Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 59 of 199
Found at i:17100606 original size:348 final size:347
Alignment explanation
Indices: 17099760--17100799 Score: 1832
Period size: 348 Copynumber: 3.0 Consensus size: 347
17099750 GGATGAAACA
* *
17099760 CTCATTTTAAATGATTCATATACATAGGATTTGCCTAAAGAATTTAGC-AAAAGGAGACAGTTAC
1 CTCATTTTAAATGATTCACAGACATAGGATTTGCCTAAAGAATTTAGCAAAAAGGAGACAGTTAC
* * * * * *
17099824 AAATCCAACTTTTATTTAAAGGGCGGATAAGTAATTCTGTGCTGGACATGAGTGAAGCTTAAAAC
66 AAATCCAACTTTTAATTGAAGGGCAGATAAGTAATTCTGCGGTGGACATGAGTGAAACTTAAAAC
17099889 CT-ATGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTCTGAAGCTTTGACCCATGGTCA
131 CTCATGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTCTGAAGCTTTGACCCATGGTCA
17099953 CTACTCGCTAGAACTAAGAGTTCAGCACTCTACCAAAAAACAACAAGGCCATTGGAAAATGCCTA
196 CTACTCGCTAGAACTAAGAGTTCAGCACTCTACCAAAAAACAACAAGGCCATTGGAAAATGCCTA
17100018 ACTTCTATGGTGACAACAGACAG-CTTTTGCACTTGGAAGCTTTTAGAATCCCAACTAAGGCCTA
261 ACTTCTATGGTGACAACAGACAGCCTTTTGCACTTGGAAGCTTTTAGAATCCCAACTAAGGCCTA
17100082 TCCTTCAGGATCTCTCCTAGTT
326 TCCTTCAGGATCTCTCCTAGTT
17100104 CTCATTTTAAATGATTCACAGACATAGGATTTGCCTAAAGAATTTAGCAAAAAGGAGACAGTTAC
1 CTCATTTTAAATGATTCACAGACATAGGATTTGCCTAAAGAATTTAGCAAAAAGGAGACAGTTAC
17100169 AAATCCAACTTTTAATTGAAGGGCAGATAAGTAATTCTGCGGTGGACATGAGTGAAACTTAAAAC
66 AAATCCAACTTTTAATTGAAGGGCAGATAAGTAATTCTGCGGTGGACATGAGTGAAACTTAAAAC
*
17100234 CTCAAGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTCTGAAGCTTTGACCCATGGTCA
131 CTCATGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTCTGAAGCTTTGACCCATGGTCA
17100299 CTACTCGCTAGAACTAAGAGTTCAGCACTCTACCAAAAAACAACAAGGCCATTGGAAAATGCCTA
196 CTACTCGCTAGAACTAAGAGTTCAGCACTCTACCAAAAAACAACAAGGCCATTGGAAAATGCCTA
17100364 ACTTCTATGGTGACAACAGACAGCCTTTTGCACTTGGAAGCTTTTAGAATCCCAACTAAGGCCTA
261 ACTTCTATGGTGACAACAGACAGCCTTTTGCACTTGGAAGCTTTTAGAATCCCAACTAAGGCCTA
17100429 TCCTTCAGGATCTCTCCTAGTT
326 TCCTTCAGGATCTCTCCTAGTT
17100451 CTCATTTTTAAATGATTCACAGACATAGGATTTGCCTAAAGAATTTAGCAAAAAGGAGACAGTTA
1 CTCA-TTTTAAATGATTCACAGACATAGGATTTGCCTAAAGAATTTAGCAAAAAGGAGACAGTTA
*
17100516 CAAATCCAACTTTTAATTGAAGGGCAGATAAGTTATTCTGCGGTGGACATGAGTGAAACTTAAAA
65 CAAATCCAACTTTTAATTGAAGGGCAGATAAGTAATTCTGCGGTGGACATGAGTGAAACTTAAAA
*
17100581 CCTCATGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTC--AAGCTTTGA-CCTTGGTC
130 CCTCATGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTCTGAAGCTTTGACCCATGGTC
* * *
17100643 A-TACTCGCTAGAACTAAGAGTTCAGCACTC--CCAAAAAACAATAAGGCTATTGGCAAATGCCT
195 ACTACTCGCTAGAACTAAGAGTTCAGCACTCTACCAAAAAACAACAAGGCCATTGGAAAATGCCT
*
17100705 AACTTCTATGGTGACAACAGACAGCCTTTTGCACTTGGAAG-TTTTAGAATCCCAACTGAGGCCT
260 AACTTCTATGGTGACAACAGACAGCCTTTTGCACTTGGAAGCTTTTAGAATCCCAACTAAGGCCT
*
17100769 ATCCTTCAGGA-CTACTCCTAATT
325 ATCCTTCAGGATCT-CTCCTAGTT
*
17100792 CTAATTTT
1 CTCATTTT
17100800 GGATTGGAGA
Statistics
Matches: 673, Mismatches: 18, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
340 6 0.01
341 44 0.07
342 70 0.10
344 75 0.11
345 85 0.13
346 158 0.23
347 67 0.10
348 168 0.25
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (347 bp):
CTCATTTTAAATGATTCACAGACATAGGATTTGCCTAAAGAATTTAGCAAAAAGGAGACAGTTAC
AAATCCAACTTTTAATTGAAGGGCAGATAAGTAATTCTGCGGTGGACATGAGTGAAACTTAAAAC
CTCATGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTCTGAAGCTTTGACCCATGGTCA
CTACTCGCTAGAACTAAGAGTTCAGCACTCTACCAAAAAACAACAAGGCCATTGGAAAATGCCTA
ACTTCTATGGTGACAACAGACAGCCTTTTGCACTTGGAAGCTTTTAGAATCCCAACTAAGGCCTA
TCCTTCAGGATCTCTCCTAGTT
Found at i:17102531 original size:1 final size:1
Alignment explanation
Indices: 17102525--17102556 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
17102515 TTTTCTCTTC
17102525 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17102557 GCATAGGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17103692 original size:33 final size:33
Alignment explanation
Indices: 17103655--17103724 Score: 124
Period size: 33 Copynumber: 2.1 Consensus size: 33
17103645 CTGAGGCACA
17103655 AGGCGCAAAAAAAGCGCTCA-CCCGAGTAAACCG
1 AGGCGCAAAAAAAGCGCT-AGCCCGAGTAAACCG
17103688 AGGCGCAAAAAAAGCGCTAGCCCGAGTAAACCG
1 AGGCGCAAAAAAAGCGCTAGCCCGAGTAAACCG
17103721 AGGC
1 AGGC
17103725 CCAAGCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 1 0.03
33 35 0.97
ACGTcount: A:0.39, C:0.29, G:0.27, T:0.06
Consensus pattern (33 bp):
AGGCGCAAAAAAAGCGCTAGCCCGAGTAAACCG
Found at i:17109457 original size:11 final size:11
Alignment explanation
Indices: 17109441--17109538 Score: 73
Period size: 11 Copynumber: 9.3 Consensus size: 11
17109431 TCAATTATTT
17109441 TCTCAATTTCC
1 TCTCAATTTCC
17109452 TCTCAATTTCC
1 TCTCAATTTCC
* *
17109463 TCTCAAATTGC
1 TCTCAATTTCC
17109474 TCTCAATTTCC
1 TCTCAATTTCC
17109485 T-TCCAAATTT-C
1 TCT-C-AATTTCC
*
17109496 TCTCAA-ATCC
1 TCTCAATTTCC
* **
17109506 -AT--ATTTAA
1 TCTCAATTTCC
*
17109514 TCTCAATTTGC
1 TCTCAATTTCC
17109525 TCTCAATTTCC
1 TCTCAATTTCC
17109536 TCT
1 TCT
17109539 TAAATTTCTC
Statistics
Matches: 66, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 4 0.06
11 51 0.77
12 6 0.09
ACGTcount: A:0.23, C:0.31, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:17109479 original size:33 final size:33
Alignment explanation
Indices: 17109441--17109503 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
17109431 TCAATTATTT
17109441 TCTCAATTTCC-TCTC-AATTTCCTCTCAAATTGC
1 TCTCAATTTCCTTC-CAAATTT-CTCTCAAATTGC
17109474 TCTCAATTTCCTTCCAAATTTCTCTCAAAT
1 TCTCAATTTCCTTCCAAATTTCTCTCAAAT
17109504 CCATATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.43
Consensus pattern (33 bp):
TCTCAATTTCCTTCCAAATTTCTCTCAAATTGC
Found at i:17109573 original size:51 final size:51
Alignment explanation
Indices: 17109463--17109562 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
17109453 CTCAATTTCC
*
17109463 TCTCAAATTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
* * *
17109514 TCTCAATTTGCTCTCAATTTCC-TCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAATTTCCTTC-CAAATTTCTCTCAAATCCATATTT
17109563 TTAGTTAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 2 0.05
51 42 0.95
ACGTcount: A:0.26, C:0.27, G:0.02, T:0.45
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
Found at i:17111376 original size:18 final size:18
Alignment explanation
Indices: 17111353--17111395 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
17111343 TGCCAGGTGC
* *
17111353 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
17111371 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
17111389 GTTTCCT
1 GTATCCT
17111396 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:17111682 original size:21 final size:22
Alignment explanation
Indices: 17111636--17111683 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
17111626 CCAACACCGA
17111636 CAACCAGATCCCCTACCGAATG
1 CAACCAGATCCCCTACCGAATG
*
17111658 -AACCAGAATCCCC-ACCGGA-G
1 CAACCAG-ATCCCCTACCGAATG
17111678 CAACCA
1 CAACCA
17111684 CAACCCCCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 16 0.70
22 6 0.26
ACGTcount: A:0.35, C:0.42, G:0.15, T:0.08
Consensus pattern (22 bp):
CAACCAGATCCCCTACCGAATG
Found at i:17112723 original size:25 final size:23
Alignment explanation
Indices: 17112666--17112723 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 23
17112656 AATTATTGAT
*
17112666 ATATTTTTGTCTGAATGTCTTAA
1 ATATTTTTGTATGAATGTCTTAA
17112689 ATATTATTTTGTATGAATGTCTTAA
1 ATA-T-TTTTGTATGAATGTCTTAA
17112714 CACTATTTTT
1 -A-TATTTTT
17112724 AACCTTACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 3 0.10
24 1 0.03
25 22 0.73
26 2 0.07
27 2 0.07
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.53
Consensus pattern (23 bp):
ATATTTTTGTATGAATGTCTTAA
Found at i:17119009 original size:110 final size:110
Alignment explanation
Indices: 17118816--17119017 Score: 334
Period size: 110 Copynumber: 1.8 Consensus size: 110
17118806 TTTTCTTAAG
* * **
17118816 TAAGCCTCTTCAAATCCTCAAGCCAACCCAGTTGGCATTCACAACACAAACTGGTATGACACAAA
1 TAAGCCTCTTCAAACCCTCAAGCCAACCCAGTTGGCATTCACAAAACAAACTGCCATGACACAAA
17118881 AAGGTAAATTTACCTATCTTCCTGTAACTCAAGTCGCAGCTAAAA
66 AAGGTAAATTTACCTATCTTCCTGTAACTCAAGTCGCAGCTAAAA
* *
17118926 TAAGCCTC-TCAAAACCCTCAAGCCAGCCCAGTTGGCATTCACAAAACAAACTGCCATGACACCA
1 TAAGCCTCTTC-AAACCCTCAAGCCAACCCAGTTGGCATTCACAAAACAAACTGCCATGACACAA
17118990 AAAGGTAAATTTACCTATCTTCCTGTAA
65 AAAGGTAAATTTACCTATCTTCCTGTAA
17119018 TAACTTAATT
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
109 2 0.02
110 83 0.98
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.23
Consensus pattern (110 bp):
TAAGCCTCTTCAAACCCTCAAGCCAACCCAGTTGGCATTCACAAAACAAACTGCCATGACACAAA
AAGGTAAATTTACCTATCTTCCTGTAACTCAAGTCGCAGCTAAAA
Found at i:17130381 original size:50 final size:50
Alignment explanation
Indices: 17130257--17130505 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
17130247 GATAATAACA
* * ** * *
17130257 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
17130308 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
17130358 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
17130408 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
17130463 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
17130506 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:17130435 original size:100 final size:104
Alignment explanation
Indices: 17130256--17130505 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
17130246 TGATAATAAC
**
17130256 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
17130321 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
17130358 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
17130421 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
17130463 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
17130506 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:17130621 original size:13 final size:13
Alignment explanation
Indices: 17130600--17130631 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
17130590 GCTTGGATCA
*
17130600 TCATCAAATAAAT
1 TCATAAAATAAAT
17130613 TCATAAAATAAAT
1 TCATAAAATAAAT
17130626 TCATAA
1 TCATAA
17130632 TTGCTGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:17137971 original size:50 final size:50
Alignment explanation
Indices: 17137847--17138095 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
17137837 GATAATAACA
* * ** * *
17137847 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
17137898 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
17137948 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
17137998 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
17138053 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
17138096 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:17138025 original size:100 final size:104
Alignment explanation
Indices: 17137846--17138095 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
17137836 TGATAATAAC
**
17137846 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
17137911 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
17137948 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
17138011 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
17138053 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
17138096 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:17138211 original size:13 final size:13
Alignment explanation
Indices: 17138190--17138221 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
17138180 GCTTAGATCA
*
17138190 TCATCAAATAAAT
1 TCATAAAATAAAT
17138203 TCATAAAATAAAT
1 TCATAAAATAAAT
17138216 TCATAA
1 TCATAA
17138222 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:17138468 original size:30 final size:30
Alignment explanation
Indices: 17138433--17138490 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
17138423 CATCGACTCT
*
17138433 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
17138463 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
17138491 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:17140786 original size:17 final size:17
Alignment explanation
Indices: 17140763--17140796 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
17140753 CTAAAGCATA
17140763 AAAAAAAGAGAAAAAAAC
1 AAAAAAA-AGAAAAAAAC
17140781 AAAAAAAAGAAAAAAA
1 AAAAAAAAGAAAAAAA
17140797 AATTTGGGGA
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:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAAAAAC
Found at i:17140797 original size:9 final size:9
Alignment explanation
Indices: 17140762--17140797 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
17140752 CCTAAAGCAT
17140762 AAAAAAAAG
1 AAAAAAAAG
*
17140771 AGAAAAAAAC
1 A-AAAAAAAG
17140781 AAAAAAAAG
1 AAAAAAAAG
17140790 AAAAAAAA
1 AAAAAAAA
17140798 ATTTGGGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:17140798 original size:19 final size:19
Alignment explanation
Indices: 17140762--17140798 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17140752 CCTAAAGCAT
*
17140762 AAAAAAAAGAGAAAAAAAC
1 AAAAAAAAGAAAAAAAAAC
17140781 AAAAAAAAGAAAAAAAAA
1 AAAAAAAAGAAAAAAAAA
17140799 TTTGGGGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAAAAC
Found at i:17145435 original size:5 final size:5
Alignment explanation
Indices: 17145425--17145450 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17145415 TGAGCATTCG
17145425 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
17145451 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:17146077 original size:20 final size:20
Alignment explanation
Indices: 17146052--17146093 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
17146042 GAGAGTAAAT
17146052 GGTGAAAAGTAAAAGTTTAG
1 GGTGAAAAGTAAAAGTTTAG
17146072 GGTGAAAAGTAAAAGTTTAG
1 GGTGAAAAGTAAAAGTTTAG
17146092 GG
1 GG
17146094 GAATAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.24
Consensus pattern (20 bp):
GGTGAAAAGTAAAAGTTTAG
Found at i:17146112 original size:16 final size:16
Alignment explanation
Indices: 17146061--17146110 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 16
17146051 TGGTGAAAAG
17146061 TAAAAGTTTAGGGTGAAAA
1 TAAAAGTTTAGGG-G--AA
17146080 GTAAAAGTTTAGGGGAA
1 -TAAAAGTTTAGGGGAA
17146097 TAAAAGTTTGAGGG
1 TAAAAGTTT-AGGG
17146111 AAAGTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 9 0.31
17 6 0.21
19 1 0.03
20 13 0.45
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (16 bp):
TAAAAGTTTAGGGGAA
Found at i:17146236 original size:30 final size:31
Alignment explanation
Indices: 17146197--17146256 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
17146187 AGAGGTGGGA
* *
17146197 TGGGAAGGGAATAAAATTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTGAGGGGAAAAG
* *
17146228 TGGG-AGGGAGTAAAAATTTGGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTGAGGGGAAAA
17146257 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTGAGGGGAAAAG
Found at i:17149372 original size:46 final size:44
Alignment explanation
Indices: 17149305--17149396 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 44
17149295 GAAATAAAAC
* *
17149305 TGTAATGGACTAGAATTGTAATCAGTGATTCAAT-TATTTGGTTGAA
1 TGTAATGGAATAGAACTGTAAT-AGT-ATT-AATGTATTTGGTTGAA
* *
17149351 TGTAATGGAATAGAACTGTAATAGTATTATTGTGTTTGGTTGAA
1 TGTAATGGAATAGAACTGTAATAGTATTAATGTATTTGGTTGAA
17149395 TG
1 TG
17149397 GAACAGATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 2 0.05
44 16 0.39
45 3 0.07
46 20 0.49
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (44 bp):
TGTAATGGAATAGAACTGTAATAGTATTAATGTATTTGGTTGAA
Found at i:17149589 original size:24 final size:24
Alignment explanation
Indices: 17149560--17149607 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
17149550 CTATAATTAT
17149560 TTTTATATTAAAATA-TTTAAAATA
1 TTTTAT-TTAAAATATTTTAAAATA
**
17149584 TTTTATTTATTATATTTTAAAATA
1 TTTTATTTAAAATATTTTAAAATA
17149608 ATACACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTATTTAAAATATTTTAAAATA
Found at i:17164956 original size:20 final size:21
Alignment explanation
Indices: 17164931--17164970 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17164921 ATATTTGTTG
17164931 ATGGA-TGTAAAAGGACTTTA
1 ATGGATTGTAAAAGGACTTTA
**
17164951 ATGGATTGTTTAAGGACTTT
1 ATGGATTGTAAAAGGACTTT
17164971 TATAACTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.38
Consensus pattern (21 bp):
ATGGATTGTAAAAGGACTTTA
Found at i:17167326 original size:16 final size:16
Alignment explanation
Indices: 17167305--17167373 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
17167295 TTTGGTTCGC
17167305 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
17167321 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
17167337 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
17167354 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
17167370 TGTA
1 TGTA
17167374 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:17167351 original size:33 final size:32
Alignment explanation
Indices: 17167305--17167373 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
17167295 TTTGGTTCGC
17167305 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
17167337 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
17167370 TGTA
1 TGTA
17167374 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:17167438 original size:44 final size:45
Alignment explanation
Indices: 17167354--17167444 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
17167344 GGATTAGAGG
* * *
17167354 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
17167399 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
17167443 TG
1 TG
17167445 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:17167630 original size:18 final size:17
Alignment explanation
Indices: 17167609--17167643 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17167599 TTATTATTAA
*
17167609 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
17167627 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
17167644 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:17167749 original size:18 final size:17
Alignment explanation
Indices: 17167728--17167762 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17167718 TTATTATTAA
*
17167728 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
17167746 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
17167763 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:17167913 original size:120 final size:120
Alignment explanation
Indices: 17167592--17168337 Score: 1282
Period size: 120 Copynumber: 6.2 Consensus size: 120
17167582 ATCATATTTA
17167592 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
17167657 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGT-AAATATAAATT
66 TATTCTTATATTAATTTACTAAAATCATAATATATGATACTGTAAAATATAAATT
17167711 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
17167776 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTAAAATCATAATATATGATACTGTAAAATATAAATT
*
17167831 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
17167896 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTAAAATCATAATATATGATACTGTAAAATATAAATT
*
17167951 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
17168016 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTAAAATCATAATATATGATACTGTAAAATATAAATT
* *
17168071 AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* * * *
17168136 TATTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAATATAATTT
66 TATTCTTATATTAATTTACTAAAATCATAATATATGATACTGTAAAATATAAATT
*
17168191 GAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAAT-ATTA
1 -AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT-
* * * *
17168254 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTT
64 AATATTCTTATATTAATTTACTAAAATCATAATATATGATACTGTAAAATATAAATT
*
17168311 AAAATAATTATTATTAAATATAATTTT
1 AACATAATTATTATTAAATAT-ATTTT
17168338 TCTAAATATA
Statistics
Matches: 609, Mismatches: 13, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
119 112 0.18
120 490 0.80
121 7 0.01
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTAAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:17168109 original size:18 final size:17
Alignment explanation
Indices: 17168086--17168122 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
17168076 AATTATTATT
17168086 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
17168102 AAATATATGATTTAATA
1 AAATATATGATTTAATA
17168119 AAAT
1 AAAT
17168123 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:17168229 original size:18 final size:17
Alignment explanation
Indices: 17168206--17168242 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
17168196 AATTATTATT
17168206 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
17168222 AAATATATGATTTAATA
1 AAATATATGATTTAATA
17168239 AAAT
1 AAAT
17168243 TCTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:17173151 original size:58 final size:57
Alignment explanation
Indices: 17173027--17173163 Score: 168
Period size: 58 Copynumber: 2.4 Consensus size: 57
17173017 TTAGTGCTTT
* * *
17173027 TTGGTGTGTTTTGGAGGGATGTGATCTATTGTCTTCAAGTTTATCACTTTAGTGCTA
1 TTGGTGTGTTTTGGAGGGATGTGATCTATTGTCTTCAAGTTTAGCAATTCAGTGCTA
** * * * *
17173084 TTCAATGTGTTTTGGAGGGATTTGATCTATTGTTTTCAATTTTAGCAATTCAGTGCTC
1 TT-GGTGTGTTTTGGAGGGATGTGATCTATTGTCTTCAAGTTTAGCAATTCAGTGCTA
17173142 TCTGGTGTG-TTTGGAGGGATGT
1 T-TGGTGTGTTTTGGAGGGATGT
17173164 AATTTGTTTC
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
57 14 0.21
58 51 0.77
59 1 0.02
ACGTcount: A:0.18, C:0.10, G:0.27, T:0.45
Consensus pattern (57 bp):
TTGGTGTGTTTTGGAGGGATGTGATCTATTGTCTTCAAGTTTAGCAATTCAGTGCTA
Found at i:17180158 original size:18 final size:18
Alignment explanation
Indices: 17180127--17180170 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
17180117 TCGAAAAATG
* * *
17180127 CATAAAAATTAAAAGAAA
1 CATAAACATAAAAACAAA
17180145 CATAAACATAAAAACAAA
1 CATAAACATAAAAACAAA
*
17180163 AATAAACA
1 CATAAACA
17180171 CACATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.73, C:0.11, G:0.02, T:0.14
Consensus pattern (18 bp):
CATAAACATAAAAACAAA
Found at i:17185995 original size:14 final size:14
Alignment explanation
Indices: 17185976--17186003 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17185966 TCATCATTTA
17185976 CCTATAACCAAAAC
1 CCTATAACCAAAAC
17185990 CCTATAACCAAAAC
1 CCTATAACCAAAAC
17186004 TCATAAACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:17187179 original size:20 final size:20
Alignment explanation
Indices: 17187108--17187179 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
17187098 AGAAATATAA
* *
17187108 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAATTTTAAAAAATT
17187128 ATTTTGAATTTT-AAAAATT
1 ATTTTGAATTTTAAAAAATT
*
17187147 AATTTGAATTTTAAAAAATT
1 ATTTTGAATTTTAAAAAATT
17187167 ATTTTGAATTTTA
1 ATTTTGAATTTTA
17187180 TTTTTGTAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
18 4 0.09
19 19 0.40
20 24 0.51
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (20 bp):
ATTTTGAATTTTAAAAAATT
Found at i:17190467 original size:13 final size:12
Alignment explanation
Indices: 17190449--17190478 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
17190439 ATTTATCCAA
17190449 TTTTTTTGAATAT
1 TTTTTTTG-ATAT
17190462 TTTTTTTGATAT
1 TTTTTTTGATAT
17190474 TTTTT
1 TTTTT
17190479 ATACCTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (12 bp):
TTTTTTTGATAT
Found at i:17190648 original size:21 final size:21
Alignment explanation
Indices: 17190602--17190645 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
17190592 TCCAACATTT
*
17190602 ATTATTATTTAAACATTATTA
1 ATTATTATTTAAACATTAATA
17190623 ATTATTATATTAAA-A-TAATA
1 ATTATTAT-TTAAACATTAATA
17190643 ATT
1 ATT
17190646 TATCATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTATTTAAACATTAATA
Found at i:17199334 original size:27 final size:28
Alignment explanation
Indices: 17199304--17199362 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
17199294 TGCTTTAAAT
**
17199304 TTATTGAATATTA-TTTCAAAATTTCTA
1 TTATTGAATATTATTTTCAAAATTGATA
* *
17199331 TTA-TGTATTTTATTTTCAAAATTGATA
1 TTATTGAATATTATTTTCAAAATTGATA
17199358 TTATT
1 TTATT
17199363 ATTGGTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 7 0.27
27 18 0.69
28 1 0.04
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (28 bp):
TTATTGAATATTATTTTCAAAATTGATA
Found at i:17204436 original size:30 final size:32
Alignment explanation
Indices: 17204374--17204436 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 32
17204364 TAGAAAGAAG
* **
17204374 AAGTATAAACATATTGGGTCATTTACGCAAAA
1 AAGTATAAACATATTGGGCCATTTACAAAAAA
*
17204406 AAGTA-AAA-ATATTGGGCCATTTATAAAAAA
1 AAGTATAAACATATTGGGCCATTTACAAAAAA
17204436 A
1 A
17204437 TAAAAAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 19 0.70
31 3 0.11
32 5 0.19
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (32 bp):
AAGTATAAACATATTGGGCCATTTACAAAAAA
Found at i:17206790 original size:24 final size:23
Alignment explanation
Indices: 17206753--17206800 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
17206743 TGCTCTCCCT
*
17206753 ATTTAAATCCATTAA-ATTATAAA
1 ATTTAAACCCATTAATATT-TAAA
17206776 ATTTAATACCCATTAATATTTAAA
1 ATTTAA-ACCCATTAATATTTAAA
17206800 A
1 A
17206801 CCCTGATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 13 0.59
25 3 0.14
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTTAAACCCATTAATATTTAAA
Found at i:17207766 original size:16 final size:16
Alignment explanation
Indices: 17207745--17207775 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17207735 TTTAAGAAAA
*
17207745 ATTTAATAAATAAATG
1 ATTTAATAAAAAAATG
17207761 ATTTAATAAAAAAAT
1 ATTTAATAAAAAAAT
17207776 TCGAATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
ATTTAATAAAAAAATG
Found at i:17209743 original size:44 final size:44
Alignment explanation
Indices: 17209650--17209744 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 44
17209640 AAAAAAATTA
* * * * *
17209650 AAAATGGAATATAGAAGTAATAGATATTACATAGTTTTGTTGGT
1 AAAATGAAATAGACAAGTAATAGATATTACATACTTTGGTTGGT
* * *
17209694 TAAATGAAATAGACAAGTAATAG-TATTAGATTCTTTGGTTGGCT
1 AAAATGAAATAGACAAGTAATAGATATTACATACTTTGGTTGG-T
17209738 AAAATGA
1 AAAATGA
17209745 TGTTAACGAT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
43 15 0.37
44 26 0.63
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (44 bp):
AAAATGAAATAGACAAGTAATAGATATTACATACTTTGGTTGGT
Found at i:17209901 original size:21 final size:20
Alignment explanation
Indices: 17209862--17209915 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
17209852 ATATAATTCA
* *
17209862 TAAAAATATAAAAAATATAAG
1 TAAAAATAT-AATATTATAAG
* *
17209883 TAAACAATTTAATATTATAAT
1 TAAA-AATATAATATTATAAG
17209904 TAAAAATATAAT
1 TAAAAATATAAT
17209916 TTAGTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 7 0.26
21 16 0.59
22 4 0.15
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
TAAAAATATAATATTATAAG
Found at i:17209958 original size:25 final size:24
Alignment explanation
Indices: 17209908--17209965 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
17209898 TATAATTAAA
* *
17209908 AATATAATTTAGTAATATATATTAT
1 AATAT-ATTTAATAATATATAGTAT
*
17209933 AATATATTTAATAGTATAATAGTAT
1 AATATATTTAATAATAT-ATAGTAT
17209958 AATATATT
1 AATATATT
17209966 ATTTATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (24 bp):
AATATATTTAATAATATATAGTAT
Found at i:17215708 original size:92 final size:92
Alignment explanation
Indices: 17215551--17215744 Score: 268
Period size: 92 Copynumber: 2.1 Consensus size: 92
17215541 TTGATTTTAG
* * * *
17215551 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATACAAGAACAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
17215616 ATTTAAT-ATTAATTATTTTAAATTGTA
66 ATGTAATAATT-ATTATTTTAAATTATA
*
17215643 TAAATTCATACAAGAA-AATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATT
1 TAAATTCATACAAGAACAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATT
17215706 ATATGTAATAATTATTATTTTAAATTATA
64 ATATGTAATAATTATTATTTTAAATTATA
*
17215735 CAAATTCATA
1 TAAATTCATA
17215745 AAATATAATT
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
90 1 0.01
91 29 0.32
92 58 0.64
93 3 0.03
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (92 bp):
TAAATTCATACAAGAACAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:17215722 original size:24 final size:25
Alignment explanation
Indices: 17215687--17215734 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
17215677 TTATGAAATT
17215687 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
17215711 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
17215735 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:17215905 original size:120 final size:120
Alignment explanation
Indices: 17215775--17216307 Score: 921
Period size: 120 Copynumber: 4.4 Consensus size: 120
17215765 AATTATTTTA
* * * * *
17215775 AATTTTATTAAATCATATATTTTAAATAAAATATA-TGATATATTAATTAT-TTCAAATTT-TCA
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTA-ATAATAATTATGTT--AATTTAT-A
* *
17215837 -TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAATAATATTAATTATTAAG
62 TTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
17215895 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
17215960 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
17216015 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
17216080 ACAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
17216135 AATTTTATTAAATTATATATTTTAATTATAATATATTTATTAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
17216200 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
17216255 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
17216308 TAAATATGAT
Statistics
Matches: 398, Mismatches: 11, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
119 6 0.02
120 388 0.97
121 4 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:17215935 original size:15 final size:15
Alignment explanation
Indices: 17215900--17216094 Score: 60
Period size: 15 Copynumber: 13.3 Consensus size: 15
17215890 TTAAGAATTT
*
17215900 TATTAAATTAT-ATA
1 TATTTAATTATAATA
17215914 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
17215928 TATTTAATAATAAT-
1 TATTTAATTATAATA
17215942 TATGTTAATT-T-ATA
1 TAT-TTAATTATAATA
* *
17215956 T-TTTACAGTATCATA
1 TATTTA-ATTATAATA
* *
17215971 TATTATGATT-TGAGTA
1 TATT-TAATTAT-AATA
* * *
17215987 -AATTCA-TATAAGA
1 TATTTAATTATAATA
*
17216000 -ATATTAATTATTAAGA
1 TAT-TTAATTA-TAATA
* *
17216016 -ATTTTATTAAATTATA
1 TATTTAATT--ATAATA
17216032 TATTTTAATTATAATA
1 TA-TTTAATTATAATA
*
17216048 TATTTAATAATAAT-
1 TATTTAATTATAATA
17216062 TATGTTAATT-T-ATA
1 TAT-TTAATTATAATA
*
17216076 T-TTTACAGTATAATA
1 TATTTA-ATTATAATA
17216091 TATT
1 TATT
17216095 ATGATTTGAG
Statistics
Matches: 135, Mismatches: 22, Indels: 46
0.67 0.11 0.23
Matches are distributed among these distances:
12 6 0.04
13 22 0.16
14 23 0.17
15 50 0.37
16 25 0.19
17 3 0.02
18 6 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:17216176 original size:51 final size:51
Alignment explanation
Indices: 17216121--17216303 Score: 132
Period size: 51 Copynumber: 3.2 Consensus size: 51
17216111 CATATAAGAA
*
17216121 TATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATT
1 TATTAATAATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATT
* * * *
17216172 TATTAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 TATTAATAATTAAG--AATTT-TA--TTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-
*
17216237 AGAA
51 ---T
*
17216241 TATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATT
1 TATTAATAATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATT
*
17216292 TAATAATAATTA
1 TATTAATAATTA
17216304 TGTTTAAATA
Statistics
Matches: 100, Mismatches: 14, Indels: 36
0.67 0.09 0.24
Matches are distributed among these distances:
51 22 0.22
53 5 0.05
54 2 0.02
55 4 0.04
56 4 0.04
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 4 0.04
65 4 0.04
66 2 0.02
67 5 0.05
69 12 0.12
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (51 bp):
TATTAATAATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATT
Found at i:17216290 original size:16 final size:16
Alignment explanation
Indices: 17216269--17216310 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
17216259 TTATTAAATT
*
17216269 ATATATTTTAATTATA
1 ATATATTTTAATAATA
17216285 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
17216300 AT-TATGTTTAA
1 ATATAT-TTTAA
17216311 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:17216295 original size:15 final size:15
Alignment explanation
Indices: 17216260--17216301 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
17216250 TTAAGAATTT
*
17216260 TATTAAATTAT-ATA
1 TATTTAATTATAATA
17216274 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
17216288 TATTTAATAATAAT
1 TATTTAATTATAAT
17216302 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:17216405 original size:157 final size:157
Alignment explanation
Indices: 17216244--17216560 Score: 573
Period size: 157 Copynumber: 2.0 Consensus size: 157
17216234 ATAAGAATAT
* *
17216244 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAAT-TATGTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAT-ATGAATGTT
* *
17216308 TAAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACA
65 TAAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
17216373 ATAATAATTTACCAAAACAAATTTATGC
130 ATAATAATTTACCAAAACAAATTTATGC
17216401 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATATGAATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATATGAATGTTT
17216466 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
17216531 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
17216558 TAA
1 TAA
17216561 GGGTATTCTA
Statistics
Matches: 154, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
156 2 0.01
157 152 0.99
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATATGAATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:17216441 original size:18 final size:17
Alignment explanation
Indices: 17216413--17216447 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17216403 ATTATTAAGA
*
17216413 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
17216430 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
17216448 TTAATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:17216705 original size:16 final size:16
Alignment explanation
Indices: 17216684--17216714 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17216674 ATTTGCTATT
17216684 ACACCTCTAATCCAAC
1 ACACCTCTAATCCAAC
17216700 ACACCTCTAATCCAA
1 ACACCTCTAATCCAA
17216715 TACAGCGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (16 bp):
ACACCTCTAATCCAAC
Found at i:17216764 original size:16 final size:16
Alignment explanation
Indices: 17216740--17216783 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
17216730 GCACCAAGAT
*
17216740 TAGAGGTGTAATGGAA
1 TAGAAGTGTAATGGAA
17216756 TAGAAGTGTAATGGAA
1 TAGAAGTGTAATGGAA
17216772 TAGAAGTGTAAT
1 TAGAAGTGTAAT
17216784 AGCAAATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.32, T:0.27
Consensus pattern (16 bp):
TAGAAGTGTAATGGAA
Found at i:17216828 original size:45 final size:44
Alignment explanation
Indices: 17216762--17216852 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
17216752 GGAATAGAAG
*
17216762 TGTAATGGAATAGAAGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAAGCGTAATAG-AAATCAACTGTTTGGTTGAA
* * ***
17216807 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAAGCGTAATAGAAATCAACTGTTTGGTTGAA
17216851 TG
1 TG
17216853 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAAGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:17217132 original size:120 final size:120
Alignment explanation
Indices: 17216996--17217612 Score: 1099
Period size: 122 Copynumber: 5.1 Consensus size: 120
17216986 TTAATCATAT
*
17216996 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* *
17217061 AAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
17217116 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA-T
*
17217181 TAAATATTCTTAAATGAATTTACTAAAATTATAATATATAATACTATAAAATATAA
65 TAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
17217237 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
17217302 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * *
17217357 TTTAAAATAATAATTATTAAAAATGTAATTTAGTAAAAATATATAATTTAATAAAATTCTTAATA
1 TTTAAAATAATTATTATT--AAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA
17217422 TTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
64 TTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
17217479 TTTAAAATAATTATTATTAAAAATATAATTTAGTAAAAATATATAATTTAATAAAATTCTTTAAT
1 TTTAAAATAATTATTATT--AAATATAATTTAATAAAAATATATAATTTAATAAAATTC-TTAAT
*
17217544 ATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
63 ATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
17217602 TTTAAAATAAT
1 TTTAAAATAAT
17217613 AAAATTTGAA
Statistics
Matches: 482, Mismatches: 11, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
120 135 0.28
121 117 0.24
122 157 0.33
123 73 0.15
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:17217516 original size:15 final size:16
Alignment explanation
Indices: 17217470--17217534 Score: 57
Period size: 18 Copynumber: 4.2 Consensus size: 16
17217460 ATAATACTAT
17217470 AAAATATAATTTAA-A
1 AAAATATAATTTAATA
* *
17217485 ATAAT-T-A-TTATTA
1 AAAATATAATTTAATA
*
17217498 AAAATATAATTTAGTAA
1 AAAATATAATTTAAT-A
17217515 AAATATATAATTTAATA
1 AAA-ATATAATTTAATA
17217532 AAA
1 AAA
17217535 TTCTTTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
12 3 0.08
13 6 0.15
14 2 0.05
15 5 0.13
16 4 0.10
17 8 0.21
18 11 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAATATAATTTAATA
Found at i:17217522 original size:18 final size:17
Alignment explanation
Indices: 17217497--17217534 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
17217487 AATTATTATT
*
17217497 AAAAATATAATTTAGTA
1 AAAAATATAATTTAATA
17217514 AAAATATATAATTTAATA
1 AAAA-ATATAATTTAATA
17217532 AAA
1 AAA
17217535 TTCTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAATATAATTTAATA
Found at i:17217923 original size:17 final size:17
Alignment explanation
Indices: 17217901--17217968 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
17217891 CTTATATGCT
17217901 TTAATTTATTGCATGTA
1 TTAATTTATTGCATGTA
*
17217918 TTAATTTATTTTTCA--TA
1 TTAATTTA--TTGCATGTA
*
17217935 TTATTTTTATAT-CATGTA
1 TTA-ATTTAT-TGCATGTA
17217953 TTAATTTATTGCATGT
1 TTAATTTATTGCATGT
17217969 TTGTATTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
16 4 0.10
17 24 0.59
18 9 0.22
19 4 0.10
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.59
Consensus pattern (17 bp):
TTAATTTATTGCATGTA
Found at i:17221776 original size:24 final size:24
Alignment explanation
Indices: 17221749--17221798 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
17221739 GCCCATTAAA
*
17221749 AACATAACTCTCGACCTTT-CATTT
1 AACATAACTATCGA-CTTTCCATTT
*
17221773 AACATAACTATTGACTTTCCATTT
1 AACATAACTATCGACTTTCCATTT
17221797 AA
1 AA
17221799 GTTTATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (24 bp):
AACATAACTATCGACTTTCCATTT
Found at i:17224221 original size:33 final size:35
Alignment explanation
Indices: 17224158--17224236 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 35
17224148 CGATCAAAAT
* * * *
17224158 ACGAGAATTTTTTTTTACACGAAGAATTTTGAAGC
1 ACGAAAATTTTTTTTAAAACGAAGAATTTTGAAAC
*
17224193 AC-AAAATTTTTTTTAAAACGAA-ATTTTTGAAAC
1 ACGAAAATTTTTTTTAAAACGAAGAATTTTGAAAC
17224226 ACGAAAATTTT
1 ACGAAAATTTT
17224237 AGAAACACGG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
33 11 0.29
34 25 0.66
35 2 0.05
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (35 bp):
ACGAAAATTTTTTTTAAAACGAAGAATTTTGAAAC
Found at i:17224233 original size:17 final size:17
Alignment explanation
Indices: 17224174--17224245 Score: 62
Period size: 17 Copynumber: 4.3 Consensus size: 17
17224164 ATTTTTTTTT
17224174 ACACGAAGAA-TTTTGAA
1 ACACGAA-AATTTTTGAA
* *
17224191 GCAC-AAAATTTTTTTTAA
1 ACACGAAAA--TTTTTGAA
17224209 A-ACG-AAATTTTTGAA
1 ACACGAAAATTTTTGAA
*
17224224 ACACGAAAATTTTAGAA
1 ACACGAAAATTTTTGAA
17224241 ACACG
1 ACACG
17224246 GGAAATTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
15 10 0.23
16 5 0.11
17 23 0.52
18 6 0.14
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
ACACGAAAATTTTTGAA
Found at i:17224253 original size:18 final size:17
Alignment explanation
Indices: 17224212--17224255 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
17224202 TTTTTAAAAC
*
17224212 GAAATTTTTGAAACACG
1 GAAATTTTAGAAACACG
*
17224229 AAAATTTTAGAAACACGG
1 GAAATTTTAGAAACAC-G
17224247 GAAATTTTA
1 GAAATTTTA
17224256 TTATTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (17 bp):
GAAATTTTAGAAACACG
Found at i:17224787 original size:9 final size:9
Alignment explanation
Indices: 17224761--17224804 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
17224751 GTTATGGGCC
17224761 TTTTTCTTT
1 TTTTTCTTT
**
17224770 TTTCCCTTT
1 TTTTTCTTT
17224779 TTTTTCTTT
1 TTTTTCTTT
*
17224788 TCTTTCTGTT
1 TTTTTCT-TT
17224798 TTTTTCT
1 TTTTTCT
17224805 GCTGGATGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:17224993 original size:16 final size:17
Alignment explanation
Indices: 17224955--17224999 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
17224945 TTCCTTCCTT
*
17224955 CTGCTGCTTGGGCCGTCA
1 CTGCTG-TTGGGCCGTAA
17224973 CTGCTGTTGGGCCG-AA
1 CTGCTGTTGGGCCGTAA
*
17224989 CTGCTGCTGGG
1 CTGCTGTTGGG
17225000 GGCCGCTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.44
17 8 0.32
18 6 0.24
ACGTcount: A:0.07, C:0.29, G:0.38, T:0.27
Consensus pattern (17 bp):
CTGCTGTTGGGCCGTAA
Found at i:17225133 original size:23 final size:22
Alignment explanation
Indices: 17225086--17225133 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
17225076 ATTTTTGCTT
* *
17225086 TTTCTTTTTTTTTCTTTTTTTC
1 TTTCCTTTTTTTTCTTTTTTCC
17225108 TTTCCTTTTTTTTCTTTTTCTCC
1 TTTCCTTTTTTTTCTTTTT-TCC
17225131 TTT
1 TTT
17225134 TTCTTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTCCTTTTTTTTCTTTTTTCC
Found at i:17225143 original size:10 final size:10
Alignment explanation
Indices: 17225083--17225158 Score: 70
Period size: 10 Copynumber: 7.9 Consensus size: 10
17225073 TTGATTTTTG
17225083 CTTTTTCTTT
1 CTTTTTCTTT
*
17225093 TTTTTTC-TT
1 CTTTTTCTTT
17225102 -TTTTTCTTT
1 CTTTTTCTTT
17225111 CCTTTTT-TTT
1 -CTTTTTCTTT
*
17225121 CTTTTTC-TC
1 CTTTTTCTTT
17225130 CTTTTTCTTT
1 CTTTTTCTTT
* *
17225140 CTTTATCTTC
1 CTTTTTCTTT
*
17225150 CTTCTTCTT
1 CTTTTTCTT
17225159 CGGGTCGCAC
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
8 6 0.11
9 18 0.33
10 25 0.46
11 5 0.09
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.76
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:17225157 original size:20 final size:18
Alignment explanation
Indices: 17225095--17225158 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
17225085 TTTTCTTTTT
17225095 TTTTCTTT-TTTTCTTTCC
1 TTTTCTTTCTTTTC-TTCC
*
17225113 TTTTTTTTCTTTT-TCTCC
1 TTTTCTTTCTTTTCT-TCC
17225131 TTTTTCTTTCTTTATCTTCC
1 -TTTTCTTTCTTT-TCTTCC
17225151 TTCTTCTT
1 TT-TTCTT
17225159 CGGGTCGCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 1 0.03
18 10 0.26
19 17 0.45
20 9 0.24
21 1 0.03
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTCTTTCTTTTCTTCC
Found at i:17225157 original size:29 final size:29
Alignment explanation
Indices: 17225102--17225157 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
17225092 TTTTTTTCTT
* * *
17225102 TTTTTCTTTCCTTTTTTTTCTTTTTCTCC
1 TTTTTCTTTCCTTTTCTTCCTTCTTCTCC
17225131 TTTTTCTTT-CTTTATCTTCCTTCTTCT
1 TTTTTCTTTCCTTT-TCTTCCTTCTTCT
17225158 TCGGGTCGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTTTCTTTCCTTTTCTTCCTTCTTCTCC
Found at i:17225899 original size:16 final size:17
Alignment explanation
Indices: 17225875--17225908 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17225865 GGGGGCAAAA
17225875 TGTA-ATTTTTATTTTT
1 TGTATATTTTTATTTTT
*
17225891 TGTATTTTTTTATTTTT
1 TGTATATTTTTATTTTT
17225908 T
1 T
17225909 TCAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (17 bp):
TGTATATTTTTATTTTT
Found at i:17225908 original size:8 final size:8
Alignment explanation
Indices: 17225880--17225909 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
17225870 CAAAATGTAA
17225880 TTTTTATT
1 TTTTTATT
17225888 TTTTGTATT
1 TTTT-TATT
17225897 TTTTTATT
1 TTTTTATT
17225905 TTTTT
1 TTTTT
17225910 CAAAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (8 bp):
TTTTTATT
Found at i:17226273 original size:16 final size:16
Alignment explanation
Indices: 17226243--17226272 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17226233 TTGAAAAGAA
17226243 AAAGAAAAGAAAAAAG
1 AAAGAAAAGAAAAAAG
17226259 AAAG-AAAGAAAAAA
1 AAAGAAAAGAAAAAA
17226273 AAATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGAAAAAAG
Found at i:17226827 original size:76 final size:77
Alignment explanation
Indices: 17226281--17227125 Score: 838
Period size: 76 Copynumber: 10.8 Consensus size: 77
17226271 AAAAATTAAA
* * * * * *****
17226281 AAATACCTCAGCTTAACTCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTT--TTTTTG
1 AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACG
** *
17226344 AAAACATAAATTG
66 AAAATTTAAA-AG
* * * * *
17226357 AAAATACCTCAGCGTGACCTGAGGCTTAACTCTCCTCTCGCATTATGAGTTGATTTTTGAAAAAC
1 -AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAC
*
17226422 AGAAAA-TT-GAA-
65 -GAAAATTTAAAAG
* *
17226433 AAATACCTCGGCATGTGACCCGGGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTG
1 AAATACCTCGGCA--TGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-----TTTTTG
* *
17226498 AAAAGCAAAAATTTAAAAG
59 AAAAACGAAAATTTAAAAG
* * * * * * **
17226517 AAATACCACGACATGTGACTCGAAGCTCAACTCACCCCTCGCAATATGAGTTGATTTTTTTTAAA
1 AAATACCTCGGCA--TGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTGAAAA
* *
17226582 A-GTAGTAA-TT-GAA-
63 ACG-A-AAATTTAAAAG
* *
17226595 AAATATCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGA
1 AAATACCTCGGCA--TGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA----TTTTTGA
17226660 AAAAC-AGAAATTTAAAAG
60 AAAACGA-AAATTTAAAAG
* * * * * *
17226678 AAAAACCACGACATGTGACTCGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA
1 AAATACCTCGGCA--TGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTGAAAA
*
17226743 ACGGAAATTTAAAAG
63 ACGAAAATTTAAAAG
*
17226758 AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTGAAAAACG
1 AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACG
17226822 AAAATTTAAAAG
66 AAAATTTAAAAG
*
17226834 AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTGAAAAACG
1 AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACG
*
17226898 GAAATTTAAAAG
66 AAAATTTAAAAG
** *
17226910 AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCT-ATATTATGAGTTGATTTTTGAAAAATG
1 AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACG
* *
17226974 GAAATTTGAAAG
66 AAAATTTAAAAG
* *
17226986 AAACACCTCGGCATGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTGAAAAAAA
1 AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTG--AAAAA
* *
17227050 CGGAAATTTGAAAG
64 CGAAAATTTAAAAG
* *
17227064 AAACACCTCGGCATGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTGAAAAA
1 AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAA
17227126 AGCAGAGATT
Statistics
Matches: 674, Mismatches: 69, Indels: 51
0.85 0.09 0.06
Matches are distributed among these distances:
75 11 0.02
76 232 0.34
77 96 0.14
78 146 0.22
79 3 0.00
80 55 0.08
81 18 0.03
82 15 0.02
83 50 0.07
84 48 0.07
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (77 bp):
AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACG
AAAATTTAAAAG
Found at i:17228040 original size:23 final size:22
Alignment explanation
Indices: 17228010--17228095 Score: 75
Period size: 22 Copynumber: 3.8 Consensus size: 22
17228000 TTCATCTTGA
17228010 TTTTTCTTTTTCTTTTCTTTGTT
1 TTTTTCTTTTTCTTTTCTTT-TT
*
17228033 TTTTTCTTTTTTCTTTTGTTTTT
1 TTTTTC-TTTTTCTTTTCTTTTT
* * *
17228056 TTATTCCTTTTT-TGTTGTTTTT
1 TT-TTTCTTTTTCTTTTCTTTTT
* *
17228078 TTGTCTCTTTTTTTTTTC
1 TT-TTTCTTTTTCTTTTC
17228096 AGGCATAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
22 18 0.35
23 18 0.35
24 16 0.31
ACGTcount: A:0.01, C:0.12, G:0.06, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTTTCTTTTCTTTTT
Found at i:17228054 original size:12 final size:12
Alignment explanation
Indices: 17228011--17228095 Score: 61
Period size: 12 Copynumber: 7.0 Consensus size: 12
17228001 TCATCTTGAT
17228011 TTTTC-TTTTTC
1 TTTTCTTTTTTC
17228022 TTTTCTTTGTTT-
1 TTTTCTTT-TTTC
17228034 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
17228046 TTTTGTTTTTT-
1 TTTTCTTTTTTC
* *
17228057 TATTCCTTTTTTG
1 T-TTTCTTTTTTC
17228070 TTGTT-TTTTTGTC
1 TT-TTCTTTTT-TC
*
17228083 TCTTTTTTTTTTC
1 T-TTTCTTTTTTC
17228096 AGGCATAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
11 9 0.15
12 34 0.57
13 11 0.18
14 6 0.10
ACGTcount: A:0.01, C:0.12, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:17228077 original size:11 final size:11
Alignment explanation
Indices: 17228028--17228091 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
17228018 TTTCTTTTCT
*
17228028 TTGTTTTTTTC
1 TTGTTTTTTTG
*
17228039 TT-TTTTCTT-
1 TTGTTTTTTTG
*
17228048 TTGTTTTTTTA
1 TTGTTTTTTTG
**
17228059 TTCCTTTTTTG
1 TTGTTTTTTTG
17228070 TTGTTTTTTTG
1 TTGTTTTTTTG
*
17228081 TCTCTTTTTTT
1 T-TGTTTTTTT
17228092 TTTCAGGCAT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
9 2 0.05
10 12 0.29
11 20 0.48
12 8 0.19
ACGTcount: A:0.02, C:0.09, G:0.08, T:0.81
Consensus pattern (11 bp):
TTGTTTTTTTG
Found at i:17228087 original size:22 final size:21
Alignment explanation
Indices: 17228016--17228090 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 21
17228006 TTGATTTTTC
17228016 TTTTTCT-TTTCTTTGTT-TTT
1 TTTTTCTCTTT-TTTGTTGTTT
17228036 TTCTTT-T-TTCTTTTGTT-TTT
1 TT-TTTCTCTT-TTTTGTTGTTT
*
17228056 TTATTC-CTTTTTTGTTGTTT
1 TTTTTCTCTTTTTTGTTGTTT
17228076 TTTTGTCTCTTTTTT
1 TTTT-TCTCTTTTTT
17228091 TTTTCAGGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
19 9 0.20
20 24 0.52
21 6 0.13
22 7 0.15
ACGTcount: A:0.01, C:0.11, G:0.07, T:0.81
Consensus pattern (21 bp):
TTTTTCTCTTTTTTGTTGTTT
Found at i:17236415 original size:9 final size:9
Alignment explanation
Indices: 17236403--17236442 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
17236393 ATTTTTGCTT
17236403 TTTTTTTTC
1 TTTTTTTTC
17236412 TTTTTTTTC
1 TTTTTTTTC
17236421 TTTCTTTTTC
1 TTT-TTTTTC
**
17236431 TCCTTTTTC
1 TTTTTTTTC
17236440 TTT
1 TTT
17236443 CTTTATCTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:17236417 original size:13 final size:13
Alignment explanation
Indices: 17236401--17236429 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17236391 TGATTTTTGC
17236401 TTTTTTT-TTTCT
1 TTTTTTTCTTTCT
17236413 TTTTTTTCTTTCT
1 TTTTTTTCTTTCT
17236426 TTTT
1 TTTT
17236430 CTCCTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTCTTTCT
Found at i:17236428 original size:19 final size:19
Alignment explanation
Indices: 17236406--17236452 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
17236396 TTTGCTTTTT
*
17236406 TTTTTCTTTTTTTTCTTTC
1 TTTTTCTTCTTTTTCTTTC
*
17236425 TTTTTCTCCTTTTTCTTTC
1 TTTTTCTTCTTTTTCTTTC
*
17236444 TTTATCTTC
1 TTTTTCTTC
17236453 CTTCTTCTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTCTTCTTTTTCTTTC
Found at i:17236451 original size:10 final size:10
Alignment explanation
Indices: 17236406--17236461 Score: 62
Period size: 10 Copynumber: 5.8 Consensus size: 10
17236396 TTTGCTTTTT
17236406 TTTTTCTTT-
1 TTTTTCTTTC
17236415 TTTTTCTTTC
1 TTTTTCTTTC
*
17236425 TTTTTC-TCC
1 TTTTTCTTTC
17236434 TTTTTCTTTC
1 TTTTTCTTTC
* *
17236444 TTTATCTTCC
1 TTTTTCTTTC
*
17236454 TTCTTCTT
1 TTTTTCTT
17236462 CGGGTCGCAC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
9 17 0.44
10 22 0.56
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:17236454 original size:20 final size:19
Alignment explanation
Indices: 17236415--17236461 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
17236405 TTTTTTCTTT
*
17236415 TTTTTCTTTCTTTTTCTCC
1 TTTTTCTTTCTTTATCTCC
17236434 TTTTTCTTTCTTTATCTTCC
1 TTTTTCTTTCTTTATC-TCC
*
17236454 TTCTTCTT
1 TTTTTCTT
17236462 CGGGTCGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTCTTTCTTTATCTCC
Found at i:17236856 original size:22 final size:22
Alignment explanation
Indices: 17236830--17236871 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17236820 CCCCCTTTTC
17236830 TCTTTCAATTTTCTCTTTTTAA
1 TCTTTCAATTTTCTCTTTTTAA
*
17236852 TCTTTCAATTTTGTCTTTTT
1 TCTTTCAATTTTCTCTTTTT
17236872 CCTTCTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.17, G:0.02, T:0.67
Consensus pattern (22 bp):
TCTTTCAATTTTCTCTTTTTAA
Found at i:17237173 original size:30 final size:29
Alignment explanation
Indices: 17237126--17237183 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
17237116 TAAATTTAGA
*
17237126 AAAAGTTAGGGGTCAAAACATAATTTTTG
1 AAAAGTTAGGGGCCAAAACATAATTTTTG
* **
17237155 AAAAGTTTGGGGGCCAAAATGTAATTTTT
1 AAAAG-TTAGGGGCCAAAACATAATTTTT
17237184 ATTTTTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (29 bp):
AAAAGTTAGGGGCCAAAACATAATTTTTG
Found at i:17237197 original size:14 final size:14
Alignment explanation
Indices: 17237178--17237205 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17237168 CCAAAATGTA
17237178 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
17237192 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
17237206 CAAAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
ATTTTTATTTTTTT
Found at i:17238212 original size:18 final size:18
Alignment explanation
Indices: 17238189--17238224 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17238179 AATATGGTTT
*
17238189 ATATTCGATTTATTCAAA
1 ATATTCGAGTTATTCAAA
17238207 ATATTCGAGTTATTCAAA
1 ATATTCGAGTTATTCAAA
17238225 TTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (18 bp):
ATATTCGAGTTATTCAAA
Found at i:17239606 original size:16 final size:17
Alignment explanation
Indices: 17239581--17239615 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
17239571 ATTTTAATTG
*
17239581 ATTAATTAATTTT-TCA
1 ATTAAATAATTTTCTCA
17239597 ATTAAATAATTTTCTCA
1 ATTAAATAATTTTCTCA
17239614 AT
1 AT
17239616 CCAATTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAAATAATTTTCTCA
Found at i:17248212 original size:21 final size:21
Alignment explanation
Indices: 17248186--17248226 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17248176 ATCTGCTCAA
* *
17248186 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
17248207 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
17248227 TTGCTCATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:17255527 original size:62 final size:62
Alignment explanation
Indices: 17255457--17255580 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
17255447 GAAAACAGAA
17255457 GCAAAATCCAGATGTTGGATGATGAAGAAAAAATTAACTTCATTACTTGAATAAGCAAAAAG
1 GCAAAATCCAGATGTTGGATGATGAAGAAAAAATTAACTTCATTACTTGAATAAGCAAAAAG
17255519 GCAAAATCCAGATGTTGGATGATGAAGAAAAAATTAACTTCATTACTTGAATAAGCAAAAAG
1 GCAAAATCCAGATGTTGGATGATGAAGAAAAAATTAACTTCATTACTTGAATAAGCAAAAAG
17255581 CCATATACAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (62 bp):
GCAAAATCCAGATGTTGGATGATGAAGAAAAAATTAACTTCATTACTTGAATAAGCAAAAAG
Found at i:17258424 original size:23 final size:22
Alignment explanation
Indices: 17258373--17258424 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
17258363 CCTCGTCTTT
*
17258373 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
17258395 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
17258418 TTCTTTT
1 TTCTTTT
17258425 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:17266894 original size:29 final size:30
Alignment explanation
Indices: 17266862--17266920 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
17266852 TAAAATAATC
17266862 ATTTAATATT-ATC-ACTTAATTAAATTAAA
1 ATTTAATATTAATCTA-TTAATTAAATTAAA
* *
17266891 ATTTATTATTAATCTATTAATTAATTTAAA
1 ATTTAATATTAATCTATTAATTAAATTAAA
17266921 TTAACGTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.35
30 16 0.62
31 1 0.04
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTTAATATTAATCTATTAATTAAATTAAA
Found at i:17270275 original size:47 final size:47
Alignment explanation
Indices: 17270201--17270304 Score: 172
Period size: 47 Copynumber: 2.2 Consensus size: 47
17270191 ACTAGCATTA
* *
17270201 ACTTTAAGTAATCTCCCTTTGACATTTTACAACAAAAACTCATCACC
1 ACTTCAAGTAATCTCCCCTTGACATTTTACAACAAAAACTCATCACC
*
17270248 ACTTCAAGTAATCTCCCCTTGACATTTTACAACAAAAACTTATCACC
1 ACTTCAAGTAATCTCCCCTTGACATTTTACAACAAAAACTCATCACC
*
17270295 ACGTCAAGTA
1 ACTTCAAGTA
17270305 GGAGTAAGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.30
Consensus pattern (47 bp):
ACTTCAAGTAATCTCCCCTTGACATTTTACAACAAAAACTCATCACC
Found at i:17271826 original size:20 final size:20
Alignment explanation
Indices: 17271801--17271840 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17271791 CGTAAAATGA
*
17271801 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
17271821 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
17271841 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:17271835 original size:34 final size:35
Alignment explanation
Indices: 17271787--17271852 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
17271777 AGTAAAATAA
*
17271787 TTTCCGTAAAATGATTT-CTGGAAAATGTTTTACT
1 TTTCCGTAAAATGATTTACTGGAAAATATTTTACT
*
17271821 TTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTCCGTAAAATGATTTACTGGAAAATATTTT
17271853 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (35 bp):
TTTCCGTAAAATGATTTACTGGAAAATATTTTACT
Found at i:17271955 original size:20 final size:20
Alignment explanation
Indices: 17271930--17271981 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
17271920 GGAAAATTTG
17271930 TTTTTACATATATT-AATAAA
1 TTTTTACATATATTAAAT-AA
* *
17271950 TTTTT--ATATTTTAAATTA
1 TTTTTACATATATTAAATAA
17271968 TTTTTACATATATT
1 TTTTTACATATATT
17271982 GCAATGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 12 0.46
19 3 0.12
20 11 0.42
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTACATATATTAAATAA
Found at i:17284831 original size:9 final size:9
Alignment explanation
Indices: 17284814--17284850 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
17284804 TGAGTTTTCA
17284814 AATTCGAAT
1 AATTCGAAT
*
17284823 AACTCGAAT
1 AATTCGAAT
17284832 AATTCGAAT
1 AATTCGAAT
17284841 AATTCGAAT
1 AATTCGAAT
17284850 A
1 A
17284851 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:17284912 original size:21 final size:21
Alignment explanation
Indices: 17284886--17284928 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
17284876 ACCCCAAACT
*
17284886 CTCAAACCTTTTTACT-TTTCC
1 CTCAAAAC-TTTTACTCTTTCC
17284907 CTCAAAACTTTTACTCTTTCC
1 CTCAAAACTTTTACTCTTTCC
17284928 C
1 C
17284929 ACTTTCCCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.21, C:0.35, G:0.00, T:0.44
Consensus pattern (21 bp):
CTCAAAACTTTTACTCTTTCC
Found at i:17285257 original size:19 final size:17
Alignment explanation
Indices: 17285202--17285265 Score: 51
Period size: 19 Copynumber: 3.6 Consensus size: 17
17285192 ACTCCCCCTA
*
17285202 TTTACTTTCCCTCAAACT
1 TTTA-TTTCTCTCAAACT
17285220 TTTA-TTCT-TCAAAACCT
1 TTTATTTCTCTC-AAA-CT
17285237 TTTATTTTCTCTCTAAACT
1 TTTA-TTTCTCTC-AAACT
*
17285256 TTTACTTCTC
1 TTTATTTCTC
17285266 ACCCTTTACC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
15 2 0.05
16 6 0.16
17 6 0.16
18 9 0.24
19 10 0.26
20 5 0.13
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTATTTCTCTCAAACT
Found at i:17285392 original size:9 final size:9
Alignment explanation
Indices: 17285378--17285406 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
17285368 AATTTCACAT
17285378 TTTATATTA
1 TTTATATTA
17285387 TTTATATTA
1 TTTATATTA
17285396 TTTATATTA
1 TTTATATTA
17285405 TT
1 TT
17285407 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:17289731 original size:34 final size:34
Alignment explanation
Indices: 17289688--17289757 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
17289678 TTATAAATTT
17289688 TAAATTATTTATTAATGTGACATATGAGATAAAA
1 TAAATTATTTATTAATGTGACATATGAGATAAAA
17289722 TAAATTATTTATTAATGTGACATATGAGATAAAA
1 TAAATTATTTATTAATGTGACATATGAGATAAAA
17289756 TA
1 TA
17289758 TTGCACGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (34 bp):
TAAATTATTTATTAATGTGACATATGAGATAAAA
Found at i:17291175 original size:3 final size:3
Alignment explanation
Indices: 17291156--17291195 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
17291146 TTGCTATTTT
* *
17291156 TTA TTAA TTA ATA TTA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17291196 CATTTCCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:17291374 original size:35 final size:35
Alignment explanation
Indices: 17291284--17291374 Score: 91
Period size: 35 Copynumber: 2.7 Consensus size: 35
17291274 TTTTTTATAC
**
17291284 TTTATAATTTATATGCATATAT-ACGTACATACATT
1 TTTATAATTTATATATATATATGACGTACATA-ATT
* *
17291319 TTGATAA--TATATATACATATGCACGTACAT-ATT
1 TTTATAATTTATATATATATATG-ACGTACATAATT
*
17291352 TTTATAATTTATTTATATATATG
1 TTTATAATTTATATATATATATG
17291375 TACATATGCA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
33 19 0.42
35 26 0.58
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (35 bp):
TTTATAATTTATATATATATATGACGTACATAATT
Found at i:17291378 original size:31 final size:31
Alignment explanation
Indices: 17291284--17291381 Score: 88
Period size: 33 Copynumber: 3.0 Consensus size: 31
17291274 TTTTTTATAC
*
17291284 TTTATAATTTATATGCATATATACGTACATACATT
1 TTTATAATTTAT-T-TATATATACGTACAT--ATT
* * * *
17291319 TTGATAATATATATACATATGCACGTACATATT
1 TTTATAATTTATTTATATAT--ACGTACATATT
*
17291352 TTTATAATTTATTTATATATATGTACATAT
1 TTTATAATTTATTTATATATACGTACATAT
17291382 GCATACTTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
31 9 0.18
33 24 0.47
35 18 0.35
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (31 bp):
TTTATAATTTATTTATATATACGTACATATT
Found at i:17291394 original size:43 final size:43
Alignment explanation
Indices: 17291325--17291407 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
17291315 CATTTTGATA
17291325 ATATATATACATATGCACGTACATATTTT-TATAATTTATTTAT
1 ATATATATACATATGCAC-TACATATTTTATATAATTTATTTAT
* *
17291368 ATATATGTACATATGCA-TACTTATATTTTATATATTTTAT
1 ATATATATACATATGCACTAC--ATATTTTATATAATTTAT
17291408 AATTTGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 3 0.09
43 23 0.66
44 9 0.26
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (43 bp):
ATATATATACATATGCACTACATATTTTATATAATTTATTTAT
Found at i:17291549 original size:8 final size:8
Alignment explanation
Indices: 17291532--17291568 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
17291522 TTATATATCT
17291532 TTTTAT-A
1 TTTTATAA
17291539 TTTTATAA
1 TTTTATAA
17291547 TTTTATAA
1 TTTTATAA
17291555 TTTTATAA
1 TTTTATAA
17291563 TTTTAT
1 TTTTAT
17291569 TTATTTACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 6 0.21
8 23 0.79
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTATAA
Found at i:17297060 original size:38 final size:38
Alignment explanation
Indices: 17297018--17297093 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
17297008 TCTTGTATTG
*
17297018 GGATCCATTTTGGTAAAGTAGTTGCTCTTTTTTCCCTT
1 GGATCCATTTTGGTAAAGTAATTGCTCTTTTTTCCCTT
*
17297056 GGATCCATTTTGGTAAAGTAATTGCTTTTTTTTCCCTT
1 GGATCCATTTTGGTAAAGTAATTGCTCTTTTTTCCCTT
17297094 TCCTCAACCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (38 bp):
GGATCCATTTTGGTAAAGTAATTGCTCTTTTTTCCCTT
Found at i:17298693 original size:16 final size:16
Alignment explanation
Indices: 17298669--17298723 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
17298659 CAAGAATACT
*
17298669 ATTACAGTTCTATTCC
1 ATTACAGTTCTATTCA
* *
17298685 ATTATAGTTCTACTCA
1 ATTACAGTTCTATTCA
* *
17298701 ATTACAGCTCTATTCT
1 ATTACAGTTCTATTCA
17298717 ATTACAG
1 ATTACAG
17298724 CGAACCAAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (16 bp):
ATTACAGTTCTATTCA
Found at i:17298903 original size:24 final size:23
Alignment explanation
Indices: 17298867--17299015 Score: 86
Period size: 26 Copynumber: 6.2 Consensus size: 23
17298857 GAACCAAAAT
* *
17298867 AATATATAGAACAATTTGAAGTA
1 AATATATAAAACAATTTAAAGTA
17298890 AATAGTATAAAACAATTTAAAGTA
1 AATA-TATAAAACAATTTAAAGTA
* * *
17298914 AATAATATGTAAACAAATTAAAATAAA
1 AAT-ATAT-AAAACAATTTAAAGT--A
* * * *
17298941 CAACATACAAAAAAATTTAAAATA
1 -AATATATAAAACAATTTAAAGTA
* *
17298965 AATAACATATAAGACAATTTAAAAT-
1 AAT---ATATAAAACAATTTAAAGTA
* *
17298990 AATATATAAAA-AGTTTAAAATA
1 AATATATAAAACAATTTAAAGTA
17299012 AATA
1 AATA
17299016 ATATGTAAAA
Statistics
Matches: 100, Mismatches: 16, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
21 9 0.09
22 11 0.11
23 6 0.06
24 24 0.24
25 16 0.16
26 28 0.28
27 4 0.04
28 2 0.02
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (23 bp):
AATATATAAAACAATTTAAAGTA
Found at i:17298967 original size:51 final size:50
Alignment explanation
Indices: 17298889--17299137 Score: 155
Period size: 51 Copynumber: 4.7 Consensus size: 50
17298879 AATTTGAAGT
* * *
17298889 AAATAGTATAAAACAATTTAAAGTAAATAATATGTAAACAAATTAAAATAA
1 AAATA-TACAAAAAAATTTAAAATAAATAATATGTAAACAAATTAAAATAA
* * * *
17298940 ACAACATACAAAAAAATTTAAAATAAATAACATATAAGACAATTTAAAAT--
1 A-AATATACAAAAAAATTTAAAATAAATAATATGTAA-ACAAATTAAAATAA
* * * *
17298990 -AATATA-TAAAAAGTTTAAAATAAATAATATGTAAAAAGAAGTTTCAAATAA
1 AAATATACAAAAAAATTTAAAATAAATAATATGTAAACA-AA--TTAAAATAA
* * * *
17299041 ATAATATACAAAACAGTTTAAAAATAAATGATATGTATAAAAACAATTTAAAATAA
1 A-AATATACAAAAAAATTT-AAAATAAATAATATG--T--AAACAAATTAAAATAA
* * * *
17299097 ATAATATATATATAACAGTTTAAAAATAAATAATATATAAA
1 A-AATATACA-A-AAAAATTT-AAAATAAATAATATGTAAA
17299138 AATGAATAAT
Statistics
Matches: 157, Mismatches: 24, Indels: 31
0.74 0.11 0.15
Matches are distributed among these distances:
46 2 0.01
47 25 0.16
48 5 0.03
49 6 0.04
51 27 0.17
52 14 0.09
53 6 0.04
54 11 0.07
55 14 0.09
56 18 0.11
57 2 0.01
58 23 0.15
59 4 0.03
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (50 bp):
AAATATACAAAAAAATTTAAAATAAATAATATGTAAACAAATTAAAATAA
Found at i:17299006 original size:21 final size:22
Alignment explanation
Indices: 17298964--17299012 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
17298954 AATTTAAAAT
17298964 AAATAACATATAAGACAATTTA
1 AAATAACATATAAGACAATTTA
*
17298986 AAATAATATATAA-A-AAGTTTA
1 AAATAACATATAAGACAA-TTTA
17299007 AAATAA
1 AAATAA
17299013 ATAATATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 11 0.44
22 12 0.48
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (22 bp):
AAATAACATATAAGACAATTTA
Found at i:17299014 original size:25 final size:24
Alignment explanation
Indices: 17298863--17299252 Score: 188
Period size: 25 Copynumber: 15.2 Consensus size: 24
17298853 AAGCGAACCA
* *
17298863 AAATAATATATAGAACAATTTGAAGT
1 AAATAATATATA-AA-AATTTAAAAT
* *
17298889 AAATAGTATA-AAACAATTTAAAGT
1 AAATAATATATAAA-AATTTAAAAT
* *
17298913 AAATAATATGTAAACAAATTAAAAT
1 AAATAATATATAAA-AATTTAAAAT
* * *
17298938 AAACAACATACAAAAAAATTTAAAAT
1 AAA-TA-ATATATAAAAATTTAAAAT
*
17298964 AAATAACATATAAGACAATTTAAAAT
1 AAATAATATATAA-A-AATTTAAAAT
*
17298990 -AAT-ATATA-AAAAGTTTAAAAT
1 AAATAATATATAAAAATTTAAAAT
* *
17299011 AAATAATATGTAAAAAGAAGTTTCAAAT
1 AAATAATA--TATAAA-AA-TTTAAAAT
*
17299039 AAATAATATACAAAACAGTTTAAAAAT
1 AAATAATATATAAAA-A-TTT-AAAAT
*
17299066 AAATGATATGTATAAAAACAATTTAAAAT
1 AAAT-A-A--TATATAAA-AATTTAAAAT
17299095 AAATAATATATATATAACAGTTTAAAAAT
1 AAATAATATATA-A-AA-A-TTT-AAAAT
*
17299124 AAATAATATATAAAAA--T-GAAT
1 AAATAATATATAAAAATTTAAAAT
* *
17299145 -AATAGT-T-TGAAATAGTTTAAAAT
1 AAATAATATAT-AAA-AATTTAAAAT
* * * * *
17299168 ACATTATATGTGAAAAACTTGAAAT
1 AAATAATATAT-AAAAATTTAAAAT
*
17299193 AAATAATAATAAAAAAATTTAAAAT
1 AAATAAT-ATATAAAAATTTAAAAT
17299218 AAATAATATATGAGAAAAAGGTTTAAAAT
1 AAATAATATAT---AAAAA--TTTAAAAT
17299247 AAATAA
1 AAATAA
17299253 ATGAATAACA
Statistics
Matches: 286, Mismatches: 40, Indels: 73
0.72 0.10 0.18
Matches are distributed among these distances:
18 1 0.00
19 4 0.01
20 6 0.02
21 12 0.04
22 5 0.02
23 9 0.03
24 35 0.12
25 60 0.21
26 55 0.19
27 25 0.09
28 21 0.07
29 41 0.14
30 3 0.01
31 8 0.03
32 1 0.00
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (24 bp):
AAATAATATATAAAAATTTAAAAT
Found at i:17299032 original size:28 final size:28
Alignment explanation
Indices: 17298991--17299139 Score: 146
Period size: 29 Copynumber: 5.4 Consensus size: 28
17298981 ATTTAAAATA
17298991 ATATAT-AAAAAGTTTAAAATAAATAAT
1 ATATATAAAAAAGTTTAAAATAAATAAT
* *
17299018 ATGTA-AAAAGAAGTTTCAAATAAAT-A-
1 ATATATAAAA-AAGTTTAAAATAAATAAT
* * *
17299044 ATATACAAAACAGTTTAAAAATAAATGAT
1 ATATATAAAAAAGTTT-AAAATAAATAAT
* *
17299073 ATGTATAAAAACAATTTAAAATAAATAAT
1 ATATATAAAAA-AGTTTAAAATAAATAAT
* *
17299102 ATATATATAACAGTTTAAAAATAAATAAT
1 ATATATAAAAAAGTTT-AAAATAAATAAT
17299131 ATATA-AAAA
1 ATATATAAAA
17299140 TGAATAATAG
Statistics
Matches: 99, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
26 9 0.09
27 20 0.20
28 22 0.22
29 44 0.44
30 4 0.04
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.30
Consensus pattern (28 bp):
ATATATAAAAAAGTTTAAAATAAATAAT
Found at i:17299094 original size:29 final size:28
Alignment explanation
Indices: 17298986--17299139 Score: 144
Period size: 28 Copynumber: 5.6 Consensus size: 28
17298976 AGACAATTTA
17298986 AAATA-ATATAT-AAAA-AGTTTAAAAT
1 AAATATATATATAAAAACAGTTTAAAAT
* * *
17299011 AAATA-ATATGTAAAAAGAAGTTTCAAAT
1 AAATATATATATAAAAA-CAGTTTAAAAT
*
17299039 AAATA-ATATA-CAAAACAGTTTAAAAAT
1 AAATATATATATAAAAACAGTTT-AAAAT
* *
17299066 AAATGATATGTATAAAAACAATTTAAAAT
1 AAAT-ATATATATAAAAACAGTTTAAAAT
*
17299095 AAATA-ATATATATATAACAGTTTAAAAAT
1 AAATATATATATA-AAAACAGTTT-AAAAT
17299124 AAATA-ATATATAAAAA
1 AAATATATATATAAAAA
17299140 TGAATAATAG
Statistics
Matches: 107, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
25 10 0.09
26 9 0.08
27 18 0.17
28 31 0.29
29 30 0.28
30 9 0.08
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (28 bp):
AAATATATATATAAAAACAGTTTAAAAT
Found at i:17299221 original size:29 final size:29
Alignment explanation
Indices: 17299189--17299260 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
17299179 GAAAAACTTG
*
17299189 AAATAAATAATAATAAAAAAATTTAAAAT
1 AAATAAATAATAAGAAAAAAATTTAAAAT
* **
17299218 AAAT-AATATATGAGAAAAAGGTTTAAAAT
1 AAATAAATA-ATAAGAAAAAAATTTAAAAT
17299247 AAATAAATGAATAA
1 AAATAAAT-AATAA
17299261 CAAATTCGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 4 0.11
29 24 0.69
30 6 0.17
31 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (29 bp):
AAATAAATAATAAGAAAAAAATTTAAAAT
Found at i:17302258 original size:12 final size:11
Alignment explanation
Indices: 17302230--17302263 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
17302220 TTTGTTTGAG
17302230 ATAAAAATTAA
1 ATAAAAATTAA
*
17302241 ATAAAAATTAT
1 ATAAAAATTAA
*
17302252 ATCAAAATTAA
1 ATAAAAATTAA
17302263 A
1 A
17302264 ATTATTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAAAAATTAA
Done.