Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2101
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: 301709
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 2
Found at i:213156 original size:22 final size:23
Alignment explanation
Indices: 213110--213156 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
213100 TATATAATGA
*
213110 TATGTGCAGTAATAAAAGAAAGT
1 TATGTGCAGCAATAAAAGAAAGT
*
213133 TATGTGTAGCAATAAAA-AAAGT
1 TATGTGCAGCAATAAAAGAAAGT
213155 TA
1 TA
213157 AATGATGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (23 bp):
TATGTGCAGCAATAAAAGAAAGT
Found at i:213808 original size:31 final size:31
Alignment explanation
Indices: 213771--213865 Score: 111
Period size: 31 Copynumber: 3.0 Consensus size: 31
213761 AAAATCATAC
213771 AACATAAATATAATATAAAATTTAAAATATT
1 AACATAAATATAATATAAAATTTAAAATATT
* * *
213802 AACATAAATATAATATAAATATATAATATTTT
1 AACATAAATATAATATAAA-ATTTAAAATATT
*
213834 AA-ATAAATTAAAATATAAAAATTTATAAATAT
1 AACATAAA-TATAATAT-AAAATTTA-AAATAT
213866 AATATGAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
31 24 0.45
32 22 0.42
33 7 0.13
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (31 bp):
AACATAAATATAATATAAAATTTAAAATATT
Found at i:213862 original size:26 final size:28
Alignment explanation
Indices: 213774--213875 Score: 63
Period size: 26 Copynumber: 3.6 Consensus size: 28
213764 ATCATACAAC
*
213774 ATAAATATAATATAAA-ATTTAAAATATT
1 ATAAATATAATATAAATATATAAAAT-TT
* *
213802 A-ACATA-AATATAATATAAATATATAATATT
1 ATAAATATAATATAA-AT--ATATAAAAT-TT
*
213832 TTAAATA-AAT-TAAA-ATATAAAAATTT
1 ATAAATATAATATAAATATAT-AAAATTT
*
213858 ATAAATATAATATGAATA
1 ATAAATATAATATAAATA
213876 AAATAGACTG
Statistics
Matches: 57, Mismatches: 8, Indels: 17
0.70 0.10 0.21
Matches are distributed among these distances:
26 19 0.33
27 12 0.21
28 4 0.07
29 2 0.04
30 13 0.23
31 7 0.12
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (28 bp):
ATAAATATAATATAAATATATAAAATTT
Found at i:216266 original size:16 final size:16
Alignment explanation
Indices: 216241--216271 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
216231 CGAGCCGTAG
*
216241 AATAATAAAATAAAAT
1 AATAAAAAAATAAAAT
216257 AATAAAAAAATAAAA
1 AATAAAAAAATAAAA
216272 ATAAAATCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
AATAAAAAAATAAAAT
Found at i:218193 original size:21 final size:22
Alignment explanation
Indices: 218167--218224 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
218157 AAATTACTTA
* *
218167 ATTTTTTAATTATTAA-ATATT
1 ATTTTTTAATTAATAATAAATT
218188 ATTTTTTAATTAATAATTAAATT
1 ATTTTTTAATTAATAA-TAAATT
218211 A-TTTTTAATTAATA
1 ATTTTTTAATTAATA
218225 TTTATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 15 0.45
22 13 0.39
23 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTTTTAATTAATAATAAATT
Found at i:218424 original size:6 final size:6
Alignment explanation
Indices: 218410--218459 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
218400 GACCTTGGAC
* * * *
218410 TTTTAT TTTTGT TTTCA- TTTTAT TTTTAT TTTTAT TTTGAT TATTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
218457 TTT
1 TTT
218460 ATTATTATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:218432 original size:17 final size:17
Alignment explanation
Indices: 218410--218459 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
218400 GACCTTGGAC
*
218410 TTTTATTTTTGTTTTCA
1 TTTTATTTTTATTTTCA
*
218427 TTTTATTTTTATTTTTA
1 TTTTATTTTTATTTTCA
*
218444 TTTTGATTATTATTTT
1 TTTT-ATTTTTATTTT
218460 ATTATTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 19 0.66
18 10 0.34
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (17 bp):
TTTTATTTTTATTTTCA
Found at i:218460 original size:23 final size:23
Alignment explanation
Indices: 218410--218467 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
218400 GACCTTGGAC
*
218410 TTTTATTTTTGTTTTCATTTTAT
1 TTTTATTTTTATTTTCATTTTAT
*
218433 TTTTATTTTTATTTTGATTATTA-
1 TTTTATTTTTATTTTCATT-TTAT
*
218456 TTTTATTATTAT
1 TTTTATTTTTAT
218468 AATATTTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 28 0.90
24 3 0.10
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.76
Consensus pattern (23 bp):
TTTTATTTTTATTTTCATTTTAT
Found at i:219266 original size:3 final size:3
Alignment explanation
Indices: 219258--219288 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
219248 ATTTTTATTA
219258 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
219289 CTTAAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:220273 original size:17 final size:17
Alignment explanation
Indices: 220251--220283 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
220241 TTAGTAGTGA
220251 AATTTTAAGTACTTATG
1 AATTTTAAGTACTTATG
*
220268 AATTTTAAGTATTTAT
1 AATTTTAAGTACTTAT
220284 TTAAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (17 bp):
AATTTTAAGTACTTATG
Found at i:221177 original size:16 final size:17
Alignment explanation
Indices: 221153--221189 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
221143 TTTAATTTGT
221153 ATTTAAATTAAA-ATATA
1 ATTTAAATTAAATAT-TA
221170 ATTT-AATTAAATATTA
1 ATTTAAATTAAATATTA
221186 ATTT
1 ATTT
221190 GATAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAAATTAAATATTA
Found at i:221220 original size:22 final size:23
Alignment explanation
Indices: 221172--221222 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
221162 AAAATATAAT
* *
221172 TTAATTAAATATTAATTTGATAA
1 TTAATTAAAGATTAATTTGAAAA
*
221195 -TAATTAAAGA-TAATTTTAAAA
1 TTAATTAAAGATTAATTTGAAAA
221216 TTAATTA
1 TTAATTA
221223 TGAGCCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
TTAATTAAAGATTAATTTGAAAA
Found at i:222090 original size:31 final size:32
Alignment explanation
Indices: 222033--222092 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
222023 AAATATACTT
222033 AAACTCAAATTTGATCTGAATCTAAAAAAGTC
1 AAACTCAAATTTGATCTGAATCTAAAAAAGTC
* *
222065 AAACTTAAA-TTGAT-TCGAATTTAAAAAA
1 AAACTCAAATTTGATCT-GAATCTAAAAAA
222093 TTTAAACGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.04
31 16 0.64
32 8 0.32
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (32 bp):
AAACTCAAATTTGATCTGAATCTAAAAAAGTC
Found at i:222137 original size:15 final size:16
Alignment explanation
Indices: 222087--222139 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
222077 ATTCGAATTT
*
222087 AAAA-AATTTAAACGTT
1 AAAATAATTTAAAC-TC
222103 AAAA-AATTTAAACTC
1 AAAATAATTTAAACTC
222118 AAAATAATTTAAA-TC
1 AAAATAATTTAAACTC
222133 AAAATAA
1 AAAATAA
222140 CCTAATTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
15 14 0.40
16 21 0.60
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAATAATTTAAACTC
Found at i:226897 original size:3 final size:3
Alignment explanation
Indices: 226879--226922 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
226869 CAAACTGTCA
*
226879 TAT TAT T-T TGT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
226923 TGCATTGGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:227383 original size:2 final size:2
Alignment explanation
Indices: 227371--227411 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
227361 GCCTCTCCAG
* *
227371 TC TC TC CC TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
227412 GCGCTGCTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:227500 original size:13 final size:13
Alignment explanation
Indices: 227482--227506 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
227472 TGATGCATTG
227482 ATTAAATTGTTTA
1 ATTAAATTGTTTA
227495 ATTAAATTGTTT
1 ATTAAATTGTTT
227507 CCTTGACTAT
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:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
ATTAAATTGTTTA
Found at i:235030 original size:11 final size:11
Alignment explanation
Indices: 235014--235054 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
235004 AATTAGATTT
*
235014 TTATATTAATA
1 TTATATTTATA
235025 TTATATTTATA
1 TTATATTTATA
235036 TTAT-TTTATA
1 TTATATTTATA
235046 TTTATATTT
1 -TTATATTT
235055 TACTGTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 6 0.22
11 18 0.67
12 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATATTTATA
Found at i:235046 original size:16 final size:17
Alignment explanation
Indices: 235013--235053 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
235003 TAATTAGATT
235013 TTTATATTAATATTATA
1 TTTATATTAATATTATA
*
235030 TTTATATT-ATTTTATA
1 TTTATATTAATATTATA
235046 TTTATATT
1 TTTATATT
235054 TTACTGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATATTAATATTATA
Found at i:235049 original size:6 final size:6
Alignment explanation
Indices: 235013--235054 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
235003 TAATTAGATT
*
235013 TTTATA TTAATA -TTATA TTTATA -TTAT- TTTATA TTTATA TTT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTT
235055 TACTGTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
5 12 0.39
6 19 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:239204 original size:20 final size:20
Alignment explanation
Indices: 239179--239222 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
239169 GCCGTTGGGC
*
239179 ACAATGTACTATGTATTGAT
1 ACAATGTACCATGTATTGAT
*
239199 ACAATGTCCCATGTATTGAT
1 ACAATGTACCATGTATTGAT
239219 ACAA
1 ACAA
239223 ACAGTGGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (20 bp):
ACAATGTACCATGTATTGAT
Found at i:239273 original size:20 final size:20
Alignment explanation
Indices: 239248--239286 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
239238 CTACTGCTAG
239248 TTTCATGTATCGATACAATT
1 TTTCATGTATCGATACAATT
239268 TTTCATGTATCGATACAAT
1 TTTCATGTATCGATACAAT
239287 GAACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (20 bp):
TTTCATGTATCGATACAATT
Found at i:240520 original size:13 final size:13
Alignment explanation
Indices: 240502--240528 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
240492 ACATTATGCT
240502 TTGTATCGATACA
1 TTGTATCGATACA
240515 TTGTATCGATACA
1 TTGTATCGATACA
240528 T
1 T
240529 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:240537 original size:19 final size:19
Alignment explanation
Indices: 240513--240587 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
240503 TGTATCGATA
240513 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGTT
240532 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGTT
* *
240551 CATTGTATTGATACATATT
1 CATTGTATCGATACATGTT
240570 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
240588 AAACTGGCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 37 0.73
20 14 0.27
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (19 bp):
CATTGTATCGATACATGTT
Found at i:240654 original size:13 final size:13
Alignment explanation
Indices: 240632--240661 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
240622 GATGCATGAG
*
240632 ACATTGTATCGAT
1 ACATTATATCGAT
240645 ACATTATATCGAT
1 ACATTATATCGAT
240658 ACAT
1 ACAT
240662 GGTAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (13 bp):
ACATTATATCGAT
Found at i:245687 original size:121 final size:121
Alignment explanation
Indices: 245518--245758 Score: 419
Period size: 121 Copynumber: 2.0 Consensus size: 121
245508 CCTCTATTTG
* * *
245518 TTTTCATTTCTCTAATTACTACCAATTTTATGCAAAAATCTCTTATTTTATTATAAAGAAATTTT
1 TTTTCATTTCTATAATTAATACCAATTTTATGCAAAAATCTCTCATTTTATTATAAAGAAATTTT
* *
245583 ATACCAATATTCTTTAATTTTTTCAATTTCTTCCTTTATAACAACTAGTCATTTTC
66 ATACCAATATTCTTCAATTTTTTCAATTTCTTCCTTTATAACAACTAATCATTTTC
*
245639 TTTTCATTTCTATAATTAATACCAATTTTATGCAAAAATCTCTCATTTTGTTATAAAGAAATTTT
1 TTTTCATTTCTATAATTAATACCAATTTTATGCAAAAATCTCTCATTTTATTATAAAGAAATTTT
*
245704 ATACTAATATTCTTCAATTTTTTCAATTTCTTCCTTTATAACAACTAATCATTTT
66 ATACCAATATTCTTCAATTTTTTCAATTTCTTCCTTTATAACAACTAATCATTTT
245759 TTCCCCCTTA
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 113 1.00
ACGTcount: A:0.32, C:0.16, G:0.02, T:0.49
Consensus pattern (121 bp):
TTTTCATTTCTATAATTAATACCAATTTTATGCAAAAATCTCTCATTTTATTATAAAGAAATTTT
ATACCAATATTCTTCAATTTTTTCAATTTCTTCCTTTATAACAACTAATCATTTTC
Found at i:245823 original size:32 final size:32
Alignment explanation
Indices: 245782--245845 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
245772 AAATATTTCC
* *
245782 CCCAAAATTATAAACTCTTTTCCTCTTTTCTA
1 CCCAAAATTATAAACTCTTTTCCCCATTTCTA
245814 CCCAAAATTATAAACTCTTTTCCCCATTTCTA
1 CCCAAAATTATAAACTCTTTTCCCCATTTCTA
245846 TTAGGCCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (32 bp):
CCCAAAATTATAAACTCTTTTCCCCATTTCTA
Found at i:250448 original size:24 final size:24
Alignment explanation
Indices: 250421--250480 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
250411 ACAATGTATC
**
250421 GATACATGAACAATGATGAGTAGT
1 GATACATGAACAATGATGAACAGT
* *
250445 GATATATGAACATTGATGAACAGT
1 GATACATGAACAATGATGAACAGT
*
250469 AATACATGAACA
1 GATACATGAACA
250481 GTAATGTATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (24 bp):
GATACATGAACAATGATGAACAGT
Found at i:250992 original size:16 final size:16
Alignment explanation
Indices: 250968--250998 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
250958 AAAGGCTTTC
*
250968 AAAATTTTTAATAGAA
1 AAAAGTTTTAATAGAA
250984 AAAAGTTTTAATAGA
1 AAAAGTTTTAATAGA
250999 GGAAATGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
AAAAGTTTTAATAGAA
Found at i:253571 original size:19 final size:20
Alignment explanation
Indices: 253524--253573 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
253514 TAGTTTCATA
**
253524 TATCGATACAATTGTGCATG
1 TATCGATACAATTGACCATG
* *
253544 TATCAATACAA-TGACCATT
1 TATCGATACAATTGACCATG
253563 TATCGATACAA
1 TATCGATACAA
253574 AGCTAATGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (20 bp):
TATCGATACAATTGACCATG
Found at i:254537 original size:33 final size:33
Alignment explanation
Indices: 254492--254564 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
254482 TACGTCGGTT
* * *
254492 AAGTGAACTAAAGTGCTCATCCATGCGCTGTGA
1 AAGTGAAATAAAGTGCTCATCCATGCACTGCGA
254525 AAGTGAAATAAAGTGCTCATCCATGCACTGCGA
1 AAGTGAAATAAAGTGCTCATCCATGCACTGCGA
254558 AAGTGAA
1 AAGTGAA
254565 GTGATCAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (33 bp):
AAGTGAAATAAAGTGCTCATCCATGCACTGCGA
Found at i:260609 original size:3 final size:3
Alignment explanation
Indices: 260601--260631 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
260591 TCCGAGTCAA
*
260601 CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
260632 TTTGATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:262229 original size:13 final size:12
Alignment explanation
Indices: 262209--262268 Score: 65
Period size: 13 Copynumber: 5.2 Consensus size: 12
262199 GCTGTAGAAG
262209 CATGTATCGATA
1 CATGTATCGATA
262221 CATTGTATCGATA
1 CA-TGTATCGATA
*
262234 CA-AT-TC-AT-
1 CATGTATCGATA
262242 CATGTATCGATA
1 CATGTATCGATA
262254 CATTGTATCGATA
1 CA-TGTATCGATA
262267 CA
1 CA
262269 AACAGTGGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
8 2 0.05
9 3 0.08
10 4 0.10
11 3 0.08
12 4 0.10
13 24 0.60
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.35
Consensus pattern (12 bp):
CATGTATCGATA
Found at i:262323 original size:20 final size:20
Alignment explanation
Indices: 262298--262352 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
262288 CCGCCAGTTT
262298 CATGTATCGATACAATTGTG-
1 CATGTATCGATACAA-TGTGC
262318 CATGTATCGATACAATGTGC
1 CATGTATCGATACAATGTGC
*
262338 CATGTATCGACACAA
1 CATGTATCGATACAA
262353 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATGTGC
Found at i:262354 original size:83 final size:83
Alignment explanation
Indices: 262257--262418 Score: 279
Period size: 83 Copynumber: 2.0 Consensus size: 83
262247 ATCGATACAT
* *
262257 TGTATCGATACAAACAGTGGTAGGGTAGCTACCGCCAGTTTCATGTATCGATACAATTGTGCATG
1 TGTATCGACACAAACAGTGGTAGGGTAGCTACCGCCAGTTTCATATATCGATACAATTGTGCATG
262322 TATCGATACAATGTGCCA
66 TATCGATACAATGTGCCA
* *
262340 TGTATCGACACAAACAGTGGTAGGGTAGCTTCTGCCAGTTTCATATATCGATACAATTGTGCATG
1 TGTATCGACACAAACAGTGGTAGGGTAGCTACCGCCAGTTTCATATATCGATACAATTGTGCATG
*
262405 TATTGATACAATGT
66 TATCGATACAATGT
262419 ATTGATACAA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 74 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (83 bp):
TGTATCGACACAAACAGTGGTAGGGTAGCTACCGCCAGTTTCATATATCGATACAATTGTGCATG
TATCGATACAATGTGCCA
Found at i:262420 original size:13 final size:13
Alignment explanation
Indices: 262402--262428 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
262392 ACAATTGTGC
262402 ATGTATTGATACA
1 ATGTATTGATACA
262415 ATGTATTGATACA
1 ATGTATTGATACA
262428 A
1 A
262429 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:277812 original size:20 final size:20
Alignment explanation
Indices: 277789--277835 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
277779 GGAGGTGTTG
277789 AACATG-TCATAAATGCATGA
1 AACATGCTCA-AAATGCATGA
277809 AACATAGCTCAAAATGCATGA
1 AACAT-GCTCAAAATGCATGA
*
277830 ATCATG
1 AACATG
277836 GGCTATTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 15 0.62
22 3 0.12
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (20 bp):
AACATGCTCAAAATGCATGA
Found at i:278750 original size:52 final size:51
Alignment explanation
Indices: 278672--278820 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
278662 CGAAATATGA
*
278672 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
278724 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
278776 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
278821 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:278827 original size:13 final size:13
Alignment explanation
Indices: 278809--278833 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
278799 CAAAGATCAG
278809 TGTATCGATACAA
1 TGTATCGATACAA
278822 TGTATCGATACA
1 TGTATCGATACA
278834 TTTAAGTGAT
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:278911 original size:33 final size:33
Alignment explanation
Indices: 278874--278940 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
278864 AGTAGCTTGA
278874 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
278907 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
278940 A
1 A
278941 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:278914 original size:13 final size:13
Alignment explanation
Indices: 278896--278920 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
278886 CAAAAAAATA
278896 TGTATCGATACAT
1 TGTATCGATACAT
278909 TGTATCGATACA
1 TGTATCGATACA
278921 ACACTTTATG
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:279849 original size:55 final size:52
Alignment explanation
Indices: 279749--280309 Score: 302
Period size: 49 Copynumber: 11.6 Consensus size: 52
279739 GAAAAGTGAT
* * * * * * * *
279749 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATG-G-A
* *
279803 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATT-GAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTAG-ACTTAAAGATGGA
*
279856 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTAGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGGA
* *
279899 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGGA
* * * * *
279948 GAAGTTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGGA
* * *
279992 -AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGATTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGGA
* ** * *
280041 -AAGGTGCCAATATGCTGATTCAAGGCCAG--AGA-T--A-TT-GGGCT--T
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGGA
* * * *
280083 AAAGGTGTCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGGA
* * * * * * *
280132 GAAGTTGCCAATATGCAGATTCAAGGCCAACGATATTGGAC-T-----T-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGGA
* *
280176 -AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGGA
* * * * *
280225 -AAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATG-GA
* *
280277 GAAAGGATGTCAATGTGCTGATTCAAGGCCAGC
1 -AAAGG-TGCCAATATGCTGATTCAAGGCCAGC
280310 GATATTGGGC
Statistics
Matches: 405, Mismatches: 61, Indels: 81
0.74 0.11 0.15
Matches are distributed among these distances:
42 2 0.00
43 135 0.33
44 4 0.01
45 2 0.00
46 3 0.01
47 2 0.00
48 3 0.01
49 145 0.36
50 1 0.00
51 2 0.00
52 31 0.08
53 7 0.02
54 10 0.02
55 58 0.14
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGGA
Found at i:279917 original size:43 final size:43
Alignment explanation
Indices: 279856--280270 Score: 389
Period size: 43 Copynumber: 9.1 Consensus size: 43
279846 TAAAGATGGA
* *
279856 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTAGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
279899 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
279942 AAAGAAGAAGTTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 --A-AAG--G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
279991 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGATTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
** * *
280034 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGAGATATTGGGCTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
280083 AAAGGTGTCAATGTGCTAATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * * *
280126 AAAGAAGAAGTTGCCAATATGCAGATTCAAGGCCAACGATATTGGACTT
1 --A-AAG--G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
280175 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * * *
280218 AAAGATGAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
280267 AAAG
1 AAAG
280271 ATGAGAGAAA
Statistics
Matches: 304, Mismatches: 44, Indels: 48
0.77 0.11 0.12
Matches are distributed among these distances:
43 145 0.48
44 2 0.01
45 4 0.01
46 12 0.04
48 2 0.01
49 139 0.46
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:279996 original size:92 final size:92
Alignment explanation
Indices: 279803--280270 Score: 720
Period size: 92 Copynumber: 5.0 Consensus size: 92
279793 AAGATGAGAA
* * *
279803 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAAT
* *
279868 ATGCTGATTCAAGGCCAGCTATATTAGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
*
279899 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
279964 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
279991 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGATTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
* *
280056 TGATTCAAGGCCAGAGATATTGGGCTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
280083 AAAGGTGTCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
* *
280148 AGATTCAAGGCCAACGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* *
280175 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
* *
280240 TAATTCAAGGCCAGCGATATTGGGCTT
66 TGATTCAAGGCCAGCGATATTGGACTT
280267 AAAG
1 AAAG
280271 ATGAGAGAAA
Statistics
Matches: 340, Mismatches: 32, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
92 294 0.86
95 41 0.12
96 5 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:280363 original size:32 final size:31
Alignment explanation
Indices: 280315--280408 Score: 120
Period size: 32 Copynumber: 3.0 Consensus size: 31
280305 CCAGCGATAT
280315 TGGGC-TTAGAAGGGTTGCCACTGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACTGACTTGTG
*
280345 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGA-AGGGTTGCCACTGACTTGTG
* *
280377 TGGGCTTTTGAAAAGGG-TGCCACTAACTTGTG
1 TGGGC-TTT-AGAAGGGTTGCCACTGACTTGTG
280409 GGCTTAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
30 5 0.09
31 5 0.09
32 37 0.66
33 7 0.12
34 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.35, T:0.30
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACTGACTTGTG
Found at i:280639 original size:87 final size:88
Alignment explanation
Indices: 280486--280747 Score: 309
Period size: 87 Copynumber: 3.0 Consensus size: 88
280476 TGGACTTTGG
* * * * *
280486 AAAAGATGCCA-TCGACTTGTGGGCTTCGAAAAAGGGTGCCACTGATTTGTGGGC-TTTGAAGGT
1 AAAAGATGACACT-GACTTGTGGGCTTTGAAAAA-GATGCCACTGACTTGTGGGCTTTTAAAGGT
280549 TGCCACTGACTTGTGGGCTTTTGAA
64 TGCCACTGACTTGTGGGCTTTTGAA
*
280574 AAAA-ATGACACTGACTTGTGGGCTTTGAAAAAGATGCCACTAACTTGTGGGCTTTTAAAGGTTG
1 AAAAGATGACACTGACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTTAAAGGTTG
*
280638 CCGCTGACTTGTGGGC-TTTGAA
66 CCACTGACTTGTGGGCTTTTGAA
* * * * * * **
280660 AAAAGATGCCACTAACTTGTGGGCTTT-TAAAGGTTGCCACTGACTTGTGGGCTTTGAAAAATAT
1 AAAAGATGACACTGACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTTAAAGGT-T
* *
280724 GCCACTGACTTATGGACTTTTGAA
65 GCCACTGACTTGTGGGCTTTTGAA
280748 GGGTGAGGAA
Statistics
Matches: 150, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
86 55 0.37
87 84 0.56
88 11 0.07
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (88 bp):
AAAAGATGACACTGACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTTAAAGGTTG
CCACTGACTTGTGGGCTTTTGAA
Found at i:280648 original size:28 final size:28
Alignment explanation
Indices: 280490--280749 Score: 209
Period size: 30 Copynumber: 9.0 Consensus size: 28
280480 CTTTGGAAAA
**
280490 GATGCCA-TCGACTTGTGGGCTTCGAAAAAG
1 GATGCCACT-GACTTGTGGGCTT--TTAAAG
* * *
280520 GGTGCCACTGATTTGTGGGC-TTTGAAG
1 GATGCCACTGACTTGTGGGCTTTTAAAG
* *
280547 GTTGCCACTGACTTGTGGGCTTTTGAAAAA
1 GATGCCACTGACTTGTGGGCTTTT--AAAG
* * * *
280577 AATGACACTGACTTGTGGGCTTTGAAAAA
1 GATGCCACTGACTTGTGGGCTTT-TAAAG
*
280606 GATGCCACTAACTTGTGGGCTTTTAAAG
1 GATGCCACTGACTTGTGGGCTTTTAAAG
* * * *
280634 GTTGCCGCTGACTTGTGGGCTTTGAAAAAA
1 GATGCCACTGACTTGTGGGCTTT--TAAAG
*
280664 GATGCCACTAACTTGTGGGCTTTTAAAG
1 GATGCCACTGACTTGTGGGCTTTTAAAG
* * *
280692 GTTGCCACTGACTTGTGGGCTTTGAAAAA
1 GATGCCACTGACTTGTGGGCTTT-TAAAG
* * * *
280721 TATGCCACTGACTTATGGACTTTTGAAG
1 GATGCCACTGACTTGTGGGCTTTTAAAG
280749 G
1 G
280750 GTGAGGAATG
Statistics
Matches: 182, Mismatches: 40, Indels: 18
0.76 0.17 0.08
Matches are distributed among these distances:
27 21 0.12
28 52 0.29
29 47 0.26
30 61 0.34
31 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (28 bp):
GATGCCACTGACTTGTGGGCTTTTAAAG
Found at i:280680 original size:58 final size:57
Alignment explanation
Indices: 280473--280749 Score: 299
Period size: 57 Copynumber: 4.8 Consensus size: 57
280463 TGCCTCGGAG
* * * ** * *
280473 TTGTGGACTTTGGAAAAGATGCCA-TCGACTTGTGGGCTTCGAAAAAGGGTGCCACTGAT
1 TTGTGGGCTTTGAAAAAGATGCCACT-AACTTGTGGGCTT--TTAAAGGTTGCCACTGAC
* * * *** *
280532 TTGTGGGCTTTG--AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAATGACACTGAC
1 TTGTGGGCTTTGAAAAAGATGCCACTAACTTGTGGGCTTTT--AAAGGTTGCCACTGAC
*
280589 TTGTGGGCTTTGAAAAAGATGCCACTAACTTGTGGGCTTTTAAAGGTTGCCGCTGAC
1 TTGTGGGCTTTGAAAAAGATGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGAC
280646 TTGTGGGCTTTGAAAAAAGATGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGAC
1 TTGTGGGCTTTG-AAAAAGATGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGAC
* * * * *
280704 TTGTGGGCTTTGAAAAATATGCCACTGACTTATGGACTTTTGAAGG
1 TTGTGGGCTTTGAAAAAGATGCCACTAACTTGTGGGCTTTTAAAGG
280750 GTGAGGAATG
Statistics
Matches: 188, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
57 96 0.51
58 57 0.30
59 35 0.19
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (57 bp):
TTGTGGGCTTTGAAAAAGATGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGAC
Found at i:282188 original size:1 final size:1
Alignment explanation
Indices: 282182--282292 Score: 87
Period size: 1 Copynumber: 111.0 Consensus size: 1
282172 ATCCGGACCC
* * * * * * * *
282182 TTTTTTTTGTTTTTTTTTGTTTGTTTTTTTGTTTGTTTTTTTTTGTTTTTGTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * *
282247 GTTTTGTTTTTGTTGTTTTTTTTTTGTTTTGTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
282293 GTGGAGGACG
Statistics
Matches: 80, Mismatches: 30, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 80 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (1 bp):
T
Found at i:282204 original size:14 final size:14
Alignment explanation
Indices: 282182--282292 Score: 121
Period size: 14 Copynumber: 8.2 Consensus size: 14
282172 ATCCGGACCC
282182 TTTTT-TTTGTTTT
1 TTTTTGTTTGTTTT
282195 TTTTTGTTTG--TT
1 TTTTTGTTTGTTTT
282207 TTTTTGTTTGTTTT
1 TTTTTGTTTGTTTT
282221 TTTTTGTTT-TTGTT
1 TTTTTGTTTGTT-TT
282235 TTTTTGTTT-TTTGT
1 TTTTTGTTTGTTT-T
282249 TTTGTT-TTTGTTGTT
1 TTT-TTGTTTGTT-TT
282264 TTTTT-TTTGTTTT
1 TTTTTGTTTGTTTT
*
282277 GTTTTGTTT-TTTT
1 TTTTTGTTTGTTTT
282290 TTT
1 TTT
282293 GTGGAGGACG
Statistics
Matches: 87, Mismatches: 2, Indels: 18
0.81 0.02 0.17
Matches are distributed among these distances:
12 12 0.14
13 20 0.23
14 46 0.53
15 8 0.09
16 1 0.01
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (14 bp):
TTTTTGTTTGTTTT
Found at i:282209 original size:21 final size:21
Alignment explanation
Indices: 282184--282294 Score: 115
Period size: 20 Copynumber: 5.4 Consensus size: 21
282174 CCGGACCCTT
282184 TTTTTTGTTTTTTTTTGTTTG
1 TTTTTTGTTTTTTTTTGTTTG
282205 TTTTTTTGTTTGTTTTTT-TTTG
1 -TTTTTTGTTT-TTTTTTGTTTG
282227 -TTTTTGTTTTTTTGTT-TTT-
1 TTTTTTGTTTTTTT-TTGTTTG
* * *
282246 TGTTTTG-TTTTTGTTGTTTT
1 TTTTTTGTTTTTTTTTGTTTG
* *
282266 TTTTTTGTTTTGTTTTGTTTT
1 TTTTTTGTTTTTTTTTGTTTG
282287 TTTTTTGT
1 TTTTTTGT
282295 GGAGGACGCC
Statistics
Matches: 78, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.03
19 12 0.15
20 25 0.32
21 19 0.24
22 14 0.18
23 6 0.08
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (21 bp):
TTTTTTGTTTTTTTTTGTTTG
Found at i:282228 original size:36 final size:34
Alignment explanation
Indices: 282182--282292 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 34
282172 ATCCGGACCC
282182 TTTTTTTTGTTTTTTTTTGTTTGTTTTTTTGTTTGT
1 TTTTTTTTGTTTTTTTTT-TTTGTTTTTTTGTTT-T
282218 TTTTTTTTGTTTTTGTTTTTTTG-TTTTTTGTTTT
1 TTTTTTTTGTTTTT-TTTTTTTGTTTTTTTGTTTT
* *
282252 GTTTTTGTTGTTTTTTTTTTGTT-TTGTTTTGTTTT
1 -TTTTTTTTGTTTTTTTTTT-TTGTTTTTTTGTTTT
282287 TTTTTT
1 TTTTTT
282293 GTGGAGGACG
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
34 11 0.16
35 35 0.51
36 18 0.26
37 4 0.06
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (34 bp):
TTTTTTTTGTTTTTTTTTTTTGTTTTTTTGTTTT
Found at i:282293 original size:35 final size:34
Alignment explanation
Indices: 282183--282294 Score: 124
Period size: 36 Copynumber: 3.3 Consensus size: 34
282173 TCCGGACCCT
282183 TTTTTTTG-TTTTTTTTTGTTTGTTTTTTTGTTTGTT
1 TTTTTTTGTTTTTTTTTTG-TTGTTTTTTT-TTTG-T
282219 TTTTTTTGTTTTTGTTTTT-TTGTTTTTTGTTTTGT
1 TTTTTTTGTTTTT-TTTTTGTTGTTTTTT-TTTTGT
* * *
282254 TTTTGTTGTTTTTTTTTTGTT-TTGTTTTGTT-T
1 TTTTTTTGTTTTTTTTTTGTTGTTTTTTTTTTGT
282286 TTTTTTTGT
1 TTTTTTTGT
282295 GGAGGACGCC
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
32 9 0.13
33 3 0.04
34 10 0.15
35 15 0.22
36 21 0.31
37 5 0.07
38 5 0.07
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (34 bp):
TTTTTTTGTTTTTTTTTTGTTGTTTTTTTTTTGT
Found at i:292001 original size:10 final size:10
Alignment explanation
Indices: 291986--292012 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
291976 ATGTATCAAG
291986 CAAAAACAAA
1 CAAAAACAAA
291996 CAAAAACAAA
1 CAAAAACAAA
292006 CAAAAAC
1 CAAAAAC
292013 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:295291 original size:20 final size:20
Alignment explanation
Indices: 295268--295314 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
295258 GGAGGTGTTG
295268 AACATG-TCATAAATGCATGA
1 AACATGCTCA-AAATGCATGA
295288 AACATAGCTCAAAATGCATGA
1 AACAT-GCTCAAAATGCATGA
*
295309 ATCATG
1 AACATG
295315 GGCTATTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 15 0.62
22 3 0.12
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (20 bp):
AACATGCTCAAAATGCATGA
Found at i:296272 original size:52 final size:52
Alignment explanation
Indices: 296163--296279 Score: 173
Period size: 52 Copynumber: 2.2 Consensus size: 52
296153 ATTTGCCTGT
***
296163 ATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATA
1 ATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGATA
*
296215 ATGTATCGATACATTTGGGCAAATTTGCCTGCATGTATCGATACA-AAGATCA
1 ATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGAT-A
*
296267 GTGTATCGATACA
1 ATGTATCGATACA
296280 ATGTATCGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 2 0.03
52 57 0.97
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (52 bp):
ATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGATA
Found at i:296286 original size:13 final size:13
Alignment explanation
Indices: 296268--296292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
296258 CAAAGATCAG
296268 TGTATCGATACAA
1 TGTATCGATACAA
296281 TGTATCGATACA
1 TGTATCGATACA
296293 TTTAAGTGAT
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:296370 original size:33 final size:33
Alignment explanation
Indices: 296333--296399 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
296323 AGTAGCTTGA
296333 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
296366 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
296399 A
1 A
296400 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:296373 original size:13 final size:13
Alignment explanation
Indices: 296355--296379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
296345 CAAAAAAATA
296355 TGTATCGATACAT
1 TGTATCGATACAT
296368 TGTATCGATACA
1 TGTATCGATACA
296380 ACACTTTATG
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:299504 original size:20 final size:20
Alignment explanation
Indices: 299479--299576 Score: 144
Period size: 20 Copynumber: 4.9 Consensus size: 20
299469 GTAAAAAGAT
299479 AGAATGTATCGATACATTAA
1 AGAATGTATCGATACATTAA
*
299499 AGAATGTATCGATACATTCAT
1 AGAATGTATCGATACATT-AA
* *
299520 A-TATGTATCGATACATTGA
1 AGAATGTATCGATACATTAA
*
299539 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTAA
299559 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
299577 TGGGCACTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
19 1 0.01
20 68 0.96
21 2 0.03
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (20 bp):
AGAATGTATCGATACATTAA
Found at i:300735 original size:27 final size:28
Alignment explanation
Indices: 300684--301392 Score: 728
Period size: 28 Copynumber: 25.1 Consensus size: 28
300674 TCATCTCTTC
* *
300684 AAGCCCATAAGTCAGTGGCACCCTTTCA
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
* *
300712 AAGCCCACAAGTCAAT-GCATCCTTTTA
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
*
300739 AAGCCCACAAG-CAGTGGCACCCTTTCA
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
*
300766 AAGCTCAC-AGTCAGTGGCATCCTTTCA
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
** * *
300793 AAGCCCATGAGTCGGTGGCAACTCTTTTCA
1 AAGCCCACAAGTCAGTGGC-A-TCCTTTCA
300823 AAGCCCACAAGTCAGTGGCATCCTTTC-
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
* * *
300850 AAGCCCACAATTCAGTGGCACCCTTTCC
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
*
300878 AAGCCC-CACGTCAGTGGCATCCTTTCA
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
* * * *
300905 AAGCCCACGAGTCGGTAGCAACTCTTTTCA
1 AAGCCCACAAGTCAGTGGC-A-TCCTTTCA
* * *
300935 AAGCCC-TAAGTCAATGGCATCCTTTTA
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
* *
300962 AAGCCCAC-AGTTAGTGGCATCTTTTCA
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
*
300989 AAGCCCACAAGTC-GATGGCAACTCTTTTCA
1 AAGCCCACAAGTCAG-TGGC-A-TCCTTTCA
*
301019 AAGCCCACAAGTCAGTGGCACCCTTTCA
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
301047 AAGCCCAC-A-TCAGTGG-ATCCTTTC-
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
301071 AAGCCCAC-AGTCAGTGGCATCCTTTCA
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
301098 AAGCCCACAAGTCAGTGGCATTTTCCTTTTCA
1 AAGCCCACAAGTCAGTGGCA---TCC-TTTCA
*
301130 AAGCCCACAAGTCAATGGCCATCCTTTCA
1 AAGCCCACAAGTCAGTGG-CATCCTTTCA
* *
301159 AAGCCCACGAA-TCGGTGTGCAACTCTTTTCA
1 AAGCCCAC-AAGTCAGTG-GC-A-TCCTTTCA
* *
301190 AAGCCCAAAAGTCAGTGGCACCCTTTCA
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
* *
301218 AAGCCCACAAGTCAGTAGCACTCTTTTCA
1 AAGCCCACAAGTCAGTGGCA-TCCTTTCA
* * * *
301247 AAACCCACAAGTCAATAGCATCCTATCA
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
* *
301275 AAGCCCATAAGTCCGTGGCA-CCATTTCA
1 AAGCCCACAAGTCAGTGGCATCC-TTTCA
* *
301303 AAGCCCACAAGTCAGTGCCACCCTTTCA
1 AAGCCCACAAGTCAGTGGCATCCTTTCA
* *
301331 AAGCCCACAAGTCGGTGGCACTCTTTTCA
1 AAGCCCACAAGTCAGTGGCA-TCCTTTCA
*
301360 AAGCCCACACGAGTCAGTGGCAACTCTTTCA
1 AAGCCCACA--AGTCAGTGGCATC-CTTTCA
301391 AA
1 AA
301393 ACCCGCAACG
Statistics
Matches: 569, Mismatches: 76, Indels: 69
0.80 0.11 0.10
Matches are distributed among these distances:
24 9 0.02
25 14 0.02
26 20 0.04
27 152 0.27
28 165 0.29
29 72 0.13
30 73 0.13
31 40 0.07
32 22 0.04
33 2 0.00
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCATCCTTTCA
Found at i:301416 original size:59 final size:56
Alignment explanation
Indices: 300684--301396 Score: 492
Period size: 57 Copynumber: 12.6 Consensus size: 56
300674 TCATCTCTTC
* * *
300684 AAGCCCATAAGTCAGTGGC-ACCCTTTCAAAGCCCACAAGTCAAT-GCATCCTTTT-A
1 AAGCCCACAAGTCAGT-GCAACCCTTTCAAAACCCACAAGTCAGTGGCA-CCTTTTCA
* *
300739 AAGCCCACAAG-CAGTGGC-ACCCTTTCAAAGCTCAC-AGTCAGTGGCATCC-TTTCA
1 AAGCCCACAAGTCAGT-GCAACCCTTTCAAAACCCACAAGTCAGTGGCA-CCTTTTCA
** * * *
300793 AAGCCCATGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTC-
1 AAGCCCACAAGTCAGT-GCAAC-CCTTTCAAAACCCACAAGTCAGTGGCA-CCTTTTCA
* * * *
300850 AAGCCCACAATTCAGTGGC-ACCCTTTCCAAGCCC-CACGTCAGTGGCATCC-TTTCA
1 AAGCCCACAAGTCAGT-GCAACCCTTTCAAAACCCACAAGTCAGTGGCA-CCTTTTCA
* * * * * *
300905 AAGCCCACGAGTCGGTAGCAACTCTTTTCAAAGCCC-TAAGTCAATGGCATCCTTTT-A
1 AAGCCCACAAGTCAGT-GCAAC-CCTTTCAAAACCCACAAGTCAGTGGCA-CCTTTTCA
* * * *
300962 AAGCCCAC-AGTTAGTGGC-ATCTTTTCAAAGCCCACAAGTC-GATGGCAACTCTTTTCA
1 AAGCCCACAAGTCAGT-GCAACCCTTTCAAAACCCACAAGTCAG-TGGC-AC-CTTTTCA
*
301019 AAGCCCACAAGTCAGTGGC-ACCCTTTCAAAGCCCAC-A-TCAGTGG-ATCC-TTTC-
1 AAGCCCACAAGTCAGT-GCAACCCTTTCAAAACCCACAAGTCAGTGGCA-CCTTTTCA
* *
301071 AAGCCCAC-AGTCAGTGGC-ATCCTTTCAAAGCCCACAAGTCAGTGGCATTTTCCTTTTCA
1 AAGCCCACAAGTCAGT-GCAACCCTTTCAAAACCCACAAGTCAGTGGCA----CCTTTTCA
* * * * *
301130 AAGCCCACAAGTCAATGGCCATCCTTTCAAAGCCCACGAA-TCGGTGTGCAACTCTTTTCA
1 AAGCCCACAAGTCAGT-GCAACCCTTTCAAAACCCAC-AAGTCAGTG-GC-AC-CTTTTCA
* * *
301190 AAGCCCAAAAGTCAGTGGC-ACCCTTTCAAAGCCCACAAGTCAGTAGCACTCTTTTCA
1 AAGCCCACAAGTCAGT-GCAACCCTTTCAAAACCCACAAGTCAGTGGCAC-CTTTTCA
* * * * * * * *
301247 AAACCCACAAGTCAATAGC-ATCCTATCAAAGCCCATAAGTCCGTGGCACCATTTCA
1 AAGCCCACAAGTCAGT-GCAACCCTTTCAAAACCCACAAGTCAGTGGCACCTTTTCA
* * *
301303 AAGCCCACAAGTCAGTGCCACCCTTTCAAAGCCCACAAGTCGGTGGCACTCTTTTCA
1 AAGCCCACAAGTCAGTGCAACCCTTTCAAAACCCACAAGTCAGTGGCAC-CTTTTCA
*
301360 AAGCCCACACGAGTCAGTGGCAACTCTTTCAAAACCC
1 AAGCCCACA--AGTCAGT-GCAACCCTTTCAAAACCC
301397 GCAACGATAG
Statistics
Matches: 559, Mismatches: 61, Indels: 71
0.81 0.09 0.10
Matches are distributed among these distances:
51 26 0.05
52 9 0.02
53 20 0.04
54 74 0.13
55 56 0.10
56 70 0.13
57 140 0.25
58 53 0.09
59 36 0.06
60 48 0.09
61 22 0.04
62 4 0.01
63 1 0.00
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (56 bp):
AAGCCCACAAGTCAGTGCAACCCTTTCAAAACCCACAAGTCAGTGGCACCTTTTCA
Done.