Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004920.1 Hibiscus syriacus cultivar Beakdansim tig00011079_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1590857
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 5 of 7
Found at i:937448 original size:20 final size:20
Alignment explanation
Indices: 937419--937528 Score: 118
Period size: 19 Copynumber: 5.5 Consensus size: 20
937409 TTCTAAACTT
* *
937419 AAAATTGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
937439 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
937459 ACTATCACAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
*
937480 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
937499 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
937518 AAAATCGCAAC
1 AAAATCGCAAC
937529 GAGATAATCG
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
19 35 0.45
20 28 0.36
21 15 0.19
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:937498 original size:19 final size:19
Alignment explanation
Indices: 937434--937529 Score: 120
Period size: 19 Copynumber: 4.9 Consensus size: 19
937424 TGCAACATGA
*
937434 AAATGAAAATCGCAACACG
1 AAATGAAAATCGCAACGCG
** * *
937453 AAAATGACTATCACAACGAGAG
1 -AAATGAAAATCGCAAC--GCG
937475 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
937494 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
937513 AAATGAAAATCGCAACG
1 AAATGAAAATCGCAACG
937530 AGATAATCGC
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
19 38 0.58
20 13 0.20
21 13 0.20
22 1 0.02
ACGTcount: A:0.50, C:0.20, G:0.19, T:0.11
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:937543 original size:33 final size:36
Alignment explanation
Indices: 937474--937559 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 36
937464 CACAACGAGA
937474 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC-CG-AATGAAAATCGCAACGC
*
937512 GAAATGAAAATCGCAA-CG-A-GATAATCGCAACGC
1 GAAATGAAAATCGCAACCGAATGAAAATCGCAACGC
**
937545 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
937560 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
33 26 0.58
34 1 0.02
36 2 0.04
38 16 0.36
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.10
Consensus pattern (36 bp):
GAAATGAAAATCGCAACCGAATGAAAATCGCAACGC
Found at i:937645 original size:20 final size:19
Alignment explanation
Indices: 937555--937653 Score: 144
Period size: 19 Copynumber: 5.1 Consensus size: 19
937545 GAAACCAAAA
*
937555 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
937574 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
937593 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
937612 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
937632 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
937652 TC
1 TC
937654 AACCAAAAGA
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
19 38 0.53
20 33 0.46
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:938726 original size:21 final size:21
Alignment explanation
Indices: 938700--938744 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
938690 GATTTCTGGG
* *
938700 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
938721 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
938742 CAA
1 CAA
938745 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:940618 original size:105 final size:103
Alignment explanation
Indices: 940432--940639 Score: 317
Period size: 105 Copynumber: 2.0 Consensus size: 103
940422 GGGTCTACGC
* *
940432 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAAACACATACTTGAT
1 GGTCATTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTAGTGAAACACATACTTGAT
* * *
940497 CCTTGGCATATGTATATAATTCTTAAGGAATGATATGT
66 CCCTAGCATATATATATAATTCTTAAGGAATGATATGT
* *
940535 GGTCATTCGGGACATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTG
1 GGTCATTCGGGAC--ATATATATATTCTTTGGAACATGTGTGAAGTCTAGTGAAACACATACTTG
* *
940600 ATCCCTAGTATATATATATGATTCTTAAGGAATGATATGT
64 ATCCCTAGCATATATATATAATTCTTAAGGAATGATATGT
940640 AGTCCTTATG
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
103 12 0.13
105 82 0.87
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (103 bp):
GGTCATTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTAGTGAAACACATACTTGAT
CCCTAGCATATATATATAATTCTTAAGGAATGATATGT
Found at i:940653 original size:105 final size:105
Alignment explanation
Indices: 940445--940662 Score: 314
Period size: 105 Copynumber: 2.1 Consensus size: 105
940435 CCTTCGGGAC
* * * *
940445 ATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAAACACATACTTGATCCTTGGCATATGT
1 ATATATATATTCTTTGGAACATGTGTGAAGTCTAGTGAAACACATACTTGATCCCTAGCATATAT
* *
940510 ATATAATTCTTAAGGAATGATATGTGGTCATTCGGGACAT
66 ATATAATTCTTAAGGAATGATATGTAGTCATTAGGGACAT
* * *
940550 ATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGTATATAT
1 ATATATATATTCTTTGGAACATGTGTGAAGTCTAGTGAAACACATACTTGATCCCTAGCATATAT
* * *
940615 ATATGATTCTTAAGGAATGATATGTAGTCCTTATGGACAT
66 ATATAATTCTTAAGGAATGATATGTAGTCATTAGGGACAT
940655 -TAT-TATAT
1 ATATATATAT
940663 GGCACTACGG
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
103 5 0.05
104 3 0.03
105 93 0.92
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (105 bp):
ATATATATATTCTTTGGAACATGTGTGAAGTCTAGTGAAACACATACTTGATCCCTAGCATATAT
ATATAATTCTTAAGGAATGATATGTAGTCATTAGGGACAT
Found at i:940696 original size:23 final size:23
Alignment explanation
Indices: 940663--940730 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
940653 ATTATTATAT
940663 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
940686 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
940709 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
940731 AGTTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:942927 original size:94 final size:94
Alignment explanation
Indices: 942765--943238 Score: 835
Period size: 94 Copynumber: 5.1 Consensus size: 94
942755 TAGATTGCTT
* * * *
942765 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
942830 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
942859 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
942924 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
942953 AGTAAATTTGTTCGGTTGCTGCCAATTTTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
943018 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
943047 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
943112 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
943141 AGTAAATTTGTTCGTTTGCTTCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
943206 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
943234 AGTAA
1 AGTAA
943239 TGCAATCCAT
Statistics
Matches: 369, Mismatches: 10, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
93 26 0.07
94 343 0.93
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:943355 original size:20 final size:20
Alignment explanation
Indices: 943330--943391 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
943320 TTTTGGTTGA
*
943330 AATGAAAATCACAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
943350 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
943369 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
943389 AAT
1 AAT
943392 CGCAACGCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 18 0.47
20 20 0.53
ACGTcount: A:0.52, C:0.16, G:0.21, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:943374 original size:19 final size:19
Alignment explanation
Indices: 943328--943387 Score: 93
Period size: 19 Copynumber: 3.1 Consensus size: 19
943318 TCTTTTGGTT
*
943328 GAAATGAAAATCACAACGA
1 GAAATGAAAATCGCAACGA
*
943347 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
943367 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
943386 GA
1 GA
943388 GAATCGCAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.52, C:0.17, G:0.22, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:943477 original size:14 final size:14
Alignment explanation
Indices: 943458--943489 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
943448 TTCGCATTGT
943458 GATTCTCTCGTTGC
1 GATTCTCTCGTTGC
943472 GATTCTCTCGTTGC
1 GATTCTCTCGTTGC
943486 GATT
1 GATT
943490 TTCATTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.25, G:0.22, T:0.44
Consensus pattern (14 bp):
GATTCTCTCGTTGC
Found at i:943505 original size:19 final size:20
Alignment explanation
Indices: 943481--943531 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
943471 CGATTCTCTC
943481 GTTGCGATTTTCA-TTTCAA
1 GTTGCGATTTTCATTTTCAA
** *
943500 GTTGCGATAGTCATTTTTCAC
1 GTTGCGATTTTCA-TTTTCAA
943521 GTTGCGATTTT
1 GTTGCGATTTT
943532 AAGTTCCAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 11 0.44
21 14 0.56
ACGTcount: A:0.18, C:0.16, G:0.20, T:0.47
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAA
Found at i:945420 original size:14 final size:14
Alignment explanation
Indices: 945401--945436 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
945391 ATTGTTTAAT
945401 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
945415 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
945429 TGATTTGT
1 TGATTTGT
945437 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:945565 original size:19 final size:19
Alignment explanation
Indices: 945543--945608 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
945533 AAAAATGACT
*
945543 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
945562 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
945576 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
945595 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
945609 CTAAATTCGC
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:945625 original size:19 final size:19
Alignment explanation
Indices: 945575--945618 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
945565 GCAACGAGAG
945575 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
945594 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
945613 ATTCGC
1 AATCGC
945619 GTTGCGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:945636 original size:19 final size:19
Alignment explanation
Indices: 945614--945731 Score: 58
Period size: 19 Copynumber: 6.7 Consensus size: 19
945604 CGAAACTAAA
945614 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
945633 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
945648 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
945666 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
945681 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
** * **
945699 TTCGTATTGTGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
945718 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
945732 AGACATTAAG
Statistics
Matches: 68, Mismatches: 20, Indels: 21
0.62 0.18 0.19
Matches are distributed among these distances:
14 16 0.24
16 6 0.09
17 6 0.09
19 32 0.47
20 8 0.12
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:945708 original size:33 final size:33
Alignment explanation
Indices: 945618--945711 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
945608 ACTAAATTCG
*
945618 CGTTGCGATTTTCATTTCGCT-TTGCGATTCCCT
1 CGTTGCGATTTTCATTTCG-TATTGTGATTCCCT
* *
945651 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGTATTGTGATTCCCT
945684 CGTTGCGATTTTCATTTCGTATTGTGAT
1 CGTTGCGATTTTCATTTCGTATTGTGAT
945712 AGTCATTTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGTATTGTGATTCCCT
Found at i:945777 original size:20 final size:19
Alignment explanation
Indices: 945685--945777 Score: 62
Period size: 20 Copynumber: 4.7 Consensus size: 19
945675 TGATTCTCTC
**
945685 GTTGCGATTTTCATTTCGT
1 GTTGCGATAGTCATTTCGT
* * *
945704 ATTGTGATAGTCATTTCCGC
1 GTTGCGATAGTCATTT-CGT
* **
945724 GTTGCGATAGACATTAAGAT
1 GTTGCGATAGTCATTTCG-T
945744 GATTGCGA-ACGTCATTTTCGT
1 G-TTGCGATA-GTCA-TTTCGT
945765 GTTGCGATAGTCA
1 GTTGCGATAGTCA
945778 AATGAATGCC
Statistics
Matches: 54, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
19 13 0.24
20 26 0.48
21 12 0.22
22 3 0.06
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.39
Consensus pattern (19 bp):
GTTGCGATAGTCATTTCGT
Found at i:948236 original size:24 final size:24
Alignment explanation
Indices: 948202--948255 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
948192 CTGAAAAATC
948202 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
948226 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
948250 ATCAAA
1 ATCAAA
948256 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:948269 original size:24 final size:24
Alignment explanation
Indices: 948202--948269 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
948192 CTGAAAAATC
* * *
948202 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
948226 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
948250 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
948270 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:949129 original size:20 final size:20
Alignment explanation
Indices: 949098--949155 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
949088 AGAATCTCGT
949098 TGCGATTTACGTAAATCGCAA
1 TGCGA-TTACGTAAATCGCAA
949119 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
*
949139 TGCGAATACGT-AATCGC
1 TGCGATTACGTAAATCGC
949156 GTTGCGAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 6 0.17
20 25 0.69
21 5 0.14
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:950425 original size:27 final size:27
Alignment explanation
Indices: 950371--950428 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
950361 AAAACCGGAA
*
950371 GAAGTTGAAATGACAGATAAGGCAGAG
1 GAAGTTGAAATGACAGATAAGACAGAG
**
950398 GAAGTTGAAATGACAGATAAGATGGAG
1 GAAGTTGAAATGACAGATAAGACAGAG
950425 GAAG
1 GAAG
950429 AAGGTTGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.34, T:0.16
Consensus pattern (27 bp):
GAAGTTGAAATGACAGATAAGACAGAG
Found at i:951251 original size:33 final size:33
Alignment explanation
Indices: 951212--951279 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
951202 ACCATTTCAA
* *
951212 GGGGCAAAGTATAATTAATCATGGAAAATGAGG
1 GGGGCAAAGTATAATTAACCATAGAAAATGAGG
* *
951245 GGGGCAAAGTATAATTTACCTTAGAAAATGAGG
1 GGGGCAAAGTATAATTAACCATAGAAAATGAGG
951278 GG
1 GG
951280 CTAAATCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.07, G:0.31, T:0.22
Consensus pattern (33 bp):
GGGGCAAAGTATAATTAACCATAGAAAATGAGG
Found at i:958843 original size:22 final size:22
Alignment explanation
Indices: 958811--958854 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
958801 TTCAGTACCA
*
958811 CATCCTGGGCTTTTTTAGCTTT
1 CATCCTAGGCTTTTTTAGCTTT
958833 CATCCTAGGCTTTTTTAGCTTT
1 CATCCTAGGCTTTTTTAGCTTT
958855 GTTCTCAGCT
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:0.11, C:0.23, G:0.16, T:0.50
Consensus pattern (22 bp):
CATCCTAGGCTTTTTTAGCTTT
Found at i:963532 original size:880 final size:871
Alignment explanation
Indices: 961563--964085 Score: 3816
Period size: 880 Copynumber: 2.9 Consensus size: 871
961553 CAGATTCACA
* * * * * *
961563 ACACATTCCACTGTATCCAAAATAAGGATGGCTTCTTCATAC-T-CGA----A-TGAATAGAATG
1 ACACATTCCACTGTATACAAAATAAGAAAGGCTTCTTCATACTTGAGAGTTGAGTGAACATAATG
* * * * *
961621 GCCACTAATATATAGAGGTGTTGACAGATGTAGCATCCAGATGTAGCTCAAATAATAACTAAACA
66 ACCACTAATATATAGAGGTGTTGAGAAATGTAGAATCCAGATGTAGCTCAAGTAATAACTAAACA
* *
961686 CAT--TACTGAGCAACGATGGACTCCTTCAAGGGATGGATA----TTCCTTATCTTTTATTTTCC
131 CATAGTACTGAGCAACGATGGACTCCTTCAAGGGATAGATATTGCTTCCCTATCTTTTATTTTCC
* * *
961745 AAATATGTAACGGTCTCTACCATCA-TAGCAAAGGTAGACATCTGGACCACATCTGGTTAGACTC
196 AGATATGTAACGGTCTCTACCAT-AGTAGCAAACGTAGACACCTGGACCACATCTGGTTAGACTC
* * * * * *
961809 ATGGGAAACAATCTAAATATTATATAATATTTCACAGATAAAGACCCAAAAGTGCATCCACAAT-
260 ATGGAAAACAATCTAAATATTATATAATATCTCACAGATAAAGA-CAAAAAATGCATCTACATTC
* * *
961873 AAATGATATAGAAGCAATGTATTTCCAAATGCAGTTATTAAGTGTTATTACCATTTACTTCACCA
324 AAATGATATGGAAGAAATGTATTTCCAAATGCAGTTATTAAGTGTTATTACCATTTACTTCACAA
* * * * * * *
961938 TGTCTAGCCCGTTAA-TAAAATAAACAGATCACCATGTGTCCCGCTATATTCAAAATAATAATGG
389 TGTCTAGCCCTTTAACAAAAAAAAACAGATCAGCATGTGTCCCACTATATACAAAATAAGAATGG
* * *
962002 CCTTCACACTTGAATGTATAGAATGATCACTGATATGAA-GAGGTACCAGAGCAATGTAGTGTCT
454 CCTTCACACTTGAATGTATAGAATGATCACTAATAT-AACGAGGTACTAGAGCAATGTAGTGTCC
* *
962066 AGATGTAGCTCAAGTAATAACTAAACGCATAGTAATGGGCAACGATGGACTCCATCAAGGGATAG
518 AGATGTAGCTCAAGTAATAACTAAA--CACAGTAATGGGCAACGATGGACTCCATCAAGGGATGG
* * * *
962131 CTAATAGATAGATTGGAAACCCAAACAATCAATTCCTTCCCCATCTTTTATTTTCCAGATGTGTA
581 CTAATAGATAGATTGGAAACACAAACCATCAATTCCTTCCCTATCTTTTATTTTCCAGATATGTA
*
962196 ACAGTCCCTACCATAATAAGCAAAGGT----ACCTAACTACATCTGGTTAGACTCATGGAAGCAG
646 ACAGTCCCTACCATAATAAGCAAAGGTAGACACCTGACTACATCTGGTTAGACTCATGGAAGCAG
* * * *
962257 AAAGCTAAATGTTAAATAATATTTCACAGGTATAAACCAAAAAATGCATATATATTCAAAATATA
711 ACAGCTAAATGTTAAATAATATTTCACAGATATAAACAAAAAAATGCATCTATATTCAAAATATA
*
962322 TTGAAGCATGGAAAGTATTGTCAAATGCGTATGTTAAGTGTTACCATTATTTTCTTCACTATGCC
776 TTGAAGCATGGAAAGTATTGTCAAATGCGTATGTTAAGTGTTACCATTATTTGCTTCACTATGCC
* * *
962387 TATCCCTTTAAGAAAAAAACAGGCTCACCAC
841 AATCCCTTCAAGAAAAAAACAGGCTCACAAC
*
962418 ACACATTCCACTGTATACAAAATAAGAAAGGCTTCTTCATGCTTGAGAGTTGAGTGAACATAATG
1 ACACATTCCACTGTATACAAAATAAGAAAGGCTTCTTCATACTTGAGAGTTGAGTGAACATAATG
962483 ACCACTAATATATAGAGGTGTTGAGAAATGTAGAATCCAGATGTAGCTCAAGTAATAACTAAACA
66 ACCACTAATATATAGAGGTGTTGAGAAATGTAGAATCCAGATGTAGCTCAAGTAATAACTAAACA
*
962548 CATAGTTCTGAGCAACGATGGACTCCTTCAAGGGATAGATATTGCTTCCCTATCTTTTATTTTCC
131 CATAGTACTGAGCAACGATGGACTCCTTCAAGGGATAGATATTGCTTCCCTATCTTTTATTTTCC
* *
962613 AGATATGTAACGGTCTCTACCATAGTAGCAAACGTAGACACCTGGACCATATCTGGTTAGATTCA
196 AGATATGTAACGGTCTCTACCATAGTAGCAAACGTAGACACCTGGACCACATCTGGTTAGACTCA
*
962678 TGGAAAACAATCTAAATA-TATGTAATATCTCACAGATAAAGACAAAAAAATGCATCTACATTCA
261 TGGAAAACAATCTAAATATTATATAATATCTCACAGATAAAGAC-AAAAAATGCATCTACATTCA
962742 AATGATATGGAAGAAATGTATTTCCAAATGCAGTTATTAAGTGTTATTACCATTTACTTCACAAT
325 AATGATATGGAAGAAATGTATTTCCAAATGCAGTTATTAAGTGTTATTACCATTTACTTCACAAT
962807 GTCTAGCCCTTTAACCAAAAAAAAACAGATCAGCATGTGTCCCACTATATACAAAATAAGAATGG
390 GTCTAGCCCTTTAA-CAAAAAAAAACAGATCAGCATGTGTCCCACTATATACAAAATAAGAATGG
962872 CCTTCACACTTGAATGTATAGAATGATCACTAATATAACGAGGTACTAGAGCAATGTAGTGTCCA
454 CCTTCACACTTGAATGTATAGAATGATCACTAATATAACGAGGTACTAGAGCAATGTAGTGTCCA
*
962937 GATGTAGCTCAAGTAATAACTAAACACAGTACTGGGCAACGATGGACTCCATCAAGGGATGGCTA
519 GATGTAGCTCAAGTAATAACTAAACACAGTAATGGGCAACGATGGACTCCATCAAGGGATGGCTA
963002 ATAGATAGATTGGAAACACAAACCATCAATTCCTTCCCTATCTTTTATTTTCCAGATATGTAACA
584 ATAGATAGATTGGAAACACAAACCATCAATTCCTTCCCTATCTTTTATTTTCCAGATATGTAACA
*
963067 GTCCCTACCATAATAAGAAAAGGTAGACACCTGACTACATCTGGTTAGACTCATGGAAGCAGACA
649 GTCCCTACCATAATAAGCAAAGGTAGACACCTGACTACATCTGGTTAGACTCATGGAAGCAGACA
*
963132 GCTAAATGTTAAACAATATTTCACAGATATAAACAAAAAAAATTGCATCTATATTCAAAATATAT
714 GCTAAATGTTAAATAATATTTCACAGATATAAAC-AAAAAAA-TGCATCTATATTCAAAATATAT
**
963197 TGAAGCATGGAAAGTATTGTCAAATGCGTATGTTAAGTGTTATTATTATTTGCTTCACTATGCCA
777 TGAAGCATGGAAAGTATTGTCAAATGCGTATGTTAAGTGTTACCATTATTTGCTTCACTATGCCA
* *
963262 ATTCCTTCAAG-AAAAAACAGGTTCACAAC
842 ATCCCTTCAAGAAAAAAACAGGCTCACAAC
*
963291 ACACATTCCACTGTATAGTGTATACAAAATAAGAATGGCTTCTTCATACTTGAGAGTTGAGTGAA
1 ACACATTCCAC-------TGTATACAAAATAAGAAAGGCTTCTTCATACTTGAGAGTTGAGTGAA
*
963356 CATAATGACCACTAATATATAGAGGTGTTGAGAAATGTAGAATCCAGATGTAGCTCACGTAATAA
59 CATAATGACCACTAATATATAGAGGTGTTGAGAAATGTAGAATCCAGATGTAGCTCAAGTAATAA
*
963421 CTAAACACATAGTACTGAGCAACGATGGACTCCTTCAAGGGATAGATATTGCTTCCCTATCTTCT
124 CTAAACACATAGTACTGAGCAACGATGGACTCCTTCAAGGGATAGATATTGCTTCCCTATCTTTT
*
963486 ATTTTCCAGATATGTAACGGTCTCTACCATAGTAGCAAATGTAGACACCTGGACCACATCTGGTT
189 ATTTTCCAGATATGTAACGGTCTCTACCATAGTAGCAAACGTAGACACCTGGACCACATCTGGTT
* * *
963551 AGACTCATGGAAAACAATCTAAATATTACATACTATCTCACAGAAAAAGACAAAAAATGCATCTA
254 AGACTCATGGAAAACAATCTAAATATTATATAATATCTCACAGATAAAGACAAAAAATGCATCTA
*
963616 CATTCAAATGATATGGAAGAAATGTATTTCCAGATGCAGTTATTAAGTGTTATTACTTATTACCA
319 CATTCAAATGATATGGAAGAAATGTATTTCCAAATGCAGTTATTAAGTG-------TTATTACCA
* * *
963681 TTTAATTCAAAATGTCTAACCCTTTAACAAAGAAAAAACCAGATCAGCATGTGTCCCACTATATA
377 TTTACTTCACAATGTCTAGCCCTTTAACAAA-AAAAAA-CAGATCAGCATGTGTCCCACTATATA
* * *
963746 CAATATAAGAATAGCCTTCACACTTGAATGTATAGAATGATCACTAATATAACAAGGTACTAGAG
440 CAAAATAAGAATGGCCTTCACACTTGAATGTATAGAATGATCACTAATATAACGAGGTACTAGAG
963811 CAATGTAGTGTCCAGATGTAGCTCAAGTAATAACTAAACACA-TAATATTGGGCAACGATGGACT
505 CAATGTAGTGTCCAGATGTAGCTCAAGTAATAACTAAACACAGT-A-A-TGGGCAACGATGGACT
* * * *
963875 CCATCAAGGGATGGCTAATAGATAGATAGGAAACGCAAACCGTCAATTCCTTCCCTATCATTTAT
567 CCATCAAGGGATGGCTAATAGATAGATTGGAAACACAAACCATCAATTCCTTCCCTATCTTTTAT
* *
963940 TTTCCAGATATGTAACAGTTCCTACCATCATAAGCAAAGGTAGACACCTGACTACATCTGGTTAG
632 TTTCCAGATATGTAACAGTCCCTACCATAATAAGCAAAGGTAGACACCTGACTACATCTGGTTAG
* * * * *
964005 ACTCATGGAAGCAAACAGCTAAATATTAAATAATATTTCACAAATGTATACCAAAAAAATGCATC
697 ACTCATGGAAGCAGACAGCTAAATGTTAAATAATATTTCACAGATATA-AACAAAAAAATGCATC
* *
964070 TATACTCAAAACATAT
761 TATATTCAAAATATAT
964086 AGATGAATAA
Statistics
Matches: 1525, Mismatches: 97, Indels: 58
0.91 0.06 0.03
Matches are distributed among these distances:
855 38 0.02
856 1 0.00
857 2 0.00
861 1 0.00
862 72 0.05
864 34 0.02
866 1 0.00
867 37 0.02
868 292 0.19
869 2 0.00
870 126 0.08
872 67 0.04
873 33 0.02
874 91 0.06
880 321 0.21
881 21 0.01
886 4 0.00
887 40 0.03
888 131 0.09
889 20 0.01
890 189 0.12
891 2 0.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (871 bp):
ACACATTCCACTGTATACAAAATAAGAAAGGCTTCTTCATACTTGAGAGTTGAGTGAACATAATG
ACCACTAATATATAGAGGTGTTGAGAAATGTAGAATCCAGATGTAGCTCAAGTAATAACTAAACA
CATAGTACTGAGCAACGATGGACTCCTTCAAGGGATAGATATTGCTTCCCTATCTTTTATTTTCC
AGATATGTAACGGTCTCTACCATAGTAGCAAACGTAGACACCTGGACCACATCTGGTTAGACTCA
TGGAAAACAATCTAAATATTATATAATATCTCACAGATAAAGACAAAAAATGCATCTACATTCAA
ATGATATGGAAGAAATGTATTTCCAAATGCAGTTATTAAGTGTTATTACCATTTACTTCACAATG
TCTAGCCCTTTAACAAAAAAAAACAGATCAGCATGTGTCCCACTATATACAAAATAAGAATGGCC
TTCACACTTGAATGTATAGAATGATCACTAATATAACGAGGTACTAGAGCAATGTAGTGTCCAGA
TGTAGCTCAAGTAATAACTAAACACAGTAATGGGCAACGATGGACTCCATCAAGGGATGGCTAAT
AGATAGATTGGAAACACAAACCATCAATTCCTTCCCTATCTTTTATTTTCCAGATATGTAACAGT
CCCTACCATAATAAGCAAAGGTAGACACCTGACTACATCTGGTTAGACTCATGGAAGCAGACAGC
TAAATGTTAAATAATATTTCACAGATATAAACAAAAAAATGCATCTATATTCAAAATATATTGAA
GCATGGAAAGTATTGTCAAATGCGTATGTTAAGTGTTACCATTATTTGCTTCACTATGCCAATCC
CTTCAAGAAAAAAACAGGCTCACAAC
Found at i:968049 original size:37 final size:37
Alignment explanation
Indices: 967971--968391 Score: 532
Period size: 37 Copynumber: 11.2 Consensus size: 37
967961 TATATTTAGC
* * ** *
967971 ATATATAATATACAGTTTTGAGAATTTTTTTTAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
*
968008 ATATATATAGTATATAGTTTTAAAAACATTTTTGAAAAT
1 ATATATA-A-TATATAGTTTTGAAAACATTTTTGAAAAT
* * *
968047 ATATATAATATATAGTTTTGAAAAAAATATTGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
968084 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
*
968121 ATATATATTATATAGTTTTGAAAACATTTTTGAATATATAT
1 ATATATAATATATAGTTTTGAAAACATTTTTG-A-A-A-AT
968162 ATATATATAGTATATAGTTTTGAAAACATTTTTGAAAAT
1 ATATATA-A-TATATAGTTTTGAAAACATTTTTGAAAAT
968201 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
*
968238 ATATATAATATATTGTTTTGAAAACATTTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
*
968275 ATATATATTATATAGTTTTGAAAACATTTTTG-AAA-
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
*
968310 ATATAT-ATA-ATA-TTTTGAAAACATTTTTTTTAAAAAT
1 ATATATAATATATAGTTTTGAAAACA---TTTTTGAAAAT
* ** *
968347 ATATATGATATATAGTTTT-AAAATGTTTTT-AATAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
968382 AATATATAAT
1 -ATATATAAT
968392 TTGAAAAAAC
Statistics
Matches: 343, Mismatches: 24, Indels: 35
0.85 0.06 0.09
Matches are distributed among these distances:
32 11 0.03
33 3 0.01
34 2 0.01
35 15 0.04
36 19 0.06
37 198 0.58
38 7 0.02
39 47 0.14
40 6 0.02
41 10 0.03
42 1 0.00
43 24 0.07
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (37 bp):
ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
Found at i:968191 original size:154 final size:154
Alignment explanation
Indices: 968006--968322 Score: 573
Period size: 154 Copynumber: 2.1 Consensus size: 154
967996 TTTTTTTAAA
968006 ATATATATATAGTATATAGTTTTAAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAA
1 ATATATATATAGTATATAGTTTTAAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAA
968071 AAATATTGAAAATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATATTATATAG
66 AAATATTGAAAATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATATTATATAG
*
968136 TTTTGAAAACATTTTTGAATATAT
131 TTTTGAAAACATTTTTGAAAATAT
*
968160 ATATATATATAGTATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAA
1 ATATATATATAGTATATAGTTTTAAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAA
* * * *
968225 CATTTTTGAAAATATATATAATATATTGTTTTGAAAACATTTTTGAAAATATATATATTATATAG
66 AAATATTGAAAATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATATTATATAG
968290 TTTTGAAAACATTTTTGAAAATAT
131 TTTTGAAAACATTTTTGAAAATAT
968314 ATATA-ATAT
1 ATATATATAT
968323 TTTGAAAACA
Statistics
Matches: 157, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
153 4 0.03
154 153 0.97
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (154 bp):
ATATATATATAGTATATAGTTTTAAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAA
AAATATTGAAAATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATATTATATAG
TTTTGAAAACATTTTTGAAAATAT
Found at i:971372 original size:20 final size:20
Alignment explanation
Indices: 971336--971373 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
971326 ATCCTATTCC
**
971336 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
971356 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
971374 GTAAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:971800 original size:17 final size:17
Alignment explanation
Indices: 971778--971814 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
971768 AAAATGATGG
*
971778 AATAATATATTATTTTT
1 AATAATATATTATTTAT
*
971795 AATAATTTATTATTTAT
1 AATAATATATTATTTAT
971812 AAT
1 AAT
971815 GAAAAACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATAATATATTATTTAT
Found at i:971939 original size:25 final size:25
Alignment explanation
Indices: 971911--971967 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
971901 AGGAAGGAAG
*
971911 AAGGTTGATGTAGAACAACAGCCAC
1 AAGGGTGATGTAGAACAACAGCCAC
971936 AAGGGTGATGTAGAACAACAGCCAC
1 AAGGGTGATGTAGAACAACAGCCAC
971961 AAGGGTG
1 AAGGGTG
971968 TTGTTGACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.30, T:0.14
Consensus pattern (25 bp):
AAGGGTGATGTAGAACAACAGCCAC
Found at i:972330 original size:29 final size:29
Alignment explanation
Indices: 972298--972393 Score: 68
Period size: 33 Copynumber: 3.1 Consensus size: 29
972288 ATTTTAACTT
972298 TTTAAATTAAATTATTAATAATATTAACA
1 TTTAAATTAAATTATTAATAATATTAACA
* * * ** **
972327 TTTATATGTTATTTAAAAAT-ATATATAAGG
1 TTTAAAT-TAAATTATTAATAATAT-TAACA
972357 TTTAATTAATTTAAATTATTAATAATATTAACA
1 TTT-A--AA-TTAAATTATTAATAATATTAACA
972390 TTTA
1 TTTA
972394 TATGTTATTT
Statistics
Matches: 46, Mismatches: 14, Indels: 11
0.65 0.20 0.15
Matches are distributed among these distances:
29 10 0.22
30 14 0.30
31 1 0.02
32 1 0.02
33 15 0.33
34 5 0.11
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTAAATTAAATTATTAATAATATTAACA
Found at i:972347 original size:27 final size:27
Alignment explanation
Indices: 972312--972411 Score: 69
Period size: 27 Copynumber: 3.4 Consensus size: 27
972302 AATTAAATTA
*
972312 TTAATAATATTAACATTTATATGTTAT
1 TTAAAAATATTAACATTTATATGTTAT
972339 TTAAAAATATATATA-AGGTTTAATTAAT-TTAAATT
1 TTAAAAATAT-TA-ACA--TTT-A-T-ATGTT--A-T
*
972374 ATTAATAATATTAACATTTATATGTTAT
1 -TTAAAAATATTAACATTTATATGTTAT
972402 TTAAAAATAT
1 TTAAAAATAT
972412 ATATAAGGTT
Statistics
Matches: 57, Mismatches: 3, Indels: 26
0.66 0.03 0.30
Matches are distributed among these distances:
27 18 0.32
28 4 0.07
29 2 0.04
30 5 0.09
31 4 0.07
32 4 0.07
33 5 0.09
34 2 0.04
35 4 0.07
36 9 0.16
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (27 bp):
TTAAAAATATTAACATTTATATGTTAT
Found at i:972381 original size:63 final size:63
Alignment explanation
Indices: 972299--972425 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
972289 TTTTAACTTT
972299 TTAAATTAAATTATTAATAATATTAACATTTATATGTTATTTAAAAATATATATAAGGTTTAA
1 TTAAATTAAATTATTAATAATATTAACATTTATATGTTATTTAAAAATATATATAAGGTTTAA
*
972362 TTAATTTAAATTATTAATAATATTAACATTTATATGTTATTTAAAAATATATATAAGGTTTAA
1 TTAAATTAAATTATTAATAATATTAACATTTATATGTTATTTAAAAATATATATAAGGTTTAA
972425 T
1 T
972426 GTAGTTAAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (63 bp):
TTAAATTAAATTATTAATAATATTAACATTTATATGTTATTTAAAAATATATATAAGGTTTAA
Found at i:974743 original size:60 final size:61
Alignment explanation
Indices: 974665--974792 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 61
974655 ATATTCTATT
** * * * *
974665 TTCATCCCTGAACAATGACTATT-ATTCTGAATTAATCCTCAAAC-TTTTGAATATTTCAAG
1 TTCATCCCCAAACAATGAC-ATTCACTCTAAATTAATCCCCAAACTTTTTGAATATTCCAAG
* ** * *
974725 TTCATCCCCAAACCATGACATTCACTCTAAATTGGTCCCCAAACTTTTTGAATGTTCCAAT
1 TTCATCCCCAAACAATGACATTCACTCTAAATTAATCCCCAAACTTTTTGAATATTCCAAG
974786 TTCATCC
1 TTCATCC
974793 TAAATTATAC
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
59 3 0.05
60 32 0.58
61 20 0.36
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (61 bp):
TTCATCCCCAAACAATGACATTCACTCTAAATTAATCCCCAAACTTTTTGAATATTCCAAG
Found at i:975069 original size:58 final size:58
Alignment explanation
Indices: 974929--975106 Score: 175
Period size: 58 Copynumber: 3.0 Consensus size: 58
974919 TGAACTTGGA
* * * *
974929 GATGAAATTGGAGTATTCAAAAGTTT-GGAGACCAATTTAGAAAGAGGGTCATAGTTTAGG
1 GATGAAATTGAAATATTCAAAAGTTTAAG-GACCAATTTAGAATGA--GTCATAGTTTAGG
* * *
974989 CATGAAATT-AGAATGAGT-AAAAGTTTAAGGACTAATTTAGAATGAGTCATTA-TTTAGG
1 GATGAAATTGA-AAT-ATTCAAAAGTTTAAGGACCAATTTAGAATGAGTCA-TAGTTTAGG
* * * *
975047 GATGAAATTGAAATATTCAAAAGTTTAAAGACCAATTTAAAATGAGTTATAGTTTGGG
1 GATGAAATTGAAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGTCATAGTTTAGG
975105 GA
1 GA
975107 CATATGATGC
Statistics
Matches: 97, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
57 4 0.04
58 55 0.57
59 3 0.03
60 32 0.33
61 3 0.03
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (58 bp):
GATGAAATTGAAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGTCATAGTTTAGG
Found at i:975320 original size:17 final size:18
Alignment explanation
Indices: 975295--975328 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
975285 ACTGAGAAAT
975295 TTTAAATTTTT-ATATAA
1 TTTAAATTTTTAATATAA
*
975312 TTTATATTTTTAATATA
1 TTTAAATTTTTAATATA
975329 TCTAATATTT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAAATTTTTAATATAA
Found at i:976677 original size:7 final size:7
Alignment explanation
Indices: 976654--976700 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
976644 TTAGAAGAGT
976654 GAAAATA
1 GAAAATA
* *
976661 GAATACA
1 GAAAATA
976668 GAAAATA
1 GAAAATA
*
976675 GAAAATT
1 GAAAATA
*
976682 GAAATTA
1 GAAAATA
976689 -AAAATA
1 GAAAATA
976695 GAAAAT
1 GAAAAT
976701 GTGAATATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.66, C:0.02, G:0.13, T:0.19
Consensus pattern (7 bp):
GAAAATA
Found at i:979502 original size:2 final size:2
Alignment explanation
Indices: 979495--979530 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
979485 TTGATATTGC
*
979495 AT AT AT AT AT AT AT AT AT AT AT AC 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
979531 TTTACTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:983354 original size:18 final size:18
Alignment explanation
Indices: 983328--983368 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
983318 GATCATGAAC
*
983328 TAAATTTTTAAATAATTA
1 TAAATTTTTAAAAAATTA
983346 -AAATATTTTAAAAAATTA
1 TAAAT-TTTTAAAAAATTA
983364 TAAAT
1 TAAAT
983369 GAATACACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 4 0.20
18 12 0.60
19 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATTTTTAAAAAATTA
Found at i:983767 original size:3 final size:3
Alignment explanation
Indices: 983759--983800 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
983749 TTACCCATTT
* *
983759 TTA TTA TTA TTA TAA TTA TTA -TA TACA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
983801 AATAAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:985433 original size:23 final size:22
Alignment explanation
Indices: 985387--985431 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
985377 ATATTATAAA
985387 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
985409 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
985432 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:985513 original size:23 final size:26
Alignment explanation
Indices: 985481--985530 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
985471 CCTTTTCTGA
*
985481 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
985504 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
985530 T
1 T
985531 TTTTCTCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:989391 original size:15 final size:15
Alignment explanation
Indices: 989371--989402 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
989361 ATCAATACCT
989371 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
989386 TTTTGCATACATTCA
1 TTTTGCATACATGCA
989401 TT
1 TT
989403 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:997775 original size:23 final size:26
Alignment explanation
Indices: 997727--997776 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
997717 AATTATGAGA
*
997727 AAAATAATTTATATATATTTATAAAT
1 AAAATAATTTATATATATTTAGAAAT
997753 AAAAT-ATTTAT-T-TATTTAGAAAT
1 AAAATAATTTATATATATTTAGAAAT
997776 A
1 A
997777 TTAGAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 6 0.26
26 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAATAATTTATATATATTTAGAAAT
Found at i:998982 original size:24 final size:23
Alignment explanation
Indices: 998955--999028 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 23
998945 CTTTCTATTT
*
998955 TTTTTCGTTCTCTGTTTTTGCTGG
1 TTTTT-GTTCTCTATTTTTGCTGG
*
998979 TTTTTTTTCTTCTATTTTTGCTGG
1 TTTTTGTTC-TCTATTTTTGCTGG
* * *
999003 TTGTTGTTCTCTCTTCTTTGCAGG
1 TTTTTGTTCTCTATT-TTTGCTGG
999027 TT
1 TT
999029 GGGTGATGGC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
23 8 0.19
24 34 0.81
ACGTcount: A:0.03, C:0.16, G:0.18, T:0.64
Consensus pattern (23 bp):
TTTTTGTTCTCTATTTTTGCTGG
Found at i:999420 original size:3 final size:3
Alignment explanation
Indices: 999412--999486 Score: 91
Period size: 3 Copynumber: 25.0 Consensus size: 3
999402 ATTTGGGCCT
* *
999412 ATA ATA ATA TTTA TTA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
999457 ATA ATA ATA ATA ATG ATA AT- ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
999487 TTTAAATGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.06
3 56 0.88
4 4 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:999850 original size:120 final size:120
Alignment explanation
Indices: 999625--999910 Score: 375
Period size: 120 Copynumber: 2.4 Consensus size: 120
999615 TGAATAAATT
* * * *
999625 CTTCTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGG---GGATGATGTTGACCT
1 CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAGGATGATGCTAACCT
* * * *
999687 ATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAA
65 ATTTCCTTCTGTGATAAAATCATTCAAAAGATTGAACAAGCTCTTCTCATTATGAA
* ** *
999743 CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAGTTTGATGCTAATCTA
1 CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTA
* * *
999808 TTTGCTTCTGTGATAAAATTATGT-AAAAGATTGAACAAGCTCTTCTCATTGTGAA
66 TTTCCTTCTGTGATAAAATCAT-TCAAAAGATTGAACAAGCTCTTCTCATTATGAA
*
999863 CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAA
1 CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
999911 AGCTGATCCA
Statistics
Matches: 147, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
117 4 0.03
118 39 0.27
119 10 0.07
120 93 0.63
121 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (120 bp):
CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTA
TTTCCTTCTGTGATAAAATCATTCAAAAGATTGAACAAGCTCTTCTCATTATGAA
Found at i:999963 original size:88 final size:89
Alignment explanation
Indices: 999867--1000053 Score: 243
Period size: 92 Copynumber: 2.1 Consensus size: 89
999857 TGTGAACTTC
* * *
999867 TTCTTCTTCAGAT-GAGTTCTTCTCATTATGAACTTCT-CTGGAAAAGCTGATCCATTAAGTGAT
1 TTCTTCTTCAGATAGAGTTCTTCTCATTATGAAC-TCTACTGGAAAAGCTAATCCATCAAATGAT
* * *
999930 GGATTTGAGCAAAAGGTTGAACAAA
65 GAATTTAAACAAAAGGTTGAACAAA
* * *
999955 TTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCATCAAATG
1 TTCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTA-CTGGAAAAGCTAATCCATCAAATG
1000020 ATGAATTTAAACAAAAGGTTGAACAAA
63 ATGAATTTAAACAAAAGGTTGAACAAA
1000047 TTCTTCT
1 TTCTTCT
1000054 CATTATGAAC
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
88 13 0.15
90 3 0.04
91 20 0.24
92 49 0.58
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (89 bp):
TTCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACTGGAAAAGCTAATCCATCAAATGATG
AATTTAAACAAAAGGTTGAACAAA
Found at i:1000091 original size:113 final size:114
Alignment explanation
Indices: 999957--1000342 Score: 442
Period size: 113 Copynumber: 3.3 Consensus size: 114
999947 TGAACAAATT
999957 CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTA-ATCCATCAAATGA
1 CTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAGATCCATCAAATGA
* *
1000021 TGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
63 TGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
* * *
1000073 CTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAATGTTGATGTTGATCTATCTCC
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTT-A----GATCCA--T-C
*** * * * *
1000137 TTCTGGGAT-AGAGTCGAGCAAAAGGTTTAA-AAAGTTCTTCTTATTATGAACTTCTTCTTC
57 AAAT--GATGA-ATTCAAGCAAAAGGTTGAACAAA-TTCTTCTCATTATGAACTTCTTCTTC
* *
1000197 TTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATG-TAGATCCATCGAATGATGA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAGATCCATCAAATGATGA
*
1000261 ATTCAAGCGAAAA-GTTGAACAAATTCTTCTCATTACGAACTTCTTCTTC
66 ATTCAAGC-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1000310 CTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1000343 CTTCTTCCTT
Statistics
Matches: 227, Mismatches: 25, Indels: 39
0.78 0.09 0.13
Matches are distributed among these distances:
112 2 0.01
113 101 0.44
114 9 0.04
115 2 0.01
116 12 0.05
118 5 0.02
119 4 0.02
121 1 0.00
122 3 0.01
123 5 0.02
124 81 0.36
125 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.38
Consensus pattern (114 bp):
CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAGATCCATCAAATGATGA
ATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
Found at i:1000341 original size:40 final size:40
Alignment explanation
Indices: 1000284--1000423 Score: 216
Period size: 40 Copynumber: 3.6 Consensus size: 40
1000274 GTTGAACAAA
*
1000284 TTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
*
1000324 TTCTTCTCATTATGAACTCCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1000364 TTCTTCTCATTATGAAC-T-TT-TT-CTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* *
1000400 TTCTTCTAATTATGAACTTTTTCT
1 TTCTTCTCATTATGAACTTCTTCT
1000424 GGAAAAGCTG
Statistics
Matches: 93, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
36 30 0.32
37 3 0.03
38 4 0.04
39 1 0.01
40 55 0.59
ACGTcount: A:0.19, C:0.24, G:0.09, T:0.49
Consensus pattern (40 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
Found at i:1000415 original size:189 final size:193
Alignment explanation
Indices: 1000169--1000530 Score: 531
Period size: 189 Copynumber: 1.9 Consensus size: 193
1000159 AGGTTTAAAA
* *
1000169 AGTTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTAATTATGAACTCTACC
* * *
1000234 TGGCAATG-TAGATCCATCGAA-TGAT-GAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATTA
66 TGGAAAAGCT-GATCCATC-AAGTGATGGAATTCAA-CAAAAAGTTGAACAAATTCTTCTCATTA
1000296 CGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTCTTCCTTCTTCAGAT
128 CGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTCTTCCTTCTTCAGAT
1000361 G
193 G
* **
1000362 AGTTCTTCTCATTATGAAC-T-TT-TTC-TTCTTCAGATGAGTTCTTCTAATTATGAACTTTTTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTAATTATGAACTCTACC
* * *
1000423 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGA
66 TGGAAAAGCTGATCCATCAAGTGATGGAATTCAACAAAAAGTTGAACAAATTCTTCTCATTACGA
**
1000488 ACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATTATGAACT
131 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1000531 TTCTCTGGAG
Statistics
Matches: 153, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
188 2 0.01
189 120 0.78
190 10 0.07
191 2 0.01
192 1 0.01
193 18 0.12
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (193 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTAATTATGAACTCTACC
TGGAAAAGCTGATCCATCAAGTGATGGAATTCAACAAAAAGTTGAACAAATTCTTCTCATTACGA
ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTCTTCCTTCTTCAGATG
Found at i:1000525 original size:113 final size:109
Alignment explanation
Indices: 1000364--1000569 Score: 331
Period size: 113 Copynumber: 1.9 Consensus size: 109
1000354 TTCAGATGAG
*
1000364 TTCTTCTCATTATGAACTTTTTCTTCTTCAGATGAGTTCTTCTAATTATGAACTTTTTCTGGAAA
1 TTCTTCTCATTATGAACTTTTTCTTCTTCAGATGAGTTCTTCTAATTATGAACTTTCTCTGGAAA
*
1000429 AGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAA
66 AGCTGATCCATCAAATGATGGATTTGAACAAAAAGTTGAACAAA
* *
1000473 TTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAA---CTT-TTTCTTCTTCAGATGAGTTCTTCTAATTATGAACTTTCTCTG
*
1000538 GAGAAGCTGATCCATCAAATGATGGATTTGAA
62 GAAAAGCTGATCCATCAAATGATGGATTTGAA
1000570 TCTTTGTTAA
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
109 16 0.18
112 3 0.03
113 69 0.78
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (109 bp):
TTCTTCTCATTATGAACTTTTTCTTCTTCAGATGAGTTCTTCTAATTATGAACTTTCTCTGGAAA
AGCTGATCCATCAAATGATGGATTTGAACAAAAAGTTGAACAAA
Found at i:1001420 original size:115 final size:113
Alignment explanation
Indices: 1001250--1001557 Score: 481
Period size: 115 Copynumber: 2.7 Consensus size: 113
1001240 TCATGCAGTC
* * * *
1001250 CATCTTTTAATTCCAATGATTGGTTATGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGAAC
1 CATCTTTCAAATCCAATGATTGGTT-TGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
*
1001315 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATT
65 ACTTCCAGAAGATGCTATTGGGTCTTCGTATTTCTACTATGAGCACATT
1001364 CATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAGAA
1 CATCTTTCAAATCCAATGATTGGTT-TGTGG-TTCATACCAAACCAGATCAGATAACTCAAAGAA
*
1001429 CACTTCCATAAGATGCTATTGGGTCTTCGTATTTCTACTATGAGCACATT
64 CACTTCCAGAAGATGCTATTGGGTCTTCGTATTTCTACTATGAGCACATT
* * *
1001479 CATCTTTCAAATTCAATGATTGGTTTTTGGGGTTAATACCAAACCAGATCAGATAACTCAAAGAA
1 CATCTTTCAAATCCAATGATTGG--TTTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
*
1001544 CACTTCTAGAAGAT
64 CACTTCCAGAAGAT
1001558 ATTATGAGCA
Statistics
Matches: 179, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
114 28 0.16
115 145 0.81
116 4 0.02
117 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (113 bp):
CATCTTTCAAATCCAATGATTGGTTTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATTGGGTCTTCGTATTTCTACTATGAGCACATT
Found at i:1001626 original size:93 final size:93
Alignment explanation
Indices: 1001466--1001848 Score: 685
Period size: 93 Copynumber: 4.1 Consensus size: 93
1001456 CGTATTTCTA
* *
1001466 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTTTTGGGGTTAATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
* *
1001531 ATAACTCAAAGAACACTTCTAGAAGATA
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
1001559 TTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
*
1001624 ATAACTCAAAGAATACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
1001652 TTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
1001717 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
1001745 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
*
1001810 ATAACTCAATGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
1001838 CTATGAGCACA
1 CTATGAGCACA
1001849 CGGCACTTGT
Statistics
Matches: 280, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 280 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (93 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:1010233 original size:15 final size:15
Alignment explanation
Indices: 1010210--1010241 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1010200 TGCAATGAAT
1010210 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1010225 AATGCATGTATGCAA
1 AATGAATGTATGCAA
1010240 AA
1 AA
1010242 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1014122 original size:23 final size:26
Alignment explanation
Indices: 1014074--1014123 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
1014064 AATTATGAGA
*
1014074 AAAATAATTTATATATATTTATAAAT
1 AAAATAATTTATATATATTTAGAAAT
1014100 AAAAT-ATTTAT-T-TATTTAGAAAT
1 AAAATAATTTATATATATTTAGAAAT
1014123 A
1 A
1014124 TCATAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 6 0.26
26 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAATAATTTATATATATTTAGAAAT
Found at i:1015296 original size:24 final size:23
Alignment explanation
Indices: 1015253--1015297 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1015243 TATTTTTTTC
* *
1015253 GTTCTCTGTTTTTGCTGGTTGTT
1 GTTCTCTCTTTTTGCAGGTTGTT
1015276 GTTCTCTCTTCTTTGCAGGTTG
1 GTTCTCTCTT-TTTGCAGGTTG
1015298 GGTGATGGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.02, C:0.18, G:0.24, T:0.56
Consensus pattern (23 bp):
GTTCTCTCTTTTTGCAGGTTGTT
Found at i:1015700 original size:3 final size:3
Alignment explanation
Indices: 1015694--1015763 Score: 108
Period size: 3 Copynumber: 23.7 Consensus size: 3
1015684 TAATATTTAT
1015694 TAA TAA TAA TAA -AA 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
*
1015741 TAA TAA TGA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TA
1015764 TTTAAATGAA
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
2 4 0.06
3 56 0.90
4 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1015764 original size:9 final size:10
Alignment explanation
Indices: 1015681--1015764 Score: 81
Period size: 9 Copynumber: 8.9 Consensus size: 10
1015671 TTTGGGCCTG
*
1015681 TAATAATATT
1 TAATAATATA
*
1015691 TATTAATA-A
1 TAATAATATA
*
1015700 TAATAAAATAA
1 TAATAATAT-A
1015711 TAATAATA-A
1 TAATAATATA
1015720 TAATAATA-A
1 TAATAATATA
1015729 TAATAATA-A
1 TAATAATATA
1015738 TAATAATA-A
1 TAATAATATA
*
1015747 TGATAATATA
1 TAATAATATA
1015757 -AATAATAT
1 TAATAATAT
1015765 TTAAATGAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
9 48 0.75
10 8 0.12
11 8 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (10 bp):
TAATAATATA
Found at i:1016069 original size:18 final size:18
Alignment explanation
Indices: 1016043--1016083 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1016033 GATCATGAAC
*
1016043 TAAATTTTTAAATAATTA
1 TAAATTTTTAAAAAATTA
1016061 -AAATATTTTAAAAAATTA
1 TAAAT-TTTTAAAAAATTA
1016079 TAAAT
1 TAAAT
1016084 GAATACACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 4 0.20
18 12 0.60
19 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATTTTTAAAAAATTA
Found at i:1016478 original size:3 final size:3
Alignment explanation
Indices: 1016470--1016527 Score: 82
Period size: 3 Copynumber: 19.3 Consensus size: 3
1016460 TTTTTTACCC
* *
1016470 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATA ATT ATT A-T ATAC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
1016515 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
1016528 AATAAATAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.92
4 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1016563 original size:26 final size:25
Alignment explanation
Indices: 1016528--1016581 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
1016518 ATTATTATTA
1016528 AATAAATAAATAA-ATAAATAATAAT
1 AATAAATAAA-AATATAAATAATAAT
*
1016553 AATAATATAAAAATATATATAATAAT
1 AATAA-ATAAAAATATAAATAATAAT
1016579 AAT
1 AAT
1016582 TACATGCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
AATAAATAAAAATATAAATAATAAT
Found at i:1016567 original size:17 final size:17
Alignment explanation
Indices: 1016526--1016576 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
1016516 TTATTATTAT
1016526 TAAATAA-ATAAATAA-A
1 TAAATAATAT-AATAATA
1016542 TAAATAATAATAATAATA
1 TAAATAAT-ATAATAATA
1016560 TAAA-AATATATATAATA
1 TAAATAATATA-ATAATA
1016577 ATAATTACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 10 0.32
17 14 0.45
18 7 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAATAATATAATAATA
Found at i:1017932 original size:14 final size:15
Alignment explanation
Indices: 1017913--1017941 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1017903 GTTCTAATTG
1017913 TAATTTTA-TTGTTT
1 TAATTTTACTTGTTT
1017927 TAATTTTACTTGTTT
1 TAATTTTACTTGTTT
1017942 ATAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.03, G:0.07, T:0.69
Consensus pattern (15 bp):
TAATTTTACTTGTTT
Found at i:1018167 original size:23 final size:22
Alignment explanation
Indices: 1018121--1018165 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1018111 ATATTATAAA
1018121 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
1018143 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
1018166 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:1018247 original size:23 final size:26
Alignment explanation
Indices: 1018215--1018264 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
1018205 CCTTTTCTGA
*
1018215 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
1018238 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
1018264 T
1 T
1018265 TTTCTCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:1044240 original size:2 final size:2
Alignment explanation
Indices: 1044233--1044265 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1044223 TAAATGAAGT
1044233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1044266 TCGAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1053512 original size:37 final size:38
Alignment explanation
Indices: 1053462--1053534 Score: 130
Period size: 37 Copynumber: 1.9 Consensus size: 38
1053452 GATTGAAAGA
1053462 TAGTTAATCAGTTGACCAGCTATAAAAAA-CTCATCGC
1 TAGTTAATCAGTTGACCAGCTATAAAAAAGCTCATCGC
*
1053499 TAGTTAATCAGTTGGCCAGCTATAAAAAAGCTCATC
1 TAGTTAATCAGTTGACCAGCTATAAAAAAGCTCATC
1053535 CCTCAAACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 28 0.82
38 6 0.18
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (38 bp):
TAGTTAATCAGTTGACCAGCTATAAAAAAGCTCATCGC
Found at i:1056313 original size:31 final size:31
Alignment explanation
Indices: 1056252--1056313 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1056242 GTTTTATGGC
* * ** *
1056252 AGAGTAAGTTGTCCTTATCATTCCTCCAAAA
1 AGAGAAAGTTGTCCTTATCACTAATACAAAA
1056283 AGAGAAAGTTGTCCTTATCACTAATACAAAA
1 AGAGAAAGTTGTCCTTATCACTAATACAAAA
1056314 GGAAAAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (31 bp):
AGAGAAAGTTGTCCTTATCACTAATACAAAA
Found at i:1067717 original size:2 final size:2
Alignment explanation
Indices: 1067705--1067736 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1067695 ATGATAAAAT
1067705 TA TA TA T- TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1067737 AAAGTTAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1067725 original size:15 final size:13
Alignment explanation
Indices: 1067703--1067736 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1067693 TTATGATAAA
1067703 ATTATATAT-TAT
1 ATTATATATATAT
1067715 A-TATATATATAT
1 ATTATATATATAT
1067727 ATTATATATA
1 ATTATATATA
1067737 AAAGTTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.35
12 5 0.25
13 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTATATATATAT
Found at i:1069394 original size:31 final size:30
Alignment explanation
Indices: 1069349--1069427 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 30
1069339 TTGATAATAA
*
1069349 AATAATTATTTTATAGT-ATTTAGATAAATTT
1 AATAA-TATTTTATAATCATTTA-ATAAATTT
* *
1069380 ATTAATAATTTTATAATCTTTTAATAAATTT
1 AATAAT-ATTTTATAATCATTTAATAAATTT
1069411 AATAAGTATTTTATAAT
1 AATAA-TATTTTATAAT
1069428 TTTTTTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 35 0.85
32 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (30 bp):
AATAATATTTTATAATCATTTAATAAATTT
Found at i:1069405 original size:19 final size:20
Alignment explanation
Indices: 1069381--1069430 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1069371 GATAAATTTA
*
1069381 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
1069400 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
1069421 TT-ATAATTTT
1 TTAATAATTTT
1069431 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:1069426 original size:11 final size:10
Alignment explanation
Indices: 1069350--1069443 Score: 52
Period size: 11 Copynumber: 9.2 Consensus size: 10
1069340 TGATAATAAA
1069350 ATAATTATTTT
1 ATAA-TATTTT
* *
1069361 ATAGTATTTAG
1 ATAATATTT-T
1069372 ATAA-A-TTT
1 ATAATATTTT
1069380 ATTAATAATTTT
1 A-TAAT-ATTTT
*
1069392 ATAATCTTTT
1 ATAATATTTT
*
1069402 AATAA-ATTTA
1 -ATAATATTTT
1069412 ATAAGTATTTT
1 ATAA-TATTTT
*
1069423 ATAATTTTTT
1 ATAATATTTT
*
1069433 TTAA-ATTTT
1 ATAATATTTT
1069442 AT
1 AT
1069444 TGACGAAAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
8 1 0.02
9 14 0.22
10 21 0.33
11 23 0.37
12 4 0.06
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (10 bp):
ATAATATTTT
Found at i:1070193 original size:31 final size:30
Alignment explanation
Indices: 1070158--1070244 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
1070148 TCAATAAAGT
1070158 TTAAAAAAATATAAAATACTTATTAAATTTA
1 TTAAAAAAATATAAAATA-TTATTAAATTTA
* * *
1070189 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAAATATAAAA-TATTATTAAATTTA
* *
1070220 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAAATATAAAAT-ATTATTA
1070245 TATTATCGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 43 0.91
32 3 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (30 bp):
TTAAAAAAATATAAAATATTATTAAATTTA
Found at i:1074045 original size:18 final size:18
Alignment explanation
Indices: 1074022--1074085 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
1074012 TTAATTGAAA
1074022 AACCGAAAAACCGAACCG
1 AACCGAAAAACCGAACCG
*
1074040 AACCGAAAAATCCAAACCG
1 AACCGAAAAA-CCGAACCG
*
1074059 TTAA---AAAACCCGAACCG
1 --AACCGAAAAACCGAACCG
1074076 AACCGAAAAA
1 AACCGAAAAA
1074086 ACCGGTTTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
15 2 0.06
17 7 0.19
18 18 0.50
19 7 0.19
21 2 0.06
ACGTcount: A:0.53, C:0.30, G:0.12, T:0.05
Consensus pattern (18 bp):
AACCGAAAAACCGAACCG
Found at i:1084450 original size:31 final size:31
Alignment explanation
Indices: 1084415--1084487 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
1084405 ATTAAAAAAA
1084415 AATATTTAGCCCATTAGACCAACTTATAAAC
1 AATATTTAGCCCATTAGACCAACTTATAAAC
* **
1084446 AATATTTAGCCCATTAGACCAACTTATTATT
1 AATATTTAGCCCATTAGACCAACTTATAAAC
1084477 AATATTTAGCC
1 AATATTTAGCC
1084488 GTTTTATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (31 bp):
AATATTTAGCCCATTAGACCAACTTATAAAC
Found at i:1087261 original size:23 final size:25
Alignment explanation
Indices: 1087220--1087269 Score: 86
Period size: 23 Copynumber: 2.1 Consensus size: 25
1087210 AACTTCTAAA
1087220 ATATGAGTTTATATAATTTTAGGAG
1 ATATGAGTTTATATAATTTTAGGAG
1087245 ATATGAG-TT-TATAATTTTAGGAG
1 ATATGAGTTTATATAATTTTAGGAG
1087268 AT
1 AT
1087270 GAAAATAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 16 0.64
24 2 0.08
25 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (25 bp):
ATATGAGTTTATATAATTTTAGGAG
Found at i:1089666 original size:32 final size:32
Alignment explanation
Indices: 1089612--1089714 Score: 93
Period size: 32 Copynumber: 3.2 Consensus size: 32
1089602 CATATCCAAT
* *
1089612 TTAACCTGAATCGGAAA-TAATCCAAATCGAAA
1 TTAACCTGAA-CTGAAAGCAATCCAAATCGAAA
* *
1089644 TTAACCTGAACTGAAAGCAATCCGAACCGAAAA
1 TTAACCTGAACTGAAAGCAATCCAAATCG-AAA
* * * *
1089677 ATAA-CTCAATTCGAAAGCAATCCAAATCGAAT
1 TTAACCTGAACT-GAAAGCAATCCAAATCGAAA
1089709 TTAACC
1 TTAACC
1089715 CAATTCGAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
31 5 0.09
32 29 0.52
33 22 0.39
ACGTcount: A:0.46, C:0.22, G:0.12, T:0.20
Consensus pattern (32 bp):
TTAACCTGAACTGAAAGCAATCCAAATCGAAA
Found at i:1089724 original size:32 final size:32
Alignment explanation
Indices: 1089630--1089724 Score: 102
Period size: 32 Copynumber: 2.9 Consensus size: 32
1089620 AATCGGAAAT
* *
1089630 AATCCAAATCGAAATTAACCTGAACT-GAAAGC
1 AATCCAAATCGAAATTAACC-CAATTCGAAAGC
* * * *
1089662 AATCCGAACCGAAAAATAACTCAATTCGAAAGC
1 AATCCAAATCG-AAATTAACCCAATTCGAAAGC
*
1089695 AATCCAAATCGAATTTAACCCAATTCGAAA
1 AATCCAAATCGAAATTAACCCAATTCGAAA
1089725 ATAACCGGGA
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
32 28 0.56
33 22 0.44
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.19
Consensus pattern (32 bp):
AATCCAAATCGAAATTAACCCAATTCGAAAGC
Found at i:1089729 original size:16 final size:16
Alignment explanation
Indices: 1089674--1089730 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
1089664 TCCGAACCGA
*
1089674 AAAATAACTCAATTCG
1 AAAATAACCCAATTCG
** * *
1089690 AAAGCAATCCAAATCG
1 AAAATAACCCAATTCG
**
1089706 AATTTAACCCAATTCG
1 AAAATAACCCAATTCG
1089722 AAAATAACC
1 AAAATAACC
1089731 GGGACCGAAA
Statistics
Matches: 29, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.49, C:0.23, G:0.07, T:0.21
Consensus pattern (16 bp):
AAAATAACCCAATTCG
Found at i:1099630 original size:19 final size:19
Alignment explanation
Indices: 1099596--1099640 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1099586 ATTTAGACAT
1099596 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
1099614 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
1099633 TTTGCATT
1 TTTGCATT
1099641 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:1102333 original size:84 final size:83
Alignment explanation
Indices: 1102210--1102914 Score: 741
Period size: 84 Copynumber: 8.5 Consensus size: 83
1102200 CGGGGGTCTT
* *
1102210 TGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGCC
1 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1102275 GAACTCGAAGGTCTTTTGG
66 GAACTCGAAGGTC-TTTGG
** * * * * * * * * *
1102294 TCACGGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
**
1102359 CGAACTCGGGGGTC-TT--
65 CGAACTCGAAGGTCTTTGG
* ** * *
1102375 TGGCAGATAGCCCTTCTCGACTTAAACTATACTGGAAATGATGTGCCGTT-GAGCTGAGCGTAGT
1 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGT
* *
1102439 CGAACTCAAAGGTCTTTTGT
65 CGAACTCGAAGGTC-TTTGG
* * * * *
1102459 TGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTC
1 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1102524 GAACTCGAAGGTCTTTGG
66 GAACTCGAAGGTCTTTGG
* *
1102542 TTGGCAGATAACTCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTT-GAGTTGAGCGTAG
1 -TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAG
* *
1102606 TCAAACTCAAAGGTCTTTGG
64 TCGAACTCGAAGGTCTTTGG
* * * * *
1102626 TTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 -TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
**
1102691 TCGAACTCGGGGGTC-TT--
64 TCGAACTCGAAGGTCTTTGG
* * *
1102708 TGGCAGATAGCCTTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGT
1 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGT
*
1102772 CGAACTCAAAGGTCTTTGG
65 CGAACTCGAAGGTCTTTGG
* * * ** *
1102791 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTATAA
1 -TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
* **
1102856 TCGAACCCGGGGGTC-TT--
64 TCGAACTCGAAGGTCTTTGG
* * *
1102873 TGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGAT
1 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
1102915 TATTTAAAAA
Statistics
Matches: 510, Mismatches: 93, Indels: 39
0.79 0.14 0.06
Matches are distributed among these distances:
80 48 0.09
81 117 0.23
82 2 0.00
83 8 0.02
84 263 0.52
85 72 0.14
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (83 bp):
TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTGG
Found at i:1102453 original size:165 final size:165
Alignment explanation
Indices: 1102175--1102914 Score: 1072
Period size: 165 Copynumber: 4.5 Consensus size: 165
1102165 AACGATATGA
* *
1102175 CCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
* * ** *
1102240 GCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGCCGAACTCGAAGGTCTTTTGG-TCACGGATA
66 GCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTTGGCAGATA
* * *
1102303 ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
129 ACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC
*
1102340 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
* * * *
1102405 ACTGGAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAAC
66 GCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAAC
* *
1102470 CCTTCTAGACTTAAGTTGTGCTGCAAATGATATG-
131 CCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC
* * ** * ** * *
1102504 CCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACTCTTCTCGACTTAAG
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAG
* * *
1102569 TTATGCTGCAAATGATGTGCCGTTGAGTTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGA
62 CTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGA
* *
1102634 TAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGC
127 TAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC
*
1102673 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCTTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1102738 GCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAAC
66 GCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAAC
* *
1102803 CCTTCTCGACTTAAGTTATACTGCAAATGATGTGC
131 CCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC
* *
1102838 CCTCGAAGCTGAGTATAATCGAACCCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
*
1102903 GTTGCAAATGAT
66 GCTGCAAATGAT
1102915 TATTTAAAAA
Statistics
Matches: 511, Mismatches: 57, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
164 30 0.06
165 335 0.66
166 3 0.01
167 1 0.00
168 116 0.23
169 26 0.05
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (165 bp):
CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
GCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAAC
CCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC
Found at i:1102816 original size:333 final size:330
Alignment explanation
Indices: 1102168--1102914 Score: 1059
Period size: 333 Copynumber: 2.3 Consensus size: 330
1102158 TGTTGTAAAC
* * ** * **
1102168 GATATGACCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTT
1 GATATGCCCTCGAAGCTGAGCATAATCGAACCCGAAGGTCTTTGGCAGATAACCCTTCTCGACTT
* *
1102233 AAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGCCGAACTCGAAGGTCTTTTGGTCAC
66 AAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGCCAAACTCAAAGGTCTTTTGGTCAC
* * * *
1102298 GGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAA
131 AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAA
*
1102363 CTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTATACTGGAAATGATGTGCCGTTGAG
196 CTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTATACTGCAAATGATGTGCCGTTGAG
* * *
1102428 CTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTG
261 CTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATACTG
1102493 CAAAT
326 CAAAT
* * * * *
1102498 GATATG-CCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACTCTTCTCG
1 GATATGCCCTCGAAGCTGAGCATAATCGAACCCGAAGGTC--T--TTGGCAGATAACCCTTCTCG
* * *
1102562 ACTTAAGTTATGCTGCAAATGATGTGCCGTT-GAGTTGAGCGTAGTCAAACTCAAAGGTC-TTTG
62 ACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGCCAAACTCAAAGGTCTTTTG
** * *
1102625 GTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGAAGCTGAGTGTA
126 G-TCACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTA
* * *
1102690 ATCGAACTCGGGGGTCTTTGGCAGATAGCCTTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
190 ATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTATACTGCAAATGATGTGCC
* *
1102755 GTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTT
255 GTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTT
1102820 ATACTGCAAAT
320 ATACTGCAAAT
* * ** *
1102831 GATGTGCCCTCGAAGCTGAGTATAATCGAACCCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTT
1 GATATGCCCTCGAAGCTGAGCATAATCGAACCCGAAGGTCTTTGGCAGATAACCCTTCTCGACTT
*
1102896 AAGCTATGTTGCAAATGAT
66 AAGCTATGCTGCAAATGAT
1102915 TATTTAAAAA
Statistics
Matches: 367, Mismatches: 43, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
329 25 0.07
330 45 0.12
331 1 0.00
332 6 0.02
333 262 0.71
334 28 0.08
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (330 bp):
GATATGCCCTCGAAGCTGAGCATAATCGAACCCGAAGGTCTTTGGCAGATAACCCTTCTCGACTT
AAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGCCAAACTCAAAGGTCTTTTGGTCAC
AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAA
CTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTATACTGCAAATGATGTGCCGTTGAG
CTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATACTG
CAAAT
Found at i:1105025 original size:37 final size:37
Alignment explanation
Indices: 1104868--1105038 Score: 186
Period size: 39 Copynumber: 4.5 Consensus size: 37
1104858 CATTTTTTTA
* *
1104868 ATATAT-ATATATAG-TTTAAAAACATTTTTAAAAAGAC
1 ATATATAATATATAGTTTTTAAAACATTTTT-GAAA-AC
* * *
1104905 GTATATATAATATATAGGTTTGAAAACATGTTTGAAAAC
1 --ATATATAATATATAGTTTTTAAAACATTTTTGAAAAC
* *
1104944 ATTTATATATTATATAGTTTTTAAAACA-TTTTGAAAAT
1 A--TATATAATATATAGTTTTTAAAACATTTTTGAAAAC
*
1104982 AAATATAATATATAGTTTTTAAAACATTTTTGAAAAC
1 ATATATAATATATAGTTTTTAAAACATTTTTGAAAAC
*
1105019 ATATATATTATATAGTTTTT
1 ATATATAATATATAGTTTTT
1105039 GAATATATAT
Statistics
Matches: 114, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
36 23 0.20
37 28 0.25
38 9 0.08
39 30 0.26
40 11 0.10
41 13 0.11
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (37 bp):
ATATATAATATATAGTTTTTAAAACATTTTTGAAAAC
Found at i:1105038 original size:26 final size:26
Alignment explanation
Indices: 1105008--1105069 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
1104998 TTTTAAAACA
1105008 TTTTTGAAAACATATATAT-TATATAG
1 TTTTTGAAAACATATATATAT-TATAG
* *
1105034 TTTTTGAATATATATATATATTATAG
1 TTTTTGAAAACATATATATATTATAG
*
1105060 TTTTTTAAAA
1 TTTTTGAAAA
1105070 AAATATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 30 0.97
27 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (26 bp):
TTTTTGAAAACATATATATATTATAG
Found at i:1105133 original size:19 final size:19
Alignment explanation
Indices: 1105111--1105171 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 19
1105101 TTTTTGAAAA
1105111 TATTTTTATTTTTATTATT
1 TATTTTTATTTTTATTATT
*
1105130 TA---TTATTGTTATTATT
1 TATTTTTATTTTTATTATT
1105146 T-TATTTTATTTATT-TTATGT
1 TAT-TTTTATTT-TTATTAT-T
1105166 TATTTT
1 TATTTT
1105172 ATTCCTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
16 14 0.42
19 11 0.33
20 7 0.21
21 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.75
Consensus pattern (19 bp):
TATTTTTATTTTTATTATT
Found at i:1105141 original size:16 final size:15
Alignment explanation
Indices: 1105111--1105169 Score: 63
Period size: 14 Copynumber: 4.1 Consensus size: 15
1105101 TTTTTGAAAA
*
1105111 TATTTTTATTTTTAT
1 TATTTTTATTGTTAT
1105126 TATTTATTATTGTTAT
1 TATTT-TTATTGTTAT
1105142 TA-TTTTATT-TTAT
1 TATTTTTATTGTTAT
1105155 T-TATTTTA-TGTTAT
1 TAT-TTTTATTGTTAT
1105169 T
1 T
1105170 TTATTCCTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
13 6 0.15
14 15 0.38
15 7 0.18
16 11 0.28
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (15 bp):
TATTTTTATTGTTAT
Found at i:1105151 original size:5 final size:5
Alignment explanation
Indices: 1105114--1105174 Score: 56
Period size: 5 Copynumber: 12.4 Consensus size: 5
1105104 TTGAAAATAT
* *
1105114 TTTTA TTTT- TATTA -TTTA TTATTG TTATTA TTTTA TTTTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TT-TTA TT-TTA TTTTA TTTTA TTTTA TTTTA
*
1105163 TGTTA TTTTA TT
1 TTTTA TTTTA TT
1105175 CCTTATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
4 10 0.22
5 27 0.59
6 9 0.20
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:1105160 original size:9 final size:9
Alignment explanation
Indices: 1105114--1105174 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
1105104 TTGAAAATAT
1105114 TTTTATTT-
1 TTTTATTTA
1105122 TTATTATTTA
1 TT-TTATTTA
*
1105132 TTATT-GTTA
1 TT-TTATTTA
*
1105141 TTAT-TTTA
1 TTTTATTTA
1105149 TTTTATTTA
1 TTTTATTTA
1105158 TTTTATGTTA
1 TTTTAT-TTA
1105168 TTTTATT
1 TTTTATT
1105175 CCTTATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
8 9 0.20
9 22 0.49
10 14 0.31
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1109880 original size:17 final size:19
Alignment explanation
Indices: 1109844--1109886 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
1109834 AAATATAGTA
*
1109844 TAAAAATTATATATTTTTT
1 TAAAATTTATATATTTTTT
1109863 TAAAATTTAT-TA-TTTTT
1 TAAAATTTATATATTTTTT
1109880 TAAAATT
1 TAAAATT
1109887 GTAAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.52
18 2 0.09
19 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TAAAATTTATATATTTTTT
Found at i:1110251 original size:56 final size:58
Alignment explanation
Indices: 1110180--1110289 Score: 152
Period size: 56 Copynumber: 1.9 Consensus size: 58
1110170 ATATACAAGG
* *
1110180 ATTAAAATATCTTTTTTATAATACAGAAATTACAA-CAAATTTTAAGTAAAATAAACTA
1 ATTAAAATA-CTTTTTTATAATAAAGAAATTAAAATCAAATTTTAAGTAAAATAAACTA
* * *
1110238 ATTAAAATA-TTTTTTATAATAAAGAGATTAAAATCAACTTTTAAGTATAATA
1 ATTAAAATACTTTTTTATAATAAAGAAATTAAAATCAAATTTTAAGTAAAATA
1110290 TATGGATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 21 0.46
57 16 0.35
58 9 0.20
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (58 bp):
ATTAAAATACTTTTTTATAATAAAGAAATTAAAATCAAATTTTAAGTAAAATAAACTA
Found at i:1113098 original size:2 final size:2
Alignment explanation
Indices: 1113091--1113117 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1113081 ATTTGCTCAT
1113091 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1113118 GATTCCACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1116076 original size:18 final size:21
Alignment explanation
Indices: 1116037--1116076 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1116027 TGAAATTTGA
1116037 ATTTTATTTGATTAGTTACTT
1 ATTTTATTTGATTAGTTACTT
1116058 ATTTT-TTTGATT-G-TACTT
1 ATTTTATTTGATTAGTTACTT
1116076 A
1 A
1116077 ACTGAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 1 0.05
20 7 0.37
21 5 0.26
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (21 bp):
ATTTTATTTGATTAGTTACTT
Found at i:1118954 original size:18 final size:18
Alignment explanation
Indices: 1118931--1118978 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1118921 AAATTGTCCT
*
1118931 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
1118949 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
1118966 TATTTATATATTT
1 TA-TTATATATTT
1118979 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:1119464 original size:14 final size:14
Alignment explanation
Indices: 1119445--1119474 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1119435 GTAATTGGTT
*
1119445 TTCTGGAAATTGAA
1 TTCTGGAAAATGAA
1119459 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
1119473 TT
1 TT
1119475 ATATTTTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (14 bp):
TTCTGGAAAATGAA
Found at i:1119728 original size:31 final size:29
Alignment explanation
Indices: 1119660--1119729 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
1119650 AATATTATTT
*
1119660 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
1119690 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
1119723 TTATATT
1 TTATATT
1119730 AATTATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:1119956 original size:47 final size:47
Alignment explanation
Indices: 1119817--1119960 Score: 121
Period size: 50 Copynumber: 3.0 Consensus size: 47
1119807 TATTATTAGA
* *
1119817 TTATTATATTAATATTAAATATATAAATA-ATATTATCATTATTAATAAT
1 TTATTATATTACTATTAAA-ATAAAAATATAT-TTAT-ATTATTAATAAT
* * * * ** * *
1119866 TTAATATTATTTCTATGAAATTAATAAATAATATAAATTTTATTGATAAT
1 TTATTA-TATTACTATTAAAATAA-AAAT-ATATTTATATTATTAATAAT
1119916 TTATTATA-TACTATTAAAATAAAAATATATCTTATATTATTAATA
1 TTATTATATTACTATTAAAATAAAAATATAT-TTATATTATTAATA
1119961 TAATTGATTA
Statistics
Matches: 72, Mismatches: 18, Indels: 12
0.71 0.18 0.12
Matches are distributed among these distances:
46 4 0.06
47 14 0.19
48 11 0.15
49 9 0.12
50 29 0.40
51 3 0.04
52 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (47 bp):
TTATTATATTACTATTAAAATAAAAATATATTTATATTATTAATAAT
Found at i:1119971 original size:49 final size:48
Alignment explanation
Indices: 1119911--1120005 Score: 111
Period size: 49 Copynumber: 2.0 Consensus size: 48
1119901 AATTTTATTG
* *
1119911 ATAATTTATTATATACTATTAAAATAAAAATA-TATCTTATATTATTAAT
1 ATAATTGATTATATACTA-TAAAATAAAAATATTATATTATA-TATTAAT
* * * *
1119960 ATAATTGATTATTTATTATATATTAAAAATATTATATTATATATTA
1 ATAATTGATTATATACTATAAAATAAAAATATTATATTATATATTA
1120006 TTAGAAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
48 16 0.41
49 23 0.59
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (48 bp):
ATAATTGATTATATACTATAAAATAAAAATATTATATTATATATTAAT
Found at i:1119978 original size:28 final size:25
Alignment explanation
Indices: 1119947--1120017 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 25
1119937 AAAATATATC
1119947 TTATATTATTAATATAATTGATTAT-TTA
1 TTATATTATTAA-A-AA-T-ATTATATTA
1119975 TTATA-TATTAAAAATATTATATTA
1 TTATATTATTAAAAATATTATATTA
*
1119999 -TATATTATTAGAAATATTA
1 TTATATTATTAAAAATATTA
1120018 ATAAATTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
23 9 0.22
24 17 0.43
25 2 0.05
26 1 0.03
27 6 0.15
28 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (25 bp):
TTATATTATTAAAAATATTATATTA
Found at i:1127679 original size:2 final size:2
Alignment explanation
Indices: 1127672--1127699 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1127662 GAGTTTCATA
1127672 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
1127700 TAAAAATAAA
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:1130771 original size:20 final size:19
Alignment explanation
Indices: 1130747--1130830 Score: 60
Period size: 20 Copynumber: 4.2 Consensus size: 19
1130737 AACTCTAATT
*
1130747 TCGCAACACAGTTTCCAAA
1 TCGCAACACAATTTCCAAA
* *
1130766 TACGCAACGCAATTTTCAAA
1 T-CGCAACACAATTTCCAAA
* * **
1130786 TTCGTAACGCGAATTTGTAAA
1 -TCGCAACAC-AATTTCCAAA
*
1130807 TCGCAACACAGTTTCCAAAA
1 TCGCAACACAATTTCC-AAA
1130827 TCGC
1 TCGC
1130831 GTTGCGATAG
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
19 5 0.10
20 36 0.72
21 9 0.18
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (19 bp):
TCGCAACACAATTTCCAAA
Found at i:1130911 original size:57 final size:57
Alignment explanation
Indices: 1130823--1130931 Score: 191
Period size: 57 Copynumber: 1.9 Consensus size: 57
1130813 CACAGTTTCC
* **
1130823 AAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
1 AAAATCGCGTTACGATAACACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
1130880 AAAATCGCGTTACGATAACACTGTTTACCTATATCGGTAATTAGCGTTGCGA
1 AAAATCGCGTTACGATAACACTGTTTACCTATATCGGTAATTAGCGTTGCGA
1130932 TTTACATATT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (57 bp):
AAAATCGCGTTACGATAACACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
Found at i:1130947 original size:20 final size:20
Alignment explanation
Indices: 1130919--1130972 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1130909 TATATCGGTA
1130919 ATTAGCGTTGCGATTTACAT
1 ATTAGCGTTGCGATTTACAT
*
1130939 ATTATCGTTGCGATTTACAT
1 ATTAGCGTTGCGATTTACAT
*
1130959 ATTCGCGTTGCGAT
1 ATTAGCGTTGCGAT
1130973 ACTGTTTACC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTAGCGTTGCGATTTACAT
Found at i:1131043 original size:20 final size:20
Alignment explanation
Indices: 1130997--1131043 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1130987 TCAGTACTTA
1130997 GCGTTGCGAATTTAAAAATC
1 GCGTTGCGAATTTAAAAATC
* * *
1131017 TCATTGCGAATTTGAAAATC
1 GCGTTGCGAATTTAAAAATC
1131037 GCGTTGC
1 GCGTTGC
1131044 AATAGTACTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (20 bp):
GCGTTGCGAATTTAAAAATC
Found at i:1131079 original size:77 final size:75
Alignment explanation
Indices: 1130869--1131088 Score: 243
Period size: 74 Copynumber: 2.9 Consensus size: 75
1130859 GTAATTAGCG
* * *
1130869 TTGCGAATTTGAAAATCGCGTTACGATAACACTGTTTACCTATATCGGTAATTAGCGTTGCGATT
1 TTGCGAATTTGAAAATCGCGTTGC-AT-ATACTGTTTACCTATATCGATAATTAGCGTTGCGATT
* * *
1130934 TACATATTATCG
64 TACAAAATATCA
* * *
1130946 TTGCG-ATTT-ACATATTCGCGTTGC-GATACTGTTTACCTATATC-AGTACTTAGCGTTGCGAA
1 TTGCGAATTTGA-A-AATCGCGTTGCATATACTGTTTACCTATATCGA-TAATTAGCGTTGCG-A
*
1131007 TTTA-AAAATCTCA
62 TTTACAAAATATCA
1131020 TTGCGAATTTGAAAATCGCGTTGCAATAGTACTGTTTACCTATATCGATAATTAGCGTTGCGATT
1 TTGCGAATTTGAAAATCGCGTTGC-ATA-TACTGTTTACCTATATCGATAATTAGCGTTGCGATT
1131085 TACA
64 TACA
1131089 TATTCGCGTT
Statistics
Matches: 119, Mismatches: 13, Indels: 22
0.77 0.08 0.14
Matches are distributed among these distances:
74 50 0.42
75 11 0.09
76 12 0.10
77 45 0.38
78 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (75 bp):
TTGCGAATTTGAAAATCGCGTTGCATATACTGTTTACCTATATCGATAATTAGCGTTGCGATTTA
CAAAATATCA
Found at i:1131101 original size:77 final size:75
Alignment explanation
Indices: 1130866--1131120 Score: 268
Period size: 77 Copynumber: 3.4 Consensus size: 75
1130856 TCGGTAATTA
* * *
1130866 GCGTTGCGAATTTGAAAATCGCGTTACGATAACACTGTTTACCTATATCGGTAATTAGCGTTGCG
1 GCGTTGCGAATTTGAAAATCGCGTTGC-AT-ATACTGTTTACCTATATCGATAATTAGCGTTGCG
*
1130931 ATTTACATATTA
64 ATTTACATATTC
* * * *
1130943 TCGTTGCG-ATTT-ACATATTCGCGTTGC-GATACTGTTTACCTATATC-AGTACTTAGCGTTGC
1 GCGTTGCGAATTTGA-A-AATCGCGTTGCATATACTGTTTACCTATATCGA-TAATTAGCGTTGC
* *
1131004 GAATTTA-AAAATC
63 G-ATTTACATATTC
* *
1131017 TCATTGCGAATTTGAAAATCGCGTTGCAATAGTACTGTTTACCTATATCGATAATTAGCGTTGCG
1 GCGTTGCGAATTTGAAAATCGCGTTGC-ATA-TACTGTTTACCTATATCGATAATTAGCGTTGCG
1131082 ATTTACATATTC
64 ATTTACATATTC
* **
1131094 GCGTTGCGAAATTGAAGTTCGCGTTGC
1 GCGTTGCGAATTTGAAAATCGCGTTGC
1131121 GAACTTGTTG
Statistics
Matches: 146, Mismatches: 21, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
74 50 0.34
75 11 0.08
76 12 0.08
77 72 0.49
78 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (75 bp):
GCGTTGCGAATTTGAAAATCGCGTTGCATATACTGTTTACCTATATCGATAATTAGCGTTGCGAT
TTACATATTC
Found at i:1133064 original size:23 final size:23
Alignment explanation
Indices: 1133034--1133103 Score: 131
Period size: 23 Copynumber: 3.0 Consensus size: 23
1133024 AAACGAATCC
1133034 AACATTTAATGAATTGTTTGGTA
1 AACATTTAATGAATTGTTTGGTA
1133057 AACATTTAATGAATTGTTTGGTA
1 AACATTTAATGAATTGTTTGGTA
*
1133080 AACATTTAATGAATTGCTTGGTA
1 AACATTTAATGAATTGTTTGGTA
1133103 A
1 A
1133104 TTAACATGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (23 bp):
AACATTTAATGAATTGTTTGGTA
Found at i:1133430 original size:145 final size:145
Alignment explanation
Indices: 1133276--1133563 Score: 450
Period size: 145 Copynumber: 2.0 Consensus size: 145
1133266 TTCGTTCATT
* * *
1133276 TATATTCAACTCAATTTCTAAATTCGTTTAAAATATTAAGACATAATAAATTATAAGGTAAATTA
1 TATATTCAACTCAATTTCTAAACTCGTTTAAAATATTAAGACATAAAAAATTATAAAGTAAATTA
* *
1133341 TATATTTAATATTTAAACTATATGTTCTGTTTCGTTTTAATATCTATTCGTTTATTTTAAAATCA
66 CATATTTAATATTTAAACTATATGTTCTGTTTCGTTTTAATATCTATTCATTTATTTTAAAATCA
1133406 TACCTAACATTTACA
131 TACCTAACATTTACA
* *
1133421 TATATTCAACTTAATTTCTAAACTCGTTTAAAATATTAAGACATAAAAAATTATAAAGTAAGTTA
1 TATATTCAACTCAATTTCTAAACTCGTTTAAAATATTAAGACATAAAAAATTATAAAGTAAATTA
* * * * * * *
1133486 CATATTTAATATTTAAATTGTCTGTTTTGTTTCGTTTTAGTATTTATTCATTTGTTTTAAAATCA
66 CATATTTAATATTTAAACTATATGTTCTGTTTCGTTTTAATATCTATTCATTTATTTTAAAATCA
1133551 TACCTAACATTTA
131 TACCTAACATTTA
1133564 TATTTTGTAC
Statistics
Matches: 129, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
145 129 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.45
Consensus pattern (145 bp):
TATATTCAACTCAATTTCTAAACTCGTTTAAAATATTAAGACATAAAAAATTATAAAGTAAATTA
CATATTTAATATTTAAACTATATGTTCTGTTTCGTTTTAATATCTATTCATTTATTTTAAAATCA
TACCTAACATTTACA
Found at i:1135076 original size:54 final size:53
Alignment explanation
Indices: 1135016--1135119 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 53
1135006 TAGAATTAGT
* *
1135016 GATATCAAAATGAAAT-AGTATTGATAATTTTAAGATTAATATAAGATATTTAAC
1 GATATCAAAAAGAAATGA-TA-CGATAATTTTAAGATTAATATAAGATATTTAAC
* * *
1135070 GATATCAAAAAGGAATGATACGATAATTTTACGATTAATATATGATATTT
1 GATATCAAAAAGAAATGATACGATAATTTTAAGATTAATATAAGATATTT
1135120 CAAATATAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
53 27 0.61
54 16 0.36
55 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (53 bp):
GATATCAAAAAGAAATGATACGATAATTTTAAGATTAATATAAGATATTTAAC
Found at i:1146107 original size:31 final size:32
Alignment explanation
Indices: 1146047--1146115 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
1146037 TTTGGGTTTG
*
1146047 GGTT-GGATCAGGTTTTTTAAAGGTAATATTC
1 GGTTCGGATCAGGTTTTTTAAAGGGAATATTC
*
1146078 GGTTCGGATC-GGATTTTTT-AAGGGGATATTC
1 GGTTCGGATCAGG-TTTTTTAAAGGGAATATTC
*
1146109 GGGTCGG
1 GGTTCGG
1146116 TCCAGATTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 22 0.67
32 11 0.33
ACGTcount: A:0.20, C:0.09, G:0.33, T:0.38
Consensus pattern (32 bp):
GGTTCGGATCAGGTTTTTTAAAGGGAATATTC
Found at i:1146309 original size:6 final size:7
Alignment explanation
Indices: 1146289--1146316 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1146279 CTTCTCTCTC
1146289 TTCTTTT
1 TTCTTTT
1146296 TTCTTTT
1 TTCTTTT
1146303 TTCTTTT
1 TTCTTTT
1146310 TTCTTTT
1 TTCTTTT
1146317 ACGTCATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTCTTTT
Found at i:1154496 original size:2 final size:2
Alignment explanation
Indices: 1154489--1154519 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1154479 TGTGTAAATA
1154489 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 A
1154520 ATCACATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1155565 original size:106 final size:106
Alignment explanation
Indices: 1155037--1155557 Score: 730
Period size: 106 Copynumber: 4.9 Consensus size: 106
1155027 TATTATTCCA
* * * * * * * *
1155037 AGTCAAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
* *
1155102 CAGTC-G-CCCTTTCG-CTGTGAAGTTGAGCTT--G-TGTCTCG
66 CAG-CGGTCCC-TTCGTC-GTGAAGTTGAACTTGCGTTGTCTGG
* * * * ** *
1155140 AGTTCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC----TGAAATTGGGAAGTTGTTTATTGA
*
1155205 CAATCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
62 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1155250 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTATTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1155315 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1155356 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1155421 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1155462 AGTCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1155527 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1155558 TGCTGTCTTA
Statistics
Matches: 379, Mismatches: 29, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
103 31 0.08
106 259 0.68
107 43 0.11
108 4 0.01
109 1 0.00
110 41 0.11
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1155602 original size:64 final size:65
Alignment explanation
Indices: 1155472--1155695 Score: 294
Period size: 64 Copynumber: 3.5 Consensus size: 65
1155462 AGTCCAATAT
* * * * * * * *
1155472 CCTTCGTTGTGAAATTGAAATTG-G--CTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAACTGGGAAATTG-TTGTTGACAACCAGCGGC
1155534 C
65 C
* *
1155535 CCTTCGTCGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGAAATT-TTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAACTGGGAAATTGTTGTTGACAACCAGCGGCC
* * *
1155599 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAATTGTTGTTAACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAACTGGGAAATTGTTGTTGACAACCAGCGGCC
1155664 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
1155696 GAGTTCCAAT
Statistics
Matches: 142, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
63 20 0.14
64 59 0.42
65 49 0.35
66 14 0.10
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.35
Consensus pattern (65 bp):
CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAACTGGGAAATTGTTGTTGACAACCAGCGGCC
Found at i:1156958 original size:22 final size:22
Alignment explanation
Indices: 1156932--1156980 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1156922 TTGTGTTTGG
* *
1156932 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
1156954 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
1156976 TCAAA
1 TCAAA
1156981 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:1156987 original size:22 final size:22
Alignment explanation
Indices: 1156944--1156987 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1156934 AAAGGTTTGG
* * *
1156944 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
1156966 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
1156988 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:1157651 original size:16 final size:17
Alignment explanation
Indices: 1157632--1157676 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
1157622 TCTTTTTGAT
*
1157632 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
1157648 TTTTGCTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
1157665 TTTT-CT-TTGTTT
1 TTTTGCTCTTGTTT
1157677 TTTTGTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 6 0.22
16 16 0.59
17 5 0.19
ACGTcount: A:0.00, C:0.20, G:0.09, T:0.71
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Done.