Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold317
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: 576627
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 3 of 7
Found at i:271037 original size:21 final size:21
Alignment explanation
Indices: 271008--271052 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
270998 AAGTTTTTAT
*
271008 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
271028 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
271050 TTT
1 TTT
271053 CAGCTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:273289 original size:13 final size:13
Alignment explanation
Indices: 273271--273296 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
273261 CAATTTTTGG
273271 TGTATCGATACAT
1 TGTATCGATACAT
273284 TGTATCGATACAT
1 TGTATCGATACAT
273297 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:273308 original size:32 final size:33
Alignment explanation
Indices: 273251--273314 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
273241 TGCAAGCCAA
**
273251 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
273284 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
273315 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:273321 original size:19 final size:18
Alignment explanation
Indices: 273251--273321 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
273241 TGCAAGCCAA
273251 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
273271 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
273284 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
273303 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
273322 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:276585 original size:13 final size:13
Alignment explanation
Indices: 276567--276592 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
276557 CATTTTTTGG
276567 TGTATCGATACAT
1 TGTATCGATACAT
276580 TGTATCGATACAT
1 TGTATCGATACAT
276593 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:276607 original size:32 final size:33
Alignment explanation
Indices: 276547--276610 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
276537 TACAAGCTAA
**
276547 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
276580 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
276611 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:276665 original size:20 final size:20
Alignment explanation
Indices: 276640--276693 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
276630 AATCCCAATG
276640 ACATGTATCGATACATTGCA
1 ACATGTATCGATACATTGCA
276660 ACATGTATCGATACATTGCA
1 ACATGTATCGATACATTGCA
276680 ACATGTATCGATAC
1 ACATGTATCGATAC
276694 TTTGAATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (20 bp):
ACATGTATCGATACATTGCA
Found at i:277138 original size:79 final size:79
Alignment explanation
Indices: 276985--277198 Score: 317
Period size: 79 Copynumber: 2.7 Consensus size: 79
276975 GATCCTAACA
* *
276985 ACTCCAACCCTGGTTTTATTTCTAAAATATCAA-TTTT--TAATCGGGGATACTCCAACCCCGTT
1 ACTCCAACCCTGATTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTT
277047 ATTTTCGAGGGGAT
66 ATTTTCGAGGGGAT
*
277061 ACTCCAACCCTGATTTTATTTCTAAAACATCAATTTTTCATAATCAGGGATACTCCAACCCCGTT
1 ACTCCAACCCTGATTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTT
*
277126 ATTTTTGAGGGGAT
66 ATTTTCGAGGGGAT
* * * * * *
277140 ACTCCAACCCCGTTTTTATTTCTAAAACATCAATTCTCCACAATCGGGGATATTCCAAC
1 ACTCCAACCCTGATTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
277199 TCCAATTTTA
Statistics
Matches: 124, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
76 31 0.25
77 4 0.03
79 89 0.72
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34
Consensus pattern (79 bp):
ACTCCAACCCTGATTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTT
ATTTTCGAGGGGAT
Found at i:277210 original size:51 final size:51
Alignment explanation
Indices: 277134--277251 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 51
277124 TTATTTTTGA
** *
277134 GGGGATACTCCAACCCCGTTTTTATTTCTAAAACA-TCAATTCTCCACAATC
1 GGGGATACTCCAACCCCAATTTTATTTCCAAAACACT-AATTCTCCACAATC
* * * * *
277185 GGGGATATTCCAACTCCAATTTTATTTCCAAAATACTAATTTTTCACAATC
1 GGGGATACTCCAACCCCAATTTTATTTCCAAAACACTAATTCTCCACAATC
277236 -GGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
277252 GTTATTTCAT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
50 14 0.25
51 41 0.73
52 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAATTTTATTTCCAAAACACTAATTCTCCACAATC
Found at i:277269 original size:28 final size:28
Alignment explanation
Indices: 277236--277308 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
277226 TTTCACAATC
*
277236 GGGATACTCCAACCCCGTTATTT-CATCG
1 GGGATACTCCAACCCCGTTATTTCCA-AG
*
277264 GGGATACTCCAACCCAGTTATTTCCAAG
1 GGGATACTCCAACCCCGTTATTTCCAAG
*
277292 GGGATACTCTAACCCCG
1 GGGATACTCCAACCCCG
277309 GCTCTATTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 38 0.95
29 2 0.05
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCCAAG
Found at i:277339 original size:157 final size:158
Alignment explanation
Indices: 277107--277429 Score: 350
Period size: 157 Copynumber: 2.1 Consensus size: 158
277097 TTCATAATCA
* *** ** * *
277107 GGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGTTTTTATTTCTAAAACATCA
1 GGGATACTCCAACCCAGTTATTTCCAAGGGGATACTCCAACCCCGGCTCTATTTCCAAAACATCA
** * **
277172 ATTCTCCACAATCGGGGATA-TTCCAACTCCAATTTTATTTCCAAAATACTAATTT-TTCACAA-
66 ATTCTCCACAATCAAGGATACTT-CAACCCCAACCTTATTTCCAAAATACTAATTTCTT-ACAAT
* *
277234 TCGGGATACTCCAACCCCGTTA-TTTCATCG
129 TAGGGATACTCCAACCCCATTATTTTCA-CG
* * **
277264 GGGATACTCCAACCCAGTTATTTCCAAGGGGATACTCTAACCCCGGCTCTATTTCCAAAATATTG
1 GGGATACTCCAACCCAGTTATTTCCAAGGGGATACTCCAACCCCGGCTCTATTTCCAAAACATCA
* * * * *
277329 ATT-TCTCACAATCAAGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTTATAATT
66 ATTCTC-CACAATCAAGGATACTTCAACCCCAACCTTATTTCCAAAATACTAATTTCTTACAATT
*
277393 AGGGATACTCCAATCCCATTATTTTCACG
130 AGGGATACTCCAACCCCATTATTTTCACG
277422 GGGATACT
1 GGGATACT
277430 TCAATCCTGA
Statistics
Matches: 136, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
156 2 0.01
157 96 0.71
158 33 0.24
159 5 0.04
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (158 bp):
GGGATACTCCAACCCAGTTATTTCCAAGGGGATACTCCAACCCCGGCTCTATTTCCAAAACATCA
ATTCTCCACAATCAAGGATACTTCAACCCCAACCTTATTTCCAAAATACTAATTTCTTACAATTA
GGGATACTCCAACCCCATTATTTTCACG
Found at i:277399 original size:51 final size:52
Alignment explanation
Indices: 277292--277401 Score: 136
Period size: 51 Copynumber: 2.2 Consensus size: 52
277282 TATTTCCAAG
*
277292 GGGATAC-TCTAACCCCGGCTCTATTTCCAAAATATTGATTTCTCACAATCA
1 GGGATACTTCTAACCCCGCCTCTATTTCCAAAATATTGATTTCTCACAATCA
* * * * *
277343 AGGATACTTC-AACCCCGACCT-TATTTCTAAAATATTGATTTCTTATAATTA
1 GGGATACTTCTAACCCCG-CCTCTATTTCCAAAATATTGATTTCTCACAATCA
277394 GGGATACT
1 GGGATACT
277402 CCAATCCCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 46 0.92
52 4 0.08
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (52 bp):
GGGATACTTCTAACCCCGCCTCTATTTCCAAAATATTGATTTCTCACAATCA
Found at i:287351 original size:23 final size:22
Alignment explanation
Indices: 287321--287370 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
287311 CTTCTCTTCT
**
287321 AAAAAAAATGAAAACAAAAACAA
1 AAAAAAAAACAAAACAAAAA-AA
*
287344 AAAAAAAAACAAAACAAAGAAA
1 AAAAAAAAACAAAACAAAAAAA
287366 AAAAA
1 AAAAA
287371 GAGAAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.02
Consensus pattern (22 bp):
AAAAAAAAACAAAACAAAAAAA
Found at i:287352 original size:18 final size:18
Alignment explanation
Indices: 287331--287370 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
287321 AAAAAAAATG
287331 AAAACAAAAACAAA-AAAA
1 AAAAC-AAAACAAAGAAAA
287349 AAAACAAAACAAAGAAAA
1 AAAACAAAACAAAGAAAA
287367 AAAA
1 AAAA
287371 GAGAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.88, C:0.10, G:0.03, T:0.00
Consensus pattern (18 bp):
AAAACAAAACAAAGAAAA
Found at i:288504 original size:55 final size:58
Alignment explanation
Indices: 288439--288695 Score: 271
Period size: 55 Copynumber: 4.5 Consensus size: 58
288429 CTCCTTTCAC
288439 CCTTT-AGTCCTCAAAGAGCAGGACGCC-TTT-C-AAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTAAAGCCCACACAAGTTGGTGGCA
* *
288493 CCTTTCAGTCCTCAAAGAGCAGGATGCC-TTT--TAAAGCCCACACGAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
288548 CCCTCCAGTCGTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACATAAGCTGGTGGGA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC---TAAAGCCCACACAAGTTGGTGGCA
* * *
288609 CC-TTCAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCATACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC---TAAAGCCCACACAAGTTGGTGGCA
* *
288669 -CTTCCTAGTCCTCAAAGAGTAGGACGC
1 CCTTTC-AGTCCTCAAAGAGCAGGACGC
288696 TCTCTCCTTT
Statistics
Matches: 173, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
54 5 0.03
55 70 0.40
56 3 0.02
59 1 0.01
60 52 0.30
61 42 0.24
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (58 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTAAAGCCCACACAAGTTGGTGGCA
Found at i:288506 original size:94 final size:97
Alignment explanation
Indices: 288327--288516 Score: 262
Period size: 94 Copynumber: 2.0 Consensus size: 97
288317 TATCTAAACC
** * *
288327 TTCTCCTTCCACTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACATAAGTT
1 TTCTCCTTCCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCC---TAAAGCCCACACAAGTT
288392 GATGGCACTTTCTAGTCCTCAAAGAGCAGGACGCT
63 GATGGCACTTTCTAGTCCTCAAAGAGCAGGACGCT
* *
288427 TTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCC-TTT-C-AAAGCCCACACAAGTTGGT
1 TTCTCCTTCCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTAAAGCCCACACAAGTTGAT
288489 GGCACCTTTC-AGTCCTCAAAGAGCAGGA
66 GGCA-CTTTCTAGTCCTCAAAGAGCAGGA
288517 TGCCTTTTAA
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
94 39 0.47
95 5 0.06
98 1 0.01
99 3 0.04
100 35 0.42
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (97 bp):
TTCTCCTTCCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTAAAGCCCACACAAGTTGAT
GGCACTTTCTAGTCCTCAAAGAGCAGGACGCT
Found at i:288641 original size:60 final size:60
Alignment explanation
Indices: 288464--288692 Score: 274
Period size: 60 Copynumber: 3.9 Consensus size: 60
288454 GAGCAGGACG
*
288464 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATG------
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGATGCCTTTT
* * * *
288519 CCTTTTAAAGCCCACACGAGTTGGTGGCACCCTCCAGTCGTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCAGGATGCCTTTT
* * * *
288580 CCTTTTAAAGCCCACATAAGCTGGTGGGACCTTCAGTCCTCAAAGAGTAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTT
* *
288640 CCTTTTAAAGCCCATACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGTAGGA
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C-AGTCCTCAAAGAGCAGGA
288693 CGCTCTCTCC
Statistics
Matches: 148, Mismatches: 17, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
55 47 0.32
56 2 0.01
59 3 0.02
60 53 0.36
61 43 0.29
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (60 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTT
Found at i:288761 original size:215 final size:214
Alignment explanation
Indices: 288501--288900 Score: 592
Period size: 215 Copynumber: 1.9 Consensus size: 214
288491 CACCTTTCAG
* *
288501 TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACGAGTTGGTGGCACCCTCCAG-TCGTCAAAG
1 TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCA-CCTCCAGTTC-TCAAAG
* * * *
288565 AGCAGGACGCCTTTTCCTTTTAAAGCCCACATAAGCTGGTGGGAC-CTTCAGTCCTCAAAGAGTA
64 AGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACTCTTCAGTCCTCAAAGAGCA
*
288629 GGATGCCTTTTCCTTTT-AAAGCCCATACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGTAGG
129 GGATG-C-TTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTCC-AGTCCTCAAAGAGTAGG
288692 ACGCTCTCTCCTTTCGCCTTTTTA
191 ACGCTCTCTCCTTTCGCCTTTTTA
*
288716 TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTTCTCAAAGAG
1 TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTCCAGTTCTCAAAGAG
* * * * *
288781 CAGGACGCCTTCTCTTTTTAAAGCCCATACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGG
66 CAGGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACTCTTCAGTCCTCAAAGAGCAGG
*
288846 ATGCTTTCTTTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAG
131 ATGCTTTCCTTTT-CAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAG
288901 GGCAGGACAC
Statistics
Matches: 166, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
213 8 0.05
214 52 0.31
215 101 0.61
216 5 0.03
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.27
Consensus pattern (214 bp):
TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTCCAGTTCTCAAAGAG
CAGGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACTCTTCAGTCCTCAAAGAGCAGG
ATGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGTAGGACGCT
CTCTCCTTTCGCCTTTTTA
Found at i:288928 original size:122 final size:115
Alignment explanation
Indices: 288709--288968 Score: 369
Period size: 122 Copynumber: 2.2 Consensus size: 115
288699 CTCCTTTCGC
*
288709 CTTTTTA-TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTTC
1 CTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCC
* * *
288773 TCAAAGAGCAGGACGCCTTCTCTTTTTAAAGCCCATACAAGTTGGTGGCA
66 TCAAAGAGCAGGACACCTTCTCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
288823 CTTTTTAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGCAAAGCCCACACAAGTTGGTGGCACCTT
1 CTTTTTAGTCCTCAAAGAGCAGGATGC---C-TTTT--AAAGCCCACACAAGCTGGTGGCACCTT
* * *
288888 CCAGTCCTCAAAGGGCAGGACACCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
60 -CAGTCCTCAAAGAGCAGGACACCTTCTCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
288945 CTTTTCAGTCCTCAAAGAGCAGGA
1 CTTTTTAGTCCTCAAAGAGCAGGA
288969 CACACTTCCT
Statistics
Matches: 129, Mismatches: 9, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
114 7 0.05
115 19 0.15
118 1 0.01
119 4 0.03
121 26 0.20
122 72 0.56
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (115 bp):
CTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCC
TCAAAGAGCAGGACACCTTCTCTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:288969 original size:61 final size:61
Alignment explanation
Indices: 288735--288971 Score: 302
Period size: 61 Copynumber: 3.9 Consensus size: 61
288725 AGCAGGATGC
* * * * *
288735 CTTTT-AAAGCCCACACAAGCTGGTGGCAC-CTTCAGTTCTCAAAGAGCAGGACGCCTTCT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTT
* * * **
288794 CTTTTTAAAGCCCATACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA-TGC-TTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTT
* * *
288853 CTTTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGGGCAGGACACCTTTT
1 C-TTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTT
*
288916 CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACAC
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACAC
288972 ACTTCCTTCC
Statistics
Matches: 152, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
59 8 0.05
60 27 0.18
61 108 0.71
62 5 0.03
63 4 0.03
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (61 bp):
CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTT
Found at i:289050 original size:42 final size:43
Alignment explanation
Indices: 288952--289055 Score: 149
Period size: 45 Copynumber: 2.4 Consensus size: 43
288942 GCACTTTTCA
*
288952 GTCCTCAAAGAGCAGGACACACTTCCTTCCCTTCTTTTCTCTTTT
1 GTCCTCAAAGAGCAGGACACACTTCATT--CTTCTTTTCTCTTTT
*
288997 GTCCTCAAAGAGCAGGACACACTTTATT-TTCCTTTT-TCTTTT
1 GTCCTCAAAGAGCAGGACACACTTCATTCTT-CTTTTCTCTTTT
289039 GTCCTCAAAGAGCAGGA
1 GTCCTCAAAGAGCAGGA
289056 TGTATTTCGT
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
42 25 0.45
43 5 0.09
45 26 0.46
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACACACTTCATTCTTCTTTTCTCTTTT
Found at i:289073 original size:42 final size:42
Alignment explanation
Indices: 288952--289089 Score: 152
Period size: 42 Copynumber: 3.2 Consensus size: 42
288942 GCACTTTTCA
** *
288952 GTCCTCAAAGAGCAGGACACACTTCCTTCCCTTCTTTTCTCTTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTCC--CTTTT-TCTTTT
*
288997 GTCCTCAAAGAGCAGGACACACTTTATTTTCCTTTTTCTTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTCCCTTTTTCTTTT
*** * *
289039 GTCCTCAAAGAGCAGGATGTA-TTTCGTTTCCCTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACACTTT-ATTTCCCTTTTTCTTTT
289081 GTCCTCAAA
1 GTCCTCAAA
289090 AAATAAGATG
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
41 3 0.04
42 47 0.57
43 5 0.06
45 27 0.33
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.40
Consensus pattern (42 bp):
GTCCTCAAAGAGCAGGACACACTTTATTTCCCTTTTTCTTTT
Found at i:289849 original size:13 final size:13
Alignment explanation
Indices: 289831--289856 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
289821 GCCAAGGAAA
289831 TGTATCGATACAT
1 TGTATCGATACAT
289844 TGTATCGATACAT
1 TGTATCGATACAT
289857 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:289922 original size:20 final size:20
Alignment explanation
Indices: 289897--289948 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
289887 TACCTAGATG
289897 TATCGATACATTTTGCATTA
1 TATCGATACATTTTGCATTA
*
289917 TATCGATACATTTTGCATTG
1 TATCGATACATTTTGCATTA
*
289937 TATCAATACATT
1 TATCGATACATT
289949 GCTCATTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (20 bp):
TATCGATACATTTTGCATTA
Found at i:289955 original size:20 final size:20
Alignment explanation
Indices: 289932--289969 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
289922 ATACATTTTG
289932 CATTGTATCAATACATTGCT
1 CATTGTATCAATACATTGCT
**
289952 CATTGTATTGATACATTG
1 CATTGTATCAATACATTG
289970 TATCGATACT
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:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (20 bp):
CATTGTATCAATACATTGCT
Found at i:289984 original size:33 final size:33
Alignment explanation
Indices: 289932--290001 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
289922 ATACATTTTG
* *
289932 CATTGTATCAATACATTGCTCATTGTATTGATA
1 CATTGTATCAATACATTGCTCATTCTATCGATA
* *
289965 CATTGTATCGATACTTTGCTCATTCTATCGATA
1 CATTGTATCAATACATTGCTCATTCTATCGATA
289998 CATT
1 CATT
290002 TTATAATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (33 bp):
CATTGTATCAATACATTGCTCATTCTATCGATA
Found at i:292554 original size:76 final size:75
Alignment explanation
Indices: 292428--292699 Score: 330
Period size: 76 Copynumber: 3.5 Consensus size: 75
292418 TACCGCAATC
* **
292428 GGGGATACTCTAACTCCAATTTTATTT-TCAAAACACCAATTTTTCATCAGGGATACTCCAACCC
1 GGGGATACTCCAAC-CCCGTTTTATTTCT-AAAACACCAATTTTTCATCAGGGATACTCCAACCC
* *
292492 CGTTATTTCCCA
64 CGTTATTTTCGA
* * *
292504 GGGGACACTACAACCCCAGTTTTATTTCTAAAACATCAATTTTTCATCAGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC-GTTTTATTTCTAAAACACCAATTTTTCATCAGGGATACTCCAACCCC
*
292569 GTCATTTTCGA
65 GTTATTTTCGA
* * * * *
292580 GGGGATACTCCAACCCCGGTTTTCTTTCTAAAACATCAATTTTTCATAATCGAAGAAACTCCAAC
1 GGGGATACTCCAACCCC-GTTTTATTTCTAAAACACCAATTTTTCATCA--G-GGATACTCCAAC
*
292645 CCCATTATTTTCGA
62 CCCGTTATTTTCGA
292659 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATT
1 GGGGATACTCCAACCCCG-TTTTATTTCTAAAACACCAATT
292700 CTCCACAATC
Statistics
Matches: 170, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
75 2 0.01
76 106 0.62
77 1 0.01
78 2 0.01
79 59 0.35
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (75 bp):
GGGGATACTCCAACCCCGTTTTATTTCTAAAACACCAATTTTTCATCAGGGATACTCCAACCCCG
TTATTTTCGA
Found at i:292733 original size:51 final size:51
Alignment explanation
Indices: 292661--292775 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 51
292651 ATTTTCGAGG
*
292661 GGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATCGA
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGA
* ** * * * *
292712 GGATATTCCAACTTCGATTTTATTTCCAAAACACTAATTTTTCACAATCGG
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGA
292763 GGATACTCCAACC
1 GGATACTCCAACC
292776 TAGTTATTTC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.30
Consensus pattern (51 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGA
Found at i:292794 original size:28 final size:29
Alignment explanation
Indices: 292758--292832 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 29
292748 ATTTTTCACA
* *
292758 ATCGGGGATACTCCAACCTAGTTATTT-C
1 ATCGGGGATACTCCAACCCAATTATTTCC
292786 ATCGGGGATACTCCAACCCAATTATTTCC
1 ATCGGGGATACTCCAACCCAATTATTTCC
* *
292815 A-AGAGGATACTCCAACCC
1 ATCGGGGATACTCCAACCC
292833 TGGCTTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 40 0.95
29 2 0.05
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCAATTATTTCC
Found at i:292867 original size:158 final size:158
Alignment explanation
Indices: 292637--292956 Score: 335
Period size: 158 Copynumber: 2.0 Consensus size: 158
292627 AATCGAAGAA
* * * * * *
292637 ACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCT
1 ACTCCAACCCAATTATTTCCAAGAGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTCT
** ** *
292702 CCACAATC-GAGGATA-TTCCAACTTCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGG
66 CCACAATCAG-GGATACTT-CAACCCCGACCTTATTTCCAAAACACTAATTTCTCACAATCGGGG
*
292765 ATACTCCAA-CCTAGTTA-TTTCATCGGGGAT
129 ATACTCCAACCCTA-TTATTTTCA-CAGGGAT
* * * ***
292795 ACTCCAACCCAATTATTTCCAAGAGGATACTCCAACCCTGGCTTTATTTCCAAAATATTGATT-T
1 ACTCCAACCCAATTATTTCCAAGAGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTCT
* * * * * * *
292859 CTCGCAATCAGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCATAATTGGGGA
66 C-CACAATCAGGGATACTTCAACCCCGACCTTATTTCCAAAACACTAATTTCTCACAATCGGGGA
292924 TACTCCAACCCTATTATTTTCACAGGGAT
130 TACTCCAACCCTATTATTTTCACAGGGAT
292953 ACTC
1 ACTC
292957 AAATCCCGAT
Statistics
Matches: 132, Mismatches: 25, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
157 2 0.02
158 118 0.89
159 12 0.09
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (158 bp):
ACTCCAACCCAATTATTTCCAAGAGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTCT
CCACAATCAGGGATACTTCAACCCCGACCTTATTTCCAAAACACTAATTTCTCACAATCGGGGAT
ACTCCAACCCTATTATTTTCACAGGGAT
Found at i:292883 original size:51 final size:51
Alignment explanation
Indices: 292819--292935 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 51
292809 ATTTCCAAGA
* * *
292819 GGATACTCCAACCCTGGCTTTATTTCCAAAATATTGATTTCTCGCAATCAG
1 GGATACTCCAACCCTGACCTTATTTCCAAAATATTGATTTCTCACAATCAG
* * * * **
292870 GGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCATAATTGG
1 GGATACTCCAACCCTGACCTTATTTCCAAAATATTGATTTCTCACAATCAG
292921 GGATACTCCAACCCT
1 GGATACTCCAACCCT
292936 ATTATTTTCA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (51 bp):
GGATACTCCAACCCTGACCTTATTTCCAAAATATTGATTTCTCACAATCAG
Found at i:294561 original size:13 final size:13
Alignment explanation
Indices: 294543--294568 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
294533 TGCACACAAG
294543 ATGTATCGATACA
1 ATGTATCGATACA
294556 ATGTATCGATACA
1 ATGTATCGATACA
294569 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:294584 original size:33 final size:32
Alignment explanation
Indices: 294525--294588 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
294515 CTTAAATGTT
* *
294525 TGTATCGATGCACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
294557 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
294589 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:300700 original size:21 final size:21
Alignment explanation
Indices: 300667--300711 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
300657 TTGCAAGTTG
*
300667 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
300689 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
300709 AAA
1 AAA
300712 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:302535 original size:15 final size:15
Alignment explanation
Indices: 302515--302553 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
302505 TAAAAATGTC
*
302515 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
302530 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
302545 CCAAATGAA
1 CAAAATGAA
302554 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:304623 original size:13 final size:13
Alignment explanation
Indices: 304605--304642 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
304595 GGAAATTCAA
304605 TGTATCGATACAT
1 TGTATCGATACAT
304618 TGTATCGATACAT
1 TGTATCGATACAT
304631 TGTATCGATACA
1 TGTATCGATACA
304643 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:307205 original size:13 final size:13
Alignment explanation
Indices: 307187--307212 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
307177 TACAGCAAGT
307187 ATGTATCGATACA
1 ATGTATCGATACA
307200 ATGTATCGATACA
1 ATGTATCGATACA
307213 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:310433 original size:8 final size:8
Alignment explanation
Indices: 310422--310447 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
310412 ATTTGTTTAA
310422 ATTTTGTG
1 ATTTTGTG
310430 ATTTTGTG
1 ATTTTGTG
310438 ATTTTGTG
1 ATTTTGTG
310446 AT
1 AT
310448 GAATGATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:310670 original size:13 final size:13
Alignment explanation
Indices: 310652--310687 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
310642 GCATTCTCTA
*
310652 TATCGATACATTG
1 TATCGATACAGTG
*
310665 TATCGATATAGTG
1 TATCGATACAGTG
310678 TATCGATACA
1 TATCGATACA
310688 AAAGGTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (13 bp):
TATCGATACAGTG
Found at i:311114 original size:32 final size:33
Alignment explanation
Indices: 311072--311135 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
311062 TAGCCAAACT
**
311072 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
*
311104 TGTATTGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
311136 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:311637 original size:34 final size:35
Alignment explanation
Indices: 311574--311640 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
311564 CTAAGTGATT
311574 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
311610 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
311641 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:314873 original size:13 final size:13
Alignment explanation
Indices: 314855--314879 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
314845 TTTTCCAGAT
314855 TGTATCGATACAA
1 TGTATCGATACAA
314868 TGTATCGATACA
1 TGTATCGATACA
314880 TTACTTCAGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:315729 original size:30 final size:32
Alignment explanation
Indices: 315693--315760 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 32
315683 GGGTGACAAC
** *
315693 GTATTAAGGGGGAGAGTTTGTATAAA-TTTT-
1 GTATTAAGGGGGAGAACTTGCATAAACTTTTG
315723 GTATTAAGGGGGAGAACTTGCATAAACTTTTG
1 GTATTAAGGGGGAGAACTTGCATAAACTTTTG
315755 GTATTA
1 GTATTA
315761 GTTGCATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 23 0.70
31 4 0.12
32 6 0.18
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.37
Consensus pattern (32 bp):
GTATTAAGGGGGAGAACTTGCATAAACTTTTG
Found at i:316890 original size:19 final size:17
Alignment explanation
Indices: 316866--316981 Score: 86
Period size: 20 Copynumber: 6.7 Consensus size: 17
316856 TAGCCAAACT
316866 TGTATCGATACACAAAGTA
1 TGTATCGATACACAAA--A
316885 TGTATCGAT--AC--AA
1 TGTATCGATACACAAAA
316898 TGTATCGATACACAAATTA
1 TGTATCGATACACAAA--A
316917 TGTATCGAT--AC--AA
1 TGTATCGATACACAAAA
316930 TGTATCGATACACAAAAAA
1 TGTATCGATACAC--AAAA
316949 TTGTATCGATACACAAAAAA
1 -TGTATCGATACAC--AAAA
316969 TTGTATCGATACA
1 -TGTATCGATACA
316982 TTGGCTTGTA
Statistics
Matches: 84, Mismatches: 0, Indels: 25
0.77 0.00 0.23
Matches are distributed among these distances:
13 20 0.24
15 6 0.07
17 5 0.06
19 21 0.25
20 32 0.38
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (17 bp):
TGTATCGATACACAAAA
Found at i:316902 original size:13 final size:13
Alignment explanation
Indices: 316884--316941 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
316874 TACACAAAGT
316884 ATGTATCGATACA
1 ATGTATCGATACA
316897 ATGTATCGATACACAAA
1 ATGTATCGAT--AC--A
316914 TTATGTATCGATACA
1 --ATGTATCGATACA
316929 ATGTATCGATACA
1 ATGTATCGATACA
316942 CAAAAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.59
15 3 0.08
17 3 0.08
19 10 0.26
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:316907 original size:32 final size:32
Alignment explanation
Indices: 316866--316961 Score: 156
Period size: 32 Copynumber: 3.0 Consensus size: 32
316856 TAGCCAAACT
*
316866 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAATATGTATCGATACAA
*
316898 TGTATCGATACACAAATTATGTATCGATACAA
1 TGTATCGATACACAAAATATGTATCGATACAA
*
316930 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAATA-TGTATCGATACA
316962 CAAAAAATTG
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 48 0.80
33 12 0.20
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAATATGTATCGATACAA
Found at i:316955 original size:20 final size:20
Alignment explanation
Indices: 316930--316981 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
316920 ATCGATACAA
316930 TGTATCGATACACAAAAAAT
1 TGTATCGATACACAAAAAAT
316950 TGTATCGATACACAAAAAAT
1 TGTATCGATACACAAAAAAT
316970 TGTATCGATACA
1 TGTATCGATACA
316982 TTGGCTTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACAAAAAAT
Found at i:317483 original size:34 final size:35
Alignment explanation
Indices: 317420--317486 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 35
317410 CTAAGTGATT
317420 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
*
317456 GAGAGGTTTTTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
317487 TGTTGTAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 8 0.28
36 9 0.31
37 12 0.41
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:319664 original size:20 final size:20
Alignment explanation
Indices: 319639--319690 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
319629 ATATATCAAA
319639 GTATCGATACATAGGTATTT
1 GTATCGATACATAGGTATTT
319659 GTATCGATACATAGGTATTT
1 GTATCGATACATAGGTATTT
319679 GTATCGATACAT
1 GTATCGATACAT
319691 TAAGGTTGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (20 bp):
GTATCGATACATAGGTATTT
Found at i:319870 original size:13 final size:13
Alignment explanation
Indices: 319852--319890 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
319842 TACACAAAGT
319852 ATGTATCGATACA
1 ATGTATCGATACA
319865 ATGTATCGATACA
1 ATGTATCGATACA
319878 ATGTATCGATACA
1 ATGTATCGATACA
319891 TTGGCTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:327733 original size:38 final size:37
Alignment explanation
Indices: 327663--327735 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
327653 GAGATTTTTT
*
327663 TTAAAAGGGGTAGAATGCTGAATTTGCTAAAATTACC
1 TTAAAAGGGGGAGAATGCTGAATTTGCTAAAATTACC
*
327700 TTAAAAGGGGGAGAATG-TACGAATTTGTTAAAATTA
1 TTAAAAGGGGGAGAATGCT--GAATTTGCTAAAATTA
327736 TTTTGATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 1 0.03
37 16 0.50
38 15 0.47
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (37 bp):
TTAAAAGGGGGAGAATGCTGAATTTGCTAAAATTACC
Found at i:328412 original size:13 final size:13
Alignment explanation
Indices: 328394--328419 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
328384 TACACAAAGT
328394 ATGTATCGATACA
1 ATGTATCGATACA
328407 ATGTATCGATACA
1 ATGTATCGATACA
328420 CCAAAAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:328417 original size:32 final size:33
Alignment explanation
Indices: 328376--328440 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
328366 TAGCCAAACT
328376 TGTATCGATACA-C-AAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAGT-TGTATCGATACAA
328408 TGTATCGATACACCAAAAAGTTGTATCGATACA
1 TGTATCGATACACC-AAAAGTTGTATCGATACA
328441 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 12 0.40
33 1 0.03
34 12 0.40
35 5 0.17
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAGTTGTATCGATACAA
Found at i:329242 original size:16 final size:16
Alignment explanation
Indices: 329217--329249 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
329207 ATTGCCTTTC
329217 TTATAAAAT-ATTAAT
1 TTATAAAATAATTAAT
329232 TTATGAAAATAATTAAT
1 TTAT-AAAATAATTAAT
329249 T
1 T
329250 ATCTCTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 5 0.31
17 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTATAAAATAATTAAT
Found at i:329396 original size:21 final size:22
Alignment explanation
Indices: 329356--329400 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
329346 CGAAATTGTT
329356 AAATTATTTTATTAAGGGGGAG
1 AAATTATTTTATTAAGGGGGAG
329378 AAATT-TTTTGATTAAGGGGGAG
1 AAATTATTTT-ATTAAGGGGGAG
329400 A
1 A
329401 GAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (22 bp):
AAATTATTTTATTAAGGGGGAG
Found at i:329974 original size:13 final size:13
Alignment explanation
Indices: 329956--329980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
329946 AGATTTCACA
329956 GTATCGATACATT
1 GTATCGATACATT
329969 GTATCGATACAT
1 GTATCGATACAT
329981 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:330077 original size:13 final size:13
Alignment explanation
Indices: 330059--330084 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
330049 TACACACAAG
330059 ATGTATCGATACA
1 ATGTATCGATACA
330072 ATGTATCGATACA
1 ATGTATCGATACA
330085 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:330101 original size:33 final size:32
Alignment explanation
Indices: 330041--330104 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
330031 CTTAACTGTT
*
330041 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
330073 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
330105 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:331939 original size:20 final size:21
Alignment explanation
Indices: 331897--331943 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
331887 TTCAACAATT
331897 TGTATCGATACAATAAGACAA
1 TGTATCGATACAATAAGACAA
**
331918 TGTATCGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGACAA
331938 TGTATC
1 TGTATC
331944 AATATATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACAATAAGACAA
Found at i:332045 original size:20 final size:21
Alignment explanation
Indices: 331994--332049 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
331984 TTCTGGAAGC
*
331994 AAATTGTATCAATACATTTAAA
1 AAATTGTATCGATACA-TTAAA
* *
332016 AAAATGTATCGATACA-TAAG
1 AAATTGTATCGATACATTAAA
332036 AAATTGTATCGATA
1 AAATTGTATCGATA
332050 TATTTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 16 0.53
22 14 0.47
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (21 bp):
AAATTGTATCGATACATTAAA
Found at i:337174 original size:45 final size:45
Alignment explanation
Indices: 337110--337206 Score: 185
Period size: 45 Copynumber: 2.1 Consensus size: 45
337100 TTGGCATAAT
337110 TTTCAAACGTGTATATTCGGGTATCATTTCATGATCTTACCATTA
1 TTTCAAACGTGTATATTCGGGTATCATTTCATGATCTTACCATTA
337155 TTTCAAACGTGTATATTCGGGTATCATTTCATGATCTTACCATTA
1 TTTCAAACGTGTATATTCGGGTATCATTTCATGATCTTACCATTA
337200 TGTTCAA
1 T-TTCAA
337207 GCTCGTGTCG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 46 0.90
46 5 0.10
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (45 bp):
TTTCAAACGTGTATATTCGGGTATCATTTCATGATCTTACCATTA
Found at i:339096 original size:21 final size:21
Alignment explanation
Indices: 339072--339118 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
339062 TTTGATGCTG
339072 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
339092 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
339113 ATTTTG
1 ATTTTG
339119 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:339257 original size:13 final size:13
Alignment explanation
Indices: 339239--339277 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
339229 ATAATCACCC
*
339239 TGTATCGATACAG
1 TGTATCGATACAA
*
339252 TGTATCGATATAA
1 TGTATCGATACAA
339265 TGTATCGATACAA
1 TGTATCGATACAA
339278 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:339288 original size:20 final size:20
Alignment explanation
Indices: 339263--339341 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
339253 GTATCGATAT
339263 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
339283 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
339308 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
339328 CATGTATCGATACA
1 AATGTATCGATACA
339342 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:341376 original size:15 final size:15
Alignment explanation
Indices: 341356--341386 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
341346 ATTTCGTTTG
*
341356 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
341371 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
341386 G
1 G
341387 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:343219 original size:21 final size:21
Alignment explanation
Indices: 343190--343234 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
343180 AAGTTTTCAT
*
343190 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
343210 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
343232 TTT
1 TTT
343235 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:345469 original size:13 final size:13
Alignment explanation
Indices: 345451--345476 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
345441 CAATTTTTTG
345451 TGTATCGATACAT
1 TGTATCGATACAT
345464 TGTATCGATACAT
1 TGTATCGATACAT
345477 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:347833 original size:79 final size:77
Alignment explanation
Indices: 347743--348394 Score: 684
Period size: 79 Copynumber: 8.3 Consensus size: 77
347733 ATTCATGTTT
*
347743 TTATTTCCGAGGGGATACTCCAACTCCGGTTTTATTTCCAAAACACCAATTTTTCACAGTCG-GC
1 TTATTT-CGAGGGGATACTCCAAC-CCGGTTTTATTTCCAAAACACCAATTTTTCACAATCGAG-
**
347807 GATACTCCAACCCTT
63 GATACTCCAACCCCG
** * *
347822 TTATCTTCGAGGGGATACTTTAACCCTGATTTTATTTCTAAAACACCAATTTTTCACAATCGAGG
1 TTAT-TTCGAGGGGATACTCCAACCC-GGTTTTATTTCCAAAACACCAATTTTTCACAATCGAGG
347887 ATACTCCAACCCCG
64 ATACTCCAACCCCG
* *
347901 TTATTTCTAAGGGGATACTCAAACCCCGG-TTTATTTCCAAAACACCAATTTTTCACAATCGAGG
1 TTATTTC-GAGGGGATACTCCAA-CCCGGTTTTATTTCCAAAACACCAATTTTTCACAATCGAGG
* *
347965 ATACTCTAATCCCG
64 ATACTCCAACCCCG
* * * *
347979 TTATTTTTGAGGGGATACTCCAACCTCGGTTTTATTTCCAAAATAGCAATTTTTCATAATC-AGA
1 TTA-TTTCGAGGGGATACTCCAACC-CGGTTTTATTTCCAAAACACCAATTTTTCACAATCGAG-
* *
348043 TATAATCCAACCCCG
63 GATACTCCAACCCCG
* * *
348058 TTATTTTCGAGGGGCTAATCCAACTCCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGAGG
1 TTA-TTTCGAGGGGATACTCCAAC-CCGGTTTTATTTCCAAAACACCAATTTTTCACAATCGAGG
* **
348123 GTACTCCAACCCTT
64 ATACTCCAACCCCG
* * * *
348137 TTATTTCTGAGGGAACACTCCAACCCCAGTTTTATTTCC-AAACTACCAATTTTTCACAATTGAG
1 TTATTTC-GAGGGGATACTCCAA-CCCGGTTTTATTTCCAAAAC-ACCAATTTTTCACAATCGAG
*
348201 GATACTCCAACCCCA
63 GATACTCCAACCCCG
* * *
348216 TTATTTCTGAGGGGATACTCCAGCCCTGGTTTTATTTTCAAAACACCAA-TTTTCGACAATCGGG
1 TTATTTC-GAGGGGATACTCCAACCC-GGTTTTATTTCCAAAACACCAATTTTTC-ACAATCGAG
*
348280 GATACTCTAACCCCG
63 GATACTCCAACCCCG
* * * * * * * * *
348295 TTATTTTCGAGGGAAAACTCCAACCCCGATTTTATTTTCAAAACATCAATTTTCCACCATTGGGG
1 TTA-TTTCGAGGGGATACTCCAA-CCCGGTTTTATTTCCAAAACACCAATTTTTCACAATCGAGG
* *
348360 ATACTCGAACCTCG
64 ATACTCCAACCCCG
*
348374 TTATTTCTGAGGGGGTACTCC
1 TTATTTC-GAGGGGATACTCC
348395 CATCCCATTT
Statistics
Matches: 484, Mismatches: 68, Indels: 42
0.81 0.11 0.07
Matches are distributed among these distances:
77 2 0.00
78 92 0.19
79 365 0.75
80 25 0.05
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (77 bp):
TTATTTCGAGGGGATACTCCAACCCGGTTTTATTTCCAAAACACCAATTTTTCACAATCGAGGAT
ACTCCAACCCCG
Found at i:348294 original size:237 final size:234
Alignment explanation
Indices: 347743--348386 Score: 735
Period size: 236 Copynumber: 2.7 Consensus size: 234
347733 ATTCATGTTT
* * *
347743 TTATTTCCGAGGGGATACTCCAACTCC-GGTTTTATTTCCAAAACACCAATTTTTCACAGTCGGC
1 TTATTTCTGAGGGGATACTCC-AC-CCTGGTTTTATTTCCAAAACACCAATTTTTCACAATCGGA
** * * ** * *
347807 GATACTCCAACCCTTTTATCTTCGAGGGGATACTTTAACCCTGATTTTATTTCTAAAACACCAAT
64 GATACTCCAACCCCGTTATTTTCGAGGGGATAATCCAACCC-GATTTTATTTCCAAAACACTAAT
* * * * *
347872 TTTTCACAATCGAGGATACTCCAACCCCGTTATTTCTAAGGGGATACTCAAACCCCGGTTTATTT
128 TTTTCACAATCGAGGGTACTCCAACCCTGTTATTTCTGAGGGAACACTCAAACCCCGGTTTATTT
* * *
347937 CCAAAACACCAATTTTTCACAATCGAGGATACTCTAATCCCG
193 CCAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCA
* * * * * * *
347979 TTATTTTTGAGGGGATACTCCAACCTCGGTTTTATTTCCAAAATAGCAATTTTTCATAATCAGAT
1 TTATTTCTGAGGGGATACTCCACCCT-GGTTTTATTTCCAAAACACCAATTTTTCACAATCGGAG
* * *
348044 ATAATCCAACCCCGTTATTTTCGAGGGGCTAATCCAACTCCGGTTTTATTTCCAAAACACTAATT
65 ATACTCCAACCCCGTTATTTTCGAGGGGATAATCCAAC-CCGATTTTATTTCCAAAACACTAATT
* * *
348109 TTTCACAATCGAGGGTACTCCAACCCTTTTATTTCTGAGGGAACACTCCAACCCCAGTTTTATTT
129 TTTCACAATCGAGGGTACTCCAACCCTGTTATTTCTGAGGGAACACTCAAACCCC-GGTTTATTT
*
348174 CC-AAACTACCAATTTTTCACAATTGAGGATACTCCAACCCCA
193 CCAAAAC-ACCAATTTTTCACAATCGAGGATACTCCAACCCCA
* *
348216 TTATTTCTGAGGGGATACTCCAGCCCTGGTTTTATTTTCAAAACACCAA-TTTTCGACAATCGGG
1 TTATTTCTGAGGGGATACTCCA-CCCTGGTTTTATTTCCAAAACACCAATTTTTC-ACAATCGGA
* * *
348280 GATACTCTAACCCCGTTATTTTCGA-GGGAAAACTCCAACCCCGATTTTATTTTCAAAACA-TCA
64 GATACTCCAACCCCGTTATTTTCGAGGGGATAA-TCCAA-CCCGATTTTATTTCCAAAACACT-A
* * * *
348343 ATTTTCCACCATTG-GGGATACTCGAA-CCTCGTTATTTCTGAGGG
126 ATTTTTCACAATCGAGGG-TACTCCAACCCT-GTTATTTCTGAGGG
348387 GGTACTCCCA
Statistics
Matches: 343, Mismatches: 53, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
234 2 0.01
235 1 0.00
236 170 0.50
237 166 0.48
238 4 0.01
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (234 bp):
TTATTTCTGAGGGGATACTCCACCCTGGTTTTATTTCCAAAACACCAATTTTTCACAATCGGAGA
TACTCCAACCCCGTTATTTTCGAGGGGATAATCCAACCCGATTTTATTTCCAAAACACTAATTTT
TCACAATCGAGGGTACTCCAACCCTGTTATTTCTGAGGGAACACTCAAACCCCGGTTTATTTCCA
AAACACCAATTTTTCACAATCGAGGATACTCCAACCCCA
Found at i:350503 original size:77 final size:77
Alignment explanation
Indices: 350343--350650 Score: 266
Period size: 77 Copynumber: 4.0 Consensus size: 77
350333 ACTATTATCA
* * ** * *
350343 AAATAACCCTAATGGACATGTTTTGACAC-GAAGATTCTTACAGGATCCT-AGACTTGATTTTAA
1 AAATAACCCCAATGGACATGTTTTGACACAAAAG-TTCCCACATGATCCTAAGACTTGGTTTTAA
* ** *
350406 GGTACCATTACCG
65 GATAGTATTACCT
* *
350419 AAATAACCCCAATGGACATGCTTTGACACAAAAGTTCACACATGATCCTAAGACTTGGTTTTAAG
1 AAATAACCCCAATGGACATGTTTTGACACAAAAGTTCCCACATGATCCTAAGACTTGGTTTTAAG
*
350484 ATAGTATTACTT
66 ATAGTATTACCT
* * * * * *
350496 AAATAACCCCAATAGACATGTTTTGGCATAAAGGTTCCCACAT-AACCTAAGGATTTGGTTTTAA
1 AAATAACCCCAATGGACATGTTTTGACACAAAAGTTCCCACATGATCCTAA-GACTTGGTTTTAA
* *
350560 GGT-GCTTTTACCT
65 GATAG-TATTACCT
* * ** * * * * *
350573 AAATGATCTTAATGGACATATTTTGACATAAAGGTTCCCACATGATCCTAAAAACTTAGTTTTAA
1 AAATAACCCCAATGGACATGTTTTGACACAAAAGTTCCCACATGATCCT-AAGACTTGGTTTTAA
350638 GATA-TATTTACCT
65 GATAGTA-TTACCT
350651 TGATGATCCT
Statistics
Matches: 188, Mismatches: 36, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
76 46 0.24
77 118 0.63
78 22 0.12
79 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (77 bp):
AAATAACCCCAATGGACATGTTTTGACACAAAAGTTCCCACATGATCCTAAGACTTGGTTTTAAG
ATAGTATTACCT
Found at i:350835 original size:58 final size:58
Alignment explanation
Indices: 350686--351022 Score: 220
Period size: 58 Copynumber: 5.8 Consensus size: 58
350676 CATATATGGT
* * * * * * * * * * *
350686 CCTAAATCATCAGAAATTACTTAGATGATCTTAAATTGTATAAAATTGCATAAATGGT-
1 CCTAAATCATAAAAAATGACTAAAATGATCCTAAAATGCATGAAATTACAT-AATGATC
* * * * **
350744 CCTAATTCATAAAAAAAT-ACTAAAATAACCCTAAAATGCATGAATTTGGATAATGATC
1 CCTAAATCAT-AAAAAATGACTAAAATGATCCTAAAATGCATGAAATTACATAATGATC
*
350802 CCTAAATCATAAAAAATGATTAAAATGATCCTAAAATGCATGAAATTACATAATTG-TC
1 CCTAAATCATAAAAAATGACTAAAATGATCCTAAAATGCATGAAATTACATAA-TGATC
** * * * * * *
350860 CCTAAATCATGCAAAATGACAAAAAT-AACCTTTAAATGGATGAATTTGCATAAT-AGTC
1 CCTAAATCATAAAAAATGACTAAAATGATCC-TAAAATGCATGAAATTACATAATGA-TC
* ** * * * *
350918 TCTAAATGCATTGAAAAT-ACCTAAAATGGTTCTAAAATGCATGAAATTATATAATTATC
1 CCTAAAT-CATAAAAAATGA-CTAAAATGATCCTAAAATGCATGAAATTACATAATGATC
* * * *
350977 CCTAATTCATGAAAAATGACTAAAATGAT-ATAAAAATGAATGAAAT
1 CCTAAATCATAAAAAATGACTAAAATGATCCT-AAAATGCATGAAAT
351023 AACACAAAAG
Statistics
Matches: 217, Mismatches: 49, Indels: 26
0.74 0.17 0.09
Matches are distributed among these distances:
57 17 0.08
58 151 0.70
59 47 0.22
60 2 0.01
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (58 bp):
CCTAAATCATAAAAAATGACTAAAATGATCCTAAAATGCATGAAATTACATAATGATC
Found at i:350979 original size:117 final size:116
Alignment explanation
Indices: 350756--351002 Score: 311
Period size: 117 Copynumber: 2.1 Consensus size: 116
350746 TAATTCATAA
*
350756 AAAAAT-ACTAAAATAACCCTAAAATGCATGAATTTGGATAATGATCCCTAAATCATAAAAAATG
1 AAAAATGACTAAAATAACCCTAAAATGCATGAATTTGCATAATGATCCCTAAATCATAAAAAATG
* *
350820 ATTAAAATGATCCTAAAATGCATGAAATTACATAATTGTCCCTAAATCATG
66 ACTAAAATGATCCTAAAATGCATGAAATTACATAATTATCCCTAAATCATG
* * * * * * **
350871 CAAAATGACAAAAATAACCTTTAAATGGATGAATTTGCATAAT-AGTCTCTAAATGCATTGAAAA
1 AAAAATGACTAAAATAACCCTAAAATGCATGAATTTGCATAATGA-TCCCTAAAT-CATAAAAAA
* * * *
350935 T-ACCTAAAATGGTTCTAAAATGCATGAAATTATATAATTATCCCTAATTCATG
64 TGA-CTAAAATGATCCTAAAATGCATGAAATTACATAATTATCCCTAAATCATG
350988 AAAAATGACTAAAAT
1 AAAAATGACTAAAAT
351003 GATATAAAAA
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
115 6 0.05
116 40 0.36
117 65 0.59
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (116 bp):
AAAAATGACTAAAATAACCCTAAAATGCATGAATTTGCATAATGATCCCTAAATCATAAAAAATG
ACTAAAATGATCCTAAAATGCATGAAATTACATAATTATCCCTAAATCATG
Found at i:351035 original size:117 final size:117
Alignment explanation
Indices: 350822--351039 Score: 274
Period size: 117 Copynumber: 1.9 Consensus size: 117
350812 AAAAAATGAT
* *
350822 TAAAATGATCCTAAAATGCATGAAATTACATAATTGTCCCTAAATCATGCAAAATGACAAAAATA
1 TAAAATGATCCTAAAATGCATGAAATTACATAATTATCCCTAAATCATGAAAAATGACAAAAATA
* ** * * ** * *
350887 ACCTTTAAATGGATGAATTTGCATAATAGTCTCTAAATGCATTGAAAATACC
66 ACATAAAAATGAATGAAATAACACAAAAGTCTCTAAATGCATTGAAAATACC
* * * * * *
350939 TAAAATGGTTCTAAAATGCATGAAATTATATAATTATCCCTAATTCATGAAAAATGACTAAAATG
1 TAAAATGATCCTAAAATGCATGAAATTACATAATTATCCCTAAATCATGAAAAATGACAAAAATA
*
351004 ATATAAAAATGAATGAAATAACACAAAAGTCTCTAA
66 ACATAAAAATGAATGAAATAACACAAAAGTCTCTAA
351040 GTAATGATAA
Statistics
Matches: 83, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
117 83 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (117 bp):
TAAAATGATCCTAAAATGCATGAAATTACATAATTATCCCTAAATCATGAAAAATGACAAAAATA
ACATAAAAATGAATGAAATAACACAAAAGTCTCTAAATGCATTGAAAATACC
Found at i:351076 original size:10 final size:10
Alignment explanation
Indices: 351048--351080 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
351038 AAGTAATGAT
351048 AAATGACATA
1 AAATGACATA
351058 CAAAT-ACATA
1 -AAATGACATA
351068 AAATGACATA
1 AAATGACATA
351078 AAA
1 AAA
351081 ATCCCTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.19
10 13 0.62
11 4 0.19
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (10 bp):
AAATGACATA
Found at i:355152 original size:20 final size:20
Alignment explanation
Indices: 355127--355202 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
355117 AAAAACCCAG
355127 AATGTATCGATACAATGAGA
1 AATGTATCGATACAATGAGA
*
355147 AATGTATCAATACAATTGTA-A
1 AATGTATCGATACAA-TG-AGA
* * * *
355168 GTATGTATCGATACATTTAGT
1 -AATGTATCGATACAATGAGA
*
355189 AATGTATTGATACA
1 AATGTATCGATACA
355203 TTTCCTTGGC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
20 27 0.61
21 4 0.09
22 13 0.30
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:355247 original size:13 final size:13
Alignment explanation
Indices: 355229--355254 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
355219 CAGGGTAGTT
355229 TTGTATCGATACA
1 TTGTATCGATACA
355242 TTGTATCGATACA
1 TTGTATCGATACA
355255 AAACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:355759 original size:16 final size:15
Alignment explanation
Indices: 355731--355778 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
355721 AGAGCTATCA
355731 TTCTTTT-TCTTTTACT
1 TTCTTTTAT-TTTT-CT
355747 TTCTTTTATTTTTCT
1 TTCTTTTATTTTTCT
* *
355762 CTCTTTTATTGTTCT
1 TTCTTTTATTTTTCT
355777 TT
1 TT
355779 AGTTTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 16 0.57
16 11 0.39
17 1 0.04
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTATTTTTCT
Found at i:358481 original size:58 final size:58
Alignment explanation
Indices: 358411--358663 Score: 174
Period size: 58 Copynumber: 4.4 Consensus size: 58
358401 TGTGCACATT
*
358411 TAGGGT-TATTTTAGTAATTTTATACATTTTAAGGCCATTTAGGTTATTTTAAATAACC
1 TAGGGTCT-TTTTAGCAATTTTATACATTTTAAGGCCATTTAGGTTATTTTAAATAACC
* * * * * * **
358469 TAGGGTCTTTTTAGAAAATTTCATACA-TTTAGGGTCATTAAGGGTA-TTTAACATATTC
1 TAGGGTCTTTTTAG-CAATTTTATACATTTTAAGGCCATTTAGGTTATTTTAA-ATAACC
* * ** *
358527 TAGGGTCTTTTTAGCAATTTCCATGCATTTTAAGGTTATTTAGG-TAATTTAAATAACC
1 TAGGGTCTTTTTAGCAATTT-TATACATTTTAAGGCCATTTAGGTTATTTTAAATAACC
* ** * * * * * * **
358585 TAAGGTCAGTTTAGCAATTTTCAT-GATTTTATGACCACTTAGGTAATTTTACATAATT
1 TAGGGTCTTTTTAGCAATTTT-ATACATTTTAAGGCCATTTAGGTTATTTTAAATAACC
** *
358643 TAGGGTCACTTTAGTAATTTT
1 TAGGGTCTTTTTAGCAATTTT
358664 TTTGCCTTAA
Statistics
Matches: 154, Mismatches: 33, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
57 23 0.15
58 102 0.66
59 29 0.19
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (58 bp):
TAGGGTCTTTTTAGCAATTTTATACATTTTAAGGCCATTTAGGTTATTTTAAATAACC
Found at i:358815 original size:80 final size:79
Alignment explanation
Indices: 358716--358863 Score: 208
Period size: 80 Copynumber: 1.9 Consensus size: 79
358706 GCATTAAGGT
*
358716 CATTTTAGTAAGTTTCATGAAAAATTCAAGTCCGTT-GAAGCATGTTGGCATTATTCACAATAAG
1 CATTTTAGTAAGTTCCATGAAAAATTCAAGTCC-TTAGAAGCATGTTGGCATT-TTCACAATAAG
358780 ACATGGACATTGAAGC
64 ACATGGACATTGAAGC
* ** * * *
358796 CATTTTAGTGAGTTCCATGAAAAATTTGAGTCCTTAGGAGCATGTTGGTATTTTCACATTAAGAC
1 CATTTTAGTAAGTTCCATGAAAAATTCAAGTCCTTAGAAGCATGTTGGCATTTTCACAATAAGAC
358861 ATG
66 ATG
358864 TATATTAGGT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
79 17 0.28
80 43 0.72
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (79 bp):
CATTTTAGTAAGTTCCATGAAAAATTCAAGTCCTTAGAAGCATGTTGGCATTTTCACAATAAGAC
ATGGACATTGAAGC
Found at i:362199 original size:24 final size:24
Alignment explanation
Indices: 362167--362238 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
362157 AACACGTGTT
362167 TCATTATGTCGATTAAGATGAAGA
1 TCATTATGTCGATTAAGATGAAGA
362191 TCATTATGTCGATTAAGATGAAGA
1 TCATTATGTCGATTAAGATGAAGA
362215 TCATTATGTCGATTAAGATGAAGA
1 TCATTATGTCGATTAAGATGAAGA
362239 GATACTTACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (24 bp):
TCATTATGTCGATTAAGATGAAGA
Found at i:370026 original size:21 final size:21
Alignment explanation
Indices: 370000--370055 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
369990 ATGGATATGT
*
370000 ACCCTAAACCTTAATTATTAA
1 ACCCTAAACCTTAAATATTAA
*
370021 ACCCTAAA-CTCTAAATCTTAA
1 ACCCTAAACCT-TAAATATTAA
*
370042 ACCCTAAACTTTAA
1 ACCCTAAACCTTAA
370056 GCTCAAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 27 0.90
22 1 0.03
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (21 bp):
ACCCTAAACCTTAAATATTAA
Found at i:377980 original size:13 final size:13
Alignment explanation
Indices: 377959--377989 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
377949 CGATACATGG
*
377959 TACAATGTATCGA
1 TACATTGTATCGA
377972 TACATTGTATCGA
1 TACATTGTATCGA
377985 TACAT
1 TACAT
377990 AATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:377985 original size:33 final size:33
Alignment explanation
Indices: 377943--378011 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
377933 CTACCACTAT
**
377943 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATAATGA-AATGTATCGATACA
*
377976 TTGTATCGATACATAATGAATTGTATCGATACA
1 TTGTATCGATACATAATGAAATGTATCGATACA
378009 TTG
1 TTG
378012 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATAATGAAATGTATCGATACA
Found at i:378999 original size:118 final size:118
Alignment explanation
Indices: 378819--379053 Score: 326
Period size: 118 Copynumber: 2.0 Consensus size: 118
378809 ATACATATCA
* * *
378819 AACCAAAATCCCTATTGAGGATTATTTTTTAGTTGGGCCCACTTCATCAACGATGACAGTTATGA
1 AACCAAAATCCCTATCGAGGATTATTTTTTAGTTGGGCCCACTTCATCAACGATAACAGTTATAA
*
378884 CAAATTGCAATTTTAATAATGTGATAATCTAAAATTAAAAGTCTTTGCTCATC
66 CAAATTACAATTTTAATAATGTGATAATCTAAAATTAAAAGTCTTTGCTCATC
* ** * * * **
378937 AACCAAAATCCCTATCGAGGATTCTTTTTTAGTTGGGTGCACTTCGTCGATGATAATTGTTATAA
1 AACCAAAATCCCTATCGAGGATTATTTTTTAGTTGGGCCCACTTCATCAACGATAACAGTTATAA
* * * *
379002 CAAATTACAATTTTAATTATGTGATAATCTAAAGTTAAAATTGTTTGCTCAT
66 CAAATTACAATTTTAATAATGTGATAATCTAAAATTAAAAGTCTTTGCTCAT
379054 TGAGTAGTTT
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
118 101 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (118 bp):
AACCAAAATCCCTATCGAGGATTATTTTTTAGTTGGGCCCACTTCATCAACGATAACAGTTATAA
CAAATTACAATTTTAATAATGTGATAATCTAAAATTAAAAGTCTTTGCTCATC
Found at i:380015 original size:16 final size:16
Alignment explanation
Indices: 379996--380038 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
379986 GTTTTTACAT
379996 TTTTAAATTTTTATTA
1 TTTTAAATTTTTATTA
* * *
380012 TTTTAAATATATATTT
1 TTTTAAATTTTTATTA
*
380028 TTTTACATTTT
1 TTTTAAATTTT
380039 AACTCTTCAC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAAATTTTTATTA
Found at i:381875 original size:18 final size:18
Alignment explanation
Indices: 381834--381875 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
381824 ATATAATTTT
* *
381834 TTAAAAAATTTTTAAATA
1 TTAAAAAATTTTAAAAAA
381852 TATAAAAAATTTTAAAAAA
1 T-TAAAAAATTTTAAAAAA
381871 TTAAA
1 TTAAA
381876 TATATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAAAAATTTTAAAAAA
Found at i:382390 original size:20 final size:19
Alignment explanation
Indices: 382359--382397 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
382349 AGATTTAATA
382359 ATTTATATATTTATATTAT
1 ATTTATATATTTATATTAT
*
382378 ATTTATAATATTTTTATTAT
1 ATTTAT-ATATTTATATTAT
382398 TAAAATTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTATATATTTATATTAT
Found at i:382477 original size:8 final size:8
Alignment explanation
Indices: 382469--382504 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
382459 TTATATAATT
*
382469 TTTTTATT
1 TTTTTATA
382477 TTTATTATA
1 TTT-TTATA
382486 TTTTTATA
1 TTTTTATA
382494 TTTTTATA
1 TTTTTATA
382502 TTT
1 TTT
382505 CATTCGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTATA
Found at i:382480 original size:19 final size:20
Alignment explanation
Indices: 382453--382502 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
382443 AATATTTGTA
*
382453 TTATATTTATATA-ATTTTT
1 TTATTTTTATATATATTTTT
382472 TTATTTTTAT-TATATTTTT
1 TTATTTTTATATATATTTTT
*
382491 ATATTTTTATAT
1 TTATTTTTATAT
382503 TTCATTCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 24 0.89
20 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTTTTATATATATTTTT
Found at i:382482 original size:28 final size:27
Alignment explanation
Indices: 382444--382504 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
382434 ATAAATATTA
382444 ATATTTGTATTATATTTATATAATTTTT
1 ATATTTGTATTATATTTATAT-ATTTTT
* * *
382472 TTATTTTTATTATATTTTTATATTTTT
1 ATATTTGTATTATATTTATATATTTTT
382499 ATATTT
1 ATATTT
382505 CATTCGTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (27 bp):
ATATTTGTATTATATTTATATATTTTT
Found at i:382500 original size:16 final size:17
Alignment explanation
Indices: 382453--382504 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
382443 AATATTTGTA
*
382453 TTATATTTATATAATTTTT
1 TTATATTTAT-T-ATATTT
*
382472 TTATTTTTATTATATTT
1 TTATATTTATTATATTT
382489 TTATATTT-TTATATTT
1 TTATATTTATTATATTT
382505 CATTCGTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 8 0.27
17 12 0.40
18 1 0.03
19 9 0.30
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATATTTATTATATTT
Found at i:382827 original size:17 final size:17
Alignment explanation
Indices: 382805--382839 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
382795 TTTTATTATT
*
382805 AAAAATAATTTGAATCA
1 AAAAATAATTTCAATCA
382822 AAAAATAATTTCAATCA
1 AAAAATAATTTCAATCA
382839 A
1 A
382840 GTGAATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAAATAATTTCAATCA
Found at i:384522 original size:51 final size:51
Alignment explanation
Indices: 384446--384567 Score: 160
Period size: 52 Copynumber: 2.4 Consensus size: 51
384436 ACTCCAACTA
384446 TAAAATAATAAAAAATTTAAAAATA-TTTATATTAAA-TCTAAAATTA-TCATT
1 TAAAATAAT-AAAAATTTAAAAATATTTTATATTAAACT-TAAAATTACT-ATT
**
384497 TAAAACTAATAAAAATTTAAAAATATTTTATATTAAACTTTGAATTACTATT
1 TAAAA-TAATAAAAATTTAAAAATATTTTATATTAAACTTAAAATTACTATT
384549 TAAAAATAATAAAAATTTA
1 T-AAAATAATAAAAATTTA
384568 TATTAATTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
51 20 0.31
52 38 0.59
53 6 0.09
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (51 bp):
TAAAATAATAAAAATTTAAAAATATTTTATATTAAACTTAAAATTACTATT
Found at i:384749 original size:52 final size:51
Alignment explanation
Indices: 384582--384748 Score: 200
Period size: 52 Copynumber: 3.3 Consensus size: 51
384572 AATTTACAAT
* * * *
384582 TTAAAAATAATAAAAATTATAA-ATATTTTATATAAAATCTTCAATTAGTAA
1 TTAAAAATAATAAAAATTAAAACATATTTTATATTAAATC-TAAATTACTAA
* **
384633 --AAAAATAA-AAAAGTTAAAACATATTTTATATTAAATCCTAAATTACTTT
1 TTAAAAATAATAAAAATTAAAACATATTTTATATTAAAT-CTAAATTACTAA
*
384682 TTAAAAATAATAAAAATGAAAACATATTTTATATTAAATCTAGAATTACTAA
1 TTAAAAATAATAAAAATTAAAACATATTTTATATTAAATCTA-AATTACTAA
384734 TTAAAAAT-ATAAAAA
1 TTAAAAATAATAAAAA
384749 AATTATATTA
Statistics
Matches: 99, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
48 9 0.09
49 30 0.30
50 1 0.01
51 18 0.18
52 41 0.41
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.36
Consensus pattern (51 bp):
TTAAAAATAATAAAAATTAAAACATATTTTATATTAAATCTAAATTACTAA
Found at i:385208 original size:16 final size:16
Alignment explanation
Indices: 385187--385221 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
385177 TTGTTCAAAG
*
385187 AAACTGACCTCTCCAT
1 AAACTGAACTCTCCAT
385203 AAACTGAACTCTCCAT
1 AAACTGAACTCTCCAT
385219 AAA
1 AAA
385222 GGAAACTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.31, G:0.06, T:0.23
Consensus pattern (16 bp):
AAACTGAACTCTCCAT
Found at i:386529 original size:17 final size:17
Alignment explanation
Indices: 386507--386540 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
386497 TAAACATTAT
386507 TTATCTAATAAATATAA
1 TTATCTAATAAATATAA
*
386524 TTATCTAATAATTATAA
1 TTATCTAATAAATATAA
386541 AATTAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATCTAATAAATATAA
Found at i:386944 original size:17 final size:17
Alignment explanation
Indices: 386922--386959 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
386912 CTTAATTGAA
* *
386922 CTATTCAATTTAGCTTT
1 CTATTCAAATTACCTTT
386939 CTATTCAAATTACCTTT
1 CTATTCAAATTACCTTT
386956 -TATT
1 CTATT
386960 TTATTAAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.53
Consensus pattern (17 bp):
CTATTCAAATTACCTTT
Found at i:388424 original size:21 final size:21
Alignment explanation
Indices: 388394--388448 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
388384 TCTAAAATTA
*
388394 ACTAAA-AGAACTAACCCTTTC
1 ACTAAAGAGAACCAA-CCTTTC
388415 AC-AAAGAGAACCAACCTTTC
1 ACTAAAGAGAACCAACCTTTC
388435 ACTAAAG-GAACCAA
1 ACTAAAGAGAACCAA
388449 ACCATCCTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.47, C:0.27, G:0.09, T:0.16
Consensus pattern (21 bp):
ACTAAAGAGAACCAACCTTTC
Found at i:388666 original size:22 final size:22
Alignment explanation
Indices: 388621--388726 Score: 95
Period size: 22 Copynumber: 4.8 Consensus size: 22
388611 ACTATATATC
* * * *
388621 TATATGACTATGATTAAGTTTA
1 TATATGACTATAACTAAATGTA
*
388643 TAAATGACTATAACTAAATGTA
1 TATATGACTATAACTAAATGTA
* * *
388665 TATATGACTAAAATTATATGTA
1 TATATGACTATAACTAAATGTA
* * *
388687 TATATAACTTTAATTAAATGTA
1 TATATGACTATAACTAAATGTA
* *
388709 CATATGACTTTAACTAAA
1 TATATGACTATAACTAAA
388727 CCAACCTCTT
Statistics
Matches: 68, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 68 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (22 bp):
TATATGACTATAACTAAATGTA
Found at i:391572 original size:79 final size:79
Alignment explanation
Indices: 391371--391586 Score: 197
Period size: 80 Copynumber: 2.7 Consensus size: 79
391361 ACAAGGTTGG
* **
391371 AGTATCCCTTGAGATGAAAATTTTGTTGTTTTAGAAGTAAAAGCAA-GGTTGGAGTATCCTTCCA
1 AGTATCCTTTGAGATGAAAATTTTAATGTTTTAGAAGTAAAA--AAGGGTTGGAGTATCCTTCCA
** *
391435 AAGATAGTGGGGTTGA
64 AAGATAGTAAGGTTAA
** * * * * * * *
391451 AGTAT-CTCTAAAGATAAAAAATTCAGTGTTTGAGAAATAAAAATAGGGTTGGAGTATCCTTTCA
1 AGTATCCT-TTGAGATGAAAATTTTAATGTTTTAGAAGTAAAAA-AGGGTTGGAGTATCCTTCCA
391515 GAA-ATA-TAAGGTTAA
64 -AAGATAGTAAGGTTAA
* *
391530 AGTATCCTTTGAGATGGAAATTTTAATGTTTTAGAAGTAAAAACGAGGTTGGAGTAT
1 AGTATCCTTTGAGATGAAAATTTTAATGTTTTAGAAGTAAAAAAG-GGTTGGAGTAT
391587 TTCCTCAAAA
Statistics
Matches: 106, Mismatches: 24, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
78 2 0.02
79 50 0.47
80 52 0.49
81 2 0.02
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (79 bp):
AGTATCCTTTGAGATGAAAATTTTAATGTTTTAGAAGTAAAAAAGGGTTGGAGTATCCTTCCAAA
GATAGTAAGGTTAA
Found at i:394786 original size:52 final size:52
Alignment explanation
Indices: 394708--394807 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
394698 CCCGAAATAT
* *
394708 GAAAAGTTGCTTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGG
1 GAAAAGTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGG
*
394760 GAAAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACAT
1 GAAAAGTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACAT
394808 TTTAAAATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 39 0.89
53 5 0.11
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (52 bp):
GAAAAGTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
Found at i:394799 original size:20 final size:20
Alignment explanation
Indices: 394774--394827 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
394764 ATTTGCCTGC
394774 ATGTATCGATACATTTTAAA
1 ATGTATCGATACATTTTAAA
394794 ATGTATCGATACATTTTAAA
1 ATGTATCGATACATTTTAAA
394814 ATGTATCGATACAT
1 ATGTATCGATACAT
394828 CTGGGCAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTAAA
Found at i:394884 original size:13 final size:13
Alignment explanation
Indices: 394866--394890 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
394856 CAAAGATCAG
394866 TGTATCGATACAA
1 TGTATCGATACAA
394879 TGTATCGATACA
1 TGTATCGATACA
394891 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:394958 original size:20 final size:20
Alignment explanation
Indices: 394929--394986 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
394919 GCAGTAGCTT
394929 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
394948 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
394968 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
394987 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:396069 original size:49 final size:49
Alignment explanation
Indices: 395860--396604 Score: 888
Period size: 49 Copynumber: 15.7 Consensus size: 49
395850 AAAAGGATGT
* * *
395860 CAATGTGCTGATTCAAGGCCAACTACATTGAACTTAAAGATGGAAAAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
395912 CGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
395955 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
396003 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
396052 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
396100 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
396149 CAATGTACTGAGTCAAGGCCAGCTACATTGGACTTAAAGATTATGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
396198 CAATATGTTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
396241 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
396290 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
396333 CAATGTGCTGATTCAAGGCCAGCTACATTGGATTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
396382 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
396425 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * * *
396477 CGATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
396520 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
396569 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
396605 GAAGGGTTGC
Statistics
Matches: 594, Mismatches: 64, Indels: 73
0.81 0.09 0.10
Matches are distributed among these distances:
43 185 0.31
45 3 0.01
47 4 0.01
48 96 0.16
49 239 0.40
52 67 0.11
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:396274 original size:92 final size:92
Alignment explanation
Indices: 395851--396609 Score: 1063
Period size: 92 Copynumber: 8.1 Consensus size: 92
395841 AGATGATGAA
* * * * * *
395851 AAAGGATGTCAATGTGCTGATTCAAGGCCAACTACATTGAACTTAAAGATGGAAAAGGTGTCGAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAAT
*
395916 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
395947 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
* *
396011 TGATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* *
396038 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGCCA
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCA
* * *
396102 ATGTGCTGATTCAAGGCCAGCTACATTGGACTT
60 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *
396135 AAAGATGAAGGTGCCAATGTACTGAGTCAAGGCCAGCTACATTGGACTTAAAGATTATGATGCCA
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCA
*
396200 ATATGTTGATTCAAGGCCAGCGATATTGGACTT
60 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
396233 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
396298 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
396325 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGATTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
396390 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
396417 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGTCGATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
396482 TGCTGATTCAAGGCCAGCGATATTGGACTT
63 TGCTGATTCAAGGCCAGCGATATTGGACTT
*
396512 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
* *
396577 TGATTCAAGGCCAGCTATATTGGGCTT
66 TGATTCAAGGCCAGCGATATTGGACTT
396604 AGAAGG
1 A-AAGG
396610 GTTGCCACCG
Statistics
Matches: 618, Mismatches: 34, Indels: 25
0.91 0.05 0.04
Matches are distributed among these distances:
91 37 0.06
92 263 0.43
93 5 0.01
94 3 0.00
95 128 0.21
96 5 0.01
97 142 0.23
98 35 0.06
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:396648 original size:33 final size:35
Alignment explanation
Indices: 396604--396673 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
396594 TATTGGGCTT
396604 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
396638 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
396672 AG
1 AG
396674 GGAGAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
Found at i:396716 original size:34 final size:32
Alignment explanation
Indices: 396678--397412 Score: 490
Period size: 34 Copynumber: 22.6 Consensus size: 32
396668 AGGAAGGGAG
* *
396678 AAAGATGCCACAGAGTTGTGGACTTAAAAGGGAAA
1 AAAG-TGCCACGGAGTTGTGGGCTTAAAA-GG-AA
* *
396713 AAGAGTGCCACTGAGTTGTGGGCTTTAAAAGAAAAA
1 AA-AGTGCCACGGAGTTGTGGGC-TTAAAAG--GAA
* *
396749 AAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAA
1 AAA-GTGCCACGGAGTTGTGGGCTTAAA-A-GGAA
* *
396784 AAAGTGCCACGGAGTTATGGGATTAAAAGG--
1 AAAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
396814 ---GTGCCACAGAGTTGTGGGCTTAGAAGGAAA
1 AAAGTGCCACGGAGTTGTGGGCTTAAAAGG-AA
* *
396844 AAGAGTGCCACAGAGTTGTGGGCTTAGAAGGAAA
1 AA-AGTGCCACGGAGTTGTGGGCTTAAAAGG-AA
*
396878 AAGAGTGCCACGGAGTTGTGGGCTT-TAA--AA
1 AA-AGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
396908 AGAGTGCCACGGAGTCGTGGGCTTTGAAAA-GAA
1 AAAGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* ** *
396941 GAAGGTGCCACAAAGTTGTGGGCTTTAAAAAGAA
1 -AAAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
396975 GAAGGTACCACGGAGTTGTGGGCTTTAAA-G--
1 -AAAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
397005 --AGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAA
1 AAAGTGCCACGGAGTTGTGGGC-TT-AAAAG-G-AA
397039 AAGAGTGCCACGGAGTTGTGGGCTTTAAACA-GAA
1 AA-AGTGCCACGGAGTTGTGGGC-TTAAA-AGGAA
*
397073 AAAGGTGCCATGGAGTTGTGGGCTTTGAAAAGGGAAA
1 AAA-GTGCCACGGAGTTGTGGGC-TT-AAAA-GG-AA
*
397110 AAGAGTGCCACAGAGTTGTGGGCTTTAAAA-GAA
1 AA-AGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
397143 AAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGAA
1 AAA-GTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
397177 AAAGGTGCCACGGAGTTGTGGGCTTAAACGG--
1 AAA-GTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
397208 ---GTGCCACGGAGTTGTGGACTTAAAGATGAAA
1 AAAGTGCCACGGAGTTGTGGGCTTAAA-A-GGAA
* *
397239 AAAGTGCCACAGAATTGTGGGCTTTAAAAGG--
1 AAAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
397270 ---GTGCCACGGAGTTGTGGACTTAAAGATGAAA
1 AAAGTGCCACGGAGTTGTGGGCTTAAA-A-GGAA
*
397301 AAAGTGCCACGGAATTGTGGGCTTTAAAAGG--
1 AAAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
397332 ---GTGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
397361 CAAGGTGCCACGGAGTTGTGGGCTTTAAA-GAA
1 -AAAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* * *
397393 AAAATGCCACTGAGTCGTGG
1 AAAGTGCCACGGAGTTGTGG
397413 ACTTTGAGAC
Statistics
Matches: 579, Mismatches: 60, Indels: 126
0.76 0.08 0.16
Matches are distributed among these distances:
27 76 0.13
28 36 0.06
29 24 0.04
30 5 0.01
31 17 0.03
32 8 0.01
33 76 0.13
34 205 0.35
35 45 0.08
36 38 0.07
37 48 0.08
38 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (32 bp):
AAAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:396819 original size:27 final size:27
Alignment explanation
Indices: 396787--396840 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
396777 GATGAAAAAA
*
396787 GTGCCACGGAGTTATGGGATTAAAAGG
1 GTGCCACAGAGTTATGGGATTAAAAGG
* * *
396814 GTGCCACAGAGTTGTGGGCTTAGAAGG
1 GTGCCACAGAGTTATGGGATTAAAAGG
396841 AAAAAGAGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.39, T:0.22
Consensus pattern (27 bp):
GTGCCACAGAGTTATGGGATTAAAAGG
Found at i:396826 original size:61 final size:61
Alignment explanation
Indices: 396747--397389 Score: 564
Period size: 61 Copynumber: 10.0 Consensus size: 61
396737 TTAAAAGAAA
* * * *
396747 AAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTATGGG-ATT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAA-ATGAAAAAAGTGCCACGGAGTTGTGGGCTTT
* * * *
396808 AAAAGGGTGCCACAGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAGAA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAATGAAAAA-AGTGCCACGGAGTTGTGGGCTT----
*
396873 GGA
61 --T
* *
396876 AAAAGAGTGCCACGGAGTTGTGGGCTT----T-AAAAAGAGTGCCACGGAGTCGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAATGAAAAA-AGTGCCACGGAGTTGTGGGCTTT
** * * * *
396933 GAAAAGAAGAAGGTGCCACAAAGTTGTGGGCTTTAAAAAGAAGAAGGTACCACGGAGTTGTGGGC
1 ---AA-AAG--GGTGCCACGGAGTTGTGGGC-TTAAAATGAAAAAAGTGCCACGGAGTTGTGGGC
396998 TTT
59 TTT
* * *
397001 -AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGGC-TT-AAAA-TGAAAAA-AGTGCCACGGAGTTGTGGGCTTT
* * *
397065 AAACAGAAAAAGGTGCCATGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTG
1 AAA-AG-----GGTGCCACGGAGTTGTGGGC-TT-AAAA-TGAAAAA-AGTGCCACGGAGTTGTG
397130 GGCTTT
56 GGCTTT
* * *
397136 AAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGC-
1 AAAAG-----GGTGCCACGGAGTTGTGGGC-TTAAAATGAAAAAAGTGCCACGGAGTTGTGGGCT
397200 TT
60 TT
* * * *
397202 AAACGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAA-ATGAAAAAAGTGCCACGGAGTTGTGGGCTTT
* *
397264 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAA-ATGAAAAAAGTGCCACGGAGTTGTGGGCTTT
* * * *
397326 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAATGAAAAAAGTGCCACGGAGTTGTGGGCTTT
397387 AAA
1 AAA
397390 GAAAAAATGC
Statistics
Matches: 497, Mismatches: 53, Indels: 64
0.81 0.09 0.10
Matches are distributed among these distances:
60 14 0.03
61 137 0.28
62 97 0.20
63 52 0.10
64 24 0.05
65 2 0.00
66 8 0.02
67 18 0.04
68 51 0.10
69 8 0.02
70 28 0.06
71 58 0.12
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTTAAAATGAAAAAAGTGCCACGGAGTTGTGGGCTTT
Found at i:396890 original size:95 final size:94
Alignment explanation
Indices: 396711--397391 Score: 599
Period size: 95 Copynumber: 7.1 Consensus size: 94
396701 TTAAAAGGGA
* * * * *
396711 AAAAGAGTGCCACTGAGTTGTGGGCTTTAAAAGAAAAAAAAGGTGCCACGGAGTTGTGGAC-TTA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAGGAAAAAGA-GTGCCACAGAGTTGTGGGCTTTA
* * *
396775 AAGATGAAAAAAGTGCCACGGAGTTATGGGATT
64 AA-A-GAAAAAGGTGCCACGGAGTTGTGGGCTT
* *
396808 AAAAGGGTGCCACAGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGC-TTAG
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTA-
*
396871 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
64 AAAGAAAAAG-GTGCCACGGAGTTGTGGGC-TT
* * * *
396904 AAAAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAAGAAG-GTGCCACAAAGTTGTGGGCTTTA
1 -AAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT-
* *
396968 AAAAGAAGAAGGTACCACGGAGTTGTGGGCTT
63 AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTT
* * *
397000 TAAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT--AAAG-GAAAAAGAGTGCCACAGAGTTGTGGGCTTT
*
397065 AAACAGAAAAAGGTGCCATGGAGTTGTGGGCTTT
63 AAA-AGAAAAAGGTGCCACGGAGTTGTGGGC-TT
* *
397099 GAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAG-GTGCCACAGAGTTGTG
1 ---------AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAAGAGTGCCACAGAGTTGTG
397163 GGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTT
57 GGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTT
* * * *
397202 AAACGGGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAA-AGTGCCACAGAATTGTGGGCTTTA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAG--GAAAAAGAGTGCCACAGAGTTGTGGGCTTTA
*
397265 AAAG-----GGTGCCACGGAGTTGTGGACTT
64 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTT
* * * *
397291 AAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTT------AAAAGGGTGCCACGGAGTTGTGGA
1 AAA-A-G-----AGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAAGAGTGCCACAGAGTTGTGGG
*
397350 C-TTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTT
59 CTTTAAAA-GAAAAAGGTGCCACGGAGTTGTGGGCTT
*
397386 TAAAGA
1 AAAAGA
397392 AAAAATGCCA
Statistics
Matches: 491, Mismatches: 51, Indels: 93
0.77 0.08 0.15
Matches are distributed among these distances:
88 1 0.00
89 34 0.07
90 17 0.03
91 1 0.00
93 6 0.01
94 33 0.07
95 115 0.23
96 37 0.08
97 92 0.19
98 64 0.13
99 4 0.01
103 2 0.00
104 47 0.10
105 10 0.02
106 3 0.01
108 25 0.05
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (94 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAA
AGAAAAAGGTGCCACGGAGTTGTGGGCTT
Found at i:397218 original size:27 final size:26
Alignment explanation
Indices: 397180--397355 Score: 109
Period size: 28 Copynumber: 6.0 Consensus size: 26
397170 AAAAGAAAAA
*
397180 GGTGCCACGGAGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGACTTAAA-G
397207 GGTGCCACGGAGTTGTGGACTTAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAG
* * *
397233 ATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAG
1 --G------GTGCCACGGAGTTGTGGAC-TT-AAAG
397269 GGTGCCACGGAGTTGTGGACTTAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAG
* *
397295 ATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAG
1 --G------GTGCCACGGAGTTGTGGAC-TT-AAAG
397331 GGTGCCACGGAGTTGTGGACTTAAA
1 GGTGCCACGGAGTTGTGGACTTAAA
397356 AGGAACAAGG
Statistics
Matches: 118, Mismatches: 11, Indels: 41
0.69 0.06 0.24
Matches are distributed among these distances:
26 8 0.07
27 28 0.24
28 35 0.30
34 35 0.30
35 4 0.03
36 8 0.07
ACGTcount: A:0.30, C:0.14, G:0.34, T:0.23
Consensus pattern (26 bp):
GGTGCCACGGAGTTGTGGACTTAAAG
Found at i:397272 original size:62 final size:61
Alignment explanation
Indices: 397071--397389 Score: 379
Period size: 62 Copynumber: 5.0 Consensus size: 61
397061 CTTTAAACAG
* * * *
397071 AAAAAGGTGCCATGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAA-GGAAAAA-AGTGCCACGGAGTTGTGGGCTTT
* * * *
397136 AAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGC-
1 AAAAG-----GGTGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAAGTGCCACGGAGTTGTGGGCT
397200 TT
60 TT
* * * *
397202 AAACGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAA-AGGAAAAAAGTGCCACGGAGTTGTGGGCTTT
* *
397264 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAA-AGGAAAAAAGTGCCACGGAGTTGTGGGCTTT
* *
397326 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTT
397387 AAA
1 AAA
397390 GAAAAAATGC
Statistics
Matches: 228, Mismatches: 19, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
60 5 0.02
61 72 0.32
62 92 0.40
65 4 0.02
66 6 0.03
67 18 0.08
68 6 0.03
69 4 0.02
70 21 0.09
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.22
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTT
Found at i:397428 original size:30 final size:31
Alignment explanation
Indices: 397333--397450 Score: 121
Period size: 30 Copynumber: 3.8 Consensus size: 31
397323 TTTAAAAGGG
* * * **
397333 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
1 TGCCACTGAGTCGTGGACTTTAAA-GAA-AAAA
* * *
397366 TGCCACGGAGTTGTGGGCTTTAAAGAAAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
* *
397397 TGCCACTGAGTCGTGGACTTT-GAGACAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
397427 TGCCACTGAGTCGTGGACTTTAAA
1 TGCCACTGAGTCGTGGACTTTAAA
397451 AAGGTATTTG
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
30 28 0.38
31 21 0.28
32 3 0.04
33 22 0.30
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
Found at i:398753 original size:16 final size:16
Alignment explanation
Indices: 398734--398771 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
398724 TGCCTTTGCA
*
398734 TTTTTT-TTGTGTGTG
1 TTTTTTGTTTTGTGTG
*
398749 TTTTTTGTTTTGTTTG
1 TTTTTTGTTTTGTGTG
398765 TTTTTTG
1 TTTTTTG
398772 ACTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (16 bp):
TTTTTTGTTTTGTGTG
Found at i:398777 original size:18 final size:17
Alignment explanation
Indices: 398747--398811 Score: 73
Period size: 16 Copynumber: 3.9 Consensus size: 17
398737 TTTTTGTGTG
*
398747 TGTTTTTT-GTTTTGTT
1 TGTTTTTTACTTTTGTT
398763 TGTTTTTTGACTTTT-TT
1 TGTTTTTT-ACTTTTGTT
398780 T-TTTTTTACTTTTGTT
1 TGTTTTTTACTTTTGTT
*
398796 TGTGTGTTTACTTTTG
1 TGT-TTTTTACTTTTG
398812 ACTGTTCCGG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.14
16 17 0.40
17 4 0.10
18 15 0.36
ACGTcount: A:0.05, C:0.05, G:0.15, T:0.75
Consensus pattern (17 bp):
TGTTTTTTACTTTTGTT
Found at i:405798 original size:52 final size:52
Alignment explanation
Indices: 405720--405819 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
405710 CCCGAAATAT
* *
405720 GAAAAGTTGCTTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGG
1 GAAAAGTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGG
*
405772 GAAAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACAT
1 GAAAAGTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACAT
405820 TTTAAAATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 39 0.89
53 5 0.11
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (52 bp):
GAAAAGTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
Found at i:405811 original size:20 final size:20
Alignment explanation
Indices: 405786--405839 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
405776 ATTTGCCTGC
405786 ATGTATCGATACATTTTAAA
1 ATGTATCGATACATTTTAAA
405806 ATGTATCGATACATTTTAAA
1 ATGTATCGATACATTTTAAA
405826 ATGTATCGATACAT
1 ATGTATCGATACAT
405840 CTGGGCAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTAAA
Found at i:405896 original size:13 final size:13
Alignment explanation
Indices: 405878--405902 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
405868 CAAAGATCAG
405878 TGTATCGATACAA
1 TGTATCGATACAA
405891 TGTATCGATACA
1 TGTATCGATACA
405903 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:405970 original size:20 final size:20
Alignment explanation
Indices: 405941--405998 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
405931 GCAGTAGCTT
405941 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
405960 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
405980 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
405999 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Done.