Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold220
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: 1016241
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 65273 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:6052 original size:49 final size:50
Alignment explanation
Indices: 5958--6052 Score: 129
Period size: 49 Copynumber: 1.9 Consensus size: 50
5948 ACCTTATTCT
* * **
5958 AATCAATGTCAAATATAAGAAGAGTAGTTCTATATTGATTCTACTTATAC
1 AATCAATGTCAAATAGAAGAAGAGTAATTCTATACGGATTCTACTTATAC
* *
6008 AATCAATGTCAAATAGAAGTA-AGTAATTCTATACGGGTTCTACTT
1 AATCAATGTCAAATAGAAGAAGAGTAATTCTATACGGATTCTACTT
6053 GTCCAACTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 20 0.51
50 19 0.49
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (50 bp):
AATCAATGTCAAATAGAAGAAGAGTAATTCTATACGGATTCTACTTATAC
Found at i:6323 original size:40 final size:40
Alignment explanation
Indices: 6269--6346 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
6259 GTTTGGACAG
* *
6269 AAAACGCCGTTATAGATCG-AGCATTAGCGGCGCTTTTTAA
1 AAAACGCCGCTATAGAT-GTACCATTAGCGGCGCTTTTTAA
* *
6309 AAAACGTCGCTATAGGTGTACCATTAGCGGCGCTTTTT
1 AAAACGCCGCTATAGATGTACCATTAGCGGCGCTTTTT
6347 GAATAACCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.03
40 32 0.97
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (40 bp):
AAAACGCCGCTATAGATGTACCATTAGCGGCGCTTTTTAA
Found at i:22728 original size:7 final size:7
Alignment explanation
Indices: 22718--22840 Score: 51
Period size: 7 Copynumber: 17.9 Consensus size: 7
22708 ATAATTTAAT
22718 GTTTAGA
1 GTTTAGA
*
22725 GTTTAGT
1 GTTTAGA
22732 GTTT-G-
1 GTTTAGA
22737 GTTTAG-
1 GTTTAGA
22743 GTTGTAG-
1 GTT-TAGA
*
22750 GTTTATA
1 GTTTAGA
22757 GTTTAGTA
1 GTTTAG-A
*
22765 -TTTAGG
1 GTTTAGA
22771 GTTTATG-
1 GTTTA-GA
* *
22778 GGTTAGG
1 GTTTAGA
* *
22785 GTTAAAA
1 GTTTAGA
22792 GTTTAGA
1 GTTTAGA
*
22799 GTTTAGG
1 GTTTAGA
*
22806 GTTTAGGG
1 GTTTA-GA
* *
22814 GCTTAGG
1 GTTTAGA
*
22821 GTTTATA
1 GTTTAGA
*
22828 GTTTAGT
1 GTTTAGA
22835 GTTTAG
1 GTTTAG
22841 GATTTTAAAC
Statistics
Matches: 90, Mismatches: 18, Indels: 16
0.73 0.15 0.13
Matches are distributed among these distances:
5 4 0.04
6 8 0.09
7 70 0.78
8 8 0.09
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (7 bp):
GTTTAGA
Found at i:25271 original size:24 final size:24
Alignment explanation
Indices: 25236--25287 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
25226 TTGTTTAAAC
*
25236 ATTT-TTACCT-AATAAAACTAAT
1 ATTTCTTACCTAAAAAAAACTAAT
25258 ATTTCTTACCCTAAAAAAAACTAAT
1 ATTTCTTA-CCTAAAAAAAACTAAT
25283 ATTTC
1 ATTTC
25288 AGTTTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 4 0.15
23 3 0.12
24 3 0.12
25 16 0.62
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.38
Consensus pattern (24 bp):
ATTTCTTACCTAAAAAAAACTAAT
Found at i:26205 original size:227 final size:232
Alignment explanation
Indices: 25798--26260 Score: 776
Period size: 227 Copynumber: 2.0 Consensus size: 232
25788 TGACGTTTCA
** * *
25798 ATTTGGGATCATTGTCGTTGGGACTATTTTATTACTGTACATTTTTCAAGTTTATTACTGTACAT
1 ATTTGGGATCATTGTAATTGGAACTATTTTATTACTGCACATTTTTCAAGTTTATTACTGTACAT
*
25863 TTTGAACTTGTGCTTCTTTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAAATAAGTTT
66 TTTGAACTTGTGCTACTTTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAAATAAGTTT
25928 TGATATTAACAATGTTTGATTTTAATATTTAATAATTTTAAAATTTTTTAAAACTTATAAATATA
131 TGATATTAACAATGTTTGATTTTAATATTTAATAATTTTAAAATTTTTTAAAACTTATAAATATA
*
25993 TTTTGTAAGAGAGTAATTTTGATCATTATTTAAATTT
196 TTTTGTAAGAGAGTAATTTTGATCATTACTTAAATTT
*
26030 ATTTGGGATCTTTGTAATTGGAACTATTTTATTACTGCACATTTTTCAAGTTTATTACTGTACAT
1 ATTTGGGATCATTGTAATTGGAACTATTTTATTACTGCACATTTTTCAAGTTTATTACTGTACAT
* *
26095 TTTGAA-TT-TG-TAC-TTTTTTTT-ATAATATTTTCAAGTATATATTTAATACTAATTAATTTT
66 TTTGAACTTGTGCTACTTTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAAATAAGTTT
26155 TGATATTAACAATGTTTGATTTTAATATTTAATAATTTT-AAATGTTTTTAAAACTTATAAATAT
131 TGATATTAACAATGTTTGATTTTAATATTTAATAATTTTAAAAT-TTTTTAAAACTTATAAATAT
* *
26219 TTTTTGTAGGAGAGTAATTTTGATCATTACTTAAATTT
195 ATTTTGTAAGAGAGTAATTTTGATCATTACTTAAATTT
26257 ATTT
1 ATTT
26261 TAATATAAAA
Statistics
Matches: 219, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
226 4 0.02
227 135 0.62
228 8 0.04
229 2 0.01
230 2 0.01
231 2 0.01
232 66 0.30
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (232 bp):
ATTTGGGATCATTGTAATTGGAACTATTTTATTACTGCACATTTTTCAAGTTTATTACTGTACAT
TTTGAACTTGTGCTACTTTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAAATAAGTTT
TGATATTAACAATGTTTGATTTTAATATTTAATAATTTTAAAATTTTTTAAAACTTATAAATATA
TTTTGTAAGAGAGTAATTTTGATCATTACTTAAATTT
Found at i:26303 original size:19 final size:19
Alignment explanation
Indices: 26279--26336 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
26269 AAATCAAAAC
26279 TTACATAACTTTAAAGAAT
1 TTACATAACTTTAAAGAAT
* *
26298 TTACATAAC-TTACATAAT
1 TTACATAACTTTAAAGAAT
26316 TTACATAACTTTAAAGAAT
1 TTACATAACTTTAAAGAAT
26335 TT
1 TT
26337 TCGATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 16 0.47
19 18 0.53
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (19 bp):
TTACATAACTTTAAAGAAT
Found at i:26310 original size:9 final size:9
Alignment explanation
Indices: 26276--26740 Score: 202
Period size: 9 Copynumber: 50.6 Consensus size: 9
26266 TAAAAATCAA
26276 AACTTACAT
1 AACTTACAT
* *
26285 AACTTTAAAG
1 AAC-TTACAT
*
26295 AATTTACAT
1 AACTTACAT
26304 AACTTACAT
1 AACTTACAT
*
26313 AATTTACAT
1 AACTTACAT
* *
26322 AACTTTAAAG
1 AAC-TTACAT
* *
26332 AATTTTCGATTTT
1 AACTTAC-A---T
26345 AACTTA-AT
1 AACTTACAT
*
26353 AACTTATAT
1 AACTTACAT
*
26362 ATATGTATATCAT
1 A-A-CT-TA-CAT
26375 AACTTACAT
1 AACTTACAT
*
26384 AACTCACATAT
1 AACTTAC--AT
*
26395 AACTTATAT
1 AACTTACAT
26404 AACTTA-AT
1 AACTTACAT
*
26412 TACTTACAT
1 AACTTACAT
*
26421 ATATCATATCAT
1 A-A-CTTA-CAT
*
26433 AACTCACAT
1 AACTTACAT
26442 AACTTA-AT
1 AACTTACAT
*
26450 AACTTATAT
1 AACTTACAT
*
26459 ATACCATATCAT
1 A-A-CTTA-CAT
26471 AACTTACAT
1 AACTTACAT
*
26480 AACTCACAT
1 AACTTACAT
*
26489 AACATACAT
1 AACTTACAT
*
26498 AACATA-AT
1 AACTTACAT
*
26506 AACTTATAT
1 AACTTACAT
*
26515 ATATCATATCAT
1 A-A-CTTA-CAT
26527 AACTTACAT
1 AACTTACAT
* *
26536 AACTCATAT
1 AACTTACAT
* *
26545 AACGTATAT
1 AACTTACAT
* *
26554 CATTTA-AT
1 AACTTACAT
*
26562 AACTTACGT
1 AACTTACAT
26571 AACTTACAT
1 AACTTACAT
*
26580 AACTCACAT
1 AACTTACAT
26589 AACTTACAT
1 AACTTACAT
26598 AA--TACAT
1 AACTTACAT
* *
26605 AA-ATATAT
1 AACTTACAT
* *
26613 ATCGTATCAT
1 AACTTA-CAT
*
26623 AATTTACAT
1 AACTTACAT
*
26632 AACTCACAT
1 AACTTACAT
26641 AACTTACAT
1 AACTTACAT
26650 AA--TACAT
1 AACTTACAT
* *
26657 AA-ATATAT
1 AACTTACAT
* *
26665 ATCGTATCAT
1 AACTTA-CAT
*
26675 AATTTACAT
1 AACTTACAT
*
26684 AACTCACAT
1 AACTTACAT
26693 AACTTACAT
1 AACTTACAT
26702 AA--TACAT
1 AACTTACAT
* *
26709 AA-ATATAT
1 AACTTACAT
* *
26717 ATCATATCAT
1 AACTTA-CAT
26727 AACTTACAT
1 AACTTACAT
26736 AACTT
1 AACTT
26741 GTTTATACTT
Statistics
Matches: 345, Mismatches: 76, Indels: 70
0.70 0.15 0.14
Matches are distributed among these distances:
7 21 0.06
8 50 0.14
9 189 0.55
10 43 0.12
11 22 0.06
12 13 0.04
13 7 0.02
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (9 bp):
AACTTACAT
Found at i:26435 original size:38 final size:36
Alignment explanation
Indices: 26373--26642 Score: 153
Period size: 38 Copynumber: 7.4 Consensus size: 36
26363 TATGTATATC
* *
26373 ATAACTTACATAACTCACATATAACTTATATAACTTA
1 ATAACTTACATAA-TCATATATAACTTACATAACTTA
* *
26410 ATTACTTACATATATCATATCATAACTCACATAACTTA
1 ATAACTTACATA-ATCATAT-ATAACTTACATAACTTA
* * *
26448 ATAACTTATATATACCATATCATAACTTACATAACTCA
1 ATAACTTACATA-ATCATAT-ATAACTTACATAACTTA
* * *
26486 CATAACATACATAA-CATA-ATAACTTATATATATCATATC
1 -ATAACTTACATAATCATATATAACTTACATA-A-C-T-TA
* * * *
26525 ATAACTTACATAA-C-TCATATAACGTATATCATTTA
1 ATAACTTACATAATCAT-ATATAACTTACATAACTTA
* * * *
26560 ATAACTTACGTAA-CTTACATAACTCACATAACTTA
1 ATAACTTACATAATCATATATAACTTACATAACTTA
* * *
26595 CATAA--TACATAA--ATATATATCGTATCATAATTTA
1 -ATAACTTACATAATCATATATAACTTA-CATAACTTA
*
26629 CATAACTCACATAA
1 -ATAACTTACATAA
26643 CTTACATAAT
Statistics
Matches: 185, Mismatches: 34, Indels: 29
0.75 0.14 0.12
Matches are distributed among these distances:
33 7 0.04
34 19 0.10
35 38 0.21
36 13 0.07
37 22 0.12
38 66 0.36
39 20 0.11
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.34
Consensus pattern (36 bp):
ATAACTTACATAATCATATATAACTTACATAACTTA
Found at i:26499 original size:56 final size:52
Alignment explanation
Indices: 26358--26739 Score: 322
Period size: 52 Copynumber: 7.6 Consensus size: 52
26348 TTAATAACTT
* * *
26358 ATATATATGTATATCATAACTTACATAACTCACATATAACTTATATAACTTA-ATTACTT
1 ATATATAT-CATATCATAACTTACATAACTCAC--ATAACTTACATAA--TACA-TA--A
* * * *
26417 ACATATATCATATCATAACTCACATAACTTA-ATAACTTATAT-ATACCAT--
1 ATATATATCATATCATAACTTACATAACTCACATAACTTACATAATA-CATAA
* * * *
26466 ATCATA-A-CTTA-CATAACTCACATAACAT-ACATAACATA-AT-A-AC-T-T
1 AT-ATATATCATATCATAACTTACATAAC-TCACATAACTTACATAATACATAA
* *
26511 ATATATATCATATCATAACTTACATAACTCATATAACGT--AT-AT-CAT--
1 ATATATATCATATCATAACTTACATAACTCACATAACTTACATAATACATAA
* * * *
26557 TTA-ATAACTTA-CGTAACTTACATAACTCACATAACTTACATAATACATAA
1 ATATATATCATATCATAACTTACATAACTCACATAACTTACATAATACATAA
* *
26607 ATATATATCGTATCATAATTTACATAACTCACATAACTTACATAATACATAA
1 ATATATATCATATCATAACTTACATAACTCACATAACTTACATAATACATAA
* *
26659 ATATATATCGTATCATAATTTACATAACTCACATAACTTACATAATACATAA
1 ATATATATCATATCATAACTTACATAACTCACATAACTTACATAATACATAA
26711 ATATATATCATATCATAACTTACATAACT
1 ATATATATCATATCATAACTTACATAACT
26740 TGTTTATACT
Statistics
Matches: 279, Mismatches: 24, Indels: 47
0.80 0.07 0.13
Matches are distributed among these distances:
44 27 0.10
45 10 0.04
46 13 0.05
47 43 0.15
48 14 0.05
49 2 0.01
50 5 0.02
51 6 0.02
52 118 0.42
53 1 0.00
54 2 0.01
55 11 0.04
58 20 0.07
59 7 0.03
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.35
Consensus pattern (52 bp):
ATATATATCATATCATAACTTACATAACTCACATAACTTACATAATACATAA
Found at i:26582 original size:35 final size:35
Alignment explanation
Indices: 26514--26582 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
26504 ATAACTTATA
* *
26514 TATATCATATCATAACTTACATAACTCATATAACG
1 TATATCATATAATAACTTACATAACTCACATAACG
* * *
26549 TATATCATTTAATAACTTACGTAACTTACATAAC
1 TATATCATATAATAACTTACATAACTCACATAAC
26583 TCACATAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (35 bp):
TATATCATATAATAACTTACATAACTCACATAACG
Found at i:26630 original size:34 final size:33
Alignment explanation
Indices: 26585--26737 Score: 112
Period size: 34 Copynumber: 4.5 Consensus size: 33
26575 TACATAACTC
*
26585 ACATAACTTACATAATACATAAATATATATCGT
1 ACATAACTTACATAATACATAAATATATATCAT
* * * *
26618 ATCATAATTTACATAACTCACATAACT-TACATAAT
1 A-CATAACTTACATAA-T-ACATAAATATATATCAT
* * ** * * *
26653 ACATAAATATATATCGTATCAT-AATTTACATAACT
1 ACATAACT-TACATAATA-CATAAATATATATCA-T
26688 CACATAACTTACATAATACATAAATATATATCAT
1 -ACATAACTTACATAATACATAAATATATATCAT
26722 ATCATAACTTACATAA
1 A-CATAACTTACATAA
26738 CTTGTTTATA
Statistics
Matches: 93, Mismatches: 17, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
33 5 0.05
34 48 0.52
35 26 0.28
36 14 0.15
ACGTcount: A:0.48, C:0.17, G:0.01, T:0.34
Consensus pattern (33 bp):
ACATAACTTACATAATACATAAATATATATCAT
Found at i:28470 original size:12 final size:12
Alignment explanation
Indices: 28453--28484 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
28443 AATATCAATG
28453 GATGAATCTGAT
1 GATGAATCTGAT
28465 GATGAATCTGAT
1 GATGAATCTGAT
28477 GATGAATC
1 GATGAATC
28485 CGATAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.31
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:29475 original size:84 final size:84
Alignment explanation
Indices: 29334--29501 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
29324 GATCAATTGC
29334 TGAAGGTTACTTGGCAGAGGAGTGTATGACTTTCTATTCTAGATATTTAGAAGATGTTGAAACAA
1 TGAAGGTTACTTGGCAGAGGAGTGTATGACTTTCTATTCTAGATATTTAGAAGATGTTGAAACAA
29399 GACTGAACAGACCAAGTAG
66 GACTGAACAGACCAAGTAG
29418 TGAAGGTTACTTGGCAGAGGAGTGTATGACTTTCTATTCTAGATATTTAGAAGATGTTGAAACAA
1 TGAAGGTTACTTGGCAGAGGAGTGTATGACTTTCTATTCTAGATATTTAGAAGATGTTGAAACAA
*
29483 GACTGAACAGATCAAGTAG
66 GACTGAACAGACCAAGTAG
29502 AAATGTTGGG
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (84 bp):
TGAAGGTTACTTGGCAGAGGAGTGTATGACTTTCTATTCTAGATATTTAGAAGATGTTGAAACAA
GACTGAACAGACCAAGTAG
Found at i:31284 original size:26 final size:26
Alignment explanation
Indices: 31248--31297 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
31238 GTAGGAGAGG
*
31248 TTTGCTTTAGAGGTCTCGGATAATAA
1 TTTGCTTTAGAGGTCTCAGATAATAA
*
31274 TTTGCTTTAGATGTCTCAGATAAT
1 TTTGCTTTAGAGGTCTCAGATAAT
31298 TATGTCAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (26 bp):
TTTGCTTTAGAGGTCTCAGATAATAA
Found at i:32701 original size:43 final size:42
Alignment explanation
Indices: 32654--32804 Score: 171
Period size: 43 Copynumber: 3.5 Consensus size: 42
32644 GAACGGTACT
* *
32654 TTTAGTGGTGTTTGTGAAAAAGGCTTCGCTAAATGTCATGTTC
1 TTTAGCGGCGTTTGTGAAAAAGGC-TCGCTAAATGTCATGTTC
*
32697 TTTAGCGGCGTTTGTGAAAAAGGCGCCGCT-AATGGTCATGTTC
1 TTTAGCGGCGTTTGTGAAAAAGGC-TCGCTAAAT-GTCATGTTC
*
32740 TTTAGCGGCGTTTGTGATAAAAGTGCT-GCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGA-AAAAG-GCTCGCTAAATGTCATGTTC
* * * *
32783 TCTAGTGGCGTTTATGTAAAAG
1 TTTAGCGGCGTTTGTGAAAAAG
32805 AAACGCTGCC
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
42 8 0.09
43 77 0.82
44 7 0.07
45 2 0.02
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGAAAAAGGCTCGCTAAATGTCATGTTC
Found at i:35209 original size:15 final size:16
Alignment explanation
Indices: 35177--35210 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
35167 ATTTAATCTT
*
35177 ATTTGCATTTAGGTTA
1 ATTTGCATCTAGGTTA
35193 ATTTGCATCTA-GTTA
1 ATTTGCATCTAGGTTA
35208 ATT
1 ATT
35211 AATTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (16 bp):
ATTTGCATCTAGGTTA
Found at i:37045 original size:19 final size:19
Alignment explanation
Indices: 36970--37046 Score: 91
Period size: 19 Copynumber: 4.0 Consensus size: 19
36960 ATATGTCAAG
*
36970 ATGCACTTTGTGTGCTAGAT
1 ATGCACTTTGTGTGCCAG-T
** *
36990 ATATACTTTGTGTGCCAAT
1 ATGCACTTTGTGTGCCAGT
*
37009 ATGCACTTTGTGCGCCAGT
1 ATGCACTTTGTGTGCCAGT
*
37028 ATGCACTTTATGTGCCAGT
1 ATGCACTTTGTGTGCCAGT
37047 TTACCCTGCT
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 33 0.70
20 14 0.30
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (19 bp):
ATGCACTTTGTGTGCCAGT
Found at i:40821 original size:55 final size:55
Alignment explanation
Indices: 40733--40881 Score: 153
Period size: 55 Copynumber: 2.7 Consensus size: 55
40723 TGGCTTTGCG
* **
40733 GAGGTTCAGGT-GGACTGTAC-G-GATATTCTTATATATGTTAAACTATGACTGTGTA
1 GAGGCTCAGGTAGG-CTGTACAGAGAT-TTC-TATATATGTTAAACTATGACTGTACA
* * * * *
40788 GAGGCTC-GAGTCGGTTGTACAGAGATTTCTATATATGTTAAATTATGGCTTTACA
1 GAGGCTCAG-GTAGGCTGTACAGAGATTTCTATATATGTTAAACTATGACTGTACA
*
40843 GAGGCTCAGGTAGGCTGTTCAGAGATTTCTATATATGTT
1 GAGGCTCAGGTAGGCTGTACAGAGATTTCTATATATGTT
40882 TACTTATGAT
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
54 1 0.01
55 68 0.86
56 7 0.09
57 3 0.04
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (55 bp):
GAGGCTCAGGTAGGCTGTACAGAGATTTCTATATATGTTAAACTATGACTGTACA
Found at i:46850 original size:16 final size:16
Alignment explanation
Indices: 46808--46843 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
46798 TAAACCCTGA
46808 AACCAGAAAAATAAAG
1 AACCAGAAAAATAAAG
46824 AACCAGAAAAATAAAG
1 AACCAGAAAAATAAAG
46840 AACC
1 AACC
46844 TTCAAAACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.67, C:0.17, G:0.11, T:0.06
Consensus pattern (16 bp):
AACCAGAAAAATAAAG
Found at i:47669 original size:52 final size:52
Alignment explanation
Indices: 47612--47720 Score: 209
Period size: 52 Copynumber: 2.1 Consensus size: 52
47602 TTTCTCATGC
*
47612 ACACAACTCCACTTTCAACCGAACTATATGTAGAAAACCATTCTCTATTGGG
1 ACACAACTCCACTTTCAACCGAACTATATGTAGAAAACAATTCTCTATTGGG
47664 ACACAACTCCACTTTCAACCGAACTATATGTAGAAAACAATTCTCTATTGGG
1 ACACAACTCCACTTTCAACCGAACTATATGTAGAAAACAATTCTCTATTGGG
47716 ACACA
1 ACACA
47721 TATGGAAAGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.26
Consensus pattern (52 bp):
ACACAACTCCACTTTCAACCGAACTATATGTAGAAAACAATTCTCTATTGGG
Found at i:50784 original size:28 final size:28
Alignment explanation
Indices: 50693--50785 Score: 143
Period size: 28 Copynumber: 3.4 Consensus size: 28
50683 TATTTAGTAG
50693 CAGT-ACAGTGTGGGCCTTAGCCCAATA
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
* * *
50720 CAGTAATACTGTGAGCCTTAGCCCAATA
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
50748 CAGTAACAGTGTGGGCCTTAGCCCAATA
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
*
50776 CAGAAACAGT
1 CAGTAACAGT
50786 CCAGTGCAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
27 4 0.07
28 54 0.93
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.22
Consensus pattern (28 bp):
CAGTAACAGTGTGGGCCTTAGCCCAATA
Found at i:50967 original size:26 final size:26
Alignment explanation
Indices: 50894--50980 Score: 95
Period size: 26 Copynumber: 3.3 Consensus size: 26
50884 CCAATATCGC
* * *
50894 AGCAAAGCTGCCAGTAATAGCATCGC
1 AGCAAAGCTGCCAGTAATAGTATTGT
* *
50920 AGCAGAGCTGCTAGT-ATCAGTATTGT
1 AGCAAAGCTGCCAGTAAT-AGTATTGT
50946 AGCAAAGCTGCCAGTAATAGTATATGT
1 AGCAAAGCTGCCAGTAATAGTAT-TGT
*
50973 GGCAAAGC
1 AGCAAAGC
50981 CACTAGTAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
25 2 0.04
26 36 0.72
27 12 0.24
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (26 bp):
AGCAAAGCTGCCAGTAATAGTATTGT
Found at i:51200 original size:27 final size:26
Alignment explanation
Indices: 51169--51403 Score: 116
Period size: 27 Copynumber: 8.7 Consensus size: 26
51159 GCATAAGGCC
51169 ATAACGGTCATTTTATCTCCTA-GGGGT
1 ATAACGGTCATTTTA-C-CCTAGGGGGT
*
51196 ATAACAGTCATTTTACCCTATGGGGGT
1 ATAACGGTCATTTTACCCTA-GGGGGT
** *
51223 ATTCCGGTCATTTTACCCTATAGGGGT
1 ATAACGGTCATTTTACCCTA-GGGGGT
** * * * *
51250 ATTTCAGTCATGTTACCCTATGAGGAT
1 ATAACGGTCATTTTACCCTA-GGGGGT
** *
51277 ATTTCGATCATTTTACCCTATGGGGGT
1 ATAACGGTCATTTTACCCTA-GGGGGT
** * *
51304 ATTTCAGTCATTTTACCCTATAGGGGT
1 ATAACGGTCATTTTACCCTA-GGGGGT
** * *
51331 ATTTCGGTTATTTTACCCTGTGGGGGT
1 ATAACGGTCATTTTACCCT-AGGGGGT
* * * *
51358 A-ATTCAGTTATTTTACCCTGTGGGGGT
1 ATA-ACGGTCATTTTACCCT-AGGGGGT
*
51385 A-ATTCGGTCATTTTACCCT
1 ATA-ACGGTCATTTTACCCT
51404 GTGAAGGTAA
Statistics
Matches: 177, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
25 4 0.02
26 1 0.01
27 172 0.97
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (26 bp):
ATAACGGTCATTTTACCCTAGGGGGT
Found at i:51235 original size:54 final size:53
Alignment explanation
Indices: 51173--51403 Score: 259
Period size: 54 Copynumber: 4.3 Consensus size: 53
51163 AAGGCCATAA
* *
51173 CGGTCATTTTATCTCC-TAGGGGTATAACAGTCATTTTACCCTATGGGGGTATTC
1 CGGTCATTTTA-C-CCTTAGGGGTATATCAGTCATTTTACCCTATGGGGGTATTT
* * * *
51227 CGGTCATTTTACCCTATAGGGGTATTTCAGTCATGTTACCCTATGAGGATATTT
1 CGGTCATTTTACCCT-TAGGGGTATATCAGTCATTTTACCCTATGGGGGTATTT
* * * *
51281 CGATCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTT
1 CGGTCATTTTACCCT-TAGGGGTATATCAGTCATTTTACCCTATGGGGGTATTT
* * * * *
51335 CGGTTATTTTACCCTGTGGGGGTA-ATTCAGTTATTTTACCCTGTGGGGGTAATT
1 CGGTCATTTTACCCT-TAGGGGTATA-TCAGTCATTTTACCCTATGGGGGTATTT
51389 CGGTCATTTTACCCT
1 CGGTCATTTTACCCT
51404 GTGAAGGTAA
Statistics
Matches: 153, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
52 2 0.01
53 1 0.01
54 150 0.98
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (53 bp):
CGGTCATTTTACCCTTAGGGGTATATCAGTCATTTTACCCTATGGGGGTATTT
Found at i:51404 original size:27 final size:27
Alignment explanation
Indices: 51202--51579 Score: 357
Period size: 27 Copynumber: 14.0 Consensus size: 27
51192 GGGTATAACA
*
51202 GTCATTTTACCCTATGGGGGT-ATTCCG
1 GTCATTTTACCCTGTGGGGGTAATT-CG
* * * *
51229 GTCATTTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTGTGGGGGTAATTCG
* * * * *
51256 GTCATGTTACCCTATGAGGATATTTCG
1 GTCATTTTACCCTGTGGGGGTAATTCG
* * * *
51283 ATCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTGTGGGGGTAATTCG
* * *
51310 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTGTGGGGGTAATTCG
* *
51337 GTTATTTTACCCTGTGGGGGTAATTCA
1 GTCATTTTACCCTGTGGGGGTAATTCG
*
51364 GTTATTTTACCCTGTGGGGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCG
**
51391 GTCATTTTACCCTGTGAAGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCG
* * **
51418 ATCATTTTACCTTGTGGGGGTAATTTA
1 GTCATTTTACCCTGTGGGGGTAATTCG
* * * * *
51445 AT-AATTTCCCCTGTGAGGCTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCG
* *
51471 GTCATTTTACCCTGTGAGGGTAATTCA
1 GTCATTTTACCCTGTGGGGGTAATTCG
* *
51498 GTAATTTT-CCTTGTGGGGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCG
*
51524 ATCATTTTACCCTGTGGGGGGGTAATTCG
1 GTCATTTTACCCTGT--GGGGGTAATTCG
* * *
51553 ATCATTTTATCCTATGGGGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCG
51580 ATTATTTATC
Statistics
Matches: 294, Mismatches: 52, Indels: 10
0.83 0.15 0.03
Matches are distributed among these distances:
26 39 0.13
27 228 0.78
28 2 0.01
29 25 0.09
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (27 bp):
GTCATTTTACCCTGTGGGGGTAATTCG
Found at i:51484 original size:80 final size:81
Alignment explanation
Indices: 51340--51539 Score: 264
Period size: 80 Copynumber: 2.5 Consensus size: 81
51330 TATTTCGGTT
* * * * *
51340 ATTTTACCCTGTGGGGGTAATTCAGTTATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTG
1 ATTTTACCTTGTGGGGGTAATTCAGATAATTTACCCTGTGAGGCTAATTCGGTCATTTTACCCTG
*
51405 TGAAGGTAATTC-GATC
66 TGAAGGTAATTCAG-TA
* *
51421 ATTTTACCTTGTGGGGGTAATTTA-ATAATTTCCCCTGTGAGGCTAATTCGGTCATTTTACCCTG
1 ATTTTACCTTGTGGGGGTAATTCAGATAATTTACCCTGTGAGGCTAATTCGGTCATTTTACCCTG
*
51485 TGAGGGTAATTCAGTA
66 TGAAGGTAATTCAGTA
*
51501 ATTTT-CCTTGTGGGGGTAATTC-GATCATTTTACCCTGTG
1 ATTTTACCTTGTGGGGGTAATTCAGAT-AATTTACCCTGTG
51540 GGGGGGTAAT
Statistics
Matches: 104, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
79 18 0.17
80 63 0.61
81 23 0.22
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (81 bp):
ATTTTACCTTGTGGGGGTAATTCAGATAATTTACCCTGTGAGGCTAATTCGGTCATTTTACCCTG
TGAAGGTAATTCAGTA
Found at i:58434 original size:21 final size:23
Alignment explanation
Indices: 58399--58440 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
58389 ATTTACTTTT
*
58399 AATTTTTTGTATAAATATTTATG
1 AATTTTTTGTATAAAAATTTATG
58422 AATTTTTT-T-TAAAAATTTA
1 AATTTTTTGTATAAAAATTTA
58441 ATCAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 1 0.06
23 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (23 bp):
AATTTTTTGTATAAAAATTTATG
Found at i:60665 original size:21 final size:23
Alignment explanation
Indices: 60619--60665 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
60609 ACGACATGGT
60619 TGTGTATTTCAGCCACACGA--G
1 TGTGTATTTCAGCCACACGACCG
60640 TGTGTGATTT-AGCCACACGACCG
1 TGTGT-ATTTCAGCCACACGACCG
60663 TGT
1 TGT
60666 CTACTCCGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 15 0.65
22 4 0.17
23 4 0.17
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (23 bp):
TGTGTATTTCAGCCACACGACCG
Found at i:60665 original size:23 final size:21
Alignment explanation
Indices: 60619--60659 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
60609 ACGACATGGT
60619 TGTGTATTTCAGCCACACGAG
1 TGTGTATTTCAGCCACACGAG
60640 TGTGTGATTT-AGCCACACGA
1 TGTGT-ATTTCAGCCACACGA
60660 CCGTGTCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
TGTGTATTTCAGCCACACGAG
Found at i:60781 original size:21 final size:21
Alignment explanation
Indices: 60742--60824 Score: 60
Period size: 21 Copynumber: 4.0 Consensus size: 21
60732 AACCATGTAA
* *
60742 CTCAGTCACACAGATGTGTGT
1 CTCAGTCACACGGACGTGTGT
*
60763 CTCAGTCACACGGCCGTGTG-
1 CTCAGTCACACGGACGTGTGT
* * *
60783 CTTCACTCACACGGGCATGTGT
1 C-TCAGTCACACGGACGTGTGT
* * * *
60805 ATCATTTACACGGTCGTGTG
1 CTCAGTCACACGGACGTGTG
60825 GCCCTATTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
20 1 0.02
21 48 0.98
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (21 bp):
CTCAGTCACACGGACGTGTGT
Found at i:63584 original size:30 final size:29
Alignment explanation
Indices: 63548--63664 Score: 155
Period size: 30 Copynumber: 4.0 Consensus size: 29
63538 GGTGAATTAA
*
63548 AGCATGCATGTGTTTAGGGAGCTGAATGG
1 AGCATGCATGTATTTAGGGAGCTGAATGG
*
63577 GGCCATGCATGTATTTAGGGAGCTGAATGG
1 AG-CATGCATGTATTTAGGGAGCTGAATGG
* *
63607 AGCA-GTATGAATTTAGGGAGCTGAATGG
1 AGCATGCATGTATTTAGGGAGCTGAATGG
* *
63635 AGCATGCATGTAATTGAAGGAGCTGAATGG
1 AGCATGCATGT-ATTTAGGGAGCTGAATGG
63665 GGATGCTAGA
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
28 26 0.34
29 7 0.09
30 43 0.57
ACGTcount: A:0.28, C:0.10, G:0.36, T:0.26
Consensus pattern (29 bp):
AGCATGCATGTATTTAGGGAGCTGAATGG
Found at i:65940 original size:21 final size:21
Alignment explanation
Indices: 65892--65940 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
65882 CAGCTACATG
65892 GGCGTGTGATTTAGCCACACA
1 GGCGTGTGATTTAGCCACACA
65913 GGCGTGTGATTTAGCCACAC-
1 GGCGTGTGATTTAGCCACACA
65933 GGCTGTGT
1 GGC-GTGT
65941 CTACTTTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.27
Consensus pattern (21 bp):
GGCGTGTGATTTAGCCACACA
Found at i:80421 original size:22 final size:22
Alignment explanation
Indices: 80370--80535 Score: 154
Period size: 22 Copynumber: 7.5 Consensus size: 22
80360 TACACCACAC
*
80370 TAGTAGGCACCGAAGTGCTTAAA
1 TAGTAGGCACCGAAGTGC-TAAT
*
80393 TAGTAGGCACCGAAGTGCTGAT
1 TAGTAGGCACCGAAGTGCTAAT
* *
80415 TAGTAGGCACCGTAGTGCAAAT
1 TAGTAGGCACCGAAGTGCTAAT
* * * *
80437 CAGTAGGTACCGAAGTGCTGAG
1 TAGTAGGCACCGAAGTGCTAAT
* * *
80459 TAGTAGGCACTGTAGTGCAAAT
1 TAGTAGGCACCGAAGTGCTAAT
* * *
80481 CAGTACGCACCGTAGTGCTAAT
1 TAGTAGGCACCGAAGTGCTAAT
* *
80503 TAGTAGGCA-CTATAGTGCAAAT
1 TAGTAGGCACCGA-AGTGCTAAT
*
80525 CAGTAGGCACC
1 TAGTAGGCACC
80536 ATAATGCTAA
Statistics
Matches: 113, Mismatches: 28, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
21 1 0.01
22 93 0.82
23 19 0.17
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (22 bp):
TAGTAGGCACCGAAGTGCTAAT
Found at i:80455 original size:44 final size:44
Alignment explanation
Indices: 80370--80535 Score: 226
Period size: 44 Copynumber: 3.8 Consensus size: 44
80360 TACACCACAC
*
80370 TAGTAGGCACCGAAGTGCTTAAAT-AGTAGGCACCGAAGTGCTGAT
1 TAGTAGGCACCGTAGTGC--AAATCAGTAGGCACCGAAGTGCTGAT
* *
80415 TAGTAGGCACCGTAGTGCAAATCAGTAGGTACCGAAGTGCTGAG
1 TAGTAGGCACCGTAGTGCAAATCAGTAGGCACCGAAGTGCTGAT
* * * *
80459 TAGTAGGCACTGTAGTGCAAATCAGTACGCACCGTAGTGCTAAT
1 TAGTAGGCACCGTAGTGCAAATCAGTAGGCACCGAAGTGCTGAT
**
80503 TAGTAGGCACTATAGTGCAAATCAGTAGGCACC
1 TAGTAGGCACCGTAGTGCAAATCAGTAGGCACC
80536 ATAATGCTAA
Statistics
Matches: 109, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
43 4 0.04
44 88 0.81
45 17 0.16
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (44 bp):
TAGTAGGCACCGTAGTGCAAATCAGTAGGCACCGAAGTGCTGAT
Found at i:80491 original size:66 final size:67
Alignment explanation
Indices: 80371--80512 Score: 178
Period size: 66 Copynumber: 2.1 Consensus size: 67
80361 ACACCACACT
** * *
80371 AGTAGGCACCGAAGTGCTTAAATAGTAGGCACCGAAGTGCTGATTAGTAGGCACCGTAGTGCAAA
1 AGTAGGCACCGAAGTGCTTAAATAGTAGGCACCGAAGTGCAAATCAGTACGCACCGTAGTGCAAA
80436 TC
66 TC
* * * * * *
80438 AGTAGGTACCGAAGTGC-TGAGTAGTAGGCACTGTAGTGCAAATCAGTACGCACCGTAGTGCTAA
1 AGTAGGCACCGAAGTGCTTAAATAGTAGGCACCGAAGTGCAAATCAGTACGCACCGTAGTGCAAA
*
80502 TT
66 TC
80504 AGTAGGCAC
1 AGTAGGCAC
80513 TATAGTGCAA
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
66 47 0.75
67 16 0.25
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (67 bp):
AGTAGGCACCGAAGTGCTTAAATAGTAGGCACCGAAGTGCAAATCAGTACGCACCGTAGTGCAAA
TC
Found at i:83044 original size:72 final size:73
Alignment explanation
Indices: 82926--83071 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 73
82916 AACATGTGTG
82926 TGTGTGTGTGTTTAATTTTTGAAGTATAATAACAGCTATTTTTCTTGAATTTCATCATGGTTATC
1 TGTGTGTGTGTTTAATTTTTGAAGTATAATAACAGCTATTTTTCTTGAATTTCATCATGGTTATC
82991 TCAATCTT
66 TCAATCTT
82999 TGTGTGTGTG-TTAATTTTTGAAGTATAATAACAGCTATTTTTCTTGAATTTCATCATGGTTATC
1 TGTGTGTGTGTTTAATTTTTGAAGTATAATAACAGCTATTTTTCTTGAATTTCATCATGGTTATC
83063 TCAATCTT
66 TCAATCTT
83071 T
1 T
83072 TAACTGTAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 63 0.86
73 10 0.14
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (73 bp):
TGTGTGTGTGTTTAATTTTTGAAGTATAATAACAGCTATTTTTCTTGAATTTCATCATGGTTATC
TCAATCTT
Found at i:83959 original size:26 final size:26
Alignment explanation
Indices: 83930--83983 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
83920 TAAATGTATG
83930 TATTTAA-TAA-TAAAATATATATTACT
1 TATTTAATTAAGT-AAATATATATTA-T
83956 TA-TTAATTAAGTAAATATATATTAT
1 TATTTAATTAAGTAAATATATATTAT
83981 TAT
1 TAT
83984 AATTAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
25 7 0.28
26 17 0.68
27 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
TATTTAATTAAGTAAATATATATTAT
Found at i:83986 original size:24 final size:26
Alignment explanation
Indices: 83942--83989 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
83932 TTTAATAATA
83942 AAATATATATTACTTATTAATTAAGT
1 AAATATATATTACTTATTAATTAAGT
83968 AAATATATATTA-TTA-TAATTAA
1 AAATATATATTACTTATTAATTAA
83990 AACAAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
AAATATATATTACTTATTAATTAAGT
Found at i:85078 original size:40 final size:40
Alignment explanation
Indices: 84957--85090 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 40
84947 AAGTTTGAGT
* *
84957 CGATGAGACACTGGGTGTCAATTTATTACTTT-AGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTTGA-ATT-ATC
* * * * ** *
84998 CGATGAGGCATTGGGTG-CCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
85035 CGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
*
85075 CGATGAGGCACTGGGT
1 CGATGAGACACTGGGT
85091 ACCAAACTGG
Statistics
Matches: 72, Mismatches: 17, Indels: 9
0.73 0.17 0.09
Matches are distributed among these distances:
37 16 0.22
38 11 0.15
39 2 0.03
40 28 0.39
41 15 0.21
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
Found at i:91130 original size:6 final size:6
Alignment explanation
Indices: 91119--91143 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
91109 CCCATTACAA
91119 TATCAG TATCAG TATCAG TATCAG T
1 TATCAG TATCAG TATCAG TATCAG T
91144 GTAGGCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (6 bp):
TATCAG
Found at i:91172 original size:46 final size:43
Alignment explanation
Indices: 91074--91178 Score: 115
Period size: 46 Copynumber: 2.4 Consensus size: 43
91064 GGTTTAAGCC
* *
91074 CAAT-TCAATAACAGTTCAGTTCAGTTGGGCCTTAGCCCATTA
1 CAATATCAGTAACAGTTCAGTTCAGTTAGGCCTTAGCCCATTA
*
91116 CAATATCAGTATCAGTATCAGTATCAGTGTAGGCCTTAGCCCATTA
1 CAATATCAGTAACAGT-TCAGT-TCAGT-TAGGCCTTAGCCCATTA
* *
91162 TAGTGA-CAGTAACAGTT
1 CAAT-ATCAGTAACAGTT
91179 TAGACATGCA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
42 4 0.08
43 9 0.17
44 5 0.10
45 6 0.12
46 27 0.52
47 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (43 bp):
CAATATCAGTAACAGTTCAGTTCAGTTAGGCCTTAGCCCATTA
Found at i:98000 original size:16 final size:17
Alignment explanation
Indices: 97967--98000 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
97957 TTATCTTTAG
*
97967 TAGTTTGTTGATCATAT
1 TAGTTTGTTGACCATAT
97984 TAGTTTGTT-ACCATAT
1 TAGTTTGTTGACCATAT
98000 T
1 T
98001 TAAAACATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.53
Consensus pattern (17 bp):
TAGTTTGTTGACCATAT
Found at i:98460 original size:34 final size:32
Alignment explanation
Indices: 98395--98466 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 32
98385 GCAATTTAGT
*
98395 TCAGTTGGGCTTAGCCCATTACAGTATCAGTA
1 TCAGTTGGGCTTAACCCATTACAGTATCAGTA
98427 TCAGTGTGGGCTTTAACCCATTACAGTGA-CAGTA
1 TCAGT-TGGGC-TTAACCCATTACAGT-ATCAGTA
*
98461 ACAGTT
1 TCAGTT
98467 CAGACATGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 5 0.14
33 6 0.17
34 23 0.66
35 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (32 bp):
TCAGTTGGGCTTAACCCATTACAGTATCAGTA
Found at i:102257 original size:156 final size:156
Alignment explanation
Indices: 101973--102284 Score: 498
Period size: 156 Copynumber: 2.0 Consensus size: 156
101963 TTAATCTTTC
* * * * * *
101973 TAGGATAAATTCAAATTACCTCAACAAAAACCACGTGCCCTAGAAAAGTCACCTCTCGCAACCAG
1 TAGGATAAACTCAAATCACCTCAACAAAAACCACGTACCCCAGAAAAGTCACCTATCACAACCAG
*
102038 AACTCACACTTGCTCAACTTAGCGTAAAGTTGTTTCTCTCGAAATATCTGAAGCACTACTCTAAT
66 AACTCACACTTGCTCAACTTAGCGTAAAGTTGTTTCTCTCGAAATATCTGAAGCACTACTCTAAG
102103 ATGTTCATCATGCTCATCCTCGGTCT
131 ATGTTCATCATGCTCATCCTCGGTCT
* * * *
102129 TAGGATAAACTCAAATCACCTCAGCAGAAACTACGTACCCCAGAAAAGTCACCTATCACAACTAG
1 TAGGATAAACTCAAATCACCTCAACAAAAACCACGTACCCCAGAAAAGTCACCTATCACAACCAG
* *
102194 AACTCACACTTGCTCAACTTAGCGTAGAGTTGTTTCTCTCGAAGTATCTGAAGCACTACTCTAAG
66 AACTCACACTTGCTCAACTTAGCGTAAAGTTGTTTCTCTCGAAATATCTGAAGCACTACTCTAAG
*
102259 ATGTTCATCATGTTCATCCTCGGTCT
131 ATGTTCATCATGCTCATCCTCGGTCT
102285 AAGAGTAAAC
Statistics
Matches: 142, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
156 142 1.00
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (156 bp):
TAGGATAAACTCAAATCACCTCAACAAAAACCACGTACCCCAGAAAAGTCACCTATCACAACCAG
AACTCACACTTGCTCAACTTAGCGTAAAGTTGTTTCTCTCGAAATATCTGAAGCACTACTCTAAG
ATGTTCATCATGCTCATCCTCGGTCT
Found at i:106939 original size:16 final size:16
Alignment explanation
Indices: 106918--106973 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
106908 CAGGGCATTA
106918 CATTACAACTCTATTC
1 CATTACAACTCTATTC
* *
106934 CATTACAGCTCTATTG
1 CATTACAACTCTATTC
* * *
106950 AATTACAGCCCTATTC
1 CATTACAACTCTATTC
106966 CATTACAA
1 CATTACAA
106974 TAAACCAAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (16 bp):
CATTACAACTCTATTC
Found at i:110712 original size:90 final size:91
Alignment explanation
Indices: 110604--110784 Score: 355
Period size: 90 Copynumber: 2.0 Consensus size: 91
110594 AAATTAATAA
110604 ATAATATTTATTTTAGGAAATAGAAAAACATGTATTAGGTTGAATTAAATTATAAAGTGCAGGAT
1 ATAATATTTATTTTAGGAAATAGAAAAACATGTATTAGGTTGAATTAAATTATAAAGTGCAGGAT
110669 TAAAAGTCTAGGAAGCACATATAATT
66 TAAAAGTCTAGGAAGCACATATAATT
110695 ATAATATTTA-TTTAGGAAATAGAAAAACATGTATTAGGTTGAATTAAATTATAAAGTGCAGGAT
1 ATAATATTTATTTTAGGAAATAGAAAAACATGTATTAGGTTGAATTAAATTATAAAGTGCAGGAT
110759 TAAAAGTCTAGGAAGCACATATAATT
66 TAAAAGTCTAGGAAGCACATATAATT
110785 GGACCTAATA
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
90 80 0.89
91 10 0.11
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.33
Consensus pattern (91 bp):
ATAATATTTATTTTAGGAAATAGAAAAACATGTATTAGGTTGAATTAAATTATAAAGTGCAGGAT
TAAAAGTCTAGGAAGCACATATAATT
Found at i:112632 original size:12 final size:12
Alignment explanation
Indices: 112614--112667 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
112604 ACCGATCTGG
112614 TTTCGTTCTCCC
1 TTTCGTTCTCCC
*
112626 GTTCGTTCT-CC
1 TTTCGTTCTCCC
112637 ---C-TTCTCCC
1 TTTCGTTCTCCC
112645 TTTCGTTCTCCC
1 TTTCGTTCTCCC
112657 TTTCGTTCTCC
1 TTTCGTTCTCC
112668 GTTGATTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
7 4 0.11
8 3 0.08
11 3 0.08
12 26 0.72
ACGTcount: A:0.00, C:0.43, G:0.09, T:0.48
Consensus pattern (12 bp):
TTTCGTTCTCCC
Found at i:112670 original size:19 final size:19
Alignment explanation
Indices: 112619--112658 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
112609 TCTGGTTTCG
112619 TTCTCCCGTTCGTTCTCCC
1 TTCTCCCGTTCGTTCTCCC
*
112638 TTCTCCCTTTCGTTCTCCC
1 TTCTCCCGTTCGTTCTCCC
112657 TT
1 TT
112659 TCGTTCTCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.45, G:0.07, T:0.47
Consensus pattern (19 bp):
TTCTCCCGTTCGTTCTCCC
Found at i:113959 original size:12 final size:12
Alignment explanation
Indices: 113942--113967 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
113932 ATTAGAATAA
113942 CTAAAATTTTTT
1 CTAAAATTTTTT
113954 CTAAAATTTTTT
1 CTAAAATTTTTT
113966 CT
1 CT
113968 TACACCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.58
Consensus pattern (12 bp):
CTAAAATTTTTT
Found at i:114090 original size:18 final size:18
Alignment explanation
Indices: 114067--114105 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
114057 TTTACCAACT
114067 TTATGGATAATAATTTAA
1 TTATGGATAATAATTTAA
114085 TTATGGATAATAATTTAA
1 TTATGGATAATAATTTAA
114103 TTA
1 TTA
114106 AAGATACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (18 bp):
TTATGGATAATAATTTAA
Found at i:114111 original size:18 final size:18
Alignment explanation
Indices: 114072--114111 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
114062 CAACTTTATG
**
114072 GATAATAATTTAATTATG
1 GATAATAATTTAATTAAA
114090 GATAATAATTTAATTAAA
1 GATAATAATTTAATTAAA
114108 GATA
1 GATA
114112 CAACATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (18 bp):
GATAATAATTTAATTAAA
Found at i:114696 original size:32 final size:33
Alignment explanation
Indices: 114660--114746 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 33
114650 AACTTTTTCG
* ** *
114660 GAAAATATTTT-CAGGAAATCTGTCAAACAGCA
1 GAAAATATTTTACAGCAAATCAATCAAACACCA
114692 GAAAATATTTTACA-CAAATTCAATCAAACACCA
1 GAAAATATTTTACAGCAAA-TCAATCAAACACCA
* *
114725 GAAAATATTTTCCAGTAAATCA
1 GAAAATATTTTACAGCAAATCA
114747 TTTTACAGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
32 14 0.30
33 29 0.63
34 3 0.07
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCAATCAAACACCA
Found at i:114744 original size:14 final size:15
Alignment explanation
Indices: 114722--114798 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
114712 CAATCAAACA
114722 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
114736 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
114751 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
114771 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
114785 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
114799 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:114763 original size:20 final size:20
Alignment explanation
Indices: 114738--114777 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
114728 AATATTTTCC
*
114738 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
114758 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
114778 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:114783 original size:34 final size:35
Alignment explanation
Indices: 114726--114792 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
114716 CAAACACCAG
*
114726 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
114761 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
114793 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:114799 original size:14 final size:14
Alignment explanation
Indices: 114761--114800 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
114751 ACAGAAAAGT
*
114761 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
114775 AAATCATTTTACGG
1 AAAACATTTTACAG
114789 AAAACATTTTAC
1 AAAACATTTTAC
114801 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:116962 original size:36 final size:35
Alignment explanation
Indices: 116902--117001 Score: 110
Period size: 37 Copynumber: 2.7 Consensus size: 35
116892 AGTCTCATAT
* *
116902 ATTACAATTATATGTTTATTTTTTTATTAGTCCAAAA
1 ATTACAATTATGTG-TTA-TTTTTTATTACTCCAAAA
*
116939 GATTACAATTATGTGCTTATTTTTTATTACTCCTAAA
1 -ATTACAATTATGTG-TTATTTTTTATTACTCCAAAA
* * *
116976 ATTATAATTATGCGTTAATTTTTATT
1 ATTACAATTATGTGTTATTTTTTATT
117002 TAATAGAAGC
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
35 11 0.20
36 12 0.22
37 16 0.29
38 16 0.29
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (35 bp):
ATTACAATTATGTGTTATTTTTTATTACTCCAAAA
Found at i:119716 original size:44 final size:44
Alignment explanation
Indices: 119666--119756 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
119656 GTAGGTCAAA
*
119666 TAATATTAAAATAACCTACACTAATAAGAGTTTAAGTG-GAAAAC
1 TAATATTAAAAAAACCTACACTAATAAGAGTTTAAGTGAG-AAAC
* * *
119710 TAATATTAAAAAAATCTACGCTAATCAGAGTTTAAGTGAGAAAC
1 TAATATTAAAAAAACCTACACTAATAAGAGTTTAAGTGAGAAAC
119754 TAA
1 TAA
119757 AAACATAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 41 0.98
45 1 0.02
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.27
Consensus pattern (44 bp):
TAATATTAAAAAAACCTACACTAATAAGAGTTTAAGTGAGAAAC
Found at i:127748 original size:13 final size:13
Alignment explanation
Indices: 127700--127755 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
127690 TATAATTCGA
*
127700 TTTGGTTTAATTT
1 TTTGTTTTAATTT
* *
127713 TGT-TTTTCATTT
1 TTTGTTTTAATTT
* *
127725 TTTCATATTAATTT
1 TTT-GTTTTAATTT
127739 TTTGTTTTAATTT
1 TTTGTTTTAATTT
127752 TTTG
1 TTTG
127756 AGCTTTTGAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
12 9 0.27
13 14 0.42
14 10 0.30
ACGTcount: A:0.16, C:0.04, G:0.09, T:0.71
Consensus pattern (13 bp):
TTTGTTTTAATTT
Found at i:132760 original size:15 final size:16
Alignment explanation
Indices: 132735--132765 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
132725 TTGATTTACT
132735 AAGGAAATTATAATGA
1 AAGGAAATTATAATGA
132751 AAGG-AATTATAATGA
1 AAGGAAATTATAATGA
132766 TTAAGCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (16 bp):
AAGGAAATTATAATGA
Found at i:133857 original size:18 final size:19
Alignment explanation
Indices: 133836--133872 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
133826 ACATGTGTAA
133836 TAATAA-ACAACATGTATT
1 TAATAATACAACATGTATT
*
133854 TAATAATACAATATGTATT
1 TAATAATACAACATGTATT
133873 GCTTATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (19 bp):
TAATAATACAACATGTATT
Found at i:134263 original size:25 final size:25
Alignment explanation
Indices: 134229--134278 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
134219 GAATTTCTAG
134229 TTAGAATTGATAAAAGGATTAAATT
1 TTAGAATTGATAAAAGGATTAAATT
*
134254 TTAGAGTTGATAAAAGGATTAAATT
1 TTAGAATTGATAAAAGGATTAAATT
134279 GTGAACTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (25 bp):
TTAGAATTGATAAAAGGATTAAATT
Found at i:135104 original size:23 final size:22
Alignment explanation
Indices: 135078--135138 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
135068 AGACACTTTA
*
135078 TGTGTCGTATTTTAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
* *
135101 TGTGTTGTA-TCAGGCACTTCG
1 TGTGTCGTATTCAGGCACCTCG
135122 TGTGTCGTA-TCAGGCAC
1 TGTGTCGTATTCAGGCAC
135139 TTATATGTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 26 0.76
23 8 0.24
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.36
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:135139 original size:21 final size:21
Alignment explanation
Indices: 135091--135140 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
135081 GTCGTATTTT
* *
135091 AGGCACCTCGTGTGTTGTATC
1 AGGCACTTCGTGTGTCGTATC
135112 AGGCACTTCGTGTGTCGTATC
1 AGGCACTTCGTGTGTCGTATC
135133 AGGCACTT
1 AGGCACTT
135141 ATATGTCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (21 bp):
AGGCACTTCGTGTGTCGTATC
Found at i:135149 original size:20 final size:21
Alignment explanation
Indices: 135107--135151 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
135097 CTCGTGTGTT
* *
135107 GTATCAGGCACTTCGTGTGTC
1 GTATCAGGCACTTCATATGTC
135128 GTATCAGGCACTT-ATATGTC
1 GTATCAGGCACTTCATATGTC
135148 GTAT
1 GTAT
135152 ACTGATCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (21 bp):
GTATCAGGCACTTCATATGTC
Found at i:135888 original size:23 final size:22
Alignment explanation
Indices: 135862--135922 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
135852 AGACACTTTA
*
135862 TGTGTCGTATTTTAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
* *
135885 TGTGTTGTA-TCAGGCACTTCG
1 TGTGTCGTATTCAGGCACCTCG
135906 TGTGTCGTA-TCAGGCAC
1 TGTGTCGTATTCAGGCAC
135923 TTATATGTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 26 0.76
23 8 0.24
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.36
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:135923 original size:21 final size:21
Alignment explanation
Indices: 135875--135924 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
135865 GTCGTATTTT
* *
135875 AGGCACCTCGTGTGTTGTATC
1 AGGCACTTCGTGTGTCGTATC
135896 AGGCACTTCGTGTGTCGTATC
1 AGGCACTTCGTGTGTCGTATC
135917 AGGCACTT
1 AGGCACTT
135925 ATATGTCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (21 bp):
AGGCACTTCGTGTGTCGTATC
Found at i:135933 original size:20 final size:21
Alignment explanation
Indices: 135891--135935 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
135881 CTCGTGTGTT
* *
135891 GTATCAGGCACTTCGTGTGTC
1 GTATCAGGCACTTCATATGTC
135912 GTATCAGGCACTT-ATATGTC
1 GTATCAGGCACTTCATATGTC
135932 GTAT
1 GTAT
135936 ACTGATCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (21 bp):
GTATCAGGCACTTCATATGTC
Found at i:139334 original size:12 final size:13
Alignment explanation
Indices: 139310--139338 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
139300 GGGCTATAAC
139310 TATTGCATTTATT
1 TATTGCATTTATT
139323 TATTGC-TTTATT
1 TATTGCATTTATT
139335 TATT
1 TATT
139339 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:142012 original size:13 final size:13
Alignment explanation
Indices: 142007--142033 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
141997 AAAAGGATGT
142007 AGGAAAAAGATTG
1 AGGAAAAAGATTG
142020 AGGAAAAAGATTG
1 AGGAAAAAGATTG
142033 A
1 A
142034 ACTAGAAGAA
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:0.56, C:0.00, G:0.30, T:0.15
Consensus pattern (13 bp):
AGGAAAAAGATTG
Found at i:145943 original size:26 final size:26
Alignment explanation
Indices: 145892--145953 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
145882 TACCTATAGT
*
145892 AGTTTCAAAATATCATAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* *
145918 AGTTTCAGAATATCATAGCATGTATC
1 AGTTTCAGAATATCATAACATATATC
145944 AGTTTCAGAA
1 AGTTTCAGAA
145954 CACTTACAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:146718 original size:34 final size:34
Alignment explanation
Indices: 146665--146732 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
146655 GCACAGTTGA
*
146665 ACAGTCTTAGACCTAAGCCCATTTCAGTATCAGTG
1 ACAGTCTTAGACCTAAGCCCATCTCAGTA-CAGTG
* *
146700 ACAGT-TTAGGCCTTAGCCCATCTCAGTACAGTG
1 ACAGTCTTAGACCTAAGCCCATCTCAGTACAGTG
146733 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (34 bp):
ACAGTCTTAGACCTAAGCCCATCTCAGTACAGTG
Found at i:149662 original size:22 final size:22
Alignment explanation
Indices: 149634--149682 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
149624 CTGCAGAGTC
*
149634 TCATACTACCCTTAAAGGGCTT
1 TCATACTACCCGTAAAGGGCTT
* *
149656 TCATACTACTCGTAAAGGGTTT
1 TCATACTACCCGTAAAGGGCTT
149678 TCATA
1 TCATA
149683 TCTATGCGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (22 bp):
TCATACTACCCGTAAAGGGCTT
Found at i:152733 original size:27 final size:27
Alignment explanation
Indices: 152703--152760 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
152693 GCATCATAGT
*
152703 TAGTCTGACAGGACATTAAACACAAGA
1 TAGTCTGACAGGACAATAAACACAAGA
* **
152730 TAGTCTGACGGGACAATAAACATGAGA
1 TAGTCTGACAGGACAATAAACACAAGA
152757 TAGT
1 TAGT
152761 ACATAGGGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (27 bp):
TAGTCTGACAGGACAATAAACACAAGA
Found at i:154282 original size:534 final size:534
Alignment explanation
Indices: 153190--154773 Score: 2767
Period size: 534 Copynumber: 3.0 Consensus size: 534
153180 ATCTTGAAGC
* *
153190 ATTCATAAACAATAACACGCTAGTAGGTGCCTGGTGTATAGGCAAACAAAAGAAGGTTTATCCGA
1 ATTCATGAACAATAACACGCTAGTAGGTGCCTGGTGTATAGGTAAACAAAAGAAGGTTTATCCGA
* *
153255 GGATCACAGATAAAGATCCACCAATAATAACCACCAAAGGGTGCTCAGTGAAAACCTACATGTTA
66 GGATCACAGATAAAGATCCACCAATAAGAACCACCAAAGGGTGCTCAGTGAAAACCTGCATGTTA
153320 GAGATTGAGCATAAATACGACGGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGTC
131 GAGATTGAGCATAAATACGACGGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGTC
* * * *
153385 AGAGTGAGTCACACAGAAGGATATATCGAGTGACAAATATGTCTGTTAATACTATTCCTCTTTAC
196 AGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTTTAA
* * * *
153450 GGGGATTATGTTGCGAAGTACTCACCAAATGGGTAGTTCCATGGGAACCAACGTGTAAGAGGAAT
261 GGGGATTATGTTGCTAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACGTGTAAGCGGAAT
*
153515 CGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAATCCATAGTTGATGGGCATGT
326 CGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGCATGT
* *
153580 TATGTATAAGAGTAAGGTAACGCATGTGAATTAGGTTACAAAGATGTAATCCCATCACTATGAAA
391 TATGTATAAGAGTAAGGTAACGCAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATGAAA
*
153645 CCCAATTGCTATTTAGCTTGCCATAGTGGTATGGGATCTCATCAGTTATTACAATAAATGGTGTG
456 CCCAATTGCTATTTAGCTTGCCATAGTGGTATGGGATCTCATCAGTTATTCCAATAAATGGTGTG
153710 GGATCTCATCAATT
521 GGATCTCATCAATT
153724 ATTCATGAACAATAACACGCTAGTAGGTGCCTGGTGTATAGGTAAACAAAAGAAGGTTTATCCGA
1 ATTCATGAACAATAACACGCTAGTAGGTGCCTGGTGTATAGGTAAACAAAAGAAGGTTTATCCGA
* * *
153789 GGATCACAGATAAAGATCCACTAATAAGAACCACCAAAAGGTGCTCAGTGAAAACTTGCATGTTA
66 GGATCACAGATAAAGATCCACCAATAAGAACCACCAAAGGGTGCTCAGTGAAAACCTGCATGTTA
* * ** *
153854 GAGAATGAGCGTAAATACGACGACTAGTCCATTGAATAAAGAGGGTTTAGCTAGAAGCCATAGTC
131 GAGATTGAGCATAAATACGACGGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGTC
153919 AGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTTTAA
196 AGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTTTAA
153984 GGGGATTATG-TGCTAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACGTGTAAGCGGAAT
261 GGGGATTATGTTGCTAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACGTGTAAGCGGAAT
* *
154048 CGTGAACTTAAATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGTCATGT
326 CGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGCATGT
154113 TATGTATAAGAGTAAGGTAACGCAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATGAAA
391 TATGTATAAGAGTAAGGTAACGCAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATGAAA
154178 CCCAATTGCTATTTAGCTTGCCATAGTGGTATGGGATCTCATCAGTTATTCCAATAAATGGTGTG
456 CCCAATTGCTATTTAGCTTGCCATAGTGGTATGGGATCTCATCAGTTATTCCAATAAATGGTGTG
154243 GGATCTCATCAATT
521 GGATCTCATCAATT
*
154257 ATTCATGAACAATAAACATGCTAGTAGGTGCCTGGTGTATAGGTAAACAAAAGAAGGTTTATCCG
1 ATTCATGAACAAT-AACACGCTAGTAGGTGCCTGGTGTATAGGTAAACAAAAGAAGGTTTATCCG
*
154322 AGGATCACAGATAAAAATCCACCAATAAGAACCACCAAAGGGTGCTCAGTGAAAACCTGCATGTT
65 AGGATCACAGATAAAGATCCACCAATAAGAACCACCAAAGGGTGCTCAGTGAAAACCTGCATGTT
154387 AGAGATTGAGCATAAATACGACGGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGT
130 AGAGATTGAGCATAAATACGACGGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGT
* *
154452 CAGAGAGAGTCACACAAAGGGATATATCAAGTGACAAATATGTCTGTTAAGACTATTCCTCTTTA
195 CAGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTTTA
* * *
154517 AGGGGATTATGTTG-TGAAGTACTTGCCAAATGGGTAGTTCGATGGTAACCAACGTGTAAGCGAA
260 AGGGGATTATGTTGCT-AAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACGTGTAAGCGGA
154581 ATCGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGCAT
324 ATCGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGCAT
* * *
154646 GTTATGTATAAGAGTGAGGTAATGCAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATTA
389 GTTATGTATAAGAGTAAGGTAACGCAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATGA
* * * * *
154711 AACCCAATTGCTATTTAGTTTGCCAGAGTGGTGTGAGATCTCATCAGTTATTCCAACAAATGG
454 AACCCAATTGCTATTTAGCTTGCCATAGTGGTATGGGATCTCATCAGTTATTCCAATAAATGG
154774 AATGTGAGTA
Statistics
Matches: 996, Mismatches: 51, Indels: 5
0.95 0.05 0.00
Matches are distributed among these distances:
533 266 0.27
534 500 0.50
535 230 0.23
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.27
Consensus pattern (534 bp):
ATTCATGAACAATAACACGCTAGTAGGTGCCTGGTGTATAGGTAAACAAAAGAAGGTTTATCCGA
GGATCACAGATAAAGATCCACCAATAAGAACCACCAAAGGGTGCTCAGTGAAAACCTGCATGTTA
GAGATTGAGCATAAATACGACGGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGTC
AGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTTTAA
GGGGATTATGTTGCTAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACGTGTAAGCGGAAT
CGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGCATGT
TATGTATAAGAGTAAGGTAACGCAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATGAAA
CCCAATTGCTATTTAGCTTGCCATAGTGGTATGGGATCTCATCAGTTATTCCAATAAATGGTGTG
GGATCTCATCAATT
Found at i:159267 original size:37 final size:38
Alignment explanation
Indices: 159217--159293 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 38
159207 GTAAAACAAG
159217 TATGTTATTACAATCATCTCAT-ACTGGTCTTTGGGCA
1 TATGTTATTACAATCATCTCATGACTGGTCTTTGGGCA
159254 TATGTTATTACAATCATCTCATGACTGGTCTTTGGGCA
1 TATGTTATTACAATCATCTCATGACTGGTCTTTGGGCA
159292 TA
1 TA
159294 CTCCATTGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
37 22 0.56
38 17 0.44
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (38 bp):
TATGTTATTACAATCATCTCATGACTGGTCTTTGGGCA
Found at i:171371 original size:10 final size:9
Alignment explanation
Indices: 171336--171372 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
171326 GGGTTTACCC
171336 ACAATTAAA
1 ACAATTAAA
171345 ACAATTAAA
1 ACAATTAAA
*
171354 AAAATTAAA
1 ACAATTAAA
171363 ACAAGTTAAA
1 ACAA-TTAAA
171373 CACTAATCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.22
Consensus pattern (9 bp):
ACAATTAAA
Found at i:173821 original size:39 final size:39
Alignment explanation
Indices: 173765--173852 Score: 158
Period size: 39 Copynumber: 2.3 Consensus size: 39
173755 TAATGAAGTT
173765 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
1 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
*
173804 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAATGTGGTGAG
1 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
*
173843 GGTGAAGGTG
1 GGTGAGGGTG
173853 AGGGTGGTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.19, C:0.02, G:0.51, T:0.27
Consensus pattern (39 bp):
GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
Found at i:173853 original size:45 final size:43
Alignment explanation
Indices: 173765--173892 Score: 149
Period size: 39 Copynumber: 3.0 Consensus size: 43
173755 TAATGAAGTT
*
173765 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGA---G-
1 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAATGTGGTGAGGTGA
173804 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAATGTGGTGAGGGTGAA
1 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAATGTGGTGA-GGTG-A
* * *
173849 GGTGAGGGTGGTGAGGTT-TCTGACAGTAAAGGTGGAGAGAGTGA
1 GGTGAGGGTGGTGAGGTTGT-TGGCAGTAAATGTGGTGAG-GTGA
173893 TAGAGGTGGT
Statistics
Matches: 77, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
39 37 0.48
43 1 0.01
44 3 0.04
45 36 0.47
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.26
Consensus pattern (43 bp):
GGTGAGGGTGGTGAGGTTGTTGGCAGTAAATGTGGTGAGGTGA
Found at i:176559 original size:82 final size:82
Alignment explanation
Indices: 176431--176633 Score: 334
Period size: 82 Copynumber: 2.5 Consensus size: 82
176421 TTGAGATTGT
* *
176431 TAACATATTTTATTTGTTTTTTGAAATGATTTCTTGAAATGGTTGGTTAACAACTTACTACTATA
1 TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAATGATTGGTTAACAACTTACTACTATA
176496 GGATCATTTTGTTAGCA
66 GGATCATTTTGTTAGCA
* * * *
176513 TAACATATTTTATTTGTTTTTTTAAATGATTTGTTGAAATGATTGGTTAACATCTTATTGCTATA
1 TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAATGATTGGTTAACAACTTACTACTATA
*
176578 GGATCATTTTGTTAGTA
66 GGATCATTTTGTTAGCA
*
176595 TAACATATTTTATTTGTTTTTTGGAATGATTTGTTGAAA
1 TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAA
176634 GATGTATATC
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 112 1.00
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.50
Consensus pattern (82 bp):
TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAATGATTGGTTAACAACTTACTACTATA
GGATCATTTTGTTAGCA
Found at i:178180 original size:113 final size:114
Alignment explanation
Indices: 177971--178182 Score: 338
Period size: 113 Copynumber: 1.9 Consensus size: 114
177961 TACTCTAATA
*
177971 TTCAAGCATGGGAAAGAAATGTTTCATCAATATCCAAATAAAAAAATAAAAAAGGAATCCCCAAT
1 TTCAAGCATGGGAAAGAAATGTTTCATCAATATCCAAATAAAAAAATAAAAAA-GAATCCACAAT
* *
178036 TTCTTATGAACCTTAAAATAAATCGGCTAAATATGCTTACTCGAATACAT
65 TTCTTATGAACCCTAAAACAAATCGGCTAAATATGCTTACTCGAATACAT
* * *
178086 TTCATGCATGGGAAAGAAATGTTTCATTAATATCC-AATTAAAAAATAAAAAA-AATCACACAAT
1 TTCAAGCATGGGAAAGAAATGTTTCATCAATATCCAAATAAAAAAATAAAAAAGAATC-CACAAT
178149 TTCTTATGAACCCTAAAACAAATCGGCTAAATAT
65 TTCTTATGAACCCTAAAACAAATCGGCTAAATAT
178183 ACAGTGATTA
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
112 4 0.04
113 37 0.41
114 16 0.18
115 33 0.37
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.27
Consensus pattern (114 bp):
TTCAAGCATGGGAAAGAAATGTTTCATCAATATCCAAATAAAAAAATAAAAAAGAATCCACAATT
TCTTATGAACCCTAAAACAAATCGGCTAAATATGCTTACTCGAATACAT
Found at i:178675 original size:18 final size:17
Alignment explanation
Indices: 178632--178680 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
178622 AGTTAGGGGT
*
178632 TTTAAATATTTTTTTTAA
1 TTTAAAT-TATTTTTTAA
*
178650 TTTTAATTATTTTTTAA
1 TTTAAATTATTTTTTAA
178667 GTTTAAATTCATTT
1 -TTTAAATT-ATTT
178681 GCTGATGCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 9 0.35
18 13 0.50
19 4 0.15
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTAAATTATTTTTTAA
Found at i:179731 original size:29 final size:31
Alignment explanation
Indices: 179699--179762 Score: 89
Period size: 29 Copynumber: 2.1 Consensus size: 31
179689 CTAGAAAAAA
179699 AATAA-TCTAGTAACTTAAATA-AA-ATTTTT
1 AATAATTC-AGTAACTTAAATAGAATATTTTT
*
179728 AATAATTCAGTAACTTAAATAGAATCTTTTT
1 AATAATTCAGTAACTTAAATAGAATATTTTT
179759 AATA
1 AATA
179763 TTTGAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 18 0.58
30 4 0.13
31 9 0.29
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (31 bp):
AATAATTCAGTAACTTAAATAGAATATTTTT
Found at i:180693 original size:27 final size:29
Alignment explanation
Indices: 180663--180716 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
180653 AAATTTAGAG
180663 AAGAGCA-AAAAAAAT-TATAAAAAATAT
1 AAGAGCACAAAAAAATATATAAAAAATAT
** *
180690 AAGATTACAAAAAAATATATTAAAAAT
1 AAGAGCACAAAAAAATATATAAAAAAT
180717 GATTCAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 8 0.36
29 9 0.41
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.22
Consensus pattern (29 bp):
AAGAGCACAAAAAAATATATAAAAAATAT
Found at i:180785 original size:16 final size:16
Alignment explanation
Indices: 180753--180790 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
180743 TAAATTAGAA
180753 AAAAAATAAAAATTAT
1 AAAAAATAAAAATTAT
*
180769 ATAAAATTAAAAA-TAT
1 A-AAAAATAAAAATTAT
180785 AAAAAA
1 AAAAAA
180791 ATCTTTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
15 4 0.21
16 5 0.26
17 10 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAATAAAAATTAT
Found at i:180790 original size:27 final size:26
Alignment explanation
Indices: 180732--180792 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
180722 AAAGTTATTC
180732 AAAAAATTATATAAATTAGAAAAAAA
1 AAAAAATTATATAAATTAGAAAAAAA
*
180758 ATAAAAATTATATAAAATTA-AAAATATA
1 A-AAAAATTATAT-AAATTAGAAAA-AAA
180786 AAAAAAT
1 AAAAAAT
180793 CTTTACAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 1 0.03
27 21 0.68
28 9 0.29
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (26 bp):
AAAAAATTATATAAATTAGAAAAAAA
Found at i:181226 original size:18 final size:18
Alignment explanation
Indices: 181205--181239 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
181195 TTTTTATATT
181205 TTTTAAATTTTTTTAAAA
1 TTTTAAATTTTTTTAAAA
* *
181223 TTTTCATTTTTTTTAAA
1 TTTTAAATTTTTTTAAA
181240 TATAAAATAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTAAATTTTTTTAAAA
Found at i:183584 original size:109 final size:109
Alignment explanation
Indices: 183435--183635 Score: 287
Period size: 109 Copynumber: 1.8 Consensus size: 109
183425 AAACTCCACT
* *
183435 TCACATGTCGGTGAATTCATCAAGTTCGTCTCAATAGGACCACTCAAATCCTAGGATATGAATTC
1 TCACATGTCAGTGAATTCATCAAGTTCGTCTCAATAGGACCACCCAAATCCTAGGATATGAATTC
*
183500 ATTAAAAGTTAGAACTCAACCTTATGCATGTACATCATTCAACC
66 ATTAAAAGTGAGAACTCAACCTTATGCATGTACATCATTCAACC
* * * * * *
183544 TCACTTGTCAGTGAATTCATCAAG-TCTGTCTCAATTGGACCACCCAAATCTTGGGATATTATTT
1 TCACATGTCAGTGAATTCATCAAGTTC-GTCTCAATAGGACCACCCAAATCCTAGGATATGAATT
* *
183608 TATTAAGAGTGAGAACTCAACCTTATGC
65 CATTAAAAGTGAGAACTCAACCTTATGC
183636 TTTTCATCGT
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
108 2 0.03
109 78 0.98
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (109 bp):
TCACATGTCAGTGAATTCATCAAGTTCGTCTCAATAGGACCACCCAAATCCTAGGATATGAATTC
ATTAAAAGTGAGAACTCAACCTTATGCATGTACATCATTCAACC
Found at i:189275 original size:55 final size:55
Alignment explanation
Indices: 189191--189317 Score: 191
Period size: 55 Copynumber: 2.3 Consensus size: 55
189181 CTAATGGAAG
* * *** *
189191 CAAGTCATTGAGTTACATGGGCTAGTCACATTGGCGTGTGGTTGGCCATGTGACC
1 CAAGTCAGTGAGTTACACGGGCTAGTCACACAAGCGTGTGGTTGACCATGTGACC
*
189246 CAAGTCAGTGAGTTACACGGGCTAGTCACACAAGCGTGTGGTTGACCGTGTGACC
1 CAAGTCAGTGAGTTACACGGGCTAGTCACACAAGCGTGTGGTTGACCATGTGACC
189301 CAAGTCAGTGAGTTACA
1 CAAGTCAGTGAGTTACA
189318 TGGCCTAAGA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 65 1.00
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (55 bp):
CAAGTCAGTGAGTTACACGGGCTAGTCACACAAGCGTGTGGTTGACCATGTGACC
Found at i:191435 original size:16 final size:16
Alignment explanation
Indices: 191414--191444 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
191404 AAGCCTATAC
191414 ATATACATCAAACAAT
1 ATATACATCAAACAAT
191430 ATATACATCAAACAA
1 ATATACATCAAACAA
191445 GTTAGCCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (16 bp):
ATATACATCAAACAAT
Found at i:191762 original size:25 final size:24
Alignment explanation
Indices: 191734--191814 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 24
191724 ATGCTTATAT
* *
191734 GAGCTGTGAATTGGAATGCTCACTC
1 GAGCTGT-AATCGGAATGCTCACAC
* * *
191759 GAGCTGTAGACCGGTATGCTCTCAC
1 GAGCTGTA-ATCGGAATGCTCACAC
*
191784 GAGCTGTAAATCGGCATGCTCACAC
1 GAGCTGT-AATCGGAATGCTCACAC
191809 GAGCTG
1 GAGCTG
191815 CAGATCAGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
24 1 0.02
25 44 0.96
26 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.23
Consensus pattern (24 bp):
GAGCTGTAATCGGAATGCTCACAC
Found at i:197904 original size:26 final size:26
Alignment explanation
Indices: 197832--197898 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
197822 ACTACAATGC
* *
197832 TCACACGAGCTGTGAAATGGGCTTGT
1 TCACACGAGCTGTGGAATGGGCCTGT
197858 TCACACGAGCTGTGGAATGGGCCTGT
1 TCACACGAGCTGTGGAATGGGCCTGT
197884 TCACACGAGCTGTGG
1 TCACACGAGCTGTGG
197899 GTTGGGATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.21, C:0.22, G:0.33, T:0.24
Consensus pattern (26 bp):
TCACACGAGCTGTGGAATGGGCCTGT
Found at i:205217 original size:25 final size:25
Alignment explanation
Indices: 205161--205221 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
205151 ACATATTTTT
*
205161 TCAAAATTTTACAAGGGCAAAATCA
1 TCAAAATTTTACAAGAGCAAAATCA
* *
205186 TCAAAATTTTACAATAGCTAAAATCG
1 TCAAAATTTTACAAGAGC-AAAATCA
*
205212 TCAAATTTTT
1 TCAAAATTTT
205222 GTTAGGGGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 16 0.52
26 15 0.48
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (25 bp):
TCAAAATTTTACAAGAGCAAAATCA
Found at i:206549 original size:26 final size:26
Alignment explanation
Indices: 206510--206594 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
206500 TCTCTGACCA
* *
206510 ACTCATACTAAAGGGTCTTCGAACCC
1 ACTCAAACTCAAGGGTCTTCGAACCC
* * *
206536 ACTCAAACTCAAGGGACATCCAACCC
1 ACTCAAACTCAAGGGTCTTCGAACCC
* * *
206562 ATTTCAAACTCAAGGGTCTTTGAGCCC
1 A-CTCAAACTCAAGGGTCTTCGAACCC
206589 ACTCAA
1 ACTCAA
206595 TCTTACTAGG
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
26 26 0.57
27 20 0.43
ACGTcount: A:0.33, C:0.32, G:0.14, T:0.21
Consensus pattern (26 bp):
ACTCAAACTCAAGGGTCTTCGAACCC
Found at i:207886 original size:34 final size:34
Alignment explanation
Indices: 207848--207919 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
207838 AATGCCAGTA
* **
207848 ATCAGTAGGGCCTTTGCCCAATTTCAGTAATAG-T
1 ATCAGTAGGGCCTTGGCCC-ATAACAGTAATAGAT
*
207882 ATCAGTGGGGCCTTGGCCCATAACAGTAATAGAT
1 ATCAGTAGGGCCTTGGCCCATAACAGTAATAGAT
207916 ATCA
1 ATCA
207920 ATCATGCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (34 bp):
ATCAGTAGGGCCTTGGCCCATAACAGTAATAGAT
Found at i:208404 original size:27 final size:26
Alignment explanation
Indices: 208374--208459 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 26
208364 ATCTCCTAGA
208374 GGTATAACAGTCATTTTACCCTATGGG
1 GGTATAAC-GTCATTTTACCCTATGGG
** **
208401 GGTATCTCGGTCATTTTACTATATGGG
1 GGTATAAC-GTCATTTTACCCTATGGG
** *
208428 GGTATTGCGATCATTTTATCCTATGGG
1 GGTATAACG-TCATTTTACCCTATGGG
208455 GGTAT
1 GGTAT
208460 TTTGGTCATT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
26 1 0.02
27 47 0.98
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (26 bp):
GGTATAACGTCATTTTACCCTATGGG
Found at i:208468 original size:27 final size:26
Alignment explanation
Indices: 208383--208473 Score: 110
Period size: 27 Copynumber: 3.4 Consensus size: 26
208373 AGGTATAACA
*
208383 GTCATTTTACCCTATGGGGGTATCTCG
1 GTCATTTTA-CCTATGGGGGTATTTCG
* *
208410 GTCATTTTACTATATGGGGGTATTGCG
1 GTCATTTTAC-CTATGGGGGTATTTCG
* *
208437 ATCATTTTATCCTATGGGGGTATTTTG
1 GTCATTTTA-CCTATGGGGGTATTTCG
208464 GTCATTTTAC
1 GTCATTTTAC
208474 TTATTTTAGG
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
27 51 0.94
28 1 0.02
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.43
Consensus pattern (26 bp):
GTCATTTTACCTATGGGGGTATTTCG
Found at i:209581 original size:12 final size:12
Alignment explanation
Indices: 209564--209605 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
209554 ATCCCAATAT
209564 TCTCTCCTCAAA
1 TCTCTCCTCAAA
*
209576 TCTCTCC-AAATA
1 TCTCTCCTCAA-A
*
209588 TCCCTCCTCAAA
1 TCTCTCCTCAAA
209600 TCTCTC
1 TCTCTC
209606 TATGACCAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.24, C:0.43, G:0.00, T:0.33
Consensus pattern (12 bp):
TCTCTCCTCAAA
Found at i:211612 original size:32 final size:32
Alignment explanation
Indices: 211571--211639 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
211561 ATGAGGCTGT
211571 TTAAATGACAACAAA-ATCTCCAACGTGACCAA
1 TTAAATGACAACAAACA-CTCCAACGTGACCAA
* * * *
211603 TTAAATGACAGCAAACACTCTAACGTGGCCAG
1 TTAAATGACAACAAACACTCCAACGTGACCAA
211635 TTAAA
1 TTAAA
211640 ATAACAAGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.20
Consensus pattern (32 bp):
TTAAATGACAACAAACACTCCAACGTGACCAA
Found at i:213641 original size:34 final size:34
Alignment explanation
Indices: 213603--213716 Score: 129
Period size: 37 Copynumber: 3.1 Consensus size: 34
213593 GAAAAAGAAG
213603 GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAA
1 GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAA
* *
213637 GAAAGAAGAAAAGGAAAGGGGAAGAAAAAAGAAAGAAAGAAA
1 G--A-AAGAAAAGGAAAGGAGAAG--AGAA-AAA-AAA-AAA
213679 GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAGAA
1 GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAA-AA
213714 GAA
1 GAA
213717 GAAGAGGGAA
Statistics
Matches: 67, Mismatches: 4, Indels: 17
0.76 0.05 0.19
Matches are distributed among these distances:
34 2 0.03
35 8 0.12
36 4 0.06
37 21 0.31
39 21 0.31
40 4 0.06
41 3 0.04
42 4 0.06
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (34 bp):
GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAA
Found at i:213695 original size:5 final size:4
Alignment explanation
Indices: 213554--213686 Score: 78
Period size: 4 Copynumber: 32.2 Consensus size: 4
213544 CAAAATATAT
* * *
213554 AGAA AGAA AGAA AGAA AGGAA GGAA GGAGA GGAA AGAA AG-A A-AA AGAA
1 AGAA AGAA AGAA AGAA A-GAA AGAA AGA-A AGAA AGAA AGAA AGAA AGAA
* * * *
213602 GGAA AGAAA AGGAA AG-G AGAA GAGAA AAAA AAAA AGAA AG-A AGAAA
1 AGAA AG-AA A-GAA AGAA AGAA -AGAA AGAA AGAA AGAA AGAA AG-AA
*
213648 AGGAA AGGGGA AGAA A-AA AGAA AGAA AGAA AGAA AGAA A
1 A-GAA A--GAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
213687 AGGAAAGGAG
Statistics
Matches: 106, Mismatches: 10, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
3 12 0.11
4 66 0.62
5 22 0.21
6 6 0.06
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:213719 original size:21 final size:22
Alignment explanation
Indices: 213661--213722 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
213651 AAAGGGGAAG
213661 AAAAAAGAAAGAAAGAA-AGAAA
1 AAAAAAGAAAG-AAGAAGAGAAA
* * *
213683 GAAAAGGAAAGGAGAAGAGAAA
1 AAAAAAGAAAGAAGAAGAGAAA
213705 AAAAAAG-AAGAAGAAGAG
1 AAAAAAGAAAGAAGAAGAG
213723 GGAATGAAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAGAAGAAGAGAAA
Found at i:213719 original size:34 final size:36
Alignment explanation
Indices: 213631--213713 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 36
213621 AAGAGAAAAA
* *
213631 AAAAAAGAAAG-AAGAAAAGGAAAGGGGAAGAAAAAA
1 AAAAAAGAAAGAAAGAAAAGGAAAGGAGAAG-AGAAA
213667 GAAAGAAAGAAAGAAAGAAAAGGAAAGGAGAAGAGAAA
1 -AAA-AAAGAAAGAAAGAAAAGGAAAGGAGAAGAGAAA
213705 AAAAAAGAA
1 AAAAAAGAA
213714 GAAGAAGAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
36 6 0.14
37 6 0.14
38 12 0.29
39 18 0.43
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (36 bp):
AAAAAAGAAAGAAAGAAAAGGAAAGGAGAAGAGAAA
Found at i:220196 original size:3 final size:3
Alignment explanation
Indices: 220188--220216 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
220178 TCTTAATACT
220188 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
220217 TAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:220494 original size:27 final size:27
Alignment explanation
Indices: 220450--220513 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
220440 ACACGAGTAA
*
220450 TGCCGCCAATGCCTTTGGCACCATTGG
1 TGCCGCCAATGCCATTGGCACCATTGG
* *
220477 TGCCGCCAATGGCATTGGCACCTTTGG
1 TGCCGCCAATGCCATTGGCACCATTGG
220504 TGCCGCCAAT
1 TGCCGCCAAT
220514 CGTTTTAGCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.16, C:0.33, G:0.27, T:0.25
Consensus pattern (27 bp):
TGCCGCCAATGCCATTGGCACCATTGG
Found at i:220612 original size:22 final size:22
Alignment explanation
Indices: 220584--220625 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
220574 TTTTTTTATG
220584 TATTTTGGTAAATAAAAAAATA
1 TATTTTGGTAAATAAAAAAATA
220606 TATTTTGGTAAATAAAAAAA
1 TATTTTGGTAAATAAAAAAA
220626 GTTATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (22 bp):
TATTTTGGTAAATAAAAAAATA
Found at i:220732 original size:22 final size:22
Alignment explanation
Indices: 220712--220756 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
220702 TATGGTTTTG
220712 TTTTTCTATTCTTTCAATTTTCA
1 TTTTT-TATTCTTTCAATTTTCA
*
220735 TTTTTTTTTCTTTC-A-TTTCA
1 TTTTTTATTCTTTCAATTTTCA
220755 TT
1 TT
220757 AAGGGTGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 1 0.05
22 8 0.38
23 5 0.24
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTATTCTTTCAATTTTCA
Found at i:236696 original size:25 final size:25
Alignment explanation
Indices: 236662--236711 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
236652 TTTGGTACCG
236662 ATTTTGGGCGTTACGAGGGTGCTAA
1 ATTTTGGGCGTTACGAGGGTGCTAA
236687 ATTTTGGGCGTTACGAGGGTGCTAA
1 ATTTTGGGCGTTACGAGGGTGCTAA
236712 TCCTTCCTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.36, T:0.32
Consensus pattern (25 bp):
ATTTTGGGCGTTACGAGGGTGCTAA
Found at i:237178 original size:3 final size:3
Alignment explanation
Indices: 237172--237211 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
237162 ATTATTATTA
237172 TTG TTG TTG -TG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
237212 TTCTTTTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:238642 original size:20 final size:20
Alignment explanation
Indices: 238617--238656 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
238607 AAAGATTTTT
238617 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
*
238637 AGTAAATCATTTTTCAGAAA
1 AGTAAATCATTTTCCAGAAA
238657 TCATTTTCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:239213 original size:3 final size:3
Alignment explanation
Indices: 239205--239244 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
239195 CTAACTGTAT
239205 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
239245 AGAATCTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:240129 original size:6 final size:6
Alignment explanation
Indices: 240118--240153 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
240108 GGAAGAGAAA
240118 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
240154 GTTGAAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:243044 original size:21 final size:21
Alignment explanation
Indices: 243020--243074 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
243010 AACAGCGGTG
* *
243020 GCGGTCAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
243041 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
243062 GCGGTGAGATTAG
1 GCGGTGAGATTAG
243075 AAACAATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.11, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:244390 original size:43 final size:43
Alignment explanation
Indices: 244339--244504 Score: 278
Period size: 43 Copynumber: 3.8 Consensus size: 43
244329 CATTCGAGCA
*
244339 CCACCGTGCCCTCCTCCCATTTTCCATTCCCATTTCCCCTCTT
1 CCACCGTGCCCTCCTCCCATTTCCCATTCCCATTTCCCCTCTT
*
244382 CCACCGTGCCCTCCTCCCATTTTCCATTCCCATTTCCCCTCTT
1 CCACCGTGCCCTCCTCCCATTTCCCATTCCCATTTCCCCTCTT
244425 CCACCGTGCCCTCCTCCCATTTCCCATTCCCATTTCCCCTCTT
1 CCACCGTGCCCTCCTCCCATTTCCCATTCCCATTTCCCCTCTT
* *
244468 CCATCGATTCCCCTCCTCCCATTTCCCATTCCCATTT
1 CCACCG--TGCCCTCCTCCCATTTCCCATTCCCATTT
244505 ACGGTTGCTT
Statistics
Matches: 118, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
43 90 0.76
45 28 0.24
ACGTcount: A:0.10, C:0.51, G:0.04, T:0.34
Consensus pattern (43 bp):
CCACCGTGCCCTCCTCCCATTTCCCATTCCCATTTCCCCTCTT
Found at i:244457 original size:13 final size:14
Alignment explanation
Indices: 244438--244504 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 14
244428 CCGTGCCCTC
244438 CTCCCATTTCCCAT
1 CTCCCATTTCCCAT
*
244452 -TCCCATTTCCCCT
1 CTCCCATTTCCCAT
* *
244465 CTTCCATCGATTCCCCT
1 CTCCCAT---TTCCCAT
244482 CCTCCCATTTCCCAT
1 -CTCCCATTTCCCAT
244497 -TCCCATTT
1 CTCCCATTT
244505 ACGGTTGCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
13 20 0.45
14 5 0.11
15 6 0.14
17 7 0.16
18 6 0.14
ACGTcount: A:0.12, C:0.49, G:0.01, T:0.37
Consensus pattern (14 bp):
CTCCCATTTCCCAT
Found at i:247010 original size:21 final size:21
Alignment explanation
Indices: 246977--247043 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
246967 CCAAGAACAA
246977 AGCAAAAA-AAGGGAGAAACC
1 AGCAAAAACAAGGGAGAAACC
* *
246997 AGCAAAAACGAGGGACAAACC
1 AGCAAAAACAAGGGAGAAACC
* * *
247018 AGTAAGAACAAGAGAGAAACC
1 AGCAAAAACAAGGGAGAAACC
247039 AGCAA
1 AGCAA
247044 GAACGAGGTA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 8 0.21
21 30 0.79
ACGTcount: A:0.57, C:0.18, G:0.24, T:0.01
Consensus pattern (21 bp):
AGCAAAAACAAGGGAGAAACC
Found at i:256131 original size:16 final size:15
Alignment explanation
Indices: 256100--256143 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
256090 GCAAAATCAA
256100 ATAAAATTAAATTAT
1 ATAAAATTAAATTAT
*
256115 ATAAAAGTTACATTAT
1 ATAAAA-TTAAATTAT
256131 ATAAAAATTAAAT
1 AT-AAAATTAAAT
256144 GAGTTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
ATAAAATTAAATTAT
Found at i:256338 original size:59 final size:60
Alignment explanation
Indices: 256255--256375 Score: 174
Period size: 59 Copynumber: 2.0 Consensus size: 60
256245 ATACTAAACT
* * * *
256255 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAACAACTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
*
256315 AAACACAA-AATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAACAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
256374 AA
1 AA
256376 TATTCATACA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
58 4 0.07
59 43 0.78
60 8 0.15
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (60 bp):
AAACACAACAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:256396 original size:19 final size:19
Alignment explanation
Indices: 256368--256407 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
256358 ATTATAAAAT
256368 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
*
256387 AATTATAATATTCATACAA
1 AATTACAATATTCATACAA
256406 AA
1 AA
256408 NNNNNNNNNN
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:256729 original size:14 final size:13
Alignment explanation
Indices: 256707--256741 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
256697 TTTTTTTTCT
256707 TTCTTTCTTCTTC
1 TTCTTTCTTCTTC
256720 TTCTTCTCTTCTTC
1 TTCTT-TCTTCTTC
*
256734 TCCTTTCT
1 TTCTTTCT
256742 CTCTCTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (13 bp):
TTCTTTCTTCTTC
Done.