Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 45 of 295
Found at i:13204688 original size:18 final size:19
Alignment explanation
Indices: 13204648--13204688 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13204638 CAGTAAGTTT
* *
13204648 TAATAAAAATGTTTAGTTT
1 TAATAAAAATGTTTAGCTC
13204667 TAATAAAAATGTTTA-CTC
1 TAATAAAAATGTTTAGCTC
13204685 TAAT
1 TAAT
13204689 CAACAGGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (19 bp):
TAATAAAAATGTTTAGCTC
Found at i:13209804 original size:48 final size:48
Alignment explanation
Indices: 13209741--13210017 Score: 288
Period size: 48 Copynumber: 5.8 Consensus size: 48
13209731 TTTGGGTGAC
* *
13209741 ATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACATTGTT
1 ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGTT
* * * *
13209789 ATGTGAGCCAGTGTAAGACCATGTCTAGGACATTGCATCGGCATTGTT
1 ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGTT
* ** * ** *
13209837 ATGTGAGCTAGTGTAAGACCATGTTTGAAACATGGCATTGATGTTGAT
1 ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGTT
* * ***
13209885 ATGTGTGCTAGTGTAAGACCATGTCTGGGACATGACATCGACAACATT
1 ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGTT
* * * * ***
13209933 -TGAGAGCTAGTGTAAGACCATGCCTGGGACATGGTATC-AGCCTTAAC
1 ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGA-CATTGTT
* *
13209980 ATGTGAACTAGTGTAAGACCATGTCTGGGCCATGGCAT
1 ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCAT
13210018 TGGTAATTTA
Statistics
Matches: 185, Mismatches: 42, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
46 1 0.01
47 35 0.19
48 149 0.81
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (48 bp):
ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGTT
Found at i:13213482 original size:15 final size:17
Alignment explanation
Indices: 13213462--13213495 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13213452 ATAAATAGAC
13213462 AAAAT-ATTAA-AATTA
1 AAAATAATTAATAATTA
13213477 AAAATAATTAATAATTA
1 AAAATAATTAATAATTA
13213494 AA
1 AA
13213496 TAAAAGCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 5 0.29
17 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATAATTAATAATTA
Found at i:13215498 original size:121 final size:121
Alignment explanation
Indices: 13215249--13215587 Score: 477
Period size: 121 Copynumber: 2.8 Consensus size: 121
13215239 ATCGAGGTGG
* * * * * * *
13215249 TTACATGTTTGAATAATCTTTTGGCTTTCAAGATAAGTTCCATCTTAAAATATTATGCTTGTGAG
1 TTACATGTTTGAACAATC-TTTAGCTTTCGAGATAAGTTCGATTTTAAAATGTTATGCATGTGAG
*
13215314 TTTGCTTCTCTGCCTGTGCTTCTTGTTCGGT-TTTGCTTACTCTAAAATTGAGGCGA
65 TTTGCTTCTCTGCCTGTGCTTCTTGTTCGGTATTTGCTGACTCTAAAATTGAGGCGA
* *
13215370 TTACATGTTTGAACAATCTTTAGCTTTTGAGATAAGTTCGATTTTAAAATGTTATGCGTGTGAGT
1 TTACATGTTTGAACAATCTTTAGCTTTCGAGATAAGTTCGATTTTAAAATGTTATGCATGTGAGT
* * *
13215435 TTGCATCTCTGCCAAG-GCTTCTTGTTCGGTATTTGCTGACTCTAGAATTGA-GCTGA
66 TTGCTTCTCTGCC-TGTGCTTCTTGTTCGGTATTTGCTGACTCTAAAATTGAGGC-GA
* * *
13215491 TTACATGTTTGAACAATCTTTAGCTTTCGAGATAAGTTTGGTTTTAAAATGTTATTCATGTGAGT
1 TTACATGTTTGAACAATCTTTAGCTTTCGAGATAAGTTCGATTTTAAAATGTTATGCATGTGAGT
*
13215556 TTGCTTCTCTGCCTGTGCTTCTTGTTCAGTAT
66 TTGCTTCTCTGCCTGTGCTTCTTGTTCGGTAT
13215588 AGATTGCCAT
Statistics
Matches: 194, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
120 69 0.36
121 125 0.64
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.43
Consensus pattern (121 bp):
TTACATGTTTGAACAATCTTTAGCTTTCGAGATAAGTTCGATTTTAAAATGTTATGCATGTGAGT
TTGCTTCTCTGCCTGTGCTTCTTGTTCGGTATTTGCTGACTCTAAAATTGAGGCGA
Found at i:13224628 original size:25 final size:25
Alignment explanation
Indices: 13224571--13224776 Score: 90
Period size: 25 Copynumber: 8.3 Consensus size: 25
13224561 CTTTTCATTT
13224571 ATGGCTCTTATGAGCTT-CTCGA-TA
1 ATGGCTCTTATGAGCTTCCT-GATTA
**
13224595 ACTTACTCTTATGAGCTTCCTGATTA
1 A-TGGCTCTTATGAGCTTCCTGATTA
**
13224621 ATGGCTCTCCTGAGCTTCCTGA-TA
1 ATGGCTCTTATGAGCTTCCTGATTA
* * * * *
13224645 TTGACTCACT-TGAACTTCTTGATTA
1 ATGGCTC-TTATGAGCTTCCTGATTA
* **
13224670 AAGGCTCTTTCATGAGCTTCCCAATTA
1 ATGGCTC-TT-ATGAGCTTCCTGATTA
**
13224697 ATGGCTC-TCGGAGCTT-CTCGA-TA
1 ATGGCTCTTATGAGCTTCCT-GATTA
* *
13224720 TTGGCTCATATGAGCTTTCC-G-TTA
1 ATGGCTCTTATGAGC-TTCCTGATTA
** *
13224744 CATGGCTCACATGAGCTTCCCG-TTA
1 -ATGGCTCTTATGAGCTTCCTGATTA
13224769 TATGGCTC
1 -ATGGCTC
13224777 AAAAGAGCTT
Statistics
Matches: 136, Mismatches: 32, Indels: 27
0.70 0.16 0.14
Matches are distributed among these distances:
23 9 0.07
24 37 0.27
25 67 0.49
26 6 0.04
27 17 0.12
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (25 bp):
ATGGCTCTTATGAGCTTCCTGATTA
Found at i:13224777 original size:25 final size:25
Alignment explanation
Indices: 13224680--13224786 Score: 94
Period size: 25 Copynumber: 4.4 Consensus size: 25
13224670 AAGGCTCTTT
* *
13224680 CATGAGCTTCCCAATTA-ATGGCTCT
1 CATGAGCTTCCC-GTTATATGGCTCA
* * *
13224705 C-GGAGCTTCTCGATAT-TGGCTCA
1 CATGAGCTTCCCGTTATATGGCTCA
* * *
13224728 TATGAGCTTTCCGTTACATGGCTCA
1 CATGAGCTTCCCGTTATATGGCTCA
13224753 CATGAGCTTCCCGTTATATGGCTCA
1 CATGAGCTTCCCGTTATATGGCTCA
* *
13224778 AAAGAGCTT
1 CATGAGCTT
13224787 TCTGTTTATG
Statistics
Matches: 63, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
23 8 0.13
24 18 0.29
25 37 0.59
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (25 bp):
CATGAGCTTCCCGTTATATGGCTCA
Found at i:13226669 original size:51 final size:50
Alignment explanation
Indices: 13226579--13226683 Score: 126
Period size: 51 Copynumber: 2.0 Consensus size: 50
13226569 AGAAATGGTG
13226579 AAATAGAGAAATAGGAAATATTTGGAAATAATTAAGGTTTTATCCAAAAAGAA
1 AAATAGAGAAATA-GAAATATTTGGAAATAATT-AGGTTTTATCCAAAAA-AA
*
13226632 AAAT-GAGAAAT-GAAATCATTTGGAAATGAATGT-GGTTTTCTCCAAAAAAA
1 AAATAGAGAAATAGAAAT-ATTTGGAAAT-AAT-TAGGTTTTATCCAAAAAAA
13226682 AA
1 AA
13226684 TAAAAAAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
50 9 0.19
51 24 0.50
52 10 0.21
53 5 0.10
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (50 bp):
AAATAGAGAAATAGAAATATTTGGAAATAATTAGGTTTTATCCAAAAAAA
Found at i:13226694 original size:51 final size:49
Alignment explanation
Indices: 13226593--13226697 Score: 115
Period size: 51 Copynumber: 2.1 Consensus size: 49
13226583 AGAGAAATAG
** *
13226593 GAAATATTTGGAAATAATTAAGGTTTTATCCAAAAAGAAAAATGAGAAAT
1 GAAATATTTGGAAATAATT-AGGTTTTATCCAAAAAGAAAAAAAAAAAAT
*
13226643 GAAATCATTTGGAAATGAATGT-GGTTTTCTCCAAAAA-AAAATAAAAAAAAT
1 GAAAT-ATTTGGAAAT-AAT-TAGGTTTTATCCAAAAAGAAAA-AAAAAAAAT
13226694 GAAA
1 GAAA
13226698 ATAAATTGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
50 9 0.19
51 34 0.72
52 3 0.06
53 1 0.02
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (49 bp):
GAAATATTTGGAAATAATTAGGTTTTATCCAAAAAGAAAAAAAAAAAAT
Found at i:13228552 original size:15 final size:15
Alignment explanation
Indices: 13228532--13228564 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
13228522 CTCGAGTCGA
*
13228532 TTCGACTACAACCGG
1 TTCGACTACAACCAG
13228547 TTCGACTACAACCAG
1 TTCGACTACAACCAG
13228562 TTC
1 TTC
13228565 AATCTAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.24
Consensus pattern (15 bp):
TTCGACTACAACCAG
Found at i:13233847 original size:21 final size:21
Alignment explanation
Indices: 13233823--13233862 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13233813 ATGTGTCATT
*
13233823 TAAACATATATATATATCTTA
1 TAAAAATATATATATATCTTA
* *
13233844 TAAAAATTTATGTATATCT
1 TAAAAATATATATATATCT
13233863 CTTTCTTAGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (21 bp):
TAAAAATATATATATATCTTA
Found at i:13237519 original size:20 final size:19
Alignment explanation
Indices: 13237491--13237547 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
13237481 ATCTGTTCTA
13237491 ATTAATATAAATATATTTT
1 ATTAATATAAATATATTTT
*
13237510 ATTAAATATATAA-ATATTAAT
1 ATT-AATATA-AATATATT-TT
13237531 ATTAATATAAAT-TATTT
1 ATTAATATAAATATATTT
13237548 ATTGAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 9 0.28
20 17 0.53
21 6 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTAATATAAATATATTTT
Found at i:13245790 original size:24 final size:26
Alignment explanation
Indices: 13245727--13245790 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
13245717 TATAGTGACT
13245727 AGTTTTTAAAAGAAGATATGGATGGG
1 AGTTTTTAAAAGAAGATATGGATGGG
*
13245753 AGTTTTTAAAAGAAGATATGG-TTGG
1 AGTTTTTAAAAGAAGATATGGATGGG
*
13245778 -GTTTTTAATAGAA
1 AGTTTTTAAAAGAA
13245791 AGTCAATTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 12 0.33
25 3 0.08
26 21 0.58
ACGTcount: A:0.38, C:0.00, G:0.27, T:0.36
Consensus pattern (26 bp):
AGTTTTTAAAAGAAGATATGGATGGG
Found at i:13249432 original size:31 final size:31
Alignment explanation
Indices: 13249397--13249464 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
13249387 AAAAAAAACC
*
13249397 CAGTGATTTAAATAAAAATTTTCAAATAATT
1 CAGTGATTTAAATAAAAACTTTCAAATAATT
* *
13249428 CAGTGGTTTAAATGAAAACTTTCAAATAATT
1 CAGTGATTTAAATAAAAACTTTCAAATAATT
*
13249459 AAGTGA
1 CAGTGA
13249465 CTATTTTGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (31 bp):
CAGTGATTTAAATAAAAACTTTCAAATAATT
Found at i:13256388 original size:17 final size:18
Alignment explanation
Indices: 13256366--13256399 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
13256356 TATTGAGGGA
13256366 TTTGGGGAA-GTAAAAGT
1 TTTGGGGAAGGTAAAAGT
13256383 TTTGGGGAAGGTAAAAG
1 TTTGGGGAAGGTAAAAG
13256400 GAAAAAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.26
Consensus pattern (18 bp):
TTTGGGGAAGGTAAAAGT
Found at i:13258846 original size:19 final size:19
Alignment explanation
Indices: 13258822--13258874 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
13258812 TGATGATAAC
13258822 TTTTAATGTTTAATTTGAG
1 TTTTAATGTTTAATTTGAG
13258841 TTTTAATGTTTAATTTGAG
1 TTTTAATGTTTAATTTGAG
*
13258860 TTTTAA-GGTTAATTT
1 TTTTAATGTTTAATTT
13258875 AATAAAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 8 0.24
19 25 0.76
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.58
Consensus pattern (19 bp):
TTTTAATGTTTAATTTGAG
Found at i:13266179 original size:17 final size:16
Alignment explanation
Indices: 13266159--13266192 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13266149 TTCATAAGTA
*
13266159 TATATCATTCATTTCAT
1 TATATCAAT-ATTTCAT
13266176 TATATCAATATTTCAT
1 TATATCAATATTTCAT
13266192 T
1 T
13266193 GTCCATCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATCAATATTTCAT
Found at i:13266734 original size:138 final size:138
Alignment explanation
Indices: 13266480--13266789 Score: 422
Period size: 138 Copynumber: 2.2 Consensus size: 138
13266470 GACATGATGT
* * * * *
13266480 CATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTAATGTTGCCATGGTAACTTTCAACCAT
1 CATAGTATCTTTCAACCATGGTCTTACTCATTTCCCGTAATGTTGCCATGGTAACTCTCAACCAT
* * * * ** *
13266545 GGTCTTATTCGTTTCATGTCACGTTGTCATGGTATCTTTCAGCCATGGTCTTATTCATTTCATGT
66 GGTCTTATTCGTTTCATGTCACATTGCCATGGTATCTTTCAACCATAGTCTTACACATTTCATAT
13266610 CACACTAC
131 CACACTAC
* * *
13266618 CATAGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTCTCAACCAT
1 CATAGTATCTTTCAACCATGGTCTTACTCATTTCCCGTAATGTTGCCATGGTAACTCTCAACCAT
*
13266683 GGTCTTATTCTTTTCATGTCACATTGCCATGGTATCTTTCAACCATAGTCTTACACATTTCATAT
66 GGTCTTATTCGTTTCATGTCACATTGCCATGGTATCTTTCAACCATAGTCTTACACATTTCATAT
*** *
13266748 CATGTTGC
131 CACACTAC
* *
13266756 CATGGTATCTTTCAACCATGGTCTTACACATTTC
1 CATAGTATCTTTCAACCATGGTCTTACTCATTTC
13266790 ATTTCAGAGA
Statistics
Matches: 149, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
138 149 1.00
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (138 bp):
CATAGTATCTTTCAACCATGGTCTTACTCATTTCCCGTAATGTTGCCATGGTAACTCTCAACCAT
GGTCTTATTCGTTTCATGTCACATTGCCATGGTATCTTTCAACCATAGTCTTACACATTTCATAT
CACACTAC
Found at i:13266782 original size:46 final size:46
Alignment explanation
Indices: 13266487--13266791 Score: 369
Period size: 46 Copynumber: 6.6 Consensus size: 46
13266477 TGTCATAGTG
* * * *
13266487 TCTTTCAACTATGGTCTTACTCATTTTC-TGTAATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCA-TTTCATGTCACGTTGCCATGGTA
* * *
13266533 ACTTTCAACCATGGTCTTATTCGTTTCATGTCACGTTGTCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
* ** * *
13266579 TCTTTCAGCCATGGTCTTATTCATTTCATGTCACACTACCATAGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
** *
13266625 TCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
* * *
13266671 TCTCTCAACCATGGTCTTATTCTTTTCATGTCACATTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
* ** * *
13266717 TCTTTCAACCATAGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
**
13266763 TCTTTCAACCATGGTCTTACACATTTCAT
1 TCTTTCAACCATGGTCTTATTCATTTCAT
13266792 TTCAGAGAGC
Statistics
Matches: 220, Mismatches: 38, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
45 4 0.02
46 216 0.98
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTA
Found at i:13268594 original size:11 final size:11
Alignment explanation
Indices: 13268578--13268625 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
13268568 CTTTATATAC
13268578 TAATAAAATAA
1 TAATAAAATAA
*
13268589 TAATAAAATATCT
1 TAATAAAATA--A
* *
13268602 TATTAAAATAT
1 TAATAAAATAA
13268613 TAATAAAATAA
1 TAATAAAATAA
13268624 TA
1 TA
13268626 TTTATTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:13269805 original size:54 final size:54
Alignment explanation
Indices: 13269737--13269858 Score: 199
Period size: 54 Copynumber: 2.3 Consensus size: 54
13269727 AACGTAAATG
**
13269737 TTAATATGAAATGAATGTAAGGTCAGCTATTGTTATGGCTAACAAATCTTGGTT
1 TTAATATGTGATGAATGTAAGGTCAGCTATTGTTATGGCTAACAAATCTTGGTT
*
13269791 TTAATATGTGATGAATGTAAGGTCAGCTATTGTTATGGCTAGCAAATCTTGGTT
1 TTAATATGTGATGAATGTAAGGTCAGCTATTGTTATGGCTAACAAATCTTGGTT
**
13269845 TTGGTATGTGATGA
1 TTAATATGTGATGA
13269859 GGTTATCTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.30, C:0.08, G:0.24, T:0.39
Consensus pattern (54 bp):
TTAATATGTGATGAATGTAAGGTCAGCTATTGTTATGGCTAACAAATCTTGGTT
Found at i:13290599 original size:7 final size:8
Alignment explanation
Indices: 13290573--13290624 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
13290563 TCTTACGAAG
13290573 ATATTAAA
1 ATATTAAA
13290581 ATATTAAA
1 ATATTAAA
13290589 ATATT-AA
1 ATATTAAA
13290596 ATATTAAGA
1 ATATTAA-A
* *
13290605 AAATATAGA
1 ATAT-TAAA
13290614 ATATTAAA
1 ATATTAAA
13290622 ATA
1 ATA
13290625 GCATTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 7 0.19
8 20 0.54
9 8 0.22
10 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (8 bp):
ATATTAAA
Found at i:13290609 original size:18 final size:18
Alignment explanation
Indices: 13290586--13290620 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13290576 TTAAAATATT
13290586 AAAATATTA-AATATTAAG
1 AAAATA-TAGAATATTAAG
13290604 AAAATATAGAATATTAA
1 AAAATATAGAATATTAA
13290621 AATAGCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
AAAATATAGAATATTAAG
Found at i:13296549 original size:26 final size:26
Alignment explanation
Indices: 13296472--13296559 Score: 108
Period size: 25 Copynumber: 3.5 Consensus size: 26
13296462 TAGCTCTTAT
* *
13296472 GAGCTTACTGTTA-TTCAACTCGGAG
1 GAGCTTACCGTTATTTCAGCTCGGAG
* **
13296497 GAGCTTATCGTTATTT-AGCTCAAAG
1 GAGCTTACCGTTATTTCAGCTCGGAG
*
13296522 GAGCTTACCATTATTTCAGCTCGGAG
1 GAGCTTACCGTTATTTCAGCTCGGAG
13296548 GAGCTTACCGTT
1 GAGCTTACCGTT
13296560 TACAGCTCGT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
25 31 0.61
26 20 0.39
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (26 bp):
GAGCTTACCGTTATTTCAGCTCGGAG
Found at i:13313357 original size:17 final size:17
Alignment explanation
Indices: 13313322--13313360 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
13313312 AAAGATAGTT
* *
13313322 TTAAAATATATTAATAA
1 TTAAAATATATCAAAAA
*
13313339 TTAAAATATGTCAAAAA
1 TTAAAATATATCAAAAA
13313356 TTAAA
1 TTAAA
13313361 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
TTAAAATATATCAAAAA
Found at i:13314552 original size:16 final size:17
Alignment explanation
Indices: 13314531--13314564 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
13314521 TTTGAATTAT
13314531 ATGTAAAAT-ATTTTAA
1 ATGTAAAATCATTTTAA
*
13314547 ATGTAAATTCATTTTAA
1 ATGTAAAATCATTTTAA
13314564 A
1 A
13314565 GTTGACAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (17 bp):
ATGTAAAATCATTTTAA
Found at i:13317436 original size:178 final size:177
Alignment explanation
Indices: 13316973--13317957 Score: 1251
Period size: 178 Copynumber: 5.6 Consensus size: 177
13316963 TTAGAAAGAT
* * * * * *
13316973 TAAGGCTGGTGGTAAAATATGCTCCATTGCCGATACATGGAGATAAAATCCACCATCTTCGATCT
1 TAAGGCTGGCGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCTTCTTCGATCT
* *
13317038 GCTCCACTGCAACTTCAGGGAGATAAGATCTTCAATCTTTAGTCTGCTTTCTTGCTACCTCAGAA
66 GCTCCGCTACAACTTCAGGGAGATAAGATCTTCAATCTTTAGTCTGCTTTCTTGCTACCTCAGAA
* *
13317103 AGATAAGACTTAATTCTTCAACCTGCTCTCTTGCTACCTCAAAGAGA
131 AGATAAGACTCAATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGA
* * * * * *
13317150 TATGGCTGGCGGTAGAATCTGCTACATTGCTGATAGATGGAGATAAGATTCGCCTTCTTCTATCT
1 TAAGGCTGGCGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCTTCTTCGATCT
* * *
13317215 GCTCCGCTACAACTTTAGGGAGATAAAATCTTCAATCTTTAGTCTACTTTCTTGCTACCTCAGAA
66 GCTCCGCTACAACTTCAGGGAGATAAGATCTTCAATCTTTAGTCTGCTTTCTTGCTACCTCAGAA
* * * *
13317280 AGATAATACTCAATTTTTCAACCCGTTCTCTTGCTACCTCAGAGAGA
131 AGATAAGACTCAATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGA
* * * *
13317327 TAAGGCTGGCGGTAAAAATATGCTCCATTGCTGATAGATGGAGATAAGATTCGCCTTCTTCAATC
1 TAAGGCTGGCGGT-AAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCTTCTTCGATC
*
13317392 TGCTCCGCTACAACTTTAGGGAGATAAGATCTTCAATCTTTAGTCTGCTTTCTTGCTACGC-CAG
65 TGCTCCGCTACAACTTCAGGGAGATAAGATCTTCAATCTTTAGTCTGCTTTCTTGCTAC-CTCAG
*
13317456 AAAGATAAGACTCAATTCTTCAACCCGCTCTCTTGCTACCTCAGAGAGA
129 AAAGATAAGACTCAATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGA
* * *
13317505 TAAGGCTGGCGGTAAAAATCCGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCAATC
1 TAAGGCTGGCGGT-AAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCTTCTTCGATC
* * * * * * * *
13317570 TGTTCTGCTACAACTTTAGGGAGATAAAATCTTCAATCTTTAGTCTACTTCCTTACTACCTCAGG
65 TGCTCCGCTACAACTTCAGGGAGATAAGATCTTCAATCTTTAGTCTGCTTTCTTGCTACCTCAGA
* * * * ** *
13317635 AAGATAAAAC-CAATATCTTCAACCTGTTC-CACTGCAATTTCAGGGAGA
130 AAGATAAGACTCAAT-TCTTCAACCTGCTCTC-TTGCTACCTCAGAGAGA
* * * * * * * * *
13317683 TAAGGCTGGTGACTTAAATCTGCTCCATTACCGGTACATGGAGATAAGATTTGTCGTCCTCGATC
1 TAAGGCTGGCG-GTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCTTCTTCGATC
* * * *
13317748 TGCTCCGCTGCAACTTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGG
65 TGCTCCGCTACAACTTCAGGGAGATAAGATCTTCAATCTTTAGTCTGCTTTCTTGCTACCTCAGA
* *
13317813 AAGATAAGACTC-ATTCTTCAACCTGCTCTCTTACTATCTCAGAGAGA
130 AAGATAAGACTCAATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGA
* * * * *
13317860 TAAGGCTGGTGGTAAAATTTGCTCCATTACCGATACATGGAGATAAGATTC-ACTATATTCGATC
1 TAAGGCTGGCGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCT-TCTTCGATC
* *
13317924 TGCTCCTCTGCAACTTCAGGGAGATAAGATCTTC
65 TGCTCCGCTACAACTTCAGGGAGATAAGATCTTC
13317958 CTTTATCAAT
Statistics
Matches: 710, Mismatches: 89, Indels: 19
0.87 0.11 0.02
Matches are distributed among these distances:
175 1 0.00
176 75 0.11
177 208 0.29
178 423 0.60
179 3 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (177 bp):
TAAGGCTGGCGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCTTCTTCGATCT
GCTCCGCTACAACTTCAGGGAGATAAGATCTTCAATCTTTAGTCTGCTTTCTTGCTACCTCAGAA
AGATAAGACTCAATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGA
Found at i:13317812 original size:45 final size:43
Alignment explanation
Indices: 13317763--13317863 Score: 105
Period size: 43 Copynumber: 2.3 Consensus size: 43
13317753 CGCTGCAACT
** *
13317763 TCAGGGAGATAAGATCTTCAATCTTCAGTCTGCT-TCCTTGCTACC
1 TCAGGGAGATAAGA-C-TCAATCTTCAACCTGCTCT-CTTACTACC
* * *
13317808 TCAGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTACTATC
1 TCAGGGAGATAAGACTCAATCTTCAACCTGCTCTCTTACTACC
*
13317851 TCAGAGAGATAAG
1 TCAGGGAGATAAG
13317864 GCTGGTGGTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
43 32 0.68
44 2 0.04
45 13 0.28
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (43 bp):
TCAGGGAGATAAGACTCAATCTTCAACCTGCTCTCTTACTACC
Found at i:13320551 original size:46 final size:47
Alignment explanation
Indices: 13320447--13320566 Score: 152
Period size: 46 Copynumber: 2.6 Consensus size: 47
13320437 TGTCTTCGAC
** * *
13320447 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCA-ATATATATAAT
* * *
13320495 ATGGGCTTACATGGCTCATTCTTGTCTCCAAAGCC-ATATATATGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATATAAT
*
13320541 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
13320567 CTGTCCTGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
46 33 0.53
48 29 0.47
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.37
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATATAAT
Found at i:13327905 original size:46 final size:47
Alignment explanation
Indices: 13327801--13327921 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 47
13327791 TGTCTTCGAC
** * *
13327801 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCA-ATATATATAAT
* * * **
13327849 ATGGGCTTACATGGCTCATTCCTGTGTCCAAAGCC-ATATATCTGGT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATATAAT
*
13327895 ATGGACTTACATGGCTCATTTCTGTCT
1 ATGGACTTACATGGCTCATTCCTGTCT
13327922 TGTCCTGTCC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 32 0.52
48 29 0.48
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATATAAT
Found at i:13336490 original size:19 final size:19
Alignment explanation
Indices: 13336466--13336505 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
13336456 TATGGTCTTT
*
13336466 AATGCATATG-ATGTAATGC
1 AATGCAAATGCATG-AATGC
13336485 AATGCAAATGCATGAATGC
1 AATGCAAATGCATGAATGC
13336504 AA
1 AA
13336506 ATGAGACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (19 bp):
AATGCAAATGCATGAATGC
Found at i:13338511 original size:46 final size:46
Alignment explanation
Indices: 13338461--13338636 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 46
13338451 TGTTTGGGCA
** *
13338461 TCCGAACTCGTTGAGTTGAGTGTGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*** * * ** *
13338507 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
* * * *
13338554 TCCGAGCTCGTTGAGTTGATTCCGAGTTCACTTATGAATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
13338600 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
13338637 GCGAGTTACA
Statistics
Matches: 102, Mismatches: 25, Indels: 6
0.77 0.19 0.05
Matches are distributed among these distances:
46 68 0.67
47 34 0.33
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:13338581 original size:93 final size:93
Alignment explanation
Indices: 13338457--13338628 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
13338447 AGGATGTTTG
** * * *
13338457 GGCATCCGAACTCGTTGAGTTGAGTGTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGAATGCAAACGCCCGAACTCGTTGAG
13338522 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
13338550 GGCATCCGAGCTCGTTGAGTTGATTCCGAGTTCACTTATGAATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGAATGCAAACGCCCGAACTCGTTGAG
13338615 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
13338629 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGAATGCAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:13351962 original size:3 final size:3
Alignment explanation
Indices: 13351956--13352043 Score: 54
Period size: 3 Copynumber: 30.0 Consensus size: 3
13351946 AATAATAATA
** * * * * * *
13351956 ATT ATT ATT ATT ACC ACT ATT ATT ATT ATT -TT ATC ACT ACT GTC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
13352003 ATT ATT A-T AGT ATT ATT AGT ATT ATT TTT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13352044 TTTGTTATCT
Statistics
Matches: 64, Mismatches: 19, Indels: 4
0.74 0.22 0.05
Matches are distributed among these distances:
2 4 0.06
3 60 0.94
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:13352003 original size:23 final size:21
Alignment explanation
Indices: 13351956--13352028 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 21
13351946 AATAATAATA
13351956 ATTATTATTATTACCACTATT
1 ATTATTATTATTACCACTATT
* *
13351977 ATTATTATT-TTATCACTACT
1 ATTATTATTATTACCACTATT
* * * *
13351997 GTCATTATTATTA-TAGTATT
1 ATTATTATTATTACCACTATT
*
13352017 ATTAGTATTATT
1 ATTATTATTATT
13352029 TTTATTATCA
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
20 29 0.71
21 12 0.29
ACGTcount: A:0.32, C:0.10, G:0.04, T:0.55
Consensus pattern (21 bp):
ATTATTATTATTACCACTATT
Found at i:13352035 original size:15 final size:15
Alignment explanation
Indices: 13352023--13352060 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
13352013 TATTATTAGT
13352023 ATTATTTTTATTATC
1 ATTATTTTTATTATC
*
13352038 ATTATTTTTGTTATC
1 ATTATTTTTATTATC
13352053 -TT-TTTTTA
1 ATTATTTTTA
13352061 AAACCATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 5 0.24
14 2 0.10
15 14 0.67
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTATTTTTATTATC
Found at i:13352170 original size:21 final size:20
Alignment explanation
Indices: 13352146--13352187 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
13352136 AAATTTTTTG
13352146 TTATTTCATTAATTATTTTAT
1 TTATTTCATT-ATTATTTTAT
*
13352167 TTATTTCATTTTTATTTTAT
1 TTATTTCATTATTATTTTAT
13352187 T
1 T
13352188 CTTGTCCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATTTCATTATTATTTTAT
Found at i:13353409 original size:20 final size:20
Alignment explanation
Indices: 13353384--13353424 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13353374 ATGTGACAGT
* *
13353384 TCATTTGTATTTTGTTTTAA
1 TCATTTATACTTTGTTTTAA
13353404 TCATTTATACTTTGTTTTAA
1 TCATTTATACTTTGTTTTAA
13353424 T
1 T
13353425 ATGTCACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (20 bp):
TCATTTATACTTTGTTTTAA
Found at i:13353476 original size:18 final size:18
Alignment explanation
Indices: 13353455--13353489 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13353445 TACTAAATGA
13353455 ATAAATA-ATTTTAAAATC
1 ATAAATATA-TTTAAAATC
13353473 ATAAATATATTTAAAAT
1 ATAAATATATTTAAAAT
13353490 AATTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAATATATTTAAAATC
Found at i:13358807 original size:17 final size:17
Alignment explanation
Indices: 13358785--13358819 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
13358775 TATATATTAG
13358785 ATTTTGTCAGTGATGAA
1 ATTTTGTCAGTGATGAA
13358802 ATTTTGTCAGTGATGAA
1 ATTTTGTCAGTGATGAA
13358819 A
1 A
13358820 AATGTAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (17 bp):
ATTTTGTCAGTGATGAA
Found at i:13361187 original size:16 final size:16
Alignment explanation
Indices: 13361168--13361216 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
13361158 TTCTTCCTTT
13361168 TTCTTAACTTTCCCAA
1 TTCTTAACTTTCCCAA
***
13361184 TTCTT--C-TTCCTTT
1 TTCTTAACTTTCCCAA
13361197 TTCTTAACTTTCCCAA
1 TTCTTAACTTTCCCAA
13361213 TTCT
1 TTCT
13361217 GATCAGCATA
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
13 9 0.38
14 1 0.04
15 1 0.04
16 13 0.54
ACGTcount: A:0.16, C:0.31, G:0.00, T:0.53
Consensus pattern (16 bp):
TTCTTAACTTTCCCAA
Found at i:13361197 original size:29 final size:29
Alignment explanation
Indices: 13361158--13361216 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
13361148 GTTATTTTAT
13361158 TTCTTCCTTTTTCTTAACTTTCCCAATTC
1 TTCTTCCTTTTTCTTAACTTTCCCAATTC
13361187 TTCTTCCTTTTTCTTAACTTTCCCAATTC
1 TTCTTCCTTTTTCTTAACTTTCCCAATTC
13361216 T
1 T
13361217 GATCAGCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.56
Consensus pattern (29 bp):
TTCTTCCTTTTTCTTAACTTTCCCAATTC
Found at i:13363145 original size:24 final size:24
Alignment explanation
Indices: 13363117--13363162 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
13363107 CATTGGAAAT
*
13363117 GATGATAAGAAGAATGTACAGGAA
1 GATGATAAGAAGAATATACAGGAA
13363141 GATGATAAGAAGAATATACAGG
1 GATGATAAGAAGAATATACAGG
13363163 TATGTGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.04, G:0.28, T:0.17
Consensus pattern (24 bp):
GATGATAAGAAGAATATACAGGAA
Found at i:13379846 original size:31 final size:31
Alignment explanation
Indices: 13379782--13379848 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
13379772 AAGTTAATCA
** *
13379782 TTGAACTTGGCAATTGTTCTCATATTAGAGC
1 TTGAACTAAGCAATTGTTCCCATATTAGAGC
* * *
13379813 TTGAACTAAGCAATTGTTCCCTTATTGGGGC
1 TTGAACTAAGCAATTGTTCCCATATTAGAGC
13379844 TTGAA
1 TTGAA
13379849 ATTTTTGTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (31 bp):
TTGAACTAAGCAATTGTTCCCATATTAGAGC
Found at i:13380136 original size:60 final size:58
Alignment explanation
Indices: 13379968--13380138 Score: 173
Period size: 60 Copynumber: 2.9 Consensus size: 58
13379958 TATCAGGGAC
* * * *** *
13379968 TAACTTAGACAAAAAAAAGTTCAAGCCCTAAATATGGTAATAATTACCAAGTTTAGAGGT
1 TAACTTGGAC-AAAAAAAGTTCAAACCC-CAATATAAAAATAATTATCAAGTTTAGAGGT
*
13380028 TAACTTGGACAAAAAAAGTTTAAACCCCAATATAAAAATAATTATCAAGTTTA-AGGAT
1 TAACTTGGACAAAAAAAGTTCAAACCCCAATATAAAAATAATTATCAAGTTTAGAGG-T
* * * * *
13380086 TAACTTGGATCACAAATAAGTTCAGACCTCAATGTAAAAATAATTGTCAAGTT
1 TAACTTGGA-CA-AAAAAAGTTCAAACCCCAATATAAAAATAATTATCAAGTT
13380139 CATATCCCAA
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
57 3 0.03
58 31 0.33
59 17 0.18
60 43 0.46
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (58 bp):
TAACTTGGACAAAAAAAGTTCAAACCCCAATATAAAAATAATTATCAAGTTTAGAGGT
Found at i:13387269 original size:13 final size:13
Alignment explanation
Indices: 13387251--13387275 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13387241 TGATACAATA
13387251 ACAAGTAAAAATT
1 ACAAGTAAAAATT
13387264 ACAAGTAAAAAT
1 ACAAGTAAAAAT
13387276 ATAATATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (13 bp):
ACAAGTAAAAATT
Found at i:13393002 original size:21 final size:20
Alignment explanation
Indices: 13392976--13393014 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
13392966 AACCCATTAA
13392976 ACCCCAAAACCCAACTAACCC
1 ACCCCAAAACCCAA-TAACCC
13392997 ACCCCAAAACCCAATAAC
1 ACCCCAAAACCCAATAAC
13393015 TAAACCTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.49, G:0.00, T:0.05
Consensus pattern (20 bp):
ACCCCAAAACCCAATAACCC
Found at i:13406366 original size:69 final size:70
Alignment explanation
Indices: 13406217--13406390 Score: 205
Period size: 69 Copynumber: 2.5 Consensus size: 70
13406207 CTTTCCAAGG
*
13406217 AAAATCAACTCATATTGCGAG-AGATGAG-TGAG-CTCAAGACACGTTGAGGTATTTTTAATTTT
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGTCGAGGTATTTTTAATTTT
*
13406279 TTTTTT
65 GTTTTT
* * *
13406285 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGTCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGTCGAGGTATTTTTAATTT-
13406349 TGTTTTT
64 TGTTTTT
** * *
13406356 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
13406391 TTTAATTTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
69 56 0.61
70 27 0.29
71 9 0.10
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGTCGAGGTATTTTTAATTTTG
TTTTT
Found at i:13406729 original size:15 final size:15
Alignment explanation
Indices: 13406709--13406737 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13406699 ACACGAGGTA
13406709 TTTTTTTTTTTCAAT
1 TTTTTTTTTTTCAAT
13406724 TTTTTTTTTTTCAA
1 TTTTTTTTTTTCAA
13406738 AAAATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTTTTTCAAT
Found at i:13421566 original size:40 final size:40
Alignment explanation
Indices: 13421500--13421724 Score: 303
Period size: 40 Copynumber: 5.7 Consensus size: 40
13421490 GGAGATAATC
* * * *
13421500 ACTCGCAC-AAGGCCTTCGGGTCTTAGCCCGG-ATATGGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
* *
13421539 ACTAGCACAAATGCCTTCAGGACTTAGCCC-GAATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
13421579 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
13421619 ACTCGCACAAATTCCTTCGGGACTTAGCCCGAAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
13421659 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAATC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
13421699 ACTAGCACAAATGTCTTCGGGACTTA
1 ACTCGCACAAATGCCTTCGGGACTTA
13421725 ACCTCGTTAG
Statistics
Matches: 167, Mismatches: 16, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
39 8 0.05
40 155 0.93
41 4 0.02
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:13425295 original size:49 final size:49
Alignment explanation
Indices: 13425242--13425340 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
13425232 GTACACGATA
13425242 ACTTAAATAATATATAAAATGTGAAAGAATAATAAAAATACATGATAAG
1 ACTTAAATAATATATAAAATGTGAAAGAATAATAAAAATACATGATAAG
13425291 ACTTAAATAATATATAAAATGTGAAAGAATAATAAAAATACATGATAAG
1 ACTTAAATAATATATAAAATGTGAAAGAATAATAAAAATACATGATAAG
13425340 A
1 A
13425341 TATAATACTA
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:0.60, C:0.04, G:0.10, T:0.26
Consensus pattern (49 bp):
ACTTAAATAATATATAAAATGTGAAAGAATAATAAAAATACATGATAAG
Found at i:13425346 original size:23 final size:22
Alignment explanation
Indices: 13425266--13425347 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 22
13425256 TAAAATGTGA
13425266 AAGAATAATAAAAATACATGAT
1 AAGAATAATAAAAATACATGAT
* * *
13425288 AAGACTTAAATAATATATAAAATG-T
1 AAGA-AT-AATAA-AAAT-ACATGAT
13425313 GAAAGAATAATAAAAATACATGAT
1 --AAGAATAATAAAAATACATGAT
13425337 AAGATATAATA
1 AAGA-ATAATA
13425348 CTAAGAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
22 8 0.17
23 11 0.24
24 9 0.20
25 9 0.20
26 5 0.11
27 4 0.09
ACGTcount: A:0.61, C:0.04, G:0.10, T:0.26
Consensus pattern (22 bp):
AAGAATAATAAAAATACATGAT
Found at i:13431386 original size:26 final size:26
Alignment explanation
Indices: 13431327--13431387 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
13431317 TTGAAAAAAT
* *
13431327 TTCTCC-ATTTTTCTTTTTTTTTTCTG
1 TTCTCCTA-TTTTCTTTTCTTTTTCTC
13431353 TTCT-CTATTTTCTTTTCTTTTTCTC
1 TTCTCCTATTTTCTTTTCTTTTTCTC
13431378 TTCTCCTATT
1 TTCTCCTATT
13431388 CTATTATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 21 0.68
26 10 0.32
ACGTcount: A:0.05, C:0.23, G:0.02, T:0.70
Consensus pattern (26 bp):
TTCTCCTATTTTCTTTTCTTTTTCTC
Found at i:13434476 original size:46 final size:45
Alignment explanation
Indices: 13434419--13434568 Score: 138
Period size: 46 Copynumber: 3.1 Consensus size: 45
13434409 ACACACCGTA
*
13434419 GCCATAGCCCAGCCATGGTCTTACATGAATCACATATCACACTGAT
1 GCCATAGCCCAGCTATGGTCTTACA-GAATCACATATCACACTGAT
* * * * *
13434465 GCCATATCCCAGATATGGTCTTATACGGAAGCACGTAATCACATATCTCTGAT
1 GCCATAGCCCAGCTATGGTC-T-TACAGAATCACAT-ATCAC--A---CTGAT
* *
13434518 GCCATAGCCCAGCTATGGTCTTACACAGATCACATATCACATTGAT
1 GCCATAGCCCAGCTATGGTCTTACAGA-ATCACATATCACACTGAT
13434564 GCCAT
1 GCCAT
13434569 GGTCTAACCA
Statistics
Matches: 82, Mismatches: 13, Indels: 18
0.73 0.12 0.16
Matches are distributed among these distances:
46 26 0.32
47 8 0.10
48 8 0.10
49 1 0.01
50 1 0.01
51 9 0.11
52 6 0.07
53 23 0.28
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (45 bp):
GCCATAGCCCAGCTATGGTCTTACAGAATCACATATCACACTGAT
Found at i:13435700 original size:23 final size:21
Alignment explanation
Indices: 13435650--13435714 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 21
13435640 CCTGATCATT
13435650 ATACGACACATAAGTGCCTG-
1 ATACGACACATAAGTGCCTGA
*
13435670 ATACGACACACAAGGTGCCTGAA
1 ATACGACACATAA-GTGCCTG-A
13435693 ATACGACACATAAAGTGCCTGA
1 ATACGACACAT-AAGTGCCTGA
13435715 TCAGTATAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 12 0.31
21 7 0.18
22 1 0.03
23 17 0.44
24 2 0.05
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (21 bp):
ATACGACACATAAGTGCCTGA
Found at i:13435946 original size:28 final size:29
Alignment explanation
Indices: 13435900--13435977 Score: 104
Period size: 28 Copynumber: 2.7 Consensus size: 29
13435890 CACCAAAATG
* * **
13435900 TCCAACCAAAACACACCAGTATCATATAA
1 TCCATCCAAAACACACCAGAAGAATATAA
*
13435929 TCC-TCCCAAACACACCAGAAGAATATAA
1 TCCATCCAAAACACACCAGAAGAATATAA
13435957 TCCATCCAAAACACACCAGAA
1 TCCATCCAAAACACACCAGAA
13435978 TAGCACAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 23 0.55
29 19 0.45
ACGTcount: A:0.47, C:0.33, G:0.05, T:0.14
Consensus pattern (29 bp):
TCCATCCAAAACACACCAGAAGAATATAA
Found at i:13439259 original size:31 final size:31
Alignment explanation
Indices: 13439193--13439259 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
13439183 TGATGTTGCT
* *
13439193 AATTG-AATGCATGCTTAAACATGCTACTGA
1 AATTGTAAAGCATGCTTAAACATGCCACTGA
13439223 AATTGTAAAGCATG-TTAAAGCATGCCACT-A
1 AATTGTAAAGCATGCTTAAA-CATGCCACTGA
13439253 ATATTGT
1 A-ATTGT
13439260 TACCGTTACC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (31 bp):
AATTGTAAAGCATGCTTAAACATGCCACTGA
Found at i:13447185 original size:22 final size:22
Alignment explanation
Indices: 13447157--13447198 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
13447147 ATATAGATAC
13447157 AACTT-AATCATGAACGAGCTCG
1 AACTTAAAT-ATGAACGAGCTCG
*
13447179 AACTTAAATATGAATGAGCT
1 AACTTAAATATGAACGAGCT
13447199 TAATTAAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (22 bp):
AACTTAAATATGAACGAGCTCG
Found at i:13456006 original size:18 final size:18
Alignment explanation
Indices: 13455979--13456071 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
13455969 CCCAACTACT
* *
13455979 GTATATGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
13455997 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
13456015 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* *
13456033 ATATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
13456051 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
13456069 GTA
1 GTA
13456072 AACGGTCGTA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:13456031 original size:36 final size:36
Alignment explanation
Indices: 13455979--13456071 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
13455969 CCCAACTACT
* *
13455979 GTATATGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
13456015 GTATACGTGAATAGTACCATATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
13456051 ATATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
13456072 AACGGTCGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:13470736 original size:23 final size:23
Alignment explanation
Indices: 13470710--13470756 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
13470700 GAGATTTCAA
13470710 TTAATCAACCTAGAGTCAGTTGT
1 TTAATCAACCTAGAGTCAGTTGT
*
13470733 TTAATCGACCTAGAGTCAGTTGT
1 TTAATCAACCTAGAGTCAGTTGT
13470756 T
1 T
13470757 CTTACTCTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (23 bp):
TTAATCAACCTAGAGTCAGTTGT
Found at i:13471276 original size:18 final size:18
Alignment explanation
Indices: 13471253--13471323 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
13471243 AAGATGTGTC
13471253 ATTCATTTTCAAAACGTT
1 ATTCATTTTCAAAACGTT
*
13471271 ATTCATTATCACAAA-GTT
1 ATTCATTTTCA-AAACGTT
*
13471289 ATAC-TCTTTCAAAACGTT
1 ATTCAT-TTTCAAAACGTT
*
13471307 ATTAATTTTCAAAACGT
1 ATTCATTTTCAAAACGT
13471324 CACTTATTGC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.09
18 36 0.82
19 4 0.09
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.41
Consensus pattern (18 bp):
ATTCATTTTCAAAACGTT
Found at i:13472307 original size:26 final size:26
Alignment explanation
Indices: 13472265--13472317 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
13472255 TTATTTTTAT
13472265 TATCATTAATAACATAAT-TACTAAAC
1 TATCATTAATAACATAATATA-TAAAC
*
13472291 TATCCTTAATGAA-ATAATATATAAAC
1 TATCATTAAT-AACATAATATATAAAC
13472317 T
1 T
13472318 TAATAATGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (26 bp):
TATCATTAATAACATAATATATAAAC
Found at i:13472756 original size:18 final size:18
Alignment explanation
Indices: 13472733--13472770 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
13472723 AGGACGTGTC
*
13472733 ATTCATTTTCA-AAACGTT
1 ATTCATTATCACAAA-GTT
13472751 ATTCATTATCACAAAGTT
1 ATTCATTATCACAAAGTT
13472769 AT
1 AT
13472771 ACTCTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (18 bp):
ATTCATTATCACAAAGTT
Found at i:13472909 original size:18 final size:18
Alignment explanation
Indices: 13472842--13472912 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
13472832 GCAATAAGTG
*
13472842 ACGTTTTGAAAATTAATA
1 ACGTTTTGAAAATGAATA
*
13472860 ACGTTTTGAAAGA-GTATA
1 ACGTTTTGAAA-ATGAATA
*
13472878 AC-TTTGTGACAATGAATA
1 ACGTTT-TGAAAATGAATA
13472896 ACGTTTTGAAAATGAAT
1 ACGTTTTGAAAATGAAT
13472913 GATACTTCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.09
18 36 0.82
19 4 0.09
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (18 bp):
ACGTTTTGAAAATGAATA
Found at i:13482729 original size:66 final size:66
Alignment explanation
Indices: 13482659--13482792 Score: 223
Period size: 66 Copynumber: 2.0 Consensus size: 66
13482649 AAAAAGAGAG
* *
13482659 TATAGAGGAAAAAGGCGAAATAAAAAATGAAGAGAATAAAGAGATGCGCCAATTTCTCTTTAGCC
1 TATAGAGGAAAAAGGCGAAATAAAAAATAAAGAGAATAAAGAGATGCACCAATTTCTCTTTAGCC
13482724 T
66 T
* * *
13482725 TATAGAGGAAAAAGGTGAAATAAAAAATAAAGAGAATAAAGAGATGCATCAATTTCTTTTTAGCC
1 TATAGAGGAAAAAGGCGAAATAAAAAATAAAGAGAATAAAGAGATGCACCAATTTCTCTTTAGCC
13482790 T
66 T
13482791 TA
1 TA
13482793 CTTTTTTAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (66 bp):
TATAGAGGAAAAAGGCGAAATAAAAAATAAAGAGAATAAAGAGATGCACCAATTTCTCTTTAGCC
T
Found at i:13483224 original size:18 final size:18
Alignment explanation
Indices: 13483162--13483225 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
13483152 TTGGCGTAGA
*
13483162 TATTTTTTTAAAAAATATT
1 TATTTTTTTAAATAAT-TT
* *
13483181 AATTTTTTTAAAT-TTTGT
1 TATTTTTTTAAATAATT-T
*
13483199 TGA-ATTTTTAAATAATTT
1 T-ATTTTTTTAAATAATTT
13483217 TATTTTTTT
1 TATTTTTTT
13483226 TTGAATTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 9
0.68 0.14 0.18
Matches are distributed among these distances:
17 2 0.06
18 18 0.53
19 14 0.41
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TATTTTTTTAAATAATTT
Found at i:13495740 original size:18 final size:18
Alignment explanation
Indices: 13495713--13495747 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13495703 GTAACGACAA
13495713 TAACTACTAACAACTAAT
1 TAACTACTAACAACTAAT
* *
13495731 TAACTGCTAACAGCTAA
1 TAACTACTAACAACTAA
13495748 CCATTACTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.26
Consensus pattern (18 bp):
TAACTACTAACAACTAAT
Found at i:13500576 original size:23 final size:22
Alignment explanation
Indices: 13500523--13500632 Score: 80
Period size: 23 Copynumber: 4.8 Consensus size: 22
13500513 TATCGATATA
* * *
13500523 TCAGCTCGTAAGAGCTTACTGTTT
1 TCAGCTCATTAGAGCTTACCG--T
*
13500547 TCAGCTCATTGGAGCTTACCGAT
1 TCAGCTCATTAGAGCTTACCG-T
* *
13500570 TCAGCTCA-TATGAGTTTACTGT
1 TCAGCTCATTA-GAGCTTACCGT
*
13500592 TCAGCTCGA-TAGAGCTTATCGTT
1 TCAGCTC-ATTAGAGCTTACCG-T
*
13500615 TCAGCTCAATAGAGCTTA
1 TCAGCTCATTAGAGCTTA
13500633 TTGTTTATCA
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
22 17 0.24
23 37 0.52
24 17 0.24
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (22 bp):
TCAGCTCATTAGAGCTTACCGT
Found at i:13500609 original size:45 final size:46
Alignment explanation
Indices: 13500523--13500647 Score: 121
Period size: 45 Copynumber: 2.7 Consensus size: 46
13500513 TATCGATATA
* *
13500523 TCAGCTCGTAAGAGCTTACTGTTTTCAGCTCATTGGAGCTTACCGAT
1 TCAGCTCATAAGAGCTTACTG-TTTCAGCTCATTAGAGCTTACCGAT
* * * *
13500570 TCAGCTCATATGAGTTTACTG-TTCAGCTCGA-TAGAGCTTATCGTT
1 TCAGCTCATAAGAGCTTACTGTTTCAGCTC-ATTAGAGCTTACCGAT
*
13500615 TCAGCTCA-ATAGAGCTTATTGTTTATCAGCTCA
1 TCAGCTCATA-AGAGCTTACTG-TT-TCAGCTCA
13500648 AGAGGAGCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
44 1 0.02
45 35 0.55
46 1 0.02
47 20 0.31
48 7 0.11
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (46 bp):
TCAGCTCATAAGAGCTTACTGTTTCAGCTCATTAGAGCTTACCGAT
Found at i:13500633 original size:23 final size:23
Alignment explanation
Indices: 13500545--13500661 Score: 96
Period size: 23 Copynumber: 5.0 Consensus size: 23
13500535 AGCTTACTGT
* * *
13500545 TTTCAGCTCATTGGAGCTTACCG
1 TTTCAGCTCAATAGAGCTTATCG
* *
13500568 ATTCAGCTC-ATATGAGTTTA-C-
1 TTTCAGCTCAATA-GAGCTTATCG
*
13500589 TGTTCAGCTCGATAGAGCTTATCG
1 T-TTCAGCTCAATAGAGCTTATCG
*
13500613 TTTCAGCTCAATAGAGCTTATTG
1 TTTCAGCTCAATAGAGCTTATCG
*
13500636 TTTATCAGCTCAAGAGGAGCTTATCG
1 -TT-TCAGCTCAATA-GAGCTTATCG
13500662 ATCATGGCTC
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
22 16 0.21
23 38 0.50
24 3 0.04
25 10 0.13
26 9 0.12
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (23 bp):
TTTCAGCTCAATAGAGCTTATCG
Found at i:13500859 original size:40 final size:40
Alignment explanation
Indices: 13500815--13500904 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
13500805 TGTTTATATG
*
13500815 GATGAATTACTGTTGATACGGATGAACTACT-GTTATTACT
1 GATGAATTACTATTGATACGGATGAACTACTGGTTA-TACT
* * * * *
13500855 GATGAACTACTATTTATATGGATGAATTACTGGTTATATT
1 GATGAATTACTATTGATACGGATGAACTACTGGTTATACT
*
13500895 AATGAATTAC
1 GATGAATTAC
13500905 AGGTTATACG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
40 37 0.90
41 4 0.10
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (40 bp):
GATGAATTACTATTGATACGGATGAACTACTGGTTATACT
Found at i:13500893 original size:20 final size:19
Alignment explanation
Indices: 13500808--13500904 Score: 88
Period size: 20 Copynumber: 4.9 Consensus size: 19
13500798 AGATATGTGT
13500808 TTATATGGATGAATTACTG
1 TTATATGGATGAATTACTG
* *
13500827 TTGATACGGATGAACTACTG
1 TT-ATATGGATGAATTACTG
* *
13500847 TTATTACT-GATGAACTACTAT
1 TTA-TA-TGGATGAATTACT-G
13500868 TTATATGGATGAATTACTGG
1 TTATATGGATGAATTACT-G
**
13500888 TTATATTAATGAATTAC
1 TTATATGGATGAATTAC
13500905 AGGTTATACG
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.06
20 57 0.89
21 3 0.05
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (19 bp):
TTATATGGATGAATTACTG
Found at i:13502471 original size:20 final size:20
Alignment explanation
Indices: 13502437--13502486 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
13502427 AGTACATGTA
13502437 TAATGTAAATG-AATGATATT
1 TAATG-AAATGAAATGATATT
13502457 TAATGAAATGAAATGATATT
1 TAATGAAATGAAATGATATT
*
13502477 TGAT-AAATGA
1 TAATGAAATGA
13502487 TTGTTCTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (20 bp):
TAATGAAATGAAATGATATT
Found at i:13518718 original size:16 final size:16
Alignment explanation
Indices: 13518697--13518736 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
13518687 TTGCCCCTAA
*
13518697 ACTTTTGCTTATTTAC
1 ACTTTTGCATATTTAC
13518713 ACTTTTGCATATTTAC
1 ACTTTTGCATATTTAC
13518729 ACTTTTGC
1 ACTTTTGC
13518737 CCCTATGCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (16 bp):
ACTTTTGCATATTTAC
Found at i:13522313 original size:120 final size:120
Alignment explanation
Indices: 13522098--13522343 Score: 429
Period size: 120 Copynumber: 2.0 Consensus size: 120
13522088 TCTAATTGCC
* *
13522098 ATTTAAGGACCTCCACTTTAAACCCTCATTTCAATCAAGTAGTTATGAATTAGAACACATATTTT
1 ATTTAAGGACCTCCACTTTAAACCCCCATTTCAATCAAGTACTTATGAATTAGAACACATATTTT
*
13522163 GCAACTTTTGCAATTTAGTCCTAAACGTCCAATTAAGCACTTTATCAATAAAATT
66 GCAACTTTTGCAATTTAGTCCTAAAAGTCCAATTAAGCACTTTATCAATAAAATT
**
13522218 ATTTAAGGACCTCCTTTTTAAACCCCCATTTCAATCAAGTACTTATGAATTAGAACACATATTTT
1 ATTTAAGGACCTCCACTTTAAACCCCCATTTCAATCAAGTACTTATGAATTAGAACACATATTTT
*
13522283 GTAACTTTTGCAATTTAGTCCTAAAAGTCCAATTAAGCACTTTATCAATAAAATT
66 GCAACTTTTGCAATTTAGTCCTAAAAGTCCAATTAAGCACTTTATCAATAAAATT
*
13522338 ACTTAA
1 ATTTAA
13522344 CGATATTTTT
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (120 bp):
ATTTAAGGACCTCCACTTTAAACCCCCATTTCAATCAAGTACTTATGAATTAGAACACATATTTT
GCAACTTTTGCAATTTAGTCCTAAAAGTCCAATTAAGCACTTTATCAATAAAATT
Found at i:13522372 original size:120 final size:119
Alignment explanation
Indices: 13522114--13522371 Score: 369
Period size: 120 Copynumber: 2.2 Consensus size: 119
13522104 GGACCTCCAC
** *
13522114 TTTAAACCCTCATTTCAATCAAGTAGTTATGAATTAGAACACATATTTTGCAACTTTTGCAATTT
1 TTTAAACCAACATTTCAATCAAGTACTTATGAATTAGAACACATATTTTGCAACTTTTGCAATTT
* * * *
13522179 AGTCCTAAACGTCCAATTAAGCACTTTATCAATAAAATTATTTAAGGACCTCCTT
66 AGTCCTAAAAGTCCAATTAAGCACTTTATCAATAAAATTACTTAACGA-CTCATT
** *
13522234 TTTAAACCCCCATTTCAATCAAGTACTTATGAATTAGAACACATATTTTGTAACTTTTGCAATTT
1 TTTAAACCAACATTTCAATCAAGTACTTATGAATTAGAACACATATTTTGCAACTTTTGCAATTT
13522299 AGTCCTAAAAGTCCAATTAAGCACTTTATCAATAAAATTACTTAACGA-T-ATT
66 AGTCCTAAAAGTCCAATTAAGCACTTTATCAATAAAATTACTTAACGACTCATT
* * *
13522351 TTTACA-CAATATTTTAATCAA
1 TTTAAACCAACATTTCAATCAA
13522372 TAAATAAACC
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
116 11 0.09
117 7 0.06
118 1 0.01
120 107 0.85
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (119 bp):
TTTAAACCAACATTTCAATCAAGTACTTATGAATTAGAACACATATTTTGCAACTTTTGCAATTT
AGTCCTAAAAGTCCAATTAAGCACTTTATCAATAAAATTACTTAACGACTCATT
Found at i:13528580 original size:5 final size:5
Alignment explanation
Indices: 13528565--13528619 Score: 58
Period size: 6 Copynumber: 10.2 Consensus size: 5
13528555 TAAGTCTTCA
13528565 AAAAT -AAAT AAAAT AAAGAT AAAAT AAAAAT AAAGAT AAAAAT AAAAAT
1 AAAAT AAAAT AAAAT AAA-AT AAAAT -AAAAT AAA-AT -AAAAT -AAAAT
13528614 AAAAT A
1 AAAAT A
13528620 GATGGACTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.09
5 18 0.40
6 20 0.44
7 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:13528594 original size:6 final size:6
Alignment explanation
Indices: 13528570--13528617 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
13528560 CTTCAAAAAT
* *
13528570 AAAT-A AAATAA AGAT-A AAATAA AAATAA AGATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
13528616 AA
1 AA
13528618 TAGATGGACT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
5 8 0.22
6 29 0.78
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:13528596 original size:17 final size:18
Alignment explanation
Indices: 13528570--13528616 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
13528560 CTTCAAAAAT
13528570 AAAT-AAAATAAAGAT-A
1 AAATAAAAATAAAGATAA
13528586 AAATAAAAATAAAGATAA
1 AAATAAAAATAAAGATAA
13528604 AAATAAAAATAAA
1 AAATAAAAATAAA
13528617 ATAGATGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.14
17 11 0.38
18 14 0.48
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (18 bp):
AAATAAAAATAAAGATAA
Found at i:13528605 original size:12 final size:11
Alignment explanation
Indices: 13528570--13528617 Score: 69
Period size: 11 Copynumber: 4.2 Consensus size: 11
13528560 CTTCAAAAAT
13528570 AAATAAAATAA
1 AAATAAAATAA
*
13528581 AGATAAAATAA
1 AAATAAAATAA
13528592 AAATAAAGATAA
1 AAATAAA-ATAA
13528604 AAATAAAAATAA
1 AAAT-AAAATAA
13528616 AA
1 AA
13528618 TAGATGGACT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 16 0.48
12 14 0.42
13 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:13534566 original size:13 final size:13
Alignment explanation
Indices: 13534548--13534572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13534538 TGTAGGTGCA
13534548 CACGGCCGTGTCG
1 CACGGCCGTGTCG
13534561 CACGGCCGTGTC
1 CACGGCCGTGTC
13534573 TGGCGTTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.40, G:0.36, T:0.16
Consensus pattern (13 bp):
CACGGCCGTGTCG
Found at i:13539777 original size:24 final size:25
Alignment explanation
Indices: 13539752--13539797 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
13539742 AATGGGGAGA
*
13539752 AAAGAA-GAGGGAAG-AAGAAAGGG
1 AAAGAAGGAGGAAAGAAAGAAAGGG
13539775 AAAGAAGGAGGAAAGAAAGAAAG
1 AAAGAAGGAGGAAAGAAAGAAAG
13539798 AAGAGAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (25 bp):
AAAGAAGGAGGAAAGAAAGAAAGGG
Found at i:13539789 original size:11 final size:10
Alignment explanation
Indices: 13539752--13539837 Score: 56
Period size: 10 Copynumber: 8.4 Consensus size: 10
13539742 AATGGGGAGA
13539752 AAAGAAGAGG
1 AAAGAAGAGG
*
13539762 GAAGAAGAAAGGG
1 AAAGAAG--A-GG
13539775 AAAGAAGGAGG
1 AAAGAA-GAGG
13539786 AAAGAA-A-G
1 AAAGAAGAGG
13539794 AAAGAAGAGAG
1 AAAGAAGAG-G
*
13539805 AAAGAA-AGAA
1 AAAGAAGAG-G
13539815 AAAGAA-AGG
1 AAAGAAGAGG
13539824 AAGAGAAGA-G
1 AA-AGAAGAGG
13539834 AAAG
1 AAAG
13539838 GGAAGGGGTT
Statistics
Matches: 63, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
8 7 0.11
9 6 0.10
10 24 0.38
11 16 0.25
12 2 0.03
13 7 0.11
14 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (10 bp):
AAAGAAGAGG
Found at i:13539794 original size:15 final size:15
Alignment explanation
Indices: 13539763--13539837 Score: 73
Period size: 15 Copynumber: 4.9 Consensus size: 15
13539753 AAGAAGAGGG
13539763 AAGAAGAAAGGGAAAGA
1 AAGAAGAAA--GAAAGA
* *
13539780 AGGAGGAAAGAAAGA
1 AAGAAGAAAGAAAGA
*
13539795 AAGAAGAGAGAAAGA
1 AAGAAGAAAGAAAGA
*
13539810 AAGAA-AAAGAAAGG
1 AAGAAGAAAGAAAGA
13539824 AAG-AGAAGAGAAAG
1 AAGAAGAA-AGAAAG
13539838 GGAAGGGGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
13 1 0.02
14 12 0.24
15 29 0.59
17 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AAGAAGAAAGAAAGA
Found at i:13539798 original size:19 final size:19
Alignment explanation
Indices: 13539774--13539837 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
13539764 AGAAGAAAGG
13539774 GAAAGAAGGAGGAAAGAAA
1 GAAAGAAGGAGGAAAGAAA
13539793 GAAAGAA-GAGAGAAAGAAA
1 GAAAGAAGGAG-GAAAGAAA
*
13539812 GAAA-AAGAAAGGAAGAGAAGA
1 GAAAGAAG-GAGGAA-AGAA-A
13539833 GAAAG
1 GAAAG
13539838 GGAAGGGGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
18 5 0.13
19 22 0.58
20 6 0.16
21 5 0.13
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (19 bp):
GAAAGAAGGAGGAAAGAAA
Found at i:13551662 original size:6 final size:6
Alignment explanation
Indices: 13551653--13551696 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
13551643 TAAGTCTAAG
*
13551653 AAAATT AAAA-T AAACA-T AAAAAT AAAATT AAAATT AAAATT AAA
1 AAAATT AAAATT AAA-ATT AAAATT AAAATT AAAATT AAAATT AAA
13551697 GAAAAAAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (6 bp):
AAAATT
Found at i:13559494 original size:37 final size:37
Alignment explanation
Indices: 13559444--13559522 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
13559434 TTATTACGAA
* * *
13559444 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
13559481 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
13559518 GTCTT
1 GTCTT
13559523 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:13559719 original size:47 final size:47
Alignment explanation
Indices: 13559641--13559950 Score: 503
Period size: 47 Copynumber: 6.6 Consensus size: 47
13559631 CCCTTCGGGA
* * * * * *
13559641 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
13559688 CCTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13559735 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13559782 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13559829 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
13559876 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
13559923 CTTATTACATATATATACACTTTCACAT
1 CTTA-T-CACATATATACACTTTCACAT
13559951 CACAATTATC
Statistics
Matches: 247, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
47 226 0.91
48 1 0.00
49 20 0.08
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:13562714 original size:40 final size:40
Alignment explanation
Indices: 13562669--13562865 Score: 232
Period size: 40 Copynumber: 4.9 Consensus size: 40
13562659 CGAATACACG
* * * * *
13562669 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * * ** * ** *
13562709 ACACCAGCACGAATGCTCTTTGGGGTTTAGCACAAATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
13562749 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
13562789 TCACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
13562829 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
13562866 TTAGTAACTC
Statistics
Matches: 130, Mismatches: 27, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 130 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:13562898 original size:80 final size:80
Alignment explanation
Indices: 13562669--13562906 Score: 214
Period size: 80 Copynumber: 3.0 Consensus size: 80
13562659 CGAATACACG
* * * * * * * *
13562669 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGG--ACATAACACCAGCACGAATGCTCTTTGG
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACAT-A-ACTAGCACCAATGCTCCTCGG
** * ** *
13562732 GGTTTAGCACAAATATA
64 GACTTAGCCCGGATACA
* *
13562749 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCCTCGGGA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATAACTAGCACCAATGCTCCTCGGGA
13562814 CTTAGCCCGGATACA
66 CTTAGCCCGGATACA
* ** * *
13562829 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAATGC-CTTC-GG
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA-TAACTAGCACCAATGCTCCTCGGG
*
13562892 ATCTTAGTCCGGATA
65 A-CTTAGCCCGGATA
13562907 TGGTCACTTA
Statistics
Matches: 132, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
79 3 0.02
80 112 0.85
81 13 0.10
82 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATAACTAGCACCAATGCTCCTCGGGA
CTTAGCCCGGATACA
Found at i:13563282 original size:29 final size:28
Alignment explanation
Indices: 13563248--13563321 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
13563238 TAATCAACCA
*
13563248 CGCACACTTAGTGCCATGTACTTT-AAAC
1 CGCACACTTAGTGCCATGCA-TTTCAAAC
*
13563276 TCGCACACTTAGTGCCATGCATTTCAAGC
1 -CGCACACTTAGTGCCATGCATTTCAAAC
13563305 CAGCACACTTAGTGCCA
1 C-GCACACTTAGTGCCA
13563322 ATCTCATAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 4 0.10
29 37 0.90
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCCATGCATTTCAAAC
Found at i:13563368 original size:43 final size:43
Alignment explanation
Indices: 13563307--13563448 Score: 275
Period size: 43 Copynumber: 3.3 Consensus size: 43
13563297 TTTCAAGCCA
*
13563307 GCACACTTAGTGCCAATCTCATAACCGTGAACACTTATTGCCC
1 GCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCC
13563350 GCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCC
1 GCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCC
13563393 GCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCC
1 GCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCC
13563436 GCACACTTAGTGC
1 GCACACTTAGTGC
13563449 TGAAAACCAA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 98 1.00
ACGTcount: A:0.27, C:0.34, G:0.15, T:0.24
Consensus pattern (43 bp):
GCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCC
Found at i:13565364 original size:37 final size:37
Alignment explanation
Indices: 13565314--13565392 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
13565304 TTATTACGAA
* * *
13565314 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
13565351 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
13565388 GTCTT
1 GTCTT
13565393 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:13565589 original size:47 final size:47
Alignment explanation
Indices: 13565511--13565914 Score: 682
Period size: 47 Copynumber: 8.6 Consensus size: 47
13565501 CCCTTCGGGA
* * * * * *
13565511 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
13565558 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
13565605 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13565652 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
13565699 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13565746 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13565793 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
13565840 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
13565887 CTTATTACATATATATACACTTTCACAT
1 CTTA-T-CACATATATACACTTTCACAT
13565915 CACAATTATC
Statistics
Matches: 339, Mismatches: 16, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
47 318 0.94
48 1 0.00
49 20 0.06
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:13579545 original size:24 final size:26
Alignment explanation
Indices: 13579508--13579560 Score: 92
Period size: 24 Copynumber: 2.1 Consensus size: 26
13579498 TAAGTCCGCA
13579508 CACTCAGTGCTATATAATC-AACTCG
1 CACTCAGTGCTATATAATCAAACTCG
13579533 CACT-AGTGCTATATAATCAAACTCG
1 CACTCAGTGCTATATAATCAAACTCG
13579558 CAC
1 CAC
13579561 ACTTAGTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.26
Consensus pattern (26 bp):
CACTCAGTGCTATATAATCAAACTCG
Found at i:13599465 original size:47 final size:47
Alignment explanation
Indices: 13599030--13599431 Score: 579
Period size: 47 Copynumber: 8.6 Consensus size: 47
13599020 ATACATGAGC
* * * * *
13599030 TAAGGCCAAATGGCAAATGTGATGAATGTGAACATGCATTTGTGTGC
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
* ** * *
13599077 TAAGGCCAAATGGAAAATGTGATGAATGTGAACATGCATTTGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
* *
13599124 TAAGACCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
* * *
13599171 TAAGGCCGAATGGCCAACGTGGTGAATATGAACATGCATATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
* * *
13599218 TAAGGCCGAATGGCCAATGTGATGAATATGAACATGTATATCTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
*
13599265 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
* *
13599312 TAAGGCCGAATGGCCAATGTGAAGAATATGAACATGCATATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
* * *
13599359 TAAGGCCGAATGACCAATGTGATAAATGTGAACATGCATACATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
*
13599406 TAAGGCAGAATGGCCAATGTGATGAA
1 TAAGGCCGAATGGCCAATGTGATGAA
13599432 CGTGGATGTG
Statistics
Matches: 325, Mismatches: 30, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 325 1.00
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (47 bp):
TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
Found at i:13599498 original size:46 final size:46
Alignment explanation
Indices: 13599445--13599535 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
13599435 GGATGTGTAT
* * *
13599445 ATATGTGGGAAAGCCGAATGGTTAATGCGAAATGCGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATACGTATGAGATGG
* * * *
13599491 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATACGTATGAGATG
13599536 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.32, T:0.26
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAATACGTATGAGATGG
Found at i:13605889 original size:40 final size:40
Alignment explanation
Indices: 13605852--13606077 Score: 305
Period size: 40 Copynumber: 5.7 Consensus size: 40
13605842 GCTACTCGTT
* *
13605852 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
13605892 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
13605932 CAAATACCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
13605972 CAAATGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
13606012 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
13606053 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
13606078 CATCATTCAA
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 3 0.02
40 153 0.91
41 13 0.08
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:13605978 original size:120 final size:121
Alignment explanation
Indices: 13605817--13606077 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 121
13605807 CCAAATCACG
* * ** *
13605817 TACCTTCGGAATTTAA-CCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTA
1 TACCTTCGGGACTTAACCCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAACCCGGATT-
* *
13605880 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACAAA
65 TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGATATAGTAACTTAGCACAAA
* * *
13605936 TACCTTCGGGACTTAACCCGGATTTAG-TAACTCGCACAAATGCCTTTGGGACTTAACCCGGATT
1 TACCTTCGGGACTTAACCCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACATAACCCGGATT
** * *
13606000 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA
65 TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAA
* *
13606057 -GCCTTCGGGACTTAGCCCGGA
1 TACCTTCGGGACTTAACCCGGA
13606078 CATCATTCAA
Statistics
Matches: 121, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
119 18 0.15
120 93 0.77
121 10 0.08
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (121 bp):
TACCTTCGGGACTTAACCCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAACCCGGATTT
AGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAA
Found at i:13618225 original size:47 final size:47
Alignment explanation
Indices: 13618159--13618584 Score: 701
Period size: 47 Copynumber: 9.1 Consensus size: 47
13618149 GAAATGATAG
*
13618159 TAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
13618206 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
13618253 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
13618300 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
13618347 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
13618394 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
13618441 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
13618488 TAAGGCCTAATGGCCGATCTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
13618534 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
13618581 TAAG
1 TAAG
13618585 TCCCGAAGGG
Statistics
Matches: 356, Mismatches: 22, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
46 39 0.11
47 317 0.89
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:13618759 original size:37 final size:37
Alignment explanation
Indices: 13618703--13618781 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
13618693 CCGAGCTCTA
* *
13618703 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCAGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCAGGT
* *
13618740 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
13618777 AAGAC
1 AAGAC
13618782 TTCGTAAAAA
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:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
Found at i:13620679 original size:43 final size:43
Alignment explanation
Indices: 13620631--13620733 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
13620621 TTGGTTTTCA
13620631 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
13620674 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
*
13620717 GCACTAAGTGTGTGGGC
1 GCACTAAGTGTGCGGGC
13620734 TTGAAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.22, C:0.15, G:0.36, T:0.27
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:13620750 original size:29 final size:29
Alignment explanation
Indices: 13620715--13620788 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
13620705 GTTGTGAGAT
* * *
13620715 TGGCACTAAGTGTGTGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
13620744 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
13620773 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
13620789 TGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:13621222 original size:40 final size:40
Alignment explanation
Indices: 13621178--13621334 Score: 224
Period size: 40 Copynumber: 3.9 Consensus size: 40
13621168 GAGTTACTAA
* *
13621178 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGCTGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
13621218 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * * *
13621258 ATCCGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * * *
13621298 ATCCGTGCTAAATCCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
13621335 CGTGTATTCG
Statistics
Matches: 104, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 104 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:13621236 original size:80 final size:80
Alignment explanation
Indices: 13621152--13621328 Score: 203
Period size: 80 Copynumber: 2.2 Consensus size: 80
13621142 GGACTAAGAT
** * * *
13621152 CCGAAG-GCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGCT
1 CCGAAGAGCATTCATGCGAGTGA-TAAATCCGGGCTAAGTCCCAAAGAGCATTCATGCTAGCGAT
* *
13621216 GTATCCGGGCTAAGTC
65 ATATCCGGGCTAAATC
* ** * * *
13621232 CCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTGATA
1 CCGAAGAGCATTCATGCGAGTGATAAATCCGGGCTAAGTCCCAAAGAGCATTCATGCTAGCGATA
*
13621297 TATCCGTGCTAAATC
66 TATCCGGGCTAAATC
*
13621312 CCGAAGAGCAATCATGC
1 CCGAAGAGCATTCATGC
13621329 TGGTGACGTG
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 69 0.85
81 12 0.15
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.24
Consensus pattern (80 bp):
CCGAAGAGCATTCATGCGAGTGATAAATCCGGGCTAAGTCCCAAAGAGCATTCATGCTAGCGATA
TATCCGGGCTAAATC
Found at i:13621314 original size:120 final size:120
Alignment explanation
Indices: 13621099--13621329 Score: 279
Period size: 120 Copynumber: 1.9 Consensus size: 120
13621089 TCGAATGATG
** * * *
13621099 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCTGGACTAAGATCCGAAGGCATTG
1 TCCGGGCTAAGTCCCGAAGGCTTCATGCTAAGTGACCATATCCGGACTAAGATCCAAAGGCATTC
* * *
13621164 GTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGCTGTA
66 GTGCGAGTGACTAAATCCGGGCTAAATCCCGAAGAGCAATCATGCTAGCGCTGTA
** * *
13621219 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TGTATCCGGGCTAAGTTCCAAAGAGCA
1 TCCGGGCTAAGTCCCGAAG-GC-TTCATGCTAAGTGACCATATCCGGACTAAGATCCAAAG-GCA
* * *
13621282 TTCGTGCTAGTGA-TATATCCGTGCTAAATCCCGAAGAGCAATCATGCT
63 TTCGTGCGAGTGACTAAATCCGGGCTAAATCCCGAAGAGCAATCATGCT
13621330 GGTGACGTGT
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
120 67 0.72
121 20 0.22
122 6 0.06
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCTTCATGCTAAGTGACCATATCCGGACTAAGATCCAAAGGCATTC
GTGCGAGTGACTAAATCCGGGCTAAATCCCGAAGAGCAATCATGCTAGCGCTGTA
Found at i:13624702 original size:47 final size:47
Alignment explanation
Indices: 13624636--13625061 Score: 701
Period size: 47 Copynumber: 9.1 Consensus size: 47
13624626 GAAATGATAG
*
13624636 TAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
13624683 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
13624730 TAAGGCCTAATAGCCGATGTGATGAATGTGGAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
13624777 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
13624824 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
13624871 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
13624918 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
13624965 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
13625011 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
13625058 TAAG
1 TAAG
13625062 TCCCGAAGGG
Statistics
Matches: 356, Mismatches: 22, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
46 40 0.11
47 316 0.89
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:13625236 original size:37 final size:37
Alignment explanation
Indices: 13625180--13625258 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
13625170 CCGAGCTCTA
* *
13625180 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
13625217 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
13625254 AAGAC
1 AAGAC
13625259 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:13627964 original size:26 final size:24
Alignment explanation
Indices: 13627934--13627983 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
13627924 AAATAAAAAA
*
13627934 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
13627960 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
13627984 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:13628840 original size:13 final size:13
Alignment explanation
Indices: 13628813--13628851 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
13628803 GGAGTAATCA
13628813 CACAC-GGCGTGT
1 CACACGGGCGTGT
*
13628825 CACACGGGCATGT
1 CACACGGGCGTGT
13628838 CACACGGGCGTGT
1 CACACGGGCGTGT
13628851 C
1 C
13628852 CCTGCCGAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.18, C:0.33, G:0.33, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:13629901 original size:3 final size:3
Alignment explanation
Indices: 13629895--13629938 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
13629885 ATAATAATAA
13629895 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
13629939 AGATATTGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:13631916 original size:30 final size:30
Alignment explanation
Indices: 13631850--13631921 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
13631840 ATACAAGGAT
* * *
13631850 GAATTTTTCATGTTAAATTATTGTTGTAAT
1 GAATTTTTCATGTTAAATGATTGTTATAAA
13631880 GAATTTTTCATGTTAAATGA-TGTTATACAA
1 GAATTTTTCATGTTAAATGATTGTTATA-AA
*
13631910 GGATTTTTCATG
1 GAATTTTTCATG
13631922 GGTTTGTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 6 0.16
30 31 0.84
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.49
Consensus pattern (30 bp):
GAATTTTTCATGTTAAATGATTGTTATAAA
Found at i:13632507 original size:25 final size:25
Alignment explanation
Indices: 13632470--13632570 Score: 132
Period size: 25 Copynumber: 4.0 Consensus size: 25
13632460 GCGGACACAC
*
13632470 TACAGCTCATATGAGCTTTCCGATT
1 TACAGCTCGTATGAGCTTTCCGATT
* * *
13632495 TACATCTTGTATGAGCTTTTCGATT
1 TACAGCTCGTATGAGCTTTCCGATT
*
13632520 TACAGCTCGTATGAGCTTCCCGATT
1 TACAGCTCGTATGAGCTTTCCGATT
*
13632545 TATAGCTCGTATGAGC-TTCACGATT
1 TACAGCTCGTATGAGCTTTC-CGATT
13632570 T
1 T
13632571 GTAGCTCATA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
24 2 0.03
25 63 0.97
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.39
Consensus pattern (25 bp):
TACAGCTCGTATGAGCTTTCCGATT
Found at i:13635444 original size:42 final size:42
Alignment explanation
Indices: 13635395--13635511 Score: 119
Period size: 42 Copynumber: 2.8 Consensus size: 42
13635385 CAAATTGTGG
*
13635395 TATCGTGTAAGACCATGTCTGGGACATTGGCATC-GTATATGA
1 TATCGTGTAAGACCATGTCTGGGACA-TGGCATCAATATATGA
* * * * *
13635437 TTTCGTGTAAGACCCTGTCTAGGACAACGGCATCAATATTTGA
1 TATCGTGTAAGACCATGTCTGGGAC-ATGGCATCAATATATGA
* * * *
13635480 TAACATGTAAGACCATATCTGGGATATGGCAT
1 TATCGTGTAAGACCATGTCTGGGACATGGCAT
13635512 TGTACAAGCT
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
42 34 0.58
43 25 0.42
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (42 bp):
TATCGTGTAAGACCATGTCTGGGACATGGCATCAATATATGA
Found at i:13637439 original size:13 final size:13
Alignment explanation
Indices: 13637421--13637447 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13637411 GCTCGACAGG
13637421 GACACGCCCGTGT
1 GACACGCCCGTGT
13637434 GACACGCCCGTGT
1 GACACGCCCGTGT
13637447 G
1 G
13637448 CGATTACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:13639630 original size:55 final size:55
Alignment explanation
Indices: 13639541--13639658 Score: 157
Period size: 55 Copynumber: 2.1 Consensus size: 55
13639531 TGTAGCTCTG
* ***
13639541 CGCACGCCCGTGTTATTTTAACAGGTTCGCCCAC-GGTTGCTTGGCACGGGCGTGT
1 CGCACGCCCGTGTTAATTTAACAGGTTCGCCCACGGGTT-AAAGGCACGGGCGTGT
* * *
13639596 CGCACGCCCTTGTTAATTTGACAGGTTCGGCCACGGGTTAAAGGCACGGGCGTGT
1 CGCACGCCCGTGTTAATTTAACAGGTTCGCCCACGGGTTAAAGGCACGGGCGTGT
13639651 CGCACGCC
1 CGCACGCC
13639659 TGTGCTGTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
55 51 0.93
56 4 0.07
ACGTcount: A:0.15, C:0.30, G:0.31, T:0.24
Consensus pattern (55 bp):
CGCACGCCCGTGTTAATTTAACAGGTTCGCCCACGGGTTAAAGGCACGGGCGTGT
Found at i:13644959 original size:43 final size:43
Alignment explanation
Indices: 13644897--13645098 Score: 266
Period size: 43 Copynumber: 4.7 Consensus size: 43
13644887 TATGTGTTCT
* *
13644897 CGTGTAAGACTACGTCTGGGACGTTGGCATCAATATCTGATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCAATATGTGATTA
* * * *
13644940 CGTGTAAGACCATGCCTGGGATGTTGGCATCGATATGTGATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCAATATGTGATTA
*
13644983 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCAATATGTGATTA
*
13645026 CATGTAAGACC-CTGTCTGGGACAG-TGGCATCGAA-ATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATC-AATATGTGATTA
* *
13645069 CATGTAAGACCACGTCTGGGATGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
13645099 TGTACGATAT
Statistics
Matches: 142, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
42 2 0.01
43 137 0.96
44 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCAATATGTGATTA
Found at i:13645032 original size:86 final size:86
Alignment explanation
Indices: 13644897--13645098 Score: 298
Period size: 86 Copynumber: 2.3 Consensus size: 86
13644887 TATGTGTTCT
* *
13644897 CGTGTAAGACTACGTCTGGGACGTTGGCATCAATATCTGATTACGTGTAAGACCATGCCTGGGA-
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCAATATCTGATTACATGTAAGACCATGCCTGGGAC
* *
13644961 TGTTGGCATCGATATGTGATTA
66 AG-TGGCATCGAAATGTGATTA
* * * *
13644983 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACATGTAAGACCCTGTCTGGGAC
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCAATATCTGATTACATGTAAGACCATGCCTGGGAC
13645048 AGTGGCATCGAAATGTGATTA
66 AGTGGCATCGAAATGTGATTA
* *
13645069 CATGTAAGACCACGTCTGGGATGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
13645099 TGTACGATAT
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
86 104 0.99
87 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (86 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCAATATCTGATTACATGTAAGACCATGCCTGGGAC
AGTGGCATCGAAATGTGATTA
Found at i:13645168 original size:56 final size:56
Alignment explanation
Indices: 13645103--13645405 Score: 394
Period size: 56 Copynumber: 5.4 Consensus size: 56
13645093 TGGCATTGTA
*
13645103 CGATATGTGTGTGCGAGTAAGACCATGTTTAATACATTGGCATCGATATGTGATTC
1 CGATATGTGTGTGCGAGTAAGACCATGTTTAATACATTGGCATCAATATGTGATTC
* * * *
13645159 CGATATGTGTGTGTGAATAAGACCACGTTTAATACGTTGGCATCAATATGTGATTC
1 CGATATGTGTGTGCGAGTAAGACCATGTTTAATACATTGGCATCAATATGTGATTC
* * * * *
13645215 CGATATGTGTGTTCGAGTAAGATCACT-TTTAATACGTTGGTATCGATATGTGATTC
1 CGATATGTGTGTGCGAGTAAGACCA-TGTTTAATACATTGGCATCAATATGTGATTC
* *
13645271 TGATATGTGTGTGCGAATAAGACCATGTTTAATACATTGGCATCAATATGTGATT-
1 CGATATGTGTGTGCGAGTAAGACCATGTTTAATACATTGGCATCAATATGTGATTC
* * ** *
13645326 CGATATGTGTGTGTGAGTAAGATCACATTTAATACTTTGGCATCAATATGTGATTC
1 CGATATGTGTGTGCGAGTAAGACCATGTTTAATACATTGGCATCAATATGTGATTC
* * * *
13645382 TGATATGTGTTTACAAGTAAGACC
1 CGATATGTGTGTGCGAGTAAGACC
13645406 CTATCTGGGA
Statistics
Matches: 212, Mismatches: 32, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
55 49 0.23
56 163 0.77
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (56 bp):
CGATATGTGTGTGCGAGTAAGACCATGTTTAATACATTGGCATCAATATGTGATTC
Found at i:13645301 original size:112 final size:111
Alignment explanation
Indices: 13645103--13645391 Score: 438
Period size: 112 Copynumber: 2.6 Consensus size: 111
13645093 TGGCATTGTA
* * *
13645103 CGATATGTGTGTGCGAGTAAGACCA-TGTTTAATACATTGGCATCGATATGTGATTCCGATATGT
1 CGATATGTGTGTTCGAGTAAGATCACT-TTTAATACATTGGCATCGATATGTGATTCTGATATGT
* *
13645167 GTGTGTGAATAAGACCACGTTTAATACGTTGGCATCAATATGTGATT
65 GTGTGCGAATAAGACCACGTTTAATACATTGGCATCAATATGTGATT
* *
13645214 CCGATATGTGTGTTCGAGTAAGATCACTTTTAATACGTTGGTATCGATATGTGATTCTGATATGT
1 -CGATATGTGTGTTCGAGTAAGATCACTTTTAATACATTGGCATCGATATGTGATTCTGATATGT
*
13645279 GTGTGCGAATAAGACCATGTTTAATACATTGGCATCAATATGTGATT
65 GTGTGCGAATAAGACCACGTTTAATACATTGGCATCAATATGTGATT
* * *
13645326 CGATATGTGTGTGT-GAGTAAGATCACATTTAATACTTTGGCATCAATATGTGATTCTGATATGT
1 CGATATGTGTGT-TCGAGTAAGATCACTTTTAATACATTGGCATCGATATGTGATTCTGATATGT
13645390 GT
65 GT
13645392 TTACAAGTAA
Statistics
Matches: 163, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
111 60 0.37
112 102 0.63
113 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (111 bp):
CGATATGTGTGTTCGAGTAAGATCACTTTTAATACATTGGCATCGATATGTGATTCTGATATGTG
TGTGCGAATAAGACCACGTTTAATACATTGGCATCAATATGTGATT
Done.