Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008120.1 Hibiscus syriacus cultivar Beakdansim tig00110670_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: 639723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:565435 original size:28 final size:28
Alignment explanation
Indices: 565403--565464 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
565393 AAAATTTAAA
*
565403 AAAATATAATTTAGACCCTTAATTTTTT
1 AAAATATAATTTAGACCCTAAATTTTTT
* * *
565431 AAAATTTAATTTGGCCCCTAAATTTTTT
1 AAAATATAATTTAGACCCTAAATTTTTT
565459 AGAAAT
1 A-AAAT
565465 TCATATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (28 bp):
AAAATATAATTTAGACCCTAAATTTTTT
Found at i:570536 original size:21 final size:20
Alignment explanation
Indices: 570485--570536 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
570475 TTTTCCCAAT
*
570485 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* * **
570505 TCACAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
570526 TCGCAATGCGA
1 TCGCAATGCGA
570537 TACTGACTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:570550 original size:20 final size:20
Alignment explanation
Indices: 570525--570638 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
570515 AATTGGGAAA
*
570525 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
570545 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
570565 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
570586 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
570606 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
570626 TTCGCAACGCGAT
1 ATCGCAACGCGAT
570639 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:570587 original size:61 final size:61
Alignment explanation
Indices: 570522--570638 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
570512 GCGAATTGGG
* * * * *
570522 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
570583 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
570639 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:571243 original size:19 final size:19
Alignment explanation
Indices: 571196--571237 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
571186 ACGAGAGAAT
*
571196 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
571215 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
571234 CGCA
1 CGCA
571238 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:571279 original size:20 final size:19
Alignment explanation
Indices: 571233--571398 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
571223 GAAACAAAAA
*
571233 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
571252 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
571271 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
571291 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* * **
571307 T--AGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
571324 TCGCGTTGCGA--TTC-TA
1 TCGCGTTGCGATTTTCATT
**
571340 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
571357 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
571377 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
571397 TC
1 TC
571399 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
14 18 0.15
16 5 0.04
17 5 0.04
19 40 0.34
20 48 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:571314 original size:39 final size:39
Alignment explanation
Indices: 571238--571314 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
571228 AAAAATCGCA
* *
571238 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTATGTCGCGG
571277 TTGCGATTTTCATTTCGCGTTGCGATTGTCTA-GTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTATGTCGCG
571315 ATAGTCATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 32 0.91
40 3 0.09
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTATGTCGCGG
Found at i:571323 original size:33 final size:33
Alignment explanation
Indices: 571286--571372 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
571276 GTTGCGATTT
* *
571286 TCATTTCGCGTTGCGATTGTCTAGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTATAGTCGCGATAG
* *
571319 TCATTTCGCGTTGCGATTCTATCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTATAGTCGCGATAG
571352 TCATTTCCGCGTTGCGATTCT
1 TCATTT-CGCGTTGCGATTCT
571373 CATTATCTCG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTATAGTCGCGATAG
Found at i:571389 original size:40 final size:34
Alignment explanation
Indices: 571276--571372 Score: 126
Period size: 33 Copynumber: 2.9 Consensus size: 34
571266 TTATTTCGCG
** * * *
571276 GTTGCGATTTTCATTT-CGCGTTGCGATTGTCTA
1 GTTGCGATAGTCATTTCCGCGTTGCGATTCTATC
*
571309 GTCGCGATAGTCATTT-CGCGTTGCGATTCTATC
1 GTTGCGATAGTCATTTCCGCGTTGCGATTCTATC
571342 GTTGCGATAGTCATTTCCGCGTTGCGATTCT
1 GTTGCGATAGTCATTTCCGCGTTGCGATTCT
571373 CATTATCTCG
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 42 0.75
34 14 0.25
ACGTcount: A:0.13, C:0.22, G:0.25, T:0.40
Consensus pattern (34 bp):
GTTGCGATAGTCATTTCCGCGTTGCGATTCTATC
Found at i:573977 original size:12 final size:12
Alignment explanation
Indices: 573960--573984 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
573950 TCTTCGGGGA
573960 CTTTTTCTTCTT
1 CTTTTTCTTCTT
573972 CTTTTTCTTCTT
1 CTTTTTCTTCTT
573984 C
1 C
573985 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:575222 original size:20 final size:20
Alignment explanation
Indices: 575197--575234 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
575187 ATTCATTTGA
*
575197 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
575217 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
575235 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:575404 original size:14 final size:15
Alignment explanation
Indices: 575385--575422 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
575375 CATCAATTAA
575385 ACAAATCAAT-ATTT
1 ACAAATCAATCATTT
*
575399 ACAAATC-ATCTTTT
1 ACAAATCAATCATTT
575413 ACAAATCAAT
1 ACAAATCAAT
575423 TAAACAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (15 bp):
ACAAATCAATCATTT
Found at i:577328 original size:19 final size:19
Alignment explanation
Indices: 577248--577365 Score: 86
Period size: 20 Copynumber: 6.4 Consensus size: 19
577238 TAGTTTACTT
* *
577248 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
577268 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
577287 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
577307 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
577326 TCGCAA--TG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
577340 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
577358 TCGCAACG
1 TCGCAACG
577366 ACAAAATCGC
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 1 0.01
17 1 0.01
18 12 0.15
19 25 0.32
20 29 0.37
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:577341 original size:14 final size:14
Alignment explanation
Indices: 577322--577379 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
577312 ATGCGAAATG
*
577322 AAAATCGCAATGAC
1 AAAATCGCAACGAC
*
577336 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
577352 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
577368 AAAATCGCAACG
1 AAAATCGCAACG
577380 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:577369 original size:32 final size:33
Alignment explanation
Indices: 577306--577384 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
577296 GGAAATGGCT
* *
577306 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
577339 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
577371 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
577385 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:577425 original size:13 final size:14
Alignment explanation
Indices: 577407--577438 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
577397 TGCGATTTTC
577407 ATTTTG-CGTTGCG
1 ATTTTGTCGTTGCG
577420 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
577434 ATTTT
1 ATTTT
577439 CATTTCGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.53
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:577451 original size:19 final size:19
Alignment explanation
Indices: 577391--577454 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
577381 GAAACACAAA
577391 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
577410 TTGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
577426 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
577443 TCGCATTGCGAT
1 TCGCATTGCGAT
577455 AGCCATTTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
14 6 0.17
15 3 0.09
16 3 0.09
17 4 0.11
18 3 0.09
19 16 0.46
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:577473 original size:20 final size:19
Alignment explanation
Indices: 577439--577493 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
577429 TTGCGATTTT
*
577439 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
577458 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
577478 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
577494 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:577573 original size:12 final size:13
Alignment explanation
Indices: 577550--577578 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
577540 TTACTTCAAC
577550 CAAAAGACAAAAA
1 CAAAAGACAAAAA
577563 CAAAA-ACAAAAA
1 CAAAAGACAAAAA
577575 CAAA
1 CAAA
577579 TACTAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.79, C:0.17, G:0.03, T:0.00
Consensus pattern (13 bp):
CAAAAGACAAAAA
Found at i:578001 original size:18 final size:18
Alignment explanation
Indices: 577975--578019 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
577965 GTCGATCAGA
*
577975 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
577993 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
578011 TGATGGCTC
1 TGATGGCTC
578020 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:579386 original size:20 final size:20
Alignment explanation
Indices: 579338--579396 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
579328 AATAGTTTCT
** *
579338 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
579358 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
579378 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
579397 AGATAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:579444 original size:19 final size:19
Alignment explanation
Indices: 579422--579472 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
579412 GAAACTAAAA
579422 TCGCGTTGCGATTTGCATT
1 TCGCGTTGCGATTTGCATT
579441 TCGCGTTGCGATTTGCATT
1 TCGCGTTGCGATTTGCATT
579460 TCGCGTTGCGATT
1 TCGCGTTGCGATT
579473 CTCGGTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.10, C:0.22, G:0.27, T:0.41
Consensus pattern (19 bp):
TCGCGTTGCGATTTGCATT
Found at i:579705 original size:22 final size:22
Alignment explanation
Indices: 579678--579721 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
579668 GATGGAGATA
579678 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
579700 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
579722 TGAGAGAGTG
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:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:580043 original size:20 final size:20
Alignment explanation
Indices: 579909--580042 Score: 153
Period size: 20 Copynumber: 6.7 Consensus size: 20
579899 GATTATGTAT
579909 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
579929 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
579949 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
579969 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
579989 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
580010 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
580030 TATCGCATTGCGA
1 TATCGCGTTGCGA
580043 TTTTCCCAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
19 3 0.03
20 83 0.83
21 12 0.12
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:580061 original size:21 final size:21
Alignment explanation
Indices: 580032--580124 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
580022 ATAGTCAGTA
580032 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
580053 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
580073 TCGCATTACGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
580094 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
580114 TCGCATTGCGA
1 TCGCATTGCGA
580125 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:580062 original size:41 final size:41
Alignment explanation
Indices: 579971--580105 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
579961 AAAGTCAGTA
* * * ** *
579971 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
580011 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
580053 TCGCGTTGCGAT-TTACTTATTCGCATTACGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
580094 TCGCGTTGCGAT
1 TCGCGTTGCGAT
580106 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:580106 original size:41 final size:41
Alignment explanation
Indices: 580032--580120 Score: 169
Period size: 41 Copynumber: 2.2 Consensus size: 41
580022 ATAGTCAGTA
*
580032 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTAT
580073 TCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTAT
580114 TCGCATT
1 TCGCATT
580121 GCGAATTGGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.42
Consensus pattern (41 bp):
TCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:584609 original size:19 final size:19
Alignment explanation
Indices: 584542--584609 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
584532 TAAAATTCAA
* **
584542 ATATATTATTTACGAATTT
1 ATATTTTATTTATAAATTT
* **
584561 ATATTTGA-TTATAATATGA
1 ATATTTTATTTATAA-ATTT
584580 ATATATTTATTTATAAATTT
1 ATAT-TTTATTTATAAATTT
584600 ATATTTTATT
1 ATATTTTATT
584610 AAATAAAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 4 0.11
19 18 0.49
20 9 0.24
21 6 0.16
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (19 bp):
ATATTTTATTTATAAATTT
Found at i:584622 original size:20 final size:20
Alignment explanation
Indices: 584560--584624 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
584550 TTTACGAATT
* **
584560 TATATTTGATTATAATATGAA
1 TATATTTTATTA-AATAAAAA
* **
584581 TATA-TTTATT-TATAAATT
1 TATATTTTATTAAATAAAAA
584599 TATATTTTATTAAATAAAAA
1 TATATTTTATTAAATAAAAA
584619 TATATT
1 TATATT
584625 ATTTATGAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
18 7 0.21
19 6 0.18
20 16 0.48
21 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (20 bp):
TATATTTTATTAAATAAAAA
Found at i:584679 original size:37 final size:38
Alignment explanation
Indices: 584517--584678 Score: 195
Period size: 38 Copynumber: 4.3 Consensus size: 38
584507 GAATATTAAA
584517 GAATTTATATTTAATTAAAAT-TCAAATATATTATTTAC
1 GAATTTATATTTAATTAAAATAT-AAATATATTATTTAC
* * * *
584555 GAATTTATATTTGATTATAATATGAATATATTTATTTAT
1 GAATTTATATTTAATTAAAATATAAATATA-TTATTTAC
* * * *
584594 AAATTTATATTTTATT-AAATAAAAATATATTATTTAT
1 GAATTTATATTTAATTAAAATATAAATATATTATTTAC
* *
584631 GAAATTATATTCAATTAAAATATAAATATATTA-TTAC
1 GAATTTATATTTAATTAAAATATAAATATATTATTTAC
584668 GAATTTATATT
1 GAATTTATATT
584679 CGATTAGAAT
Statistics
Matches: 105, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
37 33 0.31
38 50 0.48
39 22 0.21
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (38 bp):
GAATTTATATTTAATTAAAATATAAATATATTATTTAC
Found at i:584879 original size:30 final size:30
Alignment explanation
Indices: 584845--584918 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
584835 GCCTAACTAA
* * ** *
584845 AATTTTTGAAAATTTGATAGGTCTAATGAG
1 AATTTTTAAAAATTTGAGAGACCAAATGAG
*
584875 AATTTTTTAAAATTTGAGAGACCAAATGAG
1 AATTTTTAAAAATTTGAGAGACCAAATGAG
584905 AATTTTTAAAAATT
1 AATTTTTAAAAATT
584919 ATGGGAGAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (30 bp):
AATTTTTAAAAATTTGAGAGACCAAATGAG
Found at i:588465 original size:31 final size:31
Alignment explanation
Indices: 588425--588507 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
588415 TTGATACCCA
588425 TATGCATTATCTGAATACAAACCTCACATAT
1 TATGCATTATCTGAATACAAACCTCACATAT
* * * *
588456 TGTGCATTATCTAAATACAAACCTGATATAT
1 TATGCATTATCTGAATACAAACCTCACATAT
* *
588487 TACGCATTATCTGAGTACAAA
1 TATGCATTATCTGAATACAAA
588508 TCTAATTAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.33
Consensus pattern (31 bp):
TATGCATTATCTGAATACAAACCTCACATAT
Found at i:588887 original size:117 final size:117
Alignment explanation
Indices: 588681--588914 Score: 396
Period size: 117 Copynumber: 2.0 Consensus size: 117
588671 TGATACAATT
* ** *
588681 CCCACACAAACTGAAGTATTGGATTGGTCTCACATAGCCTTCAAGTCAAGCTTTAACACATCTGA
1 CCCACACAAAATGAAACATTGGATTGGTCTCACATAGCCTTCAAGCCAAGCTTTAACACATCTGA
* * *
588746 CATACTGAAATGATGGGATTATACATACATGACTGACACAAATGGACATGGG
66 CATACTGAAATGATGGGACTATACATACATGACTGACAAAAACGGACATGGG
*
588798 CCCACACAAAATGAAACATTGGTTTGGTCTCACATAGCCTTCAAGCCAAGCTTTAACACATCTGA
1 CCCACACAAAATGAAACATTGGATTGGTCTCACATAGCCTTCAAGCCAAGCTTTAACACATCTGA
588863 CATACTGAAATGATGGGACTATACATACATGACTGACAAAAACGGACATGGG
66 CATACTGAAATGATGGGACTATACATACATGACTGACAAAAACGGACATGGG
588915 ATAGGTCTGG
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 109 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (117 bp):
CCCACACAAAATGAAACATTGGATTGGTCTCACATAGCCTTCAAGCCAAGCTTTAACACATCTGA
CATACTGAAATGATGGGACTATACATACATGACTGACAAAAACGGACATGGG
Found at i:590812 original size:58 final size:58
Alignment explanation
Indices: 590713--590825 Score: 190
Period size: 58 Copynumber: 1.9 Consensus size: 58
590703 GGTAGACACA
*
590713 TACTTATCCTATGCATCTATTGTTCATAGAATATATCACTATATCAAGTCAAAATACC
1 TACTTATCCTATGCAACTATTGTTCATAGAATATATCACTATATCAAGTCAAAATACC
* * *
590771 TACTTATCCTATGCAACTATTGTTCATAGAATCTATGACTATATCGAGTCAAAAT
1 TACTTATCCTATGCAACTATTGTTCATAGAATATATCACTATATCAAGTCAAAAT
590826 GTTTTTGATA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (58 bp):
TACTTATCCTATGCAACTATTGTTCATAGAATATATCACTATATCAAGTCAAAATACC
Found at i:591139 original size:37 final size:38
Alignment explanation
Indices: 591012--591157 Score: 154
Period size: 37 Copynumber: 3.9 Consensus size: 38
591002 TTATTTAAGG
* * *
591012 ATTTACGAATTTATATTCAATTAAAATATGAATCTATA
1 ATTTACGAATTTATATTCAATTAAAATACGAATATATT
** ** * *
591050 ATTTATAAATTTATATTTGATT-AAATACAAATATAGT
1 ATTTACGAATTTATATTCAATTAAAATACGAATATATT
*
591087 ATTTATGAATTTATATTCAATTAAAATACGAATATATT
1 ATTTACGAATTTATATTCAATTAAAATACGAATATATT
* * *
591125 A-TGACGAATATATATTCAATTAGAATA-GAATAT
1 ATTTACGAATTTATATTCAATTAAAATACGAATAT
591158 TGTAATTTCG
Statistics
Matches: 89, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
36 6 0.07
37 51 0.57
38 32 0.36
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (38 bp):
ATTTACGAATTTATATTCAATTAAAATACGAATATATT
Found at i:591261 original size:28 final size:28
Alignment explanation
Indices: 591229--591315 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 28
591219 CTAACCTTTT
591229 AAGTTAAAAATATGTTTTACAAGCTTAC
1 AAGTTAAAAATATGTTTTACAAGCTTAC
** * * * * **
591257 AAGTTTTTACA-A--TTTAATAACCTTTT
1 AAG-TTAAAAATATGTTTTACAAGCTTAC
591283 AAGTTAAAAATATGTTTTACAAGCTTAC
1 AAGTTAAAAATATGTTTTACAAGCTTAC
591311 AAGTT
1 AAGTT
591316 TTTACAATTT
Statistics
Matches: 39, Mismatches: 16, Indels: 8
0.62 0.25 0.13
Matches are distributed among these distances:
25 4 0.10
26 13 0.33
28 18 0.46
29 4 0.10
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Consensus pattern (28 bp):
AAGTTAAAAATATGTTTTACAAGCTTAC
Found at i:591302 original size:54 final size:54
Alignment explanation
Indices: 591220--591331 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
591210 AATAATGTGC
591220 TAACCTTTTAAGTTAAAAATATGTTTTACAAGCTTACAAGTTTTTACAATTTAA
1 TAACCTTTTAAGTTAAAAATATGTTTTACAAGCTTACAAGTTTTTACAATTTAA
591274 TAACCTTTTAAGTTAAAAATATGTTTTACAAGCTTACAAGTTTTTACAATTTAA
1 TAACCTTTTAAGTTAAAAATATGTTTTACAAGCTTACAAGTTTTTACAATTTAA
591328 TAAC
1 TAAC
591332 GTGAAACAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (54 bp):
TAACCTTTTAAGTTAAAAATATGTTTTACAAGCTTACAAGTTTTTACAATTTAA
Found at i:594414 original size:30 final size:30
Alignment explanation
Indices: 594380--594442 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
594370 CAGAAAAAAG
594380 TATGAATTTTGATATACAATTAATCTATTT
1 TATGAATTTTGATATACAATTAATCTATTT
594410 TATGAATTTTGATATACAATTAATCTATTT
1 TATGAATTTTGATATACAATTAATCTATTT
594440 TAT
1 TAT
594443 ATAAATTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (30 bp):
TATGAATTTTGATATACAATTAATCTATTT
Found at i:599158 original size:2 final size:2
Alignment explanation
Indices: 599151--599229 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
599141 ATGCATAAGA
599151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
599193 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
599230 CATGTGTGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:599736 original size:2 final size:2
Alignment explanation
Indices: 599729--599768 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
599719 TACACGTTAG
599729 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
599769 ATGTATGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:606531 original size:37 final size:35
Alignment explanation
Indices: 606460--606531 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
606450 TTATATTTTA
* *
606460 AATTTTGTAAAAAATTATATAAATATTATGAATTT
1 AATTTTGTAAAAAAATATATAAATATTATCAATTT
* *
606495 AATTTTTTAAAGAAAATATATAAATATTTTACAATTT
1 AATTTTGTAAA-AAAATATATAAATATTAT-CAATTT
606532 GTAATATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 10 0.32
36 16 0.52
37 5 0.16
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (35 bp):
AATTTTGTAAAAAAATATATAAATATTATCAATTT
Found at i:606713 original size:20 final size:20
Alignment explanation
Indices: 606677--606714 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
606667 ATCCTATTCC
**
606677 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
606697 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
606715 GTGAACCAAA
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:611807 original size:229 final size:227
Alignment explanation
Indices: 611397--611845 Score: 790
Period size: 229 Copynumber: 2.0 Consensus size: 227
611387 GTAAATTATC
* * *
611397 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
611462 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
611527 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
611592 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
611625 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
611690 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
611755 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
611820 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
611846 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
228 40 0.19
229 170 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:611934 original size:20 final size:19
Alignment explanation
Indices: 611911--611957 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
611901 CGATATACCA
611911 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
611931 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
611951 GGTAAAA
1 GGTAAAA
611958 TTAAAAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:614466 original size:33 final size:33
Alignment explanation
Indices: 614424--614489 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
614414 AAATAGATGG
*
614424 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
614457 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
614490 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:616329 original size:19 final size:19
Alignment explanation
Indices: 616285--616328 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
616275 AATGTCGAGT
616285 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
616304 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
616323 T-ATTTT
1 TAATTTT
616329 TTATGTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:617037 original size:200 final size:199
Alignment explanation
Indices: 616410--618028 Score: 2994
Period size: 199 Copynumber: 8.1 Consensus size: 199
616400 TTAAGGGTCA
* * *
616410 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
616475 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
616540 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
616605 AATG
196 AATG
* *
616609 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
616674 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
616739 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
616804 AATG
196 AATG
616808 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
616873 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
616938 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
617003 TAATG
195 TAATG
617008 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
617073 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
617138 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
617203 TAATG
195 TAATG
* *
617208 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
617273 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
617338 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
617403 AATG
196 AATG
* *
617407 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
617472 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAA-CCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
617536 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
617601 AATG
196 AATG
*
617605 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
617670 CATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
617733 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
617798 AATG
196 AATG
617802 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
* *
617867 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
617932 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
617997 AATG
196 AATG
618001 TGTCGACACTAATATA-TTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
618029 CTAATTTAAA
Statistics
Matches: 1396, Mismatches: 20, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
196 32 0.02
197 160 0.11
198 171 0.12
199 638 0.46
200 395 0.28
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:617301 original size:399 final size:398
Alignment explanation
Indices: 616410--618028 Score: 2994
Period size: 399 Copynumber: 4.1 Consensus size: 398
616400 TTAAGGGTCA
* * *
616410 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
616475 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
616540 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
616605 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
*
616670 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
616735 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
326 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
616800 AAATAATG
391 AAATAATG
616808 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
616873 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
616938 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
617003 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGT
195 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGT
*
617068 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
260 GCACCAATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
*
617133 ATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
324 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
617198 CTAAATAATG
389 CTAAATAATG
* *
617208 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
617273 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
617338 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
617403 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
*
617468 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAA-CCAAAAGTAT
261 CACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
* *
617532 AATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCT
326 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
617597 AAATAATG
391 AAATAATG
*
617605 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
617670 CATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
617733 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
617798 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
* *
617863 CACCCATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
* *
617928 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCT
326 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
617993 AAATAATG
391 AAATAATG
618001 TGTCGACACTAATATA-TTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
618029 CTAATTTAAA
Statistics
Matches: 1189, Mismatches: 29, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
395 237 0.20
396 95 0.08
397 159 0.13
398 111 0.09
399 392 0.33
400 195 0.16
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (398 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
CACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
AAATAATG
Found at i:619516 original size:18 final size:18
Alignment explanation
Indices: 619493--619560 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
619483 ATCGGTCGCA
619493 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
619511 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
619532 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
619553 GAAGATGA
1 GAAGATGA
619561 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:619517 original size:6 final size:6
Alignment explanation
Indices: 619493--619590 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
619483 ATCGGTCGCA
* * * * * *
619493 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
619541 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
619589 GA
1 GA
619591 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:619528 original size:3 final size:3
Alignment explanation
Indices: 619508--619594 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
619498 TGAAGCTGAC
* * * * * ** *
619508 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
619556 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
619595 CCAAACAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:619543 original size:42 final size:42
Alignment explanation
Indices: 619496--619586 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
619486 GGTCGCAGAA
*
619496 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
619538 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
619580 GATGAAG
1 GATGAAG
619587 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:619594 original size:18 final size:18
Alignment explanation
Indices: 619493--619590 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
619483 ATCGGTCGCA
* *
619493 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
619511 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
619529 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
619547 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
619565 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
619583 GAAGATGA
1 GAAGATGA
619591 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:621266 original size:184 final size:184
Alignment explanation
Indices: 620957--621812 Score: 1640
Period size: 184 Copynumber: 4.7 Consensus size: 184
620947 ACTTTCACAT
**
620957 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
621022 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
621087 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
621141 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
621206 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
621271 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
621325 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
621390 GGTCTACAACATATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
621455 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATTGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
621509 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
621574 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
621639 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
621693 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
621758 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
621813 CCATTTAAAA
Statistics
Matches: 662, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 662 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:624400 original size:23 final size:23
Alignment explanation
Indices: 624369--624431 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
624359 ATAGGTAAAC
*
624369 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
624392 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
624415 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
624432 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:624439 original size:23 final size:23
Alignment explanation
Indices: 624369--624441 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
624359 ATAGGTAAAC
* * **
624369 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
624392 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
624415 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
624438 ATAT
1 ATAT
624442 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:624469 original size:20 final size:20
Alignment explanation
Indices: 624444--624482 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
624434 GGTTATATTG
* *
624444 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
624464 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
624483 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:624820 original size:23 final size:23
Alignment explanation
Indices: 624789--624851 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
624779 ATAGGTAAAC
*
624789 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
624812 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
624835 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
624852 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:624859 original size:23 final size:23
Alignment explanation
Indices: 624789--624861 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
624779 ATAGGTAAAC
* * **
624789 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
624812 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
624835 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
624858 ATAT
1 ATAT
624862 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:625184 original size:430 final size:421
Alignment explanation
Indices: 624270--625281 Score: 1911
Period size: 430 Copynumber: 2.4 Consensus size: 421
624260 AATTCGCAGT
624270 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
624335 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
624400 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
624465 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
196 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
624530 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTTTTTTTACGGTATATATTATTAAATTAA
261 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTTTTTTTACGGTATATATTATTAAATTAA
624595 AAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTA
326 AAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTA
624660 TTAAATCAATATTGTAGGTGGAAAACATGAA
391 TTAAATCAATATTGTAGGTGGAAAACATGAA
*
624691 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGAT-CATTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
624755 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
624820 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
624885 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 -AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
624950 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
260 AAGATATTAATTTAGTAATTATAGGCGTCTAATGA--T-TTTTTT---TTACGG--TATA-TATT
625015 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
316 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
625080 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
381 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
625121 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTT-AAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
625185 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
625250 TAATAGGTATCGTTTATATAATGTAATAGGTA
131 TAATAGGTATCGTTTATATAATGTAATAGGTA
625282 TCTATCTCGC
Statistics
Matches: 578, Mismatches: 2, Indels: 13
0.97 0.00 0.02
Matches are distributed among these distances:
420 138 0.24
421 154 0.27
423 1 0.00
424 6 0.01
427 6 0.01
429 18 0.03
430 255 0.44
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (421 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTTTTTTTACGGTATATATTATTAAATTAA
AAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTA
TTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:625282 original size:23 final size:23
Alignment explanation
Indices: 625219--625283 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
625209 ATAGGTAAAC
* *
625219 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
625242 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
625265 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
625284 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:625508 original size:18 final size:18
Alignment explanation
Indices: 625487--625523 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
625477 GTAATTGGAG
625487 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
625505 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
625523 T
1 T
625524 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:625531 original size:24 final size:24
Alignment explanation
Indices: 625479--625525 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
625469 TTTCATATGT
* *
625479 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
625503 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
625526 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:627640 original size:20 final size:23
Alignment explanation
Indices: 627598--627639 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
627588 ATTGATAATC
627598 TAATTATGTGTTTTAAAATTTTA
1 TAATTATGTGTTTTAAAATTTTA
*
627621 TAATTAT-T-TTTTATAATTT
1 TAATTATGTGTTTTAAAATTT
627640 AAAATTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (23 bp):
TAATTATGTGTTTTAAAATTTTA
Found at i:628682 original size:38 final size:37
Alignment explanation
Indices: 628608--628683 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
628598 GTTGAAAAAT
*
628608 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* * *
628645 ATTTATATAATTTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
628683 A
1 A
628684 AGGTTTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 8 0.24
38 21 0.64
39 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:634944 original size:42 final size:43
Alignment explanation
Indices: 634889--634975 Score: 149
Period size: 42 Copynumber: 2.0 Consensus size: 43
634879 CAAAAACCAG
* *
634889 ACTTTTCCAACAATCCAAATACTTAACAGCC-TTTCATCAACC
1 ACTTTTCCAACAATCCAAATACCTAACAGCCTTTTCATAAACC
634931 ACTTTTCCAACAATCCAAATACCTAACAGCCTTTTCATAAACC
1 ACTTTTCCAACAATCCAAATACCTAACAGCCTTTTCATAAACC
634974 AC
1 AC
634976 CTTATGCTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
42 30 0.71
43 12 0.29
ACGTcount: A:0.37, C:0.33, G:0.02, T:0.28
Consensus pattern (43 bp):
ACTTTTCCAACAATCCAAATACCTAACAGCCTTTTCATAAACC
Done.