Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold38
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: 2073527
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 13 of 15
Found at i:1785446 original size:30 final size:30
Alignment explanation
Indices: 1785411--1785488 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 30
1785401 AATAATATAA
*
1785411 ATATAATAAAAAATAAATATATTTAAATTT
1 ATATAATAAAAAATAAATATATTAAAATTT
*
1785441 ATATAA-AATAAATTATTAATATATTAAAATTT
1 ATATAATAA-AAA--ATAAATATATTAAAATTT
*
1785473 ATATAAATAAATAATA
1 ATAT-AATAAAAAATA
1785489 TTTTAAATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
29 2 0.05
30 9 0.23
31 2 0.05
32 20 0.51
33 4 0.10
34 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
ATATAATAAAAAATAAATATATTAAAATTT
Found at i:1785481 original size:20 final size:18
Alignment explanation
Indices: 1785426--1785478 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 18
1785416 ATAAAAAATA
1785426 AATATATTTAAATTTATAT
1 AATATA-TTAAATTTATAT
1785445 AA-A-A-TAAA-TTAT-T
1 AATATATTAAATTTATAT
1785458 AATATATTAAAATTTATAT
1 AATATATT-AAATTTATAT
1785477 AA
1 AA
1785479 ATAAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
13 3 0.11
14 5 0.18
15 5 0.18
16 1 0.04
17 4 0.14
18 5 0.18
19 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATATATTAAATTTATAT
Found at i:1785580 original size:17 final size:17
Alignment explanation
Indices: 1785558--1785593 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1785548 TGCTTTCCAA
1785558 TCAGACCATCAGATCAT
1 TCAGACCATCAGATCAT
1785575 TCAGACCATCAGATCAT
1 TCAGACCATCAGATCAT
1785592 TC
1 TC
1785594 CGATGGCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.31, G:0.11, T:0.25
Consensus pattern (17 bp):
TCAGACCATCAGATCAT
Found at i:1785822 original size:20 final size:19
Alignment explanation
Indices: 1785783--1785825 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1785773 ATTATAATTA
*
1785783 AAAT-TTAAATATATAAAT
1 AAATATTAAATATACAAAT
1785801 AAATATTAAATATAACAAAT
1 AAATATTAAATAT-ACAAAT
1785821 AAATA
1 AAATA
1785826 AATAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.18
19 8 0.36
20 10 0.45
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATTAAATATACAAAT
Found at i:1786290 original size:16 final size:16
Alignment explanation
Indices: 1786261--1786363 Score: 50
Period size: 16 Copynumber: 6.2 Consensus size: 16
1786251 GATGAAGATG
*
1786261 AAATAAAAAAATAATTA
1 AAAT-AAAATATAATTA
*
1786278 AAATAAAATATAAATA
1 AAATAAAATATAATTA
** *
1786294 CGATAAAAAATAATATA
1 AAATAAAATATAAT-TA
*
1786311 AATATATAAATAT-TTTA
1 AA-ATA-AAATATAATTA
*
1786328 AAA-AATATATAATATA
1 AAATAAAATATAAT-TA
* *
1786344 AATTATTAATAT-ATTA
1 AAATA-AAATATAATTA
1786360 AAAT
1 AAAT
1786364 TTATTTAAAT
Statistics
Matches: 63, Mismatches: 16, Indels: 15
0.67 0.17 0.16
Matches are distributed among these distances:
14 5 0.08
15 2 0.03
16 30 0.48
17 13 0.21
18 8 0.13
19 5 0.08
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (16 bp):
AAATAAAATATAATTA
Found at i:1786345 original size:33 final size:32
Alignment explanation
Indices: 1786303--1786388 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 32
1786293 ACGATAAAAA
1786303 ATAATATAAATATATAAATATTTTAAAAAATAT
1 ATAATATAAATATATAAATATTTTAAAAAAT-T
* *
1786336 ATAATATAAAT-TATTAATATATT--AAAATT
1 ATAATATAAATATATAAATATTTTAAAAAATT
*
1786365 -T-ATTTAAATATA-AAATATTTTAAA
1 ATAATATAAATATATAAATATTTTAAA
1786389 TATTATTATG
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
27 14 0.31
28 3 0.07
29 2 0.04
30 5 0.11
32 10 0.22
33 11 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
ATAATATAAATATATAAATATTTTAAAAAATT
Found at i:1786367 original size:18 final size:18
Alignment explanation
Indices: 1786345--1786393 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
1786335 TATAATATAA
1786345 ATTATTAATATATTAAAAT
1 ATTATTAA-ATATTAAAAT
1786364 -TTATTTAAATA-TAAAAT
1 ATTA-TTAAATATTAAAAT
1786381 ATT-TTAAATATTA
1 ATTATTAAATATTA
1786394 TTATGATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 7 0.26
17 8 0.30
18 8 0.30
19 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTATTAAATATTAAAAT
Found at i:1792532 original size:27 final size:27
Alignment explanation
Indices: 1792502--1792569 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
1792492 TATTAATTTT
*
1792502 ATTATAAATTT-AAAATATTTAAATATA
1 ATTATAAATTTAAAAATA-TAAAATATA
*
1792529 ATTAT-AATATAAAAATATAAAATATA
1 ATTATAAATTTAAAAATATAAAATATA
1792555 ATTATTAAA-TTAAAA
1 ATTA-TAAATTTAAAA
1792570 GAAAAAGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
26 16 0.46
27 17 0.49
28 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
ATTATAAATTTAAAAATATAAAATATA
Found at i:1792569 original size:26 final size:26
Alignment explanation
Indices: 1792502--1792569 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 26
1792492 TATTAATTTT
*
1792502 ATTATAAATTTAAAATATTTAAATATA
1 ATTATAAA-TTAAAATATTAAAATATA
*
1792529 ATTATAATATAAAAATA-TAAAATATA
1 ATTATAA-ATTAAAATATTAAAATATA
1792555 ATTATTAAATTAAAA
1 ATTA-TAAATTAAAA
1792570 GAAAAAGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 18 0.50
27 17 0.47
28 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATTATAAATTAAAATATTAAAATATA
Found at i:1793763 original size:27 final size:26
Alignment explanation
Indices: 1793724--1793774 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
1793714 ATCATACATT
1793724 TAATAAATATAAAAACAATATAATATA
1 TAATAAATATAAAAACAAT-TAATATA
* *
1793751 TAATAAATTTAAACACAATTAATA
1 TAATAAATATAAAAACAATTAATA
1793775 ACATAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (26 bp):
TAATAAATATAAAAACAATTAATATA
Found at i:1793780 original size:27 final size:27
Alignment explanation
Indices: 1793724--1793781 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1793714 ATCATACATT
*
1793724 TAATAAATATAAAAACAATATAATATA
1 TAATAAATATAAAAACAATATAATACA
* *
1793751 TAATAAATTTAAACACAAT-TAATAACA
1 TAATAAATATAAAAACAATATAAT-ACA
1793778 TAAT
1 TAAT
1793782 TTATTTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (27 bp):
TAATAAATATAAAAACAATATAATACA
Found at i:1796521 original size:19 final size:18
Alignment explanation
Indices: 1796490--1796566 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 18
1796480 TTAATATGTG
1796490 AATATATTAATATTTATATA
1 AATATA-TAATATTTATA-A
1796510 AATATATAATATTT-TAA
1 AATATATAATATTTATAA
*
1796527 TAAT-TATAATATATA-AA
1 -AATATATAATATTTATAA
*
1796544 AATATATAAAATATTATACA
1 AATATATAATAT-TTATA-A
1796564 AAT
1 AAT
1796567 TATCAATTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
16 3 0.06
17 19 0.40
18 7 0.15
19 9 0.19
20 10 0.21
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATATAATATTTATAA
Found at i:1796547 original size:27 final size:27
Alignment explanation
Indices: 1796490--1796550 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
1796480 TTAATATGTG
* *
1796490 AATATATTAATATTTATATAAATATAT
1 AATATATTAATAATTATATAAATATAA
* *
1796517 AATATTTTAATAATTATA-ATATATAAA
1 AATATATTAATAATTATATAAATAT-AA
1796544 AATATAT
1 AATATAT
1796551 AAAATATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AATATATTAATAATTATATAAATATAA
Found at i:1796547 original size:34 final size:35
Alignment explanation
Indices: 1796474--1796552 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 35
1796464 TAAAATAAAT
*
1796474 AAAATAT-TAATATGTGAATATATTAATATTTATA
1 AAAATATATAATATGTGAATATATTAATATATATA
* * *
1796508 TAAATATATAATATTTTAATA-ATT-ATAATATATA
1 AAAATATATAATATGTGAATATATTAAT-ATATATA
1796542 AAAATATATAA
1 AAAATATATAA
1796553 AATATTATAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
33 2 0.05
34 25 0.66
35 11 0.29
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (35 bp):
AAAATATATAATATGTGAATATATTAATATATATA
Found at i:1797029 original size:25 final size:25
Alignment explanation
Indices: 1796982--1797046 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 25
1796972 TAGTGTATAA
* *
1796982 ATTTATATATAATTAAAAAATAATATT
1 ATTTATAT-TTATT-AAAAATAAAATT
1797009 ATGTTAT-TTTATTAAAAATAAAATT
1 AT-TTATATTTATTAAAAATAAAATT
1797034 ATTTATATTTATT
1 ATTTATATTTATT
1797047 TTTAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.12
25 19 0.56
26 4 0.12
27 3 0.09
28 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
ATTTATATTTATTAAAAATAAAATT
Found at i:1798412 original size:25 final size:23
Alignment explanation
Indices: 1798384--1798452 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 23
1798374 AAAAATTAGA
*
1798384 AAATAATAATATTATTTTATTATT
1 AAAT-ATAATATTATTTTATTAAT
*
1798408 CAAAT-TAATATAATATTT-TTAAT
1 -AAATATAATATTAT-TTTATTAAT
1798431 AAATAT-ATATTATTTTATTAAT
1 AAATATAATATTATTTTATTAAT
1798453 TTTACTTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.08
22 15 0.39
23 13 0.34
24 3 0.08
25 4 0.11
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
AAATATAATATTATTTTATTAAT
Found at i:1798800 original size:18 final size:19
Alignment explanation
Indices: 1798753--1798800 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
1798743 TTATATTTAA
1798753 ATAAATTTAAAATTTTTATT
1 ATAAA-TTAAAATTTTTATT
*
1798773 AAAAATTAAAA-TTTTATT
1 ATAAATTAAAATTTTTATT
1798791 -TAAATGTAAA
1 ATAAAT-TAAA
1798801 TTAAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 4 0.16
18 11 0.44
19 6 0.24
20 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
ATAAATTAAAATTTTTATT
Found at i:1798876 original size:3 final size:3
Alignment explanation
Indices: 1798868--1798901 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1798858 TTTCAAGCTT
1798868 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1798902 TTAAGTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1798891 original size:14 final size:14
Alignment explanation
Indices: 1798872--1798900 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1798862 AAGCTTTTAT
1798872 TATTATTATTATTA
1 TATTATTATTATTA
1798886 TATTATTATTATTA
1 TATTATTATTATTA
1798900 T
1 T
1798901 TTTAAGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:1798891 original size:17 final size:17
Alignment explanation
Indices: 1798869--1798901 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1798859 TTCAAGCTTT
1798869 TATTATTATTATTATTA
1 TATTATTATTATTATTA
1798886 TATTATTATTATTATT
1 TATTATTATTATTATT
1798902 TTAAGTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:1802434 original size:20 final size:20
Alignment explanation
Indices: 1802396--1802434 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1802386 AATAATTTTA
* **
1802396 ATAGTAAATGATTGTTAAAT
1 ATAGTAAATAATTAATAAAT
1802416 ATAGTAAATAATTAATAAA
1 ATAGTAAATAATTAATAAA
1802435 AAATAGAGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (20 bp):
ATAGTAAATAATTAATAAAT
Found at i:1803571 original size:20 final size:20
Alignment explanation
Indices: 1803543--1803583 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1803533 AATCGATAAC
*
1803543 CTTGAATTTTGAATTAAATT
1 CTTGAATTTTAAATTAAATT
*
1803563 CTTGCATTTTAAATTAAATT
1 CTTGAATTTTAAATTAAATT
1803583 C
1 C
1803584 AAGCTCTAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (20 bp):
CTTGAATTTTAAATTAAATT
Found at i:1805577 original size:33 final size:33
Alignment explanation
Indices: 1805535--1805599 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
1805525 TGCAAGTGAG
1805535 ATAGAGCAGAATCAAGCCGTAATCACTAACGAT
1 ATAGAGCAGAATCAAGCCGTAATCACTAACGAT
1805568 ATAGAGCAGAATCAAGCCGTAATCACTAACGA
1 ATAGAGCAGAATCAAGCCGTAATCACTAACGA
1805600 AATCTTTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (33 bp):
ATAGAGCAGAATCAAGCCGTAATCACTAACGAT
Found at i:1805883 original size:16 final size:16
Alignment explanation
Indices: 1805851--1805899 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1805841 TTCATCATTC
* *
1805851 TAATCCAAACTCAAAA
1 TAATCTAAACCCAAAA
*
1805867 TAA-CTTAAATCCAAAA
1 TAATC-TAAACCCAAAA
1805883 TAATCTAAACCCAAAA
1 TAATCTAAACCCAAAA
1805899 T
1 T
1805900 GAACCAACCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.55, C:0.22, G:0.00, T:0.22
Consensus pattern (16 bp):
TAATCTAAACCCAAAA
Found at i:1806926 original size:11 final size:11
Alignment explanation
Indices: 1806907--1806980 Score: 55
Period size: 11 Copynumber: 6.5 Consensus size: 11
1806897 ATATTTTGAT
1806907 TTTATATTT-AA
1 TTTA-ATTTAAA
1806918 TTTAAATTTAAA
1 TTT-AATTTAAA
*
1806930 TAT-ATTTAATA
1 TTTAATTTAA-A
1806941 TTT-ATATTAAA
1 TTTAAT-TTAAA
*
1806952 TATATATTTAATA
1 TTTA-ATTTAA-A
1806965 TTTAATTTAAA
1 TTTAATTTAAA
1806976 TTTAA
1 TTTAA
1806981 ATAGTATTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
10 6 0.12
11 21 0.40
12 19 0.37
13 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:1806926 original size:24 final size:23
Alignment explanation
Indices: 1806899--1806978 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 23
1806889 TTCATTTGAT
1806899 ATTTTGATTTTATATTTAATTTAA
1 ATTTT-ATTTTATATTTAATTTAA
1806923 ATTTAAATATATTTAATATTT-ATATTAA
1 ATTT---TAT-TTT-ATATTTAAT-TTAA
* *
1806951 ATATATATTTAATATTTAATTTAA
1 AT-TTTATTTTATATTTAATTTAA
1806975 ATTT
1 ATTT
1806979 AAATAGTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 17
0.69 0.05 0.26
Matches are distributed among these distances:
23 1 0.02
24 16 0.36
25 4 0.09
26 5 0.11
27 6 0.13
28 12 0.27
29 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (23 bp):
ATTTTATTTTATATTTAATTTAA
Found at i:1806936 original size:34 final size:34
Alignment explanation
Indices: 1806907--1806979 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
1806897 ATATTTTGAT
* *
1806907 TTTATATTTAATTTAAATTTAAATATATTTAATA
1 TTTATATTAAATATAAATTTAAATATATTTAATA
* *
1806941 TTTATATTAAATATATATTTAATATTTAATTTAA-A
1 TTTATATTAAATATAAATTTAA-ATAT-ATTTAATA
1806976 TTTA
1 TTTA
1806980 AATAGTATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 19 0.58
35 8 0.24
36 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
TTTATATTAAATATAAATTTAAATATATTTAATA
Found at i:1806980 original size:6 final size:6
Alignment explanation
Indices: 1806907--1806982 Score: 54
Period size: 6 Copynumber: 13.2 Consensus size: 6
1806897 ATATTTTGAT
* * *
1806907 TTTATA TTT-AA TTTAAA TTTAAA --TATA TTTAATA TTTATA -TTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
* *
1806952 TATATA TTTAATA TTT-AA TTTAAA TTTAAA T
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA T
1806983 AGTATTAATT
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
4 3 0.06
5 12 0.22
6 30 0.56
7 9 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:1807510 original size:15 final size:15
Alignment explanation
Indices: 1807490--1807519 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1807480 CTTTTGAAAT
1807490 AAAATAAAAAATATA
1 AAAATAAAAAATATA
*
1807505 AAAATAAAATATATA
1 AAAATAAAAAATATA
1807520 GTAAGTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATAAAAAATATA
Found at i:1808560 original size:23 final size:22
Alignment explanation
Indices: 1808505--1808560 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 22
1808495 GATGATTTTA
*
1808505 TTTAAATTTAATTATAAATATTT
1 TTTAAATTTAA-TATAAATAATT
1808528 TTTAAA--TAATA-AAATAAAATT
1 TTTAAATTTAATATAAAT--AATT
1808549 TTTAAATTTAAT
1 TTTAAATTTAAT
1808561 TCGATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 4 0.14
20 2 0.07
21 12 0.43
23 10 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAAATTTAATATAAATAATT
Found at i:1810546 original size:14 final size:14
Alignment explanation
Indices: 1810529--1810560 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1810519 TTTAATTTAA
*
1810529 TAAATACAATTTTT
1 TAAATAAAATTTTT
1810543 TAAATAAAATTTTT
1 TAAATAAAATTTTT
1810557 TAAA
1 TAAA
1810561 AATAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAATAAAATTTTT
Found at i:1811287 original size:22 final size:21
Alignment explanation
Indices: 1811228--1811289 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
1811218 ATTGTATTTG
*
1811228 TATTATTTTTTCATATCATATA
1 TATTATTATTT-ATATCATATA
** *
1811250 TATCGTGTATTTATATTATATA
1 TATTAT-TATTTATATCATATA
1811272 TATTATTATTTAATATCA
1 TATTATTATTT-ATATCA
1811290 AATGTTTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 5 0.16
22 22 0.71
23 4 0.13
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.56
Consensus pattern (21 bp):
TATTATTATTTATATCATATA
Found at i:1811617 original size:14 final size:14
Alignment explanation
Indices: 1811598--1811626 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1811588 TTTATACGTG
1811598 TTCATAAAATAATA
1 TTCATAAAATAATA
1811612 TTCATAAAATAATA
1 TTCATAAAATAATA
1811626 T
1 T
1811627 GAGCGAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
TTCATAAAATAATA
Found at i:1813577 original size:16 final size:15
Alignment explanation
Indices: 1813554--1813594 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
1813544 ATTTTAATAG
1813554 TAAATAAATATTAAA
1 TAAATAAATATTAAA
*
1813569 TATAATAAATATTTAA
1 TA-AATAAATATTAAA
1813585 TAAA-AAATAT
1 TAAATAAATAT
1813595 ATTTGATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 4 0.17
16 14 0.58
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATAAATATTAAA
Found at i:1815172 original size:13 final size:12
Alignment explanation
Indices: 1815163--1815205 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
1815153 AATTTATAAT
1815163 TAATATTTATTA
1 TAATATTTATTA
*
1815175 TAATTTATTATTA
1 TAATAT-TTATTA
1815188 TAATATTTATTA
1 TAATATTTATTA
*
1815200 TTATAT
1 TAATAT
1815206 AATTAGGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAATATTTATTA
Found at i:1815173 original size:23 final size:25
Alignment explanation
Indices: 1815147--1815200 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
1815137 TATTTTTAAA
*
1815147 TATTTTAATTTA-TAAT-TAATATT
1 TATTATAATTTATTAATATAATATT
*
1815170 TATTATAATTTATTATTATAATATT
1 TATTATAATTTATTAATATAATATT
1815195 TATTAT
1 TATTAT
1815201 TATATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 11 0.41
24 3 0.11
25 13 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTATAATTTATTAATATAATATT
Found at i:1815197 original size:15 final size:14
Alignment explanation
Indices: 1815169--1815209 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1815159 TAATTAATAT
1815169 TTATTAT-AATTTA
1 TTATTATAAATTTA
1815182 TTATTATAATATTTA
1 TTATTATAA-ATTTA
1815197 TTATTATATAATT
1 TTATTATA-AATT
1815210 AGGATAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.28
14 1 0.04
15 16 0.64
16 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATTATAAATTTA
Found at i:1816361 original size:20 final size:20
Alignment explanation
Indices: 1816323--1816361 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1816313 AAAAAATCAA
*
1816323 TTAATTTAGTTAATGATTAT
1 TTAATTTAGTTAATAATTAT
*
1816343 TTAATTTAGTTATTAATTA
1 TTAATTTAGTTAATAATTA
1816362 AATTAATCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
TTAATTTAGTTAATAATTAT
Found at i:1819010 original size:29 final size:26
Alignment explanation
Indices: 1818986--1819037 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 26
1818976 ATATTATATA
1818986 TTAATATCAATAATTTTTATAATTAAAT
1 TTAA-ATCAA-AATTTTTATAATTAAAT
*
1819014 TTAAATTAAAA-TTTT-TAATTAAAT
1 TTAAATCAAAATTTTTATAATTAAAT
1819038 ATATAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 9 0.39
25 4 0.17
26 2 0.09
27 4 0.17
28 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TTAAATCAAAATTTTTATAATTAAAT
Found at i:1819025 original size:12 final size:12
Alignment explanation
Indices: 1819001--1819044 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1818991 ATCAATAATT
1819001 TTTATAATTAAA
1 TTTATAATTAAA
1819013 TTTA-AATTAAAA
1 TTTATAATT-AAA
*
1819025 TTTTTAATTAAA
1 TTTATAATTAAA
*
1819037 TATATAAT
1 TTTATAAT
1819045 AATTTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 4 0.15
12 19 0.70
13 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTATAATTAAA
Found at i:1819506 original size:18 final size:19
Alignment explanation
Indices: 1819483--1819518 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1819473 TTAATATAAA
1819483 ATAT-AATTTTTTAAAAAT
1 ATATAAATTTTTTAAAAAT
1819501 ATATAAATTTTTTAAAAA
1 ATATAAATTTTTTAAAAA
1819519 ATAAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATAAATTTTTTAAAAAT
Found at i:1819524 original size:16 final size:17
Alignment explanation
Indices: 1819480--1819524 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
1819470 TATTTAATAT
1819480 AAAATATAATTTTTTAAA
1 AAAATA-AATTTTTTAAA
1819498 AATATATAAATTTTTT-AA
1 AA-A-ATAAATTTTTTAAA
1819516 AAAATAAAT
1 AAAATAAAT
1819525 ATAATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.24
17 1 0.04
18 6 0.24
19 9 0.36
20 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATAAATTTTTTAAA
Found at i:1819558 original size:17 final size:17
Alignment explanation
Indices: 1819520--1819552 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1819510 TTTTAAAAAA
1819520 TAAATATA-A-TTATAT
1 TAAATATATATTTATAT
1819535 TAAATATATATTTATAT
1 TAAATATATATTTATAT
1819552 T
1 T
1819553 TTATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAATATATATTTATAT
Found at i:1820018 original size:23 final size:23
Alignment explanation
Indices: 1819977--1820021 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1819967 AAAATTATAA
**
1819977 ATATAAAAATTTTAATTTTAAAT
1 ATATAAAAAAATTAATTTTAAAT
*
1820000 ATATAAAAAAATTATTTTTAAA
1 ATATAAAAAAATTAATTTTAAA
1820022 AATAATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATAAAAAAATTAATTTTAAAT
Found at i:1822365 original size:30 final size:30
Alignment explanation
Indices: 1822303--1822366 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 30
1822293 ATTATGAAAA
* *
1822303 TAAAATTTTAAATAAAAAAACTTAAGCTCT
1 TAAAATTTTAAATAAAAAAAATTAAGCGCT
1822333 TAAAATTTTATAAATAAAAAAAATT-AG-GCT
1 TAAAA-TTT-TAAATAAAAAAAATTAAGCGCT
1822363 TAAA
1 TAAA
1822367 TAAAACTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 11 0.37
31 5 0.17
32 14 0.47
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.33
Consensus pattern (30 bp):
TAAAATTTTAAATAAAAAAAATTAAGCGCT
Found at i:1824224 original size:20 final size:21
Alignment explanation
Indices: 1824201--1824240 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1824191 AAATTAATTC
*
1824201 AATTTAAA-TTATTATTTAAT
1 AATTAAAATTTATTATTTAAT
*
1824221 AATTAAAATTTTTTATTTAA
1 AATTAAAATTTATTATTTAA
1824241 ATTTATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTAAAATTTATTATTTAAT
Found at i:1826492 original size:2 final size:2
Alignment explanation
Indices: 1826482--1826529 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
1826472 ATAAAAAAAT
* * *
1826482 TA TA AA TA TA TA AA TA T- TA TA TA TA AA 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
*
1826523 TG TA TA T
1 TA TA TA T
1826530 TGCAGTAGGT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1827913 original size:20 final size:20
Alignment explanation
Indices: 1827868--1827918 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1827858 ATAAATTTAT
1827868 AAATTATTTATAAATAAATA
1 AAATTATTTATAAATAAATA
* *
1827888 ATATTATTTTATTAA-AAATA
1 AAATTA-TTTATAAATAAATA
1827908 AAATTAATTTA
1 AAATT-ATTTA
1827919 AATTTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTATTTATAAATAAATA
Found at i:1828380 original size:3 final size:3
Alignment explanation
Indices: 1828372--1828414 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1828362 TCTGTAAGTT
1828372 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1828415 GTTTTCCCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1831603 original size:2 final size:2
Alignment explanation
Indices: 1831596--1831631 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1831586 AAATCTTCAA
1831596 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1831632 GTGCCAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1833903 original size:18 final size:19
Alignment explanation
Indices: 1833882--1833923 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1833872 ATTTATAAAC
1833882 TTAATTAGAT-TTTTATTT
1 TTAATTAGATATTTTATTT
*
1833900 TTAA-TATATATTTTATTT
1 TTAATTAGATATTTTATTT
1833918 TTAATT
1 TTAATT
1833924 TTAATTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 16 0.76
19 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTAATTAGATATTTTATTT
Found at i:1833961 original size:12 final size:11
Alignment explanation
Indices: 1833943--1833972 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
1833933 ATTAAAAAAT
1833943 TTTAATTTCAA
1 TTTAATTTCAA
1833954 TTTGAATTTCAA
1 TTT-AATTTCAA
1833966 TTTAATT
1 TTTAATT
1833973 ACTACTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (11 bp):
TTTAATTTCAA
Found at i:1834411 original size:23 final size:19
Alignment explanation
Indices: 1834375--1834448 Score: 64
Period size: 23 Copynumber: 3.8 Consensus size: 19
1834365 TGGTTGTCTA
1834375 ATTTAA-TTT-AATTTTTT
1 ATTTAATTTTAAATTTTTT
*
1834392 ATTTATATTTGATAATATTTATT
1 ATTTA-ATTT--TAA-ATTTTTT
*
1834415 ATTTAAATTTTAAATTATTT
1 ATTT-AATTTTAAATTTTTT
1834435 ATTTAA-TTTAAATT
1 ATTTAATTTTAAATT
1834449 AAATAAAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
17 5 0.11
18 9 0.19
19 4 0.09
20 9 0.19
21 4 0.09
22 1 0.02
23 14 0.30
24 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (19 bp):
ATTTAATTTTAAATTTTTT
Found at i:1834438 original size:20 final size:18
Alignment explanation
Indices: 1834375--1834449 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 18
1834365 TGGTTGTCTA
*
1834375 ATTTAATTT-AATTTTTT
1 ATTTAATTTAAATTATTT
*
1834392 ATTTATATTTGATAATATTTATT
1 ATTTA-ATTT-A-AAT-TAT-TT
1834415 ATTTAAATTTTAAATTATTT
1 ATTT-AA-TTTAAATTATTT
1834435 ATTTAATTTAAATTA
1 ATTTAATTTAAATTA
1834450 AATAAAATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
17 5 0.10
18 13 0.27
19 2 0.04
20 6 0.12
21 5 0.10
22 6 0.12
23 8 0.16
24 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (18 bp):
ATTTAATTTAAATTATTT
Found at i:1835042 original size:34 final size:33
Alignment explanation
Indices: 1834983--1835072 Score: 87
Period size: 34 Copynumber: 2.7 Consensus size: 33
1834973 TATATTTAAA
* *
1834983 ATATAAAATTAAATATA-TTAATAATT-TATTT
1 ATATAAATTTTAATATATTTAATAATTATATTT
*
1835014 CATATAAATTTTAATATATTTATTTAATTATATTT
1 -ATATAAATTTTAATATATTTA-ATAATTATATTT
* *
1835049 ATATTATTTTTAA-ATTATTTAATA
1 ATATAAATTTTAATA-TATTTAATA
1835073 TTTTAATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
32 15 0.31
33 6 0.12
34 22 0.46
35 5 0.10
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (33 bp):
ATATAAATTTTAATATATTTAATAATTATATTT
Found at i:1835060 original size:11 final size:10
Alignment explanation
Indices: 1835022--1835087 Score: 50
Period size: 10 Copynumber: 6.5 Consensus size: 10
1835012 TTCATATAAA
1835022 TTTTAATATATT
1 TTTTAAT-TA-T
1835034 TATTTAATTAT
1 T-TTTAATTAT
*
1835045 ATTTATATTAT
1 TTTTA-ATTAT
1835056 TTTTAA--AT
1 TTTTAATTAT
1835064 TATTTAA-TA-
1 T-TTTAATTAT
1835073 TTTTAATTAT
1 TTTTAATTAT
1835083 TTTTA
1 TTTTA
1835088 TATTCTCATC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
8 8 0.17
9 8 0.17
10 11 0.24
11 10 0.22
12 3 0.07
13 6 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTAATTAT
Found at i:1835085 original size:9 final size:9
Alignment explanation
Indices: 1835036--1835085 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 9
1835026 AATATATTTA
1835036 TTTAATTAT
1 TTTAATTAT
1835045 ATTTATATTATT
1 -TTTA-ATTA-T
1835057 TTTAAATTA-
1 TTT-AATTAT
1835066 TTTAA-TAT
1 TTTAATTAT
1835074 TTTAATTAT
1 TTTAATTAT
1835083 TTT
1 TTT
1835086 TATATTCTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
7 2 0.06
8 7 0.20
9 9 0.26
10 4 0.11
11 11 0.31
12 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTAATTAT
Found at i:1835134 original size:8 final size:8
Alignment explanation
Indices: 1835121--1835193 Score: 71
Period size: 8 Copynumber: 9.0 Consensus size: 8
1835111 CCTTTCCTGA
1835121 AATTATTT
1 AATTATTT
1835129 AATTATTT
1 AATTATTT
1835137 AAATTATTT
1 -AATTATTT
1835146 AAATTATTT
1 -AATTATTT
1835155 AA-TATTTT
1 AATTA-TTT
**
1835163 AATTAAAT
1 AATTATTT
1835171 -ATTATTT
1 AATTATTT
1835178 AA-TATTTT
1 AATTA-TTT
1835186 AATTATTT
1 AATTATTT
1835194 CCAAACAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
7 9 0.16
8 25 0.45
9 21 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
AATTATTT
Found at i:1835143 original size:9 final size:9
Alignment explanation
Indices: 1835120--1835156 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
1835110 TCCTTTCCTG
1835120 AAATTATTT
1 AAATTATTT
1835129 -AATTATTT
1 AAATTATTT
1835137 AAATTATTT
1 AAATTATTT
1835146 AAATTATTT
1 AAATTATTT
1835155 AA
1 AA
1835157 TATTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
AAATTATTT
Found at i:1835178 original size:23 final size:23
Alignment explanation
Indices: 1835120--1835191 Score: 92
Period size: 23 Copynumber: 3.0 Consensus size: 23
1835110 TCCTTTCCTG
*
1835120 AAATTATTTAATTATTTAAATTATTT
1 AAATTATTTAA-TATTTTAATTA--T
1835146 AAATTATTTAATATTTTAATTA-
1 AAATTATTTAATATTTTAATTAT
1835168 AATATTATTTAATATTTTAATTAT
1 AA-ATTATTTAATATTTTAATTAT
1835192 TTCCAAACAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
22 2 0.05
23 20 0.47
25 10 0.23
26 11 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATTATTTAATATTTTAATTAT
Found at i:1835252 original size:13 final size:13
Alignment explanation
Indices: 1835234--1835260 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1835224 ATATCCTCAT
1835234 TTTTAATTAAATA
1 TTTTAATTAAATA
1835247 TTTTAATTAAATA
1 TTTTAATTAAATA
1835260 T
1 T
1835261 ATTTTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTAATTAAATA
Found at i:1835271 original size:17 final size:16
Alignment explanation
Indices: 1835232--1835279 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
1835222 ATATATCCTC
1835232 ATTTTTAATT-AA-AT
1 ATTTTTAATTAAATAT
1835246 A-TTTTAATTAAATAT
1 ATTTTTAATTAAATAT
1835261 ATTTTTAAATTAAATAT
1 ATTTTT-AATTAAATAT
1835278 AT
1 AT
1835280 CCTCATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.27
14 3 0.10
15 3 0.10
16 4 0.13
17 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTTTAATTAAATAT
Found at i:1835315 original size:26 final size:26
Alignment explanation
Indices: 1835286--1835335 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1835276 ATATCCTCAT
1835286 TTTTAAATTATTTAATATTTTAATTA
1 TTTTAAATTATTTAATATTTTAATTA
*
1835312 TTTTTAATTATTTAATATTTTAAT
1 TTTTAAATTATTTAATATTTTAAT
1835336 GATTATTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTTAAATTATTTAATATTTTAATTA
Found at i:1835317 original size:18 final size:17
Alignment explanation
Indices: 1835287--1835332 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
1835277 TATCCTCATT
1835287 TTTAA-ATTATTTAA-TA
1 TTTAATATT-TTTAATTA
1835303 TTTTAATTATTTTTAATTA
1 -TTTAA-TATTTTTAATTA
1835322 TTTAATATTTT
1 TTTAATATTTT
1835333 AATGATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 11 0.42
18 10 0.38
19 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAATATTTTTAATTA
Found at i:1835318 original size:10 final size:9
Alignment explanation
Indices: 1835284--1835332 Score: 50
Period size: 8 Copynumber: 5.6 Consensus size: 9
1835274 ATATATCCTC
1835284 ATTTTTAA-
1 ATTTTTAAT
1835292 ATTATTTAAT
1 ATT-TTTAAT
1835302 A-TTTTAATT
1 ATTTTTAA-T
1835311 ATTTTTAAT
1 ATTTTTAAT
*
1835320 -TATTTAAT
1 ATTTTTAAT
1835328 ATTTT
1 ATTTT
1835333 AATGATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 15 0.44
9 12 0.35
10 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:1837125 original size:21 final size:21
Alignment explanation
Indices: 1837101--1837140 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1837091 TATAAAAAAA
1837101 ATTTTAAAAATAAATATATTT
1 ATTTTAAAAATAAATATATTT
* *
1837122 ATTTTAAACATATATATAT
1 ATTTTAAAAATAAATATAT
1837141 ATATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTTAAAAATAAATATATTT
Found at i:1837136 original size:2 final size:2
Alignment explanation
Indices: 1837131--1837158 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1837121 TATTTTAAAC
1837131 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
1837159 TTATGCCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1837203 original size:22 final size:22
Alignment explanation
Indices: 1837175--1837218 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1837165 CCATCATTCA
1837175 CTCTGATCTGAGTAACATAAGT
1 CTCTGATCTGAGTAACATAAGT
*
1837197 CTCTGATCTGAGTAACGTAAGT
1 CTCTGATCTGAGTAACATAAGT
1837219 TATGTTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (22 bp):
CTCTGATCTGAGTAACATAAGT
Found at i:1841380 original size:21 final size:22
Alignment explanation
Indices: 1841339--1841394 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 22
1841329 ATTTAAAAAT
* *
1841339 AATTTTATATATATATTTTTAAA
1 AATTTAATATA-ATTTTTTTAAA
1841362 AATTTAA-ATAATTTTTTTAAA
1 AATTTAATATAATTTTTTTAAA
1841383 AATTTAATATAA
1 AATTTAATATAA
1841395 AATATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 17 0.57
22 7 0.23
23 6 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTTAATATAATTTTTTTAAA
Found at i:1841477 original size:14 final size:14
Alignment explanation
Indices: 1841451--1841483 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1841441 AACTATTATA
1841451 TATTTTATTAATTTT
1 TATTTTATTAA-TTT
1841466 TATTTT-TTAATTT
1 TATTTTATTAATTT
1841479 TATTT
1 TATTT
1841484 AAAAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 4 0.22
15 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTATTAATTT
Found at i:1843877 original size:23 final size:21
Alignment explanation
Indices: 1843851--1843894 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1843841 TTTTTTATTT
*
1843851 TATATAT-TTATTTATAAAAAA
1 TATATATATAATTT-TAAAAAA
1843872 TATATATATAATTTTAAAAAA
1 TATATATATAATTTTAAAAAA
1843893 TA
1 TA
1843895 AAAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATATATATAATTTTAAAAAA
Found at i:1843903 original size:21 final size:22
Alignment explanation
Indices: 1843860--1843903 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1843850 TTATATATTT
* * *
1843860 ATTTATAAAAAATATATATATA
1 ATTTATAAAAAATAAAAAAATA
1843882 ATTT-TAAAAAATAAAAAAATA
1 ATTTATAAAAAATAAAAAAATA
1843903 A
1 A
1843904 AATAAATAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATTTATAAAAAATAAAAAAATA
Found at i:1845919 original size:3 final size:3
Alignment explanation
Indices: 1845911--1845964 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
1845901 TATTAAACAC
1845911 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1845959 TAA TAA
1 TAA TAA
1845965 AAGATCTTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1851069 original size:19 final size:20
Alignment explanation
Indices: 1851038--1851081 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1851028 ATTTAATTTT
*
1851038 TTATTTTTATAAATTAAATA
1 TTATTTTTATAAATAAAATA
*
1851058 TTATTTTT-TAAATAAAATT
1 TTATTTTTATAAATAAAATA
1851077 TTATT
1 TTATT
1851082 AAAATGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTTTTATAAATAAAATA
Found at i:1851081 original size:22 final size:22
Alignment explanation
Indices: 1851021--1851082 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
1851011 TGTAACTGTA
*
1851021 TTTTTAAATTTAATTTT-TTAT
1 TTTTTAAATTAAATTTTATTAT
1851042 TTTTATAAATTAAA---TATTAT
1 TTTT-TAAATTAAATTTTATTAT
*
1851062 TTTTTAAATAAAATTTTATTA
1 TTTTTAAATTAAATTTTATTA
1851083 AAATGATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 9 0.26
20 8 0.24
21 4 0.12
22 13 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTTAAATTAAATTTTATTAT
Found at i:1851105 original size:17 final size:17
Alignment explanation
Indices: 1851061--1851111 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
1851051 TTAAATATTA
1851061 TTTTTTAAAT-A-AAAT
1 TTTTTTAAATGATAAAT
*
1851076 TTTATTAAAATGATAAAT
1 TTT-TTTAAATGATAAAT
1851094 TTTTTTAAATGATAAAT
1 TTTTTTAAATGATAAAT
1851111 T
1 T
1851112 ACACTTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 3 0.10
16 6 0.19
17 15 0.48
18 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
TTTTTTAAATGATAAAT
Found at i:1852094 original size:15 final size:15
Alignment explanation
Indices: 1852070--1852099 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1852060 TTAACATACA
1852070 TTAAACAATAATAAT
1 TTAAACAATAATAAT
*
1852085 TTAAATAATAATAAT
1 TTAAACAATAATAAT
1852100 AATAATAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAACAATAATAAT
Found at i:1853175 original size:22 final size:24
Alignment explanation
Indices: 1853132--1853176 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
1853122 TTAAATAATT
*
1853132 ATATTCAAAAATATTTAATTATAA
1 ATATTCAAAAATATATAATTATAA
*
1853156 ATATT-AAAAATA-ATATTTATA
1 ATATTCAAAAATATATAATTATA
1853177 TGTATATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATTCAAAAATATATAATTATAA
Found at i:1853219 original size:15 final size:15
Alignment explanation
Indices: 1853196--1853233 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1853186 AAAAATTAAA
*
1853196 ATATTTATATCTAAT
1 ATATATATATCTAAT
1853211 ATATATATATCTAAT
1 ATATATATATCTAAT
1853226 ATATATAT
1 ATATATAT
1853234 GGCCAGACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATATATCTAAT
Found at i:1853517 original size:19 final size:19
Alignment explanation
Indices: 1853478--1853522 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1853468 CATCAATTTC
* *
1853478 TTAAAATAGTATTTGTATA
1 TTAAAATAATATATGTATA
*
1853497 TTAAAATAATATATGTTTA
1 TTAAAATAATATATGTATA
*
1853516 TTTAAAT
1 TTAAAAT
1853523 TTAACTATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (19 bp):
TTAAAATAATATATGTATA
Found at i:1853849 original size:30 final size:28
Alignment explanation
Indices: 1853801--1853874 Score: 67
Period size: 30 Copynumber: 2.5 Consensus size: 28
1853791 TTATGGGATT
* *
1853801 AATATATTTTTTGCTAAATTTTATAAGAGTA
1 AATATA-TTTTT--TAAATATTAAAAGAGTA
*
1853832 AATAGGTATTTTTTAAATATTAAAATAGTA
1 AATA--TATTTTTTAAATATTAAAAGAGTA
*
1853862 AGTATATTTTTTA
1 AATATATTTTTTA
1853875 TAAAGATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
28 9 0.24
30 17 0.46
31 4 0.11
32 5 0.14
33 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (28 bp):
AATATATTTTTTAAATATTAAAAGAGTA
Found at i:1857346 original size:19 final size:19
Alignment explanation
Indices: 1857324--1857361 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1857314 AATAAATAAA
1857324 TTATAATATAATTAAAATT
1 TTATAATATAATTAAAATT
* *
1857343 TTATATTATAATTTAAATT
1 TTATAATATAATTAAAATT
1857362 AATTTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATAATATAATTAAAATT
Found at i:1857350 original size:24 final size:23
Alignment explanation
Indices: 1857323--1857370 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
1857313 TAATAAATAA
1857323 ATTATAATAT-AATTAAAATTTTAT
1 ATTATAATATAAATT--AATTTTAT
*
1857347 ATTATAATTTAAATTAATTTTAT
1 ATTATAATATAAATTAATTTTAT
1857370 A
1 A
1857371 AATATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 9 0.41
24 9 0.41
25 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTATAATATAAATTAATTTTAT
Found at i:1857386 original size:18 final size:19
Alignment explanation
Indices: 1857355--1857398 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1857345 ATATTATAAT
*
1857355 TTAAATTAATTTTATAAATA
1 TTAAA-TAATTTTAAAAATA
1857375 TTAAATAA-TTTAAAAATA
1 TTAAATAATTTTAAAAATA
1857393 -TAAATA
1 TTAAATA
1857399 TTCATCTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 9 0.39
19 3 0.13
20 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAATAATTTTAAAAATA
Found at i:1857534 original size:47 final size:45
Alignment explanation
Indices: 1857468--1857558 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1857458 ATAAATGAAA
* *
1857468 AAATAAATTATTATAATATTATAATTT-CAATTAATTTTATAAAAATT
1 AAATAAATTATAAGAATATT-T-ATTTAC-ATTAATTTTATAAAAATT
*
1857515 AAATAATTTATAAGAATATTTATTTACATTAATTTTATAAAAAT
1 AAATAAATTATAAGAATATTTATTTACATTAATTTTATAAAAAT
1857559 ATTAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
45 21 0.52
46 2 0.05
47 17 0.43
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (45 bp):
AAATAAATTATAAGAATATTTATTTACATTAATTTTATAAAAATT
Found at i:1857596 original size:18 final size:19
Alignment explanation
Indices: 1857568--1857603 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1857558 TATTAAAAAA
1857568 TTTTTACTTTTTCCTTTTT
1 TTTTTACTTTTTCCTTTTT
1857587 TTTTTA-TTTTTCCTTTT
1 TTTTTACTTTTTCCTTTT
1857604 AATTAACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTACTTTTTCCTTTTT
Found at i:1858364 original size:16 final size:17
Alignment explanation
Indices: 1858343--1858376 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1858333 ATTTCTATAA
1858343 AAATAATT-TAATTTAT
1 AAATAATTATAATTTAT
*
1858359 AAATAATTATTATTTAT
1 AAATAATTATAATTTAT
1858376 A
1 A
1858377 TTTTGTCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATAATTATAATTTAT
Found at i:1858860 original size:3 final size:3
Alignment explanation
Indices: 1858852--1858878 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1858842 ATACAAAAAC
1858852 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1858879 ATAACAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1859151 original size:21 final size:20
Alignment explanation
Indices: 1859127--1859180 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
1859117 AATTATTTAT
1859127 TTTATTTAATTTAAAATAATA
1 TTTATTT-ATTTAAAATAATA
* *
1859148 TTTATATA-TTAAGATAATA
1 TTTATTTATTTAAAATAATA
1859167 TATT-TTTATTTAAA
1 T-TTATTTATTTAAA
1859181 TGTAATTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 14 0.52
20 7 0.26
21 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTATTTATTTAAAATAATA
Found at i:1859221 original size:27 final size:25
Alignment explanation
Indices: 1859191--1859241 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
1859181 TGTAATTATA
1859191 AAATATAAAAAAATATGAATATAATAT
1 AAATATAAAAAAATAT--ATATAATAT
**
1859218 AAATATATCAAAATATATATAATA
1 AAATATAAAAAAATATATATAATA
1859242 CTAATTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
27 14 0.64
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
AAATATAAAAAAATATATATAATAT
Found at i:1859614 original size:11 final size:11
Alignment explanation
Indices: 1859598--1859624 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1859588 TTAATACTTC
1859598 AAATATATACA
1 AAATATATACA
1859609 AAATATATACA
1 AAATATATACA
1859620 AAATA
1 AAATA
1859625 ATATTAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATATATACA
Found at i:1859686 original size:19 final size:20
Alignment explanation
Indices: 1859664--1859702 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1859654 AACGTAATAC
1859664 AATAAATAAATAT-AATATT
1 AATAAATAAATATAAATATT
*
1859683 AATATATAAATATAAATATT
1 AATAAATAAATATAAATATT
1859703 TTTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAAATAAATATAAATATT
Found at i:1859708 original size:20 final size:19
Alignment explanation
Indices: 1859664--1859731 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 19
1859654 AACGTAATAC
*
1859664 AATAAATAAATATAATATT
1 AATATATAAATATAATATT
1859683 AATATATAAATATAAATATT
1 AATATATAAATAT-AATATT
* * *
1859703 --TTTATAAATATTATATA
1 AATATATAAATATAATATT
*
1859720 AATTTA-AAATAT
1 AATATATAAATAT
1859732 TTTAAATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
17 4 0.10
18 16 0.38
19 16 0.38
20 6 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATATAAATATAATATT
Found at i:1859984 original size:3 final size:3
Alignment explanation
Indices: 1859978--1860031 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
1859968 AAACAACATT
*
1859978 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCG TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1860026 TCA TCA
1 TCA TCA
1860032 ACAATGAGTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1863012 original size:47 final size:47
Alignment explanation
Indices: 1862943--1863036 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
1862933 AAAAATGGGA
* *
1862943 AAGAAAACCATCCATGGTTGTCCATTTATCGTTTCTAACTTGGTCCC
1 AAGAAAACCATCCATGCTTGTCCATTTACCGTTTCTAACTTGGTCCC
* * *
1862990 AAGAAAACCATCCGTGCTTGTCCATTTGCCGTTTCTAACTTGTTCCC
1 AAGAAAACCATCCATGCTTGTCCATTTACCGTTTCTAACTTGGTCCC
1863037 TTCATCAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (47 bp):
AAGAAAACCATCCATGCTTGTCCATTTACCGTTTCTAACTTGGTCCC
Found at i:1863775 original size:2 final size:2
Alignment explanation
Indices: 1863768--1863811 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1863758 CCAGAAAATC
1863768 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
1863810 TA
1 TA
1863812 ATGTGTAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1863879 original size:16 final size:19
Alignment explanation
Indices: 1863857--1863898 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 19
1863847 ATTTTTGTTT
1863857 TTATTTTTTA-TT-CAAAA
1 TTATTTTTTAGTTACAAAA
1863874 -TA-TTTTTAGTTACAAAA
1 TTATTTTTTAGTTACAAAA
1863891 TTATTTTT
1 TTATTTTT
1863899 AATTATTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 6 0.29
16 4 0.19
17 5 0.24
18 2 0.10
19 4 0.19
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (19 bp):
TTATTTTTTAGTTACAAAA
Found at i:1863889 original size:17 final size:16
Alignment explanation
Indices: 1863861--1863899 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
1863851 TTGTTTTTAT
1863861 TTTTTATTCAAAA-TA
1 TTTTTATTCAAAATTA
1863876 TTTTTAGTTACAAAATTA
1 TTTTTA-TT-CAAAATTA
1863894 TTTTTA
1 TTTTTA
1863900 ATTATTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 2 0.10
17 5 0.24
18 8 0.38
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTTTATTCAAAATTA
Found at i:1864755 original size:20 final size:20
Alignment explanation
Indices: 1864732--1864787 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
1864722 ATATTATAAT
1864732 TTAAATTAATTTAATAAATA
1 TTAAATTAATTTAATAAATA
* *
1864752 TTAAA-CAATTTATAAAAATA
1 TTAAATTAATTTA-ATAAATA
**
1864772 AAAATATTAATTTAAT
1 TTAA-ATTAATTTAAT
1864788 TTAATTAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
19 6 0.22
20 13 0.48
21 2 0.07
22 6 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAATTAATTTAATAAATA
Found at i:1865287 original size:16 final size:16
Alignment explanation
Indices: 1865266--1865344 Score: 52
Period size: 16 Copynumber: 4.8 Consensus size: 16
1865256 TGGTATGTTT
1865266 ATAAATAAATATAAAA
1 ATAAATAAATATAAAA
*
1865282 ATAAATAATAGTATAAAT
1 ATAAATAA-A-TATAAAA
* * * *
1865300 TTAATTTAATTTAAAA
1 ATAAATAAATATAAAA
**
1865316 ATAAATATTTTATAAAA
1 ATAAATA-AATATAAAA
1865333 ATATAA-AAATAT
1 ATA-AATAAATAT
1865345 TTATTTAAAT
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
16 20 0.44
17 12 0.27
18 13 0.29
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (16 bp):
ATAAATAAATATAAAA
Found at i:1865354 original size:20 final size:20
Alignment explanation
Indices: 1865303--1865354 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
1865293 TATAAATTTA
* *
1865303 ATTTAATTTAAAAATAAATAT
1 ATTT-ATTTAAATATAAAAAT
**
1865324 -TTTATAAAAATATAAAAAT
1 ATTTATTTAAATATAAAAAT
1865343 ATTTATTTAAAT
1 ATTTATTTAAAT
1865355 TAATTTAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTATTTAAATATAAAAAT
Found at i:1865724 original size:14 final size:14
Alignment explanation
Indices: 1865701--1865736 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1865691 GATAAAAAGT
* *
1865701 ATAATAATAAAGAA
1 ATAATTATAAAAAA
1865715 ATAATTATAAAAAA
1 ATAATTATAAAAAA
1865729 ATAATTAT
1 ATAATTAT
1865737 TAATTATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
ATAATTATAAAAAA
Found at i:1865947 original size:42 final size:41
Alignment explanation
Indices: 1865830--1865965 Score: 146
Period size: 42 Copynumber: 3.3 Consensus size: 41
1865820 GATATAAAAG
* * * * *
1865830 AAATTAATTTTGAAGCTGTTTCCCGTCTACTCTCAATTCGC
1 AAATTACTTTTGAAGCTGTTTTCCGTCTACCCTTAATTAGC
* * *
1865871 TAGTTACCTTTTGAAGCTGTTTTCCGTCTACCCTTACTTAGC
1 AAATTA-CTTTTGAAGCTGTTTTCCGTCTACCCTTAATTAGC
** * *
1865913 AAATTACTTTGTGAAGCTGTTTTCCGTCTACCCTTGGTTTGT
1 AAATTACTTT-TGAAGCTGTTTTCCGTCTACCCTTAATTAGC
1865955 AAATTACTTTT
1 AAATTACTTTT
1865966 CGAAAATTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
41 9 0.11
42 70 0.89
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (41 bp):
AAATTACTTTTGAAGCTGTTTTCCGTCTACCCTTAATTAGC
Found at i:1866178 original size:12 final size:13
Alignment explanation
Indices: 1866160--1866193 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1866150 GTAAAATCGT
1866160 ATTAAATTT-AAA
1 ATTAAATTTAAAA
*
1866172 TTTAAATTTAAAA
1 ATTAAATTTAAAA
1866185 ATTAAATTT
1 ATTAAATTT
1866194 TTTTAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTAAATTTAAAA
Found at i:1866710 original size:46 final size:45
Alignment explanation
Indices: 1866642--1866762 Score: 131
Period size: 46 Copynumber: 2.7 Consensus size: 45
1866632 TATTTCTTAC
*
1866642 AGGTGATCCATGGCCCTCTTTTAAATATATTAATAAGGACAAATAT
1 AGGTGATCCATGGACCTCTTTT-AATATATTAATAAGGACAAATAT
* * *
1866688 AGGTGATCCA-GGAACCTTTTTTAATTTATTAATAAGGACAAACAGT
1 AGGTGATCCATGG-ACCTCTTTTAATATATTAATAAGGACAAATA-T
* *
1866734 AAGTTATCC-TCGGACCTCTTTT-ATATATT
1 AGGTGATCCAT-GGACCTCTTTTAATATATT
1866763 TCTCATGCCT
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
45 28 0.44
46 33 0.52
47 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (45 bp):
AGGTGATCCATGGACCTCTTTTAATATATTAATAAGGACAAATAT
Found at i:1866729 original size:45 final size:46
Alignment explanation
Indices: 1866642--1866761 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 46
1866632 TATTTCTTAC
*
1866642 AGGTGATCCATGGCCCTCTTTTAAATATATTAATAAGGACAAATAT
1 AGGTGATCCATGGACCTCTTTTAAATATATTAATAAGGACAAATAT
* * *
1866688 AGGTGATCCA-GGAACCT-TTTTTAATTTATTAATAAGGACAAACAGT
1 AGGTGATCCATGG-ACCTCTTTTAAATATATTAATAAGGACAAATA-T
* * *
1866734 AAGTTATCC-TCGGACCTCTTTTATATAT
1 AGGTGATCCAT-GGACCTCTTTTAAATAT
1866762 TTCTCATGCC
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
45 26 0.43
46 25 0.42
47 9 0.15
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (46 bp):
AGGTGATCCATGGACCTCTTTTAAATATATTAATAAGGACAAATAT
Found at i:1870585 original size:19 final size:19
Alignment explanation
Indices: 1870551--1870600 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1870541 TTTTAATTTT
1870551 TATATAAAATAAATTATATAA
1 TATATAAAAT--ATTATATAA
1870572 TATATAAAATATTATATAA
1 TATATAAAATATTATATAA
*
1870591 T-TAAAAAATA
1 TATATAAAATA
1870601 AATTAAATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 8 0.29
19 10 0.36
21 10 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATATAAAATATTATATAA
Found at i:1873148 original size:22 final size:22
Alignment explanation
Indices: 1873117--1873158 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1873107 TGCGCAGGTG
*
1873117 AAAAAGAAGGAAGAAAAAAAGA
1 AAAAAAAAGGAAGAAAAAAAGA
1873139 AAAAAAAAGGAAGAAAAAAA
1 AAAAAAAAGGAAGAAAAAAA
1873159 TTTTATGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (22 bp):
AAAAAAAAGGAAGAAAAAAAGA
Found at i:1873219 original size:21 final size:19
Alignment explanation
Indices: 1873195--1873247 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 19
1873185 TTGTATTTTA
1873195 AATATTATATTTTTATATATT
1 AATATTATATTTTTAT-TA-T
1873216 AATAATT-TA-TTTTATTAT
1 AAT-ATTATATTTTTATTAT
1873234 -ATA-TATATTTTTAT
1 AATATTATATTTTTAT
1873248 GCATAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 8 0.28
18 1 0.03
19 2 0.07
20 6 0.21
21 5 0.17
22 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATATTATATTTTTATTAT
Found at i:1873221 original size:40 final size:37
Alignment explanation
Indices: 1873170--1873247 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 37
1873160 TTTATGTGTT
*
1873170 TATATTTATAATTT-TTTGTATTTTAAATATTATATTTTTA
1 TATATTAATAATTTATTT-TA--TTAAATA-TATATTTTTA
*
1873210 TATATTAATAATTTATTTTATTATATATATATTTTTA
1 TATATTAATAATTTATTTTATTAAATATATATTTTTA
1873247 T
1 T
1873248 GCATAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 11 0.31
38 6 0.17
40 15 0.43
41 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (37 bp):
TATATTAATAATTTATTTTATTAAATATATATTTTTA
Found at i:1873548 original size:21 final size:21
Alignment explanation
Indices: 1873524--1873565 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1873514 TCGGATATTC
1873524 TTATCATG-TTTAAGTTATTTT
1 TTATCATGTTTTAA-TTATTTT
*
1873545 TTATGATGTTTTAATTATTTT
1 TTATCATGTTTTAATTATTTT
1873566 GTATTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.64
Consensus pattern (21 bp):
TTATCATGTTTTAATTATTTT
Found at i:1874543 original size:311 final size:313
Alignment explanation
Indices: 1874152--1874760 Score: 942
Period size: 311 Copynumber: 1.9 Consensus size: 313
1874142 GTATTGACAC
* * * *
1874152 GTGACATTTTTTTTGCGTTTAGCAAGATTATTTTTTAATATTGTATTTGTGTTATGTTTCAATTT
1 GTGACATTTTTTTTGCATTTAACAAGATTATTTTTTAATATTGTATTTATGTTATGTCTCAATTT
* * *
1874217 ATCTTATATTTTATATAAATTTTTATATGATTATATATT-AACTTTAAATTTATTTGTTAAATAT
66 ATCTTATAATTTATATAAATTTTTATATGATTAAAT-TTAAACTTTAAATTTATTTATTAAATAT
*
1874281 TTTAAAATAAATTTTAATAATTATAATTTTATTTAATAAAAAATTTTATAAATATTAAAA-CTCC
130 TTTAAAATAAATTTTAATAATTATAATTTTATTTAATAAAAAACTTTATAAATATTAAAACCT-C
* ** **
1874345 AACAAAGCGG-AGAGGAATTTTAGTATACTTCTATTTTTAACTACATCAATTCACTACAAAATGA
194 AACAAAACGGAAGAAAAATTTTAACATACTTCTATTTTTAACTACATCAATTCACTACAAAATGA
1874409 CACATGTCAC-TTTCTT-TTTTGCTTTCATGCTTTTTTTTACGTGATACTAGCAT
259 CACATGTCACTTTTCTTGTTTTGCTTTCATGCTTTTTTTTACGTGATACTAGCAT
**
1874462 GTGACATTTTTTTTTGCATTTAACTGGATTATTTTTTAATATT-TAATTTATGTTATGTCTCAAT
1 GTGACA-TTTTTTTTGCATTTAACAAGATTATTTTTTAATATTGT-ATTTATGTTATGTCTCAAT
1874526 TTATCTTATAATTTATATAAATTTTTATATGATTAAATTTAAACTTTAAATTTATTTATTAAATA
64 TTATCTTATAATTTATATAAATTTTTATATGATTAAATTTAAACTTTAAATTTATTTATTAAATA
*
1874591 TTTTGAAATAAATTTTAATAATTATAATTTTATTTAATAAAAAACTTTATAAATATTAAAACCTC
129 TTTTAAAATAAATTTTAATAATTATAATTTTATTTAATAAAAAACTTTATAAATATTAAAACCTC
* * *
1874656 AACAAAACGGAAGAAAAATTTTAACATATTTTTATTTTTAACTATATCAATTCACTACAAAATGA
194 AACAAAACGGAAGAAAAATTTTAACATACTTCTATTTTTAACTACATCAATTCACTACAAAATGA
*
1874721 CACATGTCACTTTTTTTTTGTTTTGCTTTCATGCTTTTTT
259 CACATGTCAC--TTTTCTTGTTTTGCTTTCATGCTTTTTT
1874761 ATTTTTACGC
Statistics
Matches: 270, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
310 9 0.03
311 177 0.66
312 59 0.22
315 5 0.02
316 20 0.07
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (313 bp):
GTGACATTTTTTTTGCATTTAACAAGATTATTTTTTAATATTGTATTTATGTTATGTCTCAATTT
ATCTTATAATTTATATAAATTTTTATATGATTAAATTTAAACTTTAAATTTATTTATTAAATATT
TTAAAATAAATTTTAATAATTATAATTTTATTTAATAAAAAACTTTATAAATATTAAAACCTCAA
CAAAACGGAAGAAAAATTTTAACATACTTCTATTTTTAACTACATCAATTCACTACAAAATGACA
CATGTCACTTTTCTTGTTTTGCTTTCATGCTTTTTTTTACGTGATACTAGCAT
Found at i:1874786 original size:4 final size:4
Alignment explanation
Indices: 1874777--1874822 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
1874767 ACGCGGTGGA
* * *
1874777 AAAG AAAG AAAA AAAG AAGG AAAG AAAG AAAG -AAG AAAA AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1874823 AAAATTTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 3 0.09
4 32 0.91
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1874793 original size:12 final size:12
Alignment explanation
Indices: 1874776--1874826 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
1874766 TACGCGGTGG
1874776 AAAAGAAAGAAA
1 AAAAGAAAGAAA
*
1874788 AAAAGAAGGAAA
1 AAAAGAAAGAAA
* *
1874800 GAAAGAAAGAAG
1 AAAAGAAAGAAA
1874812 AAAA-AAAGAAA
1 AAAAGAAAGAAA
1874823 AAAA
1 AAAA
1874827 TTTATAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 10 0.30
12 23 0.70
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAGAAAGAAA
Found at i:1874794 original size:8 final size:8
Alignment explanation
Indices: 1874775--1874826 Score: 50
Period size: 8 Copynumber: 6.0 Consensus size: 8
1874765 TTACGCGGTG
1874775 GAAAAGAAA
1 GAAAA-AAA
1874784 GAAAAAAA
1 GAAAAAAA
**
1874792 GAAGGAAA
1 GAAAAAAA
1874800 GAAAGAAAGAA
1 G-AA-AAA-AA
1874811 GAAAAAAA
1 GAAAAAAA
1874819 GAAAAAAA
1 GAAAAAAA
1874827 TTTATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
8 20 0.56
9 10 0.28
10 3 0.08
11 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:1874950 original size:16 final size:17
Alignment explanation
Indices: 1874914--1874958 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
1874904 TATTAATAAT
1874914 TTATTTTAT-T-TTATG
1 TTATTTTATATATTATG
1874929 TATATTTTATATATT-TG
1 T-TATTTTATATATTATG
1874946 TTATTTTATATAT
1 TTATTTTATATAT
1874959 GAGACAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.04
16 20 0.74
17 4 0.15
18 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (17 bp):
TTATTTTATATATTATG
Found at i:1875005 original size:12 final size:13
Alignment explanation
Indices: 1874976--1875003 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1874966 ATTTTAAGAG
1874976 TTTATATTTTTTA
1 TTTATATTTTTTA
1874989 TTTATATTTTTTA
1 TTTATATTTTTTA
1875002 TT
1 TT
1875004 ATTTAAAATA
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:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATATTTTTTA
Found at i:1876677 original size:1 final size:1
Alignment explanation
Indices: 1876639--1876669 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
1876629 TGCTATCGTC
1876639 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1876670 CAGTTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1877049 original size:18 final size:18
Alignment explanation
Indices: 1877014--1877052 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1877004 TAATATCATC
*
1877014 ATTGTTAATTGAATAAAA
1 ATTGTTAATTGAAAAAAA
*
1877032 ATTGATTAATTAAAAAAAA
1 ATTG-TTAATTGAAAAAAA
1877051 AT
1 AT
1877053 AAAAAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (18 bp):
ATTGTTAATTGAAAAAAA
Found at i:1878795 original size:2 final size:2
Alignment explanation
Indices: 1878790--1878815 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1878780 ACAGTCACAC
1878790 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
1878816 GTGTGTGTGA
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
Done.