Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 181 of 362
Found at i:59798982 original size:20 final size:21
Alignment explanation
Indices: 59798943--59798982 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
59798933 AAATTAATGG
*
59798943 CTACACGGGCATGTTGCCCTT
1 CTACACGAGCATGTTGCCCTT
59798964 CTACACGAGCATG-TGCCCT
1 CTACACGAGCATGTTGCCCT
59798983 GTTCTAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.17, C:0.35, G:0.23, T:0.25
Consensus pattern (21 bp):
CTACACGAGCATGTTGCCCTT
Found at i:59801164 original size:11 final size:11
Alignment explanation
Indices: 59801148--59801175 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
59801138 AAATTAAAGC
59801148 AGAAGGGTAGA
1 AGAAGGGTAGA
59801159 AGAAGGGTAGA
1 AGAAGGGTAGA
59801170 AGAAGG
1 AGAAGG
59801176 AATTGGCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.46, T:0.07
Consensus pattern (11 bp):
AGAAGGGTAGA
Found at i:59807598 original size:46 final size:44
Alignment explanation
Indices: 59807531--59807650 Score: 161
Period size: 46 Copynumber: 2.6 Consensus size: 44
59807521 TGCGTGAGCT
59807531 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGACGT--GCC
* * *
59807577 AGTGTAAGACATGTTTGGGACATGCATCGGCTACGAGATGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGACGTGCC
59807621 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
59807651 AGCACAGATA
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
44 11 0.16
45 15 0.22
46 41 0.61
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGACGTGCC
Found at i:59808247 original size:20 final size:21
Alignment explanation
Indices: 59808208--59808247 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
59808198 GAATTAATGG
59808208 CTACACGGGCATGTTGCCCTT
1 CTACACGGGCATGTTGCCCTT
*
59808229 CTACACGGGCGTG-TGCCCT
1 CTACACGGGCATGTTGCCCT
59808248 GTTCTAGAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.12, C:0.35, G:0.28, T:0.25
Consensus pattern (21 bp):
CTACACGGGCATGTTGCCCTT
Found at i:59812912 original size:49 final size:48
Alignment explanation
Indices: 59812846--59813066 Score: 208
Period size: 49 Copynumber: 4.7 Consensus size: 48
59812836 AGGCTATCTA
* *
59812846 GTACGCATAGTAACCTGCACTTAGTACTACACATGCGACCAATTATTCG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTA-TCG
* * * *
59812895 GTACACGTAGTAGCCTGCACTTTGTACTACACACGTGACC---TA---
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCG
* * * *
59812937 --AC-CATCGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATC-G
* *
59812985 GTACGCATAGTAGCCTGCACTTAGCACTACACATGCGACCAATTATCCG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTAT-CG
* *
59813034 GTACACGTAGTAGCCTGTACTTAGTACTACACA
1 GTACACATAGTAGCCTGCACTTAGTACTACACA
59813067 CGTGACCTCA
Statistics
Matches: 140, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
39 30 0.21
40 3 0.02
44 2 0.01
46 2 0.01
49 68 0.49
50 6 0.04
51 29 0.21
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (48 bp):
GTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCG
Found at i:59817422 original size:9 final size:9
Alignment explanation
Indices: 59817410--59817605 Score: 73
Period size: 10 Copynumber: 20.8 Consensus size: 9
59817400 TTTTATGATT
59817410 TTTTTATAA
1 TTTTTATAA
59817419 TTTTTATAA
1 TTTTTATAA
*
59817428 GTTTATATCAA
1 -TTTTTAT-AA
*
59817439 TTTTAAT-A
1 TTTTTATAA
59817447 TTTTTATAA
1 TTTTTATAA
*
59817456 TTTTTTAAGAA
1 -TTTTT-ATAA
* *
59817467 TTTTAATACG
1 TTTTTATA-A
59817477 TTTTT-TAA
1 TTTTTATAA
*
59817485 TTTTAAATAA
1 TTTT-TATAA
*
59817495 GTTTTATTAA
1 TTTTTA-TAA
59817505 -TTTTATACA
1 TTTTTATA-A
59817514 TTTTTCATAA
1 TTTTT-ATAA
* *
59817524 TTAATTCT-A
1 TT-TTTATAA
*
59817533 TTTGATT-TGA
1 TTT--TTATAA
59817543 TTTTTGAT-A
1 TTTTT-ATAA
59817552 TTTTTATAA
1 TTTTTATAA
*
59817561 GTTTTAATAA
1 -TTTTTATAA
59817571 -TTTTATAAA
1 TTTTTAT-AA
*
59817580 TTTATATCAA
1 TTTTTAT-AA
* *
59817590 TTTTAATAT
1 TTTTTATAA
59817599 TTTTTAT
1 TTTTTAT
59817606 TCTTTGATTA
Statistics
Matches: 141, Mismatches: 24, Indels: 44
0.67 0.11 0.21
Matches are distributed among these distances:
8 22 0.16
9 41 0.29
10 68 0.48
11 10 0.07
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:59817468 original size:28 final size:28
Alignment explanation
Indices: 59817418--59817517 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 28
59817408 TTTTTTTATA
* *
59817418 ATTTTTATAAGTTTATATCAATTTTAAT
1 ATTTTTATAATTTTATAACAATTTTAAT
* *
59817446 ATTTTTATAATTTTTTAAGAATTTTAAT
1 ATTTTTATAATTTTATAACAATTTTAAT
* *
59817474 ACGTTTTT-TAATTTTA-AATAAGTTTTATT
1 A--TTTTTATAATTTTATAACAA-TTTTAAT
*
59817503 AATTTTATACATTTT
1 ATTTTTATA-ATTTT
59817518 TCATAATTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
27 4 0.07
28 31 0.53
29 19 0.32
30 5 0.08
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (28 bp):
ATTTTTATAATTTTATAACAATTTTAAT
Found at i:59817469 original size:20 final size:19
Alignment explanation
Indices: 59817410--59817471 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
59817400 TTTTATGATT
59817410 TTTTTATAATTTTTATAAG-
1 TTTTTATAATTTTT-TAAGA
* *
59817429 TTTATATCAA--TTTTAATA
1 TTTTTAT-AATTTTTTAAGA
59817447 TTTTTATAATTTTTTAAGA
1 TTTTTATAATTTTTTAAGA
*
59817466 ATTTTA
1 TTTTTA
59817472 ATACGTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
17 5 0.15
18 9 0.26
19 18 0.53
20 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTTATAATTTTTTAAGA
Found at i:59817488 original size:18 final size:18
Alignment explanation
Indices: 59817465--59817518 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
59817455 ATTTTTTAAG
59817465 AATTTTAATACGTTTTTT
1 AATTTTAATACGTTTTTT
*
59817483 AATTTTAAATAAGTTTTATT
1 AATTTT-AATACGTTTT-TT
*
59817503 AATTTT-ATACATTTTT
1 AATTTTAATACGTTTTT
59817519 CATAATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 1 0.03
18 13 0.42
19 9 0.29
20 8 0.26
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (18 bp):
AATTTTAATACGTTTTTT
Found at i:59817493 original size:19 final size:20
Alignment explanation
Indices: 59817465--59817509 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
59817455 ATTTTTTAAG
*
59817465 AATTTT-AATACGTTTT-TT
1 AATTTTAAATAAGTTTTATT
59817483 AATTTTAAATAAGTTTTATT
1 AATTTTAAATAAGTTTTATT
59817503 AATTTTA
1 AATTTTA
59817510 TACATTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 6 0.25
19 9 0.38
20 9 0.38
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (20 bp):
AATTTTAAATAAGTTTTATT
Found at i:59817654 original size:21 final size:20
Alignment explanation
Indices: 59817628--59817668 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
59817618 TTTCTTTCTA
*
59817628 TTTTTTTATAATTTTTATGAG
1 TTTTTTAATAA-TTTTATGAG
*
59817649 TTTTTTAATCATTTTATGAG
1 TTTTTTAATAATTTTATGAG
59817669 AAAAATAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.63
Consensus pattern (20 bp):
TTTTTTAATAATTTTATGAG
Found at i:59823762 original size:43 final size:42
Alignment explanation
Indices: 59823712--59823849 Score: 129
Period size: 42 Copynumber: 3.2 Consensus size: 42
59823702 TCCCAGATGT
* * *
59823712 GGTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAGACAG
1 GGTCTTACACGTAATTCAA-ATCGATGCCTATGTCCCAGACAC
* * *
59823755 GGTCTTACACG-AAATCAAATACGATG-CTAATTTCCCAGACAT
1 GGTCTTACACGTAATTCAAAT-CGATGCCT-ATGTCCCAGACAC
*
59823797 GGTCTTACACGTAAATCTCAAATCGA-GCCCTGTGTCCCAGACAC
1 GGTCTTACACGT-AAT-TCAAATCGATG-CCTATGTCCCAGACAC
*
59823841 AGTCTTACA
1 GGTCTTACA
59823850 TGATATTTTA
Statistics
Matches: 78, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
41 4 0.05
42 32 0.41
43 11 0.14
44 23 0.29
45 8 0.10
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (42 bp):
GGTCTTACACGTAATTCAAATCGATGCCTATGTCCCAGACAC
Found at i:59824209 original size:14 final size:14
Alignment explanation
Indices: 59824190--59824222 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
59824180 TTAGGGCACT
59824190 TTACATTTTAGCCC
1 TTACATTTTAGCCC
59824204 TTACATTTTAGCCC
1 TTACATTTTAGCCC
59824218 TTACA
1 TTACA
59824223 GTTTCACACT
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:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (14 bp):
TTACATTTTAGCCC
Found at i:59830498 original size:25 final size:25
Alignment explanation
Indices: 59830470--59830545 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
59830460 CTCGTATGAA
*
59830470 CTTATTGATTTTCAGCTCGTGAGAG
1 CTTATCGATTTTCAGCTCGTGAGAG
* *
59830495 CTTATCGATTCTCAACTCGT-ATGAG
1 CTTATCGATTTTCAGCTCGTGA-GAG
* * * *
59830520 CTGACCGATTTACAGCTTGTGAGAG
1 CTTATCGATTTTCAGCTCGTGAGAG
59830545 C
1 C
59830546 ATGCCGATTC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
24 1 0.03
25 38 0.95
26 1 0.03
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (25 bp):
CTTATCGATTTTCAGCTCGTGAGAG
Found at i:59836385 original size:38 final size:38
Alignment explanation
Indices: 59836343--59836457 Score: 140
Period size: 38 Copynumber: 3.0 Consensus size: 38
59836333 GGCACGAAGA
* * **
59836343 CTGCTAGGCACAGAGCCCGAATATTATCGGTACAAAGC
1 CTGCTAGGCACAGAGCCCGAATATAACCGACACAAAGC
* * *
59836381 CTGCTAGGCACAGATCCCGAATATAACCGACAGAAAGT
1 CTGCTAGGCACAGAGCCCGAATATAACCGACACAAAGC
* * *
59836419 CTGCTAGGCACAGAGCCCAAATATCACTGACACAAAGC
1 CTGCTAGGCACAGAGCCCGAATATAACCGACACAAAGC
59836457 C
1 C
59836458 CGATTATCAT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.16
Consensus pattern (38 bp):
CTGCTAGGCACAGAGCCCGAATATAACCGACACAAAGC
Found at i:59844294 original size:21 final size:21
Alignment explanation
Indices: 59844270--59844316 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
59844260 TAAAAGTTGC
* *
59844270 TTTTCTATGAATAAATTT-TCA
1 TTTTCTA-CAATAAATTTCTAA
59844291 TTTTCTACAATAAATTTCTAA
1 TTTTCTACAATAAATTTCTAA
59844312 TTTTC
1 TTTTC
59844317 AGCATATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.32, C:0.13, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTCTACAATAAATTTCTAA
Found at i:59845401 original size:24 final size:24
Alignment explanation
Indices: 59845369--59845426 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
59845359 CCACATTGTT
59845369 GGAGAAATAAGGAAA-GTGAGAGAA
1 GGAGAAATAA-GAAATGTGAGAGAA
*
59845393 GGAGAAATAAGAAATGTTAGAGAA
1 GGAGAAATAAGAAATGTGAGAGAA
*
59845417 TGAGAAATAA
1 GGAGAAATAA
59845427 TGTGGTGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 4 0.13
24 27 0.87
ACGTcount: A:0.55, C:0.00, G:0.31, T:0.14
Consensus pattern (24 bp):
GGAGAAATAAGAAATGTGAGAGAA
Found at i:59848579 original size:42 final size:43
Alignment explanation
Indices: 59848499--59848636 Score: 129
Period size: 42 Copynumber: 3.2 Consensus size: 43
59848489 TCCCGGATGT
* * ** *
59848499 GGTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAGATAA
1 GGTCTTACACGTAAATCAATATCGATGCCAATGTCCCAGACAA
*
59848542 GGTCTTACACG-AAATCAAATAT-GATGCCAATGTCCCAGACAT
1 GGTCTTACACGTAAATC-AATATCGATGCCAATGTCCCAGACAA
* * ** *
59848584 GGTCTTACACATAAATCTCAA-ATCGAGGCCTGTGTCCCAGACAC
1 GGTCTTACACGTAAA--TCAATATCGATGCCAATGTCCCAGACAA
59848628 GGTCTTACA
1 GGTCTTACA
59848637 TGATATTTCA
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
42 30 0.38
43 20 0.25
44 27 0.34
45 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (43 bp):
GGTCTTACACGTAAATCAATATCGATGCCAATGTCCCAGACAA
Found at i:59854658 original size:30 final size:31
Alignment explanation
Indices: 59854601--59854659 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
59854591 TGAAATAAAG
* ***
59854601 AACGAGCTGAAAGTAAGCTCGGTTGAGCTCA
1 AACGAGCTGAAAGCAAGCTCAAATGAGCTCA
59854632 AACGAGCTGAAA-CAAGCTCAAATGAGCT
1 AACGAGCTGAAAGCAAGCTCAAATGAGCT
59854660 GAGTTGAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.17
Consensus pattern (31 bp):
AACGAGCTGAAAGCAAGCTCAAATGAGCTCA
Found at i:59854669 original size:20 final size:20
Alignment explanation
Indices: 59854622--59854669 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
59854612 AGTAAGCTCG
59854622 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
59854642 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
59854662 GTTGAGCT
1 GTTGAGCT
59854670 GGACGGAGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:59861770 original size:17 final size:18
Alignment explanation
Indices: 59861731--59861772 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
59861721 ATCTATATGT
* *
59861731 ATTCAAAATTAACCCTTTC
1 ATTCAAAA-TAACCATTTA
59861750 ATTCAAAA-AACCATTTA
1 ATTCAAAATAACCATTTA
59861767 ATTCAA
1 ATTCAA
59861773 TCCATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 13 0.62
19 8 0.38
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTCAAAATAACCATTTA
Found at i:59868478 original size:20 final size:20
Alignment explanation
Indices: 59868446--59868484 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
59868436 CAACATTTCA
59868446 CAATTAAACCATCACATAAG
1 CAATTAAACCATCACATAAG
*
59868466 CAATATAAA-CATCATATAA
1 CAAT-TAAACCATCACATAA
59868485 CTTACTTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.54, C:0.21, G:0.03, T:0.23
Consensus pattern (20 bp):
CAATTAAACCATCACATAAG
Found at i:59869432 original size:20 final size:20
Alignment explanation
Indices: 59869402--59869452 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 20
59869392 GATCTATATG
59869402 TATTC-AAAATTAACTCTTT
1 TATTCAAAAATTAACTCTTT
59869421 TATTCAAAAATTAACTCTTT
1 TATTCAAAAATTAACTCTTT
59869441 TATTCAACAAAT
1 TATTCAA-AAAT
59869453 CATTTAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 5 0.17
20 21 0.70
21 4 0.13
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (20 bp):
TATTCAAAAATTAACTCTTT
Found at i:59874937 original size:53 final size:54
Alignment explanation
Indices: 59874856--59875060 Score: 196
Period size: 53 Copynumber: 3.8 Consensus size: 54
59874846 TTTCATTTTT
* * * *
59874856 GAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCATTGCCTTAT-
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCATTGCCTTATA
* * * * *
59874909 GAACTCACCAATGTCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCATTGCCTTATA
* * * * * * *
59874963 GTAACACATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCTTTATA
1 G-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCATTGCCTTATA
* * * * * *
59875018 GAACTTATCAATTCCATGCCTTGGCATGGTCTTAAATGATATC
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATC
59875061 CTTATCTTAC
Statistics
Matches: 123, Mismatches: 27, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
53 44 0.36
54 36 0.29
55 43 0.35
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (54 bp):
GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCATTGCCTTATA
Found at i:59875017 original size:55 final size:54
Alignment explanation
Indices: 59874867--59875063 Score: 209
Period size: 55 Copynumber: 3.6 Consensus size: 54
59874857 AACTTACCAT
* * * * *
59874867 TGCCATGTCTTGACATGGTCTTACGTGGTATCATTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
* * ** *
59874920 TGTCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACACATCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATAG-AACTCATCAA
* * * *
59874975 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCTTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
* * *
59875029 TTCCATGCCTTGGCATGGTCTTAAATGATATCCTT
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTT
59875064 ATCTTACCAA
Statistics
Matches: 118, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
52 1 0.01
53 34 0.29
54 39 0.33
55 42 0.36
56 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.37
Consensus pattern (54 bp):
TGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
Found at i:59875108 original size:47 final size:47
Alignment explanation
Indices: 59875042--59875163 Score: 208
Period size: 47 Copynumber: 2.6 Consensus size: 47
59875032 CATGCCTTGG
* * *
59875042 CATGGTCTTAAATGATATCCTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
*
59875089 CATGGTCTTACATGGTATCCTTGTCTTACCATATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
59875136 CATGGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
59875164 GTGCCAATGC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
Found at i:59875351 original size:44 final size:44
Alignment explanation
Indices: 59875302--59875386 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
59875292 ATCCTTAACC
* *
59875302 GTCAATTCCTCCTTAAATGCCATGTTATGAA-CATGGACTTTTCT
1 GTCAATTCCTCCTTAAATGCCATGGTA-CAACCATGGACTTTTCT
* *
59875346 GTCAATTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 GTCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTT
59875387 GAGATATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 2 0.06
44 34 0.94
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.38
Consensus pattern (44 bp):
GTCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTTTCT
Found at i:59879319 original size:42 final size:42
Alignment explanation
Indices: 59879202--59879353 Score: 162
Period size: 42 Copynumber: 3.6 Consensus size: 42
59879192 TACCATACCA
* * *
59879202 ATGCCATATCCCAAATATGGTCTTACATG-GGATCTCGTATCG
1 ATGCCATATCCCAAATATGGTCTTACAAGAAG-TCTCATATCG
* * * ** * *
59879244 ATGCTAATAGCCTAGCTATGGTCTTCCACGAAGTCTCATATCG
1 ATGC-CATATCCCAAATATGGTCTTACAAGAAGTCTCATATCG
* *
59879287 ATGCCATTTCCCAAATATGGTCTTACAAGAAGTCTCATATAG
1 ATGCCATATCCCAAATATGGTCTTACAAGAAGTCTCATATCG
*
59879329 ATGCCATATCCCAGATATGGTCTTA
1 ATGCCATATCCCAAATATGGTCTTA
59879354 GACATAGTCT
Statistics
Matches: 88, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
42 56 0.64
43 31 0.35
44 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAAATATGGTCTTACAAGAAGTCTCATATCG
Found at i:59882817 original size:45 final size:45
Alignment explanation
Indices: 59882744--59882873 Score: 174
Period size: 45 Copynumber: 2.9 Consensus size: 45
59882734 TGTACAGTAA
* * *
59882744 TATTTGGGCCTTTGAGCCTAGCACGCTACAATGTCGGTGAAATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGAAATAC
*
59882789 TATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGAAATGC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGAAATAC
* * *
59882834 TATTCGGG-CTTTCAAGCCTAGCAGGCGA-AATGCCGATGAA
1 TATTCGGGCCTTT-GAGCCTAGCAGGCTACAATGCCGGTGAA
59882874 TGAACTCGGG
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
44 15 0.19
45 62 0.81
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGAAATAC
Found at i:59882906 original size:41 final size:44
Alignment explanation
Indices: 59882805--59882909 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 44
59882795 GGCCTTTGAG
* * * * *
59882805 CCTAGCAGGCTACAATGCCGGTGAAATGCTATTCGGGCTTTCAAG
1 CCTAGCAGGCTA-AATGCCGATGAAATGCAACTCGGGCTTTAAAA
*
59882850 CCTAGCAGGCGAAATGCCGATG-AATG-AACTCGGG-TTTAAAA
1 CCTAGCAGGCTAAATGCCGATGAAATGCAACTCGGGCTTTAAAA
*
59882891 CCTAGCACGCTAAATGCCG
1 CCTAGCAGGCTAAATGCCG
59882910 GTGATTTGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
41 22 0.42
42 6 0.12
43 4 0.08
44 9 0.17
45 11 0.21
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.21
Consensus pattern (44 bp):
CCTAGCAGGCTAAATGCCGATGAAATGCAACTCGGGCTTTAAAA
Found at i:59891240 original size:47 final size:46
Alignment explanation
Indices: 59891177--59891384 Score: 201
Period size: 46 Copynumber: 4.4 Consensus size: 46
59891167 CAATGCCATA
* * *
59891177 TCCCAAACACAGTCTTACACTGGCTTACATCTCAA-GTCGAAGCCATG
1 TCCCAAACA-TGTCTTACACTGGCTTACATCTCAAGGCCGATG-CATG
*
59891224 TCCCAGAA-ATGGTCTTACACTGG-TTATCATCTCGTA-GCCGATGCATG
1 TCCCA-AACAT-GTCTTACACTGGCTTA-CATCTC-AAGGCCGATGCATG
*
59891271 TCCCAAACATGTCTTACACTGGCTTATATCTCAAGGCCGATGCATG
1 TCCCAAACATGTCTTACACTGGCTTACATCTCAAGGCCGATGCATG
* * * * *
59891317 TCCCAGACATGTCTTACACTAGCACT-CGTCTCAATGCCGATGCCATG
1 TCCCAAACATGTCTTACACTGGC-TTACATCTCAAGGCCGATG-CATG
*
59891364 TCCCAAATATGGTCTTACACT
1 TCCCAAACAT-GTCTTACACT
59891385 AGCTCTCACA
Statistics
Matches: 137, Mismatches: 14, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
45 1 0.01
46 67 0.49
47 51 0.37
48 18 0.13
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (46 bp):
TCCCAAACATGTCTTACACTGGCTTACATCTCAAGGCCGATGCATG
Found at i:59891364 original size:93 final size:94
Alignment explanation
Indices: 59891169--59891384 Score: 253
Period size: 93 Copynumber: 2.3 Consensus size: 94
59891159 TGAGATGTCA
* * *
59891169 ATGCCATATCCCAAACACAGTCTTACACTGGCTTACATCTCAAGTCGAAGCCATGTCCCAGAAAT
1 ATGCCATGTCCCAAACA-TGTCTTACACTGGCTTACATCTCAAGCCGAAGCCATGTCCCAGAAAT
* * *
59891234 GGTCTTACACTGGTTATCATCTCGTAGCCG
65 GGTCTTACACTAGTCATCATCTCATAGCCG
* * *
59891264 ATG-CATGTCCCAAACATGTCTTACACTGGCTTATATCTCAAGGCCGATG-CATGTCCCAGACAT
1 ATGCCATGTCCCAAACATGTCTTACACTGGCTTACATCTCAA-GCCGAAGCCATGTCCCAGAAAT
*
59891327 -GTCTTACACTAG-CACTCGTCTCA-ATGCCG
65 GGTCTTACACTAGTCA-TCATCTCATA-GCCG
*
59891356 ATGCCATGTCCCAAATATGGTCTTACACT
1 ATGCCATGTCCCAAACAT-GTCTTACACT
59891385 AGCTCTCACA
Statistics
Matches: 105, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
91 2 0.02
92 24 0.23
93 49 0.47
94 27 0.26
95 3 0.03
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (94 bp):
ATGCCATGTCCCAAACATGTCTTACACTGGCTTACATCTCAAGCCGAAGCCATGTCCCAGAAATG
GTCTTACACTAGTCATCATCTCATAGCCG
Found at i:59892808 original size:4 final size:4
Alignment explanation
Indices: 59892799--59893018 Score: 440
Period size: 4 Copynumber: 55.0 Consensus size: 4
59892789 GAAAACTTAA
59892799 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
59892847 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
59892895 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
59892943 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
59892991 GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT
59893019 AGAAATATTT
Statistics
Matches: 216, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 216 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:59909051 original size:12 final size:12
Alignment explanation
Indices: 59909034--59909060 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
59909024 GATGGTTGAT
59909034 GTATATATTTTA
1 GTATATATTTTA
59909046 GTATATATTTTA
1 GTATATATTTTA
59909058 GTA
1 GTA
59909061 ATAAAAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (12 bp):
GTATATATTTTA
Found at i:59918318 original size:28 final size:29
Alignment explanation
Indices: 59918265--59918321 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
59918255 CACTTTGTGC
* *
59918265 TATTTTGGTGTGTTTTGGATGGATTATAT
1 TATTTTGATGTGTTTGGGATGGATTATAT
59918294 TATTTTGATGTGTTTGGGA-GGATTATAT
1 TATTTTGATGTGTTTGGGATGGATTATAT
59918322 GATACTGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (29 bp):
TATTTTGATGTGTTTGGGATGGATTATAT
Found at i:59918622 original size:21 final size:21
Alignment explanation
Indices: 59918574--59918625 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
59918564 ATGTTTCGTA
*
59918574 TTTCAGGCACCTTGTGTGTCG
1 TTTCAGGCACCTCGTGTGTCG
***
59918595 CAGCAGGCACCTCGTGTGTCG
1 TTTCAGGCACCTCGTGTGTCG
59918616 TTTCAGGCAC
1 TTTCAGGCAC
59918626 TTATGTGTCG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.29, G:0.29, T:0.29
Consensus pattern (21 bp):
TTTCAGGCACCTCGTGTGTCG
Found at i:59926698 original size:9 final size:11
Alignment explanation
Indices: 59926671--59926700 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
59926661 TTTCACATTT
59926671 TAATTTTTATA
1 TAATTTTTATA
59926682 TAATTTTTATA
1 TAATTTTTATA
59926693 -AATTTTTA
1 TAATTTTTA
59926701 GGGATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:59927023 original size:31 final size:29
Alignment explanation
Indices: 59926948--59927025 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
59926938 TTTGAATCAC
* *
59926948 AATTAGAGTTTCATGTGTATAATTGCACCA
1 AATTA-AGATTCATGTATATAATTGCACCA
*
59926978 AATTAA-ATTCCATGTATATAATTGCACATTA
1 AATTAAGATT-CATGTATATAATTGCAC--CA
59927009 AATTAAGATTCATGTAT
1 AATTAAGATTCATGTAT
59927026 GATTTGAGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 2 0.05
29 17 0.41
30 5 0.12
31 14 0.34
32 3 0.07
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (29 bp):
AATTAAGATTCATGTATATAATTGCACCA
Found at i:59927217 original size:20 final size:19
Alignment explanation
Indices: 59927173--59927240 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 19
59927163 TAAATGCACA
59927173 TTATTATTATTT-TATT-TT
1 TTATTATT-TTTATATTATT
59927191 TTA-TATTTTTATATTATT
1 TTATTATTTTTATATTATT
59927209 TTGATTATTTTTCTATATATATT
1 TT-ATTA-TTTT-TATAT-TATT
*
59927232 TTATAATTT
1 TTATTATTT
59927241 CTAATAATTA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
16 3 0.07
17 8 0.19
18 7 0.17
19 1 0.02
20 2 0.05
21 7 0.17
22 8 0.19
23 6 0.14
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (19 bp):
TTATTATTTTTATATTATT
Found at i:59927225 original size:22 final size:20
Alignment explanation
Indices: 59927174--59927233 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
59927164 AAATGCACAT
* *
59927174 TATTATTATTTTATTTTTTA
1 TATTTTTATATTATTTTTTA
59927194 TATTTTTATATTATTTTGATTA
1 TATTTTTATATTATTTT--TTA
59927216 T-TTTTCTATATATATTTT
1 TATTTT-TATAT-TATTTT
59927234 ATAATTTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 15 0.44
21 4 0.12
22 9 0.26
23 6 0.18
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (20 bp):
TATTTTTATATTATTTTTTA
Found at i:59927240 original size:22 final size:19
Alignment explanation
Indices: 59927185--59927236 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
59927175 ATTATTATTT
59927185 TATT-TTTTATA-TTTTTA
1 TATTATTTTATATTTTTTA
59927202 TATTATTTTGATTATTTTTCTA
1 TATTATTTT-A-TATTTTT-TA
59927224 TATATATTTTATA
1 TAT-TATTTTATA
59927237 ATTTCTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 4 0.14
18 4 0.14
19 1 0.03
20 2 0.07
21 6 0.21
22 6 0.21
23 6 0.21
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TATTATTTTATATTTTTTA
Found at i:59934053 original size:3 final size:3
Alignment explanation
Indices: 59934045--59934070 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
59934035 TGGCAGACAA
59934045 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
59934071 GGTTAAATCG
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:59935636 original size:15 final size:16
Alignment explanation
Indices: 59935613--59935650 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
59935603 TAAGGAAAAT
*
59935613 TTTTAAATTTAGTT-A
1 TTTTAAATTAAGTTAA
*
59935628 TTTTCAATTAAGTTAA
1 TTTTAAATTAAGTTAA
59935644 TTTTAAA
1 TTTTAAA
59935651 GTTTTTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (16 bp):
TTTTAAATTAAGTTAA
Found at i:59951073 original size:47 final size:45
Alignment explanation
Indices: 59950975--59951233 Score: 170
Period size: 47 Copynumber: 5.6 Consensus size: 45
59950965 GGTAAGGTGC
* * *
59950975 CATGTCCCAGACACGGTCTTACACTAGCTCAT-GTCTC-AAGTCGAATC
1 CATGTCCCAGACA-TGTCTTACACTA-CT-ATCGTCTCGAAGCCG-ATG
* *
59951022 CATGTCCCAGACATGGTCTTACACTGACTATCATCTCGTAGCCGATG
1 CATGTCCCAGACAT-GTCTTACACT-ACTATCGTCTCGAAGCCGATG
* *
59951069 CATGTCCTAGACATGTCTTACACTAGCT-TACGTCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTA-CTAT-CGTCTCGAAGCCGATG
** * * *
59951115 TTTTTCCCAGTCATGTCTTACACCAAC-ACTCGTCTC-AATGCCGATG
1 CATGTCCCAGACATGTCTTACA-CTACTA-TCGTCTCGAA-GCCGATG
* * * * **
59951161 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACT-ACTATCGT-CTCGAAGCCGATG
*
59951209 CATGCCCCAGACATGTCTTACACTA
1 CATGTCCCAGACATGTCTTACACTA
59951234 GCTCACACAA
Statistics
Matches: 167, Mismatches: 29, Indels: 34
0.73 0.13 0.15
Matches are distributed among these distances:
45 3 0.02
46 68 0.41
47 71 0.43
48 24 0.14
49 1 0.01
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTACTATCGTCTCGAAGCCGATG
Found at i:59951105 original size:46 final size:46
Alignment explanation
Indices: 59950975--59951236 Score: 178
Period size: 46 Copynumber: 5.6 Consensus size: 46
59950965 GGTAAGGTGC
* * * * *
59950975 CATGTCCCAGACACGGTCTTACACTAGCTCATGTCTC-AAGTCGAATC
1 CATGTCCCAGACA-TGTCTTACACTAGCTTACGTCTCGAAGCCG-ATG
* *
59951022 CATGTCCCAGACATGGTCTTACACT-GAC-TATCATCTCGTAGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTAG-CTTA-CGTCTCGAAGCCGATG
* *
59951069 CATGTCCTAGACATGTCTTACACTAGCTTACGTCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTACGTCTCGAAGCCGATG
** * * * * *
59951115 TTTTTCCCAGTCATGTCTTACACCAACACT-CGTCTC-AATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGC-TTACGTCTCGAA-GCCGATG
* * * **
59951161 CCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCT-TACGT-CTCGAAGCCGATG
*
59951209 CATGCCCCAGACATGTCTTACACTAGCT
1 CATGTCCCAGACATGTCTTACACTAGCT
59951237 CACACAAATG
Statistics
Matches: 168, Mismatches: 34, Indels: 27
0.73 0.15 0.12
Matches are distributed among these distances:
45 1 0.01
46 72 0.43
47 70 0.42
48 24 0.14
49 1 0.01
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTTACGTCTCGAAGCCGATG
Found at i:59951634 original size:30 final size:30
Alignment explanation
Indices: 59951600--59951660 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
59951590 TATCTTTGGT
* *
59951600 AAAATGACCATTTTGCCCCTAGATTTTAAA
1 AAAATGACCATTTTACCCCTAGATCTTAAA
* *
59951630 AAAATGGCCATTTTACCCCTAGGTCTTAAA
1 AAAATGACCATTTTACCCCTAGATCTTAAA
59951660 A
1 A
59951661 TCAAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.31
Consensus pattern (30 bp):
AAAATGACCATTTTACCCCTAGATCTTAAA
Found at i:59958798 original size:47 final size:46
Alignment explanation
Indices: 59958731--59958857 Score: 143
Period size: 46 Copynumber: 2.7 Consensus size: 46
59958721 ACGTCTCGAG
* *
59958731 GCCGATGCATGTCCTAGACATGTCTTACATTAGCACTCGTGTCAA-T
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTGT-AAGT
* ** *
59958777 GCTGATGCCATGTCCCAGACATGGTCTTACACT-G-GTTCTTGTAATGT
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCGTGTAA-GT
59958824 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
59958858 TCATACAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
45 12 0.18
46 26 0.38
47 21 0.31
48 9 0.13
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTGTAAGT
Found at i:59969652 original size:50 final size:49
Alignment explanation
Indices: 59969495--59969768 Score: 213
Period size: 50 Copynumber: 5.6 Consensus size: 49
59969485 GTAAAATCCT
** * * * *
59969495 GATGCCATGTCCTGGACATGGTCTTACACTGGCTCTCACACA-TCAGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACT-GGT-CC
* * * * * * ** * *
59969545 AATGCCATGTTCCAAACATGGTCTTGCACTGGCTCGCAT--GTTGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACTG-GTCC
* * * *
59969593 GATGTCATGTCCCAAACATGATCTTACACTAGCTCTCATAAACTGGTACT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACTGGT-CC
* * *
59969643 GATGCCATGTCCTAGACATGGTCTTACACT-G-ACACATACCAA--GG-CC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATA--AACTGGTCC
59969689 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACTGGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACTGGT-CC
*
59969739 GATGCCGTGTCCCAGACATGGTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
59969769 GACACATATC
Statistics
Matches: 178, Mismatches: 33, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
46 32 0.18
47 1 0.01
48 47 0.26
49 4 0.02
50 94 0.53
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACTGGTCC
Found at i:59969784 original size:96 final size:96
Alignment explanation
Indices: 59969495--59969784 Score: 330
Period size: 96 Copynumber: 3.0 Consensus size: 96
59969485 GTAAAATCCT
** * * * * * *
59969495 GATGCCATGTCCTGGACATGGTCTTACACTGGCTCTCACACA-TCAGTGCCAATGCCATGTTCCA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACT-GGTGCCGATGCCATGTCCCA
* * * * * * *
59969559 AACATGGTCTTGCACTGGCTCGCATGTTGAGGCT
65 GACATGGTCTTACACT-G-ACACATATCGAGGCC
* * * * * *
59969593 GATGTCATGTCCCAAACATGATCTTACACTAGCTCTCATAAACTGGTACTGATGCCATGTCCTAG
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACTGGTGCCGATGCCATGTCCCAG
* *
59969658 ACATGGTCTTACACTGACACATACCAAGGCC
66 ACATGGTCTTACACTGACACATATCGAGGCC
*
59969689 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACTGGTGCCGATGCCGTGTCCCAG
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACTGGTGCCGATGCCATGTCCCAG
59969754 ACATGGTCTTACACTGACACATATCGAGGCC
66 ACATGGTCTTACACTGACACATATCGAGGCC
59969785 TATTGTACTC
Statistics
Matches: 159, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
96 95 0.60
97 1 0.01
98 62 0.39
99 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (96 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACTGGTGCCGATGCCATGTCCCAG
ACATGGTCTTACACTGACACATATCGAGGCC
Found at i:59978699 original size:23 final size:23
Alignment explanation
Indices: 59978671--59978721 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
59978661 CATAATCATG
59978671 TTACTTATTATTTGCATGTGAAC
1 TTACTTATTATTTGCATGTGAAC
59978694 TTACTTATTATTTGCATGTGAAC
1 TTACTTATTATTTGCATGTGAAC
59978717 TTACT
1 TTACT
59978722 AAGCATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (23 bp):
TTACTTATTATTTGCATGTGAAC
Found at i:59978729 original size:23 final size:23
Alignment explanation
Indices: 59978680--59978729 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
59978670 GTTACTTATT
* **
59978680 ATTTGCATGTGAACTTACTTATT
1 ATTTGCATGTGAACTTACTAAGC
59978703 ATTTGCATGTGAACTTACTAAGC
1 ATTTGCATGTGAACTTACTAAGC
59978726 ATTT
1 ATTT
59978730 ATGCTTACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (23 bp):
ATTTGCATGTGAACTTACTAAGC
Found at i:59991274 original size:39 final size:40
Alignment explanation
Indices: 59991229--59991396 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
59991219 CGGGGTTTAG
* * *
59991229 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
59991268 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
59991308 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
59991348 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
59991389 CCGGATAT
1 CCGGATAT
59991397 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:59991379 original size:41 final size:40
Alignment explanation
Indices: 59991252--59991396 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
59991242 CTCGCACAAG
* * * * *
59991252 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
59991292 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
59991332 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
59991373 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
59991397 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:59998748 original size:46 final size:46
Alignment explanation
Indices: 59998677--59998802 Score: 155
Period size: 46 Copynumber: 2.7 Consensus size: 46
59998667 TGGTATGTAA
* * *
59998677 GCCAGTGTAAGACATGTTTGGGACATGCATCGGCA-ACATCATGAGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATACA-CACGAGG
* ** *
59998723 GCCAGTGTAAGACATGTCTGAGACATGCATCGGCATTGAGACGAGG
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATACACACGAGG
* *
59998769 GCTAGTGCAAGACATGTCTGGGACATGCATCGGC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGC
59998803 CTGAGGATAT
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
46 68 0.99
47 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATACACACGAGG
Found at i:59998834 original size:48 final size:46
Alignment explanation
Indices: 59998675--59998842 Score: 137
Period size: 46 Copynumber: 3.6 Consensus size: 46
59998665 GGTGGTATGT
* * *
59998675 AAGCCAGTGTAAGACATGTTTGGGACATGCATCGGCAACATCATG-AG-
1 AAGCTAGTGTAAGACATGTCTGGGACATGCATCGGC-AC-TGA-GAAGA
* * * * *
59998722 -TGCCAGTGTAAGACATGTCTGAGACATGCATCGGCATTGAGACGA
1 AAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCACTGAGAAGA
** * *
59998767 GGGCTAGTGCAAGACATGTCTGGGACATGCATCGGC-CTGAGGATATA
1 AAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCACTGA-GA-AGA
*
59998814 CAAGCTAGTGTAAGACATGTCCGGGACAT
1 -AAGCTAGTGTAAGACATGTCTGGGACAT
59998843 AGCGTCAGCT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 4 0.04
46 65 0.66
47 1 0.01
48 24 0.24
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (46 bp):
AAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCACTGAGAAGA
Found at i:59998966 original size:49 final size:47
Alignment explanation
Indices: 59998769--59998983 Score: 152
Period size: 49 Copynumber: 4.5 Consensus size: 47
59998759 TGAGACGAGG
* * *
59998769 GCTAGTGCAAGACATGTCTGGGACAT-GCATCGGCCTGAGGATATACAA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTGA-TATATA-AA
* * * * * * * **
59998817 GCTAGTGTAAGACATGTCCGGGACATAGCGTCAGCTTG-T-TGT-GT
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTGATATATAAA
* * * * *
59998861 G-TCAGTGTAAGACCTATCTAGGACATGGCATCGACACCGATAGATAAGA
1 GCT-AGTGTAAGACCTGTCTGGGACATGGCATCGGC-CTGATATATAA-A
*
59998910 GCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTTGATATATGAAA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCC-TGATATAT-AAA
* *
59998959 GTTAGTGTAAGACCTGTTTGGGACA
1 GCTAGTGTAAGACCTGTCTGGGACA
59998984 CTGTATCGAC
Statistics
Matches: 125, Mismatches: 32, Indels: 19
0.71 0.18 0.11
Matches are distributed among these distances:
43 1 0.01
44 25 0.20
45 1 0.01
46 3 0.02
47 1 0.01
48 25 0.20
49 67 0.54
50 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (47 bp):
GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTGATATATAAA
Found at i:60000777 original size:28 final size:28
Alignment explanation
Indices: 60000737--60000794 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
60000727 TGAAACTTAT
60000737 CAACTTCATGCCATAATTATCGTTAACA
1 CAACTTCATGCCATAATTATCGTTAACA
60000765 CAACTTCATGCCATAATTATCGTTAACA
1 CAACTTCATGCCATAATTATCGTTAACA
60000793 CA
1 CA
60000795 TTCTTACACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (28 bp):
CAACTTCATGCCATAATTATCGTTAACA
Found at i:60011777 original size:50 final size:49
Alignment explanation
Indices: 60011707--60012025 Score: 267
Period size: 50 Copynumber: 6.6 Consensus size: 49
60011697 TAAAATGTCG
* * * *
60011707 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATACATCGGTGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATCGGTGCCA
** * ** *
60011757 ATGCCATGTCCCAGACATGGTCTTACACTAACACAT-ATAA-CAATGCTA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATAATCGGTGCCA
* * * * *
60011805 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCGCAT-ATTGAG-GCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATCG-GTGCCA
* * * * * *
60011853 ATGCCATGTCCCAGGCATAGTCTTACACTAGCTCTTATAAACCGGTACCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-AATCGGTGCCA
* * * *
60011903 ATGCCATGTCCTAGACATGGTCTTACACT-G-ACACAT-ATCGAG-GTCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATCG-GTGCCA
** * *
60011949 ATGCCATGTAGCAGACATGGCCTTACACCGGCTCTCATAAATCGGTGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-AATCGGTGCCA
60011999 ATGCCATGTCCCAGACATGGTCTTACA
1 ATGCCATGTCCCAGACATGGTCTTACA
60012026 TTGACACATA
Statistics
Matches: 204, Mismatches: 52, Indels: 26
0.72 0.18 0.09
Matches are distributed among these distances:
46 29 0.14
47 3 0.01
48 74 0.36
49 4 0.02
50 93 0.46
51 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATCGGTGCCA
Found at i:60011940 original size:96 final size:94
Alignment explanation
Indices: 60011755--60012046 Score: 316
Period size: 96 Copynumber: 3.0 Consensus size: 94
60011745 ACATCGGTGT
* * * ** * *
60011755 CGATGCCATGTCCCAGACATGGTCTTACACTAACACATAT-AACAATGCTAATGCCATGTTCCAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTATAAACGGTGCCAATGCCATG-TCCAG
* * *
60011819 ACATGGTCTTACACTGGCTCGCATATTGAGGC
65 ACATGGTCTTACACT-G-ACACATATCGAGGC
* * *
60011851 CGATGCCATGTCCCAGGCATAGTCTTACACTAGCTCTTATAAACCGGTACCAATGCCATGTCCTA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTATAAA-CGGTGCCAATGCCATGTCC-A
*
60011916 GACATGGTCTTACACTGACACATATCGAGGT
64 GACATGGTCTTACACTGACACATATCGAGGC
* ** * ** *
60011947 CAATGCCATGTAGCAGACATGGCCTTACACCGGCTCTCATAAATCGGTGCCAATGCCATGTCCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTATAAA-CGGTGCCAATGCCATGT-CCA
*
60012012 GACATGGTCTTACATTGACACATATCGAGGC
64 GACATGGTCTTACACTGACACATATCGAGGC
60012043 CGAT
1 CGAT
60012047 TGTACTCGAC
Statistics
Matches: 164, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
96 128 0.78
97 8 0.05
98 28 0.17
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (94 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTATAAACGGTGCCAATGCCATGTCCAGA
CATGGTCTTACACTGACACATATCGAGGC
Found at i:60012003 original size:146 final size:145
Alignment explanation
Indices: 60011707--60012025 Score: 365
Period size: 146 Copynumber: 2.2 Consensus size: 145
60011697 TAAAATGTCG
* * * * * ** *
60011707 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATACATCGGTGTCGATGCCATGTCCCAGA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACCGGTACCAATGCCATGTCCCAGA
* * * *
60011772 CATGGTCTTACACTAACACATATAACAATGCTAATGCCATGTTCCAAACATGGTCTTACACTGGC
66 CATGGTCTTACACTAACACATAT-ACAAGGCTAATGCCATGTACCAAACATGGCCTTACACCGGC
* *
60011837 TCGCATATTGAGGCCG
130 TCGCATATCGAGGCCA
* * * *
60011853 ATGCCATGTCCCAGGCATAGTCTTACACTAGCTCTTATAAACCGGTACCAATGCCATGTCCTAGA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACCGGTACCAATGCCATGTCCCAGA
* * * *
60011918 CATGGTCTTACACTGACACATAT-CGAGG-TCAATGCCATGTAGCAGACATGGCCTTACACCGGC
66 CATGGTCTTACACTAACACATATACAAGGCT-AATGCCATGTACCAAACATGGCCTTACACCGGC
*
60011981 TCTCATAAATCG-GTGCCA
130 TCGCAT--ATCGAG-GCCA
60011999 ATGCCATGTCCCAGACATGGTCTTACA
1 ATGCCATGTCCCAGACATGGTCTTACA
60012026 TTGACACATA
Statistics
Matches: 144, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
143 1 0.01
144 36 0.25
145 1 0.01
146 106 0.74
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (145 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAACCGGTACCAATGCCATGTCCCAGA
CATGGTCTTACACTAACACATATACAAGGCTAATGCCATGTACCAAACATGGCCTTACACCGGCT
CGCATATCGAGGCCA
Found at i:60014773 original size:17 final size:16
Alignment explanation
Indices: 60014734--60014769 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
60014724 GCCAAGTTGG
60014734 AAGT-AAAAAGAACTA
1 AAGTGAAAAAGAACTA
*
60014749 AAGTGAAAAAGAATTA
1 AAGTGAAAAAGAACTA
60014765 AAGTG
1 AAGTG
60014770 GAAAGTGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.61, C:0.03, G:0.19, T:0.17
Consensus pattern (16 bp):
AAGTGAAAAAGAACTA
Found at i:60016776 original size:26 final size:26
Alignment explanation
Indices: 60016746--60016826 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
60016736 CAAGAGTTTC
60016746 AATTAACATATGATGTATGCAAGAAA
1 AATTAACATATGATGTATGCAAGAAA
* ***
60016772 AATTAA-AT-TAAT-TA-G-AGAGTTTC
1 AATTAACATATGATGTATGCA-AG-AAA
60016795 AATTAACATATGATGTATGCAAGAAA
1 AATTAACATATGATGTATGCAAGAAA
60016821 AATTAA
1 AATTAA
60016827 ATTAATTAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
21 1 0.03
22 3 0.08
23 8 0.20
24 5 0.12
25 5 0.12
26 14 0.35
27 3 0.08
28 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (26 bp):
AATTAACATATGATGTATGCAAGAAA
Found at i:60016794 original size:49 final size:49
Alignment explanation
Indices: 60016738--60016836 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
60016728 AATCAATCCA
60016738 AGAGTTTCAATTAACATATGATGTATGCAAGAAAAATTAAATTAATTAG
1 AGAGTTTCAATTAACATATGATGTATGCAAGAAAAATTAAATTAATTAG
60016787 AGAGTTTCAATTAACATATGATGTATGCAAGAAAAATTAAATTAATTAG
1 AGAGTTTCAATTAACATATGATGTATGCAAGAAAAATTAAATTAATTAG
60016836 A
1 A
60016837 TTTAAACATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.32
Consensus pattern (49 bp):
AGAGTTTCAATTAACATATGATGTATGCAAGAAAAATTAAATTAATTAG
Found at i:60035482 original size:42 final size:43
Alignment explanation
Indices: 60035372--60035527 Score: 108
Period size: 43 Copynumber: 3.7 Consensus size: 43
60035362 AACAAGTACA
** * * * *
60035372 ATGCCGACATCCCTGACGTGGTCTTACATGTAATTCAATATCG
1 ATGCCGATGTCCCAGACATGGTCTTACACGTAAATCAATATCG
** *
60035415 ATGCCTCTGTCCCAGATA-GGTTCTTACACG-AAATCAGATA-CG
1 ATGCCGATGTCCCAGACATGG-TCTTACACGTAAATCA-ATATCG
* *
60035457 ATGCCGATGTCCCAGACATGGTCTTATACATAAAT--ATCAATCG
1 ATGCCGATGTCCCAGACATGGTCTTACACGTAAATCAAT--ATCG
* *
60035500 AGGCCTATGTCCCAGACACT-GTCTTACA
1 ATGCCGATGTCCCAGACA-TGGTCTTACA
60035528 TGATATCTCA
Statistics
Matches: 88, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
40 2 0.02
42 32 0.36
43 53 0.60
44 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (43 bp):
ATGCCGATGTCCCAGACATGGTCTTACACGTAAATCAATATCG
Found at i:60038839 original size:39 final size:40
Alignment explanation
Indices: 60038679--60038901 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
60038669 GCTACTCGTT
* *
60038679 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
60038719 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
60038759 CAAATGCCTTCGGG-CTTAGCCCGGAA-TAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
60038797 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * **
60038836 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTATCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
60038877 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
60038902 CATCATTCAA
Statistics
Matches: 163, Mismatches: 12, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
38 39 0.24
39 35 0.21
40 77 0.47
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:60038886 original size:117 final size:119
Alignment explanation
Indices: 60038679--60038901 Score: 294
Period size: 117 Copynumber: 1.9 Consensus size: 119
60038669 GCTACTCGTT
*
60038679 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
60038744 ATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGAATAGTATCTCGCA
66 ATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATAGTATCTCGCA
* * **
60038797 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
60038859 GGATATGGTCACTTATCACAAA-GCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAGCCCGGA
60038902 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
116 4 0.04
117 55 0.60
118 32 0.35
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (119 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATAGTATCTCGCA
Found at i:60059999 original size:41 final size:41
Alignment explanation
Indices: 60059942--60060024 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
60059932 ACATACAATG
60059942 AGGTATATTAATGTCATTTCAGAGTATAATTAGACTATGTT
1 AGGTATATTAATGTCATTTCAGAGTATAATTAGACTATGTT
*
60059983 AGGTATATTAATGTCATTTTAGAGTATAATTAGACTATGTT
1 AGGTATATTAATGTCATTTCAGAGTATAATTAGACTATGTT
60060024 A
1 A
60060025 AGTGTTAATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (41 bp):
AGGTATATTAATGTCATTTCAGAGTATAATTAGACTATGTT
Found at i:60060441 original size:20 final size:20
Alignment explanation
Indices: 60060392--60060443 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
60060382 CAGGCCAGGG
*
60060392 ACACGGGCGTGTCCCAAAGC
1 ACACGAGCGTGTCCCAAAGC
60060412 ACAC-AGGCGTGTCCCAAAGC
1 ACACGA-GCGTGTCCCAAAGC
60060432 ACACGAGCGTGT
1 ACACGAGCGTGT
60060444 GCATTGCCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.27, C:0.33, G:0.29, T:0.12
Consensus pattern (20 bp):
ACACGAGCGTGTCCCAAAGC
Found at i:60062086 original size:26 final size:26
Alignment explanation
Indices: 60062018--60062091 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 26
60062008 AGGCCCATTG
* * * * *
60062018 GCGACCCCAGTTCGCCAAGCCGATTG
1 GCGACCCCAGTTTGCCAAACCTACTA
* *
60062044 GCGA-CCCGGTTTACCAAACCTACTA
1 GCGACCCCAGTTTGCCAAACCTACTA
60062069 GCGACCCCAGTTTGCCAAACCTA
1 GCGACCCCAGTTTGCCAAACCTA
60062092 TTGGTAAACA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
25 18 0.47
26 20 0.53
ACGTcount: A:0.24, C:0.38, G:0.20, T:0.18
Consensus pattern (26 bp):
GCGACCCCAGTTTGCCAAACCTACTA
Found at i:60062129 original size:27 final size:27
Alignment explanation
Indices: 60062099--60062156 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
60062089 CTATTGGTAA
* * *
60062099 ACACCAACTCATCAGACCTTCTGGCAT
1 ACACCAACTCACCAGACCTACTAGCAT
*
60062126 ACACCAACTTACCAGACCTACTAGCAT
1 ACACCAACTCACCAGACCTACTAGCAT
60062153 ACAC
1 ACAC
60062157 TAGCTAGCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.38, G:0.09, T:0.19
Consensus pattern (27 bp):
ACACCAACTCACCAGACCTACTAGCAT
Found at i:60064822 original size:30 final size:30
Alignment explanation
Indices: 60064788--60064845 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
60064778 TAGGCACTAC
*
60064788 CACACGGGT-GATCCACATACCCGTGTGTTA
1 CACACGGGTAGA-CCACACACCCGTGTGTTA
*
60064818 CACACGGGTAGACCACACGCCCGTGTGT
1 CACACGGGTAGACCACACACCCGTGTGT
60064846 CATGTCTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.22, C:0.33, G:0.26, T:0.19
Consensus pattern (30 bp):
CACACGGGTAGACCACACACCCGTGTGTTA
Found at i:60067326 original size:18 final size:19
Alignment explanation
Indices: 60067303--60067338 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
60067293 AACTTGGCAC
*
60067303 CATAA-TCATTTAATTTAA
1 CATAATTCAATTAATTTAA
60067321 CATAATTCAATTAATTTA
1 CATAATTCAATTAATTTA
60067339 CTAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (19 bp):
CATAATTCAATTAATTTAA
Found at i:60070723 original size:104 final size:103
Alignment explanation
Indices: 60070379--60070745 Score: 583
Period size: 103 Copynumber: 3.5 Consensus size: 103
60070369 AACCGTTATT
* * *
60070379 GGTGGATCTCGCACTTAGCACCAGCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
60070444 ATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATAC
* * *
60070482 GGTGGATATCGCACTTAGCACCACCAATTAACCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
60070547 ATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATAC
*
60070585 GGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCAATTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
* *
60070650 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAT
65 AATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATAC
* * **
60070690 GGTGGATCA-CGCACATAGTACCACCAATGAATCGGGGAATCAGCACACAGCAACCC
1 GGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCC
60070746 TTTTATATAC
Statistics
Matches: 244, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
103 125 0.51
104 80 0.33
105 38 0.16
106 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (103 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATAC
Found at i:60071109 original size:29 final size:29
Alignment explanation
Indices: 60071076--60071139 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
60071066 TAATCCACCA
60071076 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
60071105 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
60071135 CCCAA
1 CCCAA
60071140 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:60071113 original size:30 final size:30
Alignment explanation
Indices: 60071083--60071139 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
60071073 CCACCCAACT
60071083 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
60071112 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
60071140 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:60168815 original size:40 final size:40
Alignment explanation
Indices: 60168770--60168958 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 40
60168760 ATAACCACAA
* * *
60168770 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
60168810 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
60168850 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * * * *
60168890 GCATAAA-GCCTTC--GACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
60168927 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
60168959 CATTCAAATG
Statistics
Matches: 136, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
37 30 0.22
38 6 0.04
39 7 0.05
40 89 0.65
41 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:60171254 original size:27 final size:27
Alignment explanation
Indices: 60171206--60171364 Score: 182
Period size: 27 Copynumber: 5.9 Consensus size: 27
60171196 GCGAGGATGC
* * *
60171206 CAGATATTGTGACAAAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGATA
60171233 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
60171259 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
60171286 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
*
60171313 CAGATATATGTGGTAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
60171340 CAAATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
60171365 GACGCTTCCT
Statistics
Matches: 114, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
26 10 0.09
27 100 0.88
28 4 0.04
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:60171299 original size:54 final size:54
Alignment explanation
Indices: 60171206--60171364 Score: 232
Period size: 54 Copynumber: 3.0 Consensus size: 54
60171196 GCGAGGATGC
* * * *
60171206 CAGATAT-TGTGACAAAGTCACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAA
1 CAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCACCAGAA
*
60171259 CAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGCCACCAGAA
1 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGAA
* *
60171313 CAGATATATGTGGTAGAGCCACCAGATCAAATAATTGTGGCATAGCCACCAG
1 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAG
60171365 GACGCTTCCT
Statistics
Matches: 96, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
53 12 0.12
54 84 0.88
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (54 bp):
CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGAA
Found at i:60172991 original size:26 final size:26
Alignment explanation
Indices: 60172960--60173067 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
60172950 TGAAATGCCC
*
60172960 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
60172986 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
60173012 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
60173038 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
60173064 ATCA
1 ATCA
60173068 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:60179575 original size:47 final size:47
Alignment explanation
Indices: 60179509--60180079 Score: 919
Period size: 47 Copynumber: 12.1 Consensus size: 47
60179499 GAAATGATAG
60179509 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
60179556 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
60179605 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
60179652 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
60179699 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
60179746 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
60179795 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
60179842 TAAGGCCTAATAGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
60179888 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
60179935 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
**
60179982 TAAGGCCTAATGGCCGACATGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * * * *
60180029 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
60180076 TAAG
1 TAAG
60180080 TCCCGAAGGG
Statistics
Matches: 496, Mismatches: 23, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
46 45 0.09
47 358 0.72
49 93 0.19
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:60180256 original size:37 final size:37
Alignment explanation
Indices: 60180198--60180276 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
60180188 CCGAGCTCTA
* * *
60180198 AAGACCCGATGACTACTTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
60180235 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
60180272 AAGAC
1 AAGAC
60180277 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:60186152 original size:69 final size:69
Alignment explanation
Indices: 60186041--60186178 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
60186031 TATGGTCTTA
60186041 CACGAAATCACATAACGAAAACCTATGTTATGACATATGTATCCTAACTATTCCTATGGTGCATA
1 CACGAAATCACATAACGAAAACCTATGTTATGACATATGTATCCTAACTATTCCTATGGTGCATA
60186106 CATG
66 CATG
60186110 CACGAAATCACATAACGAAAACCTATGTTATGACATATGTATCCTAACTATTCCTATGGTGCATA
1 CACGAAATCACATAACGAAAACCTATGTTATGACATATGTATCCTAACTATTCCTATGGTGCATA
60186175 CATG
66 CATG
60186179 GCTTTTCAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (69 bp):
CACGAAATCACATAACGAAAACCTATGTTATGACATATGTATCCTAACTATTCCTATGGTGCATA
CATG
Found at i:60195693 original size:26 final size:26
Alignment explanation
Indices: 60195658--60195708 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
60195648 AATGTGAAAG
*
60195658 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
60195684 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
60195709 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:60195746 original size:103 final size:102
Alignment explanation
Indices: 60195581--60195801 Score: 372
Period size: 103 Copynumber: 2.2 Consensus size: 102
60195571 TGTATATAAA
** * *
60195581 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
60195646 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
66 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
*
60195683 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCG-TGATCCACCATATCT
60195747 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
64 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
60195786 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
60195802 GATATCCATT
Statistics
Matches: 112, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
102 27 0.24
103 84 0.75
104 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.32
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:60195853 original size:70 final size:71
Alignment explanation
Indices: 60195721--60195870 Score: 248
Period size: 70 Copynumber: 2.1 Consensus size: 71
60195711 TCATTGGTGG
* *
60195721 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
60195786 AGGGGT
66 AGGGGT
***
60195792 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
60195856 AGGGGT
66 AGGGGT
60195862 TGCTAAGTG
1 TGCTAAGTG
60195871 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 44 0.59
71 30 0.41
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
AGGGGT
Found at i:60195866 original size:26 final size:26
Alignment explanation
Indices: 60195831--60195882 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
60195821 AAATGAAAAG
* *
60195831 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
60195857 GGGGTTGCTAAGTGATGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
60195883 TTCAGTGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.15, C:0.21, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGATGATTCCCCGA
Found at i:60203246 original size:26 final size:26
Alignment explanation
Indices: 60203211--60203261 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
60203201 AATGTGAAAG
*
60203211 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
60203237 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
60203262 TTCATTGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:60203328 original size:101 final size:102
Alignment explanation
Indices: 60203135--60203353 Score: 347
Period size: 102 Copynumber: 2.2 Consensus size: 102
60203125 TGTATATAAA
** * *
60203135 AGGGGTTGCTGTGTGCTGATTCCCGATTTATGGTGGTGCTATGTGCGTGATCCACCATATCTTTG
1 AGGGGTTGCTAAGTGCTGATTCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTTG
60203200 AAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
66 AAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
60203236 AGGGGTTGCTAAGTGCTGATTCCCCG-TTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATT-CCCGATTCA-TGGTGGTGCTAAGTGCG-TGATCCACCATATCT
60203299 TTGAAATGTGAAA-GGGGTTGCTATGTGCTGATTCCCCCG
63 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
60203338 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
60203354 GATATCCATT
Statistics
Matches: 110, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
101 42 0.38
102 67 0.61
103 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTTG
AAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:60203374 original size:71 final size:71
Alignment explanation
Indices: 60203273--60203423 Score: 241
Period size: 71 Copynumber: 2.1 Consensus size: 71
60203263 TCATTGGTGG
* *
60203273 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAA-GGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
60203337 GAGGGGT
65 GAGGGGT
***
60203344 TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
60203409 AGGGGT
66 AGGGGT
60203415 TGCTAAGTG
1 TGCTAAGTG
60203424 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 3 0.04
71 71 0.96
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
AGGGGT
Found at i:60218289 original size:23 final size:23
Alignment explanation
Indices: 60218259--60218304 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
60218249 GAAGCATGTA
60218259 AATGCTTACCCCTCTCTTTTCCC
1 AATGCTTACCCCTCTCTTTTCCC
60218282 AATGCTTACCCCTCTCTTTTCCC
1 AATGCTTACCCCTCTCTTTTCCC
60218305 TGTCTTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.43, G:0.04, T:0.39
Consensus pattern (23 bp):
AATGCTTACCCCTCTCTTTTCCC
Found at i:60222254 original size:14 final size:13
Alignment explanation
Indices: 60222231--60222262 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
60222221 GGTATATCAA
60222231 AACAATAATTAAG
1 AACAATAATTAAG
60222244 AACACATAATTAAG
1 AACA-ATAATTAAG
60222258 AACAA
1 AACAA
60222263 GTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:60226643 original size:19 final size:19
Alignment explanation
Indices: 60226619--60226656 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
60226609 AGTTACATGG
60226619 TGTGATGTTATGTGACTAA
1 TGTGATGTTATGTGACTAA
60226638 TGTGATGTTATGTGACTAA
1 TGTGATGTTATGTGACTAA
60226657 CTTGTTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.42
Consensus pattern (19 bp):
TGTGATGTTATGTGACTAA
Found at i:60229360 original size:28 final size:28
Alignment explanation
Indices: 60229320--60229397 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 28
60229310 CTATTTAAAG
60229320 GTTTAT-GCATTATGGGTTTAGGGATT-AT
1 GTTTATGGC-TTATGGGTTTAGGG-TTGAT
* * *
60229348 GTTTATGGCTTATGGCTTAAGGGTTGGT
1 GTTTATGGCTTATGGGTTTAGGGTTGAT
* *
60229376 GTTTAAGGGTTATGGG-TTAGGG
1 GTTTATGGCTTATGGGTTTAGGG
60229398 GTTAGGGGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
27 7 0.17
28 32 0.78
29 2 0.05
ACGTcount: A:0.18, C:0.04, G:0.36, T:0.42
Consensus pattern (28 bp):
GTTTATGGCTTATGGGTTTAGGGTTGAT
Found at i:60229394 original size:7 final size:7
Alignment explanation
Indices: 60229382--60229450 Score: 66
Period size: 7 Copynumber: 9.6 Consensus size: 7
60229372 TGGTGTTTAA
*
60229382 GGGTTAT
1 GGGTTAG
60229389 GGGTTAG
1 GGGTTAG
60229396 GGGTTAG
1 GGGTTAG
60229403 GGGTTTAG
1 GGG-TTAG
*
60229411 GGGTTAT
1 GGGTTAG
*
60229418 GGGTTAAT
1 GGGTT-AG
*
60229426 GGTTTAG
1 GGGTTAG
*
60229433 GGGTTAA
1 GGGTTAG
*
60229440 GGTTTAG
1 GGGTTAG
60229447 GGGT
1 GGGT
60229451 ATTATTTTGT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
7 38 0.75
8 13 0.25
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (7 bp):
GGGTTAG
Found at i:60229399 original size:28 final size:28
Alignment explanation
Indices: 60229329--60229423 Score: 93
Period size: 28 Copynumber: 3.4 Consensus size: 28
60229319 GGTTTATGCA
* * * *
60229329 TTATGGGTTTAGGGATT-ATGTTTATGGC
1 TTATGGG-TTAGGGGTTGGTGTTTAAGGG
* *
60229357 TTATGGCTTAAGGGTTGGTGTTTAAGGG
1 TTATGGGTTAGGGGTTGGTGTTTAAGGG
* *
60229385 TTATGGGTTAGGGGTTAGGGGTTTAGGGG
1 TTATGGGTTAGGGGTT-GGTGTTTAAGGG
60229414 TTATGGGTTA
1 TTATGGGTTA
60229424 ATGGTTTAGG
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
27 7 0.13
28 28 0.51
29 20 0.36
ACGTcount: A:0.17, C:0.02, G:0.40, T:0.41
Consensus pattern (28 bp):
TTATGGGTTAGGGGTTGGTGTTTAAGGG
Found at i:60229415 original size:22 final size:22
Alignment explanation
Indices: 60229389--60229450 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
60229379 TAAGGGTTAT
*
60229389 GGGTTAGGGGTTAGGGGTTTAG
1 GGGTTAAGGGTTAGGGGTTTAG
* **
60229411 GGGTTATGGGTTAATGGTTTAG
1 GGGTTAAGGGTTAGGGGTTTAG
*
60229433 GGGTTAAGGTTTAGGGGT
1 GGGTTAAGGGTTAGGGGT
60229451 ATTATTTTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.35
Consensus pattern (22 bp):
GGGTTAAGGGTTAGGGGTTTAG
Found at i:60229443 original size:14 final size:14
Alignment explanation
Indices: 60229364--60229450 Score: 77
Period size: 14 Copynumber: 6.1 Consensus size: 14
60229354 GGCTTATGGC
*
60229364 TTAAGGGTT-GGTGT
1 TTAAGGGTTAGG-GG
*
60229378 TTAAGGGTTATGGG
1 TTAAGGGTTAGGGG
*
60229392 TTAGGGGTTAGGGG
1 TTAAGGGTTAGGGG
* *
60229406 TTTAGGGGTTATGGG
1 -TTAAGGGTTAGGGG
*
60229421 TTAATGGTTTAGGGG
1 TTAA-GGGTTAGGGG
*
60229436 TTAAGGTTTAGGGG
1 TTAAGGGTTAGGGG
60229450 T
1 T
60229451 ATTATTTTGT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
14 36 0.58
15 26 0.42
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:60233095 original size:9 final size:9
Alignment explanation
Indices: 60233073--60233432 Score: 381
Period size: 9 Copynumber: 40.3 Consensus size: 9
60233063 CATAATTAAA
60233073 TTACA-AAC
1 TTACATAAC
*
60233081 TTACATAAT
1 TTACATAAC
*
60233090 TTACATAAT
1 TTACATAAC
60233099 TTACATAAC
1 TTACATAAC
*
60233108 ATACATAAC
1 TTACATAAC
*
60233117 TTA-ACAAC
1 TTACATAAC
*
60233125 TTACATGAC
1 TTACATAAC
*
60233134 TCACATAAC
1 TTACATAAC
* *
60233143 TTATATAAT
1 TTACATAAC
60233152 TTACATAAC
1 TTACATAAC
*
60233161 TCACATAAC
1 TTACATAAC
*
60233170 ATACATAAC
1 TTACATAAC
*
60233179 TTA-ACAAC
1 TTACATAAC
*
60233187 TTACATAAT
1 TTACATAAC
60233196 TTACATAAC
1 TTACATAAC
*
60233205 TCACATAAC
1 TTACATAAC
* *
60233214 ATACAAAAC
1 TTACATAAC
*
60233223 TTA-ACAAC
1 TTACATAAC
60233231 TTACATAAC
1 TTACATAAC
*
60233240 TTACATAAT
1 TTACATAAC
60233249 TTACATAAC
1 TTACATAAC
*
60233258 TCACATAAC
1 TTACATAAC
*
60233267 ATACATAACAAC
1 TTACAT---AAC
60233279 TTACATAAC
1 TTACATAAC
*
60233288 TCACATAAC
1 TTACATAAC
*
60233297 TTACATAAT
1 TTACATAAC
60233306 TTACATAAC
1 TTACATAAC
*
60233315 TCACATAAC
1 TTACATAAC
60233324 TTACATAAC
1 TTACATAAC
*
60233333 TTA-ACAAC
1 TTACATAAC
60233341 TTACATAAC
1 TTACATAAC
*
60233350 TCACATAAC
1 TTACATAAC
* *
60233359 TTACGTAAT
1 TTACATAAC
*
60233368 TTACATAAA
1 TTACATAAC
*
60233377 TCACATAAC
1 TTACATAAC
60233386 TTACATAAC
1 TTACATAAC
*
60233395 TTA-ACAAC
1 TTACATAAC
60233403 TTACATAAC
1 TTACATAAC
*
60233412 TCACATAAC
1 TTACATAAC
60233421 TTACATAAC
1 TTACATAAC
60233430 TTA
1 TTA
60233433 ACTAATACAT
Statistics
Matches: 287, Mismatches: 56, Indels: 17
0.80 0.16 0.05
Matches are distributed among these distances:
8 40 0.14
9 239 0.83
12 8 0.03
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.31
Consensus pattern (9 bp):
TTACATAAC
Found at i:60233151 original size:53 final size:54
Alignment explanation
Indices: 60233073--60233429 Score: 397
Period size: 53 Copynumber: 6.7 Consensus size: 54
60233063 CATAATTAAA
*
60233073 TTACA-AACTTACATAATTTACATAATTTACATAACATACATAACTTA-ACAAC
1 TTACATAACTTACATAATTTACATAACTTACATAACATACATAACTTACACAAC
* * * * * * *
60233125 TTACATGACTCACATAACTTATATAATTTACATAAC-TCACATAACATACATAAC
1 TTACATAACTTACATAATTTACATAACTTACATAACAT-ACATAACTTACACAAC
* * *
60233179 TTA-ACAACTTACATAATTTACATAACTCACATAACATACAAAACTTA-ACAAC
1 TTACATAACTTACATAATTTACATAACTTACATAACATACATAACTTACACAAC
* *
60233231 TTACATAACTTACATAATTTACATAACTCACATAACATACATAACAACTTACATAAC
1 TTACATAACTTACATAATTTACATAACTTACATAACATACAT---AACTTACACAAC
* * *
60233288 TCACATAACTTACATAATTTACATAACTCACATAACTTACATAACTTA-ACAAC
1 TTACATAACTTACATAATTTACATAACTTACATAACATACATAACTTACACAAC
* * * * *
60233341 TTACATAACTCACATAACTTACGTAATTTACATAA-ATCACATAACTTACATAAC
1 TTACATAACTTACATAATTTACATAACTTACATAACAT-ACATAACTTACACAAC
* * *
60233395 TTA-ACAACTTACATAACTCACATAACTTACATAAC
1 TTACATAACTTACATAATTTACATAACTTACATAAC
60233430 TTAACTAATA
Statistics
Matches: 258, Mismatches: 35, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
52 14 0.05
53 173 0.67
54 21 0.08
56 6 0.02
57 44 0.17
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30
Consensus pattern (54 bp):
TTACATAACTTACATAATTTACATAACTTACATAACATACATAACTTACACAAC
Found at i:60233151 original size:62 final size:62
Alignment explanation
Indices: 60233073--60233432 Score: 377
Period size: 62 Copynumber: 5.8 Consensus size: 62
60233063 CATAATTAAA
* * * * * *
60233073 TTACA-AACTTACATAATTTACATAATTTACATAACATACATAACTTA-ACAACTTACATGAC
1 TTACATAACTTA-ACAACTTACATAACTCACATAACTTACATAACTTACACAACTTACATAAC
* * * * *
60233134 TCACATAACTTATATAATTTACATAACTCACATAACATACATAACTTA-ACAACTTACATAAT
1 TTACATAACTTA-ACAACTTACATAACTCACATAACTTACATAACTTACACAACTTACATAAC
* * * * * * * *
60233196 TTACATAACTCACATAACATACAAAACTTA-ACAACTTACATAACTTACATAATTTACATAAC
1 TTACATAACTTA-ACAACTTACATAACTCACATAACTTACATAACTTACACAACTTACATAAC
* * * *
60233258 TCACATAACATACATAACAACTTACATAACTCACATAACTTACATAATTTACATAACTCACATAA
1 TTACATAAC-T---TAACAACTTACATAACTCACATAACTTACATAACTTACACAACTTACATAA
60233323 C
62 C
* * * * *
60233324 TTACATAACTTAACAACTTACATAACTCACATAACTTACGTAATTTACATAAATCACATAAC
1 TTACATAACTTAACAACTTACATAACTCACATAACTTACATAACTTACACAACTTACATAAC
60233386 TTACATAACTTAACAACTTACATAACTCACATAACTTACATAACTTA
1 TTACATAACTTAACAACTTACATAACTCACATAACTTACATAACTTA
60233433 ACTAATACAT
Statistics
Matches: 259, Mismatches: 33, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
61 19 0.07
62 188 0.73
63 1 0.00
65 14 0.05
66 37 0.14
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.31
Consensus pattern (62 bp):
TTACATAACTTAACAACTTACATAACTCACATAACTTACATAACTTACACAACTTACATAAC
Found at i:60233284 original size:21 final size:21
Alignment explanation
Indices: 60233255--60233296 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
60233245 TAATTTACAT
60233255 AACTCACATAACAT-ACATAAC
1 AACTCACATAAC-TCACATAAC
*
60233276 AACTTACATAACTCACATAAC
1 AACTCACATAACTCACATAAC
60233297 TTACATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (21 bp):
AACTCACATAACTCACATAAC
Found at i:60233430 original size:44 final size:44
Alignment explanation
Indices: 60233073--60233432 Score: 340
Period size: 44 Copynumber: 8.3 Consensus size: 44
60233063 CATAATTAAA
* * * *
60233073 TTACA-AACTTACATAATTTACATAATTTACATAACATACATAAC
1 TTACATAACTTACATAACTTA-ACAACTTACATAACTTACATAAC
* * * * * *
60233117 TTA-ACAACTTACATGACTCACATAACTTATATAATTTACATAAC
1 TTACATAACTTACATAACTTA-ACAACTTACATAACTTACATAAC
* * *
60233161 TCACATAACATACATAACTTAACAACTTACATAATTTACATAAC
1 TTACATAACTTACATAACTTAACAACTTACATAACTTACATAAC
* * * *
60233205 TCACATAACATACAAAACTTAACAACTTACATAACTTACATAAT
1 TTACATAACTTACATAACTTAACAACTTACATAACTTACATAAC
* * *
60233249 TTACATAACTCACATAACAT-AC-A--TA-ACAACTTACATAAC
1 TTACATAACTTACATAACTTAACAACTTACATAACTTACATAAC
* * * *
60233288 TCACATAACTTACATAATTTACATAACTCACATAACTTACATAAC
1 TTACATAACTTACATAACTTA-ACAACTTACATAACTTACATAAC
* * * * * *
60233333 TTA-ACAACTTACATAACTCACATAACTTACGTAATTTACATAAA
1 TTACATAACTTACATAACTTA-ACAACTTACATAACTTACATAAC
* *
60233377 TCACATAACTTACATAACTTAACAACTTACATAACTCACATAAC
1 TTACATAACTTACATAACTTAACAACTTACATAACTTACATAAC
60233421 TTACATAACTTA
1 TTACATAACTTA
60233433 ACTAATACAT
Statistics
Matches: 259, Mismatches: 48, Indels: 18
0.80 0.15 0.06
Matches are distributed among these distances:
39 28 0.11
40 2 0.01
41 1 0.00
42 2 0.01
43 3 0.01
44 180 0.69
45 43 0.17
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.31
Consensus pattern (44 bp):
TTACATAACTTACATAACTTAACAACTTACATAACTTACATAAC
Found at i:60238694 original size:20 final size:20
Alignment explanation
Indices: 60238664--60238708 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
60238654 CTGTTTTATT
60238664 ATGGG-CCAACTGTATTAAA
1 ATGGGCCCAACTGTATTAAA
* *
60238683 ATGGGCCCAACTGTGTTAAT
1 ATGGGCCCAACTGTATTAAA
60238703 ATGGGC
1 ATGGGC
60238709 AAGATCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTGTATTAAA
Found at i:60238838 original size:28 final size:28
Alignment explanation
Indices: 60238737--60238850 Score: 81
Period size: 28 Copynumber: 3.9 Consensus size: 28
60238727 ACTTGTAATA
* * *
60238737 GGGCTACGGCCCAGACTGATACTGATAT
1 GGGCTAAGGCCCAGATTAATACTGATAT
* *
60238765 GGGCTAA-GCCCAGTATGCTCTGATATTG-TAAT
1 GGGCTAAGGCCCAG-A---T-TAATACTGAT-AT
*
60238797 AGGGCTATGGCCCAGATTAATACTGATAT
1 -GGGCTAAGGCCCAGATTAATACTGATAT
*
60238826 GGGCTAAGGCCCA-ATTAACACTGAT
1 GGGCTAAGGCCCAGATTAATACTGAT
60238851 TTCTGAATAG
Statistics
Matches: 69, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
27 17 0.25
28 19 0.28
29 8 0.12
30 2 0.03
31 1 0.01
32 9 0.13
33 7 0.10
34 6 0.09
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (28 bp):
GGGCTAAGGCCCAGATTAATACTGATAT
Found at i:60241230 original size:13 final size:14
Alignment explanation
Indices: 60241212--60241240 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
60241202 TTATAAATAT
60241212 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
60241225 TTATAATGGTTTAA
1 TTATAATGGTTTAA
60241239 TT
1 TT
60241241 TGTCATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:60241687 original size:21 final size:21
Alignment explanation
Indices: 60241658--60241730 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
60241648 TATAGCGGAT
60241658 GCAGCAGCGAGGGAGGCAGAG
1 GCAGCAGCGAGGGAGGCAGAG
* *
60241679 GCAGTAGCGAGGGAGGCAGCG
1 GCAGCAGCGAGGGAGGCAGAG
* *
60241700 GCAACAGCGAGGGGGGCAGAG
1 GCAGCAGCGAGGGAGGCAGAG
* *
60241721 GTAGTAGCGA
1 GCAGCAGCGA
60241731 TGGCAGCAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.27, C:0.18, G:0.51, T:0.04
Consensus pattern (21 bp):
GCAGCAGCGAGGGAGGCAGAG
Found at i:60242184 original size:86 final size:86
Alignment explanation
Indices: 60242082--60242250 Score: 250
Period size: 86 Copynumber: 2.0 Consensus size: 86
60242072 CGTTTGTAGA
* * *
60242082 AAAAGCGCCGCTAAAGGTCATGACTTTTAGCGGCGTTTCTAG-TGAAAGCACCGCTAAAGGTCAT
1 AAAAGCGCCACGAAAGGTCATGACTTTTAGCGGCGTTTCTAGAT-AAAGCACCGCTAAAAGTCAT
*
60242146 GATCTTTAGTGGCGTTTTTTGT
65 GATCTTTAGTGGCATTTTTTGT
* * * *
60242168 AAAAGCGCCACGAAAGGTCATGACTTTTAGCGGCGTTTGTGGATAAAGCGCCGCTAAAAGTCGTG
1 AAAAGCGCCACGAAAGGTCATGACTTTTAGCGGCGTTTCTAGATAAAGCACCGCTAAAAGTCATG
60242233 ATCTTTAGTGGCATTTTT
66 ATCTTTAGTGGCATTTTT
60242251 CTCTTATAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 73 0.99
87 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (86 bp):
AAAAGCGCCACGAAAGGTCATGACTTTTAGCGGCGTTTCTAGATAAAGCACCGCTAAAAGTCATG
ATCTTTAGTGGCATTTTTTGT
Found at i:60242240 original size:43 final size:43
Alignment explanation
Indices: 60242065--60242225 Score: 191
Period size: 43 Copynumber: 3.7 Consensus size: 43
60242055 TCTGTAAAAA
* *
60242065 TTAGCAGCGTTTGTAGAAAAAGCGCCGCTAAAGGTCATGACTT
1 TTAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCATGACTT
* * *
60242108 TTAGCGGCGTTTCTAGTGAAAGCACCGCTAAAGGTCATGA-TCT
1 TTAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCATGACT-T
* * * * *
60242151 TTAGTGGCGTTTTTTGTAAAAGCGCCACGAAAGGTCATGACTT
1 TTAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCATGACTT
*
60242194 TTAGCGGCGTTTGT-GGATAAAGCGCCGCTAAA
1 TTAGCGGCGTTTGTAGTA-AAAGCGCCGCTAAA
60242226 AGTCGTGATC
Statistics
Matches: 98, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
42 3 0.03
43 94 0.96
44 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (43 bp):
TTAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCATGACTT
Found at i:60254685 original size:27 final size:27
Alignment explanation
Indices: 60254641--60254693 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
60254631 AAACCTTTAG
*
60254641 ATTTTAGTTTAACAAAGAAGAAACTAAT
1 ATTTAAGTTTAACAAAGAAG-AACTAAT
*
60254669 ATTTAAGTTTAA-GAAGAAGAACTAA
1 ATTTAAGTTTAACAAAGAAGAACTAA
60254694 AGAGTATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 6 0.26
28 11 0.48
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (27 bp):
ATTTAAGTTTAACAAAGAAGAACTAAT
Found at i:60266404 original size:13 final size:13
Alignment explanation
Indices: 60266388--60266420 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
60266378 TTTGATTAAA
*
60266388 TTAGTTAATTAGT
1 TTAGATAATTAGT
60266401 TTAGATAATTAGT
1 TTAGATAATTAGT
60266414 TTA-ATAA
1 TTAGATAA
60266421 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:60269887 original size:6 final size:6
Alignment explanation
Indices: 60269868--60269908 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
60269858 ATCCTCTTAT
* *
60269868 TTTTTA TTTCTA TTTTTA TTTTTA TTTTTA TGTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
60269909 CGTTATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:60271760 original size:12 final size:11
Alignment explanation
Indices: 60271729--60271760 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
60271719 GGGTCAAGAG
*
60271729 GAGCCAAAAAC
1 GAGCTAAAAAC
60271740 GAGCTAAAAAC
1 GAGCTAAAAAC
60271751 GAGCTAAAAA
1 GAGCTAAAAA
60271761 GGGACAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.56, C:0.19, G:0.19, T:0.06
Consensus pattern (11 bp):
GAGCTAAAAAC
Found at i:60272815 original size:13 final size:13
Alignment explanation
Indices: 60272799--60272831 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
60272789 TTTGATTAAA
*
60272799 TTAGTTAATTAGT
1 TTAGATAATTAGT
60272812 TTAGATAATTAGT
1 TTAGATAATTAGT
60272825 TTA-ATAA
1 TTAGATAA
60272832 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:60276276 original size:26 final size:26
Alignment explanation
Indices: 60276246--60276297 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
60276236 CACCAATGAA
*
60276246 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
60276272 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
60276298 CCTTTTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:60276379 original size:26 final size:26
Alignment explanation
Indices: 60276350--60276401 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
60276340 ACCAATGAAA
*
60276350 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
60276376 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
60276402 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:60276400 original size:104 final size:102
Alignment explanation
Indices: 60276111--60276479 Score: 596
Period size: 103 Copynumber: 3.6 Consensus size: 102
60276101 TAGCCGTTAT
** *
60276111 TGGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
*
60276176 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
60276214 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
60276279 ATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
66 ATCAGCACATAGCAA-CCCCCTTTTCATTTCAAAGATA
60276317 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
60276382 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * * **
60276421 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
60276480 TTTATATACA
Statistics
Matches: 252, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
102 20 0.08
103 143 0.57
104 88 0.35
105 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (102 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
ATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:60276841 original size:29 final size:29
Alignment explanation
Indices: 60276808--60276871 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
60276798 TAATCCACCA
60276808 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
60276837 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
60276867 CCCAA
1 CCCAA
60276872 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:60276845 original size:30 final size:30
Alignment explanation
Indices: 60276815--60276871 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
60276805 CCACCCAACT
60276815 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
60276844 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
60276872 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:60291496 original size:30 final size:30
Alignment explanation
Indices: 60291460--60291532 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
60291450 ATAAATGAGG
*
60291460 CCACACGGGCGTGCGACATGGCCGTGTATA
1 CCACACGGGCGTGCGACATGGCAGTGTATA
*
60291490 CCACACGGGCGTGCGACATGGCAGTGTATG
1 CCACACGGGCGTGCGACATGGCAGTGTATA
*
60291520 CCATACGGGCGTG
1 CCACACGGGCGTG
60291533 TCCCAGGCCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.19, C:0.29, G:0.36, T:0.16
Consensus pattern (30 bp):
CCACACGGGCGTGCGACATGGCAGTGTATA
Found at i:60292153 original size:12 final size:13
Alignment explanation
Indices: 60292129--60292197 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 13
60292119 GTAATTATTA
*
60292129 TTATTACTATTCT
1 TTATTATTATTCT
60292142 TTATTATT-TTC-
1 TTATTATTATTCT
60292153 TTATTATTATTCT
1 TTATTATTATTCT
*
60292166 TGTCATTATTAGTCT
1 T-T-ATTATTATTCT
60292181 TT-TTAGTTATT-T
1 TTATTA-TTATTCT
60292193 TTATT
1 TTATT
60292198 CTATTGGTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
11 8 0.17
12 12 0.26
13 14 0.30
14 2 0.04
15 11 0.23
ACGTcount: A:0.20, C:0.09, G:0.04, T:0.67
Consensus pattern (13 bp):
TTATTATTATTCT
Done.