Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 49 of 153
Found at i:16317537 original size:46 final size:44
Alignment explanation
Indices: 16317433--16317540 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
16317423 TGTCTTTGAC
** * * *
16317433 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
16317477 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
16317523 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
16317541 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:16326655 original size:16 final size:17
Alignment explanation
Indices: 16326624--16326656 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16326614 TTCATAAGTA
16326624 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
16326641 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
16326657 GCACCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:16329562 original size:28 final size:28
Alignment explanation
Indices: 16329522--16329576 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
16329512 AAACCATTGG
*
16329522 TCCCAACGGCTAATTAAATAGTCGTTGA
1 TCCCAACAGCTAATTAAATAGTCGTTGA
16329550 TCCCAACAGCTAATTAAATAGTCGTTG
1 TCCCAACAGCTAATTAAATAGTCGTTG
16329577 TGGAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (28 bp):
TCCCAACAGCTAATTAAATAGTCGTTGA
Found at i:16331195 original size:30 final size:29
Alignment explanation
Indices: 16331128--16331195 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
16331118 ATTAACAAAA
*
16331128 TTAAGAATTTAGTCTTTGTATTTTTATTTC
1 TTAA-AATTTAGTCTTTCTATTTTTATTTC
*
16331158 ATAAAATTTAGTCTTTCTATTTTTCATATT-
1 TTAAAATTTAGTCTTTCTATTTTT-AT-TTC
16331188 TTAAAATT
1 TTAAAATT
16331196 CAAGTCCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 19 0.58
30 12 0.36
31 2 0.06
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.57
Consensus pattern (29 bp):
TTAAAATTTAGTCTTTCTATTTTTATTTC
Found at i:16340246 original size:20 final size:21
Alignment explanation
Indices: 16340219--16340261 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
16340209 AAGAGAATTC
*
16340219 AAGCAAGAGAAA-GAA-AGAA
1 AAGCAAGAAAAATGAAGAGAA
16340238 AAGCTAAGAAAAATGAAGAGAA
1 AAGC-AAGAAAAATGAAGAGAA
16340260 AA
1 AA
16340262 TTGATGAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 7 0.35
21 3 0.15
22 6 0.30
ACGTcount: A:0.67, C:0.05, G:0.23, T:0.05
Consensus pattern (21 bp):
AAGCAAGAAAAATGAAGAGAA
Found at i:16348159 original size:22 final size:22
Alignment explanation
Indices: 16348133--16348179 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
16348123 AAGTGATGGT
16348133 ATAAAACAACTTAAAACAAATA
1 ATAAAACAACTTAAAACAAATA
* * * *
16348155 ATAAAATAATTTTAAATAAATA
1 ATAAAACAACTTAAAACAAATA
16348177 ATA
1 ATA
16348180 TATATATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (22 bp):
ATAAAACAACTTAAAACAAATA
Found at i:16348828 original size:10 final size:12
Alignment explanation
Indices: 16348803--16348834 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
16348793 AACTTAAAAT
16348803 AAATAATATATA
1 AAATAATATATA
16348815 AAATAAT-T-TA
1 AAATAATATATA
16348825 AAATAATATA
1 AAATAATATA
16348835 CAATGAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.50
11 2 0.11
12 7 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATAATATATA
Found at i:16351039 original size:24 final size:22
Alignment explanation
Indices: 16350994--16351039 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
16350984 TTGATGGTGA
*
16350994 ACTTTATTGATAATCAATAAAT
1 ACTTTATTGATAATCAAGAAAT
*
16351016 ACTTTATTTGTATAATTAAGAAAT
1 ACTTTA-TTG-ATAATCAAGAAAT
16351040 TAAATAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (22 bp):
ACTTTATTGATAATCAAGAAAT
Found at i:16352250 original size:28 final size:29
Alignment explanation
Indices: 16352202--16352287 Score: 102
Period size: 28 Copynumber: 3.0 Consensus size: 29
16352192 TAGAGTTTAG
**
16352202 GGGTTCTGAAAAAAATAATTTTGGTGAAAT
1 GGGTTCTG-AAAAAATAATTTTGACGAAAT
* *
16352232 GGGTTCT-AAAAAATAATTTTAACGAGAT
1 GGGTTCTGAAAAAATAATTTTGACGAAAT
* *
16352260 GGGTTCTGAAGAAATAATTTTGAAGAAA
1 GGGTTCTGAAAAAATAATTTTGACGAAA
16352288 AAACTCTTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
28 24 0.51
29 16 0.34
30 7 0.15
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.31
Consensus pattern (29 bp):
GGGTTCTGAAAAAATAATTTTGACGAAAT
Found at i:16352643 original size:193 final size:192
Alignment explanation
Indices: 16352317--16352946 Score: 852
Period size: 193 Copynumber: 3.3 Consensus size: 192
16352307 CACAGTCAGT
* * *
16352317 AAAAGTACTGAAAACGCTTCCAGCTGGATGCCCTTTTCAGTACTGCTGCTTCTAAAAAATTAATT
1 AAAAGTACTGAAAACGCTTCCAGCTGGACGCCCTTTTCAGTACTGCTGCTTCTGAAAAATAAATT
* * *
16352382 TGAAGAGATGATTTTGAAAAAATATCTCT-AGATTCCCGGGATATTTAAAAGGTTTGTGAAAAAT
66 TGAGGAGATGATTCTGAAAAAATATCT-TGAGATTCCCGGGATATTTGAAAGGTTTGTGAAAAAT
* * * * * *
16352446 GCCCCGAATGGTGGGGGTTGAGGTTTGTAGAGGAACAACACTCCAAGTAGGATGCATTATTAGT
130 GCCCCGAATAGT-GGGGTTAAGGTTTGTAGAGGAAAAACGCTCCAAGTAGGATGCACTATTAGC
* * **
16352510 AAAAGTACTGAAAACGATTCCAGCTAGACATCCTTTTCAGTACTGCTGCTTCTGAAAAATAAATT
1 AAAAGTACTGAAAACGCTTCCAGCTGGACGCCCTTTTCAGTACTGCTGCTTCTGAAAAATAAATT
*
16352575 TGAGGAGATGATTCTGAAAAAATATCTTGAGATTCCCGAGATATTTGAAAGGTTTGTGAAAAATG
66 TGAGGAGATGATTCTGAAAAAATATCTTGAGATTCCCGGGATATTTGAAAGGTTTGTGAAAAATG
* * * * *
16352640 CCCCAAATAGTAGAGGCTAAGGTTTGTAGAGAAAAAAACGCTCCAA-TCAGGATACACTATTAGC
131 CCCCGAATAGT-GGGGTTAAGGTTTGTAGAG-GAAAAACGCTCCAAGT-AGGATGCACTATTAGC
* * *
16352704 AAAAGTATTGAAAATGCTTCCAGCTGGATGCCCTTTTCAGTACTGCTGCTTCTGAAAAAATAAAT
1 AAAAGTACTGAAAACGCTTCCAGCTGGACGCCCTTTTCAGTACTGCTGCTTCTG-AAAAATAAAT
* * * *
16352769 GTGAGGAGATGATTCTTAAAAAATGTCTCGAGATTCCCGGGATATTTGAAAGGTTTGTGAAAAAT
65 TTGAGGAGATGATTCTGAAAAAATATCTTGAGATTCCCGGGATATTTGAAAGGTTTGTGAAAAAT
* * * *
16352834 TCCCCGAATAGTGGGGTTAATGTTTGTAGAGGAAAAACGCTCCAAGCAGGATGCACTATCAGC
130 GCCCCGAATAGTGGGGTTAAGGTTTGTAGAGGAAAAACGCTCCAAGTAGGATGCACTATTAGC
* * *
16352897 AAAAGT-CTTGAAAATGCTTCTAGCTGGACGCCCTTTTCAGTACTTCTGCT
1 AAAAGTAC-TGAAAACGCTTCCAGCTGGACGCCCTTTTCAGTACTGCTGCT
16352947 GATAGTGCGT
Statistics
Matches: 383, Mismatches: 48, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
192 1 0.00
193 215 0.56
194 87 0.23
195 80 0.21
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (192 bp):
AAAAGTACTGAAAACGCTTCCAGCTGGACGCCCTTTTCAGTACTGCTGCTTCTGAAAAATAAATT
TGAGGAGATGATTCTGAAAAAATATCTTGAGATTCCCGGGATATTTGAAAGGTTTGTGAAAAATG
CCCCGAATAGTGGGGTTAAGGTTTGTAGAGGAAAAACGCTCCAAGTAGGATGCACTATTAGC
Found at i:16353594 original size:32 final size:32
Alignment explanation
Indices: 16353553--16353664 Score: 145
Period size: 32 Copynumber: 3.5 Consensus size: 32
16353543 TAGAAGAATA
* *
16353553 TTGTTATCATTTAACAAAATTAAAGTTGATTT
1 TTGTTATCATTTCACAAAATTAAAGTTGATAT
*
16353585 TTGTTATCATTTCACAAAATTGAAGTTG-TAAT
1 TTGTTATCATTTCACAAAATTAAAGTTGAT-AT
* * * *
16353617 TTGTTACCATTTCACAAAATGAAAGCTAATAT
1 TTGTTATCATTTCACAAAATTAAAGTTGATAT
16353649 TTGTTATCATTTCACA
1 TTGTTATCATTTCACA
16353665 GAACTGCGCG
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
31 1 0.01
32 67 0.97
33 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (32 bp):
TTGTTATCATTTCACAAAATTAAAGTTGATAT
Found at i:16353969 original size:17 final size:18
Alignment explanation
Indices: 16353947--16353990 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
16353937 CCCCAACCCT
16353947 AAACCCTAACAA-ACTAA
1 AAACCCTAACAACACTAA
*
16353964 AAACCCTAACAACCCTAA
1 AAACCCTAACAACACTAA
*
16353982 ACACCCTAA
1 AAACCCTAA
16353991 TATAACACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.52, C:0.36, G:0.00, T:0.11
Consensus pattern (18 bp):
AAACCCTAACAACACTAA
Found at i:16365583 original size:12 final size:13
Alignment explanation
Indices: 16365568--16365597 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
16365558 TAGTTCAAGG
16365568 ATCAGTTC-TTAT
1 ATCAGTTCTTTAT
16365580 ATCAGTTCTTTAT
1 ATCAGTTCTTTAT
16365593 ATCAG
1 ATCAG
16365598 ACTGATATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.47
Consensus pattern (13 bp):
ATCAGTTCTTTAT
Found at i:16370921 original size:20 final size:20
Alignment explanation
Indices: 16370896--16370935 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16370886 ATTTGAACCC
*
16370896 ATATTATTTGCATCAATAAA
1 ATATTAATTGCATCAATAAA
* *
16370916 ATATTAATTGTATCACTAAA
1 ATATTAATTGCATCAATAAA
16370936 CCAAAACTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
ATATTAATTGCATCAATAAA
Found at i:16371678 original size:22 final size:22
Alignment explanation
Indices: 16371650--16371725 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
16371640 TATATGTTTA
16371650 ATATTTTAACAATTTAATTATT
1 ATATTTTAACAATTTAATTATT
* * * *
16371672 ATATTTT-ATATTTTATTTCACATA
1 ATATTTTAACAATTTAATT---ATT
* *
16371696 ATATTTTAACAATTCAATTAAT
1 ATATTTTAACAATTTAATTATT
16371718 ATATTTTA
1 ATATTTTA
16371726 TATTTTATTA
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
21 8 0.20
22 16 0.40
24 9 0.22
25 7 0.17
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATTTTAACAATTTAATTATT
Found at i:16374622 original size:55 final size:55
Alignment explanation
Indices: 16374510--16374618 Score: 141
Period size: 54 Copynumber: 2.0 Consensus size: 55
16374500 TATCGCCGTT
* **
16374510 TAATATTTTTCACAAAACCCTTCTCTAATATCTGATTTGTAAAGTTGCCCCAAAA
1 TAATATTTTTCACAAAACCCTTCTCTAATATCTGATTTCTAAAGGGGCCCCAAAA
* * *
16374565 TAATATTTTTCACAAAA-CCTTTTTTAATGTCTGATTTCT-AAGGGGCTCCCAAAA
1 TAATATTTTTCACAAAACCCTTCTCTAATATCTGATTTCTAAAGGGGC-CCCAAAA
16374619 ATAAATGCAG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 5 0.11
54 25 0.53
55 17 0.36
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (55 bp):
TAATATTTTTCACAAAACCCTTCTCTAATATCTGATTTCTAAAGGGGCCCCAAAA
Found at i:16375511 original size:12 final size:11
Alignment explanation
Indices: 16375484--16375524 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
16375474 AATAATACAA
* *
16375484 AAATTATTAAA
1 AAATTATGAAG
16375495 AAATTATGAAG
1 AAATTATGAAG
16375506 AGAATTATGAAG
1 A-AATTATGAAG
16375518 AAATTAT
1 AAATTAT
16375525 AATTCTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (11 bp):
AAATTATGAAG
Found at i:16379274 original size:18 final size:19
Alignment explanation
Indices: 16379251--16379296 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
16379241 TAAACTGAGT
* *
16379251 TTTTTTAATTTTTTAA-AG
1 TTTTTTAATTTATTAATAA
16379269 TTTTTTAA-TTATTAATAA
1 TTTTTTAATTTATTAATAA
16379287 TTTTTTAATT
1 TTTTTTAATT
16379297 GAACTGGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 17 0.71
19 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTTAATTTATTAATAA
Found at i:16381244 original size:20 final size:20
Alignment explanation
Indices: 16381216--16381253 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16381206 CTAGGAACTA
16381216 TGTGATCTGAGCTCATGAGT
1 TGTGATCTGAGCTCATGAGT
* *
16381236 TGTGGTCTGAGTTCATGA
1 TGTGATCTGAGCTCATGA
16381254 TATAAGTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.32, T:0.37
Consensus pattern (20 bp):
TGTGATCTGAGCTCATGAGT
Found at i:16383174 original size:22 final size:23
Alignment explanation
Indices: 16383149--16383191 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
16383139 TTACAAGCAT
*
16383149 AAATGACCA-CATTTCATAACTC
1 AAATGACAATCATTTCATAACTC
*
16383171 AAATGGCAATCATTTCATAAC
1 AAATGACAATCATTTCATAAC
16383192 CATTTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (23 bp):
AAATGACAATCATTTCATAACTC
Found at i:16383370 original size:23 final size:23
Alignment explanation
Indices: 16383340--16383386 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
16383330 ACACATATAC
16383340 ATAACCAATATTTAGCCAAGTTA
1 ATAACCAATATTTAGCCAAGTTA
16383363 ATAACCAATATTTAGCCAAGTTA
1 ATAACCAATATTTAGCCAAGTTA
16383386 A
1 A
16383387 GCCAAATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.30
Consensus pattern (23 bp):
ATAACCAATATTTAGCCAAGTTA
Found at i:16384209 original size:20 final size:20
Alignment explanation
Indices: 16384102--16384209 Score: 76
Period size: 20 Copynumber: 5.4 Consensus size: 20
16384092 TTTCTATTTG
* *
16384102 TATAAACTGTAATTCATTCA
1 TATAAACAGTAATTCATCCA
* * *
16384122 TATAACCAGTAGTTCATCCG
1 TATAAACAGTAATTCATCCA
* * *
16384142 TGTAAACAGTAGTTCAT-TA
1 TATAAACAGTAATTCATCCA
* * *
16384161 T-TAATAACAATAATTCAACTA
1 TAT-A-AACAGTAATTCATCCA
*
16384182 TATCAACAGTAATTCATCCA
1 TATAAACAGTAATTCATCCA
16384202 TATAAACA
1 TATAAACA
16384210 CATATCTTAT
Statistics
Matches: 67, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
18 1 0.01
19 2 0.03
20 60 0.90
21 3 0.04
22 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (20 bp):
TATAAACAGTAATTCATCCA
Found at i:16384389 original size:23 final size:23
Alignment explanation
Indices: 16384359--16384535 Score: 194
Period size: 23 Copynumber: 7.6 Consensus size: 23
16384349 TGATCGATAG
16384359 GCTCTTTTGAGCTGAAACGGTAA
1 GCTCTTTTGAGCTGAAACGGTAA
*
16384382 GCTCTTTTGAGCTGAAACGATAA
1 GCTCTTTTGAGCTGAAACGGTAA
* * *
16384405 GCTCCTTTAAGTTGAAACGGTAA
1 GCTCTTTTGAGCTGAAACGGTAA
* * * * *
16384428 GTTCTTTCGAG-TTAAATGGTTA
1 GCTCTTTTGAGCTGAAACGGTAA
* *
16384450 GCTCCTTTAAGCTGAAACGGTAA
1 GCTCTTTTGAGCTGAAACGGTAA
16384473 GCTCTTTTGAGCTGAAACGGTAA
1 GCTCTTTTGAGCTGAAACGGTAA
* *
16384496 GCTCCTTTAAGCTGAAATATCGGTAA
1 GCTCTTTTGAGCTG-AA-A-CGGTAA
*
16384522 GCTCTTTCGAGCTG
1 GCTCTTTTGAGCTG
16384536 TGGTGAGTCC
Statistics
Matches: 124, Mismatches: 26, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
22 15 0.12
23 89 0.72
24 2 0.02
25 1 0.01
26 17 0.14
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (23 bp):
GCTCTTTTGAGCTGAAACGGTAA
Found at i:16384422 original size:46 final size:46
Alignment explanation
Indices: 16384336--16384535 Score: 224
Period size: 46 Copynumber: 4.3 Consensus size: 46
16384326 ATCATTTATC
* * * *
16384336 CTCTTTTGAGCCATG-ATCGATAGGCTCTTTTGAGCTGAAACGGTAAG
1 CTCTTTTGAG-C-TGAAACGATAAGCTCCTTTAAGCTGAAACGGTAAG
*
16384383 CTCTTTTGAGCTGAAACGATAAGCTCCTTTAAGTTGAAACGGTAAG
1 CTCTTTTGAGCTGAAACGATAAGCTCCTTTAAGCTGAAACGGTAAG
* * * * * *
16384429 TTCTTTCGAG-TTAAATGGTTAGCTCCTTTAAGCTGAAACGGTAAG
1 CTCTTTTGAGCTGAAACGATAAGCTCCTTTAAGCTGAAACGGTAAG
*
16384474 CTCTTTTGAGCTGAAACGGTAAGCTCCTTTAAGCTGAAATATCGGTAAG
1 CTCTTTTGAGCTGAAACGATAAGCTCCTTTAAGCTG-AA-A-CGGTAAG
*
16384523 CTCTTTCGAGCTG
1 CTCTTTTGAGCTG
16384536 TGGTGAGTCC
Statistics
Matches: 130, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
45 40 0.31
46 58 0.45
47 12 0.09
48 1 0.01
49 19 0.15
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (46 bp):
CTCTTTTGAGCTGAAACGATAAGCTCCTTTAAGCTGAAACGGTAAG
Found at i:16385608 original size:3 final size:3
Alignment explanation
Indices: 16385602--16385643 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
16385592 TTGTTGTGTT
16385602 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16385644 GGCTAATTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16387064 original size:23 final size:25
Alignment explanation
Indices: 16387038--16387084 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
16387028 TATCATTCAT
*
16387038 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
16387061 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
16387085 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:16388703 original size:19 final size:19
Alignment explanation
Indices: 16388667--16388704 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
16388657 TTTCATGATG
*
16388667 AAAATTTTTAAATTTTCCC
1 AAAATTTTTAAATGTTCCC
16388686 AAAAGTTTTTAAA-GTTCCC
1 AAAA-TTTTTAAATGTTCCC
16388705 GGTTTAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (19 bp):
AAAATTTTTAAATGTTCCC
Found at i:16390823 original size:21 final size:21
Alignment explanation
Indices: 16390784--16390823 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16390774 AATCTTATTT
* * *
16390784 TTTTTTTAATTTGATTTGAAA
1 TTTTTTTAAATTAAATTGAAA
16390805 TTTTTTTAAATTAAATTGA
1 TTTTTTTAAATTAAATTGA
16390824 GTGAGATGAA
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:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTTTTTAAATTAAATTGAAA
Found at i:16392107 original size:23 final size:23
Alignment explanation
Indices: 16392081--16392144 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 23
16392071 AAGTTTTTAA
*
16392081 AAAAATTAAAAATTAATTATTAT
1 AAAAATTAAAAATTAAATATTAT
*
16392104 AAAAACTAAAAA--AAATATTAT
1 AAAAATTAAAAATTAAATATTAT
* *
16392125 ATAAATATAAATATTAAATA
1 AAAAAT-TAAAAATTAAATA
16392145 AAATAATTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
21 12 0.36
22 5 0.15
23 11 0.33
24 5 0.15
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAAATTAAAAATTAAATATTAT
Found at i:16392138 original size:17 final size:16
Alignment explanation
Indices: 16392110--16392168 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
16392100 TTATAAAAAC
* *
16392110 TAAAAAAAATATTATA
1 TAAAATAAATATTAAA
16392126 TAAATATAAATATTAAA
1 TAAA-ATAAATATTAAA
16392143 TAAAATAATTATATT-AA
1 TAAAATAA--ATATTAAA
16392160 -AAAATAAAT
1 TAAAATAAAT
16392169 TTTTCCCCGC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 2 0.05
16 15 0.39
17 16 0.42
18 5 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAATAAATATTAAA
Found at i:16393200 original size:3 final size:3
Alignment explanation
Indices: 16393192--16393237 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
16393182 AAAAGCTCTG
16393192 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
16393238 ACCTACGGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:16394678 original size:18 final size:18
Alignment explanation
Indices: 16394652--16394702 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
16394642 GTACATTTGG
16394652 TCAAGTGAAGAAGAATTT
1 TCAAGTGAAGAAGAATTT
*
16394670 TCAAATGAAGAAGAATTT
1 TCAAGTGAAGAAGAATTT
*
16394688 TCAAGTAAAGAAGAA
1 TCAAGTGAAGAAGAA
16394703 CAAGATGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.24
Consensus pattern (18 bp):
TCAAGTGAAGAAGAATTT
Found at i:16395269 original size:25 final size:26
Alignment explanation
Indices: 16395223--16395274 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
16395213 TTGTATAATC
*
16395223 TTAATACAATGAATTTATAAAAATAA
1 TTAATAAAATGAATTTATAAAAATAA
*
16395249 TTAATAAAATG-ATTTATAAAAGTAA
1 TTAATAAAATGAATTTATAAAAATAA
16395274 T
1 T
16395275 AACTTGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (26 bp):
TTAATAAAATGAATTTATAAAAATAA
Found at i:16397379 original size:24 final size:24
Alignment explanation
Indices: 16397352--16397397 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
16397342 TAGACGACGG
**
16397352 ACAAATAGGATTGGATGACGATGA
1 ACAAATAGGATCAGATGACGATGA
16397376 ACAAATAGGATCAGATGACGAT
1 ACAAATAGGATCAGATGACGAT
16397398 CCATTCTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.26, T:0.20
Consensus pattern (24 bp):
ACAAATAGGATCAGATGACGATGA
Found at i:16401703 original size:27 final size:28
Alignment explanation
Indices: 16401650--16401713 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
16401640 CTAGTTTGGT
*
16401650 TCCATGCTCCCTTTTTCTCTTCTGTTCA
1 TCCATGCTCCCTTTTTCTCTTCGGTTCA
16401678 TCCATGCTCCCTTTTTCTCTT-GGTTCA
1 TCCATGCTCCCTTTTTCTCTTCGGTTCA
16401705 TCCATGCTC
1 TCCATGCTC
16401714 GGCTTCCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 14 0.40
28 21 0.60
ACGTcount: A:0.08, C:0.36, G:0.09, T:0.47
Consensus pattern (28 bp):
TCCATGCTCCCTTTTTCTCTTCGGTTCA
Found at i:16402123 original size:10 final size:9
Alignment explanation
Indices: 16402104--16402137 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
16402094 AAGAGAGGGG
16402104 AAAAAAAGA
1 AAAAAAAGA
16402113 AAAATAAAGA
1 AAAA-AAAGA
16402123 AATAAAAAGA
1 AA-AAAAAGA
16402133 AAAAA
1 AAAAA
16402138 TTAAATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 7 0.30
10 14 0.61
11 2 0.09
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:16410176 original size:8 final size:9
Alignment explanation
Indices: 16410161--16410185 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16410151 TTATAATTTA
16410161 AAATTTTTT
1 AAATTTTTT
16410170 AAATTTTTT
1 AAATTTTTT
16410179 AAATTTT
1 AAATTTT
16410186 ATTTTGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
AAATTTTTT
Found at i:16411073 original size:11 final size:11
Alignment explanation
Indices: 16411057--16411099 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
16411047 TAGAATATAT
16411057 CCCATACCTTG
1 CCCATACCTTG
*
16411068 CCCATACCTTT
1 CCCATACCTTG
*
16411079 CCCATACC-TA
1 CCCATACCTTG
16411089 CCCATACCTTG
1 CCCATACCTTG
16411100 GAAAGGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.21, C:0.47, G:0.05, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:16411084 original size:22 final size:21
Alignment explanation
Indices: 16411056--16411098 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
16411046 TTAGAATATA
*
16411056 TCCCATACCTTGCCCATACCTT
1 TCCCATACC-TACCCATACCTT
16411078 TCCCATACCTACCCATACCTT
1 TCCCATACCTACCCATACCTT
16411099 GGAAAGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.21, C:0.47, G:0.02, T:0.30
Consensus pattern (21 bp):
TCCCATACCTACCCATACCTT
Found at i:16411979 original size:226 final size:226
Alignment explanation
Indices: 16411585--16412135 Score: 1093
Period size: 226 Copynumber: 2.4 Consensus size: 226
16411575 TTCCGCGCAA
16411585 TAGGTTTTGATCACCCAACTATTTTTAATTACCTAATAACCTTTAACATTATCGAATTGTCATAT
1 TAGGTTTTGATCACCCAACTATTTTTAATTACCTAATAACCTTTAACATTATCGAATTGTCATAT
16411650 TTTTGCTACTCATCTGATACCTCTCATTAAAACATTATCGAATCACTTTAATGTTTTGTTTGCTT
66 TTTTGCTACTCATCTGATACCTCTCATTAAAACATTATCGAATCACTTTAATGTTTTGTTTGCTT
16411715 ATAATGTTATGCTATGCATAGAATCCGTGATGAATTAGTCATTAAGAAAAGTAAGAGACAAATTG
131 ATAATGTTATGCTATGCATAGAATCCGTGATGAATTAGTCATTAAGAAAAGTAAGAGACAAATTG
16411780 TACATCGTTGGCCCTTAATTTCGGTCAAGAT
196 TACATCGTTGGCCCTTAATTTCGGTCAAGAT
16411811 TAGGTTTTGATCACCCAACTATTTTTAATTACCTAATAACCTTTAACATTATCGAATTGTCATAT
1 TAGGTTTTGATCACCCAACTATTTTTAATTACCTAATAACCTTTAACATTATCGAATTGTCATAT
16411876 TTTTGCTACTCATCTGATACCTCTCATTAAAACATTATCGAATCACTTTAATGTTTTGTTTGCTT
66 TTTTGCTACTCATCTGATACCTCTCATTAAAACATTATCGAATCACTTTAATGTTTTGTTTGCTT
16411941 ATAATGTTATGCTATGCATAGAATCCGTGATGAATTAGTCATTAAGAAAAGTAAGAGACAAATTG
131 ATAATGTTATGCTATGCATAGAATCCGTGATGAATTAGTCATTAAGAAAAGTAAGAGACAAATTG
16412006 TACATCGTTGGCCCTTAATTTCGGTCAAGAT
196 TACATCGTTGGCCCTTAATTTCGGTCAAGAT
16412037 TAGGTTTTGATCACCCAACTATTTTTAATTACCTAATAACCTTTAACATTATCGAATTGTCATAT
1 TAGGTTTTGATCACCCAACTATTTTTAATTACCTAATAACCTTTAACATTATCGAATTGTCATAT
*
16412102 TTTTGCTACTCATCTAATACCTCTCATTAAAACA
66 TTTTGCTACTCATCTGATACCTCTCATTAAAACA
16412136 ATAACGTGGC
Statistics
Matches: 324, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
226 324 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.39
Consensus pattern (226 bp):
TAGGTTTTGATCACCCAACTATTTTTAATTACCTAATAACCTTTAACATTATCGAATTGTCATAT
TTTTGCTACTCATCTGATACCTCTCATTAAAACATTATCGAATCACTTTAATGTTTTGTTTGCTT
ATAATGTTATGCTATGCATAGAATCCGTGATGAATTAGTCATTAAGAAAAGTAAGAGACAAATTG
TACATCGTTGGCCCTTAATTTCGGTCAAGAT
Found at i:16412312 original size:17 final size:17
Alignment explanation
Indices: 16412276--16412336 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
16412266 TTATAAAAAC
* **
16412276 TAAATAAAAATATTCTA
1 TAAATATAAATATTAAA
16412293 TAAATATAAATATTAAA
1 TAAATATAAATATTAAA
16412310 TAAA-ATAATTATATTAAA
1 TAAATATAA--ATATTAAA
16412328 -AAATA-AAAT
1 TAAATATAAAT
16412337 TTTCCCCACC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 2 0.05
16 4 0.11
17 23 0.61
18 9 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAATATAAATATTAAA
Found at i:16414800 original size:18 final size:18
Alignment explanation
Indices: 16414752--16414802 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
16414742 GTACATTTGG
*
16414752 TCAAGTGAAGAAAAATTT
1 TCAAGTGAAGAAGAATTT
*
16414770 TCAAATGAAGAAGAATTT
1 TCAAGTGAAGAAGAATTT
*
16414788 TTAAGTGAAGAAGAA
1 TCAAGTGAAGAAGAA
16414803 CAAGATGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.51, C:0.04, G:0.20, T:0.25
Consensus pattern (18 bp):
TCAAGTGAAGAAGAATTT
Found at i:16415877 original size:25 final size:26
Alignment explanation
Indices: 16415831--16415882 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
16415821 TTGTATAATC
*
16415831 TTAATACAATGAATTTATAAAAATAA
1 TTAATAAAATGAATTTATAAAAATAA
*
16415857 TTAATAAAATG-ATTTATAAAAGTAA
1 TTAATAAAATGAATTTATAAAAATAA
16415882 T
1 T
16415883 AACTTGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (26 bp):
TTAATAAAATGAATTTATAAAAATAA
Found at i:16417970 original size:24 final size:24
Alignment explanation
Indices: 16417937--16417989 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
16417927 GCATATGTTA
**
16417937 GACGAAGAACAAATAGGATTGGAT
1 GACGAAGAACAAATAGGATCAGAT
*
16417961 GACGACGAACAAATAGGATCAGAT
1 GACGAAGAACAAATAGGATCAGAT
16417985 GACGA
1 GACGA
16417990 TCAATTCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.45, C:0.13, G:0.28, T:0.13
Consensus pattern (24 bp):
GACGAAGAACAAATAGGATCAGAT
Found at i:16419675 original size:39 final size:37
Alignment explanation
Indices: 16419610--16419684 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 37
16419600 TAATTCATTA
*
16419610 ATTTTTAAAAATTAAAAATTCAAAAAATATATAAAAATT
1 ATTTTTAAAAATTAAAAAGTCAAAAAA-A-ATAAAAATT
*
16419649 ATTTTTTAAAATTAAAAAGT-ATAAAAAAATAAAAAT
1 ATTTTTAAAAATTAAAAAGTCA-AAAAAAATAAAAAT
16419685 ATACATGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 8 0.24
38 2 0.06
39 23 0.70
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (37 bp):
ATTTTTAAAAATTAAAAAGTCAAAAAAAATAAAAATT
Found at i:16421690 original size:13 final size:13
Alignment explanation
Indices: 16421674--16421698 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16421664 TTCTTTTAAC
16421674 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
16421687 TTTTCTTTTTTT
1 TTTTCTTTTTTT
16421699 ACCATTTTCT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:16422533 original size:12 final size:12
Alignment explanation
Indices: 16422516--16422540 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16422506 AATAAGGACT
16422516 TGGTTTATTTGG
1 TGGTTTATTTGG
16422528 TGGTTTATTTGG
1 TGGTTTATTTGG
16422540 T
1 T
16422541 AGGCAAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.32, T:0.60
Consensus pattern (12 bp):
TGGTTTATTTGG
Found at i:16424488 original size:32 final size:31
Alignment explanation
Indices: 16424406--16424488 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
16424396 TCAGCCCCAC
* * **
16424406 TAACGGGTTATAATAGTTAATTTAAGCTCGT
1 TAACAGGTTATAATAGTTAGTACAAGCTCGT
* * *
16424437 TAACAAGTTAAAATGGTTAGTACAAGCCTCGT
1 TAACAGGTTATAATAGTTAGTACAAG-CTCGT
*
16424469 TAACAGGTGATAATAGTTAG
1 TAACAGGTTATAATAGTTAG
16424489 CACAGACCCT
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
31 19 0.47
32 21 0.52
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (31 bp):
TAACAGGTTATAATAGTTAGTACAAGCTCGT
Found at i:16425887 original size:13 final size:13
Alignment explanation
Indices: 16425869--16425893 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16425859 TTCTTTTTAA
16425869 TTTTAATTAATAG
1 TTTTAATTAATAG
16425882 TTTTAATTAATA
1 TTTTAATTAATA
16425894 AACATGTTAT
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTTTAATTAATAG
Found at i:16425949 original size:5 final size:5
Alignment explanation
Indices: 16425939--16425965 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
16425929 ATTTTTAAGA
16425939 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
16425966 TAATTCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:16426185 original size:21 final size:22
Alignment explanation
Indices: 16426142--16426185 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
16426132 ATATAGACAA
* * *
16426142 AATAATAAATATGTAATTCTAT
1 AATAATAAATATATAACTATAT
16426164 AATAA-AAATATATAACTATAT
1 AATAATAAATATATAACTATAT
16426185 A
1 A
16426186 TATTATTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (22 bp):
AATAATAAATATATAACTATAT
Found at i:16426596 original size:13 final size:13
Alignment explanation
Indices: 16426578--16426609 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16426568 ATAAATAAAG
*
16426578 AAAATATTAATTA
1 AAAATATGAATTA
16426591 AAAATATGAATTA
1 AAAATATGAATTA
16426604 AAAATA
1 AAAATA
16426610 AAATAAAATA
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:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
AAAATATGAATTA
Found at i:16426666 original size:22 final size:21
Alignment explanation
Indices: 16426634--16426680 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
16426624 TAAAAATGTG
*
16426634 TTTATTGATTAAAAATAATATA
1 TTTATTAATTAAAAATAATA-A
*
16426656 TTTATTAATTAAAAATATTAA
1 TTTATTAATTAAAAATAATAA
16426677 TTTA
1 TTTA
16426681 AAAAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTATTAATTAAAAATAATAA
Found at i:16437296 original size:26 final size:26
Alignment explanation
Indices: 16437267--16437339 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
16437257 CCCGTTATAT
16437267 GGCTCTTCGTGAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGCTTCCCGATTAAA
* * *
16437293 GGCTCTTTGTGAGCTTCCTGATTAAT
1 GGCTCTTCGTGAGCTTCCCGATTAAA
16437319 GGCTCTTCG-GAGCTTCCCGAT
1 GGCTCTTCGTGAGCTTCCCGAT
16437340 ATGACTCACT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 11 0.26
26 31 0.74
ACGTcount: A:0.15, C:0.26, G:0.25, T:0.34
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCGATTAAA
Found at i:16440400 original size:137 final size:138
Alignment explanation
Indices: 16440142--16440501 Score: 366
Period size: 137 Copynumber: 2.6 Consensus size: 138
16440132 GATCGTGACA
* * * *
16440142 TGTATTTTGTATTTAATGTTGCTTAAAGCTTTTTAAATTTTAATTAATTTTTTTAACATATTAAT
1 TGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTAATTAATTATTTTAACATATTAAT
* * * *
16440207 TTTTTGGTTAGATGGTTAGATAGTTGCAAATATATCCTTGAGTTTCGGATTAGATTCCTT-TCTT
66 TTTTTGGTTAGATGGTTAGATAGTTGCAAATACATCCTTAAATTTCGGATTAGATT-CTTCTATT
*
16440271 ATTCACATT
130 ACTCACATT
* * * *
16440280 TGTATTTTTTATTTCATGATGCTTCAAGTTTTTTAAATTTTTTATTAA-TATTTT-ACATATTAG
1 TGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAA-TTTTAATTAATTATTTTAACATATTAA
* *
16440343 TTATTTT-GTTAGATGGTTAGATAGTTGCAATTACATCCTTAAATCTT--GAGTTCGATTCTTCT
65 TT-TTTTGGTTAGATGGTTAGATAGTTGCAAATACATCCTTAAAT-TTCGGA-TTAGATTCTTCT
*
16440405 ATTACTCGCATT
127 ATTACTCACATT
*
16440417 TGTATTTTTTTTATTTCATGTTGCTTCAAAC--TTT---TTTTAATTAA-TATTTTTAACATATT
1 TGTA--TTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTAATTAATTA-TTTTAACATATT
* ** *
16440476 AGCTCCTTTCGTTAGATGGTTAGATA
63 A-ATTTTTTGGTTAGATGGTTAGATA
16440502 ATTACGATTA
Statistics
Matches: 188, Mismatches: 23, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
133 11 0.06
134 4 0.02
135 11 0.06
136 22 0.12
137 66 0.35
138 43 0.23
139 31 0.16
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (138 bp):
TGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTAATTAATTATTTTAACATATTAAT
TTTTTGGTTAGATGGTTAGATAGTTGCAAATACATCCTTAAATTTCGGATTAGATTCTTCTATTA
CTCACATT
Found at i:16440711 original size:25 final size:26
Alignment explanation
Indices: 16440652--16440711 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
16440642 TTATTCTTTC
*
16440652 AATTAATTATATTTATAATAATTATTA
1 AATT-ATTATATTTATAATAATTAATA
*
16440679 AATT-TTATTTTTATAA-AATTAA-A
1 AATTATTATATTTATAATAATTAATA
16440702 TAATTATTAT
1 -AATTATTAT
16440712 CATTATCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 1 0.03
24 9 0.31
25 15 0.52
27 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
AATTATTATATTTATAATAATTAATA
Found at i:16445341 original size:18 final size:18
Alignment explanation
Indices: 16445318--16445354 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
16445308 TGATCGTGGC
*
16445318 ATAATTGGTGGTTTACTA
1 ATAATTGGTGATTTACTA
16445336 ATAATTGGTGATTTACTA
1 ATAATTGGTGATTTACTA
16445354 A
1 A
16445355 CCCCGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (18 bp):
ATAATTGGTGATTTACTA
Found at i:16451650 original size:23 final size:25
Alignment explanation
Indices: 16451622--16451672 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
16451612 TGATATAAAA
*
16451622 ATTTTAAATTTT-AAAATTATTTTT
1 ATTTAAAATTTTAAAAATTATTTTT
16451646 ATTTAAAATTTTCAAAAATTATTTTT
1 ATTTAAAATTTT-AAAAATTATTTTT
16451672 A
1 A
16451673 AAAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 11 0.46
26 13 0.54
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTAAAATTTTAAAAATTATTTTT
Found at i:16451677 original size:24 final size:23
Alignment explanation
Indices: 16451627--16451678 Score: 61
Period size: 26 Copynumber: 2.2 Consensus size: 23
16451617 TAAAAATTTT
*
16451627 AAATTTTAAAATTATTTTTATTTA
1 AAATTTTAAAATTATTTTTA-TAA
16451651 AAATTTTCAAAAATTATTTTTA-AA
1 AAATTTT--AAAATTATTTTTATAA
16451675 AAAT
1 AAAT
16451679 AAAAATGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 12 0.48
26 13 0.52
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATTTTAAAATTATTTTTATAA
Found at i:16452655 original size:8 final size:8
Alignment explanation
Indices: 16452642--16452668 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
16452632 AGGCCTTTAA
16452642 AAAATTTT
1 AAAATTTT
16452650 AAAATTTT
1 AAAATTTT
16452658 AAAATTTT
1 AAAATTTT
16452666 AAA
1 AAA
16452669 TTAGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAAATTTT
Found at i:16463191 original size:17 final size:18
Alignment explanation
Indices: 16463166--16463205 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
16463156 CCATCTTTTG
* *
16463166 TTTTATTGTTGATG-AAC
1 TTTTGTTGTGGATGAAAC
16463183 TTTTGTTGTGGATGAAAC
1 TTTTGTTGTGGATGAAAC
16463201 TTTTG
1 TTTTG
16463206 AAGTGAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.20, C:0.05, G:0.23, T:0.53
Consensus pattern (18 bp):
TTTTGTTGTGGATGAAAC
Found at i:16476035 original size:9 final size:9
Alignment explanation
Indices: 16476021--16476049 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
16476011 ACACCCCCCC
16476021 TTTTTCTTT
1 TTTTTCTTT
16476030 TTTTTC-TT
1 TTTTTCTTT
16476038 TTTTTCTTT
1 TTTTTCTTT
16476047 TTT
1 TTT
16476050 GGGGGGGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:16483753 original size:27 final size:27
Alignment explanation
Indices: 16483723--16483904 Score: 136
Period size: 27 Copynumber: 6.7 Consensus size: 27
16483713 CTATCCCTTA
* * *
16483723 TTTACTGTCTCGGCAGACTACCTCGTG
1 TTTATTGTCTCGACGGACTACCTCGTG
* *
16483750 TTTATTGTCCCGACTGG-CTACCCCGTG
1 TTTATTGTCTCGAC-GGACTACCTCGTG
* * ** * *
16483777 TTTATTGTCCCAACAAACTATCTTGTG
1 TTTATTGTCTCGACGGACTACCTCGTG
*
16483804 TTTACTGT-TCTGACGGACTATCCT-GTG
1 TTTATTGTCTC-GACGGACTA-CCTCGTG
* * *
16483831 TTTATTGTCTCGATGGACAATCTCGTG
1 TTTATTGTCTCGACGGACTACCTCGTG
* * *
16483858 TTTACTGTCTCTATGGACTACCTCGTG
1 TTTATTGTCTCGACGGACTACCTCGTG
* *
16483885 TTTATTGTCCCAACGGACTA
1 TTTATTGTCTCGACGGACTA
16483905 TACTGGTTGT
Statistics
Matches: 120, Mismatches: 29, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
26 3 0.03
27 112 0.93
28 5 0.04
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (27 bp):
TTTATTGTCTCGACGGACTACCTCGTG
Found at i:16483805 original size:54 final size:55
Alignment explanation
Indices: 16483744--16483898 Score: 154
Period size: 54 Copynumber: 2.9 Consensus size: 55
16483734 GGCAGACTAC
* *
16483744 CTCGTGTTTATTGTCCCGACTGG-CTACCCCGTGTTTATTGTCCCAACAAACTAT
1 CTCGTGTTTACTGTCCCGACTGGACTACCCCGTGTTTATTGTCCCAACAAACAAT
* * * * * * * ***
16483798 CTTGTGTTTACTGTTCTGAC-GGACTATCCTGTGTTTATTGTCTCGATGGACAAT
1 CTCGTGTTTACTGTCCCGACTGGACTACCCCGTGTTTATTGTCCCAACAAACAAT
* * *
16483852 CTCGTGTTTACTGTCTCTA-TGGACTACCTCGTGTTTATTGTCCCAAC
1 CTCGTGTTTACTGTCCCGACTGGACTACCCCGTGTTTATTGTCCCAAC
16483899 GGACTATACT
Statistics
Matches: 76, Mismatches: 23, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
53 2 0.03
54 74 0.97
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (55 bp):
CTCGTGTTTACTGTCCCGACTGGACTACCCCGTGTTTATTGTCCCAACAAACAAT
Found at i:16483840 original size:108 final size:108
Alignment explanation
Indices: 16483694--16483898 Score: 252
Period size: 108 Copynumber: 1.9 Consensus size: 108
16483684 AACTGACCTA
* * * *
16483694 TGTTTACTATCCTGGCGGACTATCCCTTATTTACTGTCTCGGCAGACTACCTCGTGTTTATTGTC
1 TGTTTACTATCCTGACGGACTATCCCTTATTTACTGTCTCGACAGACAACCTCGTGTTTACTGTC
16483759 CCGACTGG-CTACCCCGTGTTTATTGTCCCAACAAACTATCTTG
66 CCGA-TGGACTACCCCGTGTTTATTGTCCCAACAAACTATCTTG
* * * * ** *
16483802 TGTTTACTGTTCTGACGGACTAT-CCTGTGTTTATTGTCTCGATGGACAATCTCGTGTTTACTGT
1 TGTTTACTATCCTGACGGACTATCCCT-TATTTACTGTCTCGACAGACAACCTCGTGTTTACTGT
* * *
16483866 CTCTATGGACTACCTCGTGTTTATTGTCCCAAC
65 CCCGATGGACTACCCCGTGTTTATTGTCCCAAC
16483899 GGACTATACT
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
107 6 0.07
108 75 0.93
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.39
Consensus pattern (108 bp):
TGTTTACTATCCTGACGGACTATCCCTTATTTACTGTCTCGACAGACAACCTCGTGTTTACTGTC
CCGATGGACTACCCCGTGTTTATTGTCCCAACAAACTATCTTG
Found at i:16486475 original size:17 final size:18
Alignment explanation
Indices: 16486447--16486480 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
16486437 TAATACTCTA
16486447 TAATATTTTTAATTTTTC
1 TAATATTTTTAATTTTTC
16486465 TAATA-TTTTAATTTTT
1 TAATATTTTTAATTTTT
16486481 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TAATATTTTTAATTTTTC
Found at i:16486562 original size:31 final size:29
Alignment explanation
Indices: 16486525--16486604 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 29
16486515 TCTAAATATT
*
16486525 TTAAAAAATAATTAAATC-TGTATAAAATAA
1 TTAAAAAATAATTAAA-CATCT-TAAAATAA
16486555 TTAAAAAATCAATTAAACAATCTTAAAATAA
1 TTAAAAAAT-AATTAAAC-ATCTTAAAATAA
*
16486586 CTAAAAATAATAATTAAAC
1 -TTAAAA-AATAATTAAAC
16486605 CTTAATATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
30 10 0.23
31 15 0.35
32 15 0.35
33 3 0.07
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.30
Consensus pattern (29 bp):
TTAAAAAATAATTAAACATCTTAAAATAA
Found at i:16489605 original size:18 final size:17
Alignment explanation
Indices: 16489577--16489611 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
16489567 ATTATTAAGA
*
16489577 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
16489594 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
16489612 TTAATAATAA
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:16489841 original size:44 final size:45
Alignment explanation
Indices: 16489776--16489866 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
16489766 ACCTCTATTC
* * *
16489776 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
16489820 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
16489865 CA
1 CA
16489867 CCTCTAATCC
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:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:16489868 original size:16 final size:16
Alignment explanation
Indices: 16489847--16489915 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
16489837 GATTAGCTAT
16489847 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
16489863 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
16489880 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
16489896 TATACCTCTAATCCAA
1 TACACCTCTAATCCAA
16489912 TACA
1 TACA
16489916 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:16489889 original size:33 final size:32
Alignment explanation
Indices: 16489847--16489915 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
16489837 GATTAGCTAT
16489847 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
16489880 TACACCTCTAATCCAATATACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
16489912 TACA
1 TACA
16489916 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:16499282 original size:12 final size:12
Alignment explanation
Indices: 16499267--16499291 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16499257 AAGTTCTTTG
16499267 CCAAGCTTGCCA
1 CCAAGCTTGCCA
16499279 CCAAGCTTGCCA
1 CCAAGCTTGCCA
16499291 C
1 C
16499292 ATGCAAGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.44, G:0.16, T:0.16
Consensus pattern (12 bp):
CCAAGCTTGCCA
Found at i:16501001 original size:16 final size:18
Alignment explanation
Indices: 16500972--16501008 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
16500962 ATGGAAATAA
*
16500972 TTTTTCTTCTTTCT-ACT
1 TTTTTCCTCTTTCTAACT
16500989 TTTTTCCTC-TTCTAACT
1 TTTTTCCTCTTTCTAACT
16501006 TTT
1 TTT
16501009 CATTTTGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTCCTCTTTCTAACT
Found at i:16502034 original size:91 final size:91
Alignment explanation
Indices: 16501875--16502057 Score: 330
Period size: 91 Copynumber: 2.0 Consensus size: 91
16501865 CATTAGAAAG
* * *
16501875 TTAAATTCATTTCCAGTCTAATGTATAAAGCTAAACGTTGGTACAAAATTAGCATTTTTATTTTC
1 TTAAATTCATTTCCAGTCTAATGTATAAAGCTAAACGGTGGTACAAAATTAGCATTTTTAGTTCC
16501940 CTTAACTTCCATCTTGACTAGATTAA
66 CTTAACTTCCATCTTGACTAGATTAA
*
16501966 TTAAATTCATTTCCAGTCTAATGTATAAAGCTAAACGGTGGTATAAAATTAGCATTTTTAGTTCC
1 TTAAATTCATTTCCAGTCTAATGTATAAAGCTAAACGGTGGTACAAAATTAGCATTTTTAGTTCC
16502031 CTTAACTTCCATCTTGACTAGATTAA
66 CTTAACTTCCATCTTGACTAGATTAA
16502057 T
1 T
16502058 AATCTTCTAT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (91 bp):
TTAAATTCATTTCCAGTCTAATGTATAAAGCTAAACGGTGGTACAAAATTAGCATTTTTAGTTCC
CTTAACTTCCATCTTGACTAGATTAA
Found at i:16504459 original size:23 final size:23
Alignment explanation
Indices: 16504433--16504479 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
16504423 TAAGAGAGGA
* *
16504433 AAATTAATGCAGAAATATCACAC
1 AAATTAATACAAAAATATCACAC
*
16504456 AAATTCATACAAAAATATCACAC
1 AAATTAATACAAAAATATCACAC
16504479 A
1 A
16504480 TGAGATTACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.55, C:0.19, G:0.04, T:0.21
Consensus pattern (23 bp):
AAATTAATACAAAAATATCACAC
Found at i:16507075 original size:12 final size:12
Alignment explanation
Indices: 16507060--16507097 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
16507050 GAGTAGTGGT
*
16507060 AGTGGTAGCGGG
1 AGTGGAAGCGGG
16507072 AGTGGAAGCGGG
1 AGTGGAAGCGGG
16507084 AGTGGAAGCGGG
1 AGTGGAAGCGGG
16507096 AG
1 AG
16507098 CGAGAGCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.58, T:0.11
Consensus pattern (12 bp):
AGTGGAAGCGGG
Found at i:16507111 original size:24 final size:24
Alignment explanation
Indices: 16507058--16507111 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
16507048 GAGAGTAGTG
* * *
16507058 GTAGTGGTAGCGGGAGTGGAAGCG
1 GTAGTGGAAGCGGGAGCGGAAGCA
*
16507082 GGAGTGGAAGCGGGAGC-GAGAGCA
1 GTAGTGGAAGCGGGAGCGGA-AGCA
16507106 GTAGTG
1 GTAGTG
16507112 ATAGTGAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.24, C:0.09, G:0.54, T:0.13
Consensus pattern (24 bp):
GTAGTGGAAGCGGGAGCGGAAGCA
Found at i:16507664 original size:3 final size:3
Alignment explanation
Indices: 16507656--16507681 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16507646 ATTGAGTTGT
16507656 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
16507682 TGGGTTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16507994 original size:50 final size:50
Alignment explanation
Indices: 16507933--16508041 Score: 200
Period size: 50 Copynumber: 2.2 Consensus size: 50
16507923 AAAGCTATTT
*
16507933 TGGGTTGAAGATGAAAATTTTAAATAAAATCAAATTAGAGAGGTTGGGGG
1 TGGGATGAAGATGAAAATTTTAAATAAAATCAAATTAGAGAGGTTGGGGG
16507983 TGGGATGAAGATGAAAATTTTAAATAAAATCAAATTAGAGAGGTTGGGGG
1 TGGGATGAAGATGAAAATTTTAAATAAAATCAAATTAGAGAGGTTGGGGG
*
16508033 TGGGGTGAA
1 TGGGATGAA
16508042 CAAAAATTGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.39, C:0.02, G:0.32, T:0.27
Consensus pattern (50 bp):
TGGGATGAAGATGAAAATTTTAAATAAAATCAAATTAGAGAGGTTGGGGG
Found at i:16511792 original size:6 final size:6
Alignment explanation
Indices: 16511781--16511813 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
16511771 TTTATCAAAC
16511781 GGATTG GGATTG GGATTG GGATTG GGATTG GGA
1 GGATTG GGATTG GGATTG GGATTG GGATTG GGA
16511814 AAAGAGAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.52, T:0.30
Consensus pattern (6 bp):
GGATTG
Found at i:16511836 original size:6 final size:6
Alignment explanation
Indices: 16511825--16511862 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
16511815 AAGAGAGTAC
16511825 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT AT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT AT
16511863 ACAGTATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (6 bp):
ATGTGT
Found at i:16515203 original size:49 final size:49
Alignment explanation
Indices: 16515150--16515381 Score: 302
Period size: 49 Copynumber: 4.7 Consensus size: 49
16515140 CTGGTACGCA
*
16515150 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
** *** * *
16515199 TAGTAGCCTGCACTTAGTACTACACACATGACCTAGCCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC-AATTATCCGGTACACG
* * * * *
16515249 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACACG
*
16515300 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
*
16515349 TAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC
16515382 TCACAATAGA
Statistics
Matches: 155, Mismatches: 25, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
49 72 0.46
50 45 0.29
51 38 0.25
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
Found at i:16515378 original size:100 final size:99
Alignment explanation
Indices: 16515150--16515381 Score: 313
Period size: 100 Copynumber: 2.3 Consensus size: 99
16515140 CTGGTACGCA
* * *
16515150 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
* * *
16515215 GTACTACACACATGACCTAGCCATCTGATACACG
66 GTACTACACACACGACCTAACCATCCGATACACG
* * *
16515249 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGTACACATAGTAGCCTGCACT
** ** *
16515314 TAGTACTACACATGCGACC-AATTATCCGGTACACG
64 TAGTACTACACACACGACCTAACCATCCGATACACG
16515349 TAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
16515382 TCACAATAGA
Statistics
Matches: 116, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
99 30 0.26
100 45 0.39
101 41 0.35
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACACACGACCTAACCATCCGATACACG
Found at i:16519012 original size:94 final size:95
Alignment explanation
Indices: 16518845--16519118 Score: 324
Period size: 94 Copynumber: 2.9 Consensus size: 95
16518835 TTACTTGTGT
* * * * *
16518845 GCTAGTGTAAGACATGTCTAGGACATGCATTGGCCAC-ATTATGA-ATGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACATGTCTGGGACACGCATCGGCCTCGATGATGATA-GCCAGTGTAAGACCATG
* *
16518908 TCTGGAACATGGCATCGGCGTAGAGATGAGTA
65 TCTGGGACATGGCATCGGCGTACAGATGAG-A
* *
16518940 -CTAGTGTAAGACATGTCTGGGACACGTATCGGCCTCGACGATGATAGCCAGTGTAAGA-CATGT
1 GCTAGTGTAAGACATGTCTGGGACACGCATCGGCCTCGATGATGATAGCCAGTGTAAGACCATGT
* * *
16519003 CCGGGACAT-GCATCAGTACGTACATATGAGA
66 CTGGGACATGGCATC-G-GCGTACAGATGAGA
* * *
16519034 GCTAGTGTAAAACCATGTCTGAGACATGGCATCGGCCTCGATGATGATAGCCAGTGTAAGACCAT
1 GCTAGTGTAAGA-CATGTCTGGGACA-CGCATCGGCCTCGATGATGATAGCCAGTGTAAGACCAT
16519099 GTCTGGGACATGGCATCGGC
64 GTCTGGGACATGGCATCGGC
16519119 AACTTATCCC
Statistics
Matches: 151, Mismatches: 19, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
93 5 0.03
94 45 0.30
95 37 0.25
96 13 0.09
97 32 0.21
98 14 0.09
99 5 0.03
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (95 bp):
GCTAGTGTAAGACATGTCTGGGACACGCATCGGCCTCGATGATGATAGCCAGTGTAAGACCATGT
CTGGGACATGGCATCGGCGTACAGATGAGA
Found at i:16519090 original size:49 final size:49
Alignment explanation
Indices: 16518848--16519118 Score: 251
Period size: 47 Copynumber: 5.7 Consensus size: 49
16518838 CTTGTGTGCT
* * * *
16518848 AGTGTAAGA-CATGTCTAGGACAT-GCATTGGCCAC-ATTATGA-ATGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATA-GCC
* * * *
16518894 AGTGTAAGACCATGTCTGGAACATGGCATCGGCGTAGA-GATGAGTA-CT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGA-TAGCC
* * *
16518942 AGTGTAAGA-CATGTCTGGGACA-CGTATCGGCCTCGACGATGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAGCC
* * * * *
16518989 AGTGTAAGA-CATGTCCGGGACAT-GCATCAGTACGTAC-AT-ATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATC-G-GCCT-CGATGATGATAGCC
* *
16519037 AGTGTAAAACCATGTCTGAGACATGGCATCGGCCTCGATGATGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAGCC
16519086 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
16519119 AACTTATCCC
Statistics
Matches: 180, Mismatches: 30, Indels: 27
0.76 0.13 0.11
Matches are distributed among these distances:
46 21 0.12
47 56 0.31
48 41 0.23
49 55 0.31
50 7 0.04
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAGCC
Found at i:16520039 original size:42 final size:42
Alignment explanation
Indices: 16519979--16520071 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
16519969 ACAGGTAGGC
16519979 CACACGGGCGTGTGTCATGGCCATGTTTTAAAGTCAGTGTTG
1 CACACGGGCGTGTGTCATGGCCATGTTTTAAAGTCAGTGTTG
* *
16520021 TACACGGGCGTGTGTCATGGCCGTGTTTTAAAGTCAGTGTTG
1 CACACGGGCGTGTGTCATGGCCATGTTTTAAAGTCAGTGTTG
16520063 CACACGGGC
1 CACACGGGC
16520072 TAAGGGCACG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.18, C:0.20, G:0.32, T:0.29
Consensus pattern (42 bp):
CACACGGGCGTGTGTCATGGCCATGTTTTAAAGTCAGTGTTG
Found at i:16523962 original size:20 final size:19
Alignment explanation
Indices: 16523925--16523962 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
16523915 AATTAAATGT
*
16523925 AAATATTTATTGTATTAAA
1 AAATATTTATTATATTAAA
16523944 AAATATTTATTTATATTAA
1 AAATATTTA-TTATATTAA
16523963 GGGTTTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
AAATATTTATTATATTAAA
Found at i:16528671 original size:18 final size:18
Alignment explanation
Indices: 16528648--16528694 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 18
16528638 AAATTTTTAT
16528648 TTATAAATATGATAAATA
1 TTATAAATATGATAAATA
16528666 TTAT-AATA--A-AAATA
1 TTATAAATATGATAAATA
16528680 TT-TAAA-ATGATAAAT
1 TTATAAATATGATAAAT
16528695 TCAACGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
13 2 0.08
14 9 0.36
15 2 0.08
16 4 0.16
17 4 0.16
18 4 0.16
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (18 bp):
TTATAAATATGATAAATA
Found at i:16530727 original size:25 final size:25
Alignment explanation
Indices: 16530693--16530743 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
16530683 TTCCTTATAA
**
16530693 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
16530718 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
16530743 A
1 A
16530744 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:16530742 original size:12 final size:12
Alignment explanation
Indices: 16530696--16530743 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
16530686 CTTATAAACT
16530696 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
16530708 TTCTATTAGGACT
1 TTAAATTAGGA-A
16530721 TTAAATTAGGAA
1 TTAAATTAGGAA
*
16530733 TTAGATTAGGA
1 TTAAATTAGGA
16530744 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:16535403 original size:25 final size:25
Alignment explanation
Indices: 16535369--16535419 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
16535359 TTCCTTATAA
**
16535369 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
16535394 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
16535419 A
1 A
16535420 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:16535418 original size:12 final size:12
Alignment explanation
Indices: 16535372--16535419 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
16535362 CTTATAAACT
16535372 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
16535384 TTCTATTAGGACT
1 TTAAATTAGGA-A
16535397 TTAAATTAGGAA
1 TTAAATTAGGAA
*
16535409 TTAGATTAGGA
1 TTAAATTAGGA
16535420 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:16536481 original size:11 final size:11
Alignment explanation
Indices: 16536465--16536490 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16536455 TAGGAAAGAT
16536465 ATATCTACAAG
1 ATATCTACAAG
16536476 ATATCTACAAG
1 ATATCTACAAG
16536487 ATAT
1 ATAT
16536491 TTGCCAGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (11 bp):
ATATCTACAAG
Found at i:16539319 original size:21 final size:21
Alignment explanation
Indices: 16539295--16539355 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
16539285 CGACACATAA
* *
16539295 GTGCTAGAAATGATACACGAG
1 GTGCTAGAAACGACACACGAG
* *
16539316 GTGCTTGATACGACACACGAG
1 GTGCTAGAAACGACACACGAG
*
16539337 GTGCTTGATATACGACACA
1 GTGCTAGA-A-ACGACACA
16539356 TAAAGTGCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 25 0.76
23 8 0.24
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (21 bp):
GTGCTAGAAACGACACACGAG
Found at i:16539353 original size:23 final size:21
Alignment explanation
Indices: 16539309--16539355 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 21
16539299 TAGAAATGAT
16539309 ACACGAGGTGCTTGATACGAC
1 ACACGAGGTGCTTGATACGAC
16539330 ACACGAGGTGCTTGATATACGAC
1 ACACGAGGTGCTTG--ATACGAC
16539353 ACA
1 ACA
16539356 TAAAGTGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 14 0.58
23 10 0.42
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (21 bp):
ACACGAGGTGCTTGATACGAC
Found at i:16539363 original size:23 final size:23
Alignment explanation
Indices: 16539316--16539368 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
16539306 GATACACGAG
* *
16539316 GTGCTTG--ATACGACACACGAG
1 GTGCTTGATATACGACACACAAA
*
16539337 GTGCTTGATATACGACACATAAA
1 GTGCTTGATATACGACACACAAA
*
16539360 GTGCCTGAT
1 GTGCTTGAT
16539369 CGGCAAAGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 7 0.27
23 19 0.73
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (23 bp):
GTGCTTGATATACGACACACAAA
Found at i:16540232 original size:23 final size:23
Alignment explanation
Indices: 16540193--16540237 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16540183 TGACTTATTA
*
16540193 TTATTATAATAATAATAAATATC
1 TTATTATAATAAAAATAAATATC
*
16540216 TTATT-TAATAACAAATATATAT
1 TTATTATAATAA-AAATAAATAT
16540238 ATTACAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
TTATTATAATAAAAATAAATATC
Found at i:16540522 original size:16 final size:16
Alignment explanation
Indices: 16540477--16540526 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
16540467 AGTAATAATT
*
16540477 TAATAAT-ATAAATTA
1 TAATAATGATAAATAA
*
16540492 TAAT-TTGATAGAATAA
1 TAATAATGATA-AATAA
16540508 TAATAATGATAAATAA
1 TAATAATGATAAATAA
16540524 TAA
1 TAA
16540527 ATATATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.03
15 7 0.24
16 16 0.55
17 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
TAATAATGATAAATAA
Found at i:16540529 original size:17 final size:17
Alignment explanation
Indices: 16540457--16540526 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 17
16540447 AATTTATTTC
*
16540457 TAATAATAATAGTAATAA
1 TAATAATGATAG-AATAA
*
16540475 TTTAATAAT-ATA-AATTA
1 --TAATAATGATAGAATAA
*
16540492 TAAT-TTGATAGAATAA
1 TAATAATGATAGAATAA
16540508 TAATAATGATA-AATAA
1 TAATAATGATAGAATAA
16540524 TAA
1 TAA
16540527 ATATATATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 1 0.02
15 7 0.16
16 16 0.37
17 9 0.21
19 3 0.07
20 7 0.16
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (17 bp):
TAATAATGATAGAATAA
Found at i:16540665 original size:25 final size:27
Alignment explanation
Indices: 16540631--16540692 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 27
16540621 TGGCTTTAAT
* *
16540631 TTAATTTAATTCATAATATGATATTTATAA
1 TTAA-TTAATTAATAATAT-AT-TGTATAA
16540661 TTAATTAATTTAATAATATATTGTATAA
1 TTAATTAA-TTAATAATATATTGTATAA
16540689 TTAA
1 TTAA
16540693 ATTATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.34
29 6 0.21
30 13 0.45
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (27 bp):
TTAATTAATTAATAATATATTGTATAA
Found at i:16542434 original size:13 final size:14
Alignment explanation
Indices: 16542418--16542453 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
16542408 CAATCTCATA
16542418 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
16542431 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
16542444 TCTC-ATTTCA
1 TCTCAATTTCA
16542454 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:16542443 original size:18 final size:19
Alignment explanation
Indices: 16542405--16542445 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
16542395 TGGTTCATGT
16542405 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
16542424 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
16542442 TTTC
1 TTTC
16542446 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:16542620 original size:29 final size:27
Alignment explanation
Indices: 16542545--16542641 Score: 89
Period size: 27 Copynumber: 3.6 Consensus size: 27
16542535 ATACGCGGAT
16542545 TCCTCCCAAACACACCAGAATATCCA-A
1 TCCTCCCAAACACACCAGAATAT-CATA
*
16542572 ----CCCAAACACACCCAGAATATTATAAA
1 TCCTCCCAAACACA-CCAGAATATCAT--A
*
16542598 TCCT-CCATAACACACCAGTATATCATA
1 TCCTCCCA-AACACACCAGAATATCATA
16542625 TCCTCCCAAACACACCA
1 TCCTCCCAAACACACCA
16542642 ATAAGGCATT
Statistics
Matches: 57, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
23 11 0.19
24 9 0.16
26 1 0.02
27 14 0.25
28 3 0.05
29 13 0.23
30 6 0.11
ACGTcount: A:0.41, C:0.38, G:0.03, T:0.18
Consensus pattern (27 bp):
TCCTCCCAAACACACCAGAATATCATA
Found at i:16542980 original size:15 final size:15
Alignment explanation
Indices: 16542960--16543006 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
16542950 TATTATATAT
16542960 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
16542975 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
16542990 TTCAATCAATATAAA
1 TTCAATCAATATAAA
16543005 TT
1 TT
16543007 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:16543982 original size:31 final size:32
Alignment explanation
Indices: 16543924--16543987 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
16543914 CATACATTTG
*
16543924 TCATAATTTAATATATTTATTACATAAAAATC
1 TCATAATATAATATATTTATTACATAAAAATC
*
16543956 TCATAATATAAT-TATTTAATTA-ATAAATATC
1 TCATAATATAATATATTT-ATTACATAAAAATC
16543987 T
1 T
16543988 TATTTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 14 0.48
32 15 0.52
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (32 bp):
TCATAATATAATATATTTATTACATAAAAATC
Found at i:16544519 original size:13 final size:14
Alignment explanation
Indices: 16544501--16544529 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
16544491 GATTAACTTC
16544501 ATAAATATTTT-TA
1 ATAAATATTTTCTA
16544514 ATAAATATTTTCTA
1 ATAAATATTTTCTA
16544528 AT
1 AT
16544530 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:16552420 original size:100 final size:100
Alignment explanation
Indices: 16552234--16552438 Score: 277
Period size: 100 Copynumber: 2.0 Consensus size: 100
16552224 TCTTCCTCGG
* * *
16552234 TGGTTTTTGCCAACAATCGCTAAATCCCCTTGGGACTACTTACGCATGCACATTGCAGCAGTATC
1 TGGTTTTTGCCAACAATCGCTAAATCCCCTTGGGACTACCTACCCATGCACATTGCAGCAGTAAC
* * *
16552299 CCAAAACCCCGTACTGAAGAACCACCGGAAAAAGA
66 CCAAAAACCAGTACTGAAGAACCACCGAAAAAAGA
* * * *
16552334 TGGTTTTTGCTAACAATCGCTAAATCCCCTTGGTACTACCTACCCATGCATATTGCAGGAGTAAC
1 TGGTTTTTGCCAACAATCGCTAAATCCCCTTGGGACTACCTACCCATGCACATTGCAGCAGTAAC
* **
16552399 CCAAAAACCAGTTA-TGCAGAACCATTGAAAAAAGA
66 CCAAAAACCAG-TACTGAAGAACCACCGAAAAAAGA
16552434 TGGTT
1 TGGTT
16552439 ACAACTCAGC
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
100 89 0.98
101 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.24
Consensus pattern (100 bp):
TGGTTTTTGCCAACAATCGCTAAATCCCCTTGGGACTACCTACCCATGCACATTGCAGCAGTAAC
CCAAAAACCAGTACTGAAGAACCACCGAAAAAAGA
Found at i:16554406 original size:18 final size:18
Alignment explanation
Indices: 16554383--16554420 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
16554373 CTGCTCCGCC
16554383 TCATATTCAATCCTTGTG
1 TCATATTCAATCCTTGTG
16554401 TCATATTCAATCCTTGTG
1 TCATATTCAATCCTTGTG
16554419 TC
1 TC
16554421 TAACACATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (18 bp):
TCATATTCAATCCTTGTG
Found at i:16555729 original size:20 final size:20
Alignment explanation
Indices: 16555704--16555746 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
16555694 TAATTTCAAA
16555704 AAATTACAATTTAAATTACT
1 AAATTACAATTTAAATTACT
*
16555724 AAATTATAATTTAAATTACT
1 AAATTACAATTTAAATTACT
16555744 AAA
1 AAA
16555747 CTATTCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATTACAATTTAAATTACT
Found at i:16562562 original size:26 final size:26
Alignment explanation
Indices: 16562531--16562638 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
16562521 TGAAATGCCC
*
16562531 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
16562557 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
16562583 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
16562609 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
16562635 ATCA
1 ATCA
16562639 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:16565555 original size:21 final size:21
Alignment explanation
Indices: 16565504--16565547 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
16565494 AGGATTATAC
16565504 ATATGATTATCACTGTGAGAA
1 ATATGATTATCACTGTGAGAA
16565525 ATATGATTATCACTGTGAGAA
1 ATATGATTATCACTGTGAGAA
16565546 AT
1 AT
16565548 GTTGTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (21 bp):
ATATGATTATCACTGTGAGAA
Found at i:16569557 original size:14 final size:15
Alignment explanation
Indices: 16569524--16569559 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
16569514 TTTTTTAAAG
16569524 AAAAATGAATATTAT
1 AAAAATGAATATTAT
* *
16569539 AAAAATGAATGTTGT
1 AAAAATGAATATTAT
16569554 AAAAAT
1 AAAAAT
16569560 ATTAATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (15 bp):
AAAAATGAATATTAT
Found at i:16570083 original size:16 final size:16
Alignment explanation
Indices: 16570050--16570094 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
16570040 AGTTGAATTC
*
16570050 TAAAAGTTATAAGGAT
1 TAAAAGTTATAAGAAT
16570066 TAAATAGTTATAA-AAT
1 TAAA-AGTTATAAGAAT
*
16570082 TAAAAGTGATAAG
1 TAAAAGTTATAAG
16570095 TCCTAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 7 0.28
16 10 0.40
17 8 0.32
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (16 bp):
TAAAAGTTATAAGAAT
Found at i:16570460 original size:20 final size:22
Alignment explanation
Indices: 16570435--16570477 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
16570425 TGGTGTAAAT
*
16570435 TGAAAGTTTA-TGATAG-GAAA
1 TGAAAGGTTATTGATAGAGAAA
16570455 TGAAAGGTTATTGATAGAGAAA
1 TGAAAGGTTATTGATAGAGAAA
16570477 T
1 T
16570478 CACTTTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 6 0.30
22 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (22 bp):
TGAAAGGTTATTGATAGAGAAA
Found at i:16571196 original size:29 final size:29
Alignment explanation
Indices: 16571129--16571197 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
16571119 TGTGTGTACC
* *
16571129 ATGTGAAAAAGGATAACTTCGGCTATCGA
1 ATGTGAAAAGGGATAACTTCGACTATCGA
* *
16571158 ATGTGAAAAGGGATAGCTTCGACTATTGA
1 ATGTGAAAAGGGATAACTTCGACTATCGA
16571187 ATGTGAAAAGG
1 ATGTGAAAAGG
16571198 AAAGGTATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.25
Consensus pattern (29 bp):
ATGTGAAAAGGGATAACTTCGACTATCGA
Found at i:16571269 original size:65 final size:65
Alignment explanation
Indices: 16571190--16571460 Score: 228
Period size: 65 Copynumber: 4.1 Consensus size: 65
16571180 CTATTGAATG
* * *
16571190 TGAAAAGGAAAGGTATACTTTGTGTATACCACATGAAAAGGCTATGTACATTTTGTGTGTACACT
1 TGAAAAGGATAGGTATACTTTGTGTATACCACATGAAAAGGATATGTACACTTTGTGTGTACACT
* * * * * * * *
16571255 TGGAAAGGTTAGGTATACTTTGTGTATACCATATGAAAATGAAAGGTATACTTTGTGTATATCAC
1 TGAAAAGGATAGGTATACTTTGTGTATACCACATGAAAAGGATATGTACACTTTGTGTGTA-CAC
16571320 T
65 T
* * * * * *
16571321 TGAAAAGGAAATGTACACTATATGTGTAT---ACTTGAAAAGGTTATGTGCACTTTGTGTGTACA
1 TGAAAAGGATAGGTATACT-T-TGTGTATACCACATGAAAAGGATATGTACACTTTGTGTGTAC-
*
16571383 AAT
63 ACT
* * * * *
16571386 TGAAAAGGGTATGTATACTTTGTGTATACCACTTGAAAAGGGA-ATGTGCACTATG-GATGTACA
1 TGAAAAGGATAGGTATACTTTGTGTATACCACATGAAAA-GGATATGTACACTTTGTG-TGTAC-
16571449 ACT
63 ACT
*
16571452 AGAAAAGGA
1 TGAAAAGGA
16571461 AGGGTCCATC
Statistics
Matches: 163, Mismatches: 34, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
63 7 0.04
64 2 0.01
65 91 0.56
66 53 0.33
67 3 0.02
68 7 0.04
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (65 bp):
TGAAAAGGATAGGTATACTTTGTGTATACCACATGAAAAGGATATGTACACTTTGTGTGTACACT
Found at i:16571310 original size:98 final size:98
Alignment explanation
Indices: 16571190--16571439 Score: 304
Period size: 98 Copynumber: 2.6 Consensus size: 98
16571180 CTATTGAATG
* ** * * *
16571190 TGAAAAGGAAAGGTATACTTTGTGTATACCACATGAAAAGGCTATGTACATTTTGTGTGTACACT
1 TGAAAAGGAAAGGTATACTTTGTGTATACCACTTGAAAAGGAAATGTACACTATATGTGTACACT
* * *
16571255 TGGAAAGGTTAGGTATACTTTGTGTATAC-CAT
66 TGAAAAGGTTAGGTACACTTTGTGTATACAAAT
* * *
16571287 ATGAAAATGAAAGGTATACTTTGTGTATATCACTTGAAAAGGAAATGTACACTATATGTGTATAC
1 -TGAAAAGGAAAGGTATACTTTGTGTATACCACTTGAAAAGGAAATGTACACTATATGTGTACAC
* * *
16571352 TTGAAAAGGTTATGTGCACTTTGTGTGTACAAAT
65 TTGAAAAGGTTAGGTACACTTTGTGTATACAAAT
** * * *
16571386 TGAAAAGGGTATGTATACTTTGTGTATACCACTTGAAAAGGGAATGTGCACTAT
1 TGAAAAGGAAAGGTATACTTTGTGTATACCACTTGAAAAGGAAATGTACACTAT
16571440 GGATGTACAA
Statistics
Matches: 129, Mismatches: 22, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
98 127 0.98
99 2 0.02
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (98 bp):
TGAAAAGGAAAGGTATACTTTGTGTATACCACTTGAAAAGGAAATGTACACTATATGTGTACACT
TGAAAAGGTTAGGTACACTTTGTGTATACAAAT
Found at i:16571427 original size:33 final size:33
Alignment explanation
Indices: 16571190--16571426 Score: 205
Period size: 33 Copynumber: 7.2 Consensus size: 33
16571180 CTATTGAATG
* * *
16571190 TGAAAAGGAAAGGTATACTTTGTGTATACCACA
1 TGAAAAGGATATGTATACTTTGTGTATACCACT
* * * *
16571223 TGAAAAGGCTATGTACATTTTGTGTGTA-CACT
1 TGAAAAGGATATGTATACTTTGTGTATACCACT
* * *
16571255 TGGAAAGGTTAGGTATACTTTGTGTATACCA-T
1 TGAAAAGGATATGTATACTTTGTGTATACCACT
* * * *
16571287 ATGAAAATGAAAGGTATACTTTGTGTATATCACT
1 -TGAAAAGGATATGTATACTTTGTGTATACCACT
* *
16571321 TGAAAAGGAAATGTACACTATATGTGTAT---ACT
1 TGAAAAGGATATGTATACT-T-TGTGTATACCACT
* ** * * *
16571353 TGAAAAGGTTATGTGCACTTTGTGTGTACAAAT
1 TGAAAAGGATATGTATACTTTGTGTATACCACT
*
16571386 TGAAAAGGGTATGTATACTTTGTGTATACCACT
1 TGAAAAGGATATGTATACTTTGTGTATACCACT
16571419 TGAAAAGG
1 TGAAAAGG
16571427 GAATGTGCAC
Statistics
Matches: 164, Mismatches: 32, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
30 6 0.04
31 1 0.01
32 45 0.27
33 103 0.63
34 2 0.01
35 7 0.04
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (33 bp):
TGAAAAGGATATGTATACTTTGTGTATACCACT
Found at i:16574386 original size:14 final size:13
Alignment explanation
Indices: 16574367--16574396 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
16574357 AATCTCCGGG
16574367 AAAAAAGAAAAAGA
1 AAAAAAG-AAAAGA
16574381 AAAAAAGAAAAGA
1 AAAAAAGAAAAGA
16574394 AAA
1 AAA
16574397 GATTTATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAGA
Found at i:16577843 original size:5 final size:6
Alignment explanation
Indices: 16577822--16577859 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
16577812 AATTCAAGTT
*
16577822 AAAATG AAAAAG AAAAAG AAAAAG AAAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG A
16577860 CATAGATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (6 bp):
AAAAAG
Done.