Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000520.1 Hibiscus syriacus cultivar Beakdansim tig00000991_pilon, whole genome shotgun sequence
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: 1956684
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1340350 original size:35 final size:34
Alignment explanation
Indices: 1340290--1340384 Score: 109
Period size: 35 Copynumber: 2.6 Consensus size: 34
1340280 TAAATTTCAA
* **
1340290 AAAAAAAAATAATAAAATATAAAAAAATTTAAAAGAG
1 AAAATAAAATAA-AAAA-ATAAAAAAA-AGAAAAGAG
*
1340327 AAAATCAAAATAAAAAAATAAAAAAAAGAAATGAG
1 AAAAT-AAAATAAAAAAATAAAAAAAAGAAAAGAG
1340362 AAAATAAAATAAAATAAATAAAA
1 AAAATAAAATAAAA-AAATAAAA
1340385 TAAATGTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
34 9 0.17
35 19 0.37
36 9 0.17
37 8 0.15
38 7 0.13
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.16
Consensus pattern (34 bp):
AAAATAAAATAAAAAAATAAAAAAAAGAAAAGAG
Found at i:1340379 original size:31 final size:29
Alignment explanation
Indices: 1340333--1340390 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
1340323 AGAGAAAATC
1340333 AAAATAAAAAAATAAAAAAAAGAAATGAG
1 AAAATAAAAAAATAAAAAAAAGAAATGAG
* *
1340362 AAAATAAAATAAAATAAATAAAATAAATG
1 AAAAT-AAA-AAAATAAAAAAAAGAAATG
1340391 TTAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 3 0.12
31 17 0.68
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.16
Consensus pattern (29 bp):
AAAATAAAAAAATAAAAAAAAGAAATGAG
Found at i:1340389 original size:9 final size:9
Alignment explanation
Indices: 1340328--1340389 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 9
1340318 TTAAAAGAGA
1340328 AAATCAAAAT
1 AAAT-AAAAT
1340338 AAA-AAAAT
1 AAATAAAAT
* *
1340346 AAAAAAAAG
1 AAATAAAAT
1340355 AAATGAGAAAAT
1 AAAT---AAAAT
1340367 AAAATAAAAT
1 -AAATAAAAT
1340377 AAATAAAAT
1 AAATAAAAT
1340386 AAAT
1 AAAT
1340390 GTTAAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
8 8 0.18
9 20 0.45
10 8 0.18
12 4 0.09
13 4 0.09
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1340407 original size:31 final size:30
Alignment explanation
Indices: 1340333--1340408 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 30
1340323 AGAGAAAATC
1340333 AAAA-TAAAAAAATAAAAAAAAGAAATGAG
1 AAAATTAAAAAAATAAAAAAAAGAAATGAG
* * * **
1340362 AAAATAAAATAAAATAAATAAAATAAATGTT
1 AAAATTAAA-AAAATAAAAAAAAGAAATGAG
*
1340393 AAATTTTAAAAAAATA
1 AAA-ATTAAAAAAATA
1340409 CAAGGAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 4 0.11
30 3 0.08
31 26 0.70
32 4 0.11
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (30 bp):
AAAATTAAAAAAATAAAAAAAAGAAATGAG
Found at i:1340449 original size:15 final size:16
Alignment explanation
Indices: 1340414--1340452 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1340404 AAATACAAGG
*
1340414 AAAAATAAAGGTATAA
1 AAAAATAAAAGTATAA
*
1340430 TAAAATAAAAG-ATAA
1 AAAAATAAAAGTATAA
1340445 AAAAATAA
1 AAAAATAA
1340453 TAGTGGTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (16 bp):
AAAAATAAAAGTATAA
Found at i:1340515 original size:13 final size:12
Alignment explanation
Indices: 1340499--1340540 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 12
1340489 TTTTAAAATA
1340499 AAATATAATAATT
1 AAATA-AATAATT
1340512 AAATAAAATAATT
1 AAAT-AAATAATT
1340525 AAATAAATAATCT
1 AAATAAATAAT-T
1340538 AAA
1 AAA
1340541 GAGATTGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.26
13 19 0.70
14 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATAAATAATT
Found at i:1341099 original size:12 final size:13
Alignment explanation
Indices: 1341082--1341110 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1341072 AAAGATAAAA
1341082 TAAAATAATAT-T
1 TAAAATAATATCT
1341094 TAAAATAATATCT
1 TAAAATAATATCT
1341107 TAAA
1 TAAA
1341111 TCCTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATAATATCT
Found at i:1341828 original size:24 final size:23
Alignment explanation
Indices: 1341801--1341845 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1341791 TTTTAATTGA
*
1341801 TTAAATTAATAATTTAAATATAAT
1 TTAAATT-ACAATTTAAATATAAT
* *
1341825 TTAACTTACAATTTTAATATA
1 TTAAATTACAATTTAAATATA
1341846 TATATCAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAAATTACAATTTAAATATAAT
Found at i:1342416 original size:17 final size:19
Alignment explanation
Indices: 1342379--1342420 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
1342369 TTTCCCAAAA
*
1342379 AGTTTCAATATTTTCCAAG
1 AGTTTCAATATTCTCCAAG
1342398 AGTTTCAATA-TCT-CAAG
1 AGTTTCAATATTCTCCAAG
1342415 AGTTTC
1 AGTTTC
1342421 GAAACTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 2 0.09
19 10 0.45
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (19 bp):
AGTTTCAATATTCTCCAAG
Found at i:1347264 original size:24 final size:22
Alignment explanation
Indices: 1347248--1347390 Score: 96
Period size: 22 Copynumber: 6.2 Consensus size: 22
1347238 TTTCTAATAT
1347248 ATATATATATATAATTTTGAAA
1 ATATATATATATAATTTTGAAA
*
1347270 A-ATATATAATATAGTTTTTGAAA
1 ATATATAT-ATATA-ATTTTGAAA
1347293 ATATAT-TATATAATTTTTGAAAA
1 ATATATATATATAA-TTTTG-AAA
*
1347316 ATATATAAATATATATAGTTTTTGAAT
1 ATATAT--ATATATA-A--TTTTGAAA
* * *
1347343 ACATAT-TATATAGTTTTGGAA
1 ATATATATATATAATTTTGAAA
* * *
1347364 ATGTATA-ATGTATGTTTTGAAA
1 ATATATATATATA-ATTTTGAAA
1347386 ATATA
1 ATATA
1347391 GAATTTTCGG
Statistics
Matches: 97, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
21 20 0.21
22 28 0.29
23 19 0.20
24 10 0.10
26 6 0.06
27 8 0.08
28 6 0.06
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (22 bp):
ATATATATATATAATTTTGAAA
Found at i:1347274 original size:23 final size:23
Alignment explanation
Indices: 1347248--1347328 Score: 105
Period size: 22 Copynumber: 3.6 Consensus size: 23
1347238 TTTCTAATAT
1347248 ATATATATATATAATTTTGAAAA
1 ATATATATATATAATTTTGAAAA
*
1347271 ATATATA-ATATAGTTTTTG-AAA
1 ATATATATATATA-ATTTTGAAAA
1347293 ATATAT-TATATAATTTTTGAAAA
1 ATATATATATATAA-TTTTGAAAA
*
1347316 ATATATAAATATA
1 ATATATATATATA
1347329 TATAGTTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
22 24 0.48
23 21 0.42
24 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (23 bp):
ATATATATATATAATTTTGAAAA
Found at i:1347336 original size:50 final size:46
Alignment explanation
Indices: 1347248--1347364 Score: 139
Period size: 50 Copynumber: 2.5 Consensus size: 46
1347238 TTTCTAATAT
1347248 ATATATATATATAA-TTTTG-AAAAATATATAATATAGTTTTTGAAA
1 ATATAT-TATATAATTTTTGAAAAAATATATAATATAGTTTTTGAAA
*
1347293 ATATATTATATAATTTTTGAAAAATATATAAATATATATAGTTTTTGAAT
1 ATATATTATATAATTTTTGAAAAA-ATAT--ATA-ATATAGTTTTTGAAA
* * *
1347343 ACATATTATATAGTTTTGGAAA
1 ATATATTATATAATTTTTGAAA
1347365 TGTATAATGT
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
44 7 0.11
45 11 0.18
46 4 0.06
47 4 0.06
49 3 0.05
50 33 0.53
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.45
Consensus pattern (46 bp):
ATATATTATATAATTTTTGAAAAAATATATAATATAGTTTTTGAAA
Found at i:1347494 original size:16 final size:16
Alignment explanation
Indices: 1347473--1347556 Score: 55
Period size: 16 Copynumber: 4.9 Consensus size: 16
1347463 TATAAATGTA
1347473 TTATTA-TTATTATTAT
1 TTATTATTTATT-TTAT
1347489 TTATTATTTATTTTAT
1 TTATTATTTATTTTAT
*
1347505 TTGTTCATCTTTATTTTATT
1 TTATT-A--TTTATTTTA-T
* * *
1347525 TTTTTCTTTCATTTTAA
1 TTATTATTT-ATTTTAT
1347542 TT-TTATTTTATTTTA
1 TTATTA-TTTATTTTA
1347557 GGTCCAATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
16 22 0.39
17 14 0.25
18 6 0.11
19 9 0.16
20 5 0.09
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (16 bp):
TTATTATTTATTTTAT
Found at i:1347526 original size:24 final size:25
Alignment explanation
Indices: 1347495--1347554 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
1347485 TTATTTATTA
1347495 TTTATTTTATTT-GTTCATCTTT-AT
1 TTTATTTTATTTCGTTCAT-TTTAAT
*
1347519 TTTATTTT-TTTCTTTCATTTTAAT
1 TTTATTTTATTTCGTTCATTTTAAT
1347543 TTTATTTTATTT
1 TTTATTTTATTT
1347555 TAGGTCCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 6 0.19
24 23 0.72
25 3 0.09
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTATTTTATTTCGTTCATTTTAAT
Found at i:1347545 original size:17 final size:17
Alignment explanation
Indices: 1347476--1347556 Score: 51
Period size: 19 Copynumber: 4.5 Consensus size: 17
1347466 AAATGTATTA
*
1347476 TTATTATTATTATTTATTAT
1 TTATT-TTA-TATTT-TTCT
1347496 TTATTTTAT-TTGTTCATCT
1 TTATTTTATATT-TT--TCT
*
1347515 TTATTTTATTTTTTTCT
1 TTATTTTATATTTTTCT
1347532 TTCATTTTA-ATTTTAT-T
1 TT-ATTTTATATTTT-TCT
1347549 TTATTTTA
1 TTATTTTA
1347557 GGTCCAATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
16 6 0.11
17 15 0.28
18 9 0.17
19 16 0.30
20 7 0.13
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (17 bp):
TTATTTTATATTTTTCT
Found at i:1348835 original size:3 final size:3
Alignment explanation
Indices: 1348827--1348864 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1348817 TATTTACAGT
*
1348827 TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1348865 CCTAACATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1350211 original size:16 final size:16
Alignment explanation
Indices: 1350192--1350230 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1350182 TTGCTTCTTC
1350192 TTCCTTCACTTTCTAA
1 TTCCTTCACTTTCTAA
*
1350208 TTCCATCACTTTCTAA
1 TTCCTTCACTTTCTAA
1350224 TTCCTTC
1 TTCCTTC
1350231 CTTCACCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (16 bp):
TTCCTTCACTTTCTAA
Found at i:1351929 original size:2 final size:2
Alignment explanation
Indices: 1351922--1351954 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1351912 TTATTTGACT
1351922 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1351955 GAAACCTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1357552 original size:26 final size:26
Alignment explanation
Indices: 1357489--1357552 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
1357479 TGTTCGTATC
* * *
1357489 TCTCTCTGTCTTTTTGTTCGTTGCTT
1 TCTCTGTGTCTTTCTGTTCGTTGCTA
*
1357515 TCTCTGTTTCTTTCTGTTTC-TTGCTA
1 TCTCTGTGTCTTTCTG-TTCGTTGCTA
*
1357541 TCTGTGTGTCTT
1 TCTCTGTGTCTT
1357553 GCTTGCCTCC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 28 0.90
27 3 0.10
ACGTcount: A:0.02, C:0.22, G:0.16, T:0.61
Consensus pattern (26 bp):
TCTCTGTGTCTTTCTGTTCGTTGCTA
Found at i:1358390 original size:113 final size:111
Alignment explanation
Indices: 1358247--1358462 Score: 396
Period size: 113 Copynumber: 1.9 Consensus size: 111
1358237 TCAAACAAAG
1358247 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA-TATGA
1358312 ACTCGAACTGGTAATGCTGAATCATCGAATGATGAATTCAAGCGAAAA
65 ACTCGAA-TGGTAATGCTGAATCATCGAATGATGAATTCAAGCGAAAA
* *
1358360 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATATGAA
1 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATATGAA
1358425 CTCGAATGGTAATGCTGAATCATCGAATGATGAATTCA
66 CTCGAATGGTAATGCTGAATCATCGAATGATGAATTCA
1358463 TATCTTTGCT
Statistics
Matches: 101, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
111 32 0.32
112 12 0.12
113 57 0.56
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (111 bp):
GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATATGAA
CTCGAATGGTAATGCTGAATCATCGAATGATGAATTCAAGCGAAAA
Found at i:1358890 original size:21 final size:21
Alignment explanation
Indices: 1358864--1358916 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1358854 CATAAAGTTT
*
1358864 TCATCTTTGAAAGAGAATCTG
1 TCATCTTTGAAAGAGAATCTA
*
1358885 TCATCTTTAAAAGAGAATCTA
1 TCATCTTTGAAAGAGAATCTA
1358906 TCATCTTTGAA
1 TCATCTTTGAA
1358917 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (21 bp):
TCATCTTTGAAAGAGAATCTA
Found at i:1361459 original size:114 final size:112
Alignment explanation
Indices: 1361237--1361459 Score: 356
Period size: 114 Copynumber: 2.0 Consensus size: 112
1361227 ACGATCATGC
* * **
1361237 AATTCATCTTTAATTCCAATGATGGTTCTGGGGTTCCTACTGAATCAGATCAGATAACTCAAAAA
1 AATTCATCTTTAAATCCAATGATGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAAA
*
1361302 ACACTTCCAGAAGATGCTATTGTGTCTCCTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
*
1361349 AATTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATC-TTTAAATCCAATGA-TGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
* *
1361414 GAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
64 AAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGA
1361460 TCACCTGGCA
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
112 8 0.08
113 13 0.13
114 80 0.79
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (112 bp):
AATTCATCTTTAAATCCAATGATGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAAA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
Found at i:1363975 original size:2 final size:2
Alignment explanation
Indices: 1363968--1363996 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1363958 ACAACAAAGG
1363968 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1363997 TAAAGGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1370920 original size:26 final size:26
Alignment explanation
Indices: 1370857--1370920 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
1370847 TGTTCGTATC
* * *
1370857 TCTCTCTGTCTTTTTGTTCGTTGCTT
1 TCTCTGTGTCTTTCTGTTCGTTGCTA
*
1370883 TCTCTGTTTCTTTCTGTTTC-TTGCTA
1 TCTCTGTGTCTTTCTG-TTCGTTGCTA
*
1370909 TCTGTGTGTCTT
1 TCTCTGTGTCTT
1370921 GCTTGCCTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 28 0.90
27 3 0.10
ACGTcount: A:0.02, C:0.22, G:0.16, T:0.61
Consensus pattern (26 bp):
TCTCTGTGTCTTTCTGTTCGTTGCTA
Found at i:1371641 original size:35 final size:35
Alignment explanation
Indices: 1371595--1371661 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
1371585 ATCCGAATTT
*
1371595 TTTATGGTAGTTATTCATTTTATTAAAAGTGTCAA
1 TTTATGGTAGTTATTCATTTTACTAAAAGTGTCAA
* * * *
1371630 TTTATGTTAGTTGTTTATTTTACTAAATGTGT
1 TTTATGGTAGTTATTCATTTTACTAAAAGTGT
1371662 TCACTGCGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.27, C:0.04, G:0.15, T:0.54
Consensus pattern (35 bp):
TTTATGGTAGTTATTCATTTTACTAAAAGTGTCAA
Found at i:1372277 original size:26 final size:24
Alignment explanation
Indices: 1372245--1372300 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1372235 ATCCTTAATA
1372245 AAAAATT-AA-TAA-TATA-TAAC
1 AAAAATTAAATTAACTATATTAAC
1372265 GAAAAATTAAATTAACTATATTAAC
1 -AAAAATTAAATTAACTATATTAAC
*
1372290 TAAAATTAAAT
1 AAAAATTAAAT
1372301 ATGGATTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.23
22 2 0.07
23 3 0.10
24 14 0.47
25 4 0.13
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (24 bp):
AAAAATTAAATTAACTATATTAAC
Found at i:1374484 original size:16 final size:17
Alignment explanation
Indices: 1374463--1374505 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1374453 ATATAAAAAT
1374463 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
1374479 AAATATAAAAATTTATT
1 AAATATTTAAATTTATA
1374496 AAATATTTAA
1 AAATATTTAA
1374506 TCAAGTAGGG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:1380166 original size:43 final size:43
Alignment explanation
Indices: 1380105--1380223 Score: 148
Period size: 43 Copynumber: 2.8 Consensus size: 43
1380095 GTGACAACAT
* *
1380105 ACCGCAAAAGGTATTGATATTTAGCGGCGTTTTGCAAAAAAAC
1 ACCGCAATAGGTGTTGATATTTAGCGGCGTTTTGCAAAAAAAC
* * * * *
1380148 ACCGCAATAGGTGTTGATATTTAACGGCATTTGGCAGACAAAC
1 ACCGCAATAGGTGTTGATATTTAGCGGCGTTTTGCAAAAAAAC
* * *
1380191 GCCGCAATAGGCGTTGATGTTTAGCGGCGTTTT
1 ACCGCAATAGGTGTTGATATTTAGCGGCGTTTT
1380224 CTTCACAAAC
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (43 bp):
ACCGCAATAGGTGTTGATATTTAGCGGCGTTTTGCAAAAAAAC
Found at i:1380718 original size:23 final size:21
Alignment explanation
Indices: 1380667--1380715 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1380657 ATATATTACT
**
1380667 TCTCTCTGTTCTGCCACTGCC
1 TCTCTCTGTGATGCCACTGCC
*
1380688 TCTCTCTGTGATGCCACTGCT
1 TCTCTCTGTGATGCCACTGCC
1380709 TCTCTCT
1 TCTCTCT
1380716 CTGCTTTCGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.39, G:0.14, T:0.41
Consensus pattern (21 bp):
TCTCTCTGTGATGCCACTGCC
Found at i:1380728 original size:21 final size:21
Alignment explanation
Indices: 1380704--1380764 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1380694 TGTGATGCCA
* *
1380704 CTGCTTCTCTCTCTGCTTTCG
1 CTGCTGCTCTCTCTGCTTCCG
** *
1380725 CTGCTGCTCTAACTACTTCCG
1 CTGCTGCTCTCTCTGCTTCCG
1380746 CTGCTGCTCTCTCTGCTTC
1 CTGCTGCTCTCTCTGCTTC
1380765 TCTTGCTTCA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.05, C:0.39, G:0.15, T:0.41
Consensus pattern (21 bp):
CTGCTGCTCTCTCTGCTTCCG
Found at i:1384490 original size:52 final size:52
Alignment explanation
Indices: 1384422--1384580 Score: 300
Period size: 52 Copynumber: 3.1 Consensus size: 52
1384412 TAACAACAAA
1384422 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
*
1384474 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
*
1384526 ATACATTATAATTTAGAAATATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1384578 ATA
1 ATA
1384581 TTGTTCAGTA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 104 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (52 bp):
ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
Found at i:1385895 original size:42 final size:42
Alignment explanation
Indices: 1385849--1385941 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
1385839 GCGTTTATTG
*
1385849 AAAAAACGCCACTATATACCAT-C-CTATGGCGGCGTTTTTA-
1 AAAAAACGCCACTATAT-CCATACTCTATGGCAGCGTTTTTAC
* ** *
1385889 ACAAAAACGCCGCTATATTTATACTCTATTGCAGCGTTTTTAC
1 A-AAAAACGCCACTATATCCATACTCTATGGCAGCGTTTTTAC
1385932 AAAAAACGCC
1 AAAAAACGCC
1385942 GCTAAAGTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
40 3 0.07
41 16 0.36
42 24 0.55
43 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (42 bp):
AAAAAACGCCACTATATCCATACTCTATGGCAGCGTTTTTAC
Found at i:1388748 original size:21 final size:21
Alignment explanation
Indices: 1388723--1388770 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1388713 CCTAATATTG
1388723 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
1388744 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
1388765 TAATGT
1 CAATGT
1388771 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:1393395 original size:21 final size:21
Alignment explanation
Indices: 1393370--1393417 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1393360 CCTAATATTG
1393370 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
1393391 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
1393412 TAATGT
1 CAATGT
1393418 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:1395346 original size:3 final size:3
Alignment explanation
Indices: 1395334--1395466 Score: 257
Period size: 3 Copynumber: 44.3 Consensus size: 3
1395324 CTACTACTAC
*
1395334 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1395382 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1395430 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1395467 GTACACACTT
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 128 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1395888 original size:34 final size:34
Alignment explanation
Indices: 1395821--1395898 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
1395811 TAAATTTTAA
* * * *
1395821 AAAAT-ATAATTTTTTATTAAAATTTATTATATT
1 AAAATAATAAGTTTTAATAAAAATATATTATATT
*
1395854 AAAATAATAAGTTTTAATAAAAATATATTTTATT
1 AAAATAATAAGTTTTAATAAAAATATATTATATT
*
1395888 ATATATAATAA
1 A-AAATAATAA
1395899 TTCTCAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
33 5 0.14
34 24 0.65
35 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (34 bp):
AAAATAATAAGTTTTAATAAAAATATATTATATT
Found at i:1399342 original size:3 final size:3
Alignment explanation
Indices: 1399334--1399367 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1399324 GAAATTAGAT
1399334 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1399368 CATCATCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1403352 original size:167 final size:164
Alignment explanation
Indices: 1403061--1403393 Score: 623
Period size: 167 Copynumber: 2.0 Consensus size: 164
1403051 TAAAATAGAT
1403061 TGAGAAATATAAAAGAGAAATGCAAAAGAAGTAAAGGGTCTGGATCAAATAGAGGCTGACATTGC
1 TGAGAAATATAAAAGAGAAATGCAAAAGAAGTAAAGGGTCTGGATCAAATAGAGGCTGACATTGC
1403126 AAATATACAAGAAGGTTTTGCTTAAAAAGATGGAAGACATACTCATAAAACATGTGGCTAAGGCT
66 AAATATACAAGAAGGTTTTGCTTAAAAAGATGGAAGACATACTCATAAAACATGTGGCTAAGGCT
1403191 AAGAATATTTTTTTATGACCATATGTGTTCTTCG
131 AAGAATATTTTTTTATGACCATATGTGTTCTTCG
1403225 TGAGAAATATAAAAGAGAAATGCAAAAAGAAGTAAAGGGTAGACTGGATCAAATAGAGGCTGACA
1 TGAGAAATATAAAAGAGAAATGC-AAAAGAAGTAAAGGGT---CTGGATCAAATAGAGGCTGACA
1403290 TTGCAAATATACAAGAAGG-TTTGCTTAAAAAGATGGAAGACATACTCATAAAACATGTGGCTAA
62 TTGCAAATATACAAGAAGGTTTTGCTTAAAAAGATGGAAGACATACTCATAAAACATGTGGCTAA
1403354 GGCTAAGAATATTTTTTTATGACCATATGTGTTCTTCG
127 GGCTAAGAATATTTTTTTATGACCATATGTGTTCTTCG
1403392 TG
1 TG
1403394 TTTCAAGACC
Statistics
Matches: 165, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
164 23 0.14
165 16 0.10
167 85 0.52
168 41 0.25
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (164 bp):
TGAGAAATATAAAAGAGAAATGCAAAAGAAGTAAAGGGTCTGGATCAAATAGAGGCTGACATTGC
AAATATACAAGAAGGTTTTGCTTAAAAAGATGGAAGACATACTCATAAAACATGTGGCTAAGGCT
AAGAATATTTTTTTATGACCATATGTGTTCTTCG
Found at i:1407100 original size:25 final size:25
Alignment explanation
Indices: 1407060--1407131 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 25
1407050 AAATCAAGTT
*
1407060 GATAAAATAGAGAGAAAGAAAAAATA
1 GATAAAA-AGAAAGAAAGAAAAAATA
*
1407086 TATAGAAAA-AAAG--A-AAAAAATA
1 GATA-AAAAGAAAGAAAGAAAAAATA
1407108 GATAAAAAGAAA-AAAGAAAAAATA
1 GATAAAAAGAAAGAAAGAAAAAATA
1407132 AGAAAGAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
21 4 0.11
22 14 0.37
23 2 0.05
24 8 0.21
25 3 0.08
26 4 0.11
27 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (25 bp):
GATAAAAAGAAAGAAAGAAAAAATA
Found at i:1407114 original size:18 final size:18
Alignment explanation
Indices: 1407063--1407122 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
1407053 TCAAGTTGAT
* *
1407063 AAAATAGAGAGAAAGAAAA
1 AAAATAGAAAAAAAG-AAA
1407082 AATATATAGAAAAAAAGAAA
1 AA-A-ATAGAAAAAAAGAAA
*
1407102 AAAATAGATAAAAAGAAA
1 AAAATAGAAAAAAAGAAA
1407120 AAA
1 AAA
1407123 GAAAAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 17 0.47
19 3 0.08
20 6 0.17
21 10 0.28
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (18 bp):
AAAATAGAAAAAAAGAAA
Found at i:1407139 original size:21 final size:22
Alignment explanation
Indices: 1407074--1407144 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
1407064 AAATAGAGAG
*
1407074 AAAGAAAAAATATATAGAAA-AAA
1 AAAG-AAAAAGATA-AGAAAGAAA
*
1407097 AGAAAAAAATAGATAA-AAAGAAA
1 A-AAGAAAA-AGATAAGAAAGAAA
1407120 AAAGAAAAA-ATAAGAAAGAAGA
1 AAAGAAAAAGATAAGAAAGAA-A
1407142 AAA
1 AAA
1407145 TAGACAGATC
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
20 4 0.10
21 7 0.17
22 13 0.32
23 10 0.25
24 6 0.15
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (22 bp):
AAAGAAAAAGATAAGAAAGAAA
Found at i:1407767 original size:15 final size:16
Alignment explanation
Indices: 1407739--1407772 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1407729 CTGCTTCATC
*
1407739 GAATCAATGAACGCCA
1 GAATCAATGAACGCAA
1407755 GAATCAA-GAACGCAA
1 GAATCAATGAACGCAA
1407770 GAA
1 GAA
1407773 GCTAGCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.50, C:0.21, G:0.21, T:0.09
Consensus pattern (16 bp):
GAATCAATGAACGCAA
Found at i:1409202 original size:44 final size:43
Alignment explanation
Indices: 1409137--1409312 Score: 262
Period size: 44 Copynumber: 4.0 Consensus size: 43
1409127 ATAAGAAACT
* *
1409137 AAGCTTGAGTGACCAATGTGATATATAGGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATATAGGGGTTCCTTGATGAC
* *
1409180 AAGCTTGAAGTGACCAACGTGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTG-AGGGACCAACGTGATATATAGGGGTTCCTTGATGAC
* * *
1409224 AAGCTGGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAT
1 AAGCTTGAGGGACCAACGTGATATATAGGGGTTCCTTGATGAC
*
1409267 AAGGCTTGAGGGACCAACGTGATATATAGAGGTTCCTTGATGAC
1 AA-GCTTGAGGGACCAACGTGATATATAGGGGTTCCTTGATGAC
1409311 AA
1 AA
1409313 CTAAGAAACT
Statistics
Matches: 122, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
43 43 0.35
44 79 0.65
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (43 bp):
AAGCTTGAGGGACCAACGTGATATATAGGGGTTCCTTGATGAC
Found at i:1409283 original size:87 final size:87
Alignment explanation
Indices: 1409137--1409312 Score: 264
Period size: 87 Copynumber: 2.0 Consensus size: 87
1409127 ATAAGAAACT
* * * *
1409137 AAGCTTGAGTGACCAATGTGATATATAGGGGTTCCTTGATGACAAGCTTGAAGTGACCAACGTGA
1 AAGCTGGAGGGACCAACGTGATATATAGGGGTTCCTTGATGACAAGCTTGAAGGGACCAACGTGA
* *
1409202 TATGTAGGGGTTCCTTGATGAC
66 TATATAGAGGTTCCTTGATGAC
* *
1409224 AAGCTGGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGATAAGGCTTG-AGGGACCAACGTG
1 AAGCTGGAGGGACCAACGTGATATATAGGGGTTCCTTGATGACAA-GCTTGAAGGGACCAACGTG
1409288 ATATATAGAGGTTCCTTGATGAC
65 ATATATAGAGGTTCCTTGATGAC
1409311 AA
1 AA
1409313 CTAAGAAACT
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
87 75 0.94
88 5 0.06
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (87 bp):
AAGCTGGAGGGACCAACGTGATATATAGGGGTTCCTTGATGACAAGCTTGAAGGGACCAACGTGA
TATATAGAGGTTCCTTGATGAC
Found at i:1409638 original size:36 final size:36
Alignment explanation
Indices: 1409591--1409714 Score: 133
Period size: 36 Copynumber: 3.4 Consensus size: 36
1409581 GCATGAGTCT
* * *
1409591 GTTTCTTTTGAAACAAAGTTTGTCTCTTTTGAGACG
1 GTTTCTCTTGAAACAAAGTTTGTCTCTCTTGAGACA
*
1409627 GTTTCTCTTGAAGA-AAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAA-ACAAAGTTTGTCTCTCTTGAGACA
* * * *
1409663 GTTTCCCTTGAAACAGAAGATTTGTCTCGCTTGCGCCA
1 GTTTCTCTTGAAACA-AAG-TTTGTCTCTCTTGAGACA
*
1409701 GTTTCCCTTGAAAC
1 GTTTCTCTTGAAAC
1409715 TAGAAATTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
35 1 0.01
36 42 0.56
37 3 0.04
38 29 0.39
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.39
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAAGTTTGTCTCTCTTGAGACA
Found at i:1410419 original size:44 final size:44
Alignment explanation
Indices: 1410171--1410873 Score: 263
Period size: 44 Copynumber: 15.9 Consensus size: 44
1410161 AAAAACTTGT
* *
1410171 TCAAC-TTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAACATT
1 TCAACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAAC--G
** * * * * * * **
1410216 TTTA-TTTTTGTTCAAATCCATCGCAGAAGGAGTTGGATTAGTG
1 TCAACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACG
* * * *
1410259 TCAACTTTTAGCTTGATTCTATCACAGAAGGAGGTAGATCAAC-
1 TCAACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACG
* * * * * * * * * ** *
1410302 ACTGACATCTCGTTCGATTTCATCAAATAAGGAGGTGGATTGACT
1 TC-AACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACG
** * * * * *
1410347 TTTA--TTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAACG
1 TCAACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACG
* * * *
1410389 TTAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACA
1 TCAACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACG
* * * * * * **
1410433 TCGACATCTTGTTCGATTCTATCACAGAAGAAGGTGGATCGACATT
1 TCAACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATC-A-ACG
** * * * *
1410479 TTTA-TTTTCT-CTCAAATCCATCGCAGAAGGAGTTGGATCAACG
1 TCAACTTTT-TGCTCGATTCCATCACAGAAGGAGGTGGATCAACG
* * * *
1410522 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCA
1 TCAACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACG
* * * * * **
1410566 CCAACATCTCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATT
1 TCAACTTTTTGCTCGA-TTCCATCACAGAAGGAGGTGGATC-A-ACG
** * * * ** * * *
1410613 TTTA-TTTTCGCTCAAATCCATCGTAGAAAGAGTTGGATCAGCG
1 TCAACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACG
* * * * *
1410656 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCA
1 TCAACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACG
* * * * * **
1410700 CCAACATCTCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATT
1 TCAACTTTTTGCTCGA-TTCCATCACAGAAGGAGGTGGATC-A-ACG
** * * * ** * *
1410747 TTTA-TTTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCAGCG
1 TCAACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACG
* * * * * *
1410790 TCAACTTTTAGCTCGATTCTAGCACAGAAGAAGGTAGATCAACA
1 TCAACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACG
* * * * ***
1410834 CCGACATCTCATTCGATTCCATCACAGAAGGAGGTGGATC
1 TCAACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATC
1410874 GACATTTACT
Statistics
Matches: 459, Mismatches: 180, Indels: 39
0.68 0.27 0.06
Matches are distributed among these distances:
42 29 0.06
43 11 0.02
44 258 0.56
45 139 0.30
46 20 0.04
47 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (44 bp):
TCAACTTTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACG
Found at i:1410658 original size:134 final size:133
Alignment explanation
Indices: 1410180--1411145 Score: 1334
Period size: 134 Copynumber: 7.3 Consensus size: 133
1410170 TTCAACTTTT
* * *
1410180 GTTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTTATTTTTGTTCAAATCCATCGCAGAAG
1 GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAG
* * * * **
1410245 GAGTTGGATTAGTGTCAACTTTTAGCTTGATTCTATCACAGAAGGAGGTAGATCAACACTGACAT
66 GAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACAT
1410310 CTC
131 CTC
* * * *
1410313 GTTCGATTTCATCAAATAAGGAGGTGGATTGAC--TTTTA-TTTCGCTCAAATCCATCGCAGAAG
1 GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAG
* * * * * *
1410375 GAGTTGGATCAACGTTAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACAT
66 GAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACAT
*
1410440 CTT
131 CTC
* * *
1410443 GTTCGATTCTATCACAGAAGAAGGTGGATCGACATTTTTATTTTCTCTCAAATCCATCGCAGAAG
1 GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAG
* *
1410508 GAGTTGGATCAACGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACAT
66 GAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACAT
1410573 CTC
131 CTC
*
1410576 GTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGTAGAA
1 GTTCGA-TTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAA
* * *
1410641 AGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCACCAACA
65 GGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACA
1410706 TCTC
130 TCTC
*
1410710 GTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGTAGAA
1 GTTCGA-TTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAA
* * * *
1410775 GGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTAGCACAGAAGAAGGTAGATCAACACCGACA
65 GGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACA
1410840 TCTC
130 TCTC
* * *
1410844 ATTCGATTCCATCACAGAAGGAGGTGGATCGACA--TTTA-CTTCGCTCAAATCCATCGCAAAAG
1 GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAG
* * * * *
1410906 AAGTTGGATCAGCATAAACTTTTAGCTCGATTCTATCGCAGAAGGAGGTAGATCAGCAACAACAT
66 GAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACAT
1410971 CTC
131 CTC
* * * * * * *
1410974 GTTTGATTCTATCACAGAAGGAGATGGATCGGCATTTTTATTTTCGTTCAAATACATTGCAGAAG
1 GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAG
* * * *
1411039 GAGTTGGATCAACGCCAACTTTTAGCTCAATTCTATCACAGAAGGAGGTAGATTAGCA-CACACA
66 GAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCA-ACA
* *
1411103 CCTT
130 TCTC
* *
1411107 GTTTTGATTCCATCACAGAAAGAGGTGGATCGACATTTT
1 G-TTCGATTCCATCACAGAAGGAGGTGGATCGACATTTT
1411146 CATTCATCAC
Statistics
Matches: 745, Mismatches: 79, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
130 217 0.29
131 9 0.01
132 11 0.01
133 223 0.30
134 285 0.38
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (133 bp):
GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAG
GAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACAT
CTC
Found at i:1410990 original size:397 final size:398
Alignment explanation
Indices: 1410180--1411145 Score: 1379
Period size: 397 Copynumber: 2.4 Consensus size: 398
1410170 TTCAACTTTT
* *
1410180 GTTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTTATTTTTGTTCAAATCCATCGCAGAAG
1 GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGTTCAAATCCATCGCAGAAG
* * * * **
1410245 GAGTTGGATTAGTGTCAACTTTTAGCTTGATTCTATCACAGAAGGAGGTAGATCAACACTGACAT
66 GAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACAT
* * *
1410310 CTCGTTCGATTT-CATCAAATAAGGAGGTGGATTGAC--TTTTATTTCGCTCAAATCCATCGCAG
131 CTCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAG
* * * * *
1410372 AAGGAGTTGGATCAACGTTAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGA
196 AAGGAGTTGGATCAACGTCAACTTTTAGCTCGATTCTAGCACAGAAGAAGGTAGATCAACACCGA
** * * *
1410437 CATCTTGTTCGATTCTATCACAGAAGAAGGTGGATCGACATTTTTATTTTCTCTCAAATCCATCG
261 CATCTCATTCGATTCCATCACAGAAGAAGGTGGATCGACA-TTTTATCTTCGCTCAAATCCATCG
* * * * * *
1410502 CAGAAGGAGTTGGATCAACGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCAC
325 CAAAAGAAGTTGGATCAACATAAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCAA
1410567 CAACATCTC
390 CAACATCTC
* *
1410576 GTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGTAGAA
1 GTTCGA-TTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGTTCAAATCCATCGCAGAA
* * *
1410641 AGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCACCAACA
65 GGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACA
*
1410706 TCTCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGT
130 TCTCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTA-TTTCGCTCAAATCCATCGC
*
1410771 AGAAGGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTAGCACAGAAGAAGGTAGATCAACACC
194 AGAAGGAGTTGGATCAACGTCAACTTTTAGCTCGATTCTAGCACAGAAGAAGGTAGATCAACACC
*
1410836 GACATCTCATTCGATTCCATCACAGAAGGAGGTGGATCGACA-TTTA-CTTCGCTCAAATCCATC
259 GACATCTCATTCGATTCCATCACAGAAGAAGGTGGATCGACATTTTATCTTCGCTCAAATCCATC
* *
1410899 GCAAAAGAAGTTGGATCAGCATAAACTTTTAGCTCGATTCTATCGCAGAAGGAGGTAGATCAGCA
324 GCAAAAGAAGTTGGATCAACATAAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCA
1410964 ACAACATCTC
389 ACAACATCTC
* * * * * *
1410974 GTTTGATTCTATCACAGAAGGAGATGGATCGGCATTTTTATTTTCGTTCAAATACATTGCAGAAG
1 GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGTTCAAATCCATCGCAGAAG
* * * *
1411039 GAGTTGGATCAACGCCAACTTTTAGCTCAATTCTATCACAGAAGGAGGTAGATTAGCA-CACACA
66 GAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCA-ACA
* * * *
1411103 CCTTGTTTTGA-TTCCATCACAGAAAGAGGTGGATCGACATTTT
130 TCTCG-TTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTT
1411146 CATTCATCAC
Statistics
Matches: 507, Mismatches: 56, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
396 8 0.02
397 263 0.52
398 112 0.22
399 4 0.01
400 5 0.01
401 115 0.23
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (398 bp):
GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGTTCAAATCCATCGCAGAAG
GAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACAT
CTCGTTCGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAG
AAGGAGTTGGATCAACGTCAACTTTTAGCTCGATTCTAGCACAGAAGAAGGTAGATCAACACCGA
CATCTCATTCGATTCCATCACAGAAGAAGGTGGATCGACATTTTATCTTCGCTCAAATCCATCGC
AAAAGAAGTTGGATCAACATAAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCAAC
AACATCTC
Found at i:1414284 original size:26 final size:28
Alignment explanation
Indices: 1414224--1414285 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
1414214 GAGTATTGCT
*
1414224 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
1414255 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
1414281 GAGCT
1 GAGCT
1414286 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:1414946 original size:2 final size:2
Alignment explanation
Indices: 1414939--1414972 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1414929 CATAACGCTA
*
1414939 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1414973 TTAATAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1419390 original size:116 final size:115
Alignment explanation
Indices: 1419152--1419560 Score: 310
Period size: 116 Copynumber: 3.5 Consensus size: 115
1419142 TGTGGAATGA
* * *
1419152 TTCATAATGAGAAGAACTCGTCTGATGAGGAGAAGAAATTTCTAATGAGAAGAACTTGTTCAACC
1 TTCATAATGAGAAGAACTCGTCCGATGAGGAGAAGAAGTTCCTAATGAGAAGAACTTGTTCAACC
* * * * **** *
1419217 TTGACTCACCCATCGTAGAATGAGGTGGACCAATATTTACTGTGGAAGGG
66 TTGAATCACCCATCATAGAATGAGATGGACCAAAATTTACTACAAAACGG
* *
1419267 TTCATAATGAAAAGAACTCGTCCGATGAGGGAGAAGAAGTCCCTAATGAGAAGAACTTGTTCAAC
1 TTCATAATGAGAAGAACTCGTCCGATGA-GGAGAAGAAGTTCCTAATGAGAAGAACTTGTTCAAC
** *
1419332 CTTGAATCGTCTATCATAGAA-GAAGATGGACCAAAATTT-CTAACAAAACGG
65 CTTGAATCACCCATCATAGAATG-AGATGGACCAAAATTTACT-ACAAAACGG
* * * * * * * *
1419383 TTTATAATGAGACGAGCTCATCCAATGAATGAGATA-AAGTTCCTAATAAGAAGAACTTGTTCCA
1 TTCATAATGAGAAGAACTCGTCCGATG-AGGAGA-AGAAGTTCCTAATGAGAAGAACTTGTTCAA
** * * * ** *
1419447 CCTTGGTTCGATTCCATCATAG-ATGAAGGA-GGATCAATATTT-CTATTAGA-GAG
64 CCTTGAATC-A-CCCATCATAGAATG-A-GATGGACCAAAATTTACTACAAAACG-G
* * * * ** *
1419500 TTCATAATGAGAATAATTCATCCAATGAGGGAGAAGAAGTTTATAATGAGAATAACTTGTT
1 TTCATAATGAGAAGAACTCGTCCGATGA-GGAGAAGAAGTTCCTAATGAGAAGAACTTGTT
1419561 TAAATCTCAG
Statistics
Matches: 236, Mismatches: 46, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
115 29 0.12
116 127 0.54
117 54 0.23
118 24 0.10
119 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (115 bp):
TTCATAATGAGAAGAACTCGTCCGATGAGGAGAAGAAGTTCCTAATGAGAAGAACTTGTTCAACC
TTGAATCACCCATCATAGAATGAGATGGACCAAAATTTACTACAAAACGG
Found at i:1420220 original size:3 final size:3
Alignment explanation
Indices: 1420214--1420254 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1420204 GTTGTTGTTG
1420214 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1420255 TACTTTTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1420817 original size:11 final size:9
Alignment explanation
Indices: 1420802--1420829 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1420792 TAGAGGGAAA
1420802 TGAGAGAGT
1 TGAGAGAGT
1420811 TGAGAGAGT
1 TGAGAGAGT
1420820 TGAGAGAGT
1 TGAGAGAGT
1420829 T
1 T
1420830 TTAGTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.43, T:0.25
Consensus pattern (9 bp):
TGAGAGAGT
Found at i:1423401 original size:14 final size:14
Alignment explanation
Indices: 1423382--1423408 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1423372 TACCTAAACT
1423382 CAAATCTTAAATCC
1 CAAATCTTAAATCC
1423396 CAAATCTTAAATC
1 CAAATCTTAAATC
1423409 TTAAACCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (14 bp):
CAAATCTTAAATCC
Found at i:1427653 original size:3 final size:3
Alignment explanation
Indices: 1427647--1427694 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
1427637 TGTGAGGAGG
*
1427647 AGA AGA AGA AGA AGAA AGA AGGA AGA TGA AGA AG- AGAA AGA AGA AGA
1 AGA AGA AGA AGA AG-A AGA A-GA AGA AGA AGA AGA AG-A AGA AGA AGA
1427694 A
1 A
1427695 ACAACCACGT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 2 0.05
3 29 0.74
4 8 0.21
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:1432518 original size:2 final size:2
Alignment explanation
Indices: 1432513--1432545 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1432503 TTAAAAAAAC
1432513 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1432546 CCATTTCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1441706 original size:5 final size:5
Alignment explanation
Indices: 1441696--1441795 Score: 67
Period size: 5 Copynumber: 18.8 Consensus size: 5
1441686 TGTTCACAGA
** * *
1441696 AAAAT AAAAT AAAAT AAAAT AAAGCAT ATGAT ACAAT AAAAT AAAAT GAAAT
1 AAAAT AAAAT AAAAT AAAAT AAA--AT AAAAT AAAAT AAAAT AAAAT AAAAT
* * *
1441748 GAAAT AAATT AAAAAT GAAAT AAAGTAT ACAAA- AAAAT AATAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAA--AT A-AAAT AAAAT AA-AAT AAAA
1441796 AATGAAAATG
Statistics
Matches: 76, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
4 3 0.04
5 55 0.72
6 10 0.13
7 6 0.08
8 2 0.03
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:1441755 original size:20 final size:21
Alignment explanation
Indices: 1441730--1441768 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1441720 CATATGATAC
1441730 AATAAAAT-AAAATGAAATGA
1 AATAAAATAAAAATGAAATGA
*
1441750 AATAAATTAAAAATGAAAT
1 AATAAAATAAAAATGAAAT
1441769 AAAGTATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (21 bp):
AATAAAATAAAAATGAAATGA
Found at i:1448083 original size:408 final size:408
Alignment explanation
Indices: 1447328--1448140 Score: 1457
Period size: 408 Copynumber: 2.0 Consensus size: 408
1447318 GTGGGGCTAA
1447328 AATTTATTAATTTGAAAGTATCGAATTAAAGTAGTAACAAGGGAAAAGTTGGGGACCAAATTATA
1 AATTTATTAATTTGAAAGTATCGAATTAAAGTAGTAACAAGGGAAAAGTTGGGGACCAAATTATA
*
1447393 AATTTCTAAAAGATATACCTTGATTTTAGAACTTATGGAAAATTCAGGGACTTGAACCCTAATTA
66 AATTTCTAAAAGATATACCTTGATTTTAGAACTTATGGAAAATTCAGGGACTTGAACCCCAATTA
* *
1447458 TCCCTTTTTAATGGGCATTGAGAAATAAACCCCCCGGATCGTCTTCTCCAATTCGAAGTGTAAAC
131 TCCCTTTTTAATGGGCATTGAGAAAAAAAACCCCCGGATCGTCTTCTCCAATTCGAAGTGTAAAC
* *
1447523 CCAAAATGGTGAGAAAATCGCTCGTTGCCTTCTTCGATTCAGCGTCAATTGGCCGGCGGTGTACG
196 CCAAAATGGTGAGAAAATCGCCCGTTGCCTTCTTCGATTCAGCGTCAATTAGCCGGCGGTGTACG
* *
1447588 TCACTGCCGGTCCCAATTGAACTGGTGACTCACCCCGACCAAAACCCCTCAACCCTCATCCCCGG
261 TCACTGCCCGTCCCAATTGAACTAGTGACTCACCCCGACCAAAACCCCTCAACCCTCATCCCCGG
* * *
1447653 ATCGACAGCCAAAAGACGTGTAATGCCTGGCAAATCTTCGACAAAAACACCCCGATCGTCGTTTG
326 ATCGACAGCCAAAAGACGTGTAATGCCTAGCAAATCTTCGACAAAAACACCCAGATCGCCGTTTG
1447718 ATTTTTCGTCAATTCCGG
391 ATTTTTCGTCAATTCCGG
1447736 AATTTATTAATTTGAAAGTATCGAATTAAAGTAGTAACAAGGGAAAAGTTGGGGACCAAATTATA
1 AATTTATTAATTTGAAAGTATCGAATTAAAGTAGTAACAAGGGAAAAGTTGGGGACCAAATTATA
* * * *
1447801 AATTTCTAAAAGATGTACCTTGATTTTGGAACTTGTGGAAAATTTAGGGACTTGAACCCCAATTA
66 AATTTCTAAAAGATATACCTTGATTTTAGAACTTATGGAAAATTCAGGGACTTGAACCCCAATTA
*
1447866 TCCCTTTTTAATGGGCATTTAGAAAAAAAACCCCCGGATCGTCTTCTCCAATTCGAAGTGTAAAC
131 TCCCTTTTTAATGGGCATTGAGAAAAAAAACCCCCGGATCGTCTTCTCCAATTCGAAGTGTAAAC
*
1447931 CCAAAATGGTGAGAAAATCGCCCGTTGCCTTC-TCTGATTCGGCGTCAATTAGCCGGCGGTGTAC
196 CCAAAATGGTGAGAAAATCGCCCGTTGCCTTCTTC-GATTCAGCGTCAATTAGCCGGCGGTGTAC
1447995 GTCACTGCCCGTCCCAATTGAACTAGTGACTCACCCCGACCAAAACCCCTCAACCCTCATCCCCG
260 GTCACTGCCCGTCCCAATTGAACTAGTGACTCACCCCGACCAAAACCCCTCAACCCTCATCCCCG
*
1448060 GATCGACCGCCAAAAGACGTGTAATGCCTAGCAAATCTTCGACAAAAACACCCAGATCGCCGTTT
325 GATCGACAGCCAAAAGACGTGTAATGCCTAGCAAATCTTCGACAAAAACACCCAGATCGCCGTTT
1448125 GATTTTTCGTCAATTC
390 GATTTTTCGTCAATTC
1448141 TGGCCGATTC
Statistics
Matches: 387, Mismatches: 17, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
407 2 0.01
408 385 0.99
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (408 bp):
AATTTATTAATTTGAAAGTATCGAATTAAAGTAGTAACAAGGGAAAAGTTGGGGACCAAATTATA
AATTTCTAAAAGATATACCTTGATTTTAGAACTTATGGAAAATTCAGGGACTTGAACCCCAATTA
TCCCTTTTTAATGGGCATTGAGAAAAAAAACCCCCGGATCGTCTTCTCCAATTCGAAGTGTAAAC
CCAAAATGGTGAGAAAATCGCCCGTTGCCTTCTTCGATTCAGCGTCAATTAGCCGGCGGTGTACG
TCACTGCCCGTCCCAATTGAACTAGTGACTCACCCCGACCAAAACCCCTCAACCCTCATCCCCGG
ATCGACAGCCAAAAGACGTGTAATGCCTAGCAAATCTTCGACAAAAACACCCAGATCGCCGTTTG
ATTTTTCGTCAATTCCGG
Found at i:1454329 original size:182 final size:182
Alignment explanation
Indices: 1454022--1454987 Score: 1360
Period size: 182 Copynumber: 5.3 Consensus size: 182
1454012 ATGTAAAAAT
* ** * * *
1454022 ATGACAAAATCAGTAAAGCGCTACTAAATATATTGAAAGTGTTC-ATACTTTAATACAAATATCG
1 ATGACAAAACCAGTAAAGCGCTACCGAATATGTTGAAAGTG-TCGATACTTTAATATAAGTATCG
* * * * *
1454086 ACACTTTTAGAATATAAAAGAGAAACAGTAATAGCGTCTATAAAATGTCGATACATTATAAAAAT
65 ACACTTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAAT
*
1454151 GTATCGATCCATAATAATATAACATGTAAAAATATGACAAAACCGGTCTCGAA
130 GTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAA
* * * *
1454204 ATGACAAAACCAGTAAAGTGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAATATTGA
1 ATGACAAAACCAGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGA
* * *
1454269 CACTTTTGGAATTTAAAATAGAAGCAATAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATG
* * * * * *
1454334 TATTGACCCATAACAATATAACAAGTAAAAATATGACAAAATCGATCTTGAA
131 TATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAA
* * *
1454386 ATGACAAAACCGGTAAAACGCTACCGAATATGTTAAAAGTGTCGATACTTTAATATAAGTATCGA
1 ATGACAAAACCAGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGA
* *
1454451 CACTTTTAGAATTTAAAAGAGAAGCAATAATAGCGCTTATAAAGTGTC-ATTACTTTATAAAAAT
66 CACTTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGA-TACTTTATAAAAAT
* * * *
1454515 GTATCGATCCATAATAATATAATATGTAAAATTATGAAAAAACCGGTCTCGAA
130 GTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAA
* * * * *
1454568 ATGACAAAACCAGTAAAACACTATCGGATATGTTGAAAGTGTCGATATTTTAATATAAGTATCGA
1 ATGACAAAACCAGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGA
* *
1454633 CACTTTTAGAATTTAAAAGAGAAGCAGTAATATCGCCTATAAAGTGTTGATACTTTATAAAAATG
66 CACTTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATG
*
1454698 TATCGATCCATAACAATATAACATGTAAAAATATAACAAAACCGGTCTCGAA
131 TATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAA
* * * * *
1454750 ATGACAAAACCGGTAAAGTGCTACCGGATATGTTGAAAGTGTCGATACTTTGATATAAGTATTGA
1 ATGACAAAACCAGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGA
* * *
1454815 CACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTAATAAAAATA
66 CACTTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATG
* * * *
1454880 TATCGATCCATAACAATATAAACAGGTAAAAATATGATAAAATCGGTCTCTAA
131 TATCGATCCATAACAATAT-AACATGTAAAAATATGACAAAACCGGTCTCGAA
* * * * *
1454933 ATGACAAAACCGGTAAAGCACTGCTGAATATGTTGAAAGTGTTGATACTTTAATA
1 ATGACAAAACCAGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATACTTTAATA
1454988 AGTACGAGTA
Statistics
Matches: 697, Mismatches: 83, Indels: 7
0.89 0.11 0.01
Matches are distributed among these distances:
181 3 0.00
182 617 0.89
183 77 0.11
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (182 bp):
ATGACAAAACCAGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGA
CACTTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATG
TATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAA
Found at i:1458108 original size:20 final size:22
Alignment explanation
Indices: 1458063--1458120 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1458053 GCATGAGTAG
1458063 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1458087 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
1458107 TGTATCGATGCACT
1 TGCATCGATGCACT
1458121 TCAAAAGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1459752 original size:23 final size:23
Alignment explanation
Indices: 1459684--1459752 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1459674 ACATCTTATA
1459684 TGGCACTACGGTGCATTTCTACG
1 TGGCACTACGGTGCATTTCTACG
** * * *
1459707 CAGTACTTCGGTGCAATTCTACG
1 TGGCACTACGGTGCATTTCTACG
* *
1459730 TGGCACTCCGGTGCATTTATACG
1 TGGCACTACGGTGCATTTCTACG
1459753 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCATTTCTACG
Found at i:1463216 original size:24 final size:20
Alignment explanation
Indices: 1463184--1463239 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
1463174 TGCATGGTAG
1463184 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
1463208 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
1463228 TGTATCGATGCA
1 TGCATCGATGCA
1463240 GTTCAAAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 14 0.48
22 1 0.03
23 2 0.07
24 12 0.41
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:1464034 original size:2 final size:2
Alignment explanation
Indices: 1464027--1464317 Score: 435
Period size: 2 Copynumber: 147.0 Consensus size: 2
1464017 AATAGAAGTA
* * *
1464027 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT GT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1464069 AT AT AT AT AT AT GT AT AT GT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1464110 AT AT AT AC AT AT AT AT AT AT AT AT AT A- AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1464151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1464193 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1464234 AT AT AT AC AT AT AT AT AT AT AT AT AC AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1464276 AC AT AT AC AT AT AT AT AT AC AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1464318 GTTATAAGTA
Statistics
Matches: 258, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
1 3 0.01
2 255 0.99
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1465117 original size:23 final size:23
Alignment explanation
Indices: 1465084--1465151 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
1465074 CATCTTATAT
1465084 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* * * * *
1465107 GGCACTTCGGTTCAATTCTATGT
1 GGCACTACGGTGCATTTCTACGC
* *
1465130 GGCACTCCGGTGCATTTATACG
1 GGCACTACGGTGCATTTCTACG
1465152 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:1466340 original size:18 final size:18
Alignment explanation
Indices: 1466317--1466356 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1466307 GAAAAAATAT
1466317 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1466335 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1466353 GAAG
1 GAAG
1466357 TGAGAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.40, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:1469369 original size:128 final size:128
Alignment explanation
Indices: 1469168--1469452 Score: 344
Period size: 128 Copynumber: 2.2 Consensus size: 128
1469158 AAAATACATT
* * * * * * *
1469168 TTTAATGACAAAATTA-GTAAACATAATGTATCGAT--ATTTTTTAAAATTGTATCGATCCCAAC
1 TTTAATGA-AAAAATAGGTATACATAATGTGTTGATACATTTATTAAAA--GTATCGATCACAAA
* * *
1469230 AACATCAAAACCAATAATTATAATGTAATAGGCAAATTTACAATGTAACCGGTAGAAATATACCG
63 AACATCAAAACCAATAATTACAATGTAATAGGCAAATTTACAATGTAACCAGTAGAAATAAACCG
1469295 G
128 G
*
1469296 TTTAATTAAAAAATAGGTCA-ACATAATGTGTTGATACATTTATTAAAAGTATCGATCACAAAAA
1 TTTAATGAAAAAATAGGT-ATACATAATGTGTTGATACATTTATTAAAAGTATCGATCACAAAAA
* * * * *
1469360 TATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAACCAGTATAAATAAACCGG
65 CATCAAAACCAATAATTACAATGTAATAGGCAAATTTACAATGTAACCAGTAGAAATAAACCGG
* *
1469424 TTTTATGAGAAAATAGGTATACATAATGT
1 TTTAATGAAAAAATAGGTATACATAATGT
1469453 ATCAACACTT
Statistics
Matches: 134, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
127 7 0.05
128 116 0.87
129 1 0.01
130 10 0.07
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.31
Consensus pattern (128 bp):
TTTAATGAAAAAATAGGTATACATAATGTGTTGATACATTTATTAAAAGTATCGATCACAAAAAC
ATCAAAACCAATAATTACAATGTAATAGGCAAATTTACAATGTAACCAGTAGAAATAAACCGG
Found at i:1469678 original size:200 final size:197
Alignment explanation
Indices: 1469317--1470283 Score: 1305
Period size: 199 Copynumber: 4.8 Consensus size: 197
1469307 AATAGGTCAA
* * * *
1469317 CATAATGTGTTGATACATTTATTAAAAGTATCGATCAC-AAAAATATCGAAACCGATAATTACAA
1 CATAAAGTGTCGATACATTTA--AAATGTATCGATC-CTAAAAACATCGAAACCGATAATTACAA
* * *
1469381 TGTAATAGGTAAATTTACAATGTAACCAGTATAAATAAACCGGTTTTATGAGAAAATAGGTATAC
63 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCTAC
1469446 ATAATGTATCAACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGACAAACTAGG
128 ATAATGTATCAACAC-TTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGACAAACTAGG
*
1469511 TGCACA
192 TGCACG
* *
1469517 CATAAAGTGTCGATACAGTTATTAAAA-GTATCGATCCTAAAAACATCAAAACCGATAATTATAA
1 CATAAAGTGTCGATACA--T-TTAAAATGTATCGATCCTAAAAACATCGAAACCGATAATTACAA
* * * * * *
1469581 TATAATAGGTAAATTTATAATGTAATCGGTATAAATATACCGGTTTTATGAGAGAATATGTCAAC
63 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCTAC
* * * *
1469646 ATAATGTATCAACACTTTCTAACTTTGTGTCGATTCATTTTGTCCAGAATGAATGTCAAACTAGG
128 ATAATGTATCAACACTTT-TAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGACAAACTAGG
1469711 TGCACG
192 TGCACG
* *
1469717 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAATACATCGAAACCGATAATTACAATG
1 CATAAAGTGTCGATACATTTAAAA-TGTATCGATCCTAAAAACATCGAAACCGATAATTACAATG
*
1469782 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
65 TAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
* * **
1469847 AAAGTATCAACACAAATTTAAA-AAGTGTCGATACTTTTTGTCCAGAATGAATGACAAACTAGGT
130 AATGTATCAACAC--TTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGACAAACTAGGT
1469911 GCACG
193 GCACG
* *
1469916 CATAAAGTGTCGATACATTTAAAATTGTATCGAT-CTCAAAAACATCGAAACTGATAATTAAAAT
1 CATAAAGTGTCGATACATTTAAAA-TGTATCGATCCT-AAAAACATCGAAACCGATAATTACAAT
* * *
1469980 GTAATAGGTAAATTTACAATGTAACCGATAGAAATATACCAGTTTTATGAGAAAATAGGTCTACA
64 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACA
* ** ** *
1470045 TAAAGTATCGACACAAATTTAAAAAT-TGTCGATATTTTTTGTCCAGAATGAATGACAAACTAGG
129 TAATGTATC-A-ACACTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGACAAACTAGG
1470109 TGCACG
192 TGCACG
* * *
1470115 CATAAAGTGTCGATACATTTAAAATTGTATCGATCCAAAAAATATCGAAACCGATAATTATAATG
1 CATAAAGTGTCGATACATTTAAAA-TGTATCGATCCTAAAAACATCGAAACCGATAATTACAATG
* * ** * * *
1470180 TAATAGGTAAATTTATAATGGAGTCGGTATAAATATATCGATTTTATGAGAAAATAGGTTTACAT
65 TAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACAT
*
1470245 AATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTT
130 AATGTATCAACAC-TTTTAAATTTGTGTCGATACTTTTT
1470284 TTAAATTACG
Statistics
Matches: 683, Mismatches: 68, Indels: 33
0.87 0.09 0.04
Matches are distributed among these distances:
197 9 0.01
198 9 0.01
199 465 0.68
200 188 0.28
201 8 0.01
202 1 0.00
203 3 0.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (197 bp):
CATAAAGTGTCGATACATTTAAAATGTATCGATCCTAAAAACATCGAAACCGATAATTACAATGT
AATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATA
ATGTATCAACACTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGACAAACTAGGTGCA
CG
Found at i:1470943 original size:20 final size:19
Alignment explanation
Indices: 1470914--1470952 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1470904 AATAGGAATT
1470914 AATACCCAATTCACCTAGA
1 AATACCCAATTCACCTAGA
1470933 AATAGCCCAATTCACCTAGA
1 AATA-CCCAATTCACCTAGA
1470953 TGTAGAGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.41, C:0.31, G:0.08, T:0.21
Consensus pattern (19 bp):
AATACCCAATTCACCTAGA
Found at i:1473080 original size:24 final size:23
Alignment explanation
Indices: 1473049--1473093 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1473039 TTCATTTCAT
1473049 ATTTAATTGGAGTTTAAATTTAA
1 ATTTAATTGGAGTTTAAATTTAA
* *
1473072 ATTTCAATTTGAGTTTGAATTT
1 ATTT-AATTGGAGTTTAAATTT
1473094 CAATATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.51
Consensus pattern (23 bp):
ATTTAATTGGAGTTTAAATTTAA
Found at i:1473104 original size:24 final size:24
Alignment explanation
Indices: 1473053--1473105 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1473043 TTTCATATTT
* * *
1473053 AATTGGAGTTTAAATTTAAATTTC
1 AATTTGAGTTTAAATTTAAATATA
* *
1473077 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTAAATTTAAATATA
1473101 AATTT
1 AATTT
1473106 CGGCTCCACC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTAAATTTAAATATA
Found at i:1474284 original size:2 final size:2
Alignment explanation
Indices: 1474279--1474325 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1474269 CTACACACAT
1474279 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1474321 TA TA T
1 TA TA T
1474326 CCATACTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1474822 original size:23 final size:23
Alignment explanation
Indices: 1474774--1474823 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1474764 ACATATTTTA
* *
1474774 TTATATAAGCGTTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
*
1474797 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
1474820 TTAT
1 TTAT
1474824 TGTGCTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:1474918 original size:157 final size:156
Alignment explanation
Indices: 1474644--1475009 Score: 633
Period size: 157 Copynumber: 2.3 Consensus size: 156
1474634 TTAAGTTACG
*
1474644 TAAGCTCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCC
1 TAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTT-CAGTAATTAACCGGTTATGTTATCC
*
1474709 TTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACATATTTTA
65 TTGGTAACATTTTAGGCATTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACATATTTTA
* *
1474774 TTATATAAGCGTTACCTATTACGTTATA
130 TTATATAAACGCTACCTATTACG-TATA
* * *
1474802 TAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTTCAGTAAATAACCGGTTATGTTATTCT
1 TAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCAGTAATTAACCGGTTATGTTATCCT
*
1474867 TGGTAACATTTTAGGCATTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTTAT
66 TGGTAACATTTTAGGCATTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACATATTTTAT
1474932 TATATAAACGCTACCTATTACGTATA
131 TATATAAACGCTACCTATTACGTATA
1474958 TAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCTAGTAATTAACC
1 TAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTC-AGTAATTAACC
1475010 TATTTTATTA
Statistics
Matches: 197, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
156 43 0.22
157 117 0.59
158 37 0.19
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (156 bp):
TAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCAGTAATTAACCGGTTATGTTATCCT
TGGTAACATTTTAGGCATTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACATATTTTAT
TATATAAACGCTACCTATTACGTATA
Found at i:1475079 original size:87 final size:86
Alignment explanation
Indices: 1474913--1475084 Score: 254
Period size: 87 Copynumber: 2.0 Consensus size: 86
1474903 TAACAAATTA
* *
1474913 AGTAATTAACCTATTTTATTATATAAACGCTACCTATTACGTATATAAGCGCTACCTAATATGTT
1 AGTAATTAACCTATTTTATTATATAAACGCTACCTATTACGTATATAAGCGCTACCCAACATGTT
* *
1474978 ATTGTGCTTGATAATGTTTCT
66 ATTGTACTTGATAATATTTCT
* * * * *
1474999 AGTAATTAACCTATTTTATTATATAAGCGTTATCTATTACATTATATAAGTGCTACCCAACATGT
1 AGTAATTAACCTATTTTATTATATAAACGCTACCTATTAC-GTATATAAGCGCTACCCAACATGT
1475064 TATTGTACTTGATAATATTTC
65 TATTGTACTTGATAATATTTC
1475085 GGTTAAATGA
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
86 37 0.49
87 39 0.51
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (86 bp):
AGTAATTAACCTATTTTATTATATAAACGCTACCTATTACGTATATAAGCGCTACCCAACATGTT
ATTGTACTTGATAATATTTCT
Found at i:1486313 original size:11 final size:11
Alignment explanation
Indices: 1486290--1486357 Score: 79
Period size: 11 Copynumber: 6.4 Consensus size: 11
1486280 ATAAAGTAAT
1486290 AAAATAAACACA
1 AAAATAAA-ACA
1486302 AAAATAAAAC-
1 AAAATAAAACA
*
1486312 AAAACAAAAC-
1 AAAATAAAACA
*
1486322 AAAA-AAAATA
1 AAAATAAAACA
1486332 AAAATAAAACA
1 AAAATAAAACA
*
1486343 AATATAAAACA
1 AAAATAAAACA
1486354 AAAA
1 AAAA
1486358 GCAAAGGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
9 4 0.08
10 17 0.35
11 20 0.41
12 8 0.16
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.09
Consensus pattern (11 bp):
AAAATAAAACA
Found at i:1486369 original size:42 final size:42
Alignment explanation
Indices: 1486290--1486380 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
1486280 ATAAAGTAAT
*
1486290 AAAATAAACACAAAAATAAAACAAAACAAAACAAAAAAAATA
1 AAAATAAACACAAAAATAAAACAAAACAAAACAAAAAAAAGA
* **
1486332 AAAATAAA-ACAAATATAAAACAAAA-AGCAAAGGAAAAAAAGA
1 AAAATAAACACAAAAATAAAACAAAACA--AAACAAAAAAAAGA
1486374 AAAATAA
1 AAAATAA
1486381 TGGAATAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 1 0.02
41 16 0.37
42 26 0.60
ACGTcount: A:0.79, C:0.09, G:0.04, T:0.08
Consensus pattern (42 bp):
AAAATAAACACAAAAATAAAACAAAACAAAACAAAAAAAAGA
Found at i:1486470 original size:2 final size:2
Alignment explanation
Indices: 1486463--1486489 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1486453 AAATAAATAA
1486463 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1486490 AAATAAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1487769 original size:2 final size:2
Alignment explanation
Indices: 1487764--1487814 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1487754 TAAATGTTTA
1487764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1487806 -T AT AT AT AT
1 AT AT AT AT AT
1487815 TAATATTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1488473 original size:85 final size:85
Alignment explanation
Indices: 1488347--1488644 Score: 400
Period size: 85 Copynumber: 3.5 Consensus size: 85
1488337 CTTGACAGTG
* * * * *
1488347 TTTGTTGACAGATAACCCTTTTCGCCTTGAGCTATGATGTAAATTTGATATGCCTCTGAGCTGAA
1 TTTGATGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTTGATATGCCTTTGAGCTGAA
1488412 TGTAATCGAACTCGAAGGTC
66 TGTAATCGAACTCGAAGGTC
* * * **
1488432 TTTGATGACAGGTAACCCTTCTTGCCTTGAGTTATGTTGTAAATTTGATATACCTTTGATATGAA
1 TTTGATGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTTGATATGCCTTTGAGCTGAA
** *
1488497 TAAAATCGAACTCGAAGGAC
66 TGTAATCGAACTCGAAGGTC
* *
1488517 TTTGATGACAGATAACCCTTCTCGCCTTGAGTTATGCTT-TAAATTTGATATGCCTTTAAGCCGA
1 TTTGATGACAGATAACCCTTCTCGCCTTGAGTTATG-TTGTAAATTTGATATGCCTTTGAGCTGA
* *
1488581 GTGTAATTGAACTCGAAGGTC
65 ATGTAATCGAACTCGAAGGTC
* * *
1488602 TTGGTTGACAGATAACCCTTCTCACCTTGAGTTATGTTGTAAA
1 TTTGATGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAA
1488645 AGGTTGGGAG
Statistics
Matches: 183, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
84 2 0.01
85 179 0.98
86 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (85 bp):
TTTGATGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTTGATATGCCTTTGAGCTGAA
TGTAATCGAACTCGAAGGTC
Found at i:1489125 original size:64 final size:64
Alignment explanation
Indices: 1489030--1489783 Score: 1177
Period size: 64 Copynumber: 11.7 Consensus size: 64
1489020 AATCTTGTGT
* * *
1489030 AAGTTGTATTGTTTCGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACCCTGAATAAAACTG
1 AAGTTGT-TTG-TT-GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTG
1489095 GA
63 GA
* * *
1489097 AAGTTGTTTGTTGAGTCCAATATCCTTCGATGTGAAGTTGAAATTAACTCTGAATGAAACTGAA
1 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGA
* * *
1489161 AAGTTGTTTGTTGAGTCCAATATCTTTCGCTT-TAAAGTTGAAATTGACTCTGAATGAAACTGAA
1 AAGTTGTTTGTTGAGTCCAATATCCTTCG-TTGTGAAGTTGAAATTGACTCTGAATGAAACTGGA
*
1489225 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAATTGGA
1 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGA
* * ** *
1489289 AAGTTGTTTTTTGTGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGAA
1 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGA
* * *
1489353 AAGATGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTGTGAATGAAACTGGA
1 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGA
* *
1489417 AAGTTGTTTGTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGGAACTGGA
1 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGA
*
1489481 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGGAACTGGA
1 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGA
* * *
1489545 AAGTTGTTTGTTGAGTCCAATATTCTTCGTTGTAAAGTTGAAATTGACTCTGAATGAAACTAGA
1 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGA
* * *
1489609 AAGTTGTTTGTTGAGTCCAATATCCTTCGCTGTGAAGCTAAAATTGACTCTGAATGAAACTGGA
1 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGA
* * *
1489673 ATGTTGTTTGTTAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGA
1 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGA
* *
1489737 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTAAAATTGAAATTGA
1 AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGA
1489784 ATCTAAAAGC
Statistics
Matches: 632, Mismatches: 53, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
63 2 0.00
64 617 0.98
65 3 0.00
66 3 0.00
67 7 0.01
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (64 bp):
AAGTTGTTTGTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGA
Found at i:1490789 original size:99 final size:98
Alignment explanation
Indices: 1490596--1490895 Score: 398
Period size: 95 Copynumber: 3.1 Consensus size: 98
1490586 GGGACAACTC
** *
1490596 AATA-TATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTTGGGGTGTTTAACCAAT
1 AATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAAT
* *
1490660 TGC-CTTAGAGGGACAGCTCAAGCTTCATTGTAT
66 TGCTC-TAGAGGGACAACTCAAGCTTTATTGTAT
* * *
1490693 AGATATTATATTCACCTTTATCAAGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAA
1 A-ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAA
* *
1490758 TTGCTCTAGAGGGACAACACAAACTTTATTG--T
65 TTGCTCTAGAGGGACAACTCAAGCTTTATTGTAT
* * **
1490790 -ATATTATAATCGCCTTTATCAGGCTAGCTAAATCTTATCCATAAAGCCATGGCGTTTAACCAAT
1 AATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAAT
*
1490854 TGCTCTAGAGGGATAACTCAAGCTTTATTGTAT
66 TGCTCTAGAGGGACAACTCAAGCTTTATTGTAT
1490887 -ATA-TATAAT
1 AATATTATAAT
1490896 ATTATAATAT
Statistics
Matches: 178, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
95 84 0.47
96 6 0.03
97 6 0.03
98 3 0.02
99 78 0.44
100 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (98 bp):
AATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAAT
TGCTCTAGAGGGACAACTCAAGCTTTATTGTAT
Found at i:1493996 original size:21 final size:21
Alignment explanation
Indices: 1493937--1494000 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
1493927 TACTCTAGAA
* *
1493937 AGGGTATCGGCACACTGTAGC
1 AGGGTATCGGTACACTGTAGT
*
1493958 AGGGTATCGGTATACTGTAGT
1 AGGGTATCGGTACACTGTAGT
* *
1493979 AGGGTATCGATACCCTGTAGT
1 AGGGTATCGGTACACTGTAGT
1494000 A
1 A
1494001 TTCTGAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (21 bp):
AGGGTATCGGTACACTGTAGT
Found at i:1497534 original size:5 final size:5
Alignment explanation
Indices: 1497516--1497631 Score: 69
Period size: 5 Copynumber: 22.8 Consensus size: 5
1497506 GAAAATGGCT
* * * *
1497516 AAATA AAAT- TAATA AAATA AAAAA GAAAGA AAGT- -AATA AAAT- AAATA
1 AAATA AAATA AAATA AAATA AAATA -AAATA AAATA AAATA AAATA AAATA
* * *
1497563 AAATA AACACAA AAATAA AAATA AAACA AAACA AAATA AAATAA AAATA
1 AAATA AA-A-TA AAAT-A AAATA AAATA AAATA AAATA AAAT-A AAATA
* *
1497612 AAACA AATATA AAACA AAAT
1 AAATA AA-ATA AAATA AAAT
1497632 GCAAAGGAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
3 2 0.02
4 7 0.08
5 54 0.63
6 20 0.23
7 3 0.03
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.16
Consensus pattern (5 bp):
AAATA
Found at i:1497579 original size:21 final size:21
Alignment explanation
Indices: 1497553--1497631 Score: 90
Period size: 21 Copynumber: 3.7 Consensus size: 21
1497543 AGAAAGTAAT
1497553 AAAAT-AAATAAAATAAACACA
1 AAAATAAAATAAAATAAA-ACA
*
1497574 AAAATAAAAATAAAACAAAAC-
1 AAAAT-AAAATAAAATAAAACA
1497595 AAAATAAAATAAAAATAAAACA
1 AAAATAAAAT-AAAATAAAACA
* *
1497617 AATATAAAACAAAAT
1 AAAATAAAATAAAAT
1497632 GCAAAGGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
20 5 0.10
21 24 0.48
22 10 0.20
23 11 0.22
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (21 bp):
AAAATAAAATAAAATAAAACA
Found at i:1497588 original size:11 final size:11
Alignment explanation
Indices: 1497562--1497630 Score: 79
Period size: 11 Copynumber: 6.3 Consensus size: 11
1497552 TAAAATAAAT
1497562 AAAATAAACACA
1 AAAATAAA-ACA
1497574 AAAATAAAA-A
1 AAAATAAAACA
*
1497584 TAAAACAAAAC-
1 -AAAATAAAACA
*
1497595 AAAATAAAATA
1 AAAATAAAACA
1497606 AAAATAAAACA
1 AAAATAAAACA
*
1497617 AATATAAAACA
1 AAAATAAAACA
1497628 AAA
1 AAA
1497631 TGCAAAGGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
10 9 0.19
11 31 0.65
12 8 0.17
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.12
Consensus pattern (11 bp):
AAAATAAAACA
Found at i:1497600 original size:15 final size:15
Alignment explanation
Indices: 1497529--1497631 Score: 62
Period size: 16 Copynumber: 6.3 Consensus size: 15
1497519 TAAAATTAAT
*
1497529 AAAATAAAAAAGAAAG
1 AAAATAAAAAA-AAAC
* *
1497545 AAAGTAATAAAATAAAT
1 AAAATAA-AAAA-AAAC
*
1497562 AAAATAAACACAAAAATA
1 AAAATAAA-A-AAAAA-C
*
1497580 AAAATAAAACAAAAC
1 AAAATAAAAAAAAAC
*
1497595 AAAATAAAATAAAAAT
1 AAAATAAAA-AAAAAC
* *
1497611 AAAACAAATATAAAAC
1 AAAATAAA-AAAAAAC
1497627 AAAAT
1 AAAAT
1497632 GCAAAGGAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
15 9 0.13
16 30 0.44
17 19 0.28
18 10 0.15
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.14
Consensus pattern (15 bp):
AAAATAAAAAAAAAC
Found at i:1497609 original size:32 final size:33
Alignment explanation
Indices: 1497562--1497631 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
1497552 TAAAATAAAT
1497562 AAAATAAACACAAAAATAAAA-ATAAAACAAAAC
1 AAAATAAACACAAAAATAAAACA-AAAACAAAAC
* * *
1497595 AAAATAAA-ATAAAAATAAAACAAATATAAAAC
1 AAAATAAACACAAAAATAAAACAAAAACAAAAC
1497627 AAAAT
1 AAAAT
1497632 GCAAAGGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 24 0.73
33 9 0.27
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.13
Consensus pattern (33 bp):
AAAATAAACACAAAAATAAAACAAAAACAAAAC
Found at i:1498981 original size:2 final size:2
Alignment explanation
Indices: 1498974--1499032 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
1498964 AACATAAATA
1498974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1499016 AT AT -T A- AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1499033 GTGTAATGCG
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.06
2 51 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1501415 original size:21 final size:22
Alignment explanation
Indices: 1501382--1501426 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1501372 TAAGAATTTT
1501382 TATTTTTATATTATT-AAAATA
1 TATTTTTATATTATTAAAAATA
1501403 TATTCTTTA-ATTATTAAAAATA
1 TATT-TTTATATTATTAAAAATA
1501425 TA
1 TA
1501427 AATATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTTTATATTATTAAAAATA
Found at i:1501422 original size:22 final size:21
Alignment explanation
Indices: 1501382--1501447 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
1501372 TAAGAATTTT
1501382 TATTTTTATATTATTAAAATA
1 TATTTTTATATTATTAAAATA
1501403 TATTCTTTA-ATTATTAAAA-A
1 TATT-TTTATATTATTAAAATA
***
1501423 TATAAATATTATTA-TAAAATA
1 TATTTTTA-TATTATTAAAATA
1501444 TATT
1 TATT
1501448 ATTTTAATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 2 0.05
20 9 0.24
21 22 0.59
22 4 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTTTATATTATTAAAATA
Found at i:1501454 original size:42 final size:43
Alignment explanation
Indices: 1501390--1501516 Score: 136
Period size: 42 Copynumber: 3.0 Consensus size: 43
1501380 TTTATTTTTA
* *
1501390 TATTATTAAAATATATT-CTTTAATTA-TTAAAAATATAAATAT
1 TATTA-TAAAATATATTATTTTAATTAGTTTAAAATATAAATAT
* *
1501432 TATTATAAAATATATTATTTTAA-TAGTTTTAAATATAACAAAT
1 TATTATAAAATATATTATTTTAATTAGTTTAAAATATAA-ATAT
* * * *
1501475 AACTAT-AAATATATTATTTTAATTATTTTAAAATATTAATAT
1 TATTATAAAATATATTATTTTAATTAGTTTAAAATATAAATAT
1501517 ATTTGAATCA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
41 13 0.18
42 39 0.55
43 19 0.27
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (43 bp):
TATTATAAAATATATTATTTTAATTAGTTTAAAATATAAATAT
Found at i:1506294 original size:3 final size:3
Alignment explanation
Indices: 1506286--1506325 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
1506276 GTAACATGTA
1506286 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AATT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT A
1506326 TTTTTTAGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1506815 original size:131 final size:133
Alignment explanation
Indices: 1506513--1506839 Score: 363
Period size: 135 Copynumber: 2.5 Consensus size: 133
1506503 GTTCTGGTGT
* * * ** * *
1506513 TCTATGGGTGACACGGCTCCTACATTATGAGGATATATGGTCGGTGGATGACACAGTTCCTATGC
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTATGC
* ** ** * *
1506578 GTTGATTACAGCTGGCCATCTTTAGGGAATAGTGATAACACGATTCCTACGCGAAGAGGAAGGCT
66 GATGAGAACAGCAAGCCATCTTTAGGGAATA--GATAACACGATTCCTACGCGAAGAGGAAGACA
*
1506643 GGTTA
129 GATTA
* * * * *
1506648 TCTAGGGGTGAAATGGCTCCTACGCGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTATGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTATGC
* * * * * *
1506713 GATGAGAACGGCAAGCCATCTTTAGGG-ATA-ATAACATGGTTCCTACGTGATGAGGACGACAGA
66 GATGAGAACAGCAAGCCATCTTTAGGGAATAGATAACACGATTCCTACGCGAAGAGGAAGACAGA
1506776 TTA
131 TTA
* *
1506779 TCTAAGGTTGACACGGCTCCTACGTGATGAAGAGGTCTGGTCGG-GGATGACACGGTTCCTA
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTA
1506840 CACGATGAAA
Statistics
Matches: 161, Mismatches: 31, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
130 17 0.11
131 66 0.41
134 3 0.02
135 75 0.47
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.26
Consensus pattern (133 bp):
TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTATGC
GATGAGAACAGCAAGCCATCTTTAGGGAATAGATAACACGATTCCTACGCGAAGAGGAAGACAGA
TTA
Found at i:1506983 original size:67 final size:66
Alignment explanation
Indices: 1506869--1507070 Score: 277
Period size: 65 Copynumber: 3.1 Consensus size: 66
1506859 TATCTTTAGG
* * *
1506869 GATTTATTTCAAGAGAAACTGTCTCAAGGGAGACAAAAATTTGTTTCAAGGGAAACAAT-AC-CA
1 GATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAC-ATGACTCA
1506932 AA
65 AA
* *
1506934 GGTTGGTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAC-TGACTC
1 GATT--TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACATGACTC
1506998 AAA
64 AAA
* * *
1507001 GATTTTTTTCAAGAAAAACTGTCTCAAGAGAGAAAAAACTTTGTTTCAAGGGAAACA-GACTCAA
1 GATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACATGACTCAA
1507065 A
66 A
1507066 GATTT
1 GATTT
1507071 TATCAATTTT
Statistics
Matches: 122, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
65 65 0.53
66 2 0.02
67 55 0.45
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (66 bp):
GATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACATGACTCAA
A
Found at i:1506990 original size:37 final size:36
Alignment explanation
Indices: 1506940--1507056 Score: 124
Period size: 37 Copynumber: 3.4 Consensus size: 36
1506930 CAAAGGTTGG
1506940 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGA-AAAACTT
*
1506977 TGTTTCAAGGGAAACTGACTC-A-A-AG----A-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAACTT
* **
1507005 TTTTTCAAGAAAAACTGTCTCAAGAGAGAAAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAG-AAAAACTT
1507042 TGTTTCAAGGGAAAC
1 TGTTTCAAGGGAAAC
1507057 AGACTCAAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
28 19 0.30
29 2 0.03
30 1 0.02
31 2 0.03
34 2 0.03
35 1 0.02
36 2 0.03
37 34 0.54
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAACTT
Found at i:1508421 original size:23 final size:24
Alignment explanation
Indices: 1508390--1508434 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1508380 GTGCTTATTC
*
1508390 TCTTCTTTTTTCTTTGTTTTTTCT
1 TCTTCTTTTATCTTTGTTTTTTCT
1508414 TCTT-TTTTATCTTTGTTTTTT
1 TCTTCTTTTATCTTTGTTTTTT
1508435 GTCTTTGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.80
Consensus pattern (24 bp):
TCTTCTTTTATCTTTGTTTTTTCT
Found at i:1508433 original size:14 final size:14
Alignment explanation
Indices: 1508415--1508448 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1508405 GTTTTTTCTT
1508415 CTTTTTTATCTTTG
1 CTTTTTTATCTTTG
*
1508429 -TTTTTTGTCTTTG
1 CTTTTTTATCTTTG
1508442 CTTTTTT
1 CTTTTTT
1508449 CTTTTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.03, C:0.12, G:0.09, T:0.76
Consensus pattern (14 bp):
CTTTTTTATCTTTG
Found at i:1508441 original size:36 final size:35
Alignment explanation
Indices: 1508395--1508468 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 35
1508385 TATTCTCTTC
1508395 TTTTTTCTTTG-TTTTTTCTTCTTTTTTATCTTTGT
1 TTTTTTCTTTGCTTTTTTCTT-TTTTTTATCTTTGT
* *
1508430 TTTTTGTCTTTGCTTTTTTCTTTTTTTTGTTTTTGT
1 TTTTT-TCTTTGCTTTTTTCTTTTTTTTATCTTTGT
1508466 TTT
1 TTT
1508469 GATGTGATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
35 5 0.14
36 21 0.60
37 9 0.26
ACGTcount: A:0.01, C:0.09, G:0.08, T:0.81
Consensus pattern (35 bp):
TTTTTTCTTTGCTTTTTTCTTTTTTTTATCTTTGT
Found at i:1508455 original size:23 final size:23
Alignment explanation
Indices: 1508394--1508468 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 23
1508384 TTATTCTCTT
1508394 CTTTTTTCTTTGTTTTT-TC-TT-
1 CTTTTTTCTTT-TTTTTGTCTTTG
1508415 CTTTTTTATCTTTGTTTTTTGTCTTTG
1 C-TTTTT-TC-TT-TTTTTTGTCTTTG
*
1508442 CTTTTTTCTTTTTTTTGTTTTTG
1 CTTTTTTCTTTTTTTTGTCTTTG
1508465 -TTTT
1 CTTTT
1508469 GATGTGATCT
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
21 1 0.02
22 9 0.20
23 14 0.30
24 9 0.20
25 5 0.11
26 7 0.15
27 1 0.02
ACGTcount: A:0.01, C:0.11, G:0.08, T:0.80
Consensus pattern (23 bp):
CTTTTTTCTTTTTTTTGTCTTTG
Found at i:1508593 original size:69 final size:69
Alignment explanation
Indices: 1508510--1508717 Score: 398
Period size: 69 Copynumber: 3.0 Consensus size: 69
1508500 CTTTTTGAGA
* *
1508510 TCTTATGTGTATTGATGGTCTTCACTCATGTGAGCATATTTTCTTTGCCTTTCCCCCTCAGTGTG
1 TCTTATGTGGATTGATGGTCTTCACTCATGTGAGCATATTTTCTTTGCCTTGCCCCCTCAGTGTG
1508575 GAGG
66 GAGG
1508579 TCTTATGTGGATTGATGGTCTTCACTCATGTGAGCATATTTTCTTTGCCTTGCCCCCTCAGTGTG
1 TCTTATGTGGATTGATGGTCTTCACTCATGTGAGCATATTTTCTTTGCCTTGCCCCCTCAGTGTG
1508644 GAGG
66 GAGG
1508648 TCTTATGTGGATTGATGGTCTTCACTCATGTGAGCATATTTTCTTTGCCTTGCCCCCTCAGTGTG
1 TCTTATGTGGATTGATGGTCTTCACTCATGTGAGCATATTTTCTTTGCCTTGCCCCCTCAGTGTG
1508713 GAGG
66 GAGG
1508717 T
1 T
1508718 GATACTTGGT
Statistics
Matches: 137, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 137 1.00
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (69 bp):
TCTTATGTGGATTGATGGTCTTCACTCATGTGAGCATATTTTCTTTGCCTTGCCCCCTCAGTGTG
GAGG
Found at i:1520464 original size:21 final size:19
Alignment explanation
Indices: 1520438--1520499 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 19
1520428 TTTTGTGCAC
1520438 AGTGTATCGATACACTATGAT
1 AGTGTA-CGATAC-CTATGAT
1520459 AGTGTACGATACCTATG-T
1 AGTGTACGATACCTATGAT
* *
1520477 ATTG-A-TATA-CTATGAT
1 AGTGTACGATACCTATGAT
1520493 AGTGTAC
1 AGTGTAC
1520500 TGATGCATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 5 0.14
16 7 0.20
17 2 0.06
18 4 0.11
19 5 0.14
20 6 0.17
21 6 0.17
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
AGTGTACGATACCTATGAT
Found at i:1521055 original size:12 final size:12
Alignment explanation
Indices: 1521025--1521058 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1521015 GTATCATAAT
*
1521025 TTTTCAAACATTG
1 TTTTCAAA-ATTA
1521038 TTTTCAAAATTA
1 TTTTCAAAATTA
1521050 TTTTCAAAA
1 TTTTCAAAA
1521059 ATTTCCCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (12 bp):
TTTTCAAAATTA
Found at i:1522540 original size:20 final size:20
Alignment explanation
Indices: 1522498--1522556 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
1522488 TTAAATGTTT
* *
1522498 ATTTGGTTTTGATT-GTTTGA
1 ATTTGG-TTTGATTAATTTAA
1522518 ATTTGGTTTGATTAATTTAA
1 ATTTGGTTTGATTAATTTAA
1522538 ATTTAGTGTTT-ATTAATTT
1 ATTT-G-GTTTGATTAATTT
1522557 TTGCATCGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 7 0.21
20 14 0.41
21 9 0.26
22 4 0.12
ACGTcount: A:0.24, C:0.00, G:0.17, T:0.59
Consensus pattern (20 bp):
ATTTGGTTTGATTAATTTAA
Found at i:1523323 original size:20 final size:20
Alignment explanation
Indices: 1523298--1523353 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1523288 ATTTTACACT
1523298 GAGTGTACCGATACACTAGA
1 GAGTGTACCGATACACTAGA
*
1523318 GAGTGTACCAATACACTAGA
1 GAGTGTACCGATACACTAGA
1523338 GAGTGTACCGATACAC
1 GAGTGTACCGATACAC
1523354 CGACGATCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (20 bp):
GAGTGTACCGATACACTAGA
Found at i:1526720 original size:3 final size:3
Alignment explanation
Indices: 1526712--1526781 Score: 124
Period size: 3 Copynumber: 23.3 Consensus size: 3
1526702 GTAACAGGTA
1526712 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1526760 AAT AAT AA- AAT AATT AAT AAT A
1 AAT AAT AAT AAT AA-T AAT AAT A
1526782 TTTTTAGACC
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 60 0.92
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1527122 original size:2 final size:2
Alignment explanation
Indices: 1527115--1527150 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1527105 GTAATTGAAT
*
1527115 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1527151 ATTAAATGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1530076 original size:3 final size:3
Alignment explanation
Indices: 1530070--1530110 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
1530060 TATATCATTA
*
1530070 ATT ATT ATT ATT ATT ATT ATT -TT ATT AAT ATT ATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1530111 CATTTTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1530096 original size:14 final size:14
Alignment explanation
Indices: 1530070--1530110 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1530060 TATATCATTA
*
1530070 ATTATTATTATTATT
1 ATTATT-TTATTAAT
1530085 ATTATTTTATTAAT
1 ATTATTTTATTAAT
1530099 ATTATTTTATTA
1 ATTATTTTATTA
1530111 CATTTTGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTATTTTATTAAT
Found at i:1534647 original size:3 final size:3
Alignment explanation
Indices: 1534639--1534716 Score: 138
Period size: 3 Copynumber: 26.0 Consensus size: 3
1534629 TTTTTATCCA
*
1534639 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1534687 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1534717 AAATATATAT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1535202 original size:24 final size:24
Alignment explanation
Indices: 1535175--1535226 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1535165 GATATAGAAC
* *
1535175 GAGACAGAGAGACAAAAAAAAATA
1 GAGACAGACAGACAAAAAAAAACA
* * *
1535199 GAGAGAGACATAGAAAAAAAAACA
1 GAGACAGACAGACAAAAAAAAACA
1535223 GAGA
1 GAGA
1535227 AAATACAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.65, C:0.08, G:0.23, T:0.04
Consensus pattern (24 bp):
GAGACAGACAGACAAAAAAAAACA
Found at i:1536033 original size:17 final size:17
Alignment explanation
Indices: 1536011--1536056 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
1536001 TAGATTTTTA
*
1536011 ATTTTATTTTTTCGTTT
1 ATTTTATTTTTTCATTT
*
1536028 ATTTTATGTTTTCATTT
1 ATTTTATTTTTTCATTT
1536045 ATTTTATTTTTT
1 ATTTTATTTTTT
1536057 TAAATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.76
Consensus pattern (17 bp):
ATTTTATTTTTTCATTT
Found at i:1536836 original size:21 final size:23
Alignment explanation
Indices: 1536811--1536852 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1536801 TCAAATTTTT
1536811 TATTTAT-T-TATTATTTTATAA
1 TATTTATATGTATTATTTTATAA
*
1536832 TATTTATATGTTTTATTTTAT
1 TATTTATATGTATTATTTTAT
1536853 TTGCAAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TATTTATATGTATTATTTTATAA
Found at i:1536876 original size:13 final size:15
Alignment explanation
Indices: 1536845--1536881 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1536835 TTATATGTTT
1536845 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
1536860 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
1536873 TA-TTTATTT
1 TATTTTATTT
1536882 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:1547472 original size:12 final size:12
Alignment explanation
Indices: 1547455--1547503 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
1547445 GCTTGAAGAG
1547455 AATAGAAAAAAA
1 AATAGAAAAAAA
1547467 AATAGAAAAAAA
1 AATAGAAAAAAA
*
1547479 AA-AGAGAAGAAA
1 AATAGA-AAAAAA
*
1547491 AAGAGAAGAAAAA
1 AATAGAA-AAAAA
1547504 GAAAGGGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 3 0.09
12 22 0.69
13 7 0.22
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (12 bp):
AATAGAAAAAAA
Found at i:1547478 original size:13 final size:13
Alignment explanation
Indices: 1547455--1547492 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1547445 GCTTGAAGAG
1547455 AATAG-AAAAAAA
1 AATAGAAAAAAAA
1547467 AATAGAAAAAAAA
1 AATAGAAAAAAAA
* *
1547480 AAGAGAAGAAAAA
1 AATAGAAAAAAAA
1547493 GAGAAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (13 bp):
AATAGAAAAAAAA
Found at i:1547504 original size:11 final size:11
Alignment explanation
Indices: 1547477--1547505 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1547467 AATAGAAAAA
1547477 AAAAAGAGAAG
1 AAAAAGAGAAG
1547488 AAAAAGAGAAG
1 AAAAAGAGAAG
1547499 AAAAAGA
1 AAAAAGA
1547506 AAGGGGGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAGAGAAG
Found at i:1548771 original size:83 final size:84
Alignment explanation
Indices: 1548628--1549059 Score: 782
Period size: 83 Copynumber: 5.2 Consensus size: 84
1548618 ATATCTTAGT
1548628 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1548693 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
1548712 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1548776 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
*
1548795 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTTTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1548859 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
1548878 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATC-TCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1548942 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
1548961 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* *
1549026 CTAATCTG-GTTGGACAGAA
66 CTGATCTGATTTGG-CAGAA
*
1549045 CCAATCGTTGGAATT
1 CCAATCATT-GAATT
1549060 AAAAGATGAA
Statistics
Matches: 339, Mismatches: 5, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
83 251 0.74
84 83 0.24
85 5 0.01
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (84 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTTGGCAGAA
Found at i:1550009 original size:112 final size:112
Alignment explanation
Indices: 1549769--1550546 Score: 1360
Period size: 113 Copynumber: 6.9 Consensus size: 112
1549759 TCAAATCCAC
* *
1549769 TTGATGGATCATTCATTGCCAGA-TAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCA-ACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1549833 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
65 AAGTTCATAATGAGAAGAACTTGTTCAAC-TTTTGTTTAAATTCATCAT
1549882 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1549947 AGTTCATAATGAGAAGAACTTGTTCAACTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTGTTTAAATTCATCAT
1549994 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1550059 AGTTCATAATGAGAAGAACTTGTTCAACTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTGTTTAAATTCATCAT
1550106 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1550171 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAAC-TTTTGTTTAAATTCATCAT
*
1550219 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1550284 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAAC-TTTTGTTTAAATTCATCAT
1550332 TTGATGGATCAACATTGCCAGAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCAACATTGCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * *
1550397 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCAC
65 AAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTGTTTAAATTCATCAT
* * *** *
1550446 TAGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
1550511 AGTTCATAAGGAGAAGAGCTTGTTCAACCTTTGTTT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTGTTT
1550547 GATACTATCA
Statistics
Matches: 644, Mismatches: 17, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
112 242 0.38
113 300 0.47
114 101 0.16
115 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.29
Consensus pattern (112 bp):
TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTGTTTAAATTCATCAT
Found at i:1550509 original size:337 final size:335
Alignment explanation
Indices: 1549766--1550546 Score: 1357
Period size: 337 Copynumber: 2.3 Consensus size: 335
1549756 ATTTCAAATC
*
1549766 CACTTGATGGATCATTCATTGCCAGATAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 CACTTGATGGATCATT-ATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGA
1549831 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACA
64 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACA
*
1549896 TTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
129 TTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGA
1549961 AGAACTTGTTCAACTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCAT
194 AGAACTTGTTCAACTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCAT
1550026 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTT
259 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTT
1550091 GTTTAAATTCAT
324 GTTTAAATTCAT
* **
1550103 CATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 CACTTGATGGATCATTATTGCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGA
1550168 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACA
64 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACA
1550233 TTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGA
129 TTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGA
1550298 AGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCA
194 AGAACTTGTTCAAC-TTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCA
*
1550363 TGAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCT
258 T-AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CT
*
1550428 TTTGTTTGAATTCAT
321 TTTGTTTAAATTCAT
* * *
1550443 CACTAGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 CACTTGATGGATCATTATTGCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGA
* * *
1550508 AGAAGTTCATAAGGAGAAGAGCTTGTTCAAC-CTTTGTTT
64 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
1550547 GATACTATCA
Statistics
Matches: 423, Mismatches: 16, Indels: 8
0.95 0.04 0.02
Matches are distributed among these distances:
336 9 0.02
337 194 0.46
338 51 0.12
339 68 0.16
340 101 0.24
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (335 bp):
CACTTGATGGATCATTATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAG
AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATT
GCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAG
AACTTGTTCAACTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAA
TGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTGT
TTAAATTCAT
Done.