Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001111.1 Hibiscus syriacus cultivar Beakdansim tig00002193_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: 3891333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 17
Found at i:266653 original size:17 final size:16
Alignment explanation
Indices: 266632--266684 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
266622 ATTAGAGTGC
266632 AAAAAGAAAGAAAAGA
1 AAAAAGAAAGAAAAGA
266648 CAAAAAG-AAGAAAAGA
1 -AAAAAGAAAGAAAAGA
266664 AGAAAAGAATA-AAAAGA
1 A-AAAAGAA-AGAAAAGA
266681 AAAA
1 AAAA
266685 TATTTCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
15 1 0.03
16 17 0.52
17 14 0.42
18 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAGAAAAGA
Found at i:266661 original size:25 final size:25
Alignment explanation
Indices: 266633--266681 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
266623 TTAGAGTGCA
266633 AAAAGAAAGAAAAG-ACAAAAAGAAG
1 AAAAG-AAGAAAAGAACAAAAAGAAG
*
266658 AAAAGAAGAAAAGAATAAAAAGAA
1 AAAAGAAGAAAAGAACAAAAAGAA
266682 AAATATTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (25 bp):
AAAAGAAGAAAAGAACAAAAAGAAG
Found at i:267951 original size:15 final size:16
Alignment explanation
Indices: 267919--267960 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
267909 GATTTTTTTA
267919 TTATCTTATTTCATCTT
1 TTAT-TTATTTCATCTT
267936 TTATTTATTT-ATCTT
1 TTATTTATTTCATCTT
*
267951 TTGTTTATTT
1 TTATTTATTT
267961 TATTCTAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 6 0.25
17 4 0.17
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTATTTCATCTT
Found at i:276860 original size:17 final size:18
Alignment explanation
Indices: 276832--276866 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
276822 GGTTAGGGTA
276832 GAAAGAGTAGAAAAAATG
1 GAAAGAGTAGAAAAAATG
*
276850 GAAAG-GTAGAAGAAATG
1 GAAAGAGTAGAAAAAATG
276867 ATTCAAAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.57, C:0.00, G:0.31, T:0.11
Consensus pattern (18 bp):
GAAAGAGTAGAAAAAATG
Found at i:279286 original size:25 final size:26
Alignment explanation
Indices: 279230--279287 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
279220 TTTGAAATTC
279230 TTCTTTTTTTCTTTTCTTCTATTCTG
1 TTCTTTTTTTCTTTTCTTCTATTCTG
* *
279256 AT-TTTTTTTCTTTT-TGTCTTTTCT-
1 TTCTTTTTTTCTTTTCT-TCTATTCTG
279280 TTCTTTTT
1 TTCTTTTT
279288 GCACTCCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 2 0.07
25 24 0.89
26 1 0.04
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (26 bp):
TTCTTTTTTTCTTTTCTTCTATTCTG
Found at i:281680 original size:19 final size:21
Alignment explanation
Indices: 281637--281688 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
281627 GAAACCCCTT
281637 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
281658 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
281677 TGAAGATACATG
1 TGAAAATACATG
281689 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:285081 original size:19 final size:20
Alignment explanation
Indices: 285040--285090 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
285030 GAAACCCCTT
*
285040 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
285060 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
285079 TGAAGATACATG
1 TGAAAATACATG
285091 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:286835 original size:13 final size:11
Alignment explanation
Indices: 286813--286878 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
286803 CATCACGCCT
286813 ATATCATCACC
1 ATATCATCACC
286824 ATAGTCCATCACC
1 ATA-T-CATCACC
*
286837 ATTATCA-CGCC
1 A-TATCATCACC
286848 TATATCATCACC
1 -ATATCATCACC
286860 ATATTCCATCACC
1 ATA-T-CATCACC
286873 ATATCA
1 ATATCA
286879 CGCCTATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:286845 original size:36 final size:35
Alignment explanation
Indices: 286804--286895 Score: 157
Period size: 36 Copynumber: 2.6 Consensus size: 35
286794 GCTTCTAACC
286804 ATCACGCCTATATCATCACCATAGTCCATCACCATT
1 ATCACGCCTATATCATCACCATAGTCCATCACCA-T
*
286840 ATCACGCCTATATCATCACCATATTCCATCACCAT
1 ATCACGCCTATATCATCACCATAGTCCATCACCAT
*
286875 ATCACGCCTATATTATCACCA
1 ATCACGCCTATATCATCACCA
286896 ACTTATAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
35 21 0.39
36 33 0.61
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (35 bp):
ATCACGCCTATATCATCACCATAGTCCATCACCAT
Found at i:299971 original size:2 final size:2
Alignment explanation
Indices: 299954--299992 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
299944 TATCATAAAC
*
299954 TA TA GA TA TA -A TA TA TA TA TA TA TA TA -A TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
299993 GAAAATAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:299977 original size:15 final size:14
Alignment explanation
Indices: 299954--299992 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
299944 TATCATAAAC
*
299954 TATAGATATA-ATA
1 TATATATATATATA
299967 TATATATATATATA
1 TATATATATATATA
299981 -ATATATATATAT
1 TATATATATATAT
299993 GAAAATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 21 0.88
14 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
TATATATATATATA
Found at i:299979 original size:17 final size:17
Alignment explanation
Indices: 299954--299992 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
299944 TATCATAAAC
*
299954 TATAGATATAATATATA
1 TATATATATAATATATA
299971 TATATATATAATATATA
1 TATATATATAATATATA
299988 TATAT
1 TATAT
299993 GAAAATAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TATATATATAATATATA
Found at i:300903 original size:19 final size:21
Alignment explanation
Indices: 300860--300911 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
300850 GAAACCCCTT
300860 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
300881 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
300900 TGAAGATACATG
1 TGAAAATACATG
300912 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:303261 original size:35 final size:34
Alignment explanation
Indices: 303210--303309 Score: 139
Period size: 35 Copynumber: 2.9 Consensus size: 34
303200 GATACTATTT
*
303210 TCATCACCATAATCCATCTCCATTATCACGCCTAA
1 TCATCACCATAATCCATCACCATTATCACGCCT-A
* *
303245 TCATCACCATAGTCCATCACCATTATCACACCTA
1 TCATCACCATAATCCATCACCATTATCACGCCTA
* *
303279 TAATCACCATATTCCATCACCA-TATCACGCC
1 TCATCACCATAATCCATCACCATTATCACGCC
303310 AATAACATCA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 8 0.14
34 21 0.36
35 30 0.51
ACGTcount: A:0.32, C:0.38, G:0.03, T:0.27
Consensus pattern (34 bp):
TCATCACCATAATCCATCACCATTATCACGCCTA
Found at i:303262 original size:13 final size:11
Alignment explanation
Indices: 303244--303345 Score: 59
Period size: 11 Copynumber: 9.0 Consensus size: 11
303234 ATCACGCCTA
303244 ATCATCACCAT
1 ATCATCACCAT
303255 AGTCCATCACCATT
1 A-T-CATCACCA-T
303269 ATCA-CACC-T
1 ATCATCACCAT
*
303278 ATAATCACCAT
1 ATCATCACCAT
303289 ATTCCATCACCAT
1 A-T-CATCACCAT
*
303302 ATCA-CGCCAAT
1 ATCATCACC-AT
*
303313 AACATCATCC-T
1 ATCATCA-CCAT
* *
303324 ACCATTACCAT
1 ATCATCACCAT
*
303335 TTCATCACCAT
1 ATCATCACCAT
303346 TAAATCATCC
Statistics
Matches: 70, Mismatches: 10, Indels: 22
0.69 0.10 0.22
Matches are distributed among these distances:
9 4 0.06
10 9 0.13
11 29 0.41
12 6 0.09
13 20 0.29
14 2 0.03
ACGTcount: A:0.34, C:0.36, G:0.02, T:0.27
Consensus pattern (11 bp):
ATCATCACCAT
Found at i:303334 original size:33 final size:33
Alignment explanation
Indices: 303258--303356 Score: 80
Period size: 33 Copynumber: 3.0 Consensus size: 33
303248 TCACCATAGT
*
303258 CCATCACCATTATCA-CACCTAT-AATCA-CCATA
1 CCATCACCA-TATCATCACCAATAAATCATCC-TA
*
303290 TTCCATCACCATATCA-CGCCAATAACATCATCCTA
1 --CCATCACCATATCATCACCAATAA-ATCATCCTA
* * *
303325 CCATTACCATTTCATCACCATTAAATCATCCT
1 CCATCACCATATCATCACCAATAAATCATCCT
303357 TCATTCATCA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
33 30 0.55
34 17 0.31
35 6 0.11
36 2 0.04
ACGTcount: A:0.34, C:0.36, G:0.01, T:0.28
Consensus pattern (33 bp):
CCATCACCATATCATCACCAATAAATCATCCTA
Found at i:303709 original size:30 final size:31
Alignment explanation
Indices: 303668--303726 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
303658 ACATGCTGCC
*
303668 ATGATATCT-AAATGATATGCAAACATAATAA
1 ATGATATCTAAAACG-TATGCAAACATAATAA
*
303699 ATGA-ATCTAAAACGTATGTAAACATAAT
1 ATGATATCTAAAACGTATGCAAACATAAT
303727 TTAAAGCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (31 bp):
ATGATATCTAAAACGTATGCAAACATAATAA
Found at i:304117 original size:25 final size:24
Alignment explanation
Indices: 304076--304123 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
304066 TTGAACGTTT
304076 ATGTCCTTTATCATTCCAAAAATC
1 ATGTCCTTTATCATTCCAAAAATC
* * *
304100 ATGTCCCTTTGTCCTTCCATAAAT
1 ATGT-CCTTTATCATTCCAAAAAT
304124 GTATGCGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.40
Consensus pattern (24 bp):
ATGTCCTTTATCATTCCAAAAATC
Found at i:306513 original size:14 final size:13
Alignment explanation
Indices: 306496--306535 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
306486 TGAAATTCTA
306496 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
306509 CTTC-TTTT-TTTT
1 -TTCTTTTTCTTTT
306521 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
306534 TT
1 TT
306536 TTGTCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.12
12 8 0.33
13 10 0.42
14 3 0.12
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTCTTTTTCTTTT
Found at i:306513 original size:19 final size:19
Alignment explanation
Indices: 306491--306527 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
306481 CTTTTTGAAA
306491 TTCTATTCTTTTTCTTTTC
1 TTCTATTCTTTTTCTTTTC
* *
306510 TTCTTTTTTTTTTCTTTT
1 TTCTATTCTTTTTCTTTT
306528 TCTTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (19 bp):
TTCTATTCTTTTTCTTTTC
Found at i:306524 original size:25 final size:25
Alignment explanation
Indices: 306496--306554 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 25
306486 TGAAATTCTA
306496 TTCTTTTTCTTTTCTTCTT-T-TTTTT
1 TTCTTTTTCTTTT-TT-TTGTCTTTTT
306521 TTCTTTTTCTTTTTTTTGTCTTTTT
1 TTCTTTTTCTTTTTTTTGTCTTTTT
306546 TGTCTTTTT
1 T-TCTTTTT
306555 TTTACTCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 2 0.06
24 3 0.10
25 19 0.61
26 7 0.23
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (25 bp):
TTCTTTTTCTTTTTTTTGTCTTTTT
Found at i:306528 original size:20 final size:18
Alignment explanation
Indices: 306499--306557 Score: 75
Period size: 17 Copynumber: 3.2 Consensus size: 18
306489 AATTCTATTC
306499 TTTTTCTTTTCTTCTTTTT
1 TTTTTCTTTT-TTCTTTTT
306518 TTTTTC-TTTTTCTTTTT
1 TTTTTCTTTTTTCTTTTT
*
306535 TTTGTCTTTTTTGTCTTTTT
1 TTTTTC-TTTTT-TCTTTTT
306555 TTT
1 TTT
306558 ACTCCAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
17 13 0.36
18 3 0.08
19 10 0.28
20 10 0.28
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (18 bp):
TTTTTCTTTTTTCTTTTT
Found at i:306536 original size:14 final size:14
Alignment explanation
Indices: 306496--306536 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
306486 TGAAATTCTA
*
306496 TTCTTTTTCTTTTC
1 TTCTTTTTCTTTTT
306510 TTC--TTT-TTTTT
1 TTCTTTTTCTTTTT
306521 TTCTTTTTCTTTTT
1 TTCTTTTTCTTTTT
306535 TT
1 TT
306537 TGTCTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 7 0.30
12 3 0.13
13 3 0.13
14 10 0.43
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTCTTTTTCTTTTT
Found at i:306545 original size:11 final size:10
Alignment explanation
Indices: 306496--306557 Score: 65
Period size: 10 Copynumber: 6.1 Consensus size: 10
306486 TGAAATTCTA
306496 TTCTTTTTCTT
1 TTCTTTTT-TT
306507 TTCTTCTTTTT
1 TTCTT-TTTTT
*
306518 TT-TTTCTTT
1 TTCTTTTTTT
306527 TTCTTTTTTT
1 TTCTTTTTTT
306537 TGTC-TTTTTT
1 T-TCTTTTTTT
*
306547 GTCTTTTTTT
1 TTCTTTTTTT
306557 T
1 T
306558 ACTCCAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
9 8 0.19
10 21 0.49
11 11 0.26
12 3 0.07
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:307805 original size:26 final size:26
Alignment explanation
Indices: 307766--307830 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
307756 CCCTAGAACA
*
307766 CCCATGTGCTTTGCATATGATCAGCC
1 CCCATGTGCCTTGCATATGATCAGCC
307792 CCCATGTGCCTTGCATATGATCAGCC
1 CCCATGTGCCTTGCATATGATCAGCC
307818 CCCATGTGCCTTG
1 CCCATGTGCCTTG
307831 TATGTGGTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.17, C:0.34, G:0.20, T:0.29
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGATCAGCC
Found at i:309909 original size:34 final size:33
Alignment explanation
Indices: 309840--309909 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
309830 CATCACCATA
* *
309840 TTCCATCACCATATCACGCCAATAACATCATCC
1 TTCCATCACCATATCACACCAATAAAATCATCC
* * *
309873 TTCCATTACCATTTCATCACCATTAAAATCATCC
1 TTCCATCACCATATCA-CACCAATAAAATCATCC
309907 TTC
1 TTC
309910 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
33 14 0.45
34 17 0.55
ACGTcount: A:0.31, C:0.36, G:0.01, T:0.31
Consensus pattern (33 bp):
TTCCATCACCATATCACACCAATAAAATCATCC
Found at i:314331 original size:33 final size:33
Alignment explanation
Indices: 314252--314355 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
314242 ATACAATCTG
* *
314252 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
314288 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
314321 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
314354 TC
1 TC
314356 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:316236 original size:90 final size:91
Alignment explanation
Indices: 316083--316262 Score: 247
Period size: 90 Copynumber: 2.0 Consensus size: 91
316073 GAAATGATGC
* * * *
316083 TTGGCCGAATAGGGAGAGAGCTCTTCATTTTGGTGCCTAAATAAACTACATGCAAGGCACAT-GG
1 TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACTACATACAAGGCACATGGG
*
316147 GGCTGTTCACATGCAAAACACATGGT
66 GGCTGGTCACATGCAAAACACATGGT
**
316173 TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCT-CATACAAGGCACATGG
1 TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAAT-AAACTACATACAAGGCACATGG
* **
316237 GGGCTGGTCATATGCAAGGCACATGG
65 GGGCTGGTCACATGCAAAACACATGG
316263 GTGTTCTAGG
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
90 52 0.67
91 26 0.33
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (91 bp):
TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACTACATACAAGGCACATGGG
GGCTGGTCACATGCAAAACACATGGT
Found at i:318685 original size:33 final size:33
Alignment explanation
Indices: 318643--318711 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
318633 GTTGATGATT
*
318643 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
318676 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
318709 GAA
1 GAA
318712 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:319132 original size:19 final size:20
Alignment explanation
Indices: 319085--319134 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
319075 GAAACCCCTT
**
319085 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
319105 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
319124 TGAAGATACAT
1 TGAAAATACAT
319135 TCTCTTGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:322659 original size:33 final size:33
Alignment explanation
Indices: 322617--322685 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
322607 GTTGATGATT
*
322617 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
322650 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
322683 GAA
1 GAA
322686 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:323106 original size:19 final size:20
Alignment explanation
Indices: 323059--323108 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
323049 GAAAACCCTT
**
323059 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
323079 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
323098 TGAAGATACAT
1 TGAAAATACAT
323109 TCTCTTGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:328688 original size:24 final size:21
Alignment explanation
Indices: 328654--328696 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
328644 TGCACAAGTT
*
328654 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
328676 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
328697 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:330370 original size:26 final size:26
Alignment explanation
Indices: 330331--330395 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
330321 CCCTAGAACA
* *
330331 CCCATGTGCTTTGCATATGATCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
330357 CCCATGTGCCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
*
330383 CCCATGAGCCTTG
1 CCCATGTGCCTTG
330396 TATGTGGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.18, C:0.35, G:0.20, T:0.26
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGCC
Found at i:332474 original size:2 final size:2
Alignment explanation
Indices: 332462--332494 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
332452 TCATAATAAC
*
332462 TA TA GA 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
332495 GAAAATAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:335226 original size:15 final size:16
Alignment explanation
Indices: 335183--335228 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
335173 TGTGAAATAA
*
335183 GAAATGGAAGAAGAATG
1 GAAATGG-AGAAGAAAG
*
335200 GAAAT-GATAAGAAAG
1 GAAATGGAGAAGAAAG
335215 GAAATGGA-AAGAAA
1 GAAATGGAGAAGAAA
335229 AGATAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 18 0.69
16 3 0.12
17 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (16 bp):
GAAATGGAGAAGAAAG
Found at i:335427 original size:14 final size:14
Alignment explanation
Indices: 335395--335435 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
335385 ATAGGCGTGA
* *
335395 ATGGTGATAGAGA-
1 ATGGTGATGGAAAG
335408 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
335422 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
335436 GTAGTATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:338865 original size:12 final size:13
Alignment explanation
Indices: 338848--338876 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
338838 TTATATATTG
338848 GAAAT-AAGAAAT
1 GAAATAAAGAAAT
338860 GAAATAAAGAAAT
1 GAAATAAAGAAAT
338873 GAAA
1 GAAA
338877 GGATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:341228 original size:12 final size:12
Alignment explanation
Indices: 341200--341235 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
341190 TTATATTTTT
341200 TTATCTTG-TTC
1 TTATCTTGTTTC
*
341211 TAATCTTGTTTC
1 TTATCTTGTTTC
341223 TTATCTTGTTTC
1 TTATCTTGTTTC
341235 T
1 T
341236 AGCACTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:350160 original size:28 final size:27
Alignment explanation
Indices: 350129--350186 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
350119 GAAAATCAGA
* *
350129 AAAGAAATTAAAGCACTCCAAAAGAAAG
1 AAAGAAAATAAAGCACTCAAAAAG-AAG
**
350157 AAAGAAAATCCAGCACTCAAAAAGAAG
1 AAAGAAAATAAAGCACTCAAAAAGAAG
350184 AAA
1 AAA
350187 AACAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.62, C:0.16, G:0.14, T:0.09
Consensus pattern (27 bp):
AAAGAAAATAAAGCACTCAAAAAGAAG
Found at i:351372 original size:20 final size:21
Alignment explanation
Indices: 351335--351373 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
351325 GATGGTCTTG
*
351335 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
351356 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
351374 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:351750 original size:20 final size:21
Alignment explanation
Indices: 351710--351762 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
351700 GAAAACCCCT
351710 TTGAAAATACATGACTTTTAA
1 TTGAAAATACATGACTTTTAA
*
351731 TTGACAATACATGA-TTTTAA
1 TTGAAAATACATGACTTTTAA
*
351751 -TGAAGATACATG
1 TTGAAAATACATG
351763 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.34
20 6 0.21
21 13 0.45
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (21 bp):
TTGAAAATACATGACTTTTAA
Found at i:351761 original size:19 final size:20
Alignment explanation
Indices: 351714--351762 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
351704 ACCCCTTTGA
351714 AAATACATGACTTTTAATTG
1 AAATACATGACTTTTAATTG
351734 ACAATACATGA-TTTTAA-TG
1 A-AATACATGACTTTTAATTG
351753 AAGATACATG
1 AA-ATACATG
351763 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.04
19 10 0.37
20 7 0.26
21 9 0.33
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (20 bp):
AAATACATGACTTTTAATTG
Found at i:355489 original size:20 final size:21
Alignment explanation
Indices: 355452--355490 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
355442 GATGGTCTTG
*
355452 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
355473 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
355491 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:355865 original size:19 final size:21
Alignment explanation
Indices: 355822--355873 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
355812 GAAACCCCTT
*
355822 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTGTTAAA
355843 TGAAAATACATGA-TGTT-AA
1 TGAAAATACATGACTGTTAAA
*
355862 TGAAGATACATG
1 TGAAAATACATG
355874 CTCTTGGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (21 bp):
TGAAAATACATGACTGTTAAA
Found at i:360415 original size:28 final size:28
Alignment explanation
Indices: 360353--360415 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
360343 AAAGAAAATC
* * *
360353 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAAATCAAGCACTCAAAAAGA
*
360381 A-AGAAAGAAAATCCAGCACTCAAAAAGA
1 AGA-AAAGAAAATCAAGCACTCAAAAAGA
360409 AGAAAAG
1 AGAAAAG
360416 CAAAGAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 27 0.93
29 1 0.03
ACGTcount: A:0.60, C:0.14, G:0.17, T:0.08
Consensus pattern (28 bp):
AGAAAAGAAAATCAAGCACTCAAAAAGA
Found at i:362559 original size:96 final size:96
Alignment explanation
Indices: 362457--362634 Score: 356
Period size: 96 Copynumber: 1.9 Consensus size: 96
362447 GTAAGGCTGG
362457 GTCTTTGCTCTTTATAGCACTGGTTCTTCCTTGGTTATTCTAAGATACTATCCATTCCTTATTTA
1 GTCTTTGCTCTTTATAGCACTGGTTCTTCCTTGGTTATTCTAAGATACTATCCATTCCTTATTTA
362522 CCATCCCTTATTGGAGCAATATAAAGTCTGA
66 CCATCCCTTATTGGAGCAATATAAAGTCTGA
362553 GTCTTTGCTCTTTATAGCACTGGTTCTTCCTTGGTTATTCTAAGATACTATCCATTCCTTATTTA
1 GTCTTTGCTCTTTATAGCACTGGTTCTTCCTTGGTTATTCTAAGATACTATCCATTCCTTATTTA
362618 CCATCCCTTATTGGAGC
66 CCATCCCTTATTGGAGC
362635 TCATTATGAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 82 1.00
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (96 bp):
GTCTTTGCTCTTTATAGCACTGGTTCTTCCTTGGTTATTCTAAGATACTATCCATTCCTTATTTA
CCATCCCTTATTGGAGCAATATAAAGTCTGA
Found at i:362893 original size:362 final size:359
Alignment explanation
Indices: 362268--362941 Score: 1249
Period size: 362 Copynumber: 1.9 Consensus size: 359
362258 TGCATTATAA
362268 TGGAGCTCATCATGATGAATTAAGTGAGATTATTCTCTTGTTTAAGTCCTTGTGACTTTATCGAC
1 TGGAGCTCATCATGATGAATTAAGTGAGATTATTCTCTTGTTTAAGTCCTTGTGACTTTATCGAC
*
362333 CAAACAAGTAACTTGTTACTTGTGGCGTCAATTCCTTTCATTATGATAATTTTGGTTCCTATCTC
66 CAAACAAGTAACTTGTTACTTGTGGCGTCAATTCCTTTCATTATGATAATTCTGGTTCCTATCTC
*
362398 TATATAGATAGTGGGTCAAATTCCTTGTTACCACCCCTTAGAATGATTTGTAAGGCTGGGTCTTT
131 TATATAGATAGTGGGTCAAATTCCTTGTTACCACCCCTTAGAACGATTTGTAAGGCTGGGTCTTT
362463 GCTCTTTATAGCACTGGTTCTTCCTTGGTTATTCTAAGATACTATCCATTCCTTATTTACCATCC
196 GCTCTTTATAGCACTGGTTCTTCCTTGGTTATTCTAAGATACTATCCATTCCTTATTTACCATCC
362528 CTTATTGGAGCAATATAAAGTCTGAGTCTTTGCTCTTTATAGCACTGGTTCTTCCTTGGTTATTC
261 CTTATTGGAGCAATATAAAGTCTGAGTCTTTGCTCTTTA-A-CACTGGTTCTTCCTTGGTTATTC
362593 TAAGATACTATCCATTCCTTATTTACCATCCCTTAT
324 TAAGATACTATCCATTCCTTATTTACCATCCCTTAT
*
362629 TGGAGCTCATTATGATGAATTAAGTGAGATTATTCTCTTGTTTAAGTCCTTGTGACTTTTATCGA
1 TGGAGCTCATCATGATGAATTAAGTGAGATTATTCTCTTGTTTAAGTCCTTGTGAC-TTTATCGA
*
362694 CCAAACAAGTAACTTGTTACTTGTGGTGTCAATTCCTTTCATTATGATAATTCTGGTTCCTATCT
65 CCAAACAAGTAACTTGTTACTTGTGGCGTCAATTCCTTTCATTATGATAATTCTGGTTCCTATCT
362759 CTATATAGATAGTGGGTCAAATTCCTTGTTACCACCCCTTAGAACGATTTGTAAGGCTGGGTCTT
130 CTATATAGATAGTGGGTCAAATTCCTTGTTACCACCCCTTAGAACGATTTGTAAGGCTGGGTCTT
*
362824 TGCTCTTTATAGCACTGGTTCTTCCTTGGTTATTCTAAGATACTATCCATTCCTTATTTATCATC
195 TGCTCTTTATAGCACTGGTTCTTCCTTGGTTATTCTAAGATACTATCCATTCCTTATTTACCATC
* * *
362889 CCTTATTGGAGCAATATAAAGTCTGGGTCTTTGTTCTTTAACATTGGTTCTTC
260 CCTTATTGGAGCAATATAAAGTCTGAGTCTTTGCTCTTTAACACTGGTTCTTC
362942 TTTGAGTCTT
Statistics
Matches: 304, Mismatches: 8, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
360 11 0.04
361 56 0.18
362 237 0.78
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.41
Consensus pattern (359 bp):
TGGAGCTCATCATGATGAATTAAGTGAGATTATTCTCTTGTTTAAGTCCTTGTGACTTTATCGAC
CAAACAAGTAACTTGTTACTTGTGGCGTCAATTCCTTTCATTATGATAATTCTGGTTCCTATCTC
TATATAGATAGTGGGTCAAATTCCTTGTTACCACCCCTTAGAACGATTTGTAAGGCTGGGTCTTT
GCTCTTTATAGCACTGGTTCTTCCTTGGTTATTCTAAGATACTATCCATTCCTTATTTACCATCC
CTTATTGGAGCAATATAAAGTCTGAGTCTTTGCTCTTTAACACTGGTTCTTCCTTGGTTATTCTA
AGATACTATCCATTCCTTATTTACCATCCCTTAT
Found at i:366462 original size:14 final size:13
Alignment explanation
Indices: 366443--366483 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
366433 AGATACTATA
366443 TTTCCATCACCAT
1 TTTCCATCACCAT
366456 CTTTCCATCACCAT
1 -TTTCCATCACCAT
* *
366470 TCTCTATCACCAT
1 TTTCCATCACCAT
366483 T
1 T
366484 CACGCCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.22, C:0.39, G:0.00, T:0.39
Consensus pattern (13 bp):
TTTCCATCACCAT
Found at i:366480 original size:13 final size:13
Alignment explanation
Indices: 366445--366484 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
366435 ATACTATATT
*
366445 TCCATCACCATCTT
1 TCCATCACCAT-TC
366459 TCCATCACCATTC
1 TCCATCACCATTC
*
366472 TCTATCACCATTC
1 TCCATCACCATTC
366485 ACGCCTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (13 bp):
TCCATCACCATTC
Found at i:374590 original size:13 final size:12
Alignment explanation
Indices: 374562--374596 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
374552 TACATACTAA
374562 ATACC-TTTCAC
1 ATACCTTTTCAC
374573 ATACCTTTTCACC
1 ATACCTTTTCA-C
374586 ATACCTTTTCA
1 ATACCTTTTCA
374597 TCTTTGGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 5 0.23
12 5 0.23
13 12 0.55
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (12 bp):
ATACCTTTTCAC
Found at i:379901 original size:30 final size:30
Alignment explanation
Indices: 379867--379947 Score: 153
Period size: 30 Copynumber: 2.7 Consensus size: 30
379857 GTCCAAAGCT
379867 CTCCTCCAGCTAAGTTCAGCTACATGCTAG
1 CTCCTCCAGCTAAGTTCAGCTACATGCTAG
379897 CTCCTCCAGCTAAGTTCAGCTACATGCTAG
1 CTCCTCCAGCTAAGTTCAGCTACATGCTAG
*
379927 CTCCTCCAGCTAAGTTGAGCT
1 CTCCTCCAGCTAAGTTCAGCT
379948 TTCCTTAGTG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.27
Consensus pattern (30 bp):
CTCCTCCAGCTAAGTTCAGCTACATGCTAG
Found at i:385880 original size:91 final size:91
Alignment explanation
Indices: 385725--385907 Score: 303
Period size: 91 Copynumber: 2.0 Consensus size: 91
385715 GGTAGTTGAT
385725 GCTTGGCTGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATGAACCAAATGCAAGGCACATG
1 GCTTGGCTGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATGAACCAAATGCAAGGCACATG
385790 GGGGCTGATCACATGCAAAACACATG
66 GGGGCTGATCACATGCAAAACACATG
* * *
385816 GCTTGGCTGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATG
1 GCTTGGCTGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATGAACCAAATGCAAGGCACATG
* * **
385881 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGATCACATGCAAAACACATG
385907 G
1 G
385908 GTGTTCTAGG
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (91 bp):
GCTTGGCTGAATAGGGAGAGAACTCTTCATATTGGCGCCTAAATGAACCAAATGCAAGGCACATG
GGGGCTGATCACATGCAAAACACATG
Found at i:395107 original size:23 final size:23
Alignment explanation
Indices: 395064--395109 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
395054 TATTTTATTC
*
395064 TTGCTTTGATTTTGTCTTTTCTT
1 TTGCTTTGATTTTGTCGTTTCTT
*
395087 TTGCTTT-CTTTTGTACGTTTCTT
1 TTGCTTTGATTTTGT-CGTTTCTT
395110 CAATGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.04, C:0.15, G:0.13, T:0.67
Consensus pattern (23 bp):
TTGCTTTGATTTTGTCGTTTCTT
Found at i:395953 original size:33 final size:33
Alignment explanation
Indices: 395911--395979 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
395901 GTTGATGAAT
*
395911 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
395944 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
395977 GAA
1 GAA
395980 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:395984 original size:13 final size:12
Alignment explanation
Indices: 395965--396029 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
395955 TTATTGGCGT
395965 GATATGGTGATG
1 GATATGGTGATG
395977 GAATATGGTGAT-
1 G-ATATGGTGATG
*
395989 GATATAGGCG-T-
1 GATAT-GGTGATG
396000 GATAATGGTGATG
1 GAT-ATGGTGATG
396013 GACTATGGTGAT-
1 GA-TATGGTGATG
396025 GATAT
1 GATAT
396030 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:396020 original size:36 final size:36
Alignment explanation
Indices: 395950--396058 Score: 166
Period size: 36 Copynumber: 3.1 Consensus size: 36
395940 AATGGAAGGA
* *
395950 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
395985 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
396021 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
396057 TG
1 TG
396059 GTGAAAATAG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 16 0.24
36 52 0.76
ACGTcount: A:0.27, C:0.04, G:0.37, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:396449 original size:19 final size:20
Alignment explanation
Indices: 396402--396452 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
396392 GAAATCCCTT
**
396402 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
396422 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
396441 TGAAGATACATG
1 TGAAAATACATG
396453 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:398015 original size:18 final size:19
Alignment explanation
Indices: 397977--398015 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
397967 TAATTCCTAA
397977 AAAATAATAAATCTGATCCT
1 AAAATAATAAATC-GATCCT
*
397997 AAAATAATTAATC-ATCCT
1 AAAATAATAAATCGATCCT
398015 A
1 A
398016 TATTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAATAATAAATCGATCCT
Found at i:401809 original size:14 final size:15
Alignment explanation
Indices: 401773--401810 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
401763 TTTTGGCTCT
401773 TTTTTTGTTTTTTGCC
1 TTTTTT-TTTTTTGCC
401789 TTTTTTTTTTTTGCC
1 TTTTTTTTTTTTGCC
401804 TTTTTTT
1 TTTTTTT
401811 GTTTGTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTTGCC
Found at i:401815 original size:14 final size:14
Alignment explanation
Indices: 401783--401823 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
401773 TTTTTTGTTT
*
401783 TTTGCCTTTTTTTTT
1 TTTGCC-TTTTTTTG
401798 TTTGCCTTTTTTTG
1 TTTGCCTTTTTTTG
401812 TTTG--TTTTTTTG
1 TTTGCCTTTTTTTG
401824 AAAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 8 0.32
14 11 0.44
15 6 0.24
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.78
Consensus pattern (14 bp):
TTTGCCTTTTTTTG
Found at i:402637 original size:43 final size:50
Alignment explanation
Indices: 402576--402683 Score: 126
Period size: 51 Copynumber: 2.3 Consensus size: 50
402566 ATAATTAAAG
402576 AATAAAAT-AT-AATAAACT-AAACA-TGTTTT-AA-C-CC-TAATTCCT
1 AATAAAATAATAAATAAACTAAAACATTGTTTTAAACCACCTTAATTCCT
*
402618 AATAAAATAATAAAT-AACTAAAATATTGTTTTAAACCCAACCTTAATTCCT
1 AATAAAATAATAAATAAACTAAAACATTGTTTTAAA-CC-ACCTTAATTCCT
402669 AATAAAATAATAAAT
1 AATAAAATAATAAAT
402684 CTGATCCTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
42 8 0.15
43 6 0.11
44 7 0.13
45 6 0.11
46 2 0.04
48 1 0.02
50 2 0.04
51 23 0.42
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (50 bp):
AATAAAATAATAAATAAACTAAAACATTGTTTTAAACCACCTTAATTCCT
Found at i:402691 original size:23 final size:21
Alignment explanation
Indices: 402665--402718 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
402655 CAACCTTAAT
402665 TCCTAATAAAATAATAAATCTGA
1 TCCTAATAAAATAATAAATC--A
* *
402688 TCCTAA-AAGATAATTAATCA
1 TCCTAATAAAATAATAAATCA
402708 TCCTATATAAA
1 TCCTA-ATAAA
402719 TTATATTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 6 0.23
21 1 0.04
22 13 0.50
23 6 0.23
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.31
Consensus pattern (21 bp):
TCCTAATAAAATAATAAATCA
Found at i:405738 original size:13 final size:12
Alignment explanation
Indices: 405719--405783 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
405709 TGATTGGCGT
405719 GATATGGTGATG
1 GATATGGTGATG
405731 GAATATGGTGAT-
1 G-ATATGGTGATG
*
405743 GATATAGGCG-T-
1 GATAT-GGTGATG
405754 GATAATGGTGATG
1 GAT-ATGGTGATG
405767 GACTATGGTGAT-
1 GA-TATGGTGATG
405779 GATAT
1 GATAT
405784 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:405744 original size:36 final size:36
Alignment explanation
Indices: 405704--405821 Score: 166
Period size: 36 Copynumber: 3.3 Consensus size: 36
405694 GTAATGGAAG
*
405704 GATGATGATTGGCGTGAT-ATGGTGATGGAATATGGT
1 GATGAT-ATAGGCGTGATAATGGTGATGGAATATGGT
*
405740 GATGATATAGGCGTGATAATGGTGATGGACTATGGT
1 GATGATATAGGCGTGATAATGGTGATGGAATATGGT
* *
405776 GATGATATAGGCGTGATAATGGAGATGGATTATGGT
1 GATGATATAGGCGTGATAATGGTGATGGAATATGGT
* *
405812 GGTGAAATAG
1 GATGATATAG
405822 TATCTTATAA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
35 10 0.13
36 65 0.87
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
GATGATATAGGCGTGATAATGGTGATGGAATATGGT
Found at i:406201 original size:19 final size:20
Alignment explanation
Indices: 406154--406204 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
406144 GAAATCCCTT
**
406154 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
406174 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
406193 TGAAGATACATG
1 TGAAAATACATG
406205 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:411064 original size:19 final size:21
Alignment explanation
Indices: 411021--411072 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
411011 GAAACCCCTT
411021 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
411042 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
411061 TGAAGATACATG
1 TGAAAATACATG
411073 CTCTTGGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:416081 original size:23 final size:24
Alignment explanation
Indices: 416055--416106 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
416045 AATCAGCAAG
*
416055 GAAAATAAAAGCAC-TCAAAAGAA
1 GAAAATAAAAGCACTTAAAAAGAA
* * *
416078 GAAATTGAAAGCACTTAAAAAGCA
1 GAAAATAAAAGCACTTAAAAAGAA
416102 GAAAA
1 GAAAA
416107 AAGAAAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.62, C:0.12, G:0.15, T:0.12
Consensus pattern (24 bp):
GAAAATAAAAGCACTTAAAAAGAA
Found at i:417358 original size:24 final size:21
Alignment explanation
Indices: 417324--417366 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
417314 TGCACAAGAT
*
417324 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
417346 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
417367 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:424184 original size:27 final size:27
Alignment explanation
Indices: 424154--424206 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
424144 ATGATTAATA
* *
424154 AAGGAATATTAATGAAAT-GATAAAGAT
1 AAGGAATA-AAATGAAATAAATAAAGAT
424181 AAGGAATAAAATGAAATAAATAAAGA
1 AAGGAATAAAATGAAATAAATAAAGA
424207 ATATAGATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (27 bp):
AAGGAATAAAATGAAATAAATAAAGAT
Found at i:428255 original size:21 final size:21
Alignment explanation
Indices: 428216--428255 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
428206 AAGAAAGATT
*
428216 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
428237 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
428256 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:428313 original size:22 final size:21
Alignment explanation
Indices: 428278--428318 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
428268 GTTACGGAAT
428278 TGATGGTCTCGATGGATGAAGA
1 TGATGGTCTCGAT-GATGAAGA
* *
428300 TGATGGTGTTGATGATGAA
1 TGATGGTCTCGATGATGAA
428319 ATGGAGATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.27, C:0.05, G:0.37, T:0.32
Consensus pattern (21 bp):
TGATGGTCTCGATGATGAAGA
Found at i:432531 original size:26 final size:26
Alignment explanation
Indices: 432502--432559 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
432492 CCCATGTTCT
432502 TTGCATATGATCAGCCCCAATGTGCC
1 TTGCATATGATCAGCCCCAATGTGCC
*
432528 TTGCATATGATCAGCCCCTATGTGCC
1 TTGCATATGATCAGCCCCAATGTGCC
432554 TTGCAT
1 TTGCAT
432560 GTGGTTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (26 bp):
TTGCATATGATCAGCCCCAATGTGCC
Found at i:433427 original size:5 final size:5
Alignment explanation
Indices: 433417--433441 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
433407 ACTCAAAAAG
433417 AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA
433442 TGAAGTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:434769 original size:24 final size:25
Alignment explanation
Indices: 434723--434777 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
434713 ACAGTTATGC
*
434723 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
434747 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
434772 CA-TTGA
1 CACTTGA
434778 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:438764 original size:12 final size:12
Alignment explanation
Indices: 438749--438778 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
438739 TTCTTTATCT
438749 TTTTTAATCTTA
1 TTTTTAATCTTA
438761 TTTTTAATCTTA
1 TTTTTAATCTTA
438773 TTTTTA
1 TTTTTA
438779 GCACTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTAATCTTA
Found at i:443430 original size:12 final size:12
Alignment explanation
Indices: 443415--443444 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
443405 TTCTTTATCT
443415 TTTTTAATCTTA
1 TTTTTAATCTTA
443427 TTTTTAATCTTA
1 TTTTTAATCTTA
443439 TTTTTA
1 TTTTTA
443445 GCACTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTAATCTTA
Found at i:443755 original size:23 final size:22
Alignment explanation
Indices: 443725--443769 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
443715 TGGTACTGAG
443725 AATAAGAT-AAGAAATAAGATTAA
1 AATAAGATAAAG-AA-AAGATTAA
443748 AATAAGATAAAGAAAAGATTAA
1 AATAAGATAAAGAAAAGATTAA
443770 GGAATTGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
23 10 0.48
24 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (22 bp):
AATAAGATAAAGAAAAGATTAA
Found at i:447084 original size:16 final size:16
Alignment explanation
Indices: 447063--447095 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
447053 TAGTTAGCTC
447063 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
447079 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
447095 A
1 A
447096 GGTGGCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:451257 original size:4 final size:5
Alignment explanation
Indices: 451229--451254 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
451219 ACTCAAAAAG
451229 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
451255 GAAGTTGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:452579 original size:24 final size:25
Alignment explanation
Indices: 452533--452587 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
452523 ACAGTTATGC
*
452533 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
452557 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
452582 CA-TTGA
1 CACTTGA
452588 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:457707 original size:18 final size:19
Alignment explanation
Indices: 457683--457725 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
457673 GCTACAACAA
*
457683 AAAAAAAGCAATAAG-AAAG
1 AAAAAAA-CAAAAAGAAAAG
457702 AAAAAAACAAAAAGAAAAG
1 AAAAAAACAAAAAGAAAAG
457721 AAAAA
1 AAAAA
457726 GACTCCTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (19 bp):
AAAAAAACAAAAAGAAAAG
Found at i:457953 original size:16 final size:15
Alignment explanation
Indices: 457913--457964 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
457903 GTAAGTTATC
457913 TTCATTTTTTTATCAT
1 TTCA-TTTTTTATCAT
457929 TTCATTTTTTATTC-T
1 TTCATTTTTTA-TCAT
* * *
457944 TTCATCTTTTCTTAT
1 TTCATTTTTTATCAT
457959 TTCATT
1 TTCATT
457965 ACCATATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 1 0.03
15 23 0.77
16 6 0.20
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (15 bp):
TTCATTTTTTATCAT
Found at i:464018 original size:7 final size:6
Alignment explanation
Indices: 463999--464042 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
463989 CAAAAGCAAC
*
463999 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG AGAAAA- AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG A-AAAAG AAAAAG A
464043 CTCCTACAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.12
6 19 0.58
7 10 0.30
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:464024 original size:25 final size:24
Alignment explanation
Indices: 463996--464042 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
463986 CAACAAAAGC
463996 AACAAAAAGA-AAAAGAAAGAAGAAA
1 AACAAAAAGAGAAAA-AAA-AAGAAA
464021 AACAAAAAGAGAAAAAAAAAGA
1 AACAAAAAGAGAAAAAAAAAGA
464043 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.19
25 13 0.62
26 4 0.19
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (24 bp):
AACAAAAAGAGAAAAAAAAAGAAA
Found at i:464030 original size:12 final size:12
Alignment explanation
Indices: 463996--464042 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
463986 CAACAAAAGC
463996 AACAAAAAGAAA
1 AACAAAAAGAAA
*
464008 AAGAAAGAAGAAA
1 AACAAA-AAGAAA
464021 AACAAAAAGAGAA
1 AACAAAAAGA-AA
464034 AA-AAAAAGA
1 AACAAAAAGA
464043 CTCCTACAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 16 0.52
13 15 0.48
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (12 bp):
AACAAAAAGAAA
Found at i:464040 original size:19 final size:19
Alignment explanation
Indices: 463999--464039 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
463989 CAAAAGCAAC
* *
463999 AAAAAGAAAAAGAAAGAAG
1 AAAAACAAAAAGAAAGAAA
464018 AAAAACAAAAAG--AGAAA
1 AAAAACAAAAAGAAAGAAA
464035 AAAAA
1 AAAAA
464040 AGACTCCTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAAGAAAGAAA
Found at i:468257 original size:17 final size:16
Alignment explanation
Indices: 468230--468272 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
468220 AATTCAAAAC
*
468230 AAAAG-AGAAAAGCATA
1 AAAAGAAGAAAAGC-CA
468246 AAAAGAAGAAAAGCCA
1 AAAAGAAGAAAAGCCA
468262 AAAAGAA-AAAA
1 AAAAGAAGAAAA
468273 ATTTCCAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 4 0.16
16 13 0.52
17 8 0.32
ACGTcount: A:0.74, C:0.07, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAAAAGCCA
Found at i:470098 original size:36 final size:36
Alignment explanation
Indices: 470058--470162 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
470048 AACACCATCT
470058 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
* * **
470094 TCCATCACCATTATCACGCCTTTATCATCATTATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
*
470130 TCCATCTCCATTATCACGCCTATATTATCACCA
1 TCCATCTCCATTATCACGCCTATATCATCACCA
470163 ACTTATAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.28, C:0.34, G:0.05, T:0.33
Consensus pattern (36 bp):
TCCATCTCCATTATCACGCCTATATCATCACCATAG
Found at i:470582 original size:24 final size:24
Alignment explanation
Indices: 470542--470588 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
470532 AAAGTGCTAC
470542 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
470567 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
470589 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:474488 original size:36 final size:36
Alignment explanation
Indices: 474448--474552 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
474438 AACACCATCT
474448 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
* * **
474484 TCCATCACCATTATCACGCCTTTATCATCATTATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
*
474520 TCCATCTCCATTATCACGCCTATATTATCACCA
1 TCCATCTCCATTATCACGCCTATATCATCACCA
474553 ACTTATAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.28, C:0.34, G:0.05, T:0.33
Consensus pattern (36 bp):
TCCATCTCCATTATCACGCCTATATCATCACCATAG
Found at i:474972 original size:24 final size:24
Alignment explanation
Indices: 474932--474978 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
474922 AAAGTGCTAC
474932 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
474957 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
474979 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:478877 original size:36 final size:36
Alignment explanation
Indices: 478837--478941 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
478827 AACACCATCT
478837 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
* * *
478873 TCCATCACCATTATCACGCCTTTATCATCACTATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
*
478909 TCCATCTCCATTATCACGCCTATATTATCACCA
1 TCCATCTCCATTATCACGCCTATATCATCACCA
478942 ACTTATAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.28, C:0.35, G:0.05, T:0.32
Consensus pattern (36 bp):
TCCATCTCCATTATCACGCCTATATCATCACCATAG
Found at i:495926 original size:17 final size:17
Alignment explanation
Indices: 495904--495944 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
495894 TTCATTTACA
495904 TTTTTTTGAATTTTTTG
1 TTTTTTTGAATTTTTTG
**
495921 TTTTTTTGCCTTTTTTG
1 TTTTTTTGAATTTTTTG
495938 TTTTTTT
1 TTTTTTT
495945 TAAAAAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.05, C:0.05, G:0.10, T:0.80
Consensus pattern (17 bp):
TTTTTTTGAATTTTTTG
Found at i:500699 original size:15 final size:16
Alignment explanation
Indices: 500671--500701 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
500661 CATTTCTATC
500671 CATTTCCTTTTCTTAT
1 CATTTCCTTTTCTTAT
500687 CATTTCC-TTTCTTAT
1 CATTTCCTTTTCTTAT
500702 TTCATATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTCCTTTTCTTAT
Found at i:501037 original size:16 final size:17
Alignment explanation
Indices: 501006--501043 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
500996 AAAACTAAGG
*
501006 AGAAAAGCATAAAAAGA
1 AGAAAAGCACAAAAAGA
501023 AGAAAAGC-CAAAAAGA
1 AGAAAAGCACAAAAAGA
501039 A-AAAA
1 AGAAAA
501044 ATTTCTAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 8 0.40
17 8 0.40
ACGTcount: A:0.74, C:0.08, G:0.16, T:0.03
Consensus pattern (17 bp):
AGAAAAGCACAAAAAGA
Found at i:505701 original size:11 final size:11
Alignment explanation
Indices: 505687--505711 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
505677 AATAAAAAAA
505687 GAAGTGCAAGT
1 GAAGTGCAAGT
505698 GAAGTGCAAGT
1 GAAGTGCAAGT
505709 GAA
1 GAA
505712 AGAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:516005 original size:11 final size:11
Alignment explanation
Indices: 515989--516016 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
515979 AATTCCTTCT
515989 TTTCTTTATCA
1 TTTCTTTATCA
516000 TTTCTTTATCA
1 TTTCTTTATCA
516011 TTTCTT
1 TTTCTT
516017 AGCCATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTCTTTATCA
Found at i:524268 original size:19 final size:20
Alignment explanation
Indices: 524244--524289 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
524234 CGGCCAAGAG
**
524244 CATGTATCTTCAT-TTAAAT
1 CATGTATCTTCATCAAAAAT
*
524263 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCATCAAAAAT
524283 CATGTAT
1 CATGTAT
524290 TTTAAATGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (20 bp):
CATGTATCTTCATCAAAAAT
Found at i:528149 original size:20 final size:19
Alignment explanation
Indices: 528103--528149 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
528093 ACATGCCCAT
*
528103 TAATAT-TTAAGCATCTTA
1 TAATATATTAAGCATATTA
528121 TAATCATATTAAGCATGATTA
1 TAAT-ATATTAAGCAT-ATTA
*
528142 TCATATAT
1 TAATATAT
528150 ACATCAAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.17
19 2 0.08
20 12 0.50
21 6 0.25
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (19 bp):
TAATATATTAAGCATATTA
Found at i:529642 original size:23 final size:25
Alignment explanation
Indices: 529607--529661 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
529597 AAATCTAGTA
*
529607 AAGAAAATCAAAGCACTC-AAAA-G
1 AAGAAAATCAAAGAACTCAAAAAGG
* *
529630 AAGAAATTGAAAGAACTCAAAAAGG
1 AAGAAAATCAAAGAACTCAAAAAGG
529655 AAGAAAA
1 AAGAAAA
529662 AGAAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 15 0.58
24 4 0.15
25 7 0.27
ACGTcount: A:0.64, C:0.11, G:0.16, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGAACTCAAAAAGG
Found at i:535969 original size:35 final size:36
Alignment explanation
Indices: 535898--535974 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
535888 ATAAGATACT
* *
535898 GCCTA-AACATCACCATCTTCCATTACTATTTTCAC
1 GCCTATAACATCACCATCTGCCATTACTATTTGCAC
535933 GCCTATAACATCACCATCTGCCATTACTA-TTGCAC
1 GCCTATAACATCACCATCTGCCATTACTATTTGCAC
535968 GCCTATA
1 GCCTATA
535975 TCCTAACCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 17 0.44
36 22 0.56
ACGTcount: A:0.29, C:0.34, G:0.06, T:0.31
Consensus pattern (36 bp):
GCCTATAACATCACCATCTGCCATTACTATTTGCAC
Found at i:535984 original size:35 final size:36
Alignment explanation
Indices: 535898--535986 Score: 110
Period size: 35 Copynumber: 2.5 Consensus size: 36
535888 ATAAGATACT
* * *
535898 GCCTA-AACATCACCATCTTCCATTACTATTTTCAC
1 GCCTATAACATAACCATCTGCCATTACTATTTGCAC
*
535933 GCCTATAACATCACCATCTGCCATTACTA-TTGCAC
1 GCCTATAACATAACCATCTGCCATTACTATTTGCAC
* *
535968 GCCTATATCCTAACCATCT
1 GCCTATAACATAACCATCT
535987 TTTTATCACC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 26 0.54
36 22 0.46
ACGTcount: A:0.28, C:0.35, G:0.06, T:0.31
Consensus pattern (36 bp):
GCCTATAACATAACCATCTGCCATTACTATTTGCAC
Found at i:536685 original size:17 final size:17
Alignment explanation
Indices: 536627--536686 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
536617 GAGTTGTAAG
*
536627 TTATCTTCACTTTC-TTA
1 TTAT-TTCATTTTCTTTA
*
536644 CTATTTCA-TTTCTTTA
1 TTATTTCATTTTCTTTA
* * *
536660 TTCTTTCATTTTTTTTC
1 TTATTTCATTTTCTTTA
536677 TTATTTCATT
1 TTATTTCATT
536687 ACCATATCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 4 0.11
16 13 0.37
17 18 0.51
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTCATTTTCTTTA
Found at i:542348 original size:19 final size:20
Alignment explanation
Indices: 542307--542357 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
542297 GAAACCCCTT
*
542307 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
542327 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
542346 TGAAGATACATG
1 TGAAAATACATG
542358 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:543896 original size:10 final size:10
Alignment explanation
Indices: 543881--543937 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
543871 ATTGGAGTGC
543881 AAAAAGAAAG
1 AAAAAGAAAG
*
543891 AAAAAG--AC
1 AAAAAGAAAG
543899 AAAAAGAGAAG
1 AAAAAGA-AAG
543910 AAAAA-AGAAG
1 AAAAAGA-AAG
543920 -AAAAGAAAAG
1 AAAAAG-AAAG
543930 AAAAAGAA
1 AAAAAGAA
543938 TTCAAAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
8 7 0.18
9 4 0.10
10 16 0.41
11 12 0.31
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:543910 original size:23 final size:24
Alignment explanation
Indices: 543884--543937 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
543874 GGAGTGCAAA
*
543884 AAGAAAGAAA-AAGACAAA-AAGAG
1 AAGAAAGAAAGAAGA-AAAGAAAAG
543907 AAGAAA-AAAGAAGAAAAGAAAAG
1 AAGAAAGAAAGAAGAAAAGAAAAG
543930 AA-AAAGAA
1 AAGAAAGAA
543938 TTCAAAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (24 bp):
AAGAAAGAAAGAAGAAAAGAAAAG
Found at i:543937 original size:19 final size:18
Alignment explanation
Indices: 543881--543937 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 18
543871 ATTGGAGTGC
543881 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
*
543898 CAAAAAGAGAAGAAAAAAGA
1 -AAAAAGAAAAG-AAAAAGA
543918 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
543937 A
1 A
543938 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 6 0.18
19 12 0.35
20 16 0.47
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:546354 original size:30 final size:31
Alignment explanation
Indices: 546302--546361 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
546292 CTTAGCTTTA
**
546302 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
546332 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
546362 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:547289 original size:19 final size:21
Alignment explanation
Indices: 547265--547316 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
547255 CGGCCAAGAG
*
547265 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
547284 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
547305 CATGTATTTTCA
1 CATGTATTTTCA
547317 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:548058 original size:14 final size:13
Alignment explanation
Indices: 548041--548090 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
548031 GTGCAAAAAG
548041 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
548055 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
548068 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
548079 AAAGAAAAAGAA
1 AAAGAAAAAGAA
548091 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:548087 original size:19 final size:18
Alignment explanation
Indices: 548035--548090 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
548025 ATTGGAGTGC
548035 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
548052 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
548071 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
548090 A
1 A
548091 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:548088 original size:11 final size:11
Alignment explanation
Indices: 548035--548090 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
548025 ATTGGAGTGC
548035 AAAAAG-AAAG
1 AAAAAGAAAAG
548045 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
548059 AAGAAGAAAAG
1 AAAAAGAAAAG
548070 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
548083 AAAAAGAA
1 AAAAAGAA
548091 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:551635 original size:19 final size:20
Alignment explanation
Indices: 551594--551644 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
551584 GAAACCCCTT
*
551594 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
551614 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
551633 TGAAGATACATG
1 TGAAAATACATG
551645 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:553072 original size:20 final size:21
Alignment explanation
Indices: 553035--553073 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
553025 GATGGTCTTG
*
553035 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
553056 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
553074 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:557252 original size:12 final size:13
Alignment explanation
Indices: 557235--557275 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
557225 AATTCTTTTC
557235 TTTCTTTT-TTCT
1 TTTCTTTTCTTCT
557247 TTTCTTCTTCTT-T
1 TTTCTT-TTCTTCT
557260 TTTCTTTTCTTCT
1 TTTCTTTTCTTCT
557273 TTT
1 TTT
557276 TGCACTCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 11 0.42
13 13 0.50
14 2 0.08
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTCTTTTCTTCT
Found at i:557259 original size:18 final size:18
Alignment explanation
Indices: 557227--557273 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
557217 TCTTTTTGAA
557227 TTCTTTTC-T-TTCTTTT
1 TTCTTTTCTTCTTCTTTT
557243 TTCTTTTCTTCTTCTTTT
1 TTCTTTTCTTCTTCTTTT
557261 TTCTTTTCTTCTT
1 TTCTTTTCTTCTT
557274 TTTGCACTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.28
17 1 0.03
18 20 0.69
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTCTTTTCTTCTTCTTTT
Found at i:561841 original size:16 final size:16
Alignment explanation
Indices: 561822--561873 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 16
561812 TCTTTTTGAA
561822 TTCTTTTTCTTTTCTT
1 TTCTTTTTCTTTTCTT
561838 TTC---TTCTTTTCTT
1 TTCTTTTTCTTTTCTT
*
561851 CTT-TTTGTCTTTTC-T
1 -TTCTTTTTCTTTTCTT
561866 TTCTTTTT
1 TTCTTTTT
561874 GCACTCCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 11
0.69 0.05 0.26
Matches are distributed among these distances:
13 10 0.34
14 4 0.14
15 5 0.17
16 10 0.34
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (16 bp):
TTCTTTTTCTTTTCTT
Found at i:561846 original size:8 final size:8
Alignment explanation
Indices: 561833--561872 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
561823 TCTTTTTCTT
561833 TTCTTTTC
1 TTCTTTTC
561841 TTCTTTTC
1 TTCTTTTC
561849 TTCTTTT-
1 TTCTTTTC
561856 TGTCTTTTC
1 T-TCTTTTC
561865 TTTCTTTT
1 -TTCTTTT
561873 TGCACTCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 1 0.03
8 21 0.72
9 6 0.21
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (8 bp):
TTCTTTTC
Found at i:566408 original size:36 final size:35
Alignment explanation
Indices: 566357--566432 Score: 118
Period size: 36 Copynumber: 2.2 Consensus size: 35
566347 TAAGATACTA
* *
566357 CCTA-AACATCACCATCTTCCATTACTATTTTCACG
1 CCTATAACATCACCATCTGCCATTACTA-TTGCACG
566392 CCTATAACATCACCATCTGCCATTACTATTGCACG
1 CCTATAACATCACCATCTGCCATTACTATTGCACG
566427 CCTATA
1 CCTATA
566433 TCCTAACCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 16 0.42
36 22 0.58
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTGCCATTACTATTGCACG
Done.