
1 AAA-AA-AGA-AAGAAAGAAA
33633024 AAACAAAG-AAGAAA-AAA
1 AAA-AAAGAAAGAAAGAAA
33633041 AAGAAAAGAAGAGAAAGAAA
1 AA-AAAAGAA-AGAAAGAAA
33633061 A
1 A
33633062 GGGAGGAGCG
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
17 9 0.19
18 10 0.21
19 9 0.19
20 20 0.42
ACGTcount: A:0.78, C:0.07, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAGAAAGAAA
Found at i:33633159 original size:11 final size:11
Alignment explanation
Indices: 33633145--33633206 Score: 83
Period size: 11 Copynumber: 5.5 Consensus size: 11
33633135 CTGAACGGGG
33633145 AAGAAAGAAAA
1 AAGAAAGAAAA
33633156 AAG-AAGAAAA
1 AAGAAAGAAAA
33633166 GAAGAAAGAAAA
1 -AAGAAAGAAAA
33633178 AAG-AAGAAGAAA
1 AAGAAAG-A-AAA
33633190 AAGAAAGAAAA
1 AAGAAAGAAAA
33633201 AAGAAA
1 AAGAAA
33633207 AAAGAAAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.22
11 19 0.41
12 14 0.30
13 3 0.07
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAAA
Found at i:33633160 original size:7 final size:7
Alignment explanation
Indices: 33633148--33633215 Score: 84
Period size: 7 Copynumber: 9.3 Consensus size: 7
33633138 AACGGGGAAG
33633148 AAAGAAA
1 AAAGAAA
33633155 AAAGAAGA
1 AAAGAA-A
*
33633163 AAAGAAG
1 AAAGAAA
33633170 AAAGAAA
1 AAAGAAA
33633177 AAAGAAGA
1 AAAGAA-A
33633185 AGAA-AAA
1 A-AAGAAA
33633192 GAAAGAAA
1 -AAAGAAA
33633200 AAAGAAA
1 AAAGAAA
33633207 AAAGAAA
1 AAAGAAA
33633214 AA
1 AA
33633216 TAAATAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
7 37 0.69
8 15 0.28
9 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:33633170 original size:22 final size:22
Alignment explanation
Indices: 33633144--33633212 Score: 113
Period size: 22 Copynumber: 3.1 Consensus size: 22
33633134 GCTGAACGGG
33633144 GAAGAAAGAAAAAAGAAGAAAA
1 GAAGAAAGAAAAAAGAAGAAAA
33633166 GAAGAAAGAAAAAAGAAGAAGAA
1 GAAGAAAGAAAAAAGAAGAA-AA
*
33633189 AAAGAAAGAAAAAAGAA-AAAA
1 GAAGAAAGAAAAAAGAAGAAAA
33633210 GAA
1 GAA
33633213 AAATAAATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
21 4 0.09
22 22 0.50
23 18 0.41
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (22 bp):
GAAGAAAGAAAAAAGAAGAAAA
Found at i:33633481 original size:13 final size:12
Alignment explanation
Indices: 33633462--33633491 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
33633452 AGCAGGCCAT
33633462 AAAAAAAAGAGA
1 AAAAAAAAGAGA
33633474 AGAAAAAAAGAGA
1 A-AAAAAAAGAGA
33633487 AAAAA
1 AAAAA
33633492 GAAAAAAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAGA
Found at i:33633482 original size:15 final size:15
Alignment explanation
Indices: 33633464--33633513 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
33633454 CAGGCCATAA
*
33633464 AAAAAAGAG-AAGA-
1 AAAAAAGAGAAAAAG
33633477 AAAAAAGAGAAAAAAG
1 AAAAAAGAG-AAAAAG
*
33633493 AAAAAAGGGAAAAAG
1 AAAAAAGAGAAAAAG
33633508 AAAAAA
1 AAAAAA
33633514 AAGGTTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 9 0.28
15 15 0.47
16 8 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAAGAGAAAAAG
Found at i:33633514 original size:8 final size:8
Alignment explanation
Indices: 33633473--33633514 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
33633463 AAAAAAAGAG
33633473 AAGAAAAA
1 AAGAAAAA
33633481 AAGAGAAAA
1 AAGA-AAAA
33633490 AAG-AAAA
1 AAGAAAAA
**
33633497 AAGGGAAA
1 AAGAAAAA
33633505 AAGAAAAA
1 AAGAAAAA
33633513 AA
1 AA
33633515 AGGTTCAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 7 0.24
8 15 0.52
9 7 0.24
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:33633629 original size:26 final size:25
Alignment explanation
Indices: 33633600--33633656 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
33633590 TTTAATGCTC
* *
33633600 GTATTTTTTTCATTTTAATATTATTA
1 GTATTTTGTGCATTTTAATATT-TTA
* *
33633626 GTATTTTGTGCATTTTTATATTTTT
1 GTATTTTGTGCATTTTAATATTTTA
33633651 GTATTT
1 GTATTT
33633657 ATATTTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.21, C:0.04, G:0.09, T:0.67
Consensus pattern (25 bp):
GTATTTTGTGCATTTTAATATTTTA
Found at i:33633670 original size:6 final size:6
Alignment explanation
Indices: 33633661--33633710 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
33633651 GTATTTATAT
* *
33633661 TTTTAA TTTTAAA TTTTAA ATTTAA -TTCAA TTTTAA TTTT-A TTTT-A
1 TTTTAA TTTT-AA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
33633707 TTTT
1 TTTT
33633711 GAATACTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
5 14 0.36
6 19 0.49
7 6 0.15
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTTAA
Found at i:33633917 original size:20 final size:20
Alignment explanation
Indices: 33633834--33633938 Score: 60
Period size: 20 Copynumber: 5.4 Consensus size: 20
33633824 ATTGAAAATA
* *
33633834 TTCAAAAAAAATTCTCATGAT
1 TTCAAAAAAATTTCTCGTG-T
* *
33633855 TTC-AAAAAATTTCT-ATCT
1 TTCAAAAAAATTTCTCGTGT
* *
33633873 TTC---AAAATTTTTTGTGT
1 TTCAAAAAAATTTCTCGTGT
* *
33633890 CTTTAAAAAATTTTCTCGTGT
1 -TTCAAAAAAATTTCTCGTGT
*
33633911 TTCAAAAAAATAT-TCGTGTT
1 TTCAAAAAAATTTCTCGTG-T
33633931 TTCAAAAA
1 TTCAAAAA
33633939 TAAGGCAGCG
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
16 8 0.12
17 2 0.03
18 6 0.09
19 7 0.11
20 29 0.44
21 14 0.21
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (20 bp):
TTCAAAAAAATTTCTCGTGT
Found at i:33634087 original size:18 final size:18
Alignment explanation
Indices: 33634055--33634286 Score: 205
Period size: 17 Copynumber: 13.1 Consensus size: 18
33634045 GTTTATGTAA
33634055 AAAAATTTCTCGTGTTTTC
1 AAAAATTT-TCGTGTTTTC
*
33634074 AAAAATTTTAGTG-TTTC
1 AAAAATTTTCGTGTTTTC
**
33634091 AAAAATTCCCGTGTTTT-
1 AAAAATTTTCGTGTTTTC
33634108 AAAAATATTT-GTGTTTTC
1 AAAAAT-TTTCGTGTTTTC
* *
33634126 AAAAATTTTTGTATTTTC
1 AAAAATTTTCGTGTTTTC
**
33634144 AAAAAAAATTCGTG-TTTC
1 -AAAAATTTTCGTGTTTTC
***
33634162 AAAAATCCACGTGTTTTC
1 AAAAATTTTCGTGTTTTC
33634180 AAAAA-TTTCAGTG-TTTC
1 AAAAATTTTC-GTGTTTTC
*
33634197 AAAAATCTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
33634215 -AAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
33634232 TAAAAA-TTTC-TGTGCTTC
1 -AAAAATTTTCGTGT-TTTC
*
33634250 AAAAAATTTCGT-TTTTC
1 AAAAATTTTCGTGTTTTC
* *
33634267 ACAAATTTCCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
33634285 AA
1 AA
33634287 TGACTCTAGT
Statistics
Matches: 172, Mismatches: 26, Indels: 31
0.75 0.11 0.14
Matches are distributed among these distances:
17 88 0.51
18 62 0.36
19 22 0.13
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:33634106 original size:35 final size:35
Alignment explanation
Indices: 33634055--33634286 Score: 190
Period size: 35 Copynumber: 6.6 Consensus size: 35
33634045 GTTTATGTAA
* *
33634055 AAAAATTTCTCGTGTTTTCAAAAATTTTAGTGTTTC
1 AAAAA-TTCCCGTGTTTTCAAAAATTTTCGTGTTTC
33634091 AAAAATTCCCGTGTTTT-AAAAATATTT-GTGTTTTC
1 AAAAATTCCCGTGTTTTCAAAAAT-TTTCGTG-TTTC
*** * **
33634126 AAAAATTTTTGTATTTTCAAAAAAAATTCGTGTTTC
1 AAAAATTCCCGTGTTTTC-AAAAATTTTCGTGTTTC
33634162 AAAAA-TCCACGTGTTTTCAAAAA-TTTCAGTGTTTC
1 AAAAATTCC-CGTGTTTTCAAAAATTTTC-GTGTTTC
*
33634197 AAAAA-TCTTCGTGTTTTC-AAAATTTTCGTGTTTTC
1 AAAAATTC-CCGTGTTTTCAAAAATTTTCGTG-TTTC
* * * * *
33634232 TAAAAATTTCTGTG-CTTCAAAAAATTTCGTTTTTC
1 -AAAAATTCCCGTGTTTTCAAAAATTTTCGTGTTTC
* *
33634267 ACAAATTTCCGTGTTTTCAA
1 AAAAATTCCCGTGTTTTCAA
33634287 TGACTCTAGT
Statistics
Matches: 160, Mismatches: 22, Indels: 29
0.76 0.10 0.14
Matches are distributed among these distances:
34 30 0.19
35 80 0.50
36 41 0.26
37 9 0.06
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (35 bp):
AAAAATTCCCGTGTTTTCAAAAATTTTCGTGTTTC
Found at i:33634390 original size:19 final size:21
Alignment explanation
Indices: 33634358--33634398 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
33634348 CTCGTGTGTC
33634358 AAAAATTGTAGTGTTT-TAAA
1 AAAAATTGTAGTGTTTCTAAA
*
33634378 AAAAATT-TCGTGTTTCTAAA
1 AAAAATTGTAGTGTTTCTAAA
33634398 A
1 A
33634399 TTTTCGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.39
Consensus pattern (21 bp):
AAAAATTGTAGTGTTTCTAAA
Found at i:33634398 original size:17 final size:17
Alignment explanation
Indices: 33634378--33634431 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
33634368 GTGTTTTAAA
33634378 AAAAATTTCGTGTTTCT
1 AAAAATTTCGTGTTTCT
*
33634395 AAAATTTTCGTG-TTC-
1 AAAAATTTCGTGTTTCT
* * *
33634410 GAAAATTTCGTTTTTTT
1 AAAAATTTCGTGTTTCT
33634427 AAAAA
1 AAAAA
33634432 ACAAAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 9 0.31
16 5 0.17
17 15 0.52
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.46
Consensus pattern (17 bp):
AAAAATTTCGTGTTTCT
Found at i:33634400 original size:16 final size:16
Alignment explanation
Indices: 33634379--33634430 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
33634369 TGTTTTAAAA
33634379 AAAATTTCGTGTTTCT
1 AAAATTTCGTGTTTCT
*
33634395 AAAATTTTCGTG-TTCG
1 AAAA-TTTCGTGTTTCT
* *
33634411 AAAATTTCGTTTTTTT
1 AAAATTTCGTGTTTCT
33634427 AAAA
1 AAAA
33634431 AACAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 6 0.20
16 17 0.57
17 7 0.23
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (16 bp):
AAAATTTCGTGTTTCT
Found at i:33640577 original size:10 final size:10
Alignment explanation
Indices: 33640564--33640620 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
33640554 AAAAAAGGAC
33640564 AAAAAAAACA
1 AAAAAAAACA
*
33640574 AAAACAAAC-
1 AAAAAAAACA
33640583 AAAAAAAACA
1 AAAAAAAACA
*
33640593 AAAACAAACA
1 AAAAAAAACA
33640603 AAAACAAAACA
1 AAAA-AAAACA
33640614 AAGAAAA
1 AA-AAAA
33640621 GAAAAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
9 8 0.20
10 21 0.52
11 9 0.22
12 2 0.05
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:33640578 original size:6 final size:6
Alignment explanation
Indices: 33640567--33640615 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
33640557 AAAGGACAAA
*
33640567 AAAAAC AAAAAC AAACAAA AAAAAC AAAAAC --AAAC AAAAAC -AAAAC
1 AAAAAC AAAAAC AAA-AAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
33640613 AAA
1 AAA
33640616 GAAAAGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 4 0.11
5 5 0.14
6 23 0.62
7 5 0.14
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:33640580 original size:15 final size:15
Alignment explanation
Indices: 33640562--33640632 Score: 69
Period size: 15 Copynumber: 4.9 Consensus size: 15
33640552 AAAAAAAAGG
33640562 ACAAAAA-AAACAAAA
1 ACAAAAACAAA-AAAA
33640577 AC--AAACAAAAAAA
1 ACAAAAACAAAAAAA
33640590 ACAAAAACAAACAAAA
1 ACAAAAACAAA-AAAA
*
33640606 AC-AAAACAAAGAAA
1 ACAAAAACAAAAAAA
* *
33640620 AGAAAAAGAAAAA
1 ACAAAAACAAAAA
33640633 TCAAGATGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
13 9 0.19
14 7 0.15
15 25 0.53
16 6 0.13
ACGTcount: A:0.83, C:0.13, G:0.04, T:0.00
Consensus pattern (15 bp):
ACAAAAACAAAAAAA
Found at i:33640584 original size:19 final size:19
Alignment explanation
Indices: 33640562--33640606 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
33640552 AAAAAAAAGG
33640562 ACAAAAAAAACAAAAACAA
1 ACAAAAAAAACAAAAACAA
33640581 ACAAAAAAAACAAAAACAA
1 ACAAAAAAAACAAAAACAA
33640600 ACAAAAA
1 ACAAAAA
33640607 CAAAACAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (19 bp):
ACAAAAAAAACAAAAACAA
Found at i:33640607 original size:25 final size:25
Alignment explanation
Indices: 33640567--33640620 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
33640557 AAAGGACAAA
33640567 AAAAACAAAAACAAACAAAAAAAAC
1 AAAAACAAAAACAAACAAAAAAAAC
* *
33640592 AAAAACAAACAA-AAACAAAACAAAG
1 AAAAACAAA-AACAAACAAAAAAAAC
33640617 AAAA
1 AAAA
33640621 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (25 bp):
AAAAACAAAAACAAACAAAAAAAAC
Found at i:33640625 original size:19 final size:17
Alignment explanation
Indices: 33640564--33640625 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 17
33640554 AAAAAAGGAC
33640564 AAAAAAAACAAAAACAAA
1 AAAAAAAAC-AAAACAAA
*
33640582 CAAAAAAAACAAAA-ACA
1 -AAAAAAAACAAAACAAA
*
33640599 AACAAAAACAAAACAAA
1 AAAAAAAACAAAACAAA
33640616 GAAAAGAAAA
1 -AAAA-AAAA
33640626 AGAAAAATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 12 0.33
17 4 0.11
18 7 0.19
19 13 0.36
ACGTcount: A:0.84, C:0.13, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAAAAAACAAAACAAA
Found at i:33641452 original size:78 final size:78
Alignment explanation
Indices: 33641259--33641590 Score: 431
Period size: 78 Copynumber: 4.3 Consensus size: 78
33641249 TTTATGTCTT
* * * **
33641259 TTTTTAAAAAAATCAACTCATAATAC-AGAGGTGAATTGAGCCTCGGGTCACGCTGAGGTA--T-
1 TTTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGACCACGCTGAGGTATTTC
33641320 TTTT-AATTTATG
66 TTTTAAATTTATG
** * ** *
33641332 TCTTTTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACTGAGGTAT
1 ---TTTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGACCACGCTGAGGTAT
33641397 TTCTTTTAAATTTATG
63 TTCTTTTAAATTTATG
* * * *
33641413 TTTTTCAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCTGATGTATTTC
1 TTTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGACCACGCTGAGGTATTTC
33641478 TTTTAAATTTATG
66 TTTTAAATTTATG
* * * *
33641491 TTTTTCAAAAAATCAACTCATATTACGAGATGTGAGTTGAGCCTAGGACCATGCCGAGGTATTTC
1 TTTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGACCACGCTGAGGTATTTC
33641556 TTTTAAATTTATG
66 TTTTAAATTTATG
33641569 TTTTTCAAAAAATCAACTCATA
1 TTTTTCAAAAAATCAACTCATA
33641591 GTAGAGCAAG
Statistics
Matches: 231, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
76 22 0.10
77 32 0.14
78 164 0.71
79 1 0.00
80 4 0.02
81 8 0.03
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (78 bp):
TTTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGACCACGCTGAGGTATTTC
TTTTAAATTTATG
Found at i:33641908 original size:76 final size:76
Alignment explanation
Indices: 33641691--33642598 Score: 936
Period size: 78 Copynumber: 11.9 Consensus size: 76
33641681 TTTCAAGAAA
* * * *
33641691 TATTTTTCACTTTCTGTTTTTTTTTAAATATCAACTCATAATACTAGAGGTGAGTTGAGCCTCGG
1 TATTTTT-AATTTATGTTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
33641756 GTCACGCTGAGG
65 GTCACGCTGAGG
** *
33641768 TATTTTTAATTTCGGTTTTTTTTT-AAAATCAACTCATAATA-TAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTATGTTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
*
33641831 TCACACTGAGG
66 TCACGCTGAGG
33641842 TATTTTTAATTTATGTCTTTTTTTTAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGG
1 TATTTTTAATTTATGT-TTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
33641906 GTCACGCTGAGG
65 GTCACGCTGAGG
** *
33641918 TATTTTTAATTTCGGTTTTTTTTT-AAAATCAACTCATAATA-TAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTATGTTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
*
33641981 TCACACTGAGG
66 TCACGCTGAGG
33641992 TATTTTTAATTTATGTCTTTTTTTTAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGG
1 TATTTTTAATTTATGT-TTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
*
33642056 GTCACGCTTAGG
65 GTCACGCTGAGG
* *
33642068 TATTTTTAATTTATGTCTTTTTTTAAAAAAATCAACTCATAATAC-AGAGGTGAATTGAGCCTCG
1 TATTTTTAATTTATGT-TTTTTTT-TAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
33642132 GGTCACGCTGAGG
64 GGTCACGCTGAGG
* *
33642145 TATTTTTAATTTATGTCTTTTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 TATTTTTAATTTATGT-TTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
*
33642210 GTCACACTGAGG
65 GTCACGCTGAGG
** * * *
33642222 TATTTCTTTTAAATTTATG--TTTTTCAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TA--T-TTTT-AATTTATGTTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCT
** * *
33642285 CGGACCATGCTGATG
62 CGGGTCACGCTGAGG
** * *
33642300 TATTTCTTTTAAATTTATG--TTTTTCAAAAAATCAACTCATATTACGAGATGTGAGTTGAGCCT
1 TA--T-TTTT-AATTTATGTTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCT
* ** * *
33642363 AGGACCATGCCGAGG
62 CGGGTCACGCTGAGG
** *
33642378 TATTTCTTTTAAATTTATG--TTTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCT
1 TA--T-TTTT-AATTTATGTTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCT
* ** * *
33642441 TGGACCATGCCGAGG
62 CGGGTCACGCTGAGG
* ** * *
33642456 TATTTCT--TTTAAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TATTTTTAATTTATGTTT-T-TTTTT-AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
*
33642519 GGGGCACATG-TCGAGG
63 GGGTCAC--GCT-GAGG
** * ** * * * *
33642535 TATTTTCGA-TT-T-TTGTTTTTCGAAGATCAACTCATAATCCAAGAGGTGAGTTGAGTCTCGGG
1 TATTTTTAATTTATGTTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
33642597 TC
66 TC
33642599 GCACGCCGAG
Statistics
Matches: 747, Mismatches: 61, Indels: 48
0.87 0.07 0.06
Matches are distributed among these distances:
72 4 0.01
74 109 0.15
75 80 0.11
76 173 0.23
77 153 0.20
78 203 0.27
79 11 0.01
80 6 0.01
81 8 0.01
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (76 bp):
TATTTTTAATTTATGTTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
TCACGCTGAGG
Found at i:33641963 original size:150 final size:151
Alignment explanation
Indices: 33641691--33642598 Score: 953
Period size: 150 Copynumber: 5.9 Consensus size: 151
33641681 TTTCAAGAAA
* * * *
33641691 TATTTTTCACTTTCTGT-TTTTTTTTAAATATCAACTCATAATACTAGAGGTGAGTTGAGCCTCG
1 TATTTTT-AATTTATGTCTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
** * *
33641755 GGTCACGCTGAGGTATTTTTAATTTCGGTTTTTTTTTAAAATCAACTCATAATATAGAGGTGAGT
65 GGTCACGCTGAGGTATTTTTAATTTATGTTTTTTTTAAAAATCAACTCATAATAGAGAGGTGAGT
*
33641820 TGAGCCTCGGGTCACACTGAGG
130 TGAGCCTCGGGTCACGCTGAGG
33641842 TATTTTTAATTTATGTCTTTTTTTTAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGG
1 TATTTTTAATTTATGTCTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
** * *
33641906 GTCACGCTGAGGTATTTTTAATTTCGGTTTTTTTTTAAAATCAACTCATAATATAGAGGTGAGTT
66 GTCACGCTGAGGTATTTTTAATTTATGTTTTTTTTAAAAATCAACTCATAATAGAGAGGTGAGTT
*
33641971 GAGCCTCGGGTCACACTGAGG
131 GAGCCTCGGGTCACGCTGAGG
33641992 TATTTTTAATTTATGTCTTTTTTTTAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGG
1 TATTTTTAATTTATGTCTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
* *
33642056 GTCACGCTTAGGTATTTTTAATTTATGTCTTTTTTTAAAAAAATCAACTCATAATACAGAGGTGA
66 GTCACGCTGAGGTATTTTTAATTTATGT-TTTTTTT--AAAAATCAACTCATAATAGAGAGGTGA
*
33642121 ATTGAGCCTCGGGTCACGCTGAGG
128 GTTGAGCCTCGGGTCACGCTGAGG
* *
33642145 TATTTTTAATTTATGTCTTTTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 TATTTTTAATTTATGTCTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
* ** * * *
33642210 GTCACACTGAGGTATTTCTTTTAAATTTATG-TTTTTCAAAAAATTAACTCATATTGCGAGAGGT
66 GTCACGCTGAGGTA--T-TTTT-AATTTATGTTTTTTTTAAAAATCAACTCATAAT-AGAGAGGT
** * *
33642274 GAGTTGAGCCTCGGACCATGCTGATG
126 GAGTTGAGCCTCGGGTCACGCTGAGG
** * *
33642300 TATTTCTTTTAAATTTATG---TTTTTCAAAAAATCAACTCATATTACGAGATGTGAGTTGAGCC
1 TA--T-TTTT-AATTTATGTCTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCC
* ** * * ** *
33642362 TAGGACCATGCCGAGGTATTTCTTTTAAATTTATG-TTTTTCAAAAAATCAACTCATATTACGAG
62 TCGGGTCACGCTGAGGTA--T-TTTT-AATTTATGTTTTTTTTAAAAATCAACTCATAATA-GAG
* ** * *
33642426 AGGTGAGTTGAGCCTTGGACCATGCCGAGG
122 AGGTGAGTTGAGCCTCGGGTCACGCTGAGG
* * * * * *
33642456 TATTTCTT--TTAAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TATTT-TTAATT-TATGTCTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
* ** * ** *
33642519 GGGGCACATG-TCGAGGTATTTTCGATTT-T-TGTTTTTCGAAGATCAACTCATAATCCA-AGAG
64 GGGTCAC--GCT-GAGGTATTTTTAATTTATGTTTTTTTTAAAAATCAACTCATAAT--AGAGAG
*
33642580 GTGAGTTGAGTCTCGGGTC
124 GTGAGTTGAGCCTCGGGTC
33642599 GCACGCCGAG
Statistics
Matches: 667, Mismatches: 64, Indels: 51
0.85 0.08 0.07
Matches are distributed among these distances:
150 202 0.30
151 42 0.06
152 40 0.06
153 95 0.14
154 54 0.08
155 73 0.11
156 129 0.19
157 12 0.02
158 12 0.02
159 8 0.01
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (151 bp):
TATTTTTAATTTATGTCTTTTTTTTAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
GTCACGCTGAGGTATTTTTAATTTATGTTTTTTTTAAAAATCAACTCATAATAGAGAGGTGAGTT
GAGCCTCGGGTCACGCTGAGG
Found at i:33642845 original size:30 final size:30
Alignment explanation
Indices: 33642790--33642937 Score: 156
Period size: 30 Copynumber: 5.0 Consensus size: 30
33642780 TTTTTTTGCT
* * *
33642790 TTTTGACCTCTAAACTTT-TCTAAAATTGCA
1 TTTTAACCCCTAAACTTTCTC-AAAATTACA
*
33642820 TTTTAACCCCTAAAATTTCTCAAAATTACA
1 TTTTAACCCCTAAACTTTCTCAAAATTACA
* * * *
33642850 ATTCAACACCTAAACTTT-TCTAAATTACA
1 TTTTAACCCCTAAACTTTCTCAAAATTACA
* **
33642879 TTTTGACCCCTAAACTTTCTTGAAATTACA
1 TTTTAACCCCTAAACTTTCTCAAAATTACA
* *
33642909 TTTGAACCCTTAAACTTTCTCAAAATTAC
1 TTTTAACCCCTAAACTTTCTCAAAATTAC
33642938 GATTCAGCCC
Statistics
Matches: 96, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
29 24 0.25
30 70 0.73
31 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
TTTTAACCCCTAAACTTTCTCAAAATTACA
Found at i:33642888 original size:59 final size:58
Alignment explanation
Indices: 33642799--33642937 Score: 170
Period size: 59 Copynumber: 2.3 Consensus size: 58
33642789 TTTTTGACCT
*
33642799 CTAAACTTTTCTAAAATTGCATTTTAACCCCTAAAATTTCTCAAAATTACAATTCAACAC
1 CTAAACTTTTCT-AAATTACATTTTAACCCCTAAAATTTCTCAAAATTACAATTCAAC-C
* * ** * *
33642859 CTAAACTTTTCTAAATTACATTTTGACCCCTAAACTTTCTTGAAATTACATTTGAACC
1 CTAAACTTTTCTAAATTACATTTTAACCCCTAAAATTTCTCAAAATTACAATTCAACC
*
33642917 CTTAAACTTTCTCAAAATTAC
1 C-TAAACTTT-TCTAAATTAC
33642938 GATTCAGCCC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 2 0.03
59 46 0.67
60 21 0.30
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (58 bp):
CTAAACTTTTCTAAATTACATTTTAACCCCTAAAATTTCTCAAAATTACAATTCAACC
Found at i:33643111 original size:20 final size:20
Alignment explanation
Indices: 33643088--33643126 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
33643078 GGGACTTTCT
33643088 CCCCCAAAAAATAAAAAAAC
1 CCCCCAAAAAATAAAAAAAC
*
33643108 CCCCCACAAAATAAAAAAA
1 CCCCCAAAAAATAAAAAAA
33643127 AGAAGAAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.31, G:0.00, T:0.05
Consensus pattern (20 bp):
CCCCCAAAAAATAAAAAAAC
Found at i:33643449 original size:7 final size:7
Alignment explanation
Indices: 33643437--33643540 Score: 104
Period size: 7 Copynumber: 14.3 Consensus size: 7
33643427 AACGGGGAAG
33643437 AAAGAAA
1 AAAGAAA
33643444 AAAGAAA
1 AAAGAAA
33643451 AAAGAAA
1 AAAGAAA
33643458 AAAG-AA
1 AAAGAAA
*
33643464 AAAGAAG
1 AAAGAAA
33643471 AAAGAAA
1 AAAGAAA
33643478 AAAGAAGAA
1 AAAG-A-AA
*
33643487 AAAGAAG
1 AAAGAAA
33643494 AAAGAAA
1 AAAGAAA
*
33643501 GAAGGAAGA
1 -AAAGAA-A
33643510 AGAA-AAA
1 A-AAGAAA
33643517 GAAAGAAA
1 -AAAGAAA
*
33643525 AAATAAA
1 AAAGAAA
33643532 AAAGAAA
1 AAAGAAA
33643539 AA
1 AA
33643541 TAAAAAAATT
Statistics
Matches: 81, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
6 6 0.07
7 53 0.65
8 14 0.17
9 8 0.10
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (7 bp):
AAAGAAA
Found at i:33643467 original size:20 final size:20
Alignment explanation
Indices: 33643437--33643547 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 20
33643427 AACGGGGAAG
33643437 AAAGAAAAAAGAAAAAAGAAA
1 AAAG-AAAAAGAAAAAAGAAA
*
33643458 AAAGAAAAAGAAGAAAGAAA
1 AAAGAAAAAGAAAAAAGAAA
*
33643478 AAAG---AAG-AAAAAGAAG
1 AAAGAAAAAGAAAAAAGAAA
* *
33643494 AAAGAAAGAAGGAAGAAG-AA
1 AAAGAAA-AAGAAAAAAGAAA
*
33643514 AAAG--AAAGAAAAAATAAA
1 AAAGAAAAAGAAAAAAGAAA
*
33643532 AAAGAAAAATAAAAAA
1 AAAGAAAAAGAAAAAA
33643548 ATTAATTCAG
Statistics
Matches: 73, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
16 11 0.15
17 10 0.14
18 7 0.10
20 36 0.49
21 9 0.12
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (20 bp):
AAAGAAAAAGAAAAAAGAAA
Found at i:33643474 original size:27 final size:27
Alignment explanation
Indices: 33643437--33643540 Score: 114
Period size: 23 Copynumber: 4.1 Consensus size: 27
33643427 AACGGGGAAG
*
33643437 AAAGAAAAAAGAAAAAAGAAAAAAGAA
1 AAAGAAGAAAGAAAAAAGAAAAAAGAA
33643464 AAAGAAGAAAGAAAAAAG----AAGAA
1 AAAGAAGAAAGAAAAAAGAAAAAAGAA
* * *
33643487 AAAGAAGAAAGAAAGAAGGAAGAAG-A
1 AAAGAAGAAAGAAAAAAGAAAAAAGAA
*
33643513 AAA--AGAAAGAAAAAATAAAAAAGAA
1 AAAGAAGAAAGAAAAAAGAAAAAAGAA
33643538 AAA
1 AAA
33643541 TAAAAAAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
23 22 0.33
24 16 0.24
25 4 0.06
26 4 0.06
27 20 0.30
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (27 bp):
AAAGAAGAAAGAAAAAAGAAAAAAGAA
Found at i:33643802 original size:17 final size:17
Alignment explanation
Indices: 33643782--33643837 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
33643772 AGCAGGCCAG
*
33643782 AAAAAA-AAAAAGAAGA
1 AAAAAAGAAAAAAAAGA
*
33643798 AAAAAAGAGAAAAAAGA
1 AAAAAAGAAAAAAAAGA
* * *
33643815 AAAAAGGGAAAAAGA-A
1 AAAAAAGAAAAAAAAGA
33643831 AAAAAAG
1 AAAAAAG
33643838 TTCAATTTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAGA
Found at i:33643810 original size:7 final size:7
Alignment explanation
Indices: 33643782--33643834 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
33643772 AGCAGGCCAG
33643782 AAAAA-A
1 AAAAAGA
33643788 AAAAAGA
1 AAAAAGA
*
33643795 AGAAA-A
1 AAAAAGA
*
33643801 AAAGAGA
1 AAAAAGA
33643808 AAAAAGA
1 AAAAAGA
*
33643815 AAAAAGGG
1 AAAAA-GA
33643823 AAAAAGA
1 AAAAAGA
33643830 AAAAA
1 AAAAA
33643835 AAGTTCAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
6 9 0.24
7 23 0.61
8 6 0.16
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:33643826 original size:15 final size:16
Alignment explanation
Indices: 33643780--33643834 Score: 62
Period size: 15 Copynumber: 3.5 Consensus size: 16
33643770 GAAGCAGGCC
33643780 AGAAAAAA-A-AAAAGA
1 AGAAAAAAGAGAAAA-A
33643795 AGAAAAAAAGAGAAAAA
1 AG-AAAAAAGAGAAAAA
*
33643812 AGAAAAAAG-GGAAAA
1 AGAAAAAAGAGAAAAA
33643827 AGAAAAAA
1 AGAAAAAA
33643835 AAGTTCAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 15 0.42
16 13 0.36
17 4 0.11
18 4 0.11
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AGAAAAAAGAGAAAAA
Found at i:33643826 original size:24 final size:25
Alignment explanation
Indices: 33643780--33643837 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
33643770 GAAGCAGGCC
*
33643780 AGAAAAAAAAAAAGAAGAAAAAAAG
1 AGAAAAAAGAAAAGAAGAAAAAAAG
**
33643805 AGAAAAAAGAAAA-AAGGGAAAAAG
1 AGAAAAAAGAAAAGAAGAAAAAAAG
*
33643829 AAAAAAAAG
1 AGAAAAAAG
33643838 TTCAATTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (25 bp):
AGAAAAAAGAAAAGAAGAAAAAAAG
Found at i:33643835 original size:16 final size:16
Alignment explanation
Indices: 33643780--33643835 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
33643770 GAAGCAGGCC
33643780 AGAAAAAAA-A-AAAGA
1 AGAAAAAAAGAGAAA-A
33643795 AGAAAAAAAGAGAAAA
1 AGAAAAAAAGAGAAAA
*
33643811 A-AGAAAAAAGGGAAAA
1 AGA-AAAAAAGAGAAAA
33643827 AGAAAAAAA
1 AGAAAAAAA
33643836 AGTTCAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
15 10 0.28
16 22 0.61
17 4 0.11
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAGAGAAAA
Found at i:33643991 original size:6 final size:6
Alignment explanation
Indices: 33643982--33644031 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
33643972 GTATTTATAT
* *
33643982 TTTTAA TTTTTAA TTTTAA ATTTAA -TTCAA TTTTAA TTTT-A TTTT-A
1 TTTTAA -TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
33644028 TTTT
1 TTTT
33644032 GAATACTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
5 14 0.36
6 19 0.49
7 6 0.15
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:33644396 original size:18 final size:17
Alignment explanation
Indices: 33644375--33644696 Score: 162
Period size: 17 Copynumber: 18.3 Consensus size: 17
33644365 TTATGTAAAA
33644375 AAAAATTCTCGTGTTTTC
1 AAAAATT-TCGTGTTTTC
*
33644393 AAAATTTTCAGTG-TTTC
1 AAAAATTTC-GTGTTTTC
* *
33644410 AAAAATCTACGTATTTTC
1 AAAAAT-TTCGTGTTTTC
33644428 AAAAATTTCG-GTGTTTC
1 AAAAATTTCGTGT-TTTC
33644445 AAAAATCTTCGTGTTTTC
1 AAAAAT-TTCGTGTTTTC
*
33644463 AAAAATTTCG-GTGATTC
1 AAAAATTTCGTGT-TTTC
*
33644480 AAAATTTTCGTGTTTTC
1 AAAAATTTCGTGTTTTC
*
33644497 TAAAAATTTC-TGTGCTTC
1 -AAAAATTTCGTGT-TTTC
*
33644515 AAAAAATTTCGT-TTGTC
1 -AAAAATTTCGTGTTTTC
*
33644532 ACAAATTTCCGTGTTTTC
1 AAAAATTT-CGTGTTTTC
* * * *
33644550 AATGACTCTAGTG-TTTC
1 AA-AAATTTCGTGTTTTC
* * *
33644567 ACAAATTGTCATGTTTTTTTTTTA
1 AAAAATT-TC--G----TGTTTTC
*
33644591 ATAAAATTT-GTGTTTTG
1 A-AAAATTTCGTGTTTTC
33644608 AAAAATTCTCGTG-TTTC
1 AAAAATT-TCGTGTTTTC
*
33644625 AAAAATTGTCGTGTTTTA
1 AAAAATT-TCGTGTTTTC
**
33644643 AAAAAAATCGTG-TTTC
1 AAAAATTTCGTGTTTTC
*
33644659 TAAAATTTTCGTG--TTC
1 -AAAAATTTCGTGTTTTC
* * *
33644675 GAAAATTTCGTTTTTTT
1 AAAAATTTCGTGTTTTC
33644692 AAAAA
1 AAAAA
33644697 CAAAAAAAAT
Statistics
Matches: 230, Mismatches: 45, Indels: 59
0.69 0.13 0.18
Matches are distributed among these distances:
15 9 0.04
16 24 0.10
17 101 0.44
18 77 0.33
19 7 0.03
21 1 0.00
23 1 0.00
24 5 0.02
25 5 0.02
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:33644551 original size:35 final size:34
Alignment explanation
Indices: 33644375--33644547 Score: 195
Period size: 35 Copynumber: 5.0 Consensus size: 34
33644365 TTATGTAAAA
* *
33644375 AAAAATTCTCGTGTTTTCAAAATTTTCAGTGTTTC
1 AAAAATT-TCGTGTTTTCAAAAATTTCGGTGTTTC
* *
33644410 AAAAATCTACGTATTTTCAAAAATTTCGGTGTTTC
1 AAAAAT-TTCGTGTTTTCAAAAATTTCGGTGTTTC
*
33644445 AAAAATCTTCGTGTTTTCAAAAATTTCGGTGATTC
1 AAAAAT-TTCGTGTTTTCAAAAATTTCGGTGTTTC
* * *
33644480 AAAATTTTCGTGTTTTCTAAAAATTTCTGTGCTTC
1 AAAAATTTCGTGTTTTC-AAAAATTTCGGTGTTTC
* * *
33644515 AAAAAATTTCGT-TTGTCACAAATTTCCGTGTTT
1 -AAAAATTTCGTGTTTTCAAAAATTTCGGTGTTT
33644548 TCAATGACTC
Statistics
Matches: 120, Mismatches: 15, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
34 24 0.20
35 85 0.71
36 11 0.09
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (34 bp):
AAAAATTTCGTGTTTTCAAAAATTTCGGTGTTTC
Done.