Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1830
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: 215889
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:164353 original size:23 final size:22
Alignment explanation
Indices: 164327--164386 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
164317 TAATAAATAT
164327 TTATAATAATTTTTATATTTATA
1 TTATAATAA-TTTTATATTTATA
* * *
164350 TTATATTAAATTTATTTTTATA
1 TTATAATAATTTTATATTTATA
* *
164372 TCATTATAAATTTTA
1 TTATAAT-AATTTTA
164387 ATTATTTTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATAATAATTTTATATTTATA
Found at i:164381 original size:22 final size:22
Alignment explanation
Indices: 164338--164384 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
164328 TATAATAATT
*
164338 TTTATATTTATATTATATTAAA
1 TTTATATTTATATCATATTAAA
*
164360 TTTATTTTTATATCAT-TATAAA
1 TTTATATTTATATCATAT-TAAA
164382 TTT
1 TTT
164385 TAATTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTATATTTATATCATATTAAA
Found at i:164765 original size:3 final size:3
Alignment explanation
Indices: 164757--164786 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
164747 ATATTTATTA
*
164757 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
164787 TTTTTAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:172308 original size:14 final size:14
Alignment explanation
Indices: 172289--172324 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
172279 AGACATTAAT
*
172289 TATAAAAATATGAA
1 TATAAAAATATAAA
172303 TATAAAAATATAAA
1 TATAAAAATATAAA
*
172317 TACAAAAA
1 TATAAAAA
172325 ATCTTTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (14 bp):
TATAAAAATATAAA
Found at i:172420 original size:22 final size:20
Alignment explanation
Indices: 172395--172444 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
172385 TATGTTTTTA
*
172395 TTATTAATAAGATTTATCTAAT
1 TTATTAATAAGAATT-T-TAAT
*
172417 TTATAAATAAGAATTTTAAT
1 TTATTAATAAGAATTTTAAT
172437 TTCATTAA
1 TT-ATTAA
172445 ATGTTTCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 5 0.21
22 13 0.54
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (20 bp):
TTATTAATAAGAATTTTAAT
Found at i:172757 original size:2 final size:2
Alignment explanation
Indices: 172750--172783 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
172740 ATGACTATTC
*
172750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
172784 GAGACAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:173408 original size:2 final size:2
Alignment explanation
Indices: 173401--173431 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
173391 AGTCTCCATT
173401 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
173432 AAATTGATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:175080 original size:1 final size:1
Alignment explanation
Indices: 175074--175103 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
175064 TAGAATCTCA
175074 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
175104 AAAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:176020 original size:29 final size:29
Alignment explanation
Indices: 175978--176036 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
175968 TATTGCAGTC
175978 AGCACACTCCTTTAAAATGCTTTTCTCTG
1 AGCACACTCCTTTAAAATGCTTTTCTCTG
176007 AGCACACTCCTTTAAAATGCTTTTCTCTG
1 AGCACACTCCTTTAAAATGCTTTTCTCTG
176036 A
1 A
176037 TAATTTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.37
Consensus pattern (29 bp):
AGCACACTCCTTTAAAATGCTTTTCTCTG
Found at i:180628 original size:2 final size:2
Alignment explanation
Indices: 180621--180663 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
180611 TTAAAGATCC
180621 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180663 A
1 A
180664 ACCTCATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:181253 original size:21 final size:21
Alignment explanation
Indices: 181211--181275 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
181201 AATAAAAGTG
*
181211 ATAAATATTAAAATTTAAAATTTA
1 ATAAAT-TTTAAATTT--AATTTA
*
181235 A-AATTTTTAAATATTAA-TTA
1 ATAAATTTTAAAT-TTAATTTA
181255 ATTAAATTTTAAATTTAATTT
1 A-TAAATTTTAAATTTAATTT
181276 TTTTAGATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
20 4 0.12
21 6 0.18
22 18 0.53
23 5 0.15
24 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAATTTTAAATTTAATTTA
Found at i:181263 original size:37 final size:37
Alignment explanation
Indices: 181221--181293 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
181211 ATAAATATTA
181221 AAATTTAAAATTTAAAATTTTTAAATATTAATTAATT
1 AAATTTAAAATTTAAAATTTTTAAATATTAATTAATT
* ** * *
181258 AAATTTTAAATTTAATTTTTTTAGATATTACTTAAT
1 AAATTTAAAATTTAAAATTTTTAAATATTAATTAAT
181294 ACAACACAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (37 bp):
AAATTTAAAATTTAAAATTTTTAAATATTAATTAATT
Found at i:181570 original size:21 final size:22
Alignment explanation
Indices: 181546--181605 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
181536 AATTATTACG
* *
181546 TATTATATTTATATT-ATTTTT
1 TATTATAATTAAATTAATTTTT
181567 TATTATAATTAAATTAATTTTT
1 TATTATAATTAAATTAATTTTT
*
181589 TGTCCTATAATTAAATT
1 TAT--TATAATTAAATT
181606 TAAAAGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.39
22 8 0.24
24 12 0.36
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (22 bp):
TATTATAATTAAATTAATTTTT
Found at i:181647 original size:21 final size:20
Alignment explanation
Indices: 181623--181668 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
181613 TTTACATATA
181623 TATAAATTTTGACAAATTATG
1 TATAAATTTTGACAAATT-TG
* * *
181644 TATATATTTTTACATATTTG
1 TATAAATTTTGACAAATTTG
181664 TATAA
1 TATAA
181669 TAATATCATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (20 bp):
TATAAATTTTGACAAATTTG
Found at i:181859 original size:23 final size:24
Alignment explanation
Indices: 181833--181882 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
181823 TTTTTTGTAT
181833 TATAATAAA-TTTAAAATATTATA
1 TATAATAAATTTTAAAATATTATA
* *
181856 TAT-ATAAATTTTAACATGTTATA
1 TATAATAAATTTTAAAATATTATA
181879 TATA
1 TATA
181883 GATTTTGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TATAATAAATTTTAAAATATTATA
Found at i:181997 original size:17 final size:16
Alignment explanation
Indices: 181975--182008 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
181965 ATTGTGTTAG
*
181975 TATTATTTTTTATATTT
1 TATTATGTTTTA-ATTT
181992 TATTATGTTTTAATTT
1 TATTATGTTTTAATTT
182008 T
1 T
182009 TTTGTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TATTATGTTTTAATTT
Found at i:183126 original size:16 final size:18
Alignment explanation
Indices: 183094--183130 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
183084 TAATTTTTAC
183094 TTCATAATTTTTGATATA
1 TTCATAATTTTTGATATA
183112 TTCAT-ATTTTT-ATATA
1 TTCATAATTTTTGATATA
183128 TTC
1 TTC
183131 TTTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (18 bp):
TTCATAATTTTTGATATA
Found at i:183432 original size:17 final size:16
Alignment explanation
Indices: 183394--183446 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
183384 GATATGATTA
*
183394 TATACTTATATCTTATT
1 TATA-TTATATTTTATT
*
183411 TATATTATTTTTTATT
1 TATATTATATTTTATT
*
183427 TCATATTATATTTTAAT
1 T-ATATTATATTTTATT
183444 TAT
1 TAT
183447 TTTTATCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 13 0.42
17 18 0.58
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATTATATTTTATT
Found at i:185290 original size:29 final size:27
Alignment explanation
Indices: 185208--185279 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
185198 CTTTTTTACA
* * *
185208 TATTT-TTTTACTTTTCT-ATACTCCAT
1 TATTTCTTTTACTTTTTTCATAATTC-T
185234 TATTTCTTTTACTTTTTTCATAATTCT
1 TATTTCTTTTACTTTTTTCATAATTCT
*
185261 TATTTTTTTCTACTTTTTT
1 TATTTCTTT-TACTTTTTT
185280 TCAAATTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 5 0.13
27 20 0.51
28 14 0.36
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (27 bp):
TATTTCTTTTACTTTTTTCATAATTCT
Found at i:188678 original size:21 final size:19
Alignment explanation
Indices: 188654--188708 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
188644 TTCTATAATT
188654 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGT-AA
* **
188675 TGTATCGATACATAAGTTT
1 TGTATCGATACAAAAGTAA
188694 TGTATCGATACAAAA
1 TGTATCGATACAAAA
188709 CTACCTTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:188699 original size:19 final size:21
Alignment explanation
Indices: 188651--188707 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
188641 AATTTCTATA
188651 ATTTGTATCGATACAAACAGT
1 ATTTGTATCGATACAAACAGT
** *
188672 AAATGTATCGATACATA-AGT
1 ATTTGTATCGATACAAACAGT
188692 -TTTGTATCGATACAAA
1 ATTTGTATCGATACAAA
188708 ACTACCTTAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (21 bp):
ATTTGTATCGATACAAACAGT
Found at i:199214 original size:52 final size:52
Alignment explanation
Indices: 199066--199194 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
199056 CGAAATATGA
*
199066 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
199118 AAATTTGCCTGCATGTATTGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
199170 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
199195 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:199221 original size:13 final size:13
Alignment explanation
Indices: 199203--199227 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
199193 CAAAGATCAG
199203 TGTATCGATACAA
1 TGTATCGATACAA
199216 TGTATCGATACA
1 TGTATCGATACA
199228 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:199294 original size:19 final size:19
Alignment explanation
Indices: 199270--199367 Score: 94
Period size: 19 Copynumber: 5.7 Consensus size: 19
199260 TAGCTTAAAT
199270 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
199289 TGTATCGATAC---A-TTA
1 TGTATCGATACAAAACTTA
*
199304 --TATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
199321 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
199334 TGTATCGATACAAAACTTTA
1 TGTATCGATACAAAAC-TTA
199354 TGTATCGATACAAA
1 TGTATCGATACAAA
199368 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 20 0.30
14 1 0.02
15 3 0.05
16 4 0.06
17 3 0.05
19 21 0.32
20 14 0.21
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:199313 original size:32 final size:32
Alignment explanation
Indices: 199272--199365 Score: 161
Period size: 32 Copynumber: 2.9 Consensus size: 32
199262 GCTTAAATTG
199272 TATCGATACAAAACTTATGTATCGATACATTA
1 TATCGATACAAAACTTATGTATCGATACATTA
* *
199304 TATCGATACAACACTTATGTATCGATACATTG
1 TATCGATACAAAACTTATGTATCGATACATTA
199336 TATCGATACAAAACTTTATGTATCGATACA
1 TATCGATACAAAAC-TTATGTATCGATACA
199366 AATCGTTGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 43 0.74
33 15 0.26
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (32 bp):
TATCGATACAAAACTTATGTATCGATACATTA
Found at i:203372 original size:51 final size:51
Alignment explanation
Indices: 203312--203446 Score: 153
Period size: 51 Copynumber: 2.6 Consensus size: 51
203302 CCTTCGGAAT
* *
203312 ATGGGGTTGGAATATCCCCGAGATAAAAAATTTAATATTTTTAAAATAAAA
1 ATGGGGTTGGAGTATCCCCGAGATAAAAAATTTAATATTTTGAAAATAAAA
* ** * **
203363 ATGGGGTTGGAGTATTCTTGAGATATAAAATTTAATATTTTGGGAATAAAA
1 ATGGGGTTGGAGTATCCCCGAGATAAAAAATTTAATATTTTGAAAATAAAA
* * * *
203414 GTAGGGTTGGAGTATCCCCTAAGATGAAAAATT
1 ATGGGGTTGGAGTATCCCC-GAGATAAAAAATT
203447 CGATACCATT
Statistics
Matches: 67, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
51 57 0.85
52 10 0.15
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (51 bp):
ATGGGGTTGGAGTATCCCCGAGATAAAAAATTTAATATTTTGAAAATAAAA
Found at i:206553 original size:20 final size:21
Alignment explanation
Indices: 206515--206553 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
206505 AGTGACTTCA
* *
206515 AATCCTCAAAATTATCACAAT
1 AATCCTCAAAACTACCACAAT
206536 AATCCT-AAAACTACCACA
1 AATCCTCAAAACTACCACA
206554 TCCAAAGCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (21 bp):
AATCCTCAAAACTACCACAAT
Found at i:207457 original size:52 final size:52
Alignment explanation
Indices: 207309--207437 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
207299 CGAAATATGA
207309 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATTGATACATCTGGGC
* *
207361 AAATTTGCCTGCATGTATTGATACATTTTATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATTGATACATCTGGGC
* *
207413 AAATTTTCCTACATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
207438 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATTGATACATCTGGGC
Found at i:207537 original size:19 final size:20
Alignment explanation
Indices: 207513--207565 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
207503 TAGCTTATAT
207513 TGTATCGATACAAAAC-TTA
1 TGTATCGATACAAAACTTTA
*
207532 TGTATCGATACAACACTTTA
1 TGTATCGATACAAAACTTTA
207552 TGTATCGATACAAA
1 TGTATCGATACAAA
207566 TCGTTGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (20 bp):
TGTATCGATACAAAACTTTA
Found at i:208378 original size:67 final size:68
Alignment explanation
Indices: 208281--208407 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
208271 ATTGGGTTTT
* * *
208281 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGGCTTAAAGATGAAGATG
208346 AGA
66 AGA
* * **
208349 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAATGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGGCTTAAAGATGA
208408 GAAAAAGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGGCTTAAAGATGAAGATG
AGA
Found at i:208600 original size:92 final size:92
Alignment explanation
Indices: 208411--208696 Score: 446
Period size: 92 Copynumber: 3.1 Consensus size: 92
208401 AAGATGAGAA
* *
208411 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AAAAGGTGCCAAT
*
208476 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
*
208507 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGTTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
*
208572 TGATTCAAGGTCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* **
208599 AAAGGTGCCAATGTACTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
*
208664 TGATTCAAGGCCAGCGATATTGGGCTT
66 TGATTCAAGGCCAGCGATATTGGACTT
208691 AGAAGG
1 A-AAGG
208697 GTTGCCACCG
Statistics
Matches: 178, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
92 128 0.72
93 4 0.02
95 41 0.23
96 5 0.03
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:208686 original size:49 final size:49
Alignment explanation
Indices: 208362--208691 Score: 299
Period size: 43 Copynumber: 6.8 Consensus size: 49
208352 GTGATAAAGA
* * * *
208362 TGCCAATATGTTGATTCACGGCCA-ATGATATTGGGCTTAAAGATGAGAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCT-ATATTGGACTTAAAGAT--G---AAGG
* * * *
208416 ATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGG
1 -TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGG
208469 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* * ** *
208512 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGT
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
208561 TGCCAATATGCTGATTCAAGGTCAGCGATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* * *
208604 TGCCAATGTACTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
208653 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
208692 GAAGGGTTGC
Statistics
Matches: 231, Mismatches: 31, Indels: 32
0.79 0.11 0.11
Matches are distributed among these distances:
43 76 0.33
45 1 0.00
47 2 0.01
48 1 0.00
49 75 0.32
52 34 0.15
53 6 0.03
54 1 0.00
55 34 0.15
56 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
Found at i:208732 original size:32 final size:32
Alignment explanation
Indices: 208684--208914 Score: 337
Period size: 32 Copynumber: 7.2 Consensus size: 32
208674 CCAGCGATAT
208684 TGGGC-TTAGA-AGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
208714 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
* *
208746 TGGGCTTT-GAAAAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAG-AGAGGGTTGCCACCGACTTGTG
*
208778 TGGGCTTTAGAG-GGGATTGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGG-TTGCCACCGACTTGTG
*
208810 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAG-AGAGGGTTGCCACCGACTTGTG
*
208843 TGGGCTTT-GAGGGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
208874 TGGGCTTTGGAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
208907 TGGGCTTT
1 TGGGCTTT
208915 TGAAAAGGAG
Statistics
Matches: 182, Mismatches: 10, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
30 5 0.03
31 36 0.20
32 86 0.47
33 53 0.29
34 2 0.01
ACGTcount: A:0.16, C:0.19, G:0.36, T:0.29
Consensus pattern (32 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
Found at i:208962 original size:27 final size:27
Alignment explanation
Indices: 208930--208983 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
208920 AGGAGAAAGA
* *
208930 TGCCACGGAGTTGTAGACTTAAAAGGG
1 TGCCACGGAATTATAGACTTAAAAGGG
*
208957 TGCCACGGAATTATGGACTTAAAAGGG
1 TGCCACGGAATTATAGACTTAAAAGGG
208984 AAAAAGAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.22
Consensus pattern (27 bp):
TGCCACGGAATTATAGACTTAAAAGGG
Found at i:209056 original size:58 final size:58
Alignment explanation
Indices: 208985--209254 Score: 235
Period size: 58 Copynumber: 4.5 Consensus size: 58
208975 TTAAAAGGGA
* *
208985 AAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGATGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGATGCCACGGAGTTGTGGACTT
* * * * * *
209043 AAAAGGGTGCCACAAAATTGTGGACTTTGAAGAA-AAAATGCCACTGAGTCGTGGACTTT
1 AAAAGGGTGCCACAGAGTTGTGGGCTTTGAA-AAGAAGATGCCACGGAGTTGTGGAC-TT
* * * * * *
209102 GGAAAGAGATGCCACTGAGTTGTGGGC-TT-AAAAG--GGTGCCACGGAATTGTGAACTT
1 -AAAAG-GGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGATGCCACGGAGTTGTGGACTT
*
209158 AAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGATGCCACGGAGTTGTGGGCT
1 AAAA--G-----G-GTGCCACAGAGTTGTGGGCTTTGAAAAGAAGATGCCACGGAGTTGTGGACT
209223 T
58 T
* * *
209224 AAAAGGGTGCCACGGAATTGTGGACTTTGAA
1 AAAAGGGTGCCACAGAGTTGTGGGCTTTGAA
209255 GAAAAAATAC
Statistics
Matches: 166, Mismatches: 30, Indels: 32
0.73 0.13 0.14
Matches are distributed among these distances:
55 3 0.02
56 2 0.01
57 15 0.09
58 69 0.42
59 7 0.04
60 6 0.04
61 17 0.10
62 17 0.10
63 2 0.01
64 6 0.04
66 22 0.13
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.22
Consensus pattern (58 bp):
AAAAGGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGATGCCACGGAGTTGTGGACTT
Found at i:209131 original size:88 final size:88
Alignment explanation
Indices: 208927--209395 Score: 555
Period size: 88 Copynumber: 5.2 Consensus size: 88
208917 AAAAGGAGAA
* * * **
208927 AGATGCCACGGAGTTGTAGACTTAAAAGGGTGCCACGGAATTATGGACTTAAAAGGGAAAAAGAG
1 AGATGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTGGACTTTGAA--GAAAAA-A-
* * *
208992 TGCCACAGAGTTGTGGGCTTTGAAAAG
62 TGCCACTGAGTCGTGGGCTTTGGAAAG
**
209019 AAGATGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACAAAATTGTGGACTTTGAAGAAAAAATGC
1 -AGATGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTGGACTTTGAAGAAAAAATGC
*
209084 CACTGAGTCGTGGACTTTGGAAAG
65 CACTGAGTCGTGGGCTTTGGAAAG
* * **
209108 AGATGCCACTGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTGAACTTAAAAGGGAAAAAGAG
1 AGATGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTGGACTTTGAA--GAAAAA-A-
* * *
209173 TGCCACAGAGTTGTGGGCTTTGAAAAG
62 TGCCACTGAGTCGTGGGCTTTGGAAAG
*
209200 AAGATGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTGGACTTTGAAGAAAAAATAC
1 -AGATGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTGGACTTTGAAGAAAAAATGC
* *
209265 CATTGAGTCGTGGACTTTGGAAAG
65 CACTGAGTCGTGGGCTTTGGAAAG
* * * * *
209289 AGATGCCACTGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGGCTTTG-AGACAAAATGCC
1 AGATGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTGGACTTTGAAGAAAAAATGCC
*
209353 ACTGAGTCGTGGGCATT-GAGAAG
66 ACTGAGTCGTGGGCTTTGGA-AAG
* *
209376 AGATTGCCACTGAGTCGTGG
1 AGA-TGCCACGGAGTTGTGG
209396 ACTTTAAGAA
Statistics
Matches: 328, Mismatches: 41, Indels: 19
0.85 0.11 0.05
Matches are distributed among these distances:
86 2 0.01
87 30 0.09
88 111 0.34
89 44 0.13
90 8 0.02
91 13 0.04
92 23 0.07
93 97 0.30
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.22
Consensus pattern (88 bp):
AGATGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTGGACTTTGAAGAAAAAATGCC
ACTGAGTCGTGGGCTTTGGAAAG
Found at i:209225 original size:66 final size:63
Alignment explanation
Indices: 209104--209230 Score: 166
Period size: 66 Copynumber: 2.0 Consensus size: 63
209094 TGGACTTTGG
* *
209104 AAAGAGATGCCACTGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTGAACTTAAAAGGGAA
1 AAAGAGATGCCACAGAGTTGTGGGCTTAAAAGGATGCCACGGAATTGTGAACTTAAAAGGGAA
* **
209167 AAAGAG-TGCCACAGAGTTGTGGGCTTTGAAAAGAAGATGCCACGGAGTTGTGGGCTTAAAAGGG
1 AAAGAGATGCCACAGAGTTGTGGGC-TT-AAAAG--GATGCCACGGAATTGTGAACTTAAAAGGG
209231 TGCCACGGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
62 17 0.31
63 8 0.15
64 5 0.09
66 25 0.45
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (63 bp):
AAAGAGATGCCACAGAGTTGTGGGCTTAAAAGGATGCCACGGAATTGTGAACTTAAAAGGGAA
Found at i:209231 original size:181 final size:181
Alignment explanation
Indices: 208927--209333 Score: 715
Period size: 181 Copynumber: 2.2 Consensus size: 181
208917 AAAAGGAGAA
* * * * *
208927 AGATGCCACGGAGTTGTAGACTTAAAAGGGTGCCACGGAATTATGGACTTAAAAGGGAAAAAGAG
1 AGATGCCACTGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTGAACTTAAAAGGGAAAAAGAG
208992 TGCCACAGAGTTGTGGGCTTTGAAAAGAAGATGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACA
66 TGCCACAGAGTTGTGGGCTTTGAAAAGAAGATGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACA
*
209057 AAATTGTGGACTTTGAAGAAAAAATGCCACTGAGTCGTGGACTTTGGAAAG
131 AAATTGTGGACTTTGAAGAAAAAATACCACTGAGTCGTGGACTTTGGAAAG
209108 AGATGCCACTGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTGAACTTAAAAGGGAAAAAGAG
1 AGATGCCACTGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTGAACTTAAAAGGGAAAAAGAG
*
209173 TGCCACAGAGTTGTGGGCTTTGAAAAGAAGATGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACG
66 TGCCACAGAGTTGTGGGCTTTGAAAAGAAGATGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACA
* *
209238 GAATTGTGGACTTTGAAGAAAAAATACCATTGAGTCGTGGACTTTGGAAAG
131 AAATTGTGGACTTTGAAGAAAAAATACCACTGAGTCGTGGACTTTGGAAAG
* *
209289 AGATGCCACTGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTG
1 AGATGCCACTGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTG
209334 GGCTTTGAGA
Statistics
Matches: 215, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
181 215 1.00
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.22
Consensus pattern (181 bp):
AGATGCCACTGAGTTGTGGGCTTAAAAGGGTGCCACGGAATTGTGAACTTAAAAGGGAAAAAGAG
TGCCACAGAGTTGTGGGCTTTGAAAAGAAGATGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACA
AAATTGTGGACTTTGAAGAAAAAATACCACTGAGTCGTGGACTTTGGAAAG
Found at i:209244 original size:27 final size:29
Alignment explanation
Indices: 208985--209341 Score: 181
Period size: 31 Copynumber: 12.0 Consensus size: 29
208975 TTAAAAGGGA
* *
208985 AAAAGAGTGCCACAGAGTTGTGGGCTTTG
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTG
*
209014 AAAAGAAGATGCCACGGAGTTGTGGGC-TT-
1 AAAAG--GGTGCCACGGAGTTGTGGGCTTTG
** * *
209043 AAAAGGGTGCCACAAAATTGTGGACTTTG
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTG
*** * * *
209072 AAGAAAAAATGCCACTGAGTCGTGGACTTTG
1 -A-AAAGGGTGCCACGGAGTTGTGGGCTTTG
* * *
209103 GAAAGAGATGCCACTGAGTTGTGGGC-TT-
1 AAAAG-GGTGCCACGGAGTTGTGGGCTTTG
* ** *
209131 AAAAGGGTGCCACGGAATTGTGAACTTAAAAGGG
1 AAAAGGGTGCCACGGAGTTGTGGGCTT-----TG
* *
209165 AAAAAGAGTGCCACAGAGTTGTGGGCTTTG
1 -AAAAGGGTGCCACGGAGTTGTGGGCTTTG
*
209195 AAAAGAAGATGCCACGGAGTTGTGGGC-TT-
1 AAAAG--GGTGCCACGGAGTTGTGGGCTTTG
* *
209224 AAAAGGGTGCCACGGAATTGTGGACTTTG
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTG
*** * ** * *
209253 AAGAAAAAATACCATTGAGTCGTGGACTTTG
1 -A-AAAGGGTGCCACGGAGTTGTGGGCTTTG
* * *
209284 GAAAGAGATGCCACTGAGTTGTGGGC-TT-
1 AAAAG-GGTGCCACGGAGTTGTGGGCTTTG
*
209312 AAAAGGGTGCCACAGAGTTGTGGGCTTTG
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTG
209341 A
1 A
209342 GACAAAATGC
Statistics
Matches: 247, Mismatches: 57, Indels: 48
0.70 0.16 0.14
Matches are distributed among these distances:
27 65 0.26
28 15 0.06
29 31 0.13
30 39 0.16
31 75 0.30
35 22 0.09
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.23
Consensus pattern (29 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTTTG
Found at i:209406 original size:31 final size:30
Alignment explanation
Indices: 208987--209406 Score: 156
Period size: 31 Copynumber: 14.1 Consensus size: 30
208977 AAAAGGGAAA
* *
208987 AAGAG-TGCCACAGAGTTGTGGGCTTTGAA-
1 AAGAGATGCCACTGAGTCGTGGGCTTT-AAG
* *
209016 AAGAAGATGCCACGGAGTTGTGGGC-TTAA-
1 AAG-AGATGCCACTGAGTCGTGGGCTTTAAG
* ** * * *
209045 AAG-GGTGCCACAAAATTGTGGACTTTGAAG
1 AAGAGATGCCACTGAGTCGTGGGCTTT-AAG
* * * *
209075 AAAAAATGCCACTGAGTCGTGGACTTT-GG
1 AAGAGATGCCACTGAGTCGTGGGCTTTAAG
*
209104 AAAGAGATGCCACTGAGTTGTGGGC-TTAA-
1 -AAGAGATGCCACTGAGTCGTGGGCTTTAAG
* * * * ** *
209133 AAG-GGTGCCACGGAATTGTGAACTTAAAAGGG
1 AAGAGATGCCACTGAGTCGTGGGCTT-TAA--G
* * *
209165 AAAAAGAGTGCCACAGAGTTGTGGGCTTTGAA-
1 -AAGAGA-TGCCACTGAGTCGTGGGCTTT-AAG
* *
209197 AAGAAGATGCCACGGAGTTGTGGGC-TTAA-
1 AAG-AGATGCCACTGAGTCGTGGGCTTTAAG
* * * * *
209226 AAG-GGTGCCACGGAATTGTGGACTTTGAAG
1 AAGAGATGCCACTGAGTCGTGGGCTTT-AAG
* * * * * *
209256 AAAAAATACCATTGAGTCGTGGACTTT-GG
1 AAGAGATGCCACTGAGTCGTGGGCTTTAAG
*
209285 AAAGAGATGCCACTGAGTTGTGGGC-TTAA-
1 -AAGAGATGCCACTGAGTCGTGGGCTTTAAG
* * * *
209314 AAG-GGTGCCACAGAGTTGTGGGCTTTGAG
1 AAGAGATGCCACTGAGTCGTGGGCTTTAAG
* * *
209343 ACA-AAATGCCACTGAGTCGTGGGCATTGAG
1 A-AGAGATGCCACTGAGTCGTGGGCTTTAAG
*
209373 AAGAGATTGCCACTGAGTCGTGGACTTTAAG
1 AAGAGA-TGCCACTGAGTCGTGGGCTTTAAG
209404 AAG
1 AAG
209407 GTATTTGACG
Statistics
Matches: 296, Mismatches: 65, Indels: 58
0.71 0.16 0.14
Matches are distributed among these distances:
27 65 0.22
28 14 0.05
29 27 0.09
30 73 0.25
31 93 0.31
32 3 0.01
33 2 0.01
34 1 0.00
35 18 0.06
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.23
Consensus pattern (30 bp):
AAGAGATGCCACTGAGTCGTGGGCTTTAAG
Found at i:210408 original size:17 final size:15
Alignment explanation
Indices: 210352--210407 Score: 78
Period size: 16 Copynumber: 3.7 Consensus size: 15
210342 GGTTCTTCCC
210352 TTCTTTTTTTTTTGT
1 TTCTTTTTTTTTTGT
210367 TTCTTCTTTTTTTT-T
1 TTCTT-TTTTTTTTGT
*
210382 TCCTTTTTTGTTTTGT
1 TTCTTTTTT-TTTTGT
210398 TTCTTTTTTT
1 TTCTTTTTTT
210408 GGAAAAGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
14 4 0.11
15 15 0.42
16 17 0.47
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (15 bp):
TTCTTTTTTTTTTGT
Found at i:210679 original size:10 final size:10
Alignment explanation
Indices: 210666--210691 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
210656 GTGTTTTTTG
210666 TTTTTTTGTT
1 TTTTTTTGTT
210676 TTTTTTTGTT
1 TTTTTTTGTT
210686 TTTTTT
1 TTTTTT
210692 CATCACTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:214620 original size:19 final size:18
Alignment explanation
Indices: 214596--214663 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
214586 CAGTAGCTAA
214596 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
214615 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
214630 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
214647 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
214664 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:214636 original size:13 final size:13
Alignment explanation
Indices: 214618--214642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
214608 ACAATACTTA
214618 TGTATCGATACAT
1 TGTATCGATACAT
214631 TGTATCGATACA
1 TGTATCGATACA
214643 AAACTTATGT
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):
TGTATCGATACAT
Found at i:214640 original size:32 final size:32
Alignment explanation
Indices: 214599--214661 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
214589 TAGCTAATTA
*
214599 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
214631 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
214662 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Done.