Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold63
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: 2211945
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 524 characters in sequence are not A, C, G, or T
File 11 of 16
Found at i:1577512 original size:30 final size:29
Alignment explanation
Indices: 1577459--1577553 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 29
1577449 ATTTATATTA
* *
1577459 AAGGATGTATTTAGGTAAAAATTTAAAGGTT
1 AAGGAT-TATTTGGGT-ACAATTTAAAGGTT
1577490 AGAGGATTATTTGGGTACAATTTAAAGGTT
1 A-AGGATTATTTGGGTACAATTTAAAGGTT
* * * *
1577520 AAGGGATAATTTGAGTACAAATTAAAGATT
1 AA-GGATTATTTGGGTACAATTTAAAGGTT
1577550 AAGG
1 AAGG
1577554 GCTTACTTGA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
29 3 0.05
30 39 0.70
31 9 0.16
32 5 0.09
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (29 bp):
AAGGATTATTTGGGTACAATTTAAAGGTT
Found at i:1577564 original size:30 final size:30
Alignment explanation
Indices: 1577504--1577565 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
1577494 GATTATTTGG
* * *
1577504 GTACAATTTAAAGGTTAAGGGATAATTTGA
1 GTACAAATTAAAGATTAAGGGATAACTTGA
* *
1577534 GTACAAATTAAAGATTAAGGGCTTACTTGA
1 GTACAAATTAAAGATTAAGGGATAACTTGA
1577564 GT
1 GT
1577566 GTAATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (30 bp):
GTACAAATTAAAGATTAAGGGATAACTTGA
Found at i:1577898 original size:19 final size:19
Alignment explanation
Indices: 1577870--1577923 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1577860 TAAGCCAAAG
*
1577870 ACTAATTAATATAAAATAAT
1 ACTAAATAATATAAAA-AAT
*
1577890 -CTAAATAATCTAAAAAAT
1 ACTAAATAATATAAAAAAT
*
1577908 ACTATATATATATAAA
1 ACTAAATA-ATATAAA
1577924 TACAATTAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 3 0.11
19 19 0.68
20 6 0.21
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
ACTAAATAATATAAAAAAT
Found at i:1583147 original size:16 final size:16
Alignment explanation
Indices: 1583126--1583157 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1583116 AAAAAAAAAG
1583126 ACAAGAAACAGAGACT
1 ACAAGAAACAGAGACT
*
1583142 ACAAGAAACGGAGACT
1 ACAAGAAACAGAGACT
1583158 TTTAAGGTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.19, G:0.22, T:0.06
Consensus pattern (16 bp):
ACAAGAAACAGAGACT
Found at i:1584351 original size:17 final size:19
Alignment explanation
Indices: 1584312--1584367 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
1584302 TAAAATAATA
*
1584312 AAAAATATGAATAATAAAT
1 AAAAATATGAATAATAAAC
*
1584331 AAAAATAT-AA-ATTAAAC
1 AAAAATATGAATAATAAAC
*
1584348 AAAAAATATTAAATAATAAA
1 -AAAAATA-TGAATAATAAA
1584368 AGATTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 5 0.17
18 9 0.30
19 9 0.30
20 2 0.07
21 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (19 bp):
AAAAATATGAATAATAAAC
Found at i:1584994 original size:18 final size:19
Alignment explanation
Indices: 1584971--1585011 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1584961 TTCACATTAT
*
1584971 AAATCAAATTATA-ATAAA
1 AAATCAAATAATATATAAA
*
1584989 AAATCAAATAATATATTAA
1 AAATCAAATAATATATAAA
1585008 AAAT
1 AAAT
1585012 TTTCTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATCAAATAATATATAAA
Found at i:1586029 original size:23 final size:23
Alignment explanation
Indices: 1586001--1586048 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1585991 AAAAATAAAC
1586001 ATACTCGTATTTAACACATCCGA
1 ATACTCGTATTTAACACATCCGA
1586024 ATACTCGTATTTAACACATCCGA
1 ATACTCGTATTTAACACATCCGA
1586047 AT
1 AT
1586049 CTGAGTGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.31
Consensus pattern (23 bp):
ATACTCGTATTTAACACATCCGA
Found at i:1590047 original size:3 final size:3
Alignment explanation
Indices: 1590039--1590076 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1590029 TTAAGATCAA
1590039 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1590077 CCCAATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1590689 original size:24 final size:23
Alignment explanation
Indices: 1590662--1590719 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 23
1590652 AATATTATTA
1590662 TTTAATATATTAATAATAAAAATT
1 TTTAATATATTAATAAT-AAAATT
* *
1590686 TTTAAATTTATAAATAATAAAATT
1 TTT-AATATATTAATAATAAAATT
*
1590710 ATT-ATATATT
1 TTTAATATATT
1590720 TTTAATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 5 0.18
24 11 0.39
25 12 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTAATATATTAATAATAAAATT
Found at i:1590797 original size:51 final size:52
Alignment explanation
Indices: 1590718--1590820 Score: 138
Period size: 51 Copynumber: 2.0 Consensus size: 52
1590708 TTATTATATA
1590718 TTTTTAATATATATTTAAAAAATAAAAATAATTAATTAAATATATAATAAAT
1 TTTTTAATATATATTTAAAAAATAAAAATAATTAATTAAATATATAATAAAT
* * * * *
1590770 TTTTTAAT-T-TATTTATAAAATTAAAAATATTTTATTAATTATATATTAAAT
1 TTTTTAATATATATTTA-AAAAATAAAAATAATTAATTAAATATATAATAAAT
1590821 AATAATTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
50 6 0.13
51 31 0.69
52 8 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (52 bp):
TTTTTAATATATATTTAAAAAATAAAAATAATTAATTAAATATATAATAAAT
Found at i:1591052 original size:3 final size:3
Alignment explanation
Indices: 1591044--1591109 Score: 87
Period size: 3 Copynumber: 22.0 Consensus size: 3
1591034 CCCTTTCCTC
* * * * *
1591044 CAT CAT CAT CAT CAC CAT CAC CAT CAC CAG CAT TAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1591092 CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT
1591110 AATTCAATCA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.29
Consensus pattern (3 bp):
CAT
Found at i:1591223 original size:21 final size:20
Alignment explanation
Indices: 1591168--1591226 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1591158 ACTAAATTTA
* *
1591168 AATAAAAATTTTAATTAATT
1 AATAAAAATTTTTATTTATT
** *
1591188 AATTTAAATTATTATTTATT
1 AATAAAAATTTTTATTTATT
1591208 AATAAAAAATTTTTATTTA
1 AAT-AAAAATTTTTATTTA
1591227 AATTTAATTA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAAAAATTTTTATTTATT
Found at i:1591649 original size:29 final size:30
Alignment explanation
Indices: 1591617--1591673 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
1591607 CTTGAATTAT
1591617 TATTTT-AATAATAAAA-AATATTTTAAATA
1 TATTTTAAATAATAAAATAAT-TTTTAAATA
1591646 TATTTTAAATAATAAAATAATTTTTAAA
1 TATTTTAAATAATAAAATAATTTTTAAA
1591674 CGAATAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 6 0.23
30 17 0.65
31 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TATTTTAAATAATAAAATAATTTTTAAATA
Found at i:1591821 original size:28 final size:29
Alignment explanation
Indices: 1591789--1591843 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
1591779 CTTAAATTAT
1591789 TATTTT-AATAATAAAA-ATATTTTTAATA
1 TATTTTAAATAATAAAATA-ATTTTTAATA
1591817 TATTTTAAATAATAAAATAATTTTTAA
1 TATTTTAAATAATAAAATAATTTTTAA
1591844 ACAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 6 0.24
29 18 0.72
30 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TATTTTAAATAATAAAATAATTTTTAATA
Found at i:1591877 original size:171 final size:172
Alignment explanation
Indices: 1591549--1591886 Score: 554
Period size: 171 Copynumber: 2.0 Consensus size: 172
1591539 TATCTACTCT
* * * *
1591549 AATAATTTTAATTCGAATCAAATTAGATATAAAATAATTTTTTGATAATCTAAATTAACTTGAAT
1 AATAATTTCAATTCGAATCAAATTAGATATAAAATAAATTTTTAATAATCTAAATTAACTTAAAT
*
1591614 TATTATTTTAATAATAAAAAATATTTTAAATATATTTTAAATAATAAAATAATTTTTAAACGAAT
66 TATTATTTTAATAATAAAAAATATTTTAAATATATTTTAAATAATAAAATAATTTTTAAACAAAT
** *
1591679 AAAACCTGAACAAATAAATTTTTTTATTTGGATTCATATTTC
131 AAAACCCAAACAAATAAATTATTTTATTTGGATTCATATTTC
*
1591721 AATAATTTCAACTT-GAATTAAATTAGATATAAAATAAATTTTTAATAATCTAAATTAACTTAAA
1 AATAATTTCAA-TTCGAATCAAATTAGATATAAAATAAATTTTTAATAATCTAAATTAACTTAAA
*
1591785 TTATTATTTTAATAAT-AAAAATATTTTTAATATATTTTAAATAATAAAATAATTTTTAAACAAA
65 TTATTATTTTAATAATAAAAAATATTTTAAATATATTTTAAATAATAAAATAATTTTTAAACAAA
*
1591849 TAAAACCCAAATAAATAAATTATTTTATTTGGATTCAT
130 TAAAACCCAAACAAATAAATTATTTTATTTGGATTCAT
1591887 CTCATCTATA
Statistics
Matches: 154, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
171 80 0.52
172 72 0.47
173 2 0.01
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (172 bp):
AATAATTTCAATTCGAATCAAATTAGATATAAAATAAATTTTTAATAATCTAAATTAACTTAAAT
TATTATTTTAATAATAAAAAATATTTTAAATATATTTTAAATAATAAAATAATTTTTAAACAAAT
AAAACCCAAACAAATAAATTATTTTATTTGGATTCATATTTC
Found at i:1592383 original size:28 final size:28
Alignment explanation
Indices: 1592352--1592419 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
1592342 TAATTTATTT
**
1592352 AAATTATTATTTAAAATATGTTAAAATA
1 AAATTATTATTTAAAATAAATTAAAATA
* *
1592380 AAATATATT-TTTATAATAAATTTAAATA
1 AAAT-TATTATTTAAAATAAATTAAAATA
1592408 AAATTTATTATT
1 AAA-TTATTATT
1592420 ATTATATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 26 0.79
29 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (28 bp):
AAATTATTATTTAAAATAAATTAAAATA
Found at i:1595019 original size:78 final size:78
Alignment explanation
Indices: 1594890--1595037 Score: 215
Period size: 78 Copynumber: 1.9 Consensus size: 78
1594880 TACATAAATA
* ** * *
1594890 CTTCGCTCTCTTTCCCCGAAAGTTCTGATTTATTGAACGGGGACCAAATACAGCCTCAATCTATT
1 CTTCGCTCTCTTTCCCCAAAAGTTCTGACATATCGAACAGGGACCAAATACAGCCTCAATCTATT
1594955 CAATCTTAATGTT
66 CAATCTTAATGTT
* ** *
1594968 CTTCGCTCTCTTTCCCCAAAAGTTCTGACATATCGAATAGGGACTGAATACAGCCTTAATCTATT
1 CTTCGCTCTCTTTCCCCAAAAGTTCTGACATATCGAACAGGGACCAAATACAGCCTCAATCTATT
1595033 CAATC
66 CAATC
1595038 CGAATCTATC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 61 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (78 bp):
CTTCGCTCTCTTTCCCCAAAAGTTCTGACATATCGAACAGGGACCAAATACAGCCTCAATCTATT
CAATCTTAATGTT
Found at i:1595058 original size:15 final size:15
Alignment explanation
Indices: 1595022--1595069 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1595012 TGAATACAGC
*
1595022 CTTAATCTATTCAAT
1 CTTAATCTATCCAAT
** *
1595037 CCGAATCTATCCGAT
1 CTTAATCTATCCAAT
*
1595052 CTTAATCTTTCCAAT
1 CTTAATCTATCCAAT
1595067 CTT
1 CTT
1595070 CTAATCCTAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.04, T:0.42
Consensus pattern (15 bp):
CTTAATCTATCCAAT
Found at i:1595967 original size:13 final size:13
Alignment explanation
Indices: 1595945--1595977 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1595935 TTTTTTATAA
*
1595945 AATATTTATATTT
1 AATATATATATTT
1595958 AATATATATATTT
1 AATATATATATTT
1595971 AA-ATATA
1 AATATATA
1595978 AATATAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATATATATATTT
Found at i:1596195 original size:6 final size:6
Alignment explanation
Indices: 1596178--1596230 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
1596168 ACGAAAATAC
1596178 TTAAATT TTAAAT TTAAAT TT-AAT TTAAA- TT--AT TTAAAT TTAATAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-A-AAT
1596225 TTAAAT
1 TTAAAT
1596231 ATATTAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
3 1 0.03
4 2 0.05
5 7 0.17
6 18 0.45
7 7 0.17
8 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:1596226 original size:14 final size:14
Alignment explanation
Indices: 1596184--1596230 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
1596174 ATACTTAAAT
1596184 TTTAAATTT-A-AA
1 TTTAAATTTAATAA
*
1596196 TTT-AATTTAAATTA
1 TTTAAATTT-AATAA
1596210 TTTAAATTTAATAA
1 TTTAAATTTAATAA
1596224 TTTAAAT
1 TTTAAAT
1596231 ATATTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 5 0.17
12 3 0.10
13 1 0.03
14 15 0.52
15 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTAAATTTAATAA
Found at i:1596274 original size:21 final size:21
Alignment explanation
Indices: 1596249--1596289 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1596239 ATAATACAAA
*
1596249 ATATTTT-TATTTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
1596270 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
1596290 AATAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:1596333 original size:15 final size:15
Alignment explanation
Indices: 1596279--1596365 Score: 56
Period size: 15 Copynumber: 5.7 Consensus size: 15
1596269 TATATTTTAT
*
1596279 AATTAAATTTAAATAA
1 AATT-AATTTAAATTA
*
1596295 AATTATTATTT-ATTTA
1 AATTA--ATTTAAATTA
*
1596311 ATAATAATTTAAATTA
1 A-ATTAATTTAAATTA
1596327 AATTAATTTAAA-TA
1 AATTAATTTAAATTA
* *
1596341 AA-AAATATAAATTTA
1 AATTAATTTAAA-TTA
1596356 AA-TAATTTAA
1 AATTAATTTAA
1596366 TTTTTTAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
13 7 0.12
14 4 0.07
15 25 0.45
16 13 0.23
17 7 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAATTTAAATTA
Found at i:1596374 original size:17 final size:18
Alignment explanation
Indices: 1596352--1596385 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1596342 AAAATATAAA
1596352 TTTAAAT-AATTTAATTT
1 TTTAAATAAATTTAATTT
1596369 TTTAAATAAATTTAATT
1 TTTAAATAAATTTAATT
1596386 AACACGACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAATAAATTTAATTT
Found at i:1597205 original size:17 final size:18
Alignment explanation
Indices: 1597180--1597213 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1597170 GGTACTGACC
*
1597180 AAAAGGAAAAA-AAAAAA
1 AAAAAGAAAAAGAAAAAA
1597197 AAAAAGAAAAAGAAAAA
1 AAAAAGAAAAAGAAAAA
1597214 GCAAGAGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAAAA
Found at i:1597456 original size:6 final size:7
Alignment explanation
Indices: 1597437--1597462 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1597427 TTTTAAATAT
1597437 ATAAAAA
1 ATAAAAA
1597444 ATAAAAA
1 ATAAAAA
1597451 ATAAAAA
1 ATAAAAA
1597458 ATAAA
1 ATAAA
1597463 TACACTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAA
Found at i:1597709 original size:13 final size:13
Alignment explanation
Indices: 1597674--1597712 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1597664 ATCTAACATC
1597674 TTTTTAAATATAAA
1 TTTTTAAATAT-AA
* *
1597688 TATTAAAATATAA
1 TTTTTAAATATAA
1597701 TTTTTAAATATA
1 TTTTTAAATATA
1597713 TAAAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTTTAAATATAA
Found at i:1598741 original size:19 final size:18
Alignment explanation
Indices: 1598717--1598760 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
1598707 TGGTGCTTAA
*
1598717 AAATAAATAAAACTATAAT
1 AAATAAATAAAA-TAAAAT
1598736 AAATAAAATAAAATAAAAT
1 AAAT-AAATAAAATAAAAT
1598755 AAATAA
1 AAATAA
1598761 TACTTCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 13 0.57
20 8 0.35
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAAATAAAATAAAAT
Found at i:1598746 original size:5 final size:5
Alignment explanation
Indices: 1598716--1598757 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
1598706 ATGGTGCTTA
*
1598716 AAAAT -AAAT AAAACT ATAAT -AAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1598758 TAATACTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 7 0.22
5 21 0.66
6 4 0.12
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:1599269 original size:2 final size:2
Alignment explanation
Indices: 1599262--1599287 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1599252 TTGCATTGGA
1599262 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
1599288 GAATGAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1602838 original size:24 final size:24
Alignment explanation
Indices: 1602804--1602869 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 24
1602794 TCATTTAAAC
*
1602804 ATATTACTATTTAAAATAATTTTA
1 ATATTAATATTTAAAATAATTTTA
1602828 ATATTAATATTTAATTAAATAATTTTA
1 ATATTAATATTT-A--AAATAATTTTA
* *
1602855 TTATATAAAATTTAA
1 ATAT-TAATATTTAA
1602870 TTAAAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
24 11 0.31
25 2 0.06
27 15 0.43
28 7 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATTAATATTTAAAATAATTTTA
Found at i:1602847 original size:27 final size:28
Alignment explanation
Indices: 1602817--1602874 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
1602807 TTACTATTTA
*
1602817 AAATAATTTTAATAT-TAATATTTAATT
1 AAATAATTTTAATATATAAAATTTAATT
*
1602844 AAATAATTTTATTATATAAAATTTAATT
1 AAATAATTTTAATATATAAAATTTAATT
1602872 AAA
1 AAA
1602875 AATAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
AAATAATTTTAATATATAAAATTTAATT
Found at i:1602867 original size:28 final size:27
Alignment explanation
Indices: 1602817--1602892 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 27
1602807 TTACTATTTA
*
1602817 AAATAATTTTAATATTAATATTTAATT
1 AAATAATTTTAATATTAAAATTTAATT
*
1602844 AAATAATTTTATTATATAAAATTTAATT
1 AAATAATTTTAATAT-TAAAATTTAATT
*
1602872 AAAAATAAATTTAA-ATTAAAA
1 --AAATAATTTTAATATTAAAA
1602893 AATATAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 14 0.33
28 16 0.38
29 2 0.05
30 10 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATAATTTTAATATTAAAATTTAATT
Found at i:1602883 original size:16 final size:17
Alignment explanation
Indices: 1602862--1602893 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1602852 TTATTATATA
1602862 AAATTT-AATTAAAAAT
1 AAATTTAAATTAAAAAT
1602878 AAATTTAAATTAAAAA
1 AAATTTAAATTAAAAA
1602894 ATATAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTTAAATTAAAAAT
Found at i:1602910 original size:20 final size:18
Alignment explanation
Indices: 1602862--1602902 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1602852 TTATTATATA
1602862 AAATTT-AATT-AAAAAT
1 AAATTTAAATTAAAAAAT
1602878 AAATTTAAATTAAAAAAT
1 AAATTTAAATTAAAAAAT
1602896 ATAATTT
1 A-AATTT
1602903 TAACTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.27
17 4 0.18
18 7 0.32
19 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTTAAATTAAAAAAT
Found at i:1604587 original size:13 final size:13
Alignment explanation
Indices: 1604569--1604596 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1604559 AGATTTCAAT
1604569 TATGTGAAATAAG
1 TATGTGAAATAAG
1604582 TATGTGAAATAAG
1 TATGTGAAATAAG
1604595 TA
1 TA
1604597 AAAGTATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.32
Consensus pattern (13 bp):
TATGTGAAATAAG
Found at i:1610314 original size:2 final size:2
Alignment explanation
Indices: 1610307--1610338 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1610297 TATGAATTTG
1610307 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
1610339 TTGTTTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1618876 original size:26 final size:26
Alignment explanation
Indices: 1618840--1618890 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1618830 GATATACCGA
*
1618840 AAACTCTTTTAAACACTCTAATTTCC
1 AAACTCTTTTAAACACACTAATTTCC
*
1618866 AAACTCTTTTAAGCACACTAATTTC
1 AAACTCTTTTAAACACACTAATTTC
1618891 AAAAAGTGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.37
Consensus pattern (26 bp):
AAACTCTTTTAAACACACTAATTTCC
Found at i:1619361 original size:20 final size:20
Alignment explanation
Indices: 1619339--1619427 Score: 142
Period size: 20 Copynumber: 4.5 Consensus size: 20
1619329 ATAACCATTG
**
1619339 TTGGAACTTTATATGTTGGG
1 TTGGAACTTTATATGTTGAA
1619359 TTGGAACTTTATATGTTGAA
1 TTGGAACTTTATATGTTGAA
1619379 TTGGAACTTTATATGTTGAA
1 TTGGAACTTTATATGTTGAA
*
1619399 TTGGAACTTTATATGTTGGA
1 TTGGAACTTTATATGTTGAA
*
1619419 TCGGAACTT
1 TTGGAACTT
1619428 GGTATTTCGA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.44
Consensus pattern (20 bp):
TTGGAACTTTATATGTTGAA
Found at i:1625678 original size:24 final size:25
Alignment explanation
Indices: 1625646--1625696 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
1625636 GTTTTTTAGT
1625646 GATAAGTGG-TAAACAATGGGAATA
1 GATAAGTGGATAAACAATGGGAATA
**
1625670 GATAAGTGGATAAATGATGGGAATA
1 GATAAGTGGATAAACAATGGGAATA
1625695 GA
1 GA
1625697 GCTGGCAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.45, C:0.02, G:0.31, T:0.22
Consensus pattern (25 bp):
GATAAGTGGATAAACAATGGGAATA
Found at i:1626106 original size:3 final size:3
Alignment explanation
Indices: 1626098--1626149 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
1626088 CCCTTTCTGA
1626098 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1626146 TAT T
1 TAT T
1626150 TTTTGTTTAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1627786 original size:6 final size:7
Alignment explanation
Indices: 1627770--1627795 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1627760 TAGTGCCTTC
1627770 TTTTTAT
1 TTTTTAT
1627777 TTTTTAT
1 TTTTTAT
1627784 TTTTTAT
1 TTTTTAT
1627791 TTTTT
1 TTTTT
1627796 TCTGTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:1631159 original size:21 final size:21
Alignment explanation
Indices: 1631130--1631170 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1631120 AATTTATTTT
*
1631130 TAAATACACATATGTCATATA
1 TAAACACACATATGTCATATA
1631151 TAAACACACATATGTCATAT
1 TAAACACACATATGTCATAT
1631171 TATTATGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (21 bp):
TAAACACACATATGTCATATA
Found at i:1631230 original size:18 final size:17
Alignment explanation
Indices: 1631201--1631234 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1631191 TCAAAGTATT
1631201 ATTTATTTATATGAATA
1 ATTTATTTATATGAATA
1631218 ATTTATATTATATGAAT
1 ATTTAT-TTATATGAAT
1631235 TTAATAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTTATTTATATGAATA
Found at i:1631493 original size:6 final size:6
Alignment explanation
Indices: 1631484--1631513 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1631474 CAGCAACAGC
*
1631484 TAGCCA TAGCCA TAGCCA TAGCTA TAGCCA
1 TAGCCA TAGCCA TAGCCA TAGCCA TAGCCA
1631514 GGGACGTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (6 bp):
TAGCCA
Found at i:1632594 original size:23 final size:24
Alignment explanation
Indices: 1632567--1632615 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
1632557 TATAAAAAAT
*
1632567 TTATTTAAAGTTT-AATATATTAA
1 TTATTTAAAGTTTAAAAATATTAA
* *
1632590 TTATTTATATTTTAAAAATATTAA
1 TTATTTAAAGTTTAAAAATATTAA
1632614 TT
1 TT
1632616 TATTACATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TTATTTAAAGTTTAAAAATATTAA
Found at i:1632610 original size:24 final size:25
Alignment explanation
Indices: 1632583--1632649 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
1632573 AAAGTTTAAT
1632583 ATATTAATTATTTATATTTTA-AAA
1 ATATTAATTATTTATATTTTATAAA
* *
1632607 ATATTAATT-TATTACATATTTATATA
1 ATATTAATTAT-TTATAT-TTTATAAA
1632633 ATATTAA-TA-TTATATTT
1 ATATTAATTATTTATATTT
1632650 AATTATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
23 3 0.08
24 19 0.53
25 5 0.14
26 9 0.25
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATTAATTATTTATATTTTATAAA
Found at i:1632620 original size:32 final size:33
Alignment explanation
Indices: 1632578--1632676 Score: 85
Period size: 32 Copynumber: 2.9 Consensus size: 33
1632568 TATTTAAAGT
*
1632578 TTAATATATTA-ATTATTTATATTTTAAAAATA
1 TTAATTTATTACATTATTTATATTTTAAAAATA
** **
1632610 TTAATTTATTACA-TATTTATATAATATTAATA
1 TTAATTTATTACATTATTTATATTTTAAAAATA
* *
1632642 TTATATTTAATTATATTATATCATATTTTTAAAAA
1 TTA-ATTT-ATTACATTAT-TTATA-TTTTAAAAA
1632677 ACAATTGTCC
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
32 28 0.56
33 5 0.10
34 5 0.10
35 3 0.06
36 4 0.08
37 5 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (33 bp):
TTAATTTATTACATTATTTATATTTTAAAAATA
Found at i:1632631 original size:21 final size:19
Alignment explanation
Indices: 1632607--1632668 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 19
1632597 TATTTTAAAA
1632607 ATATTAATTTATTACATATT
1 ATATTAATTTATTA-ATATT
1632627 -TATATAA--TATTAATATT
1 ATAT-TAATTTATTAATATT
*
1632644 ATATTTAATTATATT-ATATC
1 ATA-TTAATT-TATTAATATT
1632664 ATATT
1 ATATT
1632669 TTTAAAAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
17 5 0.14
18 10 0.29
19 6 0.17
20 10 0.29
21 4 0.11
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTAATTTATTAATATT
Found at i:1634674 original size:18 final size:19
Alignment explanation
Indices: 1634651--1634696 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1634641 TTAATAATTT
1634651 ATTTTAT-TTTTTAAAATA
1 ATTTTATATTTTTAAAATA
1634669 ATTTTATAATTTTTAAAATA
1 ATTTTAT-ATTTTTAAAATA
*
1634689 TTTTTATA
1 ATTTTATA
1634697 ATAATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
19 1 0.04
20 17 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATTTTTAAAATA
Found at i:1634681 original size:20 final size:20
Alignment explanation
Indices: 1634658--1634698 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1634648 TTTATTTTAT
1634658 TTTTTAAAATAATTTTATAA
1 TTTTTAAAATAATTTTATAA
*
1634678 TTTTTAAAATATTTTTATAA
1 TTTTTAAAATAATTTTATAA
1634698 T
1 T
1634699 AATATTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTAAAATAATTTTATAA
Found at i:1634780 original size:21 final size:22
Alignment explanation
Indices: 1634756--1634807 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
1634746 ATTTAACTTA
1634756 AAACAAATTAAATAAA-TTATT
1 AAACAAATTAAATAAATTTATT
**
1634777 AAACTCA-TAAATAAATTTATT
1 AAACAAATTAAATAAATTTATT
*
1634798 -AATAAATTAA
1 AAACAAATTAA
1634808 TATATATGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (22 bp):
AAACAAATTAAATAAATTTATT
Found at i:1634854 original size:18 final size:19
Alignment explanation
Indices: 1634832--1634876 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1634822 TATTATTTTT
1634832 TAAATATTT-TAAAAATAAA
1 TAAATATTTATAAAAA-AAA
1634851 -AAATAATTTATAAAAAAAA
1 TAAAT-ATTTATAAAAAAAA
1634870 TAAATAT
1 TAAATAT
1634877 AACATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.17
19 9 0.39
20 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAATATTTATAAAAAAAA
Found at i:1635112 original size:2 final size:2
Alignment explanation
Indices: 1635107--1635145 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1635097 TCTCTCTCTC
1635107 TA TA TA 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 TA TA TA T
1635146 TATTTTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1635449 original size:15 final size:15
Alignment explanation
Indices: 1635429--1635514 Score: 56
Period size: 15 Copynumber: 5.7 Consensus size: 15
1635419 ATTTTTCTAT
1635429 TTATATTATATTTTA
1 TTATATTATATTTTA
*
1635444 TTATATTATAATTATA
1 TTATATTAT-ATTTTA
*
1635460 TT-TAATATATTATATA
1 TTATATTATATT-T-TA
*
1635476 TT-TATATAAATTTTA
1 TTATAT-TATATTTTA
*
1635491 ATATATTA-A--TTA
1 TTATATTATATTTTA
1635503 TTCATATTATAT
1 TT-ATATTATAT
1635515 AAATTTTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
12 4 0.07
13 6 0.11
14 5 0.09
15 19 0.34
16 17 0.30
17 5 0.09
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATTATATTTTA
Found at i:1635463 original size:20 final size:21
Alignment explanation
Indices: 1635429--1635482 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
1635419 ATTTTTCTAT
*
1635429 TTAT-ATTATATTTTATTATA
1 TTATAATTATATTTTAATATA
1635449 TTATAATTATA-TTTAATATA
1 TTATAATTATATTTTAATATA
1635469 TTATATATTTATAT
1 TTATA-A-TTATAT
1635483 AAATTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 17 0.59
21 7 0.24
22 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATAATTATATTTTAATATA
Found at i:1635470 original size:35 final size:34
Alignment explanation
Indices: 1635430--1635528 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 34
1635420 TTTTTCTATT
*
1635430 TATATTATATTTTAT-TATATTATAATTATATTTAA
1 TATATTATATTTTATATAAATTATAA-TATA-TTAA
*
1635465 TATATTATATATTTATATAAATTTTAATATATTAA
1 TATATTATAT-TTTATATAAATTATAATATATTAA
* *
1635500 T-TATTCATA--TTATATAAATTTTAAAATAT
1 TATATT-ATATTTTATATAAATTATAATATAT
1635529 ATTTTTATCA
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
32 19 0.33
34 4 0.07
35 18 0.31
36 9 0.16
37 8 0.14
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (34 bp):
TATATTATATTTTATATAAATTATAATATATTAA
Found at i:1635540 original size:32 final size:31
Alignment explanation
Indices: 1635460--1635542 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 31
1635450 TATAATTATA
1635460 TTTAATATATT-A-TAT-AT-TTATATAAAT
1 TTTAATATATTAATTATCATATTATATAAAT
1635487 TTTAATATATTAATTATTCATATTATATAAAT
1 TTTAATATATTAATTA-TCATATTATATAAAT
*
1635519 TTTAAAATATATT-TTTATCATATT
1 TTT--AATATATTAATTATCATATT
1635543 TTAATAATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
27 11 0.23
28 1 0.02
29 2 0.04
30 1 0.02
31 2 0.04
32 20 0.42
33 3 0.06
34 8 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (31 bp):
TTTAATATATTAATTATCATATTATATAAAT
Found at i:1635939 original size:22 final size:22
Alignment explanation
Indices: 1635912--1635959 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1635902 CTATTTTAAT
1635912 ATAAAT-T-TTTTTATATATATTA
1 ATAAATATATTTTTAT-TATA-TA
1635934 ATAAATATATTTTTATTATATA
1 ATAAATATATTTTTATTATATA
1635956 ATAA
1 ATAA
1635960 TTAATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 12 0.50
23 5 0.21
24 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAAATATATTTTTATTATATA
Found at i:1635953 original size:25 final size:24
Alignment explanation
Indices: 1635908--1635967 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
1635898 ACTTCTATTT
1635908 TAAT-ATAAAT-T-TTTTTATATA
1 TAATAATAAATATATTTTTATATA
*
1635929 TATTAATAAATATATTTTTATTATA
1 TAATAATAAATATATTTTTA-TATA
*
1635954 TAATAATTAATATA
1 TAATAATAAATATA
1635968 AATTAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 3 0.09
22 6 0.19
23 1 0.03
24 6 0.19
25 16 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TAATAATAAATATATTTTTATATA
Found at i:1635976 original size:25 final size:25
Alignment explanation
Indices: 1635925--1635976 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
1635915 AATTTTTTTA
* ** *
1635925 TATATATTAATAAATATATTTTTAT
1 TATATAATAATAAATATAAATTAAT
*
1635950 TATATAATAATTAATATAAATTAAT
1 TATATAATAATAAATATAAATTAAT
1635975 TA
1 TA
1635977 AAAATAAATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TATATAATAATAAATATAAATTAAT
Found at i:1636040 original size:17 final size:17
Alignment explanation
Indices: 1636004--1636050 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
1635994 AAATAATAAA
1636004 AATATATTATTATCATTTTT
1 AATAT-TTATT-T-ATTTTT
*
1636024 AATTTTTATTTATTTTT
1 AATATTTATTTATTTTT
1636041 AATATTTATT
1 AATATTTATT
1636051 AAAAGAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 15 0.60
18 1 0.04
19 5 0.20
20 4 0.16
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
AATATTTATTTATTTTT
Found at i:1636513 original size:19 final size:20
Alignment explanation
Indices: 1636491--1636531 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1636481 AAAATAAAAT
* *
1636491 AATTTTATT-AATATCTTAA
1 AATTATATTAAATATATTAA
1636510 AATTATATTAAATATATTAA
1 AATTATATTAAATATATTAA
1636530 AA
1 AA
1636532 ATAGAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTATATTAAATATATTAA
Found at i:1636685 original size:25 final size:26
Alignment explanation
Indices: 1636657--1636713 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
1636647 ATGTTTAACA
1636657 TTTTTTT-ATAATT-TATAAAATTCAT
1 TTTTTTTCA-AATTATATAAAATTCAT
*
1636682 TTTTTTTCAAATTATATAAAATTCCT
1 TTTTTTTCAAATTATATAAAATTCAT
1636708 TTTTTT
1 TTTTTT
1636714 CTCTATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTTTTCAAATTATATAAAATTCAT
Found at i:1636714 original size:25 final size:26
Alignment explanation
Indices: 1636657--1636714 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
1636647 ATGTTTAACA
*
1636657 TTTTTTT-ATAATTTATAAAATTCAT
1 TTTTTTTCATAATTTATAAAATTCAC
1636682 TTTTTTTCA-AATTATATAAAATTC-C
1 TTTTTTTCATAATT-TATAAAATTCAC
1636707 TTTTTTTC
1 TTTTTTTC
1636715 TCTATTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 19 0.63
26 11 0.37
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTTTTCATAATTTATAAAATTCAC
Found at i:1638387 original size:2 final size:2
Alignment explanation
Indices: 1638382--1638407 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1638372 TTTTTTTTTC
1638382 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
1638408 TTAGAAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1638976 original size:2 final size:2
Alignment explanation
Indices: 1638971--1639000 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1638961 GTGTGTGTGT
1638971 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1639001 CCTACTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1645390 original size:18 final size:17
Alignment explanation
Indices: 1645363--1645397 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1645353 ATTTTTACAC
*
1645363 AAAATATTTTTAATTAT
1 AAAATATTTTCAATTAT
1645380 AAAATTATTTTCAATTAT
1 AAAA-TATTTTCAATTAT
1645398 TATAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
AAAATATTTTCAATTAT
Found at i:1645574 original size:17 final size:17
Alignment explanation
Indices: 1645535--1645576 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1645525 AACAATAAAT
1645535 ATTTTAAATTTATATTTA
1 ATTTT-AATTTATATTTA
1645553 A-TTTAA-TTATATATTA
1 ATTTTAATTTATAT-TTA
1645569 ATTTTAAT
1 ATTTTAAT
1645577 ATTAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 6 0.29
16 6 0.29
17 8 0.38
18 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTAATTTATATTTA
Found at i:1646120 original size:16 final size:16
Alignment explanation
Indices: 1646092--1646125 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1646082 TAAAATTAAC
1646092 TTAAAAAATAATA-AT
1 TTAAAAAATAATATAT
1646107 TTAAAAAATAAATATAT
1 TTAAAAAAT-AATATAT
1646124 TT
1 TT
1646126 TTAATTACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 4 0.24
17 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAAAATAATATAT
Found at i:1646183 original size:16 final size:15
Alignment explanation
Indices: 1646144--1646174 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1646134 CCTTTAAAAA
1646144 TAAATAAATATTTTT
1 TAAATAAATATTTTT
1646159 TAAATAAATATTTTT
1 TAAATAAATATTTTT
1646174 T
1 T
1646175 TATTAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATAAATATTTTT
Found at i:1646305 original size:21 final size:19
Alignment explanation
Indices: 1646281--1646328 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1646271 GACATTTTAA
*
1646281 TTATTTTAAATTAAATTAAAT
1 TTATTTAAAATTAAA-T-AAT
*
1646302 TTATTAAAAAATTAAATAAT
1 TTATT-TAAAATTAAATAAT
1646322 TTATTTA
1 TTATTTA
1646329 TTTTTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.04
20 8 0.35
21 6 0.26
22 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTTAAAATTAAATAAT
Found at i:1646419 original size:17 final size:16
Alignment explanation
Indices: 1646399--1646442 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1646389 GACTCAACTT
1646399 ATTATTTATTAATTAAA
1 ATTATTT-TTAATTAAA
*
1646416 ATTATTTTTATTTAAA
1 ATTATTTTTAATTAAA
* *
1646432 TTTAATTTTAA
1 ATTATTTTTAA
1646443 AATATAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTTTTAATTAAA
Found at i:1647743 original size:29 final size:30
Alignment explanation
Indices: 1647710--1647768 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1647700 CGATGACATT
1647710 ATATGAAAT-ATAATAAAAAAATAAT-TAAA
1 ATATGAAATCAT-ATAAAAAAATAATATAAA
* *
1647739 ATATGATATCATATAAAAATATAATATAAA
1 ATATGAAATCATATAAAAAAATAATATAAA
1647769 TAAAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (30 bp):
ATATGAAATCATATAAAAAAATAATATAAA
Found at i:1647776 original size:29 final size:27
Alignment explanation
Indices: 1647715--1647778 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
1647705 ACATTATATG
1647715 AAATATAATAAAAAAATAATTAAAATA
1 AAATATAATAAAAAAATAATTAAAATA
** *
1647742 TGATATCATATAAAAATATAA-TATAAATA
1 AAATAT-A-ATAAAAAAATAATTA-AAATA
1647771 AAATATAA
1 AAATATAA
1647779 ATATTTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
27 5 0.17
28 4 0.14
29 20 0.69
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (27 bp):
AAATATAATAAAAAAATAATTAAAATA
Found at i:1647802 original size:16 final size:15
Alignment explanation
Indices: 1647776--1647835 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 15
1647766 AAATAAAATA
1647776 TAAATATTTATATATCT
1 TAAA-ATTTATATAT-T
*
1647793 TAAAATTTATATAATA
1 TAAAATTTATAT-ATT
*
1647809 TAAATTATTA-ATATAT
1 TAAAAT-TTATATAT-T
1647825 TAAAATTTATA
1 TAAAATTTATA
1647836 AATTATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
15 5 0.14
16 21 0.60
17 9 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATTTATATATT
Found at i:1647832 original size:32 final size:33
Alignment explanation
Indices: 1647772--1647835 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1647762 ATATAAATAA
*
1647772 AATATAAATATTTATATATCTTAAAATTTATAT
1 AATATAAATATTTATATATATTAAAATTTATAT
1647805 AATATAAAT-TATTA-ATATATTAAAATTTATA
1 AATATAAATAT-TTATATATATTAAAATTTATA
1647836 AATTATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (33 bp):
AATATAAATATTTATATATATTAAAATTTATAT
Found at i:1647839 original size:40 final size:39
Alignment explanation
Indices: 1647762--1647878 Score: 98
Period size: 39 Copynumber: 3.0 Consensus size: 39
1647752 TAAAAATATA
* * *
1647762 ATATAAATAAAATATAAATAT-TTATATATCTTA-AAATTT
1 ATATAAATAAATTATTAATATATTA-AAAT-TTATAAATTT
1647801 ATATAATATAAATTATTAATATATTAAAATTTATAAA-TT
1 ATATAA-ATAAATTATTAATATATTAAAATTTATAAATTT
* * * *
1647840 ATTTTAAATATAATTA-TGATATAATAAAATATATAAATT
1 A-TATAAATA-AATTATTAATATATTAAAATTTATAAATT
1647879 ATTAAAATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
39 33 0.51
40 29 0.45
41 3 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (39 bp):
ATATAAATAAATTATTAATATATTAAAATTTATAAATTT
Found at i:1647869 original size:39 final size:41
Alignment explanation
Indices: 1647805--1647881 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 41
1647795 AAATTTATAT
* *
1647805 AATATAAATTATTAATATATTAAAATTTATAAATTATTTTA
1 AATATAAATTATTAATATAATAAAATATATAAATTATTTTA
*
1647846 AATAT-AATTA-TGATATAATAAAATATATAAATTATT
1 AATATAAATTATTAATATAATAAAATATATAAATTATT
1647882 AAAATTAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 23 0.70
40 5 0.15
41 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (41 bp):
AATATAAATTATTAATATAATAAAATATATAAATTATTTTA
Found at i:1648204 original size:14 final size:15
Alignment explanation
Indices: 1648179--1648219 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1648169 ATTTTTTATA
1648179 AATTTAAAATAATTT
1 AATTTAAAATAATTT
1648194 AATTT-AAATAA-TT
1 AATTTAAAATAATTT
1648207 -ATTTAATAATAAT
1 AATTTAA-AATAAT
1648220 AAATATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 4 0.17
13 3 0.13
14 11 0.48
15 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTTAAAATAATTT
Found at i:1648284 original size:22 final size:25
Alignment explanation
Indices: 1648233--1648295 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 25
1648223 TATTTTTATT
1648233 TAAAT-TTAATTATAAAAATATATA
1 TAAATATTAATTATAAAAATATATA
*
1648257 TAAATATTAA-TATAAAAATAT-TG
1 TAAATATTAATTATAAAAATATATA
*
1648280 T-AATATTATTTATAAA
1 TAAATATTAATTATAAA
1648296 TTGTAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 7 0.20
23 8 0.23
24 16 0.46
25 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
TAAATATTAATTATAAAAATATATA
Found at i:1649171 original size:12 final size:12
Alignment explanation
Indices: 1649150--1649186 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1649140 TTAAATTAAA
*
1649150 AAATTAAATTTT
1 AAATTTAATTTT
*
1649162 AAATTTAATTAT
1 AAATTTAATTTT
1649174 AAATTTAATTTT
1 AAATTTAATTTT
1649186 A
1 A
1649187 TTTGATTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AAATTTAATTTT
Found at i:1649181 original size:25 final size:25
Alignment explanation
Indices: 1649137--1649186 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1649127 TGATGAATGG
1649137 AATTTAAATTAAAAAATTAAATTTTA
1 AATTTAAATTAAAAAATT-AATTTTA
* *
1649163 AATTT-AATTATAAATTTAATTTTA
1 AATTTAAATTAAAAAATTAATTTTA
1649187 TTTGATTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 10 0.45
26 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AATTTAAATTAAAAAATTAATTTTA
Found at i:1649212 original size:35 final size:35
Alignment explanation
Indices: 1649164--1649257 Score: 84
Period size: 35 Copynumber: 2.7 Consensus size: 35
1649154 TAAATTTTAA
1649164 ATTTAATTATAAATTTAAT-TTTATTTGATTTACAT
1 ATTTAATTATAAA-TTAATATTTATTTGATTTACAT
* * * *
1649199 ATTTAAATT-TAAATTATTATTTATTTTATTTAAAA
1 ATTT-AATTATAAATTAATATTTATTTGATTTACAT
* * * *
1649234 AATTATTTTTATATTAATATTTAT
1 ATTTAATTATAAATTAATATTTAT
1649258 ATATTTTATA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
34 7 0.15
35 37 0.77
36 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (35 bp):
ATTTAATTATAAATTAATATTTATTTGATTTACAT
Found at i:1649298 original size:19 final size:19
Alignment explanation
Indices: 1649274--1649314 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1649264 TATAATTAAA
1649274 TTTAATA-AAAATATATTAT
1 TTTAATATAAAA-ATATTAT
*
1649293 TTTAATATAAAAATGTTAT
1 TTTAATATAAAAATATTAT
1649312 TTT
1 TTT
1649315 GAGCTGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTAATATAAAAATATTAT
Found at i:1651562 original size:27 final size:26
Alignment explanation
Indices: 1651515--1651566 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1651505 TATCAAAAGG
1651515 TTTAAATATTTTCACAAATATAAAAT
1 TTTAAATATTTTCACAAATATAAAAT
*
1651541 TTTACATATTTT-ACAAATATATAAAT
1 TTTAAATATTTTCACAAATATA-AAAT
1651567 AAATTGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (26 bp):
TTTAAATATTTTCACAAATATAAAAT
Found at i:1653868 original size:4 final size:5
Alignment explanation
Indices: 1653846--1653877 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1653836 ATGAACTCAA
1653846 AATTT AATTT AATTT AA-TT AA-TT AATTT AATT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATT
1653878 ATTATTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:1655667 original size:23 final size:22
Alignment explanation
Indices: 1655641--1655688 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
1655631 TTTAAAAAAT
*
1655641 TTTA-AAAATATAATTTATTTTTA
1 TTTATAAAAT-TAATTTA-ATTTA
1655664 TTTATAAAATTAATTTAATTTA
1 TTTATAAAATTAATTTAATTTA
1655686 TTT
1 TTT
1655689 TTATGAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 11 0.48
24 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATAAAATTAATTTAATTTA
Found at i:1655672 original size:24 final size:23
Alignment explanation
Indices: 1655641--1655703 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
1655631 TTTAAAAAAT
1655641 TTTA-AAAATATAATTTATTTTTA
1 TTTATAAAAT-TAATTTATTTTTA
1655664 TTTATAAAATTAATTTAATTTATT-
1 TTTATAAAATTAATTT-ATTT-TTA
* *
1655688 TTTATGAAATTTATTT
1 TTTATAAAATTAATTT
1655704 TTTATTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 10 0.29
24 23 0.66
25 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTATAAAATTAATTTATTTTTA
Found at i:1655716 original size:24 final size:25
Alignment explanation
Indices: 1655645--1655717 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 25
1655635 AAAAATTTTA
*
1655645 AAAATATAATTTATTT-TTAT-TTAT
1 AAAAT-TAATTTATTTATTTTATTAT
1655669 AAAATTAATTTAATTTA-TTT-TTAT
1 AAAATTAATTT-ATTTATTTTATTAT
* *
1655693 GAAATTTATTT-TTTATTTTATTAT
1 AAAATTAATTTATTTATTTTATTAT
1655717 A
1 A
1655718 TATAAATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 4 0.10
23 9 0.22
24 28 0.68
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (25 bp):
AAAATTAATTTATTTATTTTATTAT
Found at i:1655760 original size:15 final size:16
Alignment explanation
Indices: 1655735--1655766 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1655725 TTAAAATATT
1655735 AATTATAAAAATAAAA
1 AATTATAAAAATAAAA
1655751 AATT-TAAAAATAAAA
1 AATTATAAAAATAAAA
1655766 A
1 A
1655767 GAGTCACGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AATTATAAAAATAAAA
Found at i:1656533 original size:346 final size:340
Alignment explanation
Indices: 1655894--1658584 Score: 4014
Period size: 339 Copynumber: 8.0 Consensus size: 340
1655884 GAGGAGTTCT
* * * **
1655894 TTTCAATTTGGAGAGAGTTCTTCAAAAAGATTTTGGCAGGGGAA-ATATATTTTTCTGTTAGGCC
1 TTTCAGTTTGGAGAGAGCTCTTCAAAAAGATTTTGGCA-GGGAATATATATTTTCCTGTCGGGCC
**
1655958 TTCTACC-CTAATAATTGAGGTGGGGGGTTTTAATATGTAGAGGAGCTCTTTTCAGTTTGGAGAG
65 CCCTACCTC-AATAATTGAGGTGGGGGGTTTTAATATGTAGAGGAG------TCAGTTTGGAGAG
* * *
1656022 AGCTCTCAATAATTGAAGTAAGATCTTAACACATAGAGGAGCTTATGGAGAGAACTCTTTAAAAT
123 AGCTCTCAATAATTGAGGTAGGATCTTAACACATAGAGGAGCTCATGGAGAGAACTCTTTAAAAT
1656087 ATAAAAATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTAT
188 ATAAAAATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTAT
* * *
1656152 TAAAATATTTATTAGTATGATTATATACATTTAATTTAATTTTTTTATAAATATTTTTAAGTTAT
253 TAAAATATTTATTAGTATGATTATATAAATTTAATTTAATTTTTTTATAAATAGTTTAAAGTTAT
1656217 TTTATTTAATTTAATTATTAAAA
318 TTTATTTAATTTAATTATTAAAA
* *
1656240 TTTCAGTTTGGAGAGAGCTTTTCAAAAAAATTTTGGCAGGGAATATATATTTTCCTGTCGGGCCC
1 TTTCAGTTTGGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGAATATATATTTTCCTGTCGGGCCC
* * *
1656305 TCTACCTCAATAATTGAGGTGGGGGGTTTGAATACGTAGAGGAGCTCTTTTCAGTTTGGAGAGAG
66 CCTACCTCAATAATTGAGGTGGGGGGTTTTAATATGTAGAGGAG------TCAGTTTGGAGAGAG
*
1656370 CTCTCAATAATTGAGGTAGGATCTTAACACATAAAGGAGCTCATGGAGAGAACTCTTTAAAATAT
125 CTCTCAATAATTGAGGTAGGATCTTAACACATAGAGGAGCTCATGGAGAGAACTCTTTAAAATAT
*
1656435 AAAAATAAAAAATTTCATTTTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTA
190 AAAAATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTA
1656500 AAATATTTATTAGTATGATTATATAAATTTAATTTAA----TTTATAAATAGTTTAAAGTTATTT
255 AAATATTTATTAGTATGATTATATAAATTTAATTTAATTTTTTTATAAATAGTTTAAAGTTATTT
1656561 TATTTAATTTAATTATTAAAA
320 TATTTAATTTAATTATTAAAA
1656582 TTTCAGTTTGGAAAGAGAGCTCTTCAAAAAGATTTTGGCA-GGAGATATATATTTTCCTGTCGGG
1 TTTCAGTTTGG--AGAGAGCTCTTCAAAAAGATTTTGGCAGGGA-ATATATATTTTCCTGTCGGG
*
1656646 CCCCCTACCTCAATAATTGAGGTGGGGGGTTTTAATATGTAGATGAGCTCTTTTCAGTTTGGAGA
63 CCCCCTACCTCAATAATTGAGGTGGGGGGTTTTAATATGTAGAGGAG------TCAGTTTGGAGA
** ** *
1656711 GAATTCTCAATAATTAATTGAGGTAGGATCTTAACACATAGAGGAGCTCATAAAGAAAACTCTTT
122 GAGCTCTC---AA-TAATTGAGGTAGGATCTTAACACATAGAGGAGCTCATGGAGAGAACTCTTT
*
1656776 AAAATAT-AAAATAAAAAATTTTATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTA
183 AAAATATAAAAATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTA
* *
1656840 ATTATTAAAATATTTATTAGTATCATTATATAAATTTAATTT-ATTTTTTTATAAATATTTTAAA
248 ATTATTAAAATATTTATTAGTATGATTATATAAATTTAATTTAATTTTTTTATAAATAGTTTAAA
1656904 GTTATTTTATTTAATTTAATTATTAAAA
313 GTTATTTTATTTAATTTAATTATTAAAA
* * * *
1656932 TTTCAATTTGAAGAGAGCTCTTCAAAAAGATTTTGACA-GGAGATATATATTTTCCTGTC-GGAC
1 TTTCAGTTTGGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGA-ATATATATTTTCCTGTCGGGCC
* * * *
1656995 CCCTACCTCAATAATTGAGGTGAGAGGTTTTAATATGTAAAGGA-ACAGTTTGGAGAGAGCTCTC
65 CCCTACCTCAATAATTGAGGTGGGGGGTTTTAATATGTAGAGGAGTCAGTTTGGAGAGAGCTCTC
*
1657059 AATAATTGAGGTAGGATCTTAACATATAGAGGAGCTCATGGAGAGAACTCTTTAAAATATAAAAA
130 AATAATTGAGGTAGGATCTTAACACATAGAGGAGCTCATGGAGAGAACTCTTTAAAATATAAAAA
* * *
1657124 TAATAAATTTTATTCTTAACAGTTTTTTTAAATAAAGATATAATTTATTTTTAATTATTAAAATA
195 TAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATA
* *
1657189 TTTATTAATATGATTATATAAATTTAATTTAATTTTTTTATAAATAGCTTAAAGTTATTTTATTT
260 TTTATTAGTATGATTATATAAATTTAATTTAATTTTTTTATAAATAGTTTAAAGTTATTTTATTT
1657254 AATTTAATTATTAAAA
325 AATTTAATTATTAAAA
* *
1657270 TTTCAGTTTGGAGAGAACTCTTCAAAAAGATTTTGGC-----------A--------T-GAGCCC
1 TTTCAGTTTGGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGAATATATATTTTCCTGTCGGGCCC
* *
1657315 CC-ACCTCAATAATTGAGGTGAGGGATTTTAATATGTAGAGGAGT-AGTTTGGAGAGAGCTCTCA
66 CCTACCTCAATAATTGAGGTGGGGGGTTTTAATATGTAGAGGAGTCAGTTTGGAGAGAGCTCTCA
* *
1657378 ATAATTGAGGTTGGATCTTAACACATAGAGGATCTCATGGAGAGAACTCTTTAAAATATAAAAAT
131 ATAATTGAGGTAGGATCTTAACACATAGAGGAGCTCATGGAGAGAACTCTTTAAAATATAAAAAT
*
1657443 AAAAAATTTTATTCTTAACAGTTTTTTAAAATAAAGATATAA-TTATTTTTAATTATTAAAATAT
196 AAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATAT
*
1657507 TTATTAGTATCATTATATAAATTTAATTTAATTTTTTTATAAATAGTTTAAAGTTATTTTATTTA
261 TTATTAGTATGATTATATAAATTTAATTTAATTTTTTTATAAATAGTTTAAAGTTATTTTATTTA
1657572 ATTTAATTATTAAAA
326 ATTTAATTATTAAAA
* * *
1657587 TTTCAGTTTAGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGGATATATATTTTCCTGTCGAGCCC
1 TTTCAGTTTGGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGAATATATATTTTCCTGTCGGGCCC
* * * * *
1657652 CCTACCTCAATAATTGAGGTGAGAGGTTTTAATATGTAGATGAG-CACTTTGGAGGGAGCTCTCA
66 CCTACCTCAATAATTGAGGTGGGGGGTTTTAATATGTAGAGGAGTCAGTTTGGAGAGAGCTCTCA
* *
1657716 ATAATTGAGGTAGGATCTTAACACATAGAGGAGCTTAGGGAGAGAACTCTTTAAAATAT--AAA-
131 ATAATTGAGGTAGGATCTTAACACATAGAGGAGCTCATGGAGAGAACTCTTTAAAATATAAAAAT
*
1657778 AAAAAATTT-ATTTTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATAT
196 AAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATAT
* *
1657842 TTATTAGTATGATTATATAAATTTAATTTAATTTTTTTATAAATAATTTAAAGTTATTTAATTTA
261 TTATTAGTATGATTATATAAATTTAATTTAATTTTTTTATAAATAGTTTAAAGTTATTTTATTTA
1657907 ATTTAATTATTAAAA
326 ATTTAATTATTAAAA
* * * *
1657922 TTTCAATTGGGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGGATATATATTTTCCTGTCTGGCCC
1 TTTCAGTTTGGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGAATATATATTTTCCTGTCGGGCCC
* *
1657987 CCCACCTTAATAATTGAGGT-GGGGGTTTTAATATGTAGAGGAG-CAGTTTGGAGAGAGCTCTCA
66 CCTACCTCAATAATTGAGGTGGGGGGTTTTAATATGTAGAGGAGTCAGTTTGGAGAGAGCTCTC-
*
1658050 AATAATTGAGGTAGGATCTTAACACATAGAGGAGTTCATGGAGAGAACTCTTTAAAATATAAAAA
130 AATAATTGAGGTAGGATCTTAACACATAGAGGAGCTCATGGAGAGAACTCTTTAAAATATAAAAA
1658115 TAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATA
195 TAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATA
* * * *
1658180 TTTATTAATATAATTATAAAAATTTAATTTAATTTTTTTATAAATAATTTAAAGTTATTTTATTT
260 TTTATTAGTATGATTATATAAATTTAATTTAATTTTTTTATAAATAGTTTAAAGTTATTTTATTT
1658245 AATTTAATTATTAAAA
325 AATTTAATTATTAAAA
* *
1658261 TTTCAGTTGGGAGAAAGCTCTTCAAAAAGATTTTGGCAGAGG-ATATATATTTTCCTGTCGGGCC
1 TTTCAGTTTGGAGAGAGCTCTTCAAAAAGATTTTGGCAG-GGAATATATATTTTCCTGTCGGGCC
* * * * *
1658325 TCCC-ACTTGAATAATTGAGGTGGAGGGTTTTAATATATAGAGGAG-CAGTTTGAAGAGAGCTCT
65 -CCCTACCTCAATAATTGAGGTGGGGGGTTTTAATATGTAGAGGAGTCAGTTTGGAGAGAGCTCT
*
1658388 CAATAATTGAGGTAGGATCTTAACACATAGAGAAGCTCATGGAGAGAACTCTTTAAAATATAAAA
129 CAATAATTGAGGTAGGATCTTAACACATAGAGGAGCTCATGGAGAGAACTCTTTAAAATATAAAA
*
1658453 ATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAAATATAATTTATTTTTAATTATTAAAAT
194 ATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAAT
*
1658518 ATTTTTTAGTATGATTATATAAATTTAATTTAATTTTTTTTATAAATAGTTTAAAGTTATTTTAT
259 ATTTATTAGTATGATTATATAAATTTAATTTAA-TTTTTTTATAAATAGTTTAAAGTTATTTTAT
1658583 TT
323 TT
1658585 GTAGGTATGA
Statistics
Matches: 2172, Mismatches: 124, Indels: 104
0.90 0.05 0.04
Matches are distributed among these distances:
317 134 0.06
318 158 0.07
319 6 0.00
327 1 0.00
328 1 0.00
334 68 0.03
335 243 0.11
336 58 0.03
337 108 0.05
338 200 0.09
339 358 0.16
340 93 0.04
342 54 0.02
343 3 0.00
344 112 0.05
345 5 0.00
346 274 0.13
347 142 0.07
348 101 0.05
350 53 0.02
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (340 bp):
TTTCAGTTTGGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGAATATATATTTTCCTGTCGGGCCC
CCTACCTCAATAATTGAGGTGGGGGGTTTTAATATGTAGAGGAGTCAGTTTGGAGAGAGCTCTCA
ATAATTGAGGTAGGATCTTAACACATAGAGGAGCTCATGGAGAGAACTCTTTAAAATATAAAAAT
AAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATAT
TTATTAGTATGATTATATAAATTTAATTTAATTTTTTTATAAATAGTTTAAAGTTATTTTATTTA
ATTTAATTATTAAAA
Found at i:1658211 original size:24 final size:23
Alignment explanation
Indices: 1658166--1658231 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
1658156 AATTTATTTT
1658166 TAATTATTAAAATATTT-ATTAATA
1 TAATTA-TAAAA-ATTTAATTAATA
*
1658190 TAATTATAAAAATTTAATTTAATT
1 TAATTATAAAAATTTAA-TTAATA
**
1658214 TTTTTATAAATAATTTAA
1 TAATTATAAA-AATTTAA
1658232 AGTTATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.11
23 6 0.17
24 19 0.53
25 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTATAAAAATTTAATTAATA
Found at i:1658211 original size:991 final size:998
Alignment explanation
Indices: 1655894--1658584 Score: 3960
Period size: 991 Copynumber: 2.6 Consensus size: 998
1655884 GAGGAGTTCT
* * *
1655894 TTTCAATTTGGAGAGAGTTCTTCAAAAAGATTTTGGCAGGGGAAATATATTTTTCTGT-TAGGCC
1 TTTCAATTTGGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGGATATATATTTTCCTGTCT-GGCC
** *
1655958 TTCTACCCTAATAATTGAGGTGGGGGGTTTTAATATGTAGAGGAGCTCTTTTCAGTTTGGAGAGA
65 CCCTACCTTAATAATTGAGGT-GGGGGTTTTAATATGTAGAGGAG-------CAGTTTGGAGAGA
* *
1656023 GCTCTCAATAATTGAAGTAAGATCTTAACACATAGAGGAGCTT-ATGGAGAGAACTCTTTAAAAT
122 GCTCTCAATAATTGAGGTAGGATCTTAACACATAGAGGAG-TTCATGGAGAGAACTCTTTAAAAT
1656087 ATAAAAATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTAT
186 ATAAAAATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTAT
* * * *
1656152 TAAAATATTTATTAGTATGATTATATACATTTAATTTAATTTTTTTATAAATATTTTTAAGTTAT
251 TAAAATATTTATTAATATGATTATATAAATTTAATTTAATTTTTTTATAAATAATTTAAAGTTAT
* * *
1656217 TTTATTTAATTTAATTATTAAAATTTCAGTTTGGAGAGAGCTTTTCAAAAAAATTTTGGCAGGGA
316 TTTATTTAATTTAATTATTAAAATTTCAGTTTGGAGAGAACTCTTCAAAAAGATTTTGGC-----
* * * *
1656282 ATATATATTTTCCTGTCGGGCCCTCTACCTCAATAATTGAGGTGGGGGGTTTGAATACGTAGAGG
376 A-ATAGA-------G-C---CCC-C-ACCTCAATAATTGAGGT-GAGGGTTTTAATATGTAGAGG
*
1656347 AGCTCTTTTCAGTTTGGAGAGAGCTCTCAATAATTGAGGTAGGATCTTAACACATAAAGGAGCTC
426 AG------T-AGTTTGGAGAGAGCTCTCAATAATTGAGGTAGGATCTTAACACATAGAGGAGCTC
*
1656412 ATGGAGAGAACTCTTTAAAATATAAAAATAAAAAATTTCATTTTTAACAGTTTTTTAAAATAAAG
484 ATGGAGAGAACTCTTTAAAATATAAAAATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAG
1656477 ATATAATTTATTTTTAATTATTAAAATATTTATTAGTATGATTATATAAATTTAATTTAA----T
549 ATATAATTTATTTTTAATTATTAAAATATTTATTAGTATGATTATATAAATTTAATTTAATTTTT
1656538 TTATAAATAGTTTAAAGTTATTTTATTTAATTTAATTATTAAAATTTCAGTTTGGAAAGAGAGCT
614 TTATAAATAGTTTAAAGTTATTTTATTTAATTTAATTATTAAAATTTCAGTTT-GAAAGAGAGCT
*
1656603 CTTCAAAAAGATTTTGGCAGGAGATATATATTTTCCTGTCGGGCCCCCTACCTCAATAATTGAGG
678 CTTCAAAAAGATTTTGGCAGGAGATATATATTTTCCTGTCGAGCCCCCTACCTCAATAATTGAGG
* * * *
1656668 TGGGGGGTTTTAATATGTAGATGAGCTCTTTTCAGTTTGGAGAGAATTCTCAATAATTAATTGAG
743 TGAGAGGTTTTAATATGTAGATGAG------TCACTTTGGAGAGAACTCTC-A-AATTAATTGAG
*
1656733 GTAGGATCTTAACACATAGAGGAGCTCATAAAGAAAACTCTTTAAAATATAAAATAAAAAATTTT
800 GTAGGATCTTAACACATAGAGGAGCTCAGAAAGAAAACTCTTTAAAATATAAAATAAAAAATTTT
1656798 ATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATATTTATTAGTAT
865 ATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATATTTATTAGTAT
* *
1656863 CATTATATAAATTTAATTTATTTTTTTATAAATATTTTAAAGTTATTTTATTTAATTTAATTATT
930 CATTATATAAATTTAATTTATTTTTTTATAAATAATTTAAAGTTATTTAATTTAATTTAATTATT
1656928 AAAA
995 AAAA
* * * *
1656932 TTTCAATTTGAAGAGAGCTCTTCAAAAAGATTTTGACAGGAGATATATATTTTCCTGTC-GGACC
1 TTTCAATTTGGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGGATATATATTTTCCTGTCTGGCCC
* * * *
1656996 CCTACCTCAATAATTGAGGTGAGAGGTTTTAATATGTAAAGGAACAGTTTGGAGAGAGCTCTCAA
66 CCTACCTTAATAATTGAGGTG-GGGGTTTTAATATGTAGAGGAGCAGTTTGGAGAGAGCTCTCAA
* *
1657061 TAATTGAGGTAGGATCTTAACATATAGAGGAGCTCATGGAGAGAACTCTTTAAAATATAAAAATA
130 TAATTGAGGTAGGATCTTAACACATAGAGGAGTTCATGGAGAGAACTCTTTAAAATATAAAAATA
* * *
1657126 ATAAATTTTATTCTTAACAGTTTTTTTAAATAAAGATATAATTTATTTTTAATTATTAAAATATT
195 AAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATATT
**
1657191 TATTAATATGATTATATAAATTTAATTTAATTTTTTTATAAATAGCTTAAAGTTATTTTATTTAA
260 TATTAATATGATTATATAAATTTAATTTAATTTTTTTATAAATAATTTAAAGTTATTTTATTTAA
1657256 TTTAATTATTAAAATTTCAGTTTGGAGAGAACTCTTCAAAAAGATTTTGGC-AT-GAGCCCCCAC
325 TTTAATTATTAAAATTTCAGTTTGGAGAGAACTCTTCAAAAAGATTTTGGCAATAGAGCCCCCAC
1657319 CTCAATAATTGAGGTGAGGGATTTTAATATGTAGAGGAGTAGTTTGGAGAGAGCTCTCAATAATT
390 CTCAATAATTGAGGTGAGGG-TTTTAATATGTAGAGGAGTAGTTTGGAGAGAGCTCTCAATAATT
* *
1657384 GAGGTTGGATCTTAACACATAGAGGATCTCATGGAGAGAACTCTTTAAAATATAAAAATAAAAAA
454 GAGGTAGGATCTTAACACATAGAGGAGCTCATGGAGAGAACTCTTTAAAATATAAAAATAAAAAA
*
1657449 TTTTATTCTTAACAGTTTTTTAAAATAAAGATATAA-TTATTTTTAATTATTAAAATATTTATTA
519 TTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATATTTATTA
*
1657513 GTATCATTATATAAATTTAATTTAATTTTTTTATAAATAGTTTAAAGTTATTTTATTTAATTTAA
584 GTATGATTATATAAATTTAATTTAATTTTTTTATAAATAGTTTAAAGTTATTTTATTTAATTTAA
* *
1657578 TTATTAAAATTTCAGTTT-AGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGGATATATATTTTCC
649 TTATTAAAATTTCAGTTTGAAAGAGAGCTCTTCAAAAAGATTTTGGCAGGAGATATATATTTTCC
1657642 TGTCGAGCCCCCTACCTCAATAATTGAGGTGAGAGGTTTTAATATGTAGATGAG-CACTTTGGAG
714 TGTCGAGCCCCCTACCTCAATAATTGAGGTGAGAGGTTTTAATATGTAGATGAGTCACTTTGGAG
* * * ** *
1657706 GGAGCTCTC-AA-TAATTGAGGTAGGATCTTAACACATAGAGGAGCTTAGGGAGAGAACTCTTTA
779 AGAACTCTCAAATTAATTGAGGTAGGATCTTAACACATAGAGGAGCTCAGAAAGAAAACTCTTTA
*
1657769 AAATAT-AAA-AAAAAA-TTTATTTTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAAT
844 AAATATAAAATAAAAAATTTTATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAAT
*
1657831 TATTAAAATATTTATTAGTATGATTATATAAATTTAATTTAATTTTTTTATAAATAATTTAAAGT
909 TATTAAAATATTTATTAGTATCATTATATAAATTTAATTT-ATTTTTTTATAAATAATTTAAAGT
1657896 TATTTAATTTAATTTAATTATTAAAA
973 TATTTAATTTAATTTAATTATTAAAA
*
1657922 TTTCAATTGGGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGGATATATATTTTCCTGTCTGGCCC
1 TTTCAATTTGGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGGATATATATTTTCCTGTCTGGCCC
*
1657987 CCCACCTTAATAATTGAGGTGGGGGTTTTAATATGTAGAGGAGCAGTTTGGAGAGAGCTCTCAAA
66 CCTACCTTAATAATTGAGGTGGGGGTTTTAATATGTAGAGGAGCAGTTTGGAGAGAGCTCTC-AA
1658052 TAATTGAGGTAGGATCTTAACACATAGAGGAGTTCATGGAGAGAACTCTTTAAAATATAAAAATA
130 TAATTGAGGTAGGATCTTAACACATAGAGGAGTTCATGGAGAGAACTCTTTAAAATATAAAAATA
1658117 AAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATATT
195 AAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATATT
* *
1658182 TATTAATATAATTATAAAAATTTAATTTAATTTTTTTATAAATAATTTAAAGTTATTTTATTTAA
260 TATTAATATGATTATATAAATTTAATTTAATTTTTTTATAAATAATTTAAAGTTATTTTATTTAA
*
1658247 TTTAATTATTAAAATTTCAGTTGGGAGA-AAGCTCTTCAAAAAGATTTTGGCAGAGGATATATAT
325 TTTAATTATTAAAATTTCAGTTTGGAGAGAA-CTCTTCAAAAAGATTTTGGC-------A-ATA-
* * * * *
1658311 TTTCCTGTCGGGCCTCCCACTTGAATAATTGAGGTGGAGGGTTTTAATATATAGAGGAGCAGTTT
380 ---------GAGCC-CCCACCTCAATAATTGAGGT-GAGGGTTTTAATATGTAGAGGAGTAGTTT
* *
1658376 GAAGAGAGCTCTCAATAATTGAGGTAGGATCTTAACACATAGAGAAGCTCATGGAGAGAACTCTT
434 GGAGAGAGCTCTCAATAATTGAGGTAGGATCTTAACACATAGAGGAGCTCATGGAGAGAACTCTT
*
1658441 TAAAATATAAAAATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAAATATAATTTATTTTT
499 TAAAATATAAAAATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTT
*
1658506 AATTATTAAAATATTTTTTAGTATGATTATATAAATTTAATTTAATTTTTTTTATAAATAGTTTA
564 AATTATTAAAATATTTATTAGTATGATTATATAAATTTAATTTAA-TTTTTTTATAAATAGTTTA
1658571 AAGTTATTTTATTT
628 AAGTTATTTTATTT
1658585 GTAGGTATGA
Statistics
Matches: 1527, Mismatches: 90, Indels: 96
0.89 0.05 0.06
Matches are distributed among these distances:
989 85 0.06
990 149 0.10
991 261 0.17
992 53 0.03
993 2 0.00
996 15 0.01
1000 2 0.00
1001 52 0.03
1002 121 0.08
1003 96 0.06
1005 54 0.04
1008 4 0.00
1009 33 0.02
1010 1 0.00
1011 7 0.00
1012 155 0.10
1013 56 0.04
1014 34 0.02
1015 1 0.00
1022 1 0.00
1023 2 0.00
1029 1 0.00
1030 250 0.16
1036 1 0.00
1037 39 0.03
1038 52 0.03
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (998 bp):
TTTCAATTTGGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGGATATATATTTTCCTGTCTGGCCC
CCTACCTTAATAATTGAGGTGGGGGTTTTAATATGTAGAGGAGCAGTTTGGAGAGAGCTCTCAAT
AATTGAGGTAGGATCTTAACACATAGAGGAGTTCATGGAGAGAACTCTTTAAAATATAAAAATAA
AAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATATTT
ATTAATATGATTATATAAATTTAATTTAATTTTTTTATAAATAATTTAAAGTTATTTTATTTAAT
TTAATTATTAAAATTTCAGTTTGGAGAGAACTCTTCAAAAAGATTTTGGCAATAGAGCCCCCACC
TCAATAATTGAGGTGAGGGTTTTAATATGTAGAGGAGTAGTTTGGAGAGAGCTCTCAATAATTGA
GGTAGGATCTTAACACATAGAGGAGCTCATGGAGAGAACTCTTTAAAATATAAAAATAAAAAATT
TCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAATATTTATTAGT
ATGATTATATAAATTTAATTTAATTTTTTTATAAATAGTTTAAAGTTATTTTATTTAATTTAATT
ATTAAAATTTCAGTTTGAAAGAGAGCTCTTCAAAAAGATTTTGGCAGGAGATATATATTTTCCTG
TCGAGCCCCCTACCTCAATAATTGAGGTGAGAGGTTTTAATATGTAGATGAGTCACTTTGGAGAG
AACTCTCAAATTAATTGAGGTAGGATCTTAACACATAGAGGAGCTCAGAAAGAAAACTCTTTAAA
ATATAAAATAAAAAATTTTATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTA
TTAAAATATTTATTAGTATCATTATATAAATTTAATTTATTTTTTTATAAATAATTTAAAGTTAT
TTAATTTAATTTAATTATTAAAA
Found at i:1658239 original size:25 final size:25
Alignment explanation
Indices: 1658193--1658245 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
1658183 ATTAATATAA
*
1658193 TTATAAAAATTTAATTTAATTTT-T
1 TTATAAAAATTTAAGTTAATTTTAT
1658217 TTATAAATAATTTAAAGTT-ATTTTAT
1 TTATAAA-AATTT-AAGTTAATTTTAT
1658243 TTA
1 TTA
1658246 ATTTAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 7 0.28
25 10 0.40
26 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTATAAAAATTTAAGTTAATTTTAT
Found at i:1658292 original size:674 final size:677
Alignment explanation
Indices: 1657312--1658584 Score: 2175
Period size: 674 Copynumber: 1.9 Consensus size: 677
1657302 TTGGCATGAG
*
1657312 CCCCCACCTCAATAATTGAGGTGAGGGATTTTAATATGTAGAGGAGTAGTTTGGAGAGAGCTCTC
1 CCCCCACCTCAATAATTGAGGTGAGGGATTTTAATATGTAGAGGAGCAGTTTGGAGAGAGCTCTC
*
1657377 AATAATTGAGGTTGGATCTTAACACATAGAGGATCTCATGGAGAGAACTCTTTAAAATATAAAAA
66 AATAATTGAGGTAGGATCTTAACACATAGAGGATCTCATGGAGAGAACTCTTTAAAATATAAAAA
*
1657442 TAAAAAATTTTATTCTTAACAGTTTTTTAAAATAAAGATATAATTATTTTTAATTATTAAAATAT
131 TAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTATTTTTAATTATTAAAATAT
* * * *
1657507 TTATTAGTATCATTATATAAATTTAATTTAATTTTTTTATAAATAGTTTAAAGTTATTTTATTTA
196 TTATTAATATAATTATAAAAATTTAATTTAATTTTTTTATAAATAATTTAAAGTTATTTTATTTA
* * *
1657572 ATTTAATTATTAAAATTTCAGTTTAGAGAGAGCTCTTCAAAAAGATTTTGGCAGGGGATATATAT
261 ATTTAATTATTAAAATTTCAGTTGAGAGAAAGCTCTTCAAAAAGATTTTGGCAGAGGATATATAT
* *
1657637 TTTCCTGTCGAGCC-CCCTACCTCAATAATTGAGGT-GAGAGGTTTTAATATGTAGATGAGCACT
326 TTTCCTGTCGAGCCTCCC-ACCTCAATAATTGAGGTGGAG-GGTTTTAATATATAGAGGAGCACT
* * * *
1657700 TTGGAGGGAGCTCTCAATAATTGAGGTAGGATCTTAACACATAGAGGAGCTTAGGGAGAGAACTC
389 TTGAAGAGAGCTCTCAATAATTGAGGTAGGATCTTAACACATAGAGAAGCTCAGGGAGAGAACTC
* *
1657765 TTTAAAATAT-AAA-AAAAAATTT-ATTTTTAACAGTTTTTTAAAATAAAGATATAATTTATTTT
454 TTTAAAATATAAAATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAAATATAATTTATTTT
1657827 TAATTATTAAAATATTTATTAGTATGATTATATAAATTTAATTTAA-TTTTTTTATAAATAATTT
519 TAATTATTAAAATATTTATTAGTATGATTATATAAATTTAATTTAATTTTTTTTATAAATAATTT
1657891 AAAGTTATTTAATTTAATTTAATTATTAAAATTTCAATTGGGAGAGAGCTCTTCAAAAAGATTTT
584 AAAGTTATTTAATTTAATTTAATTATTAAAATTTCAATTGGGAGAGAGCTCTTCAAAAAGATTTT
1657956 GGCAGGGGATATATATTTTCCTGTCTGGC
649 GGCAGGGGATATATATTTTCCTGTCTGGC
* *
1657985 CCCCCACCTTAATAATTGAGGTG-GGGGTTTTAATATGTAGAGGAGCAGTTTGGAGAGAGCTCTC
1 CCCCCACCTCAATAATTGAGGTGAGGGATTTTAATATGTAGAGGAGCAGTTTGGAGAGAGCTCTC
1658049 AAATAATTGAGGTAGGATCTTAACACATAGAGGAGT-TCATGGAGAGAACTCTTTAAAATATAAA
66 -AATAATTGAGGTAGGATCTTAACACATAGAGGA-TCTCATGGAGAGAACTCTTTAAAATATAAA
1658113 AATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTTATTTTTAATTATTAAAA
129 AATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAA-TTATTTTTAATTATTAAAA
1658178 TATTTATTAATATAATTATAAAAATTTAATTTAATTTTTTTATAAATAATTTAAAGTTATTTTAT
193 TATTTATTAATATAATTATAAAAATTTAATTTAATTTTTTTATAAATAATTTAAAGTTATTTTAT
*
1658243 TTAATTTAATTATTAAAATTTCAGTTGGGAGAAAGCTCTTCAAAAAGATTTTGGCAGAGGATATA
258 TTAATTTAATTATTAAAATTTCAGTTGAGAGAAAGCTCTTCAAAAAGATTTTGGCAGAGGATATA
* * * *
1658308 TATTTTCCTGTCGGGCCTCCCACTTGAATAATTGAGGTGGAGGGTTTTAATATATAGAGGAGCAG
323 TATTTTCCTGTCGAGCCTCCCACCTCAATAATTGAGGTGGAGGGTTTTAATATATAGAGGAGCAC
*
1658373 TTTGAAGAGAGCTCTCAATAATTGAGGTAGGATCTTAACACATAGAGAAGCTCATGGAGAGAACT
388 TTTGAAGAGAGCTCTCAATAATTGAGGTAGGATCTTAACACATAGAGAAGCTCAGGGAGAGAACT
1658438 CTTTAAAATATAAAAATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAAATATAATTTATT
453 CTTTAAAATAT-AAAATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAAATATAATTTATT
* *
1658503 TTTAATTATTAAAATATTTTTTAGTATGATTATATAAATTTAATTTAATTTTTTTTATAAATAGT
517 TTTAATTATTAAAATATTTATTAGTATGATTATATAAATTTAATTTAATTTTTTTTATAAATAAT
*
1658568 TTAAAGTTATTTTATTT
582 TTAAAGTTATTTAATTT
1658585 GTAGGTATGA
Statistics
Matches: 561, Mismatches: 29, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
672 39 0.07
673 126 0.22
674 264 0.47
675 6 0.01
676 3 0.01
677 9 0.02
678 83 0.15
679 31 0.06
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (677 bp):
CCCCCACCTCAATAATTGAGGTGAGGGATTTTAATATGTAGAGGAGCAGTTTGGAGAGAGCTCTC
AATAATTGAGGTAGGATCTTAACACATAGAGGATCTCATGGAGAGAACTCTTTAAAATATAAAAA
TAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAGATATAATTATTTTTAATTATTAAAATAT
TTATTAATATAATTATAAAAATTTAATTTAATTTTTTTATAAATAATTTAAAGTTATTTTATTTA
ATTTAATTATTAAAATTTCAGTTGAGAGAAAGCTCTTCAAAAAGATTTTGGCAGAGGATATATAT
TTTCCTGTCGAGCCTCCCACCTCAATAATTGAGGTGGAGGGTTTTAATATATAGAGGAGCACTTT
GAAGAGAGCTCTCAATAATTGAGGTAGGATCTTAACACATAGAGAAGCTCAGGGAGAGAACTCTT
TAAAATATAAAATAAAAAATTTCATTCTTAACAGTTTTTTAAAATAAAAATATAATTTATTTTTA
ATTATTAAAATATTTATTAGTATGATTATATAAATTTAATTTAATTTTTTTTATAAATAATTTAA
AGTTATTTAATTTAATTTAATTATTAAAATTTCAATTGGGAGAGAGCTCTTCAAAAAGATTTTGG
CAGGGGATATATATTTTCCTGTCTGGC
Found at i:1658651 original size:27 final size:29
Alignment explanation
Indices: 1658621--1658682 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 29
1658611 TGTAATATTA
*
1658621 ATTTGATTAGAA--TTATTATTTA-TTTTT
1 ATTTGATTAGAAGTTTA-AATTTATTTTTT
1658648 ATTTG--TAGAAGTTTAAATTTATTTTTT
1 ATTTGATTAGAAGTTTAAATTTATTTTTT
1658675 ATTTGATT
1 ATTTGATT
1658683 TTATGGGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
25 5 0.17
26 5 0.17
27 18 0.62
29 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (29 bp):
ATTTGATTAGAAGTTTAAATTTATTTTTT
Found at i:1659718 original size:27 final size:25
Alignment explanation
Indices: 1659657--1659725 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 25
1659647 TGATTTTTAA
*
1659657 AATTTAATTATATTTTTTATTAGGT
1 AATTTAATTTTATTTTTTATTAGGT
* *
1659682 ATGATATAATTTTAATTTTTTATTTATGT
1 A--ATTTAATTTT-ATTTTTTA-TTAGGT
*
1659711 AATTTAATTTGATTT
1 AATTTAATTTTATTT
1659726 ATAATAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
25 1 0.03
26 4 0.11
27 16 0.46
28 8 0.23
29 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (25 bp):
AATTTAATTTTATTTTTTATTAGGT
Found at i:1660197 original size:24 final size:21
Alignment explanation
Indices: 1660145--1660197 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 21
1660135 TCATATTTTT
1660145 TTAATTTTTATTATTTATTTA
1 TTAATTTTTATTATTTATTTA
**
1660166 TTCTTTTTTAGTTAAATTTATTTA
1 TTAATTTTTA-TT--ATTTATTTA
1660190 TTAATTTT
1 TTAATTTT
1660198 ATCTAGTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 8 0.32
22 2 0.08
24 15 0.60
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (21 bp):
TTAATTTTTATTATTTATTTA
Found at i:1662357 original size:24 final size:23
Alignment explanation
Indices: 1662330--1662378 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1662320 ATTAATGTAA
*
1662330 ATTTTTTAAATTTAATTAAATATT
1 ATTTTTT-AATTTAATTAAAAATT
* *
1662354 ATTTTTTTATTTTATTAAAAATT
1 ATTTTTTAATTTAATTAAAAATT
1662377 AT
1 AT
1662379 AATAAAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTTTAATTTAATTAAAAATT
Found at i:1662421 original size:132 final size:131
Alignment explanation
Indices: 1662272--1662541 Score: 400
Period size: 133 Copynumber: 2.1 Consensus size: 131
1662262 AAAAAATTAA
* *
1662272 TTTAAAATTTTTTA-TTTTAAAAAAATATAATAATTAATATTTTAATTTATTAATGTAAATTTTT
1 TTTAAAATTTGTTATTTTTAAAAAAACATAATAATTAATATTTTAATTTATTAATGTAAATTTTT
* * **
1662336 TAAATTTAATTAAATATTATTTTTTTATTTTATTAAAAATTATAATAA-AAAACTTTTTTATTTT
66 TAAACTTAATTAAATATTA-TTTTTAATTTTATTAAAAA--ATAATAATAAAACCATTTTATTTT
1662400 TTAT
128 TTAT
* * * *
1662404 TTTAAAATTTGTTATTTTTATAAAAACATAATAATTAATATTTTATTTTGTTAATGTAATTTTTT
1 TTTAAAATTTGTTATTTTTAAAAAAACATAATAATTAATATTTTAATTTATTAATGTAAATTTTT
*
1662469 TAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAATAAACCCATTTTATTTTTTA
66 TAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAATAAAACCATTTTATTTTTTA
1662534 T
131 T
1662535 TTTAAAA
1 TTTAAAA
1662542 ATAATTAATA
Statistics
Matches: 125, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
130 7 0.06
131 24 0.19
132 31 0.25
133 63 0.50
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (131 bp):
TTTAAAATTTGTTATTTTTAAAAAAACATAATAATTAATATTTTAATTTATTAATGTAAATTTTT
TAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAATAAAACCATTTTATTTTTTA
T
Found at i:1664361 original size:2 final size:2
Alignment explanation
Indices: 1664354--1664390 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1664344 GCAAAGTGAC
1664354 AT AT 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 AT AT A
1664391 GAAGTTGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1670703 original size:2 final size:2
Alignment explanation
Indices: 1670696--1670733 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1670686 AAGTCTCTAC
1670696 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
1670734 GCATAACGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1674045 original size:30 final size:28
Alignment explanation
Indices: 1674011--1674066 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 28
1674001 AAAATTAGTA
1674011 TTTAAATAATAAAATATATATTTTATATAT
1 TTTAAATAATAAAAT-TA-ATTTTATATAT
*
1674041 TTTAAATAATCAAATTAATTTTATAT
1 TTTAAATAATAAAATTAATTTTATAT
1674067 CATACTTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 9 0.36
29 2 0.08
30 14 0.56
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
TTTAAATAATAAAATTAATTTTATATAT
Found at i:1676808 original size:14 final size:15
Alignment explanation
Indices: 1676781--1676813 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1676771 ACTTATTATT
1676781 TTTTAAATAAAATAA
1 TTTTAAATAAAATAA
1676796 TTTTAAA-AAAATAA
1 TTTTAAATAAAATAA
1676810 TTTT
1 TTTT
1676814 TTAATTCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTTAAATAAAATAA
Found at i:1676814 original size:15 final size:16
Alignment explanation
Indices: 1676780--1676814 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1676770 AACTTATTAT
1676780 TTTTTAAATAAAATAA
1 TTTTTAAATAAAATAA
1676796 -TTTTAAA-AAAATAA
1 TTTTTAAATAAAATAA
1676810 TTTTT
1 TTTTT
1676815 TAATTCGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTTTAAATAAAATAA
Found at i:1681009 original size:2 final size:2
Alignment explanation
Indices: 1681002--1681042 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1680992 ATTACTGATT
*
1681002 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA 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
1681043 CTTTGGAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1681149 original size:2 final size:2
Alignment explanation
Indices: 1681142--1681185 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1681132 ATGGAAGTTT
1681142 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1681182 TA TA
1 TA TA
1681186 GCAGTCTTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1682380 original size:22 final size:22
Alignment explanation
Indices: 1682346--1682397 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1682336 TAATAATAAA
* *
1682346 AAAATTATTTAAAT-TTAATTAT
1 AAAATAATATAAATATTAA-TAT
*
1682368 AATATAATATAAATATTAATAT
1 AAAATAATATAAATATTAATAT
1682390 AAAATAAT
1 AAAATAAT
1682398 TTCAAATCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATAATATAAATATTAATAT
Found at i:1684801 original size:19 final size:19
Alignment explanation
Indices: 1684763--1684803 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1684753 CTTTTAATTG
*
1684763 ATTTATAAAATATTTTTAA
1 ATTTATAAAATATTTATAA
1684782 ATTTA-AAAATATTTAATAA
1 ATTTATAAAATATTT-ATAA
1684801 ATT
1 ATT
1684804 CAAATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTATAAAATATTTATAA
Found at i:1687991 original size:3 final size:3
Alignment explanation
Indices: 1687983--1688029 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1687973 GATCAGCACT
1687983 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1688030 TTTTGGTACG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1689106 original size:20 final size:21
Alignment explanation
Indices: 1689067--1689108 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1689057 TAAAAAAATT
*
1689067 ATTTTTTTATAATATTTTTAA
1 ATTTTTTTATAATATATTTAA
*
1689088 ATTTTTTTATATTA-ATTTAA
1 ATTTTTTTATAATATATTTAA
1689108 A
1 A
1689109 AATAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTTTTATAATATATTTAA
Found at i:1689684 original size:22 final size:23
Alignment explanation
Indices: 1689643--1689686 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1689633 TAAAATTTGA
*
1689643 TTTTTAAATTTATTAAATATTATT
1 TTTTTAAATTAATT-AATATTATT
1689667 TTTTTAAATTAATT-ATATTA
1 TTTTTAAATTAATTAATATTA
1689687 ATTAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
24 13 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTTAAATTAATTAATATTATT
Found at i:1689689 original size:13 final size:13
Alignment explanation
Indices: 1689673--1689723 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
1689663 TATTTTTTTA
1689673 AATTAATTATATT
1 AATTAATTATATT
1689686 AATTAATTATATT
1 AATTAATTATATT
*
1689699 AATT--TTAAATT
1 AATTAATTATATT
**
1689710 CCTTAATTATATT
1 AATTAATTATATT
1689723 A
1 A
1689724 TTGGATGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
11 8 0.26
13 23 0.74
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTAATTATATT
Found at i:1689864 original size:2 final size:2
Alignment explanation
Indices: 1689857--1689899 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1689847 GCTTTGCTTT
1689857 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
1689899 T
1 T
1689900 GTAGAGAGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1689907 original size:2 final size:2
Alignment explanation
Indices: 1689902--1689934 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1689892 ATATATATGT
1689902 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1689935 ATCGAAGCTG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1690217 original size:22 final size:20
Alignment explanation
Indices: 1690190--1690242 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 20
1690180 GAGAATATTC
1690190 AAATAAAAATATTAAATTTAAA
1 AAATAAAAATATTAAA--TAAA
1690212 AAAT--AAAT-TTAAATAAA
1 AAATAAAAATATTAAATAAA
1690229 AAATAAAATATATT
1 AAATAAAA-ATATT
1690243 GAAAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
17 8 0.30
19 7 0.26
20 6 0.22
21 2 0.07
22 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAAAAATATTAAATAAA
Found at i:1690494 original size:30 final size:31
Alignment explanation
Indices: 1690428--1690505 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
1690418 AATAATATTA
* **
1690428 AAAAAATTTAATAAAAAATATATTTAATTAT
1 AAAAAATTAAATAAAAAATATATTTAAAAAT
* *
1690459 TAAAAATTAAAT-TAAAATATATTTAAAAAT
1 AAAAAATTAAATAAAAAATATATTTAAAAAT
1690489 AAAAAATATAATATAAA
1 AAAAAAT-TAA-ATAAA
1690506 TGAGAATAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 21 0.57
31 13 0.35
32 2 0.05
33 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
AAAAAATTAAATAAAAAATATATTTAAAAAT
Found at i:1692786 original size:21 final size:22
Alignment explanation
Indices: 1692762--1692809 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1692752 GTTTTATTAT
1692762 TTTAAAAT-TTTTAT-ATTAATA
1 TTTAAAATGTTTTATAATTAA-A
*
1692783 TTT-ATATGTTTTATAATTAAA
1 TTTAAAATGTTTTATAATTAAA
1692804 TTTAAA
1 TTTAAA
1692810 TTCGAGCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
20 3 0.14
21 13 0.59
22 6 0.27
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAAATGTTTTATAATTAAA
Found at i:1694368 original size:16 final size:16
Alignment explanation
Indices: 1694347--1694381 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1694337 ATAATTTAGG
*
1694347 TTTCAATTTTAAATTA
1 TTTCAAGTTTAAATTA
*
1694363 TTTCAAGTTTGAATTA
1 TTTCAAGTTTAAATTA
1694379 TTT
1 TTT
1694382 TGGACTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (16 bp):
TTTCAAGTTTAAATTA
Done.