Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 13 of 185
Found at i:3515244 original size:29 final size:30
Alignment explanation
Indices: 3515126--3515289 Score: 116
Period size: 29 Copynumber: 5.5 Consensus size: 30
3515116 AAATGTCCAA
3515126 ATAACTTATATAATTCACATAATAACTTAC
1 ATAACTTATATAATTCACATAATAACTTAC
* *
3515156 ATAACAACTTA-ACAACTCACATAAT---TTAC
1 AT---AACTTATATAATTCACATAATAACTTAC
*
3515185 ATAATACATATATATATGTCATACCAT-ATAACTT-C
1 AT-A-ACTTATATA-AT-TC--A-CATAATAACTTAC
3515220 ATAACTTATATAATTCACATAATAACTTAC
1 ATAACTTATATAATTCACATAATAACTTAC
* *
3515250 ATAACTTA-ACAACTCACATAAT---TTAC
1 ATAACTTATATAATTCACATAATAACTTAC
3515276 ATAACTTA-ATAATT
1 ATAACTTATATAATT
3515290 TTAAAATATA
Statistics
Matches: 108, Mismatches: 11, Indels: 34
0.71 0.07 0.22
Matches are distributed among these distances:
26 16 0.15
27 1 0.01
28 7 0.06
29 28 0.26
30 12 0.11
31 4 0.04
32 14 0.13
33 17 0.16
34 4 0.04
35 3 0.03
36 2 0.02
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.35
Consensus pattern (30 bp):
ATAACTTATATAATTCACATAATAACTTAC
Found at i:3515253 original size:9 final size:9
Alignment explanation
Indices: 3515241--3515287 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
3515231 AATTCACATA
3515241 ATAACTTAC
1 ATAACTTAC
3515250 ATAACTTA-
1 ATAACTTAC
* *
3515258 ACAACTCAC
1 ATAACTTAC
*
3515267 ATAATTTAC
1 ATAACTTAC
3515276 ATAACTTA-
1 ATAACTTAC
3515284 ATAA
1 ATAA
3515288 TTTTAAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
8 10 0.32
9 21 0.68
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:3515431 original size:25 final size:26
Alignment explanation
Indices: 3515391--3515454 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
3515381 CATAATAACT
* *
3515391 TACATAACTTAGTAACTTATA-TATA
1 TACATAACTTAATAACTCATATTATA
* *
3515416 TGCATAACTTAATAACTCATATTATT
1 TACATAACTTAATAACTCATATTATA
3515442 TACATAACTTAAT
1 TACATAACTTAAT
3515455 CATTGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 18 0.55
26 15 0.45
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.41
Consensus pattern (26 bp):
TACATAACTTAATAACTCATATTATA
Found at i:3516022 original size:43 final size:43
Alignment explanation
Indices: 3515953--3516174 Score: 320
Period size: 43 Copynumber: 5.2 Consensus size: 43
3515943 CACCAAACAA
* * *
3515953 TAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAAAACATGACCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGCCTT
* *
3515996 TAACGGCATTTGTGGGAAAAGCGCCGCTAAAGAACATGGCCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGCCTT
* *
3516039 TAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGCCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGCCTT
* * * *
3516082 TAGCAGCGTTTGTGAGAGAAGCGTCGCTAAAGAACATGGCCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGCCTT
*
3516125 TAGCGGCGTTT-TCGGGAAAAGCGCCACTAAAGAACATGGCCTT
1 TAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGAACATGGCCTT
3516168 TAGCGGC
1 TAGCGGC
3516175 ATTTATTTCT
Statistics
Matches: 158, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
42 1 0.01
43 157 0.99
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGCCTT
Found at i:3521364 original size:28 final size:28
Alignment explanation
Indices: 3521332--3521386 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
3521322 AATGGAATTT
3521332 GTTCCCTTGGGTTCAAATCTTTTTTCAA
1 GTTCCCTTGGGTTCAAATCTTTTTTCAA
3521360 GTTCCCTTGGGTTCAAATCTTTTTTCA
1 GTTCCCTTGGGTTCAAATCTTTTTTCA
3521387 CCCAAGTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.16, C:0.22, G:0.15, T:0.47
Consensus pattern (28 bp):
GTTCCCTTGGGTTCAAATCTTTTTTCAA
Found at i:3521517 original size:57 final size:57
Alignment explanation
Indices: 3521453--3521567 Score: 196
Period size: 57 Copynumber: 2.0 Consensus size: 57
3521443 AGATGGAATT
*
3521453 TGTTCCTC-GCGTTCAAATCTTAATTTTAATCTTTTTTCATAGATGGAATTAAATTCC
1 TGTTCCTCAG-GTTCAAATCTTAATCTTAATCTTTTTTCATAGATGGAATTAAATTCC
*
3521510 TGTTCCTCAGGTTCAAATCTTAATCTTAATCTTTTTTCATATATGGAATTAAATTCC
1 TGTTCCTCAGGTTCAAATCTTAATCTTAATCTTTTTTCATAGATGGAATTAAATTCC
3521567 T
1 T
3521568 TTTTGAATCT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
57 54 0.98
58 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (57 bp):
TGTTCCTCAGGTTCAAATCTTAATCTTAATCTTTTTTCATAGATGGAATTAAATTCC
Found at i:3521660 original size:15 final size:15
Alignment explanation
Indices: 3521642--3521694 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
3521632 GTTTTTAAAA
*
3521642 TTAATATATTATATT
1 TTAATATATTATAGT
*
3521657 TTAATATTATT-TGGT
1 TTAATA-TATTATAGT
*
3521672 ATAATATATTATAGT
1 TTAATATATTATAGT
*
3521687 TTGATATA
1 TTAATATA
3521695 ATTAATATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 4 0.13
15 22 0.73
16 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (15 bp):
TTAATATATTATAGT
Found at i:3521861 original size:19 final size:18
Alignment explanation
Indices: 3521839--3521881 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
3521829 AAATTCGTAA
3521839 AAAAAATGTAAAAAATTAT
1 AAAAAAT-TAAAAAATTAT
*
3521858 AAAATTATTAAAAAATTAT
1 AAAA-AATTAAAAAATTAT
3521877 AAAAA
1 AAAAA
3521882 TTTATCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAAAATTAAAAAATTAT
Found at i:3522044 original size:17 final size:17
Alignment explanation
Indices: 3522010--3522042 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3522000 GTTTATCGTT
*
3522010 TTTATTTTTTTCCTCCC
1 TTTATTTTTCTCCTCCC
3522027 TTTATTTTTCT-CTCCC
1 TTTATTTTTCTCCTCCC
3522043 CTCGAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.06, C:0.30, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATTTTTCTCCTCCC
Found at i:3522988 original size:8 final size:8
Alignment explanation
Indices: 3522975--3522999 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3522965 CTTTTAAAAT
3522975 TTATATTA
1 TTATATTA
3522983 TTATATTA
1 TTATATTA
3522991 TTATATTA
1 TTATATTA
3522999 T
1 T
3523000 AAAAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTATATTA
Found at i:3528317 original size:20 final size:20
Alignment explanation
Indices: 3528292--3528331 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3528282 ATAATGGCAT
3528292 GTATAAGTTAAATTGGTTAA
1 GTATAAGTTAAATTGGTTAA
3528312 GTATAAGTTAAATTGGTTAA
1 GTATAAGTTAAATTGGTTAA
3528332 CGTTGGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (20 bp):
GTATAAGTTAAATTGGTTAA
Found at i:3530156 original size:3 final size:3
Alignment explanation
Indices: 3530150--3530178 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3530140 TCTTAATACT
3530150 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
3530179 TAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:3530183 original size:3 final size:3
Alignment explanation
Indices: 3530177--3530216 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3530167 CAACAACAAC
3530177 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3530217 CTATCAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3530548 original size:27 final size:27
Alignment explanation
Indices: 3530464--3530540 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
3530454 CCAATCAGTA
**
3530464 TGGCACCATTGGTGCTGCCAATGGCTT
1 TGGCACCATTGGTGCCACCAATGGCTT
3530491 TGGCACCATTGGTGCCACCAATGGCTT
1 TGGCACCATTGGTGCCACCAATGGCTT
*
3530518 TGGCACCTTTGGTGCCACCAATG
1 TGGCACCATTGGTGCCACCAATG
3530541 CCATTGGCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.17, C:0.29, G:0.27, T:0.27
Consensus pattern (27 bp):
TGGCACCATTGGTGCCACCAATGGCTT
Found at i:3532134 original size:22 final size:23
Alignment explanation
Indices: 3532106--3532439 Score: 94
Period size: 23 Copynumber: 14.7 Consensus size: 23
3532096 AGTTGCTAGA
* *
3532106 AATTGAGATGTTTTATTGTTG-T
1 AATTGAGATGTTTAAATGTTGTT
* *
3532128 AATTGAGGTGTATAAATGTTGTT
1 AATTGAGATGTTTAAATGTTGTT
* * * **
3532151 AATTGATATGTTTAAGTGCTGCA
1 AATTGAGATGTTTAAATGTTGTT
* * *
3532174 AATTTA-AGTGTTTAAATGCTGTA
1 AATTGAGA-TGTTTAAATGTTGTT
* * **
3532197 AATTGA-AGTGTTTAAGTGCTGCA
1 AATTGAGA-TGTTTAAATGTTGTT
** * **
3532220 AATTGA-AGTGTTTAGTTGATGGA
1 AATTGAGA-TGTTTAAATGTTGTT
* *
3532243 AATTGAGATGTTT-TATCGCTG-T
1 AATTGAGATGTTTAAAT-GTTGTT
* *
3532265 AATTGAGGTGTATAAATGTTGTT
1 AATTGAGATGTTTAAATGTTGTT
* * * **
3532288 AATTGATATGTTTAAGTGCTGCA
1 AATTGAGATGTTTAAATGTTGTT
* * *
3532311 AATTTA-AGTGTTTAAATGCTGTA
1 AATTGAGA-TGTTTAAATGTTGTT
* * **
3532334 AATTGA-AGTGTTTAAGTGCTGCA
1 AATTGAGA-TGTTTAAATGTTGTT
* ** * **
3532357 AATTGA-AGTATTTAGTTGCTGGA
1 AATTGAGA-TGTTTAAATGTTGTT
* **
3532380 AATTGAGATGTTTTACCGTTG-T
1 AATTGAGATGTTTAAATGTTGTT
* *
3532402 AATTGAGGTGTATAAATGTTGTT
1 AATTGAGATGTTTAAATGTTGTT
*
3532425 AATTGATATGTTTAA
1 AATTGAGATGTTTAA
3532440 GTGCTGCAAA
Statistics
Matches: 242, Mismatches: 61, Indels: 17
0.76 0.19 0.05
Matches are distributed among these distances:
22 50 0.21
23 190 0.79
24 2 0.01
ACGTcount: A:0.30, C:0.04, G:0.23, T:0.42
Consensus pattern (23 bp):
AATTGAGATGTTTAAATGTTGTT
Found at i:3532177 original size:23 final size:22
Alignment explanation
Indices: 3532151--3532536 Score: 237
Period size: 23 Copynumber: 16.9 Consensus size: 22
3532141 AAATGTTGTT
3532151 AATTGATATGTTTAAGTGCTGCA
1 AATTGA-ATGTTTAAGTGCTGCA
* * *
3532174 AATTTAAGTGTTTAAATGCTGTA
1 AATTGAA-TGTTTAAGTGCTGCA
3532197 AATTGAAGTGTTTAAGTGCTGCA
1 AATTGAA-TGTTTAAGTGCTGCA
* *
3532220 AATTGAAGTGTTT-AGTTGATGGA
1 AATTGAA-TGTTTAAG-TGCTGCA
* *
3532243 AATTGAGATGTTTTA-TCGCTG-T
1 AATTGA-ATGTTTAAGT-GCTGCA
* * * * **
3532265 AATTGAGGTGTATAAATGTTGTT
1 AATTGA-ATGTTTAAGTGCTGCA
3532288 AATTGATATGTTTAAGTGCTGCA
1 AATTGA-ATGTTTAAGTGCTGCA
* * *
3532311 AATTTAAGTGTTTAAATGCTGTA
1 AATTGAA-TGTTTAAGTGCTGCA
3532334 AATTGAAGTGTTTAAGTGCTGCA
1 AATTGAA-TGTTTAAGTGCTGCA
* *
3532357 AATTGAA-GTATTTAGTTGCTGGA
1 AATTGAATGT-TTAAG-TGCTGCA
* ** * *
3532380 AATTGAGATGTTTTACCGTTG-T
1 AATTGA-ATGTTTAAGTGCTGCA
* * * * **
3532402 AATTGAGGTGTATAAATGTTGTT
1 AATTGA-ATGTTTAAGTGCTGCA
3532425 AATTGATATGTTTAAGTGCTGCA
1 AATTGA-ATGTTTAAGTGCTGCA
3532448 AATTGAAGTGTTTAAGTGCTGCA
1 AATTGAA-TGTTTAAGTGCTGCA
3532471 AATTGAAGTGTTT-AGTTGCTGCA
1 AATTGAA-TGTTTAAG-TGCTGCA
* *
3532494 AATTGAGATGTTTTA-TCGCTGTA
1 AATTGA-ATGTTTAAGT-GCTGCA
*
3532517 AATTGAAGTGTTAAAGTGCT
1 AATTGAA-TGTTTAAGTGCT
3532537 ACTTTCCATT
Statistics
Matches: 295, Mismatches: 48, Indels: 40
0.77 0.13 0.10
Matches are distributed among these distances:
21 2 0.01
22 45 0.15
23 236 0.80
24 10 0.03
25 2 0.01
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (22 bp):
AATTGAATGTTTAAGTGCTGCA
Found at i:3532462 original size:114 final size:113
Alignment explanation
Indices: 3532174--3532536 Score: 396
Period size: 114 Copynumber: 3.2 Consensus size: 113
3532164 AAGTGCTGCA
*
3532174 AATTTAAGTGTTTAAATGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTT-AGTTG
1 AATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAG-TG
* * * * * * * *
3532238 ATGGAAATTGAGATGTTTTA-TCGCT-GTAATTGAGGTGTATAAATGTTGTT
65 CTGCAAATTGA-A-GTTTTAGTTGCTGGAAATTGAGATGTTTTAACGTTG-T
* * * * *
3532288 AATTGATA-TGTTTAAGTGCTGCAAATTTAAGTGTTTAAATGCTGTAAATTGAAGTGTTTAAGTG
1 AATTGA-AGTGTTTAAATGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTG
*
3532352 CTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTTTTACCGTTGT
65 CTGCAAATTGAAGT-TTTAGTTGCTGGAAATTGAGATGTTTTAACGTTGT
* * * *
3532402 AATTGAGGTGTATAAATGTTGTTAATTGATA-TGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTG
1 AATTGAAGTGTTTAAATGCTGTAAATTGA-AGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTG
* * *
3532466 CTGCAAATTGAAGTGTTTAGTTGCTGCAAATTGAGATGTTTTATCGCTGT
65 CTGCAAATTGAAGT-TTTAGTTGCTGGAAATTGAGATGTTTTAACGTTGT
3532516 AAATTGAAGTG-TTAAAGTGCT
1 -AATTGAAGTGTTTAAA-TGCT
3532537 ACTTTCCATT
Statistics
Matches: 209, Mismatches: 31, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
112 2 0.01
113 5 0.02
114 169 0.81
115 33 0.16
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (113 bp):
AATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGC
TGCAAATTGAAGTTTTAGTTGCTGGAAATTGAGATGTTTTAACGTTGT
Found at i:3532522 original size:137 final size:137
Alignment explanation
Indices: 3532074--3532499 Score: 755
Period size: 137 Copynumber: 3.1 Consensus size: 137
3532064 GAAATTTGAT
* *
3532074 AGTGCTGCAAATTGAAGTATTTAGTTGCTAGAAATTGAGATGTTTTATTGTTGTAATTGAGGTGT
1 AGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTTTTATCGTTGTAATTGAGGTGT
3532139 ATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGTGTTTAAATGCTGTAAATTGAA
66 ATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGTGTTTAAATGCTGTAAATTGAA
3532204 GTGTTTA
131 GTGTTTA
* * *
3532211 AGTGCTGCAAATTGAAGTGTTTAGTTGATGGAAATTGAGATGTTTTATCGCTGTAATTGAGGTGT
1 AGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTTTTATCGTTGTAATTGAGGTGT
3532276 ATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGTGTTTAAATGCTGTAAATTGAA
66 ATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGTGTTTAAATGCTGTAAATTGAA
3532341 GTGTTTA
131 GTGTTTA
*
3532348 AGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTTTTACCGTTGTAATTGAGGTGT
1 AGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTTTTATCGTTGTAATTGAGGTGT
* * *
3532413 ATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAA
66 ATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGTGTTTAAATGCTGTAAATTGAA
3532478 GTGTTT-
131 GTGTTTA
3532484 AGTTGCTGCAAATTGA
1 AG-TGCTGCAAATTGA
3532500 GATGTTTTAT
Statistics
Matches: 276, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
136 2 0.01
137 274 0.99
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.41
Consensus pattern (137 bp):
AGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTTTTATCGTTGTAATTGAGGTGT
ATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGTGTTTAAATGCTGTAAATTGAA
GTGTTTA
Found at i:3533596 original size:42 final size:43
Alignment explanation
Indices: 3533514--3533636 Score: 185
Period size: 42 Copynumber: 2.9 Consensus size: 43
3533504 AGGTCTTGGT
* **
3533514 AAGGTCTTTGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTA
1 AAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTA
*
3533557 AAGGTCTTGGTCTTTAACGGCG-TTGTGGGAAAAGCGCCGCTA
1 AAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTA
* *
3533599 AAGATCTTGGTCTTTAGCGGTGTTTGTGGGAAAAGCGC
1 AAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGC
3533637 TTTTCGGCGC
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 37 0.51
43 35 0.49
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (43 bp):
AAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTA
Found at i:3533691 original size:21 final size:22
Alignment explanation
Indices: 3533647--3533688 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3533637 TTTTCGGCGC
* *
3533647 TAAAAAGCGTCGCTAAAGGCCT
1 TAAAAAGCGCCGCTAAAAGCCT
3533669 TAAAAAGCGCCGCTAAAAGC
1 TAAAAAGCGCCGCTAAAAGC
3533689 TTATTTTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.14
Consensus pattern (22 bp):
TAAAAAGCGCCGCTAAAAGCCT
Found at i:3534716 original size:19 final size:20
Alignment explanation
Indices: 3534691--3534738 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
3534681 AAATTCACAT
*
3534691 TAATATTTTAATCATAAT-AA
1 TAATATTTTAAAC-TAATCAA
3534711 -AATA-TTTAAACTAATCAA
1 TAATATTTTAAACTAATCAA
3534729 TAATATTTTA
1 TAATATTTTA
3534739 TATACACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 4 0.17
18 8 0.33
19 8 0.33
20 4 0.17
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATATTTTAAACTAATCAA
Found at i:3535740 original size:14 final size:14
Alignment explanation
Indices: 3535718--3535765 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
3535708 AGCATATGCG
*
3535718 AATAAATATTTACA
1 AATAAATATATACA
*
3535732 AATATATATATACA
1 AATAAATATATACA
*
3535746 AATACA-ATATACA
1 AATAAATATATACA
*
3535759 AGTAAAT
1 AATAAAT
3535766 TCACAAATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 11 0.39
14 17 0.61
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.31
Consensus pattern (14 bp):
AATAAATATATACA
Found at i:3536240 original size:3 final size:3
Alignment explanation
Indices: 3536227--3536262 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
3536217 ATATGTATAG
*
3536227 ATA AT- ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3536263 ATGGGGATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3538506 original size:26 final size:26
Alignment explanation
Indices: 3538475--3538529 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
3538465 AACTATTTTG
*
3538475 TAATTATTTTTATTTATAGTTTAGCA
1 TAATTATTTTTATTTATAATTTAGCA
3538501 TAATTATTTTTATTTATAATTTAGCA
1 TAATTATTTTTATTTATAATTTAGCA
3538527 TAA
1 TAA
3538530 GTTAAAGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (26 bp):
TAATTATTTTTATTTATAATTTAGCA
Found at i:3542996 original size:33 final size:33
Alignment explanation
Indices: 3542947--3543012 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
3542937 CAATCGATCT
*
3542947 TTGCTTCACATTCTGCTTCTTGGCTAACTTGCC
1 TTGCTTCACATACTGCTTCTTGGCTAACTTGCC
*
3542980 TTGCTTCGCATACTGCTTCTTGGCTAACTTGCC
1 TTGCTTCACATACTGCTTCTTGGCTAACTTGCC
3543013 AATCCATCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.12, C:0.30, G:0.17, T:0.41
Consensus pattern (33 bp):
TTGCTTCACATACTGCTTCTTGGCTAACTTGCC
Found at i:3543053 original size:15 final size:16
Alignment explanation
Indices: 3543033--3543064 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3543023 TGCTTCACAT
3543033 ACTTCTTCTT-GGCTA
1 ACTTCTTCTTAGGCTA
3543048 ACTTCTTCTTAGGCTA
1 ACTTCTTCTTAGGCTA
3543064 A
1 A
3543065 TAATCTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.44
Consensus pattern (16 bp):
ACTTCTTCTTAGGCTA
Found at i:3543435 original size:1 final size:1
Alignment explanation
Indices: 3543429--3543457 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
3543419 TTTAGCATTG
3543429 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3543458 ACTTTGATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3544540 original size:8 final size:7
Alignment explanation
Indices: 3544522--3544558 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
3544512 TTGCGATTGG
3544522 TTTTTTA
1 TTTTTTA
3544529 TTTTTTA
1 TTTTTTA
3544536 TTTTTTTA
1 -TTTTTTA
3544544 TTTTTTA
1 TTTTTTA
3544551 TTTTTTA
1 TTTTTTA
3544558 T
1 T
3544559 ATATATATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:3544542 original size:15 final size:15
Alignment explanation
Indices: 3544522--3544556 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3544512 TTGCGATTGG
3544522 TTTTTTATTTTTTAT
1 TTTTTTATTTTTTAT
3544537 TTTTTTATTTTTTAT
1 TTTTTTATTTTTTAT
3544552 TTTTT
1 TTTTT
3544557 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTATTTTTTAT
Found at i:3544906 original size:14 final size:14
Alignment explanation
Indices: 3544872--3544899 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3544862 ATATTTTATA
3544872 TAATTAAAATATTT
1 TAATTAAAATATTT
3544886 TAATTAAAATATTT
1 TAATTAAAATATTT
3544900 ATGTTAATAA
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:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTAAAATATTT
Found at i:3546145 original size:3 final size:3
Alignment explanation
Indices: 3546139--3546199 Score: 88
Period size: 3 Copynumber: 20.3 Consensus size: 3
3546129 CGATTTTCTG
*
3546139 TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
3546187 TTA CTA TTA TTA T
1 TTA TTA TTA TTA T
3546200 ATTTTTCTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3548104 original size:15 final size:15
Alignment explanation
Indices: 3548092--3548125 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3548082 TAAATTAAAT
3548092 TTTATCATTTTAATAA
1 TTTAT-ATTTTAATAA
*
3548108 TTTATATTTTTATAA
1 TTTATATTTTAATAA
3548123 TTT
1 TTT
3548126 TTGAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATATTTTAATAA
Found at i:3551277 original size:15 final size:16
Alignment explanation
Indices: 3551257--3551288 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3551247 CGCCTGACAT
3551257 ACTTCTTCTT-GGCTA
1 ACTTCTTCTTAGGCTA
3551272 ACTTCTTCTTAGGCTA
1 ACTTCTTCTTAGGCTA
3551288 A
1 A
3551289 TAATCTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.44
Consensus pattern (16 bp):
ACTTCTTCTTAGGCTA
Found at i:3552755 original size:8 final size:7
Alignment explanation
Indices: 3552737--3552773 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
3552727 TTGCGATTGG
3552737 TTTTTTA
1 TTTTTTA
3552744 TTTTTTA
1 TTTTTTA
3552751 TTTTTTTA
1 -TTTTTTA
3552759 TTTTTTA
1 TTTTTTA
3552766 TTTTTTA
1 TTTTTTA
3552773 T
1 T
3552774 ATATATATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:3552757 original size:15 final size:15
Alignment explanation
Indices: 3552737--3552771 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3552727 TTGCGATTGG
3552737 TTTTTTATTTTTTAT
1 TTTTTTATTTTTTAT
3552752 TTTTTTATTTTTTAT
1 TTTTTTATTTTTTAT
3552767 TTTTT
1 TTTTT
3552772 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTATTTTTTAT
Found at i:3553122 original size:14 final size:14
Alignment explanation
Indices: 3553088--3553115 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3553078 ATATTTTATA
3553088 TAATTAAAATATTT
1 TAATTAAAATATTT
3553102 TAATTAAAATATTT
1 TAATTAAAATATTT
3553116 ATGTTAATAA
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:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTAAAATATTT
Found at i:3558143 original size:24 final size:26
Alignment explanation
Indices: 3558111--3558160 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
3558101 ATGGTAAAAC
*
3558111 TATAATTTTATCA-TTTT-AATAATT
1 TATAATTTTATAATTTTTAAATAATT
*
3558135 TATATTTTTATAATTTTTAAATAATT
1 TATAATTTTATAATTTTTAAATAATT
3558161 AAGAGAGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 4 0.18
26 7 0.32
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TATAATTTTATAATTTTTAAATAATT
Found at i:3558147 original size:15 final size:16
Alignment explanation
Indices: 3558111--3558150 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
3558101 ATGGTAAAAC
3558111 TATAATTTTATCATTTT
1 TATAA-TTTATCATTTT
*
3558128 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
3558143 TATAATTT
1 TATAATTT
3558151 TTAAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:3559144 original size:42 final size:42
Alignment explanation
Indices: 3559097--3559194 Score: 160
Period size: 42 Copynumber: 2.3 Consensus size: 42
3559087 AGGAACATCA
*
3559097 GCTTCTTGGCTAACTTGCCAATCCATCTTTGCTTCACATACT
1 GCTTCTTGGCTAACTTGCCAATCCATCTTCGCTTCACATACT
*
3559139 GCTTCTTGGCTAACTTGCCAATCCATCTTCGCTTCAGATACT
1 GCTTCTTGGCTAACTTGCCAATCCATCTTCGCTTCACATACT
*
3559181 TCTTCTTAGGCTAA
1 GCTTCTT-GGCTAA
3559195 TAATCTCTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 46 0.88
43 6 0.12
ACGTcount: A:0.19, C:0.30, G:0.13, T:0.38
Consensus pattern (42 bp):
GCTTCTTGGCTAACTTGCCAATCCATCTTCGCTTCACATACT
Found at i:3559707 original size:42 final size:42
Alignment explanation
Indices: 3559622--3559768 Score: 240
Period size: 42 Copynumber: 3.4 Consensus size: 42
3559612 GCCAATCCAT
3559622 CTGCTTCTTGGCTAACTTGCCAATATTCCATCTTTGCTTCACATA
1 CTGCTTCTTGGCTAACTTGCC-A-A-TCCATCTTTGCTTCACATA
3559667 CTGCTTCTTGGCTAACTTGCCAATCCATCTTTGCTTCACATA
1 CTGCTTCTTGGCTAACTTGCCAATCCATCTTTGCTTCACATA
*
3559709 CTGCTTCTTGGCTAACTTGCCAATCCATCTTTGCTTCAGATA
1 CTGCTTCTTGGCTAACTTGCCAATCCATCTTTGCTTCACATA
* *
3559751 CTTCCTCTTGGCTAACTT
1 CTGCTTCTTGGCTAACTT
3559769 CTTCTTAGGC
Statistics
Matches: 99, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
42 76 0.77
43 1 0.01
44 1 0.01
45 21 0.21
ACGTcount: A:0.18, C:0.30, G:0.12, T:0.39
Consensus pattern (42 bp):
CTGCTTCTTGGCTAACTTGCCAATCCATCTTTGCTTCACATA
Found at i:3564912 original size:11 final size:13
Alignment explanation
Indices: 3564879--3564908 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3564869 TAATTATTAA
3564879 AATATAAAATATT
1 AATATAAAATATT
3564892 AATATAAAATATT
1 AATATAAAATATT
3564905 AATA
1 AATA
3564909 AAATCATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAAAATATT
Found at i:3576797 original size:32 final size:32
Alignment explanation
Indices: 3576756--3576820 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3576746 TGTACAAGAT
3576756 ATGGTTTAGAAATGTCTAAATTATCCAGATTA
1 ATGGTTTAGAAATGTCTAAATTATCCAGATTA
3576788 ATGGTTTAGAAATGTCTAAATTATCCAGATTA
1 ATGGTTTAGAAATGTCTAAATTATCCAGATTA
3576820 A
1 A
3576821 GTGTTGCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (32 bp):
ATGGTTTAGAAATGTCTAAATTATCCAGATTA
Found at i:3584545 original size:26 final size:27
Alignment explanation
Indices: 3584516--3584572 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 27
3584506 GTAATAAAAA
3584516 ATATTA-ACCATAAATTTCAA-TATTTT
1 ATATTATACCAT-AATTTCAAGTATTTT
*
3584542 ATA-TATACCATAATTTTAAGTTATTTT
1 ATATTATACCATAATTTCAAG-TATTTT
3584569 ATAT
1 ATAT
3584573 ATAATTCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
25 9 0.35
26 8 0.31
27 9 0.35
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATACCATAATTTCAAGTATTTT
Found at i:3585089 original size:21 final size:20
Alignment explanation
Indices: 3585041--3585090 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
3585031 TCTTTAAACT
*
3585041 ATGAACCCCAAACTCATAAC
1 ATGAACCCCAAACCCATAAC
**
3585061 CCGTAACCCCAAACCCATAAC
1 ATG-AACCCCAAACCCATAAC
3585082 AATGAACCC
1 -ATGAACCC
3585091 TGAACCTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.04
21 21 0.91
22 1 0.04
ACGTcount: A:0.42, C:0.40, G:0.06, T:0.12
Consensus pattern (20 bp):
ATGAACCCCAAACCCATAAC
Found at i:3591068 original size:88 final size:88
Alignment explanation
Indices: 3590885--3591051 Score: 221
Period size: 88 Copynumber: 1.9 Consensus size: 88
3590875 AACAGTGTAA
*
3590885 AAAAAAGAAGTAATTAAGCCTCTTTTTTTTTTGCACTTAATTGAGTAATTGAACTTTCAAAATGC
1 AAAAAA-AAGTAATTAAGCCTCTTTTTTTTTTGCACTGAATTGAGTAATTGAACTTTCAAAATGC
* **
3590950 ATAAAACGGGCCTCAAACTTCTTC
65 ATAAAAAGACCCTCAAACTTCTTC
* * *
3590974 AAAAAAAAGCAATTAAGCCAT-TGTTTTTTTTT-CACTGAATTGGGTACTTGAACTTTCAAAATG
1 AAAAAAAAGTAATTAAGCC-TCT-TTTTTTTTTGCACTGAATTGAGTAATTGAACTTTCAAAATG
3591037 CATCAAAAAGACCCT
64 CAT-AAAAAGACCCT
3591052 TAATTTTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
88 44 0.65
89 24 0.35
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (88 bp):
AAAAAAAAGTAATTAAGCCTCTTTTTTTTTTGCACTGAATTGAGTAATTGAACTTTCAAAATGCA
TAAAAAGACCCTCAAACTTCTTC
Found at i:3591164 original size:19 final size:19
Alignment explanation
Indices: 3591141--3591185 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3591131 TAAATTTTAG
* *
3591141 AAAAATTATTAAATATTAAT
1 AAAAA-TATAAAAAATTAAT
*
3591161 AAAAATATAAAAAATTATT
1 AAAAATATAAAAAATTAAT
3591180 AAAAAT
1 AAAAAT
3591186 TAGAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATATAAAAAATTAAT
Found at i:3591327 original size:19 final size:19
Alignment explanation
Indices: 3591304--3591356 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
3591294 GACATGTGAC
3591304 GAAAAATAATAAAAAAGAT
1 GAAAAATAATAAAAAAGAT
**
3591323 -AAAAATCAATAAAAACTAT
1 GAAAAAT-AATAAAAAAGAT
*
3591342 AGAAAAATTATAAAA
1 -GAAAAATAATAAAA
3591357 TGCTTCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 6 0.21
21 6 0.21
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.19
Consensus pattern (19 bp):
GAAAAATAATAAAAAAGAT
Found at i:3591547 original size:19 final size:19
Alignment explanation
Indices: 3591478--3591540 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
3591468 TTGCTATATA
3591478 TTTTATAATATTTTACGAT
1 TTTTATAATATTTTACGAT
* * *
3591497 TTTTATAAAATATTAC-AA
1 TTTTATAATATTTTACGAT
*
3591515 TTTT-TAATGTTTTTACGAT
1 TTTTATAAT-ATTTTACGAT
3591534 TTTTATA
1 TTTTATA
3591541 TTTTTTTCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
17 3 0.09
18 10 0.29
19 19 0.56
20 2 0.06
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTATAATATTTTACGAT
Found at i:3591555 original size:56 final size:55
Alignment explanation
Indices: 3591495--3591619 Score: 139
Period size: 56 Copynumber: 2.2 Consensus size: 55
3591485 ATATTTTACG
* *
3591495 ATTTTTATAAAATATT-ACAATTTTTA-ATGTTTTTACGATTTTTATAT-TTTTTTCTA
1 ATTTTTATAAAAT-TTAACAATATTTATA-G-TTTTA-AATTTTTATATATTTTTTCTA
* *
3591551 ATTTTTATTAAAATTTAATAATATTTATAGTTTTAAATTTTTTTATATTTTTTCTA
1 ATTTTTA-TAAAATTTAACAATATTTATAGTTTTAAATTTTTATATATTTTTTCTA
3591607 ATTTTTAATAAAA
1 ATTTTT-ATAAAA
3591620 GCAAGTGCGT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
55 9 0.15
56 34 0.57
57 16 0.27
58 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (55 bp):
ATTTTTATAAAATTTAACAATATTTATAGTTTTAAATTTTTATATATTTTTTCTA
Found at i:3592433 original size:30 final size:30
Alignment explanation
Indices: 3592374--3592446 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
3592364 GATTTCTAAA
* **
3592374 TTAAAAAGTA-AAAAATTAAATTTTTAATTT
1 TTAAAAA-TATAAAAATTAAATCTGAAATTT
3592404 TTAAAAATATAAAAATTAAATCTGAAATTT
1 TTAAAAATATAAAAATTAAATCTGAAATTT
*
3592434 TATAAAAGTATAA
1 T-TAAAAATATAA
3592447 GGACTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 2 0.05
30 25 0.68
31 10 0.27
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (30 bp):
TTAAAAATATAAAAATTAAATCTGAAATTT
Found at i:3596679 original size:19 final size:20
Alignment explanation
Indices: 3596639--3596682 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
3596629 ACAAAAAAAG
*
3596639 AATTCAAAATATTTTTTAAA
1 AATTCAAAATATTTTATAAA
*
3596659 AATTCGAAATA-TTTATAAA
1 AATTCAAAATATTTTATAAA
3596678 AATTC
1 AATTC
3596683 CAACATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (20 bp):
AATTCAAAATATTTTATAAA
Found at i:3596690 original size:18 final size:19
Alignment explanation
Indices: 3596655--3596694 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3596645 AAATATTTTT
*
3596655 TAAAAATTCGAAATATTTA
1 TAAAAATTCGAAACATTTA
*
3596674 TAAAAATTC-CAACATTTA
1 TAAAAATTCGAAACATTTA
3596692 TAA
1 TAA
3596695 TTTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.35
Consensus pattern (19 bp):
TAAAAATTCGAAACATTTA
Found at i:3605814 original size:13 final size:13
Alignment explanation
Indices: 3605778--3605823 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
3605768 CACGTTTAAT
3605778 TTTTAATTAATT-
1 TTTTAATTAATTA
* *
3605790 TTGTATTTAATTA
1 TTTTAATTAATTA
3605803 TTTTAATTAATTA
1 TTTTAATTAATTA
3605816 TTTTAATT
1 TTTTAATT
3605824 TTTTATTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
TTTTAATTAATTA
Found at i:3605829 original size:13 final size:13
Alignment explanation
Indices: 3605800--3605849 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
3605790 TTGTATTTAA
**
3605800 TTATTTTAATTAA
1 TTATTTTAATTTT
3605813 TTATTTTAATTTT
1 TTATTTTAATTTT
*
3605826 TTATTTGAATTTT
1 TTATTTTAATTTT
*
3605839 TTATTATAATT
1 TTATTTTAATT
3605850 GAAATATAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TTATTTTAATTTT
Found at i:3609343 original size:24 final size:24
Alignment explanation
Indices: 3609311--3609358 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3609301 AAGCAGGCTC
3609311 CTTAGTTAACAGCAAGTAAGTGAT
1 CTTAGTTAACAGCAAGTAAGTGAT
3609335 CTTAGTTAACAGCAAGTAAGTGAT
1 CTTAGTTAACAGCAAGTAAGTGAT
3609359 GGCACCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (24 bp):
CTTAGTTAACAGCAAGTAAGTGAT
Found at i:3617046 original size:60 final size:61
Alignment explanation
Indices: 3616974--3617103 Score: 140
Period size: 59 Copynumber: 2.2 Consensus size: 61
3616964 TAAGTTTTTA
* * * *
3616974 AAATTT-TGAATTTTTAAGAATCAAGATTAAAATTGTCATAATATATAGA-GT-TGAGGGTT
1 AAATTTGTTAATTTTTAAGAATCAAGA-TAAAATTGTCATAATATATAAACATATGAGGGCT
* * * * * *
3617033 AAATTTGTTAATTTTTTAGAATTAGGATCAAATTGTTATAATCTATAAACATATGAGGGCT
1 AAATTTGTTAATTTTTAAGAATCAAGATAAAATTGTCATAATATATAAACATATGAGGGCT
3617094 AAATTTGTTA
1 AAATTTGTTA
3617104 TTATTCTAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
59 24 0.41
60 17 0.29
61 17 0.29
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (61 bp):
AAATTTGTTAATTTTTAAGAATCAAGATAAAATTGTCATAATATATAAACATATGAGGGCT
Found at i:3622497 original size:23 final size:23
Alignment explanation
Indices: 3622471--3622515 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3622461 GAGTAATTTA
*
3622471 AATTTTTTCTTTTATGTTCTTTT
1 AATTTTTCCTTTTATGTTCTTTT
* *
3622494 AATTTTTCCTTTTTTTTTCTTT
1 AATTTTTCCTTTTATGTTCTTT
3622516 ATTTTCCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.76
Consensus pattern (23 bp):
AATTTTTCCTTTTATGTTCTTTT
Found at i:3629918 original size:28 final size:28
Alignment explanation
Indices: 3629872--3629942 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
3629862 GATTAAATGA
* *
3629872 AAAAAAAAAGAGTAAATGACTATTACTTC
1 AAAATAAAAGA-TTAATGACTATTACTTC
3629901 AAAATAAAAGATTAATGACTATTACTTC
1 AAAATAAAAGATTAATGACTATTACTTC
3629929 AAAATAAAAGATTA
1 AAAATAAAAGATTA
3629943 TCAATTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 30 0.75
29 10 0.25
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.27
Consensus pattern (28 bp):
AAAATAAAAGATTAATGACTATTACTTC
Found at i:3637172 original size:19 final size:19
Alignment explanation
Indices: 3637149--3637193 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3637139 AAAATTTTAA
3637149 AATTTTTA-ATTTTTATAT
1 AATTTTTAGATTTTTATAT
*
3637167 ATATTTTTAGATTTTTTTAT
1 A-ATTTTTAGATTTTTATAT
3637187 AATTTTT
1 AATTTTT
3637194 TTAAAACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 13 0.54
20 10 0.42
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
AATTTTTAGATTTTTATAT
Found at i:3637719 original size:27 final size:28
Alignment explanation
Indices: 3637663--3637735 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 28
3637653 GTAAATTTAA
* *
3637663 AATTATAATATGTGTAAATGATAATATT
1 AATTATAAAATGTATAAATGATAATATT
*
3637691 AATTATAAAATG-ATAAATG-TATATTTT
1 AATTATAAAATGTATAAATGATA-ATATT
*
3637718 AATTA-ATAATAGTATAAA
1 AATTATAAAAT-GTATAAA
3637736 ATAGTAGATG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
26 6 0.16
27 16 0.42
28 16 0.42
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (28 bp):
AATTATAAAATGTATAAATGATAATATT
Found at i:3638138 original size:141 final size:142
Alignment explanation
Indices: 3637928--3638190 Score: 345
Period size: 141 Copynumber: 1.9 Consensus size: 142
3637918 ATTGTATTAG
* * * * *
3637928 AATCACCATCATTCGTATCGATAATATATAAATAACTTCAAGCTATGAGCTCTTTCTCGTGAATT
1 AATCACCATCATTCATATCAATAATATATAAATAACTTCAAACTATGAGCTCTCTCTCATGAATT
* *
3637993 TCTTTAAAGGAAGAAACTCGAAA-AGTTTATGAAAATA-CTGAGCATGGGAGTGTTCTCTAGTTA
66 TCTTTAAAGGAAGAAACTCGAAAGAGCTTATGAAAATAGC-GAGCATGCGAGTGTTCTCTAGTTA
3638056 AAATGGGATTAAA
130 AAATGGGATTAAA
* * * *
3638069 AATCATCATCGTTCATATCAATAATATATAAATAACTTTAAACTA-GAAGTTCTCTCTCAT-AAG
1 AATCACCATCATTCATATCAATAATATATAAATAACTTCAAACTATG-AGCTCTCTCTCATGAA-
* * *
3638132 TTTCTTTAGAGGAAGAAACTCTAAAGAGCTTATGAAAATAGCGAGTATGCGAGTGTTCT
64 TTTCTTTAAAGGAAGAAACTCGAAAGAGCTTATGAAAATAGCGAGCATGCGAGTGTTCT
3638191 TTGGCTAATA
Statistics
Matches: 104, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
140 3 0.03
141 72 0.69
142 28 0.27
143 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (142 bp):
AATCACCATCATTCATATCAATAATATATAAATAACTTCAAACTATGAGCTCTCTCTCATGAATT
TCTTTAAAGGAAGAAACTCGAAAGAGCTTATGAAAATAGCGAGCATGCGAGTGTTCTCTAGTTAA
AATGGGATTAAA
Found at i:3638537 original size:74 final size:74
Alignment explanation
Indices: 3638458--3638620 Score: 196
Period size: 69 Copynumber: 2.3 Consensus size: 74
3638448 ATCAATGTAG
** * *
3638458 GATTAAAATTAACTTTTTAATTTAATGAAAATAGTGAAGATTTTAGCTATATGAGT-ATTCTCTA
1 GATTAAAATTAACTTTTTAATTTAATGAAAATAGTGAAGAGGTGAGCTATAAGAGTAATT-TCTA
3638522 GTCAACATG-
65 GTCAACATGA
*
3638531 GAATTAAAATTAA---TTT--TTTAATGAAAATAGTGAAGAGGTGAGCTATAAGAGTAATTTTTA
1 G-ATTAAAATTAACTTTTTAATTTAATGAAAATAGTGAAGAGGTGAGCTATAAGAGTAATTTCTA
* *
3638591 GTTAACGTGA
65 GTCAACATGA
3638601 GATTAAAATTAACTTTTTAA
1 GATTAAAATTAACTTTTTAA
3638621 CAAAAATAGT
Statistics
Matches: 75, Mismatches: 7, Indels: 15
0.77 0.07 0.15
Matches are distributed among these distances:
69 53 0.71
70 4 0.05
71 3 0.04
72 3 0.04
73 1 0.01
74 11 0.15
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.39
Consensus pattern (74 bp):
GATTAAAATTAACTTTTTAATTTAATGAAAATAGTGAAGAGGTGAGCTATAAGAGTAATTTCTAG
TCAACATGA
Found at i:3638700 original size:237 final size:238
Alignment explanation
Indices: 3638239--3638714 Score: 550
Period size: 237 Copynumber: 2.0 Consensus size: 238
3638229 AAAATTAGCT
* * * ** *
3638239 TTTAATTAAAATAGTGAAGAATTAAGCTATATGAGTGTTCTCTAGTTAATTTAGGATTCTAAATA
1 TTTAATGAAAATAGTGAAGAATTAAGCTATATGAGTATTCTCTAGTCAACATAGGATTCAAAATA
* * * ** *
3638304 ACTTTTTTTAATGAAACTAGTAAAAAAAGTGAGTTATGAGAGTATTTTCTAGTCAATTTGGGATT
66 AC-TTTTTTAATGAAAATAGTAAAAAAAGTGAGCTATAAGAGTATTTTCTAGTCAACGTGAGATT
* * *
3638369 AGAATTAAAATCTAATAAAAATAGTGAAGAAATTGTCACTTATTTATAAGGTAAGTGTGAGATAT
130 AAAATTAAAATCTAACAAAAATAGTGAAGAAATTATCACTTATTTATAAGGTAAGTGTGAGATAT
* * * *
3638434 GGGAGTGCTCTCTAATCAATGTAGGATTAAAATTAACTTTTTAA
195 GAGAGTACTCTCTAATCAACGTAGGATTAAAATGAACTTTTTAA
* *
3638478 TTTAATGAAAATAGTGAAGATTTTAGCTATATGAGTATTCTCTAGTCAACAT-GGAATT-AAAAT
1 TTTAATGAAAATAGTGAAGAATTAAGCTATATGAGTATTCTCTAGTCAACATAGG-ATTCAAAA-
* * * *
3638541 TAA-TTTTTTAATGAAAATAGT-GAAGAGGTGAGCTATAAGAGTAATTTT-TAGTTAACGTGAGA
64 TAACTTTTTTAATGAAAATAGTAAAAAAAGTGAGCTATAAGAGT-ATTTTCTAGTCAACGTGAGA
** * * *
3638603 TTAAAATTAACTTTTTAACAAAAATAGTGAAGAAATTATCACTTATTTATAAGGTAATTGTGATA
128 TTAAAATTAA-AATCTAACAAAAATAGTGAAGAAATTATCACTTATTTATAAGGTAAGTGTGAGA
* * * *
3638668 TATGAGAGTATTCTCTGA-CTGACGTCGGATTAAAATGAACTTTTTAA
192 TATGAGAGTACTCTCTAATC-AACGTAGGATTAAAATGAACTTTTTAA
3638715 AGAAAATAGT
Statistics
Matches: 198, Mismatches: 34, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
236 36 0.18
237 106 0.54
238 5 0.03
239 51 0.26
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (238 bp):
TTTAATGAAAATAGTGAAGAATTAAGCTATATGAGTATTCTCTAGTCAACATAGGATTCAAAATA
ACTTTTTTAATGAAAATAGTAAAAAAAGTGAGCTATAAGAGTATTTTCTAGTCAACGTGAGATTA
AAATTAAAATCTAACAAAAATAGTGAAGAAATTATCACTTATTTATAAGGTAAGTGTGAGATATG
AGAGTACTCTCTAATCAACGTAGGATTAAAATGAACTTTTTAA
Found at i:3639304 original size:6 final size:6
Alignment explanation
Indices: 3639293--3639322 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3639283 TAAAGTATTT
3639293 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
3639323 ATATATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:3640351 original size:23 final size:23
Alignment explanation
Indices: 3640324--3640369 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3640314 TATTGCTGGT
*
3640324 TTTGAGCATCGTTTTATGATAAA
1 TTTGAGCATCGCTTTATGATAAA
* *
3640347 TTTGAGCTTTGCTTTATGATAAA
1 TTTGAGCATCGCTTTATGATAAA
3640370 AGTTGCAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.46
Consensus pattern (23 bp):
TTTGAGCATCGCTTTATGATAAA
Found at i:3643225 original size:13 final size:13
Alignment explanation
Indices: 3643184--3643225 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3643174 TTAAAAAATC
3643184 TAAA-AAAAACCT
1 TAAACAAAAACCT
* *
3643196 AAAACAAAAACCC
1 TAAACAAAAACCT
*
3643209 TAAACAAAAATCT
1 TAAACAAAAACCT
3643222 TAAA
1 TAAA
3643226 AACCCTAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
12 3 0.12
13 21 0.88
ACGTcount: A:0.67, C:0.19, G:0.00, T:0.14
Consensus pattern (13 bp):
TAAACAAAAACCT
Found at i:3645355 original size:30 final size:33
Alignment explanation
Indices: 3645287--3645365 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
3645277 ATATCCCATT
*
3645287 AAAGAATAGATACTAATTTTCTTAAAAAAAAGA
1 AAAGAATAGATACTAAATTTCTTAAAAAAAAGA
*
3645320 AAAGAATAGATACTAAATTTC-T-CAAAAAA-A
1 AAAGAATAGATACTAAATTTCTTAAAAAAAAGA
*
3645350 CAAGAATAGATACTAA
1 AAAGAATAGATACTAA
3645366 GTTCTAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 16 0.37
31 6 0.14
32 1 0.02
33 20 0.47
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.24
Consensus pattern (33 bp):
AAAGAATAGATACTAAATTTCTTAAAAAAAAGA
Found at i:3645631 original size:12 final size:12
Alignment explanation
Indices: 3645614--3645652 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
3645604 TGGCCGGCCC
3645614 ATATTAATTTTT
1 ATATTAATTTTT
*
3645626 ATATTATTTTTT
1 ATATTAATTTTT
*
3645638 ATA-TAATTTTA
1 ATATTAATTTTT
3645649 ATAT
1 ATAT
3645653 ATATATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:3645805 original size:30 final size:30
Alignment explanation
Indices: 3645771--3645833 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
3645761 ACTTAACAAG
3645771 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
** *
3645801 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
3645831 CAA
1 CAA
3645834 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:3645883 original size:14 final size:14
Alignment explanation
Indices: 3645864--3645894 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3645854 ATACAAACAA
3645864 TAACAACAAAATAG
1 TAACAACAAAATAG
*
3645878 TAACAACATAATAG
1 TAACAACAAAATAG
3645892 TAA
1 TAA
3645895 AATGGAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (14 bp):
TAACAACAAAATAG
Found at i:3653151 original size:19 final size:20
Alignment explanation
Indices: 3653127--3653181 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
3653117 TTTAACTGAG
3653127 AATGAATGACCAATTTAT-A
1 AATGAATGACCAATTTATGA
* *
3653146 AATGAATG-CCAAATTTTTGT
1 AATGAATGACC-AATTTATGA
*
3653166 AATGAATGACAAATTT
1 AATGAATGACCAATTT
3653182 GTCTAAGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.07
19 14 0.47
20 13 0.43
21 1 0.03
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGAATGACCAATTTATGA
Found at i:3653550 original size:20 final size:20
Alignment explanation
Indices: 3653499--3653550 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3653489 CCAGGCTAAA
*
3653499 AAGTATTGATACTTTTTGTC
1 AAGTATTGATAGTTTTTGTC
* *
3653519 AAGTATCGATAGTTTTTGTT
1 AAGTATTGATAGTTTTTGTC
*
3653539 GAGTATTGATAG
1 AAGTATTGATAG
3653551 AATCAAGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (20 bp):
AAGTATTGATAGTTTTTGTC
Found at i:3657548 original size:19 final size:21
Alignment explanation
Indices: 3657509--3657549 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
3657499 AATTTATATT
3657509 TTAAAATATAATATAAACATA
1 TTAAAATATAATATAAACATA
*
3657530 TTAAAAT-TTATAT-AACATA
1 TTAAAATATAATATAAACATA
3657549 T
1 T
3657550 ACTCACAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 5 0.26
21 7 0.37
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAAAATATAATATAAACATA
Found at i:3663010 original size:9 final size:9
Alignment explanation
Indices: 3662998--3663050 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
3662988 AAATATATTT
3662998 ATTTTTTTA
1 ATTTTTTTA
3663007 ATTTTTTTA
1 ATTTTTTTA
3663016 ATTTTTTTTA
1 A-TTTTTTTA
***
3663026 ATTTTAAAA
1 ATTTTTTTA
3663035 TATTTTTTTA
1 -ATTTTTTTA
3663045 ATTTTT
1 ATTTTT
3663051 AAATTTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 21 0.58
10 15 0.42
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:3663014 original size:10 final size:10
Alignment explanation
Indices: 3662999--3663030 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3662989 AATATATTTA
3662999 TTTTTTTAA-
1 TTTTTTTAAT
3663008 TTTTTTTAAT
1 TTTTTTTAAT
3663018 TTTTTTTAAT
1 TTTTTTTAAT
3663028 TTT
1 TTT
3663031 AAAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTTAAT
Found at i:3663023 original size:19 final size:20
Alignment explanation
Indices: 3662997--3663096 Score: 84
Period size: 19 Copynumber: 5.1 Consensus size: 20
3662987 TAAATATATT
**
3662997 TATTTTTTTAATTTTTTTAA
1 TATTTTTTTAATTTTTAAAA
3663017 T-TTTTTTTAA-TTTTAAAA
1 TATTTTTTTAATTTTTAAAA
3663035 TATTTTTTTAATTTTT--AA
1 TATTTTTTTAATTTTTAAAA
***
3663053 -ATTTTAAAATATTTTTAAAA
1 TATTTTTTTA-ATTTTTAAAA
*
3663073 TACTTTTTTAAAATTTTTAAAA
1 TA-TTTTTT-TAATTTTTAAAA
3663095 TA
1 TA
3663097 AATTTTTAGT
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
17 6 0.09
18 15 0.23
19 18 0.28
20 7 0.11
21 1 0.02
22 16 0.25
23 2 0.03
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTTTTAATTTTTAAAA
Found at i:3663040 original size:27 final size:28
Alignment explanation
Indices: 3663010--3663070 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
3663000 TTTTTTAATT
*
3663010 TTTTTAATT-TTTTTTAATTTTAAAATA
1 TTTTTAATTATTTTTAAATTTTAAAATA
3663037 TTTTT--TTAATTTTTAAATTTTAAAATA
1 TTTTTAATT-ATTTTTAAATTTTAAAATA
3663064 TTTTTAA
1 TTTTTAA
3663071 AATACTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 2 0.07
27 27 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTTAATTATTTTTAAATTTTAAAATA
Found at i:3663041 original size:11 final size:11
Alignment explanation
Indices: 3663027--3663096 Score: 55
Period size: 10 Copynumber: 6.9 Consensus size: 11
3663017 TTTTTTTTAA
3663027 TTTTAAAATAT
1 TTTTAAAATAT
**
3663038 TTTT-TTA-AT
1 TTTTAAAATAT
3663047 TTTT-AAA--T
1 TTTTAAAATAT
3663055 TTT-AAAATAT
1 TTTTAAAATAT
3663065 TTTTAAAATACT
1 TTTTAAAATA-T
*
3663077 TTTTTAAA-AT
1 TTTTAAAATAT
3663087 TTTTAAAATA
1 TTTTAAAATA
3663097 AATTTTTAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
8 7 0.15
9 7 0.15
10 13 0.28
11 12 0.26
12 8 0.17
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3663102 original size:22 final size:23
Alignment explanation
Indices: 3663050--3663104 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
3663040 TTTTAATTTT
*
3663050 TAAATTTTAAAATATTTTTAAAA
1 TAAATTTTTAAATATTTTTAAAA
**
3663073 TACTTTTTTAAA-ATTTTTAAAA
1 TAAATTTTTAAATATTTTTAAAA
3663095 TAAATTTTTA
1 TAAATTTTTA
3663105 GTATTTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAATTTTTAAATATTTTTAAAA
Found at i:3670078 original size:17 final size:19
Alignment explanation
Indices: 3670046--3670081 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
3670036 AGAATGCAGG
3670046 ATAATTAAATAATTCAAAT
1 ATAATTAAATAATTCAAAT
3670065 ATAA-TAAA-AATTCAAAT
1 ATAATTAAATAATTCAAAT
3670082 CTCGAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATTAAATAATTCAAAT
Found at i:3673279 original size:8 final size:8
Alignment explanation
Indices: 3673266--3673293 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3673256 ACTAGAGACT
3673266 AGTGTTAC
1 AGTGTTAC
3673274 AGTGTTAC
1 AGTGTTAC
3673282 AGTGTTAC
1 AGTGTTAC
3673290 AGTG
1 AGTG
3673294 AGTCCCGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.36
Consensus pattern (8 bp):
AGTGTTAC
Found at i:3673407 original size:23 final size:23
Alignment explanation
Indices: 3673380--3673455 Score: 111
Period size: 23 Copynumber: 3.3 Consensus size: 23
3673370 AGTGTTATTG
3673380 ATCAGTGGTAGCTTCGGCTACA-
1 ATCAGTGGTAGCTTCGGCTACAT
*
3673402 ATTCAGTGGAAGCTAT-GGCTACAT
1 A-TCAGTGGTAGCT-TCGGCTACAT
3673426 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
3673449 ATCAGTG
1 ATCAGTG
3673456 TGGCACTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
22 2 0.04
23 44 0.92
24 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:3681751 original size:7 final size:7
Alignment explanation
Indices: 3681739--3681785 Score: 94
Period size: 7 Copynumber: 6.7 Consensus size: 7
3681729 TTTCAGAAAC
3681739 CCCTTTA
1 CCCTTTA
3681746 CCCTTTA
1 CCCTTTA
3681753 CCCTTTA
1 CCCTTTA
3681760 CCCTTTA
1 CCCTTTA
3681767 CCCTTTA
1 CCCTTTA
3681774 CCCTTTA
1 CCCTTTA
3681781 CCCTT
1 CCCTT
3681786 AACTCTAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.13, C:0.45, G:0.00, T:0.43
Consensus pattern (7 bp):
CCCTTTA
Found at i:3694713 original size:31 final size:31
Alignment explanation
Indices: 3694678--3694744 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
3694668 TTGAACTTGT
* * *
3694678 CAATTTTTCCTACATTAAGG-CCGAAATTAGG
1 CAATTGTTCCCACATTAAGGCCCG-AATTAGA
*
3694709 CAATTGTTCCCACATTAGGGCCCGAATTAGA
1 CAATTGTTCCCACATTAAGGCCCGAATTAGA
3694740 CAATT
1 CAATT
3694745 ATTTTCACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (31 bp):
CAATTGTTCCCACATTAAGGCCCGAATTAGA
Found at i:3694830 original size:90 final size:88
Alignment explanation
Indices: 3694709--3694883 Score: 237
Period size: 90 Copynumber: 2.0 Consensus size: 88
3694699 CGAAATTAGG
* * * * *
3694709 CAATTGTTCCCACATTAGGGCCCGAATTAGACAATTATT-TTCACATTGGGGTTTGAACTTTTTT
1 CAATTATTCCCACATTAGGGCACGAACTAGACAATTATTCCT-ACATTGGGGCTTGAAC--TTTT
*
3694773 TTTGTCCAAGTTAGTCTTTGAACTCGA
63 TTT-TCCAAGTTAGTCCTTGAACTCGA
*
3694800 CAATTATT-CCACATTAGGGCATGAACTAGACAATTATTCCTACATTGGGGCTTGAACTTTTTTT
1 CAATTATTCCCACATTAGGGCACGAACTAGACAATTATTCCTACATTGGGGCTTGAACTTTTTTT
3694864 TCCAAGTTAGTCCTTGAACT
66 TCCAAGTTAGTCCTTGAACT
3694884 TAACATTTGT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
87 19 0.25
88 7 0.09
90 42 0.55
91 8 0.11
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (88 bp):
CAATTATTCCCACATTAGGGCACGAACTAGACAATTATTCCTACATTGGGGCTTGAACTTTTTTT
TCCAAGTTAGTCCTTGAACTCGA
Found at i:3694832 original size:30 final size:31
Alignment explanation
Indices: 3694791--3694857 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
3694781 AGTTAGTCTT
*
3694791 TGAACTCGACAATTATTCC-ACATTAGGGCA
1 TGAACTAGACAATTATTCCTACATTAGGGCA
* *
3694821 TGAACTAGACAATTATTCCTACATTGGGGCT
1 TGAACTAGACAATTATTCCTACATTAGGGCA
3694852 TGAACT
1 TGAACT
3694858 TTTTTTTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 18 0.55
31 15 0.45
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (31 bp):
TGAACTAGACAATTATTCCTACATTAGGGCA
Found at i:3697171 original size:29 final size:29
Alignment explanation
Indices: 3697139--3697195 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3697129 TTAACAGCGC
3697139 TCCTCCACTAGGGTGCC-GCTTGACACATG
1 TCCTCCACTAGGGT-CCTGCTTGACACATG
* *
3697168 TCCTCTACTTGGGTCCTGCTTGACACAT
1 TCCTCCACTAGGGTCCTGCTTGACACAT
3697196 CTCCACCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.16, C:0.33, G:0.21, T:0.30
Consensus pattern (29 bp):
TCCTCCACTAGGGTCCTGCTTGACACATG
Found at i:3700134 original size:21 final size:22
Alignment explanation
Indices: 3700096--3700151 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 22
3700086 TTTGTAATTG
* *
3700096 TAATA-AATATTTATTA-TTAA
1 TAATATAATATTAAATATTTAA
3700116 -AATATTAATATTAAATATTTTAA
1 TAATA-TAATATTAAATA-TTTAA
3700139 TAATATAATATTA
1 TAATATAATATTA
3700152 TTTAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 4 0.14
21 9 0.31
23 12 0.41
24 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATATAATATTAAATATTTAA
Found at i:3700147 original size:23 final size:24
Alignment explanation
Indices: 3700107--3700151 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
3700097 AATAAATATT
3700107 TATTATTAAAATATTAATATTAAA
1 TATTATTAAAATATTAATATTAAA
3700131 TATT-TTAATAATA-TAATATTA
1 TATTATTAA-AATATTAATATTA
3700152 TTTAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTATTAAAATATTAATATTAAA
Found at i:3700192 original size:17 final size:17
Alignment explanation
Indices: 3700154--3700205 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
3700144 TAATATTATT
*
3700154 TAAAA-TTATTATTTAA
1 TAAAATTTATTATTAAA
3700170 -AAAATTTATTATTAAA
1 TAAAATTTATTATTAAA
* *
3700186 TAAAATTGAATATTAAA
1 TAAAATTTATTATTAAA
3700203 TAA
1 TAA
3700206 TTTATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 4 0.13
16 10 0.32
17 17 0.55
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAAATTTATTATTAAA
Found at i:3700210 original size:29 final size:29
Alignment explanation
Indices: 3700178--3700241 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
3700168 AAAAAATTTA
*
3700178 TTATTAAATAAAATTGAA-TATTAA-ATAAT
1 TTATTAAA-AAAA-TAAATTATTAATATAAT
*
3700207 TTATTAAAATAATAAATTATTAATATAAT
1 TTATTAAAAAAATAAATTATTAATATAAT
3700236 TTATTA
1 TTATTA
3700242 TATGATTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 3 0.10
28 9 0.29
29 19 0.61
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
TTATTAAAAAAATAAATTATTAATATAAT
Found at i:3700226 original size:16 final size:16
Alignment explanation
Indices: 3700201--3700235 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3700191 TTGAATATTA
*
3700201 AATAATTTATTAAAAT
1 AATAAATTATTAAAAT
*
3700217 AATAAATTATTAATAT
1 AATAAATTATTAAAAT
3700233 AAT
1 AAT
3700236 TTATTATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAAATTATTAAAAT
Found at i:3700241 original size:16 final size:15
Alignment explanation
Indices: 3700099--3700242 Score: 78
Period size: 13 Copynumber: 10.0 Consensus size: 15
3700089 GTAATTGTAA
3700099 TAAAT-ATTTATTAT
1 TAAATAATTTATTAT
*
3700113 T-AA-AATATTAATAT
1 TAAATAAT-TTATTAT
*
3700127 TAAAT-A-TT-TTAA
1 TAAATAATTTATTAT
3700139 TAATATAA--TATTAT
1 TAA-ATAATTTATTAT
*
3700153 TTAA-AA-TTATTATT
1 TAAATAATTTATTA-T
*
3700167 TAAAAAATTTATTAT
1 TAAATAATTTATTAT
* *
3700182 TAAATAAAATTGAATAT
1 TAAAT--AATTTATTAT
3700199 TAAATAATTTATTA-
1 TAAATAATTTATTAT
**
3700213 -AAATAATAAATTAT
1 TAAATAATTTATTAT
3700227 TAATATAATTTATTAT
1 TAA-ATAATTTATTAT
3700243 ATGATTAGAT
Statistics
Matches: 99, Mismatches: 15, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
12 7 0.07
13 26 0.26
14 18 0.18
15 19 0.19
16 16 0.16
17 13 0.13
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (15 bp):
TAAATAATTTATTAT
Found at i:3706392 original size:3 final size:3
Alignment explanation
Indices: 3706386--3706476 Score: 182
Period size: 3 Copynumber: 30.3 Consensus size: 3
3706376 ACAAGAAGAC
3706386 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3706434 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3706477 CAAATCGCAC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3707443 original size:31 final size:31
Alignment explanation
Indices: 3707404--3707473 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
3707394 CTTGTCAATT
*
3707404 TTTC-CATTAAGGCCAAAATTAGGCAATTG-
1 TTTCACATTAAGGCCAAAATTAGACAATTGC
* **
3707433 TTCTCACATTAGGGCCCGAATTAGACAATTGC
1 TT-TCACATTAAGGCCAAAATTAGACAATTGC
3707465 TTTCACATT
1 TTTCACATT
3707474 GGGGTTTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 2 0.06
30 2 0.06
31 28 0.82
32 2 0.06
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (31 bp):
TTTCACATTAAGGCCAAAATTAGACAATTGC
Found at i:3707542 original size:30 final size:31
Alignment explanation
Indices: 3707508--3707574 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
3707498 AGTTAGTCTT
* *
3707508 TGAACTCGACAATTGTTCC-ACATTAGGGCA
1 TGAACTAGACAATTATTCCTACATTAGGGCA
*
3707538 TGAACTAGACAATTATTCCTACATTAGGGCT
1 TGAACTAGACAATTATTCCTACATTAGGGCA
3707569 TGAACT
1 TGAACT
3707575 TTTTTTTTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (31 bp):
TGAACTAGACAATTATTCCTACATTAGGGCA
Found at i:3707548 original size:89 final size:89
Alignment explanation
Indices: 3707427--3707622 Score: 252
Period size: 89 Copynumber: 2.2 Consensus size: 89
3707417 CAAAATTAGG
* * * * * *
3707427 CAATTGTTCTCACATTAGGGCCCGAATTAGACAATTGCTTTC-ACATTGGGGTTTGAACTTTTTT
1 CAATTGTTCTCACATTAGGGCACGAACTAGACAATT-ATTCCTACATTAGGGCTTGAACTTTTTT
*
3707491 TTGTCCAAGTTAGTCTTTGAACTCGA
65 TT-TCCAAGTTAGTCCTTGAACTCGA
*
3707517 CAATTGTTC-CACATTAGGGCATGAACTAGACAATTATTCCTACATTAGGGCTTGAACTTTTTTT
1 CAATTGTTCTCACATTAGGGCACGAACTAGACAATTATTCCTACATTAGGGCTTGAACTTTTTTT
*
3707581 TTCCAAGTTAGTCCTTGAACTTGA
66 TTCCAAGTTAGTCCTTGAACTCGA
* * *
3707605 CATTTGTTATCATATTAG
1 CAATTGTTCTCACATTAG
3707623 AGTTTAAACA
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
88 31 0.34
89 52 0.57
90 9 0.10
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (89 bp):
CAATTGTTCTCACATTAGGGCACGAACTAGACAATTATTCCTACATTAGGGCTTGAACTTTTTTT
TTCCAAGTTAGTCCTTGAACTCGA
Found at i:3712811 original size:148 final size:151
Alignment explanation
Indices: 3712531--3712904 Score: 508
Period size: 148 Copynumber: 2.5 Consensus size: 151
3712521 TTTAGTGTGT
3712531 TTTTTATTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT
1 TTTTTATT-AAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAA-GG--TTTT
* * * *
3712596 TTTAAATTTATTTAAAAAATAAACTAAATGAATACATTTCGAACATAATGTACTAAAATAATGTA
62 TTTAATTTTATTTAAAAAACAAACTAAATGAATACATTTCAAACATAATGTACTAAAAGAATGTA
3712661 AAATAATAAAATTA-G-AA-AATAGTA
127 AAATAATAAAA-TACGAAACAATA-TA
** *
3712685 -TTTT-TT-AAGTAATAAAATCCGGGGGAAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTTT
1 TTTTTATTAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAG-GTTTTTTT
* * *
3712747 AATTTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAAGAATGTAAAA
65 AATTTTATTTAAAAAACAAACTAAATGAATACATTTCAAACATAATGTACTAAAAGAATGTAAAA
3712812 TAATAAAATACGAAAACAATATA
130 TAATAAAATACG-AAACAATATA
* * *
3712835 TTTTTATTGAAAGTAATAAAATCTGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTA
1 TTTTTATT-AAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTT
3712900 AATTT
65 AATTT
3712905 ATTNNNNNNN
Statistics
Matches: 195, Mismatches: 16, Indels: 19
0.85 0.07 0.08
Matches are distributed among these distances:
147 2 0.01
148 74 0.38
149 1 0.01
150 48 0.25
151 8 0.04
152 4 0.02
153 15 0.08
154 43 0.22
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (151 bp):
TTTTTATTAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTA
ATTTTATTTAAAAAACAAACTAAATGAATACATTTCAAACATAATGTACTAAAAGAATGTAAAAT
AATAAAATACGAAACAATATA
Found at i:3723475 original size:41 final size:43
Alignment explanation
Indices: 3723409--3723499 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 43
3723399 CTTTCTCTTT
** * *
3723409 ATTATTAATATTTTATAATTGTAATAA-ATATTTATTA-TTAAA
1 ATTATTAATATTGAATAATTCTAATAATATA-ATATTATTTAAA
*
3723451 A-TATTAATATTGAATATTTCTAATAATATAATATTATTTAAA
1 ATTATTAATATTGAATAATTCTAATAATATAATATTATTTAAA
3723493 ATTATTA
1 ATTATTA
3723500 TTTTAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
41 26 0.63
42 10 0.24
43 5 0.12
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (43 bp):
ATTATTAATATTGAATAATTCTAATAATATAATATTATTTAAA
Found at i:3723614 original size:34 final size:34
Alignment explanation
Indices: 3723576--3723657 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
3723566 AATATGTATG
* * *
3723576 TTTAATAATATTGAAAATCATAATGTT-TTATTAA
1 TTTAATAATATTAAAAATAAAAAT-TTATTATTAA
*
3723610 TTTAA-ATATTTTAAAAATAAAAATTTATTATTAA
1 TTTAATA-ATATTAAAAATAAAAATTTATTATTAA
*
3723644 TATAATAATATTAA
1 TTTAATAATATTAA
3723658 GCTTAACTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
33 3 0.08
34 35 0.90
35 1 0.03
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (34 bp):
TTTAATAATATTAAAAATAAAAATTTATTATTAA
Found at i:3724586 original size:158 final size:155
Alignment explanation
Indices: 3724001--3724667 Score: 945
Period size: 154 Copynumber: 4.4 Consensus size: 155
3723991 TTTAGTGTGT
3724001 TTTTTATTGAAAGTAATAAAATCC-GGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTT
1 TTTTTATT-AAAGTAATAAAATCCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGG-TTTT
*
3724065 TTTTAAATTTATTTAAAAATA-A-ACTAAATGAATACATTTCGAACATAATGTACTAAAATAATG
64 TTTTAAATTTATTTAAAAA-ACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATG
*
3724128 TAAAATAAT-AAATTAGAAAAT-A-GTA
128 TAAAATAATAAAATTAGAAAATAATATA
* * *
3724153 -TTTT-TT-AAGTAATAAAATCCGGGG-GAAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTT
1 TTTTTATTAAAGTAATAAAATCCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT
* * * *
3724214 TTAATTTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAAGAATGTAA
66 TTAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
*
3724279 AATAATAAAA-TACGAAAACAATATA
131 AATAATAAAATTA-GAAAATAATATA
* *
3724304 TTTTTATTGAAAGTAATAAAAT-CTGGGAAAAAAATACGAACAAAGGGCCGAAATAA-GGATTTT
1 TTTTTATT-AAAGTAATAAAATCCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTT
* *
3724367 TTTAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTA
65 TTTAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTA
3724432 AAATAATAAAATTATG-AAATAATATA
130 AAATAATAAAATTA-GAAAATAATATA
3724458 TTTTTATTAAAAGTAATAAAATCCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTT
1 TTTTTATT-AAAGTAATAAAATCCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGG-TTTT
3724523 TTTTAAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATG
64 TTTT-AAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATG
*
3724588 TAAAATAATAAAATTAGAAAATAGTATA
128 TAAAATAATAAAATTAGAAAATAATATA
* ** * * *
3724616 -TTTT-TTAAAGTAATAAAATTCAAGG-AAAAAATAAGAACAACGGGCCAAAATA
1 TTTTTATTAAAGTAATAAAATCCGGGGAAAAAAATACGAACAAAGGGCCGAAATA
3724668 CGAACATGTT
Statistics
Matches: 466, Mismatches: 31, Indels: 34
0.88 0.06 0.06
Matches are distributed among these distances:
146 1 0.00
147 23 0.05
148 90 0.19
149 11 0.02
150 3 0.01
151 6 0.01
152 4 0.01
153 2 0.00
154 137 0.29
155 90 0.19
156 4 0.01
157 12 0.03
158 83 0.18
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.30
Consensus pattern (155 bp):
TTTTTATTAAAGTAATAAAATCCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT
TTAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
AATAATAAAATTAGAAAATAATATA
Found at i:3725724 original size:20 final size:20
Alignment explanation
Indices: 3725699--3725737 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3725689 GGGCTAAATT
*
3725699 TATTCACTTCACCCTCTTGC
1 TATTCACCTCACCCTCTTGC
3725719 TATTCACCTCACCCTCTTG
1 TATTCACCTCACCCTCTTG
3725738 TTAGGGCCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.41, G:0.05, T:0.38
Consensus pattern (20 bp):
TATTCACCTCACCCTCTTGC
Found at i:3726156 original size:30 final size:30
Alignment explanation
Indices: 3726117--3726173 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
3726107 TTTTATAGAT
3726117 AATTAATATTT-AT-TATTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
3726147 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
3726174 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:3726388 original size:26 final size:26
Alignment explanation
Indices: 3726349--3726412 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
3726339 TTTAAACCAA
*
3726349 ACTTTTCAAAAGCACTTCTCAAAATT
1 ACTTTTCAAAAGCACTTCTCAAAAGT
* * *
3726375 ACTTTTCCACAGCACTTTTCAAAAGT
1 ACTTTTCAAAAGCACTTCTCAAAAGT
3726401 ACTTTTCAAAAG
1 ACTTTTCAAAAG
3726413 TATTGCCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.34
Consensus pattern (26 bp):
ACTTTTCAAAAGCACTTCTCAAAAGT
Found at i:3726413 original size:13 final size:13
Alignment explanation
Indices: 3726349--3726414 Score: 78
Period size: 13 Copynumber: 5.1 Consensus size: 13
3726339 TTTAAACCAA
*
3726349 ACTTTTCAAAAGC
1 ACTTTTCAAAAGT
* *
3726362 ACTTCTCAAAATT
1 ACTTTTCAAAAGT
* * *
3726375 ACTTTTCCACAGC
1 ACTTTTCAAAAGT
3726388 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
3726401 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
3726414 A
1 A
3726415 TTGCCAAACT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:3726520 original size:13 final size:13
Alignment explanation
Indices: 3726502--3726529 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3726492 GCCTAGTCTT
3726502 AACCCATAAATAG
1 AACCCATAAATAG
3726515 AACCCATAAATAG
1 AACCCATAAATAG
3726528 AA
1 AA
3726530 GGATAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.21, G:0.07, T:0.14
Consensus pattern (13 bp):
AACCCATAAATAG
Found at i:3732256 original size:6 final size:6
Alignment explanation
Indices: 3732245--3732270 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3732235 TATGGTCAAA
3732245 ATAAAT ATAAAT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT ATAAAT AT
3732271 TTTATCATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATAAAT
Found at i:3737094 original size:18 final size:18
Alignment explanation
Indices: 3737056--3737091 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3737046 TTATTATTTT
*
3737056 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
3737074 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
3737092 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:3737207 original size:13 final size:13
Alignment explanation
Indices: 3737189--3737215 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3737179 AATATTAAAA
3737189 ATATTAATATTTT
1 ATATTAATATTTT
3737202 ATATTAATATTTT
1 ATATTAATATTTT
3737215 A
1 A
3737216 AATATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTAATATTTT
Found at i:3737556 original size:3 final size:3
Alignment explanation
Indices: 3737550--3737579 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3737540 TAAAAAAATA
3737550 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3737580 CATCATCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3737584 original size:3 final size:3
Alignment explanation
Indices: 3737578--3737602 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3737568 AATAATAATA
3737578 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
3737603 AATCGCACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:3739489 original size:43 final size:43
Alignment explanation
Indices: 3739436--3739556 Score: 135
Period size: 43 Copynumber: 2.8 Consensus size: 43
3739426 ATAGGATTTA
*
3739436 CGATATGTGTTATCGTGTAAGACCACGTCTGGGACA-TTGACAT
1 CGATATGTGTTATCGTGTAAGACCACGTCTGGGACAGTCG-CAT
*
3739479 CGACT-TGTGTT-TACGTGTAAGACC-CTGTCTAGGACAGTCGCAT
1 CGA-TATGTGTTAT-CGTGTAAGACCAC-GTCTGGGACAGTCGCAT
*
3739522 CGATATGTGATTA-CATGTAAGACCACGTCTGGGAC
1 CGATATGTG-TTATCGTGTAAGACCACGTCTGGGAC
3739557 GTTGGCATTG
Statistics
Matches: 66, Mismatches: 4, Indels: 16
0.77 0.05 0.19
Matches are distributed among these distances:
42 3 0.05
43 57 0.86
44 6 0.09
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.29
Consensus pattern (43 bp):
CGATATGTGTTATCGTGTAAGACCACGTCTGGGACAGTCGCAT
Found at i:3740629 original size:23 final size:23
Alignment explanation
Indices: 3740475--3740638 Score: 123
Period size: 23 Copynumber: 7.0 Consensus size: 23
3740465 ATATACATAT
* * *
3740475 TTTGATGTTTAAATGCTGCCCAA
1 TTTGGTGTATAAATGCTGTCCAA
* * *
3740498 TTTGTTGTATATACGCTGTCCAA
1 TTTGGTGTATAAATGCTGTCCAA
*
3740521 TTTTGGTGTAAAAATGCTG-CTCAA
1 -TTTGGTGTATAAATGCTGTC-CAA
* * * *
3740545 ATTGTTGTATATATGCTGCCCAA
1 TTTGGTGTATAAATGCTGTCCAA
* * **
3740568 ATTGTTGTATTTATGCTGTCCAAA
1 TTTGGTGTATAAATGCTGTCC-AA
*
3740592 TTTTGGTGTAAAAATGCTGTCCAA
1 -TTTGGTGTATAAATGCTGTCCAA
* *
3740616 TTTGGTATATAAATGTTGTCCAA
1 TTTGGTGTATAAATGCTGTCCAA
3740639 ATTGATAGGG
Statistics
Matches: 113, Mismatches: 23, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
23 75 0.66
24 22 0.19
25 16 0.14
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (23 bp):
TTTGGTGTATAAATGCTGTCCAA
Found at i:3740639 original size:71 final size:72
Alignment explanation
Indices: 3740484--3740642 Score: 218
Period size: 70 Copynumber: 2.2 Consensus size: 72
3740474 TTTTGATGTT
*
3740484 TAAATGCTGCCCAATTTGTTGTATATACGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAAATTG
1 TAAATGCTGCCCAAATTGTTGTATATACGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAAATTG
*
3740549 TTGTATA
66 TGGTATA
* * *
3740556 T--ATGCTGCCCAAATTGTTGTATTTATGCTGTCCAAATTTTGGTGTAAAAATGCTG-TCCAATT
1 TAAATGCTGCCCAAATTGTTGTATATACGCTGTCC-AATTTTGGTGTAAAAATGCTGCTCAAATT
3740618 -TGGTATA
65 GTGGTATA
* *
3740625 TAAATGTTGTCCAAATTG
1 TAAATGCTGCCCAAATTG
3740643 ATAGGGTAGT
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
69 7 0.09
70 35 0.45
71 34 0.44
72 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (72 bp):
TAAATGCTGCCCAAATTGTTGTATATACGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAAATTG
TGGTATA
Found at i:3741040 original size:5 final size:5
Alignment explanation
Indices: 3741030--3741091 Score: 74
Period size: 5 Copynumber: 12.2 Consensus size: 5
3741020 AAGTATGTTT
*
3741030 TTATA TTATA -T-TA TTATAA ATATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTATA TTATA
3741079 TATATA TATATA T
1 T-TATA T-TATA T
3741092 AAGACAAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 32 0.63
6 15 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TTATA
Found at i:3741082 original size:2 final size:2
Alignment explanation
Indices: 3741031--3741092 Score: 59
Period size: 2 Copynumber: 35.0 Consensus size: 2
3741021 AGTATGTTTT
*
3741031 TA TA T- TA TA T- TA T- TA TA AA TA TA T- TA TA T- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3741067 TA T- TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3741093 AGACAAAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
1 8 0.16
2 42 0.84
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:3742119 original size:19 final size:19
Alignment explanation
Indices: 3742095--3742169 Score: 68
Period size: 19 Copynumber: 4.0 Consensus size: 19
3742085 TTATGTGTGA
3742095 ATATGTGAATTGTGAATTG
1 ATATGTGAATTGTGAATTG
*
3742114 ATATGTGAATTG-GAAATCG
1 ATATGTGAATTGTG-AATTG
* *
3742133 AGATATGAGATT-TGAA-T-
1 ATATGTGA-ATTGTGAATTG
3742150 ATATGTGAATATGTGAATTG
1 ATATGTGAAT-TGTGAATTG
3742170 TGTATTGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
16 2 0.05
17 7 0.16
18 5 0.12
19 25 0.58
20 4 0.09
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.37
Consensus pattern (19 bp):
ATATGTGAATTGTGAATTG
Found at i:3748745 original size:14 final size:14
Alignment explanation
Indices: 3748726--3748757 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3748716 ATTAAATTTG
*
3748726 AAAATAATTAAATA
1 AAAATAAATAAATA
3748740 AAAATAAATAAATA
1 AAAATAAATAAATA
3748754 AAAA
1 AAAA
3748758 CGAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAAATAAATA
Found at i:3750204 original size:30 final size:30
Alignment explanation
Indices: 3750170--3750236 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
3750160 AAGTTAGTCT
* *
3750170 TTGAACTCGACAATTGTTCC-ACATTAGGGC
1 TTGAACTAGACAATT-ATCCTACATTAGGGC
* *
3750200 TTGAACTAGACAATTATCCTCCATTGGGGC
1 TTGAACTAGACAATTATCCTACATTAGGGC
3750230 TTGAACT
1 TTGAACT
3750237 TTTTTCCAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (30 bp):
TTGAACTAGACAATTATCCTACATTAGGGC
Found at i:3750226 original size:88 final size:85
Alignment explanation
Indices: 3750091--3750260 Score: 218
Period size: 88 Copynumber: 2.0 Consensus size: 85
3750081 CTGAATTAGG
* * * *
3750091 CAATTGTTCCCATATTAGGGCCCAATTAGACAATTGTCTTCACATTGGGGCTTGAACTTTTTTTT
1 CAATTGTTCCCACATTAGGGCCCAACTAGACAATTATCCTCACATTGGGGCTTGAAC---TTTTT
*
3750156 GTCCAAGTTAGTCTTTGAACTCGA
63 -TCCAAGTTAGTCCTTGAACTCGA
**
3750180 CAATTGTT-CCACATTAGGGCTTGAACTAGACAATTATCCTC-CATTGGGGCTTGAACTTTTTTC
1 CAATTGTTCCCACATTAGGGC-CCAACTAGACAATTATCCTCACATTGGGGCTTGAACTTTTTTC
3750243 CAAGTTAGTCCTTGAACT
65 CAAGTTAGTCCTTGAACT
3750261 TGCCATTTGT
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
84 19 0.26
85 5 0.07
88 26 0.36
89 23 0.32
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (85 bp):
CAATTGTTCCCACATTAGGGCCCAACTAGACAATTATCCTCACATTGGGGCTTGAACTTTTTTCC
AAGTTAGTCCTTGAACTCGA
Done.