Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold102
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: 331322
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.28
Warning! 50393 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:209917 original size:13 final size:13
Alignment explanation
Indices: 209899--209923 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
209889 CATTTTATGG
209899 TGTATCGATACAA
1 TGTATCGATACAA
209912 TGTATCGATACA
1 TGTATCGATACA
209924 TACTGTGTGT
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:209939 original size:32 final size:33
Alignment explanation
Indices: 209876--209943 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
209866 CGTTATAAGC
**
209876 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
209909 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
209941 CAA
1 CAA
209944 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:211592 original size:21 final size:21
Alignment explanation
Indices: 211566--211613 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
211556 TGAATCGGAA
211566 GTGTTTTGGTGCAAAACTGAG
1 GTGTTTTGGTGCAAAACTGAG
211587 GTGTTTTGGTGCAAAACTGAG
1 GTGTTTTGGTGCAAAACTGAG
211608 GTGTTT
1 GTGTTT
211614 CGGATATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.08, G:0.33, T:0.38
Consensus pattern (21 bp):
GTGTTTTGGTGCAAAACTGAG
Found at i:212141 original size:13 final size:13
Alignment explanation
Indices: 212123--212161 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
212113 ATAATCCCCC
*
212123 TGTATCGATACAG
1 TGTATCGATACAA
212136 TGTATCGATACAA
1 TGTATCGATACAA
212149 TGTATCGATACAA
1 TGTATCGATACAA
212162 AGAATGCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:218357 original size:13 final size:13
Alignment explanation
Indices: 218339--218363 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
218329 CATTTTATGG
218339 TGTATCGATACAA
1 TGTATCGATACAA
218352 TGTATCGATACA
1 TGTATCGATACA
218364 TACTGTGTGT
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:218379 original size:32 final size:33
Alignment explanation
Indices: 218316--218383 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
218306 CGTTACAAGC
**
218316 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
218349 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
218381 CAA
1 CAA
218384 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:220160 original size:12 final size:11
Alignment explanation
Indices: 220143--220186 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
220133 CGTATTTTCT
*
220143 CTTTTTCTTAG
1 CTTTTTCTTTG
220154 CCTTTTTCTTTG
1 -CTTTTTCTTTG
*
220166 ATTTTTCTTTG
1 CTTTTTCTTTG
220177 CTTTTTCTTT
1 CTTTTTCTTT
220187 TTTACTTGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.05, C:0.18, G:0.07, T:0.70
Consensus pattern (11 bp):
CTTTTTCTTTG
Found at i:220172 original size:23 final size:22
Alignment explanation
Indices: 220144--220186 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
220134 GTATTTTCTC
220144 TTTTTCTTAGCCTTTTTCTTTGA
1 TTTTTCTTAG-CTTTTTCTTTGA
*
220167 TTTTTCTTTGCTTTTTCTTT
1 TTTTTCTTAGCTTTTTCTTT
220187 TTTACTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.05, C:0.16, G:0.07, T:0.72
Consensus pattern (22 bp):
TTTTTCTTAGCTTTTTCTTTGA
Found at i:227037 original size:80 final size:80
Alignment explanation
Indices: 226933--227107 Score: 237
Period size: 80 Copynumber: 2.2 Consensus size: 80
226923 AAAATTTGCA
* * *
226933 TTTTAAAAGTAAAAACATGGTTAGAGTATCTCTTCGA-AGATGGTAGGGTTGGAATATCCCTAAA
1 TTTTAGAAGTAAAAACATGGTTAGAGTATCT-TTCCAGAGATGGTAGGGTTGGAATATCCCCAAA
** *
226997 TCAGAAAAATTTAGTG
65 GAAGAAAAATTTAGAG
* *
227013 TTTTAGAAGTAAAAACA-GGATTAGATTATCTTTCCAGAGATGGTGGGGTTGGAATATCCCCAAA
1 TTTTAGAAGTAAAAACATGG-TTAGAGTATCTTTCCAGAGATGGTAGGGTTGGAATATCCCCAAA
227077 GAAGAAAAATTTAGAG
65 GAAGAAAAATTTAGAG
*
227093 TTTTAGAAGTTAAAA
1 TTTTAGAAGTAAAAA
227108 TAGGGGTTGG
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
79 6 0.07
80 78 0.93
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (80 bp):
TTTTAGAAGTAAAAACATGGTTAGAGTATCTTTCCAGAGATGGTAGGGTTGGAATATCCCCAAAG
AAGAAAAATTTAGAG
Found at i:229665 original size:20 final size:20
Alignment explanation
Indices: 229640--229681 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
229630 CATTACAAGC
*
229640 ATATATCAATACATTCACTT
1 ATATATCAATACATTAACTT
*
229660 ATATATTAATACATTAACTT
1 ATATATCAATACATTAACTT
229680 AT
1 AT
229682 TGTATCGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATATCAATACATTAACTT
Found at i:233409 original size:20 final size:21
Alignment explanation
Indices: 233386--233438 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
233376 CACATTTAGA
*
233386 TGTATCGATACATTATTC-AT
1 TGTATCGATACATTACTCAAT
233406 TGTATCGATACA-TACTCAAT
1 TGTATCGATACATTACTCAAT
*
233426 TGTATTGATACAT
1 TGTATCGATACAT
233439 GAAACTGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTACTCAAT
Found at i:233507 original size:13 final size:13
Alignment explanation
Indices: 233489--233513 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
233479 CATGGCACAT
233489 TGTATCGATACAG
1 TGTATCGATACAG
233502 TGTATCGATACA
1 TGTATCGATACA
233514 TGAAGAATTG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:233512 original size:33 final size:32
Alignment explanation
Indices: 233469--233533 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
233459 TATCACTGTT
*
233469 TGTATTGATACATG-GCACATTGTATCGATACAG
1 TGTATCGATACATGAG-A-ATTGTATCGATACAG
233502 TGTATCGATACATGAAGAATTGTATCGATACA
1 TGTATCGATACATG-AGAATTGTATCGATACA
233534 TTGTCCTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATACAG
Found at i:238288 original size:16 final size:17
Alignment explanation
Indices: 238264--238299 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
238254 AAAGGCTTTC
*
238264 AAAATTTTTAATAGA-A
1 AAAAGTTTTAATAGAGA
238280 AAAAGTTTTAATAGAGA
1 AAAAGTTTTAATAGAGA
238297 AAA
1 AAA
238300 TGTTGATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (17 bp):
AAAAGTTTTAATAGAGA
Found at i:239726 original size:13 final size:13
Alignment explanation
Indices: 239708--239747 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
239698 ATAAGGATCT
*
239708 TTGTATCAATACA
1 TTGTATCGATACA
239721 TTGTATCGATACA
1 TTGTATCGATACA
* *
239734 ATGTGTCGATACA
1 TTGTATCGATACA
239747 T
1 T
239748 GGGTTACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:242767 original size:23 final size:23
Alignment explanation
Indices: 242740--242783 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
242730 GCATTCAACC
*
242740 TTGGGTTATAATCTCTT-AAGAAT
1 TTGGGGTATAAT-TCTTGAAGAAT
242763 TTGGGGTATAATTCTTGAAGA
1 TTGGGGTATAATTCTTGAAGA
242784 GATTGTGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (23 bp):
TTGGGGTATAATTCTTGAAGAAT
Found at i:243234 original size:23 final size:23
Alignment explanation
Indices: 243200--243243 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
243190 CCTCTCAATC
*
243200 TCTTCAAGAATTATACCCTAAAT
1 TCTTCAAGAATTATAACCTAAAT
*
243223 TCTT-AAGAAATTGTAACCTAA
1 TCTTCAAG-AATTATAACCTAA
243244 GGTTAAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (23 bp):
TCTTCAAGAATTATAACCTAAAT
Found at i:243599 original size:20 final size:20
Alignment explanation
Indices: 243574--243624 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
243564 TCATGCTCCT
*
243574 ATGTATTGATACTTTTCATA
1 ATGTATCGATACTTTTCATA
243594 ATGTATCGATACTTTTCATA
1 ATGTATCGATACTTTTCATA
243614 ATGTATCGATA
1 ATGTATCGATA
243625 GATGCATTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACTTTTCATA
Found at i:246557 original size:21 final size:22
Alignment explanation
Indices: 246523--246580 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 22
246513 TTTCACTGTT
246523 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
246545 CATCACT-TTCATGTATCGATAAA
1 CATCACTGTTCATGTATCGAT--A
*
246568 AATCACTGTTCAT
1 CATCACTGTTCAT
246581 ACTGTTCACG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 13 0.41
22 7 0.22
23 7 0.22
24 5 0.16
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.36
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:246610 original size:47 final size:47
Alignment explanation
Indices: 246547--246636 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
246537 TATCGATACA
*
246547 TCACTTTCATGTATCGATAAAAATCACTGTTCAT-ACTGTTCACGTT
1 TCACTTTCATGTATCGATAAAAATCACTGTTCATCACTATTCACGTT
246593 TCACTATTCATGTATCGATAAAAATCACTGTTCATCACTATTCA
1 TCACT-TTCATGTATCGATAAAAATCACTGTTCATCACTATTCA
246637 TGTATCGATA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
46 5 0.12
47 29 0.71
48 7 0.17
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (47 bp):
TCACTTTCATGTATCGATAAAAATCACTGTTCATCACTATTCACGTT
Found at i:246763 original size:20 final size:19
Alignment explanation
Indices: 246715--246753 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
246705 ATAATTTCAA
246715 ATGCATGTATCGATACATT
1 ATGCATGTATCGATACATT
*
246734 ATGAATTGTATCGATACATT
1 ATGCA-TGTATCGATACATT
246754 GGAGCATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
ATGCATGTATCGATACATT
Found at i:255860 original size:39 final size:39
Alignment explanation
Indices: 255806--255883 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
255796 ACCTTGGTTG
255806 CATTGTTGGTGATTTTAGTTGCATAAAAATACTAGCCCA
1 CATTGTTGGTGATTTTAGTTGCATAAAAATACTAGCCCA
*
255845 CATTGTTGGTGATTTTAGTTGCATAAAAATATTAGCCCA
1 CATTGTTGGTGATTTTAGTTGCATAAAAATACTAGCCCA
255884 TAATAGGAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (39 bp):
CATTGTTGGTGATTTTAGTTGCATAAAAATACTAGCCCA
Found at i:258687 original size:19 final size:18
Alignment explanation
Indices: 258644--258691 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
258634 ATATTAAACA
258644 TATTATATTA-ATAATTT
1 TATTATATTATATAATTT
*
258661 TAAATATATTATATAATATT
1 T-ATTATATTATATAAT-TT
258681 TATTATATTAT
1 TATTATATTAT
258692 TTTCATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 8 0.31
19 14 0.54
20 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTATATTATATAATTT
Found at i:259357 original size:16 final size:16
Alignment explanation
Indices: 259336--259373 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
259326 AAGTTTATTT
*
259336 TTTATTTAAATT-TAAA
1 TTTATTT-AATTCAAAA
259352 TTTATTTAATTCAAAA
1 TTTATTTAATTCAAAA
259368 TTTATT
1 TTTATT
259374 ATATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATTTAATTCAAAA
Found at i:259480 original size:20 final size:20
Alignment explanation
Indices: 259455--259530 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
259445 AAATTTATTA
259455 AAAATATAATTTATATAAAT
1 AAAATATAATTTATATAAAT
* * *
259475 AAAATATAAAATATAATGATTTTATT
1 AAAATAT--AAT-T--T-ATATAAAT
259501 AAAAATATAATTTATATAAAT
1 -AAAATATAATTTATATAAAT
259522 AAAATATAA
1 AAAATATAA
259531 AATATAATGA
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
20 16 0.37
21 5 0.12
22 4 0.09
23 1 0.02
24 1 0.02
25 4 0.09
26 5 0.12
27 7 0.16
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (20 bp):
AAAATATAATTTATATAAAT
Found at i:259485 original size:27 final size:27
Alignment explanation
Indices: 259455--259538 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 27
259445 AAATTTATTA
259455 AAAATATAATTTATATAAATAAAATAT
1 AAAATATAATTTATATAAATAAAATAT
* * * *
259482 AAAATATAA-TGATTTTATTAAAA-AT
1 AAAATATAATTTATATAAATAAAATAT
259507 ---ATA-A-TTTATATAAATAAAATAT
1 AAAATATAATTTATATAAATAAAATAT
259529 AAAATATAAT
1 AAAATATAAT
259539 GATAAAATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
21 11 0.26
22 5 0.12
25 5 0.12
26 11 0.26
27 10 0.24
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (27 bp):
AAAATATAATTTATATAAATAAAATAT
Found at i:259510 original size:47 final size:47
Alignment explanation
Indices: 259448--259541 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
259438 TTATTTTAAA
259448 TTTATTAAAAATATAATTTATATAAATAAAATATAAAATATAATGAT
1 TTTATTAAAAATATAATTTATATAAATAAAATATAAAATATAATGAT
259495 TTTATTAAAAATATAATTTATATAAATAAAATATAAAATATAATGAT
1 TTTATTAAAAATATAATTTATATAAATAAAATATAAAATATAATGAT
259542 AAAATAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (47 bp):
TTTATTAAAAATATAATTTATATAAATAAAATATAAAATATAATGAT
Found at i:259536 original size:20 final size:20
Alignment explanation
Indices: 259455--259598 Score: 59
Period size: 20 Copynumber: 7.2 Consensus size: 20
259445 AAATTTATTA
**
259455 AAAATATAATTTATATAAAT
1 AAAATATAAAATATATAAAT
*
259475 AAAATATAAAATATAATGATTTTATT
1 AAAATATAAAATAT-AT-A----AAT
**
259501 AAAAATATAATTTATATAAAT
1 -AAAATATAAAATATATAAAT
*
259522 AAAATATAAAATATA-ATGAT
1 AAAATATAAAATATATA-AAT
* * *
259542 AAAATA-AATAGATATTAAT
1 AAAATATAAAATATATAAAT
* *
259561 CATATA-AAAATAT-TAAA-
1 AAAATATAAAATATATAAAT
*
259578 AAAACATAAAAT-TA-AAAT
1 AAAATATAAAATATATAAAT
259596 AAA
1 AAA
259599 TTTACGCCGA
Statistics
Matches: 91, Mismatches: 21, Indels: 26
0.66 0.15 0.19
Matches are distributed among these distances:
17 7 0.08
18 11 0.12
19 18 0.20
20 33 0.36
21 4 0.04
22 1 0.01
25 1 0.01
26 4 0.04
27 12 0.13
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAATATAAAATATATAAAT
Found at i:259970 original size:2 final size:2
Alignment explanation
Indices: 259963--260003 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
259953 TGCTTCATCT
* * *
259963 TA TA TA TA TA TA AA TA TA AA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
260004 TGTGTTTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:261976 original size:1 final size:1
Alignment explanation
Indices: 261966--262008 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
261956 GATGGAGAGA
* * * *
261966 TTTTTCTTTTTTCTTTTTTTCTTTTTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
262009 GGGGGGGGGG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.07, G:0.02, T:0.91
Consensus pattern (1 bp):
T
Found at i:261983 original size:8 final size:8
Alignment explanation
Indices: 261966--262008 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
261956 GATGGAGAGA
261966 TTTTTC-T
1 TTTTTCTT
261973 TTTTTCTT
1 TTTTTCTT
261981 TTTTTCTT
1 TTTTTCTT
261989 TTTTT-TT
1 TTTTTCTT
261996 GTTTTT-TT
1 -TTTTTCTT
262004 TTTTT
1 TTTTT
262009 GGGGGGGGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 13 0.38
8 21 0.62
ACGTcount: A:0.00, C:0.07, G:0.02, T:0.91
Consensus pattern (8 bp):
TTTTTCTT
Found at i:261986 original size:15 final size:14
Alignment explanation
Indices: 261966--262008 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
261956 GATGGAGAGA
261966 TTTTTCTTTTTTCTT
1 TTTTTCTTTTTT-TT
261981 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
261995 TGTTTT-TTTTTTTT
1 T-TTTTCTTTTTTTT
262009 GGGGGGGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.00, C:0.07, G:0.02, T:0.91
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:261995 original size:18 final size:17
Alignment explanation
Indices: 261966--262008 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
261956 GATGGAGAGA
*
261966 TTTTTCTTTTTTCTTTT
1 TTTTTTTTTTTTCTTTT
*
261983 TTTCTTTTTTTTTGTTTT
1 TTT-TTTTTTTTTCTTTT
262001 TTTTTTTT
1 TTTTTTTT
262009 GGGGGGGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.00, C:0.07, G:0.02, T:0.91
Consensus pattern (17 bp):
TTTTTTTTTTTTCTTTT
Found at i:264973 original size:27 final size:27
Alignment explanation
Indices: 264942--264994 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
264932 CGGTTATGAA
264942 TAGGATAGAATTTGTAACTTATGGGAT
1 TAGGATAGAATTTGTAACTTATGGGAT
*
264969 TAGGATAGGATTTGTAACTTATGGGA
1 TAGGATAGAATTTGTAACTTATGGGA
264995 CTCCTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (27 bp):
TAGGATAGAATTTGTAACTTATGGGAT
Found at i:265921 original size:151 final size:151
Alignment explanation
Indices: 265656--266112 Score: 914
Period size: 151 Copynumber: 3.0 Consensus size: 151
265646 GGATGTTATT
265656 AAGCAAACCTATTCCAAAGCATGAGATGCAGCCCAAGTCTATGAGATCAAGGTTAAGGCTGGTGC
1 AAGCAAACCTATTCCAAAGCATGAGATGCAGCCCAAGTCTATGAGATCAAGGTTAAGGCTGGTGC
265721 AATGAAGTAGGGAAACAAGTCTGTCACCAAATATGCCAACTCCTTTCAGAATTTGTGGCAAGAGA
66 AATGAAGTAGGGAAACAAGTCTGTCACCAAATATGCCAACTCCTTTCAGAATTTGTGGCAAGAGA
265786 TGGATCATTATCGATGTATAA
131 TGGATCATTATCGATGTATAA
265807 AAGCAAACCTATTCCAAAGCATGAGATGCAGCCCAAGTCTATGAGATCAAGGTTAAGGCTGGTGC
1 AAGCAAACCTATTCCAAAGCATGAGATGCAGCCCAAGTCTATGAGATCAAGGTTAAGGCTGGTGC
265872 AATGAAGTAGGGAAACAAGTCTGTCACCAAATATGCCAACTCCTTTCAGAATTTGTGGCAAGAGA
66 AATGAAGTAGGGAAACAAGTCTGTCACCAAATATGCCAACTCCTTTCAGAATTTGTGGCAAGAGA
265937 TGGATCATTATCGATGTATAA
131 TGGATCATTATCGATGTATAA
265958 AAGCAAACCTATTCCAAAGCATGAGATGCAGCCCAAGTCTATGAGATCAAGGTTAAGGCTGGTGC
1 AAGCAAACCTATTCCAAAGCATGAGATGCAGCCCAAGTCTATGAGATCAAGGTTAAGGCTGGTGC
266023 AATGAAGTAGGGAAACAAGTCTGTCACCAAATATGCCAACTCCTTTCAGAATTTGTGGCAAGAGA
66 AATGAAGTAGGGAAACAAGTCTGTCACCAAATATGCCAACTCCTTTCAGAATTTGTGGCAAGAGA
266088 TGGATCATTATCGATGTATAA
131 TGGATCATTATCGATGTATAA
266109 AAGC
1 AAGC
266113 CAACTGTTCT
Statistics
Matches: 306, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 306 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (151 bp):
AAGCAAACCTATTCCAAAGCATGAGATGCAGCCCAAGTCTATGAGATCAAGGTTAAGGCTGGTGC
AATGAAGTAGGGAAACAAGTCTGTCACCAAATATGCCAACTCCTTTCAGAATTTGTGGCAAGAGA
TGGATCATTATCGATGTATAA
Found at i:267654 original size:32 final size:33
Alignment explanation
Indices: 267585--267651 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
267575 TCTTCAATAA
267585 TTAAAGTTTTTTTATTAAACACATGATAAGCTT
1 TTAAAGTTTTTTTATTAAACACATGATAAGCTT
267618 TTAAAGTTTTTTTATTAAACACATGATAAGCTT
1 TTAAAGTTTTTTTATTAAACACATGATAAGCTT
267651 T
1 T
267652 AAAATTTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (33 bp):
TTAAAGTTTTTTTATTAAACACATGATAAGCTT
Found at i:269517 original size:15 final size:16
Alignment explanation
Indices: 269477--269517 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
269467 TTCAATGTTG
269477 TTGTAGCCGTTGGAGT
1 TTGTAGCCGTTGGAGT
**
269493 TTG-ATTCGTT-GAGT
1 TTGTAGCCGTTGGAGT
269507 TTGTAGCCGTT
1 TTGTAGCCGTT
269518 ATTGACTTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 7 0.35
15 10 0.50
16 3 0.15
ACGTcount: A:0.12, C:0.12, G:0.32, T:0.44
Consensus pattern (16 bp):
TTGTAGCCGTTGGAGT
Found at i:269670 original size:13 final size:13
Alignment explanation
Indices: 269652--269676 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
269642 CATTTTATGG
269652 TGTATCGATACAA
1 TGTATCGATACAA
269665 TGTATCGATACA
1 TGTATCGATACA
269677 TACTGTGTGT
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:269692 original size:32 final size:33
Alignment explanation
Indices: 269631--269696 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
269621 TTACAAGCCG
**
269631 ATGTATCGATACATTTTATGGTGTATCGATACA
1 ATGTATCGATACATACTATGGTGTATCGATACA
*
269664 ATGTATCGATACATACTGT-GTGTATCGATACA
1 ATGTATCGATACATACTATGGTGTATCGATACA
269696 A
1 A
269697 GTTTGGCTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATACTATGGTGTATCGATACA
Found at i:278091 original size:13 final size:13
Alignment explanation
Indices: 278073--278097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
278063 CATTTTATGG
278073 TGTATCGATACAA
1 TGTATCGATACAA
278086 TGTATCGATACA
1 TGTATCGATACA
278098 TATTGTGTGT
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:278113 original size:32 final size:33
Alignment explanation
Indices: 278050--278117 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
278040 CGTTACAAGC
*
278050 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATATTATGGTGTATCGATA
*
278083 CAATGTATCGATACATATTGT-GTGTATCGATA
1 CAATGTATCGATACATATTATGGTGTATCGATA
278115 CAA
1 CAA
278118 GTTTGGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATATTATGGTGTATCGATA
Found at i:278721 original size:19 final size:19
Alignment explanation
Indices: 278683--278751 Score: 111
Period size: 19 Copynumber: 3.6 Consensus size: 19
278673 ATCTCGTGTT
**
278683 TCGATACAATTGTCCATGTA
1 TCGATACAA-TGAACATGTA
278703 TCGATACAATGAACATGTA
1 TCGATACAATGAACATGTA
278722 TCGATACAATGAACATGTA
1 TCGATACAATGAACATGTA
278741 TCGATACAATG
1 TCGATACAATG
278752 TATCGATACA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 38 0.81
20 9 0.19
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (19 bp):
TCGATACAATGAACATGTA
Found at i:278754 original size:13 final size:13
Alignment explanation
Indices: 278736--278767 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
278726 TACAATGAAC
278736 ATGTATCGATACA
1 ATGTATCGATACA
278749 ATGTATCGATACA
1 ATGTATCGATACA
*
278762 AAGTAT
1 ATGTAT
278768 AATGTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:286517 original size:13 final size:13
Alignment explanation
Indices: 286499--286533 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
286489 CCGTTACAAG
286499 CAATGTATCGATA
1 CAATGTATCGATA
286512 CAATGTATCGATA
1 CAATGTATCGATA
*
286525 CATTGTATC
1 CAATGTATC
286534 ATGTATCGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:287664 original size:20 final size:20
Alignment explanation
Indices: 287633--287689 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
287623 GTCAAAACCC
*
287633 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
287653 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
287673 TGCATTGTATCGATACA
1 TGAAATGTATCGATACA
287690 TTGTATCAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:287813 original size:13 final size:13
Alignment explanation
Indices: 287795--287820 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
287785 ACACACAGTA
287795 TGTATCGATACAT
1 TGTATCGATACAT
287808 TGTATCGATACAT
1 TGTATCGATACAT
287821 CATAAAATGT
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:287836 original size:33 final size:32
Alignment explanation
Indices: 287775--287842 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
287765 GTAGCCAAAC
**
287775 TTGTATCGATACACACAGTATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
287807 TTGTATCGATACATCATAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
287840 TTG
1 TTG
287843 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:292704 original size:20 final size:20
Alignment explanation
Indices: 292679--292732 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
292669 GTTACAAGCA
* *
292679 ATGTATCAATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
292699 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
292719 ATGTATCGATACAA
1 ATGTATCGATACAA
292733 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:295024 original size:34 final size:32
Alignment explanation
Indices: 294933--295091 Score: 162
Period size: 31 Copynumber: 4.9 Consensus size: 32
294923 AAGTGATTGA
* * *
294933 GAGGTTCTATCATAGCTTTTGAAAAAGATAGGGAG
1 GAGGTTCTATCTTAGCCTGTG-AAAAGATA--GAG
* * *
294968 AAAGGTTCTATCTTAGCTTGTGAAAATATAGAG
1 -GAGGTTCTATCTTAGCCTGTGAAAAGATAGAG
* *
295001 AAGATGTTTTATCTTAGCCTGTGAAAAGATA-AG
1 --GAGGTTCTATCTTAGCCTGTGAAAAGATAGAG
295034 GAGGTTCTATCTTAGCCTGTGAAAAGATAG-G
1 GAGGTTCTATCTTAGCCTGTGAAAAGATAGAG
*
295065 GAGGTTCTATCTTAGCCT-TCAAAAGAT
1 GAGGTTCTATCTTAGCCTGTGAAAAGAT
295092 TATGTTGTAA
Statistics
Matches: 109, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
30 8 0.07
31 46 0.42
33 5 0.05
34 25 0.23
35 7 0.06
36 18 0.17
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31
Consensus pattern (32 bp):
GAGGTTCTATCTTAGCCTGTGAAAAGATAGAG
Found at i:300639 original size:52 final size:52
Alignment explanation
Indices: 300569--300708 Score: 181
Period size: 52 Copynumber: 2.7 Consensus size: 52
300559 TCTGGAAAGA
* * * *
300569 AAATGTATCGATACATTTTTCATTGTATCAATACATTTTGGGTTTTTGACCC
1 AAATATATCGATACATTTTTCATTGTATCGATACATTCTAGGTTTTTGACCC
* * * * *
300621 AAATATGTTGATACATTTTTTATTATATTGATACATTCTAGGTTTTTGACCC
1 AAATATATCGATACATTTTTCATTGTATCGATACATTCTAGGTTTTTGACCC
* *
300673 AAATATATCGATACATTCTTCAATGTATCGATACAT
1 AAATATATCGATACATTTTTCATTGTATCGATACAT
300709 ATAAGCAATT
Statistics
Matches: 72, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (52 bp):
AAATATATCGATACATTTTTCATTGTATCGATACATTCTAGGTTTTTGACCC
Found at i:307214 original size:13 final size:13
Alignment explanation
Indices: 307196--307221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
307186 CAATTTTTTG
307196 TGTATCGATACAT
1 TGTATCGATACAT
307209 TGTATCGATACAT
1 TGTATCGATACAT
307222 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:307236 original size:32 final size:33
Alignment explanation
Indices: 307176--307239 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
307166 TACAAGCCAA
** *
307176 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
307209 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
307240 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:313478 original size:157 final size:156
Alignment explanation
Indices: 313013--314686 Score: 1344
Period size: 157 Copynumber: 10.7 Consensus size: 156
313003 TACTTTCATA
* * * * * ** * *
313013 TCGAAGGTATACC-CTAGAGGCATTTTTGTATTTTCCTAGAACCGAGTCTTAGGTCATCATCGGG
1 TCGAAGGTATACCAATAG-GGCATTTTCGTATTTTCTTAGAACCAAGTCCTAGGTTGTCACCGAG
* * * * *
313077 TCTACTTTTATGCCAAAGGTAGGCATTTAAGATAGGTTCATC-CCATTTCTCGTCTTTTTAGGTC
65 TCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGTC
*
313141 CTTTAGGGTTGCCGGGATACTTTTACA
130 CTTTAGGGTTGCCGGGATACTTTTACG
* * * * * * ** *
313168 TCGAAGGTATACCCATTGGGGATTTTTTGTATTTTCATAGAACCAGGTATTAGGTTGTCACCGGG
1 TCGAAGGTATACCAATAGGGCA-TTTTCGTATTTTCTTAGAACCAAGTCCTAGGTTGTCACCGAG
* *
313233 TCTGCTTTTATGCCGAAGGT-GGCATTTAGGATAGGTTCATCACCATTTATAGTCTTTTTAGCTC
65 TCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGTC
* *
313297 CTTTAAGGTTGCCGAGATACTTTTACG
130 CTTTAGGGTTGCCGGGATACTTTTACG
* * * * *
313324 TCGAAGCTATACTCACA-AGGCCATTTTCGTATTTTCTTAGAACTAAGTCTTAGGTTGTCACCAA
1 TCGAAGGTATAC-CA-ATAGGGCATTTTCGTATTTTCTTAGAACCAAGTCCTAGGTTGTCACCGA
* * * * *
313388 GTTTGCTTTTATGGCGAAGGTGGGCATCTAGGATAGGTCCATCATCATTTCTAGTCTTTTTAGGT
64 GTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGT
* *
313453 CATTTAGGGTTGCTGGGATACTTTTACG
129 CCTTTAGGGTTGCCGGGATACTTTTACG
* * * * * * *
313481 TCGAAAGTATACCCATAGGGGCATTTTTGAATTTTCCTAG-ACCAAGTCCTAAGTTGTCACCGGG
1 TCGAAGGTATACCAATA-GGGCATTTTCGTATTTTCTTAGAACCAAGTCCTAGGTTGTCACCGAG
* * * *
313545 TCTGTTTTTATACCGAAGGTGGGCATTTAAGATAGGTTCATCGCCATTTCTAGTCTTTTTAGGTC
65 TCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGTC
* *
313610 CTTTAAGGTTGCCGGGATACTTTTACT
130 CTTTAGGGTTGCCGGGATACTTTTACG
* * * * *
313637 TCGAAGTTATACCAATAGGGGTATTTTCGTATTTTTTTAAAACCAAGTCCTAGGTTGTCACTGCA
1 TCGAAGGTATACCAATA-GGGCATTTTCGTATTTTCTTAGAACCAAGTCCTAGGTTGTCACCG-A
*
313702 -TCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTATTTTTAGGT
64 GTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGT
**
313766 CCTTTAGGGTTGTTGGGATACTTTTACG
129 CCTTTAGGGTTGCCGGGATACTTTTACG
* * * *
313794 TCGAAGGTATACTC-ATAGGGTCATTTTCGAATTTTCCTAG-ACTAAGTCCTAAGTTG-CACCGA
1 TCGAAGGTATAC-CAATAGGG-CATTTTCGTATTTTCTTAGAACCAAGTCCTAGGTTGTCACCGA
* * * *
313856 GTCCGTTTTTATACCGAAGGTAGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGT
64 GTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGT
* * *
313921 CCTTTAAGGTTGCCGAGATACTTTTACA
129 CCTTTAGGGTTGCCGGGATACTTTTACG
* * * * * *
313949 TCGAAGTTATACCAATAGGGGTATTTTCATATTTTTTTAAAACCAAGTCCTAGGTTGTCA-CTAC
1 TCGAAGGTATACCAATA-GGGCATTTTCGTATTTTCTTAGAACCAAGTCCTAGGTTGTCACCGA-
*
314013 GTCCGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGT
64 GTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGT
* ** *
314078 CCTTTAGGGTTACTATGG-CACTTTTACG
129 CCTTTAGGGTTGC-CGGGATACTTTTACG
* * * * * * * * * * * ** *
314106 TCAAAAGTATACTC-GTAAGGGCATTTTCATAATTTCCTAAAATCGATTCCTAGGTTATCGTCGG
1 TCGAAGGTATAC-CAAT-AGGGCATTTTCGTATTTTCTTAGAACCAAGTCCTAGGTTGTCACCGA
* * * ** * * *
314170 GTCCGTTTTTATGCCGAAGGTAGATATTTAGGATAGGTTCATC-CC-TTCTATAATCTTTTTTAA
64 GTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATT-TCTAGTC-TTTTTAG
* *** * *
314233 GTCCTTTAGGGATATTGGGATCCTTTCACG
127 GTCCTTTAGGGTTGCCGGGATACTTTTACG
* * * * * * * * * * **
314263 TTGAAGGTATACCTATAAAGGTATTTTGGTAATTTCTTAAAACTAATTCCTCGGTCATCACCGAG
1 TCGAAGGTATACCAAT-AGGGCATTTTCGTATTTTCTTAGAACCAAGTCCTAGGTTGTCACCGAG
* * * ** * * * *
314328 TTTGCTTTTATGCTGAAGGTAGGTGTTTAGGATAGGTTCATC-CCATCTATAATTCTTTTTAAGT
65 TCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCT-AGTCTTTTTAGGT
* * ** * **
314392 CTTTTAGGGGTATC-GGTTACTTCCACG
129 CCTTTAGGGTTGCCGGGATACTTTTACG
* ** ** * * * * *
314419 TCAAAGGTAT-CCCCTAAGTACATTTTCGTAATTTTC-TAGAACAAACTCCTAAGG-CGACACCA
1 TCGAAGGTATACCAAT-AGGGCATTTTCGT-ATTTTCTTAGAACCAAGTCCT-AGGTTGTCACCG
* * * * *
314481 AGTCTGCTTTTATGCGGATGGTGGGTATTTAGGATAGGTTCATC-CAACTTTCTAATCCTTTTTA
63 AGTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCA-TTTCTAGT-CTTTTTA
** * ** ** * *
314545 AATCCTTTAGGGATATCTAG-CACTTCTACG
126 GGTCCTTTAGGGTTGCCGGGATACTTTTACG
* ** * ** * * * * *
314575 TCGAAGATAT-CCCCTAGGGGTATTTTAATAATTTT-TTTGAATCGAGTCGTAGGTTGTCATCGA
1 TCGAAGGTATACCAATA-GGGCATTTTCGT-ATTTTCTTAGAACCAAGTCCTAGGTTGTCACCGA
* * * * *
314638 GTCCGCTTTTATACCAAAGGTGGGTATTTAGGATAGGTACATC-CCATTT
64 GTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTT
314687 ATAATCCTTT
Statistics
Matches: 1240, Mismatches: 243, Indels: 72
0.80 0.16 0.05
Matches are distributed among these distances:
154 2 0.00
155 230 0.19
156 474 0.38
157 524 0.42
158 10 0.01
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (156 bp):
TCGAAGGTATACCAATAGGGCATTTTCGTATTTTCTTAGAACCAAGTCCTAGGTTGTCACCGAGT
CTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGTCC
TTTAGGGTTGCCGGGATACTTTTACG
Found at i:313614 original size:313 final size:312
Alignment explanation
Indices: 313076--314400 Score: 1470
Period size: 313 Copynumber: 4.2 Consensus size: 312
313066 TCATCATCGG
* * * * *
313076 GTCTACTTTTATGCCAAAGGTAGGCATTTAAGATAGGTTCATC-CCATTTCTCGTCTTTTTAGGT
1 GTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGT
* * * * *
313140 CCTTTAGGGTTGCCGGGATACTTTTACATCGAAGGTATACCCATTGGGG-ATTTTTTGTATTTTC
66 CCTTTAGGGTTGCTGGGATACTTTTACGTCGAAAGTATACCCATAGGGGCA-TTTTTGAATTTTC
* * ** * * *
313204 ATAGAACCAGGTATTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGCATTTAGGATAGGT
130 CTAG-ACCAAGTCCTAAGTTGTCACCGGGTCTGTTTTTATACCGAAGGTGGCATTTAGGATAGGT
* * * *
313269 TCATCACCATTTATAGTCTTTTTAGCTCCTTTAAGGTTGCCGAGATACTTTTACGTCGAAGCTAT
194 TCATCACCATTTCTAGTCTTTTTAGGTCCTTTAAGGTTGCCGAGATACTTTTACATCGAAGTTAT
** * * * *
313334 ACTCACA-A-GGCCATTTTCGTATTTTCTTAGAACTAAGTCTTAGGTTGTCACCAA
259 AC-CA-ATAGGGGTATTTTCGTATTTTTTTAAAACCAAGTCCTAGGTTGTCACCAA
* * * * *
313388 GTTTGCTTTTATGGCGAAGGTGGGCATCTAGGATAGGTCCATCATCATTTCTAGTCTTTTTAGGT
1 GTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGT
*
313453 CATTTAGGGTTGCTGGGATACTTTTACGTCGAAAGTATACCCATAGGGGCATTTTTGAATTTTCC
66 CCTTTAGGGTTGCTGGGATACTTTTACGTCGAAAGTATACCCATAGGGGCATTTTTGAATTTTCC
*
313518 TAGACCAAGTCCTAAGTTGTCACCGGGTCTGTTTTTATACCGAAGGTGGGCATTTAAGATAGGTT
131 TAGACCAAGTCCTAAGTTGTCACCGGGTCTGTTTTTATACCGAAGGT-GGCATTTAGGATAGGTT
* * *
313583 CATCGCCATTTCTAGTCTTTTTAGGTCCTTTAAGGTTGCCGGGATACTTTTACTTCGAAGTTATA
195 CATCACCATTTCTAGTCTTTTTAGGTCCTTTAAGGTTGCCGAGATACTTTTACATCGAAGTTATA
313648 CCAATAGGGGTATTTTCGTATTTTTTTAAAACCAAGTCCTAGGTTGTCACTGC-A
260 CCAATAGGGGTATTTTCGTATTTTTTTAAAACCAAGTCCTAGGTTGTCAC--CAA
*
313702 -TCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTATTTTTAGGT
1 GTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGT
* * * * *
313766 CCTTTAGGGTTGTTGGGATACTTTTACGTCGAAGGTATACTCATAGGGTCATTTTCGAATTTTCC
66 CCTTTAGGGTTGCTGGGATACTTTTACGTCGAAAGTATACCCATAGGGGCATTTTTGAATTTTCC
* * *
313831 TAGACTAAGTCCTAAGTTG-CACCGAGTCCGTTTTTATACCGAAGGTAGGCATTTAGGATAGGTT
131 TAGACCAAGTCCTAAGTTGTCACCGGGTCTGTTTTTATACCGAAGGT-GGCATTTAGGATAGGTT
313895 CATCACCATTTCTAGTCTTTTTAGGTCCTTTAAGGTTGCCGAGATACTTTTACATCGAAGTTATA
195 CATCACCATTTCTAGTCTTTTTAGGTCCTTTAAGGTTGCCGAGATACTTTTACATCGAAGTTATA
* * *
313960 CCAATAGGGGTATTTTCATATTTTTTTAAAACCAAGTCCTAGGTTGTCACTAC
260 CCAATAGGGGTATTTTCGTATTTTTTTAAAACCAAGTCCTAGGTTGTCACCAA
*
314013 GTCCGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGT
1 GTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGT
* * * * * * *
314078 CCTTTAGGGTTACTATGG-CACTTTTACGTCAAAAGTATACTCGTAAGGGCATTTTCAT-AA-TT
66 CCTTTAGGGTTGCT-GGGATACTTTTACGTCGAAAGTATACCCATAGGGGCATTTT--TGAATTT
* * * * * * ** * * **
314140 TCCTAAAATCGATTCCTAGGTTATCGTCGGGTCCGTTTTTATGCCGAAGGTAGATATTTAGGATA
128 TCCT-AGACCAAGTCCTAAGTTGTCACCGGGTCTGTTTTTATACCGAAGGT-GGCATTTAGGATA
* * * * * *** * * * * *
314205 GGTTCATC-CC-TTCTATAATCTTTTTTAAGTCCTTTAGGGATATTGGGATCCTTTCACGTTGAA
191 GGTTCATCACCATT-TCTAGTC-TTTTTAGGTCCTTTAAGGTTGCCGAGATACTTTTACATCGAA
* * ** * * * * * * ** *
314268 GGTATACCTATAAAGGTATTTTGGTAATTTCTTAAAACTAATTCCTCGGTCATCACCGA
254 GTTATACCAATAGGGGTATTTTCGTATTTTTTTAAAACCAAGTCCTAGGTTGTCACCAA
* * * ** * * * *
314327 GTTTGCTTTTATGCTGAAGGTAGGTGTTTAGGATAGGTTCATC-CCATCTATAATTCTTTTTAAG
1 GTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCT-AGTCTTTTTAGG
*
314391 TCTTTTAGGG
65 TCCTTTAGGG
314401 GTATCGGTTA
Statistics
Matches: 872, Mismatches: 124, Indels: 32
0.85 0.12 0.03
Matches are distributed among these distances:
311 1 0.00
312 341 0.39
313 354 0.41
314 175 0.20
315 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (312 bp):
GTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGT
CCTTTAGGGTTGCTGGGATACTTTTACGTCGAAAGTATACCCATAGGGGCATTTTTGAATTTTCC
TAGACCAAGTCCTAAGTTGTCACCGGGTCTGTTTTTATACCGAAGGTGGCATTTAGGATAGGTTC
ATCACCATTTCTAGTCTTTTTAGGTCCTTTAAGGTTGCCGAGATACTTTTACATCGAAGTTATAC
CAATAGGGGTATTTTCGTATTTTTTTAAAACCAAGTCCTAGGTTGTCACCAA
Found at i:313993 original size:312 final size:311
Alignment explanation
Indices: 313081--314212 Score: 1461
Period size: 312 Copynumber: 3.6 Consensus size: 311
313071 ATCGGGTCTA
* * * *
313081 CTTTTATGCCAAAGGTAGGCATTTAAGATAGGTTCATC-CCATTTCTCGTCTTTTTAGGTCCTTT
1 CTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGTCCTTT
* * * * * * * *
313145 AGGGTTGCCGGGATACTTTTACATCGAAGGTATACCCATTGGGGATTTTTTGTATTTTCATAGAA
66 AGGGTTGCTGGGATACTTTTACGTCGAAAGTATACCCATAGGGCA-TTTTCGAATTTTCCTAG-A
* ** * * * *
313210 CCAGGTATTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGT-GGCATTTAGGATAGGTTCATC
129 CCAAGTCCTAAGTTGTCACCGGGTCCGTTTTTATACCGAAGGTAGGCATTTAGGATAGGTTCATC
* * * *
313274 ACCATTTATAGTCTTTTTAGCTCCTTTAAGGTTGCCGAGATACTTTTACGTCGAAGCTATACTCA
194 ACCATTTCTAGTCTTTTTAGGTCCTTTAAGGTTGCCGAGATACTTTTACATCGAAGTTATAC-CA
** * * * * *
313339 CA-A-GGCCATTTTCGTATTTTCTTAGAACTAAGTCTTAGGTTGTCAC-CAAGTTTG
258 -ATAGGGGTATTTTCGTATTTTTTTAAAACCAAGTCCTAGGTTGTCACTC-A-TCTG
* * * * *
313393 CTTTTATGGCGAAGGTGGGCATCTAGGATAGGTCCATCATCATTTCTAGTCTTTTTAGGTCATTT
1 CTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGTCCTTT
*
313458 AGGGTTGCTGGGATACTTTTACGTCGAAAGTATACCCATAGGGGCATTTTTGAATTTTCCTAGAC
66 AGGGTTGCTGGGATACTTTTACGTCGAAAGTATACCCATA-GGGCATTTTCGAATTTTCCTAGAC
* * * *
313523 CAAGTCCTAAGTTGTCACCGGGTCTGTTTTTATACCGAAGGTGGGCATTTAAGATAGGTTCATCG
130 CAAGTCCTAAGTTGTCACCGGGTCCGTTTTTATACCGAAGGTAGGCATTTAGGATAGGTTCATCA
* *
313588 CCATTTCTAGTCTTTTTAGGTCCTTTAAGGTTGCCGGGATACTTTTACTTCGAAGTTATACCAAT
195 CCATTTCTAGTCTTTTTAGGTCCTTTAAGGTTGCCGAGATACTTTTACATCGAAGTTATACCAAT
313653 AGGGGTATTTTCGTATTTTTTTAAAACCAAGTCCTAGGTTGTCACTGCATCTG
260 AGGGGTATTTTCGTATTTTTTTAAAACCAAGTCCTAGGTTGTCACT-CATCTG
*
313706 CTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTATTTTTAGGTCCTTT
1 CTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGTCCTTT
* * *
313771 AGGGTTGTTGGGATACTTTTACGTCGAAGGTATACTCATAGGGTCATTTTCGAATTTTCCTAGAC
66 AGGGTTGCTGGGATACTTTTACGTCGAAAGTATACCCATAGGG-CATTTTCGAATTTTCCTAGAC
* *
313836 TAAGTCCTAAGTTG-CACCGAGTCCGTTTTTATACCGAAGGTAGGCATTTAGGATAGGTTCATCA
130 CAAGTCCTAAGTTGTCACCGGGTCCGTTTTTATACCGAAGGTAGGCATTTAGGATAGGTTCATCA
313900 CCATTTCTAGTCTTTTTAGGTCCTTTAAGGTTGCCGAGATACTTTTACATCGAAGTTATACCAAT
195 CCATTTCTAGTCTTTTTAGGTCCTTTAAGGTTGCCGAGATACTTTTACATCGAAGTTATACCAAT
* * *
313965 AGGGGTATTTTCATATTTTTTTAAAACCAAGTCCTAGGTTGTCACTACGTCCG
260 AGGGGTATTTTCGTATTTTTTTAAAACCAAGTCCTAGGTTGTCACT-CATCTG
314018 CTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGTCCTTT
1 CTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGTCCTTT
* * * * * * *
314083 AGGGTTACTATGG-CACTTTTACGTCAAAAGTATACTCGTAAGGGCATTTTC-ATAATTTCCTAA
66 AGGGTTGCT-GGGATACTTTTACGTCGAAAGTATACCCAT-AGGGCATTTTCGA-ATTTTCCT-A
* * * * * * ** * **
314146 AATCGATTCCTAGGTTATCGTCGGGTCCGTTTTTATGCCGAAGGTAGATATTTAGGATAGGTTCA
127 GACCAAGTCCTAAGTTGTCACCGGGTCCGTTTTTATACCGAAGGTAGGCATTTAGGATAGGTTCA
314211 TC
192 TC
314213 CCTTCTATAA
Statistics
Matches: 727, Mismatches: 80, Indels: 24
0.87 0.10 0.03
Matches are distributed among these distances:
311 2 0.00
312 340 0.47
313 336 0.46
314 48 0.07
315 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (311 bp):
CTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACCATTTCTAGTCTTTTTAGGTCCTTT
AGGGTTGCTGGGATACTTTTACGTCGAAAGTATACCCATAGGGCATTTTCGAATTTTCCTAGACC
AAGTCCTAAGTTGTCACCGGGTCCGTTTTTATACCGAAGGTAGGCATTTAGGATAGGTTCATCAC
CATTTCTAGTCTTTTTAGGTCCTTTAAGGTTGCCGAGATACTTTTACATCGAAGTTATACCAATA
GGGGTATTTTCGTATTTTTTTAAAACCAAGTCCTAGGTTGTCACTCATCTG
Found at i:314600 original size:156 final size:155
Alignment explanation
Indices: 314176--314609 Score: 340
Period size: 156 Copynumber: 2.8 Consensus size: 155
314166 TCGGGTCCGT
* * ** * *
314176 TTTTATGCCGAAGGTAGATATTTAGGATAGGTTCATCCCTTCTATAATCTTTTTTAAGTCCTTTA
1 TTTTATGCGGAAGGTAGGTATTTAGGATAGGTTCATCCAATCTATAATCCTTTTTAAATCCTTTA
** * ** * ** * ** *
314241 GGGATATTGGGATC-CTTTCACGTTGAAGGTATACCTATAAAGG-TATTTTGGTAA-TTTCTTAA
66 GGGATA-TCAG-TCACTTCCACGTCAAAGATAT-CCCCT-AAGGACATTTTAATAATTTTC-TAG
* * * * *
314303 AACTAATTCCT-CGGTC-ATCACCGAGTTTGC
126 AACAAACTCCTAAGG-CGA-CACCAAGTCTGC
* * * * * *
314333 TTTTATGCTGAAGGTAGGTGTTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCTTTTA
1 TTTTATGCGGAAGGTAGGTATTTAGGATAGGTTCATCCAATCTATAATCCTTTTTAAATCCTTTA
* * * * * **
314398 GGGGTATCGGTTACTTCCACGTCAAAGGTATCCCCTAAGTACATTTTCGTAATTTTCTAGAACAA
66 GGGATATCAGTCACTTCCACGTCAAAGATATCCCCTAAGGACATTTTAATAATTTTCTAGAACAA
314463 ACTCCTAAGGCGACACCAAGTCTGC
131 ACTCCTAAGGCGACACCAAGTCTGC
* * * *
314488 TTTTATGCGGATGGTGGGTATTTAGGATAGGTTCATCCAACTTTCTAATCCTTTTTAAATCCTTT
1 TTTTATGCGGAAGGTAGGTATTTAGGATAGGTTCATCCAA-TCTATAATCCTTTTTAAATCCTTT
* * * **
314553 AGGGATATCTAG-CACTTCTACGTCGAAGATATCCCCTAGGGGTATTTTAATAATTTT
65 AGGGATATC-AGTCACTTCCACGTCAAAGATATCCCCTAAGGACATTTTAATAATTTT
314610 TTTGAATCGA
Statistics
Matches: 224, Mismatches: 46, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
154 3 0.01
155 70 0.31
156 87 0.39
157 64 0.29
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (155 bp):
TTTTATGCGGAAGGTAGGTATTTAGGATAGGTTCATCCAATCTATAATCCTTTTTAAATCCTTTA
GGGATATCAGTCACTTCCACGTCAAAGATATCCCCTAAGGACATTTTAATAATTTTCTAGAACAA
ACTCCTAAGGCGACACCAAGTCTGC
Found at i:315809 original size:1 final size:1
Alignment explanation
Indices: 315803--315976 Score: 105
Period size: 1 Copynumber: 174.0 Consensus size: 1
315793 GGCGTCCTCC
* * * ** ** * * * *
315803 AAAAAAACAAAAAAAAACAAAACAAAAAAAAACGAAAAAATGAAAAAACAAAACAAAACAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** ** * * * * *
315868 AAACAAAAAAAAACGAAAAAAATGAAAAAACAAAAAAAAAACAAAACAAAAAAAACAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
315933 AAAAAAAAAACAAAAACAATAAAAAAATAAACAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
315977 GGGGGTCCGA
Statistics
Matches: 123, Mismatches: 50, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 123 1.00
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:315818 original size:10 final size:10
Alignment explanation
Indices: 315803--315974 Score: 142
Period size: 10 Copynumber: 16.7 Consensus size: 10
315793 GGCGTCCTCC
315803 AAAAAAACAA
1 AAAAAAACAA
315813 AAAAAAACAA
1 AAAAAAACAA
315823 AACAAAAA-AA
1 AA-AAAAACAA
*
315833 AACGAAAAA-AT
1 AA--AAAAACAA
*
315844 GAAAAAACAA
1 AAAAAAACAA
*
315854 AACAAAACAA
1 AAAAAAACAA
*
315864 AACAAAACAA
1 AAAAAAACAA
315874 AAAAAAACGAA
1 AAAAAAAC-AA
315885 AAAAATGAA-AA
1 AAAAA--AACAA
315896 AACAAAAA-AA
1 AA-AAAAACAA
315906 AAACAAAAC-A
1 AAA-AAAACAA
315916 AAAAAAAC-A
1 AAAAAAACAA
315925 AAAAAAACAAA
1 AAAAAAAC-AA
315936 AAAAAAACAA
1 AAAAAAACAA
315946 AAACAATAA-AA
1 AAA-AA-AACAA
*
315957 AAATAAACAA
1 AAAAAAACAA
315967 AACAAAAA
1 AA-AAAAA
315975 AAGGGGGTCC
Statistics
Matches: 138, Mismatches: 9, Indels: 29
0.78 0.05 0.16
Matches are distributed among these distances:
9 22 0.16
10 66 0.48
11 43 0.31
12 5 0.04
13 2 0.01
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.02
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:315866 original size:46 final size:46
Alignment explanation
Indices: 315806--315976 Score: 202
Period size: 46 Copynumber: 3.6 Consensus size: 46
315796 GTCCTCCAAA
*
315806 AAAACAAAAAAAAACAAAACAAAAAAAAACGAAAAAATGAAAAAAC
1 AAAACAAAACAAAACAAAACAAAAAAAAACGAAAAAATGAAAAAAC
315852 AAAACAAAACAAAACAAAACAAAAAAAAACGAAAAAAATGAAAAAAC
1 AAAACAAAACAAAACAAAACAAAAAAAAACG-AAAAAATGAAAAAAC
* * * **
315899 AAAAAAAAAACAAAACAAAAAAAACAAAAAAAACAAAAAAAAAACAAAAAC
1 -AAAACAAAACAAAAC--AAAACA-AAAAAAAACGAAAAAATGA-AAAAAC
315950 AATAA-AAAA-ATAAACAAAACAAAAAAA
1 AA-AACAAAACA-AAACAAAACAAAAAAA
315977 GGGGGTCCGA
Statistics
Matches: 110, Mismatches: 7, Indels: 15
0.83 0.05 0.11
Matches are distributed among these distances:
46 30 0.27
47 21 0.19
48 19 0.17
49 1 0.01
50 22 0.20
51 17 0.15
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.02
Consensus pattern (46 bp):
AAAACAAAACAAAACAAAACAAAAAAAAACGAAAAAATGAAAAAAC
Found at i:317484 original size:30 final size:29
Alignment explanation
Indices: 317415--317738 Score: 313
Period size: 30 Copynumber: 11.1 Consensus size: 29
317405 TTTATCACCC
*
317415 TTCAAAAGTCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ATTT
*
317445 TTC-AAAGCCCACAAGTCAGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ATTT
**
317474 TTCAAAAGCCCACAAGTCAGTGGCAA-CC
1 TTCAAAAGCCCACAAGTCAGTGGCAATTT
* *
317502 TTC-AAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA--ATTT
**
317532 TTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCAATTT
* **
317561 TT-AAAAGCCCACAAGTTAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ATTT
*
317590 TTCAAAAGCCCACAAGTTAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ATTT
**
317620 TTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCAATTT
* **
317649 TT-AAAAGTCCACAAGTCAGTGGCAA-CC
1 TTCAAAAGCCCACAAGTCAGTGGCAATTT
* *
317676 TTC-AAAGCCCACAAATCAGTGGCACCTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA--ATTT
* * *
317706 TTC-GAAGCCCACAAGTCGGTGGCACCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ATTT
317735 TTCA
1 TTCA
317739 TCTTTAAGTC
Statistics
Matches: 249, Mismatches: 33, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
27 42 0.17
28 46 0.18
29 45 0.18
30 96 0.39
31 20 0.08
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (29 bp):
TTCAAAAGCCCACAAGTCAGTGGCAATTT
Found at i:317551 original size:58 final size:58
Alignment explanation
Indices: 317415--317733 Score: 382
Period size: 58 Copynumber: 5.5 Consensus size: 58
317405 TTTATCACCC
* ** **
317415 TTCAAAAGTCCACAAGTCAGTGGCATATTTTTCAAAGCCCACAAGTCAGTGGCA-TTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-A-CCTTCAAAGCCCACAAGTCAGTGGCACCCTTT
*
317474 TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAGTCAGTGGCACCCTTT
* *
317532 TTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTTAGTGGCACCC-TT
1 TTCAAAAGCCCACAAGTCAGTGGCAACC-TTCAAAGCCCACAAGTCAGTGGCACCCTTT
* ** *
317590 TTCAAAAGCCCACAAGTTAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACC--T
1 TTCAAAAGCCCACAAGTCAGTGGCA-A-CCTTC-AAAGCCCACAAGTCAGTGGCACCCTTT
* * *
317649 TT-AAAAGTCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAGTCAGTGGCACCCTTT
* *
317706 TTC-GAAGCCCACAAGTCGGTGGC-ACCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTT
317734 TTTCATCTTT
Statistics
Matches: 227, Mismatches: 25, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
55 21 0.09
56 8 0.04
57 44 0.19
58 78 0.34
59 54 0.24
60 22 0.10
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (58 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAGTCAGTGGCACCCTTT
Found at i:317621 original size:88 final size:85
Alignment explanation
Indices: 317413--317734 Score: 409
Period size: 88 Copynumber: 3.7 Consensus size: 85
317403 CATTTATCAC
* * ***
317413 CCTTCAAAAGTCCACAAGTCAGTGGCA-TATTTTTCAAAGCCCACAAGTCAGTGGCATTTTTTTC
1 CCTTC-AAAGCCCACAAATCAGTGGCACTATTTTTCAAAGCCCACAAGTCAGTGGCA-ACCTTT-
317477 AAAAGCCCACAAGTCAGTGGCAA
63 AAAAGCCCACAAGTCAGTGGCAA
**
317500 CCTTCAAAGCCCACAAATCAGTGGCACCCTTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAA
1 CCTTCAAAGCCCACAAATCAGTGGCACTATTTTTC-AAAGCCCACAAGTCAGTGGCAACCTTTAA
* *
317565 AAGCCCACAAGTTAGTGGCAC
65 AAGCCCACAAGTCAGTGGCAA
* *
317586 CCTTTTCAAAAGCCCACAAGTTAGTGGCA-TATTTTTCAAAAGCCCACAAGTCAGTGGCAACCTT
1 CC--TTC-AAAGCCCACAAATCAGTGGCACTATTTTTC-AAAGCCCACAAGTCAGTGGCAACCTT
*
317650 TAAAAGTCCACAAGTCAGTGGCAA
62 TAAAAGCCCACAAGTCAGTGGCAA
* *
317674 CCTTCAAAGCCCACAAATCAGTGGCACCT-TTTTTCGAAGCCCACAAGTCGGTGGC-ACCTTT
1 CCTTCAAAGCCCACAAATCAGTGGCA-CTATTTTTCAAAGCCCACAAGTCAGTGGCAACCTTT
317735 TTCATCTTTA
Statistics
Matches: 208, Mismatches: 20, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
84 6 0.03
85 37 0.18
86 51 0.25
87 15 0.07
88 80 0.38
89 19 0.09
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (85 bp):
CCTTCAAAGCCCACAAATCAGTGGCACTATTTTTCAAAGCCCACAAGTCAGTGGCAACCTTTAAA
AGCCCACAAGTCAGTGGCAA
Found at i:317782 original size:52 final size:52
Alignment explanation
Indices: 317725--317944 Score: 199
Period size: 52 Copynumber: 4.4 Consensus size: 52
317715 CACAAGTCGG
*
317725 TGGCACCTTTTTCATCTTTAAGTCCAATGTAGCTGACCTTGAATCAGCACAT
1 TGGCACCTTTTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
* *
317777 TGGCA-------C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATAT
1 TGGCACCTTTTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
* *
317820 TGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACAT
1 TGGCACCTTTTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
* * * * * * * * *
317872 TGACATCCTTTTTCTCAGCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATAT
1 TGGCA-CC-TTTT-TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
* *
317927 TGGCATCTTTATCA-CTTT
1 TGGCACCTTTTTCATCTTT
317945 TCTCATCTTC
Statistics
Matches: 136, Mismatches: 20, Indels: 25
0.75 0.11 0.14
Matches are distributed among these distances:
43 39 0.29
45 1 0.01
50 1 0.01
51 4 0.03
52 46 0.34
53 5 0.04
54 5 0.04
55 35 0.26
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (52 bp):
TGGCACCTTTTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
Found at i:317801 original size:43 final size:43
Alignment explanation
Indices: 317740--317829 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
317730 CCTTTTTCAT
*
317740 CTTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
* *
317783 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
317826 CTTT
1 CTTT
317830 TCCATCTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
Found at i:318738 original size:13 final size:13
Alignment explanation
Indices: 318720--318744 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
318710 CATAAAGTGT
318720 TGTATCGATACAA
1 TGTATCGATACAA
318733 TGTATCGATACA
1 TGTATCGATACA
318745 TATTTTTTTG
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:318742 original size:33 final size:33
Alignment explanation
Indices: 318700--318766 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
318690 TTCAACGATT
318700 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
318733 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
318766 T
1 T
318767 TTAAGCTACT
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:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:318825 original size:13 final size:13
Alignment explanation
Indices: 318807--318831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
318797 ATCACTTAAA
318807 TGTATCGATACAT
1 TGTATCGATACAT
318820 TGTATCGATACA
1 TGTATCGATACA
318832 CTGATCTTTG
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:318896 original size:52 final size:52
Alignment explanation
Indices: 318840--319020 Score: 317
Period size: 52 Copynumber: 3.5 Consensus size: 52
318830 CACTGATCTT
*
318840 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
318892 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
318944 TGTATCTATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
318996 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
319021 TCATATTTCG
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 123 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:323162 original size:10 final size:10
Alignment explanation
Indices: 323147--323173 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
323137 TGCTAACTAA
323147 GTTTTTGTTT
1 GTTTTTGTTT
323157 GTTTTTGTTT
1 GTTTTTGTTT
323167 GTTTTTG
1 GTTTTTG
323174 CTTGATACAT
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:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Done.