Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 131 of 187
Found at i:39711536 original size:102 final size:102
Alignment explanation
Indices: 39711426--39711645 Score: 395
Period size: 102 Copynumber: 2.2 Consensus size: 102
39711416 AATTATATAT
*
39711426 TTTTATTAAATTATATTTAATAATAATTATTTTAGATTATATTTTATAGTATTATATATTATGAT
1 TTTTATTAAATTATATTTAATAATAATGATTTTAGATTATATTTTATAGTATTATATATTATGAT
*
39711491 TTTAGTAAATTCATTTAAGAATATTTAATATTAAGAA
66 TTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
39711528 TTTTATTAAATTATATTTAATAATTATGATTTTAGATTATATTTTATAGTATTATATATTATGAT
1 TTTTATTAAATTATATTTAATAATAATGATTTTAGATTATATTTTATAGTATTATATATTATGAT
* *
39711593 TTTATTAAATTCATATAAGAATATTTAATATTAAGAC
66 TTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
39711630 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
39711646 ATTTTTATTA
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 113 1.00
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (102 bp):
TTTTATTAAATTATATTTAATAATAATGATTTTAGATTATATTTTATAGTATTATATATTATGAT
TTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
Found at i:39711543 original size:59 final size:58
Alignment explanation
Indices: 39711361--39711544 Score: 196
Period size: 56 Copynumber: 3.1 Consensus size: 58
39711351 TATAGTATTA
*
39711361 TATATTATGATTTTAGTAAATTCATATAAGAATAATTATATTAAGAATTTTATTAAAT
1 TATATTATGATTTTAGTAAATTCATTTAAGAATAATTATATTAAGAATTTTATTAAAT
* * * * * *
39711419 TATA-TAT--TTTTATTAAATTATATTTAATAATAATTATTTTAGATTATATTTTA-TAGTATT
1 TATATTATGATTTTAGTAAATT-CATTTAAGAATAATTATATTA-A-GA-ATTTTATTA--AAT
*
39711479 ATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTAAGAATTTTATTAAAT
1 -TATATTATGATTTTAGTAAATTCATTTAAGAATAATT-ATATTAAGAATTTTATTAAAT
39711539 TATATT
1 TATATT
39711545 TAATAATTAT
Statistics
Matches: 100, Mismatches: 14, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
55 11 0.11
56 17 0.17
57 4 0.04
58 7 0.07
59 12 0.12
60 4 0.04
61 10 0.10
62 6 0.06
63 13 0.13
64 16 0.16
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (58 bp):
TATATTATGATTTTAGTAAATTCATTTAAGAATAATTATATTAAGAATTTTATTAAAT
Found at i:39711559 original size:29 final size:29
Alignment explanation
Indices: 39711511--39711608 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
39711501 TCATTTAAGA
*
39711511 ATATTTAAT-ATTAAGAATTTTATTAAATT
1 ATATTTAATAATTATG-ATTTTATTAAATT
*
39711540 ATATTTAATAATTATGATTTTAGATTATATTTT
1 ATATTTAATAATTATGATTTT--ATTA-A-ATT
39711573 ATAGTATT-ATATATTATGATTTTATTAAATT
1 ATA-T-TTAATA-ATTATGATTTTATTAAATT
39711604 CATAT
1 -ATAT
39711609 AAGAATATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
29 14 0.25
30 5 0.09
31 7 0.12
32 5 0.09
33 9 0.16
34 4 0.07
35 13 0.23
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (29 bp):
ATATTTAATAATTATGATTTTATTAAATT
Found at i:39718518 original size:17 final size:17
Alignment explanation
Indices: 39718498--39718532 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39718488 ATAAGAATTC
39718498 AAAAAAG-AGAAGAAAAG
1 AAAAAAGCAG-AGAAAAG
39718515 AAAAAAGCAGAGAAAAG
1 AAAAAAGCAGAGAAAAG
39718532 A
1 A
39718533 TGGAGATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAAAAGCAGAGAAAAG
Found at i:39723814 original size:26 final size:26
Alignment explanation
Indices: 39723741--39723801 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
39723731 ATATTTTCTG
*
39723741 AAAATTTTACCAGAGG-CAAAA-TAGTC
1 AAAATTTTACCAG-GGATAAAATTA-TC
39723767 AAAATTTTACCAGGGATAAAATTATC
1 AAAATTTTACCAGGGATAAAATTATC
39723793 AAAATTTTA
1 AAAATTTTA
39723802 TTGGGGATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 2 0.06
26 28 0.88
27 2 0.06
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (26 bp):
AAAATTTTACCAGGGATAAAATTATC
Found at i:39738487 original size:6 final size:6
Alignment explanation
Indices: 39738476--39738530 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 6
39738466 ACGTTAGCGA
**
39738476 ATAAAT ATAAAT AT-AA- ATAAAT ATTTAT ATAAAT -TAAAT -TAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
39738520 -TAAAT -TAAAT A
1 ATAAAT ATAAAT A
39738531 ATTTATATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
4 2 0.05
5 24 0.57
6 16 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
ATAAAT
Found at i:39738496 original size:16 final size:17
Alignment explanation
Indices: 39738477--39738530 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 17
39738467 CGTTAGCGAA
39738477 TAAATATAAATATAAA-
1 TAAATATAAATATAAAT
**
39738493 TAAATATTTATATAAAT
1 TAAATATAAATATAAAT
39738510 TAAAT-TAAAT-TAAAT
1 TAAATATAAATATAAAT
39738525 TAAATA
1 TAAATA
39738531 ATTTATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 10 0.31
16 17 0.53
17 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATATAAATATAAAT
Found at i:39738737 original size:25 final size:25
Alignment explanation
Indices: 39738709--39738760 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
39738699 ATGAGCCTTT
* *
39738709 AAATCAATTTGAATAAAATCAAATC
1 AAATCAATTGGAATAAAATAAAATC
** *
39738734 AAATTGATTGGAATCAAATAAAATC
1 AAATCAATTGGAATAAAATAAAATC
39738759 AA
1 AA
39738761 GATACATGTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.27
Consensus pattern (25 bp):
AAATCAATTGGAATAAAATAAAATC
Found at i:39740147 original size:22 final size:22
Alignment explanation
Indices: 39740119--39740175 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
39740109 AAACAACTTA
39740119 GTCAACGGAAAATGACTTACAG
1 GTCAACGGAAAATGACTTACAG
39740141 GTCAACGGAAAATGACTTACAG
1 GTCAACGGAAAATGACTTACAG
*
39740163 GTCAACGAAAAAT
1 GTCAACGGAAAAT
39740176 AAGTCTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (22 bp):
GTCAACGGAAAATGACTTACAG
Found at i:39741890 original size:21 final size:22
Alignment explanation
Indices: 39741866--39741908 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
39741856 TAAAATAAAT
39741866 CAATT-TAATAAATATAT-TTTA
1 CAATTATAA-AAATATATATTTA
39741887 CAATTATAAAAATATATATTTA
1 CAATTATAAAAATATATATTTA
39741909 ATAAATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (22 bp):
CAATTATAAAAATATATATTTA
Found at i:39742079 original size:3 final size:3
Alignment explanation
Indices: 39742071--39742133 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
39742061 AATACACAAG
39742071 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39742119 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
39742134 AGACAGTTCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39743490 original size:26 final size:27
Alignment explanation
Indices: 39743451--39743505 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
39743441 AGTTGTACAA
*
39743451 AAATAAAAATATTAACTTATG-AAAAG
1 AAATAAAAATATTAAATTATGTAAAAG
*
39743477 AAAT-AAAATAATTAAATTTTGTAAAAG
1 AAATAAAAAT-ATTAAATTATGTAAAAG
39743504 AA
1 AA
39743506 GAAAATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 13 0.52
27 7 0.28
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (27 bp):
AAATAAAAATATTAAATTATGTAAAAG
Found at i:39743510 original size:26 final size:25
Alignment explanation
Indices: 39743456--39743511 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
39743446 TACAAAAATA
* *
39743456 AAAATATTAACTTATGAAAAGAAAT
1 AAAATATTAAATTATGAAAAGAAAG
*
39743481 AAAATAATTAAATTTTGTAAAAG-AAG
1 AAAAT-ATTAAATTATG-AAAAGAAAG
39743507 AAAAT
1 AAAAT
39743512 GTTTGTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
26 16 0.62
27 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.29
Consensus pattern (25 bp):
AAAATATTAAATTATGAAAAGAAAG
Found at i:39754459 original size:3 final size:3
Alignment explanation
Indices: 39754451--39754478 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39754441 ATTTACTGTT
39754451 GCA GCA GCA GCA GCA GCA GCA GCA GCA G
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA G
39754479 TCTGTTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.36, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:39758445 original size:7 final size:7
Alignment explanation
Indices: 39758402--39758434 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
39758392 ATTAATTATA
*
39758402 ATAACAC
1 ATAAAAC
39758409 ATAAAAC
1 ATAAAAC
39758416 ATAAAAC
1 ATAAAAC
39758423 ATAAAAC
1 ATAAAAC
39758430 A-AAAA
1 ATAAAA
39758435 AAAAGATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 4 0.16
7 21 0.84
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.12
Consensus pattern (7 bp):
ATAAAAC
Found at i:39770144 original size:16 final size:16
Alignment explanation
Indices: 39770120--39770170 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
39770110 GGTTGAGGGG
39770120 AATGAAATA-AGGTTGT
1 AATGAAATAGA-GTTGT
* *
39770136 AATGGAATAGAATTGT
1 AATGAAATAGAGTTGT
*
39770152 AATGTAATAGAGTTGT
1 AATGAAATAGAGTTGT
39770168 AAT
1 AAT
39770171 CAGTAATTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 29 0.97
17 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (16 bp):
AATGAAATAGAGTTGT
Found at i:39770419 original size:26 final size:23
Alignment explanation
Indices: 39770379--39770471 Score: 72
Period size: 21 Copynumber: 4.0 Consensus size: 23
39770369 AATTTTATAA
*
39770379 TAATAAATAATTT-AATCATATTT
1 TAATAAATAATTTAAAT-ATAATT
39770402 TAATATAATAATTATTAAATATAATT
1 TAATA-AATAA-T-TTAAATATAATT
39770428 TAATAAA-AA--TAATATATAATT
1 TAATAAATAATTTAA-ATATAATT
*
39770449 TAAT-AAT-ATTCTTAATATAATT
1 TAATAAATAATT-TAAATATAATT
39770471 T
1 T
39770472 GGTTCATCTA
Statistics
Matches: 59, Mismatches: 2, Indels: 19
0.74 0.03 0.24
Matches are distributed among these distances:
20 6 0.10
21 12 0.20
22 9 0.15
23 7 0.12
24 7 0.12
25 3 0.05
26 12 0.20
27 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TAATAAATAATTTAAATATAATT
Found at i:39770427 original size:55 final size:57
Alignment explanation
Indices: 39770343--39770469 Score: 168
Period size: 55 Copynumber: 2.2 Consensus size: 57
39770333 TTGTTATTAA
** * * *
39770343 ATTTTAATAGGATTATTATTAAATATAATTT-T-ATAATAATAAATAATTTAATCAT
1 ATTTTAATATAATAATTATTAAATATAATTTATAAAAATAATAAATAATTTAATAAT
*
39770398 ATTTTAATATAATAATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAAT
1 ATTTTAATATAATAATTATTAAATATAATTT-ATAAAAATAATAAATAATTTAATAAT
39770456 ATTCTTAATATAAT
1 ATT-TTAATATAAT
39770470 TTGGTTCATC
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
55 28 0.45
57 1 0.02
58 23 0.37
59 10 0.16
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (57 bp):
ATTTTAATATAATAATTATTAAATATAATTTATAAAAATAATAAATAATTTAATAAT
Found at i:39778417 original size:18 final size:19
Alignment explanation
Indices: 39778396--39778438 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
39778386 CATGGGTGGG
*
39778396 TTTTTTT-TTTTTTTG-GA
1 TTTTTTTCTTTATTTGTGA
*
39778413 TTTTTTTCTTTATTTGTTA
1 TTTTTTTCTTTATTTGTGA
39778432 TTTTTTT
1 TTTTTTT
39778439 GTTACTGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 7 0.32
19 8 0.36
ACGTcount: A:0.07, C:0.02, G:0.07, T:0.84
Consensus pattern (19 bp):
TTTTTTTCTTTATTTGTGA
Found at i:39785834 original size:12 final size:12
Alignment explanation
Indices: 39785819--39785849 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
39785809 AATATTTTTA
*
39785819 ATTTTATAATTT
1 ATTTAATAATTT
39785831 ATTTAATAATTT
1 ATTTAATAATTT
39785843 ATTTAAT
1 ATTTAAT
39785850 TGAACCAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTAATAATTT
Found at i:39794436 original size:3 final size:3
Alignment explanation
Indices: 39794428--39794459 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
39794418 AATATGGTTC
39794428 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
39794460 CCCCTTATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
TGT
Found at i:39796947 original size:9 final size:9
Alignment explanation
Indices: 39796933--39796963 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39796923 GTTAAACGAA
39796933 TCGAGTTAT
1 TCGAGTTAT
*
39796942 TCGAGTTAA
1 TCGAGTTAT
39796951 TCGAGTTAT
1 TCGAGTTAT
39796960 TCGA
1 TCGA
39796964 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:39798573 original size:29 final size:29
Alignment explanation
Indices: 39798540--39798598 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
39798530 TTGCGAATTC
*
39798540 TTGGACCGCCCACCATTTTGGCTTGCACT
1 TTGGACCGCCCACCAATTTGGCTTGCACT
* *
39798569 TTGGACTGTCCACCAATTTGGCTTGCACT
1 TTGGACCGCCCACCAATTTGGCTTGCACT
39798598 T
1 T
39798599 GGATTGTCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.15, C:0.31, G:0.20, T:0.34
Consensus pattern (29 bp):
TTGGACCGCCCACCAATTTGGCTTGCACT
Found at i:39798620 original size:28 final size:29
Alignment explanation
Indices: 39798540--39798621 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 29
39798530 TTGCGAATTC
* * * *
39798540 TTGGACCGCCCACCATTTTGGCTTGCACT
1 TTGGACTGTCCACCAATTTAGCTTGCACT
*
39798569 TTGGACTGTCCACCAATTTGGCTTGCAC-
1 TTGGACTGTCCACCAATTTAGCTTGCACT
* ** *
39798597 TTGGATTGTCTGCCACTTTAGCTTG
1 TTGGACTGTCCACCAATTTAGCTTG
39798622 TACTGTCCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 20 0.44
29 25 0.56
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.35
Consensus pattern (29 bp):
TTGGACTGTCCACCAATTTAGCTTGCACT
Found at i:39798675 original size:29 final size:29
Alignment explanation
Indices: 39798631--39798704 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 29
39798621 GTACTGTCCA
*
39798631 TCATTTTGGCTTGCACTTTGGACTATCCG
1 TCATTTTGGCTTGCACTTTGGACTACCCG
*
39798660 TTATTTTGGCTTGCAC-TTGGACTACCCG
1 TCATTTTGGCTTGCACTTTGGACTACCCG
*
39798688 TCACTTTGGCTTGCACT
1 TCATTTTGGCTTGCACT
39798705 GTCTACCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 25 0.62
29 15 0.38
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.41
Consensus pattern (29 bp):
TCATTTTGGCTTGCACTTTGGACTACCCG
Found at i:39798693 original size:79 final size:79
Alignment explanation
Indices: 39798549--39798728 Score: 234
Period size: 79 Copynumber: 2.3 Consensus size: 79
39798539 CTTGGACCGC
* * ** *
39798549 CCACCATTTTGGCTTGCACTTTGGACTGTCCACCAATTTGGCTTGCACTTGGATTGTCTGCCACT
1 CCACCATTTTGGCTTGCACTTTGGACTATCCACCAATTTGGCTTGCACTTGGACTACCCGCCACT
*
39798614 TTAGCTTGTACTGT
66 TTAGCTTGCACTGT
* *** * *
39798628 CCATCATTTTGGCTTGCACTTTGGACTATCCGTTATTTTGGCTTGCACTTGGACTACCCGTCACT
1 CCACCATTTTGGCTTGCACTTTGGACTATCCACCAATTTGGCTTGCACTTGGACTACCCGCCACT
*
39798693 TTGGCTTGCACTGT
66 TTAGCTTGCACTGT
*
39798707 CTACCATTTTGGCTTGCACTTT
1 CCACCATTTTGGCTTGCACTTT
39798729 TTCATCTCGT
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 86 1.00
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.39
Consensus pattern (79 bp):
CCACCATTTTGGCTTGCACTTTGGACTATCCACCAATTTGGCTTGCACTTGGACTACCCGCCACT
TTAGCTTGCACTGT
Found at i:39801023 original size:3 final size:3
Alignment explanation
Indices: 39801015--39801058 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
39801005 NNNNNNNNNN
39801015 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39801059 GATTTTTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39803722 original size:3 final size:3
Alignment explanation
Indices: 39803714--39803751 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
39803704 GTTTAAGGTA
39803714 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
39803752 TTAGAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:39809403 original size:21 final size:21
Alignment explanation
Indices: 39809370--39809419 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
39809360 TTATTTTATA
**
39809370 TATTTTATTATTTTCATATTAT
1 TATTTTAAAATTTTCATATT-T
*
39809392 T-TTTTAAAATTTTTATATTT
1 TATTTTAAAATTTTCATATTT
39809412 TATTTTAA
1 TATTTTAA
39809420 TATAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 21 0.88
22 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTTAAAATTTTCATATTT
Found at i:39810207 original size:13 final size:13
Alignment explanation
Indices: 39810189--39810219 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
39810179 TCATGAGTGT
39810189 GGAAAACTTTTAG
1 GGAAAACTTTTAG
39810202 GGAAAACTTTTAG
1 GGAAAACTTTTAG
*
39810215 AGAAA
1 GGAAA
39810220 TATACTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (13 bp):
GGAAAACTTTTAG
Found at i:39815455 original size:21 final size:21
Alignment explanation
Indices: 39815421--39815474 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
39815411 TTTCCCTAAA
*
39815421 ATTTCCTTTCCTCAA-TTTTCAC
1 ATTTTCTTT-CTCAACTTTT-AC
* *
39815443 GTTTTTTTTCTCAACTTTTAC
1 ATTTTCTTTCTCAACTTTTAC
39815464 ATTTTCTTTCT
1 ATTTTCTTTCT
39815475 TTCTTTTTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.15, C:0.24, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTTCTTTCTCAACTTTTAC
Found at i:39816623 original size:2 final size:2
Alignment explanation
Indices: 39816618--39816648 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39816608 TAGCCGAATG
39816618 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 T
39816649 TTATGAAAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39825972 original size:18 final size:18
Alignment explanation
Indices: 39825949--39825983 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39825939 ACGGTGAGAC
39825949 TAAATGTGATAACGATAT
1 TAAATGTGATAACGATAT
*
39825967 TAAATGTGATAGCGATA
1 TAAATGTGATAACGATA
39825984 CTATAGTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (18 bp):
TAAATGTGATAACGATAT
Found at i:39829295 original size:30 final size:31
Alignment explanation
Indices: 39829227--39829296 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
39829217 CAGCACAAGG
39829227 GGTCACGCCTAGGGAAGAGGCGGCACCCCTT
1 GGTCACGCCTAGGGAAGAGGCGGCACCCCTT
*
39829258 GGTCACGCCTAGGGCAGAGGCGGCACCACC-T
1 GGTCACGCCTAGGGAAGAGGCGGCACC-CCTT
39829289 -GTCACGCC
1 GGTCACGCC
39829297 ATCTCCATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
30 8 0.22
31 27 0.73
32 2 0.05
ACGTcount: A:0.19, C:0.36, G:0.34, T:0.11
Consensus pattern (31 bp):
GGTCACGCCTAGGGAAGAGGCGGCACCCCTT
Found at i:39832159 original size:12 final size:12
Alignment explanation
Indices: 39832144--39832201 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
39832134 TGCCCGATAT
* *
39832144 AGAGGCCGAGCA
1 AGAGCCCGAGCC
*
39832156 AGAGCCAGAGCC
1 AGAGCCCGAGCC
39832168 AGAGCCCGAGCC
1 AGAGCCCGAGCC
*
39832180 CGAGCCCGAGCC
1 AGAGCCCGAGCC
39832192 AGAGCCCGAG
1 AGAGCCCGAG
39832202 TGATCGCATA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.28, C:0.36, G:0.36, T:0.00
Consensus pattern (12 bp):
AGAGCCCGAGCC
Found at i:39832165 original size:6 final size:6
Alignment explanation
Indices: 39832151--39832197 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
39832141 TATAGAGGCC
* * * *
39832151 GAGCAA GAGCCA GAGCCA GAGCCC GAGCCC GAGCCC GAGCCA GAGCC
1 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCC
39832198 CGAGTGATCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.28, C:0.38, G:0.34, T:0.00
Consensus pattern (6 bp):
GAGCCA
Found at i:39834786 original size:28 final size:28
Alignment explanation
Indices: 39834746--39834802 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
39834736 GGTCTATGAG
39834746 AAGCATGTGTGGCCCAGGATTATTGTGT
1 AAGCATGTGTGGCCCAGGATTATTGTGT
39834774 AAGCATGTGTGGCCCAGGATTATTGTGT
1 AAGCATGTGTGGCCCAGGATTATTGTGT
39834802 A
1 A
39834803 TCACAATACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.14, G:0.32, T:0.32
Consensus pattern (28 bp):
AAGCATGTGTGGCCCAGGATTATTGTGT
Found at i:39835927 original size:13 final size:14
Alignment explanation
Indices: 39835900--39835930 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
39835890 TAATATTTTT
39835900 TCTTTCTTCTCTTC
1 TCTTTCTTCTCTTC
39835914 TCTTTCTT-TCTTC
1 TCTTTCTTCTCTTC
39835927 TCTT
1 TCTT
39835931 CCCTCTCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (14 bp):
TCTTTCTTCTCTTC
Found at i:39835939 original size:18 final size:18
Alignment explanation
Indices: 39835900--39835939 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
39835890 TAATATTTTT
* *
39835900 TCTTTCTTCTCTTCTCTT
1 TCTTTCTTCTCTTCCCTC
39835918 TCTTTCTTCTCTTCCCTC
1 TCTTTCTTCTCTTCCCTC
39835936 TCTT
1 TCTT
39835940 GTTCTGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (18 bp):
TCTTTCTTCTCTTCCCTC
Found at i:39836070 original size:27 final size:27
Alignment explanation
Indices: 39836005--39836079 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
39835995 GGAATGCTAT
*
39836005 TGGTGCCACCTATCAGATAGGTGTCAC
1 TGGTGCCACCTATCAGATAGGGGTCAC
** *
39836032 CAGTTCCACCTATCAGATAGGGGTCAC
1 TGGTGCCACCTATCAGATAGGGGTCAC
* *
39836059 TGGTGCCGCCTATTAGATAGG
1 TGGTGCCACCTATCAGATAGG
39836080 CACCATACCC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (27 bp):
TGGTGCCACCTATCAGATAGGGGTCAC
Found at i:39837409 original size:16 final size:16
Alignment explanation
Indices: 39837367--39837410 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
39837357 TTATATATGA
*
39837367 TATTTTAAAATTTATT
1 TATTTTAAAATTAATT
39837383 TATCTTT-AAATTAATT
1 TAT-TTTAAAATTAATT
39837399 TATTTTAAAATT
1 TATTTTAAAATT
39837411 CCTCTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 3 0.12
16 19 0.76
17 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTTAAAATTAATT
Found at i:39837737 original size:18 final size:18
Alignment explanation
Indices: 39837714--39837748 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39837704 AAGTTCTCCA
*
39837714 TTTTATATATATTACTTC
1 TTTTATATATACTACTTC
39837732 TTTTATATATACTACTT
1 TTTTATATATACTACTT
39837749 ATATAGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATATATACTACTTC
Found at i:39837785 original size:15 final size:13
Alignment explanation
Indices: 39837748--39837777 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
39837738 ATATACTACT
39837748 TATATAG-ATTAA
1 TATATAGTATTAA
39837760 TATATAGTATTAA
1 TATATAGTATTAA
39837773 TATAT
1 TATAT
39837778 TAGTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (13 bp):
TATATAGTATTAA
Found at i:39843063 original size:30 final size:30
Alignment explanation
Indices: 39843008--39843069 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
39842998 CACTAAGCAA
39843008 GTTTCATATACATGTATCATCCATTT-CAT
1 GTTTCATATACATGTATCATCCATTTCCAT
39843037 GTTTCAATATATCATGTAAT-AT-CATTTCCAT
1 GTTTC-ATATA-CATGT-ATCATCCATTTCCAT
39843068 GT
1 GT
39843070 ATCTCATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
31 12 0.41
32 2 0.07
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (30 bp):
GTTTCATATACATGTATCATCCATTTCCAT
Found at i:39843246 original size:25 final size:25
Alignment explanation
Indices: 39843222--39843333 Score: 79
Period size: 25 Copynumber: 4.5 Consensus size: 25
39843212 ATACATGTAT
* *
39843222 GCTCATACAAGCTATGAATTGGTAT
1 GCTCATACGAGCTATGAATTGGTAA
* * *
39843247 GCT-TTCACGAGCTGTAAATTGGTAA
1 GCTCAT-ACGAGCTATGAATTGGTAA
* *
39843272 GCTCATACGAGCTAAGAATCGGTAA
1 GCTCATACGAGCTATGAATTGGTAA
* *
39843297 GCTC-TCATGAG-T-TGCAATCGGTAA
1 GCTCAT-ACGAGCTATG-AATTGGTAA
*
39843321 GCTTATACGAGCT
1 GCTCATACGAGCT
39843334 GAGAATCAGT
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
23 1 0.01
24 19 0.28
25 46 0.69
26 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (25 bp):
GCTCATACGAGCTATGAATTGGTAA
Found at i:39844317 original size:12 final size:12
Alignment explanation
Indices: 39844300--39844343 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
39844290 AACTAATCCT
39844300 CTCTCAAATTTC
1 CTCTCAAATTTC
39844312 CTCTCAAATTTC
1 CTCTCAAATTTC
39844324 CT-TCAAAATTT-
1 CTCTC-AAATTTC
39844335 CTCTCAAAT
1 CTCTCAAAT
39844344 CCATATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.27
12 22 0.73
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:39844541 original size:14 final size:15
Alignment explanation
Indices: 39844509--39844540 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39844499 ATTTTTAAAA
39844509 TTTATTTAAGAATTT
1 TTTATTTAAGAATTT
*
39844524 TTTATTTATGAATTT
1 TTTATTTAAGAATTT
39844539 TT
1 TT
39844541 AGATAATTAT
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:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (15 bp):
TTTATTTAAGAATTT
Found at i:39846695 original size:25 final size:25
Alignment explanation
Indices: 39846663--39846836 Score: 191
Period size: 25 Copynumber: 7.2 Consensus size: 25
39846653 TTTAATATTG
39846663 TTTGATGTAATAAAATAGAAGTTTA
1 TTTGATGTAATAAAATAGAAGTTTA
*
39846688 TTTGATGTAATAAAATAAAAGTTTA
1 TTTGATGTAATAAAATAGAAGTTTA
* *
39846713 TTTGATGTAATAAAGTAGAAATTT-
1 TTTGATGTAATAAAATAGAAGTTTA
* * ***
39846737 TTT--TG-AAT-TATTTTTA-TATTA
1 TTTGATGTAATAAAATAGAAGT-TTA
*
39846758 TGTGATGTAATAAAATAGAAGTTTA
1 TTTGATGTAATAAAATAGAAGTTTA
*
39846783 TTTGATGTAATAAAATAAAAGTTTA
1 TTTGATGTAATAAAATAGAAGTTTA
*
39846808 TTTGATGTAATAAAATAGAAATTT-
1 TTTGATGTAATAAAATAGAAGTTTA
39846832 TTTGA
1 TTTGA
39846837 GTTATTTTGA
Statistics
Matches: 123, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
19 1 0.01
20 5 0.04
21 5 0.04
22 2 0.02
23 2 0.02
24 11 0.09
25 96 0.78
26 1 0.01
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.44
Consensus pattern (25 bp):
TTTGATGTAATAAAATAGAAGTTTA
Found at i:39846756 original size:95 final size:95
Alignment explanation
Indices: 39846616--39846864 Score: 403
Period size: 95 Copynumber: 2.6 Consensus size: 95
39846606 AATTTTGATA
* * * *
39846616 TTATTTTATGCAATAAAATAG-AATTTTTTTTAGTTATTTTAATATTGTTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTAATATTATTTGATGTAATAAAATA
39846680 GAAGTTTATTTGATGTAATAAAATAAAAGT
66 GAAGTTTATTTGATGTAATAAAATAAAAGT
* * * *
39846710 TTATTTGATGTAATAAAGTAGAAATTTTTTTGAATTATTTTTATATTATGTGATGTAATAAAATA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTAATATTATTTGATGTAATAAAATA
39846775 GAAGTTTATTTGATGTAATAAAATAAAAGT
66 GAAGTTTATTTGATGTAATAAAATAAAAGT
*
39846805 TTATTTGATGTAATAAAATAGAAA-TTTTTTGAGTTATTTTGATATTATTTGATGTAATAA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTAATATTATTTGATGTAATAA
39846865 CATGAGCTTA
Statistics
Matches: 142, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
94 51 0.36
95 91 0.64
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (95 bp):
TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTAATATTATTTGATGTAATAAAATA
GAAGTTTATTTGATGTAATAAAATAAAAGT
Found at i:39852985 original size:18 final size:17
Alignment explanation
Indices: 39852964--39853007 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
39852954 TTTTTAAAAA
39852964 TATAAATTTTGGAAATTT
1 TATAAATTTTGG-AATTT
*
39852982 TATAAATATTTTGAATTT
1 TATAAAT-TTTGGAATTT
*
39853000 TAAAAATT
1 TATAAATT
39853008 ATTTTAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 18 0.78
19 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (17 bp):
TATAAATTTTGGAATTT
Found at i:39853012 original size:19 final size:19
Alignment explanation
Indices: 39852977--39853038 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
39852967 AAATTTTGGA
*
39852977 AATTTTATAAA-TATTTTG
1 AATTTTAAAAATTATTTTG
*
39852995 AATTTTAAAAATTATTTTA
1 AATTTTAAAAATTATTTTG
* * *
39853014 AATGTTCAAAATTAATTTG
1 AATTTTAAAAATTATTTTG
39853033 AATTTT
1 AATTTT
39853039 TTTTTTTTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
18 10 0.28
19 26 0.72
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTG
Found at i:39854755 original size:49 final size:49
Alignment explanation
Indices: 39854693--39854811 Score: 139
Period size: 49 Copynumber: 2.4 Consensus size: 49
39854683 CTCGTGTGGT
* * * * *
39854693 CCACACGGTCTACCCACACGACCTGCTTGATTTCACTCGCCCGTGTGCC
1 CCACACGGCCTACCCACACGACCTGCATGATTTCACACGACCATGTGCC
* * * * * *
39854742 CTACATGGGCTACCCACATGGCCTGCATGATTTTACACGACCATGTGCC
1 CCACACGGCCTACCCACACGACCTGCATGATTTCACACGACCATGTGCC
39854791 CCACACGGCCTACCCACACGA
1 CCACACGGCCTACCCACACGA
39854812 TTGTATGGCA
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.21, C:0.40, G:0.18, T:0.20
Consensus pattern (49 bp):
CCACACGGCCTACCCACACGACCTGCATGATTTCACACGACCATGTGCC
Found at i:39857937 original size:3 final size:3
Alignment explanation
Indices: 39857929--39857965 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
39857919 TCGGTATCAA
39857929 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
39857966 GGTAGGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39861109 original size:39 final size:39
Alignment explanation
Indices: 39861024--39861122 Score: 130
Period size: 39 Copynumber: 2.6 Consensus size: 39
39861014 AAAAACCTTT
* *
39861024 TTATAATT-TTGTAATTATAA-TTTACGATCCAATATTA
1 TTATAATTATTGTAATTATAATTTTACGATCAAACATTA
* * *
39861061 TTATAATTATTGTAATTGTAATTTTTCGGTCAAACATTA
1 TTATAATTATTGTAATTATAATTTTACGATCAAACATTA
*
39861100 TTATAATTATGGTAATTATAATT
1 TTATAATTATTGTAATTATAATT
39861123 ATTATGATTC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
37 8 0.15
38 11 0.21
39 34 0.64
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.49
Consensus pattern (39 bp):
TTATAATTATTGTAATTATAATTTTACGATCAAACATTA
Found at i:39863772 original size:125 final size:124
Alignment explanation
Indices: 39863552--39863807 Score: 388
Period size: 125 Copynumber: 2.1 Consensus size: 124
39863542 AAATAGTGGG
** * * * *
39863552 AAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATTGTGGCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
39863617 TCGCTACAGTGGTCATGTAAGAAATAAATTTTTTTTGACGTTTTCTGAGAAAATAGTATA
66 TCGCTACAGTGGTCATGTAAGAAATAAATTTTTTTTGACG-TTTCTGAGAAAATAGTATA
39863677 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
* * * * *
39863742 TCGCTACAATTGGTCATGTAGGAAAT-AATTTTTTTTGACGTTTCTGAGCAAATAGTGTC
66 TCGCTAC-AGTGGTCATGTAAGAAATAAATTTTTTTTGACGTTTCTGAGAAAATAGTATA
39863801 AAATCGC
1 AAATCGC
39863808 GCCCTCGTGG
Statistics
Matches: 119, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
124 23 0.19
125 80 0.67
126 16 0.13
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (124 bp):
AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
TCGCTACAGTGGTCATGTAAGAAATAAATTTTTTTTGACGTTTCTGAGAAAATAGTATA
Found at i:39867120 original size:34 final size:27
Alignment explanation
Indices: 39867092--39867436 Score: 155
Period size: 29 Copynumber: 12.7 Consensus size: 27
39867082 TTTTACATTA
*
39867092 ATTAAATTAGGTTAGGGTTAGGGATTTT
1 ATTAAAATAGGTTAGGGTTAGGG-TTTT
*
39867120 AATTAAAATAGGTTAGGTTTAGGGTTTT
1 -ATTAAAATAGGTTAGGGTTAGGGTTTT
39867148 CATGTAAAATAGGTTAGGGTTAGGGTTTTT
1 -AT-TAAAATAGGTTAGGGTTAGGG-TTTT
* * *
39867178 AACTAAATTAGGTTAGGGTT----TTTA
1 -ATTAAAATAGGTTAGGGTTAGGGTTTT
* **
39867202 ATTAAATTAAATTA-GGTTAGGGTTTTT
1 ATTAAAATAGGTTAGGGTTAGGG-TTTT
** ** *
39867229 AATTAAGTTAAATTA-GGTTAGAGTTTTT
1 -ATTAAAATAGGTTAGGGTTAG-GGTTTT
* *
39867257 AGGTAAATTAGGTTAGGGTTAGGGTTTTT
1 A-TTAAAATAGGTTAGGGTTAGGG-TTTT
* *
39867286 AATTAAATTAAGTTA-GGTTAGGGTTTTT
1 -ATTAAAATAGGTTAGGGTTAGGG-TTTT
* *
39867314 AATTAAATTAGGTTAGGGTT----TTTA
1 -ATTAAAATAGGTTAGGGTTAGGGTTTT
* ***
39867338 ATTAAATTAAACTA-GGTTAGGG-TTT
1 ATTAAAATAGGTTAGGGTTAGGGTTTT
* * *
39867363 -TT-AATTAAGTTA-AGTTAGGGTTTTT
1 ATTAAAATAGGTTAGGGTTAGGG-TTTT
*
39867388 AATTAAAATAGGCTAGGGTTAGGGTTTTT
1 -ATTAAAATAGGTTAGGGTTAGGG-TTTT
* *
39867417 AACTAAATTAGGTTAGGGTT
1 -ATTAAAATAGGTTAGGGTT
39867437 TTTAATTAAA
Statistics
Matches: 255, Mismatches: 37, Indels: 48
0.75 0.11 0.14
Matches are distributed among these distances:
22 8 0.03
23 37 0.15
24 8 0.03
25 5 0.02
27 6 0.02
28 73 0.29
29 112 0.44
30 6 0.02
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.43
Consensus pattern (27 bp):
ATTAAAATAGGTTAGGGTTAGGGTTTT
Found at i:39867581 original size:28 final size:28
Alignment explanation
Indices: 39867089--39867581 Score: 507
Period size: 28 Copynumber: 18.3 Consensus size: 28
39867079 GGTTTTTACA
** *
39867089 TTAATTAAATTAGGTTAGGGTTAGGGATT
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
* **
39867118 TTAATTAAAATAGGTTAGGTTTAGGG-TT
1 TTAATTAAATTAAATTAGG-TTAGGGTTT
* * **
39867146 TTCATGTAAAATAGGTTAGGGTTAGGG--T
1 TTAAT-TAAATTAAATTA-GGTTAGGGTTT
*
39867174 TT--TT-AACTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
39867199 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
* *
39867227 TTAATTAAGTTAAATTAGGTTAGAGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
** **
39867255 TTAGGTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
*
39867284 TTAATTAAATTAAGTTAGGTTAGGG--T
1 TTAATTAAATTAAATTAGGTTAGGGTTT
39867310 TT--TT-AATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
39867335 TTAATTAAATTAAACTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
39867363 TTAATTAAGTT--A--A-GTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
* ***
39867386 TTAATTAAAATAGGCTAGGGTTAGGG--T
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
*
39867413 TT--TT-AACTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
39867438 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
39867466 TTAATTAAATTAAATTAGGTTAGGCTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
39867494 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
39867522 TTAATTAAGTT--A--A-GTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
39867545 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
39867573 TTAATTAAA
1 TTAATTAAA
39867582 ATGTCTGGTT
Statistics
Matches: 402, Mismatches: 32, Indels: 61
0.81 0.06 0.12
Matches are distributed among these distances:
23 72 0.18
24 17 0.04
25 13 0.03
26 6 0.01
27 11 0.03
28 210 0.52
29 71 0.18
30 2 0.00
ACGTcount: A:0.33, C:0.01, G:0.22, T:0.44
Consensus pattern (28 bp):
TTAATTAAATTAAATTAGGTTAGGGTTT
Found at i:39870712 original size:14 final size:15
Alignment explanation
Indices: 39870695--39870728 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39870685 AATAAATATC
39870695 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
39870709 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
39870724 TAAAA
1 TAAAA
39870729 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:39870861 original size:29 final size:29
Alignment explanation
Indices: 39870827--39870887 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
39870817 TGAAAATATT
39870827 AAAAATTTTAAAATTATT-TTAAAAAAATA
1 AAAAATTTTAAAATT-TTCTTAAAAAAATA
*
39870856 AAAAATTTTAAAATTTTCTTAAAATAATA
1 AAAAATTTTAAAATTTTCTTAAAAAAATA
39870885 AAA
1 AAA
39870888 TTTAATGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAAATTTTAAAATTTTCTTAAAAAAATA
Found at i:39870950 original size:22 final size:22
Alignment explanation
Indices: 39870925--39870966 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39870915 ATTTGGAGAT
*
39870925 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
39870947 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
39870967 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:39870974 original size:30 final size:30
Alignment explanation
Indices: 39870938--39870996 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
39870928 TTGAAGGAAA
*
39870938 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAATTTGAGAGT
39870968 TTGAGAGAATTTTGGAAGGAATTTGAGAG
1 TTGAGAGAATTTTGGAAGGAATTTGAGAG
39870997 AATTTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAATTTGAGAGT
Found at i:39870986 original size:52 final size:51
Alignment explanation
Indices: 39870916--39871018 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
39870906 TTAATATGGA
* * *
39870916 TTTGGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAA-TTGAGAG
* *
39870967 TTTGAGAGAATTTTGGAAGGAATTTGAGAGAATTTTTGAACGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAATTGAGAG
39871019 AATTTTTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 4 0.09
52 37 0.82
53 4 0.09
ACGTcount: A:0.33, C:0.01, G:0.32, T:0.34
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAATTGAGAG
Found at i:39870992 original size:22 final size:22
Alignment explanation
Indices: 39870967--39871037 Score: 108
Period size: 22 Copynumber: 3.2 Consensus size: 22
39870957 AATTTGAGAG
*
39870967 TTTGAGAGAATTTTGGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
39870989 TTTGAGAGAATTTTTGAACGGAA
1 TTTGAGAGAATTTTTGAA-GGAA
39871012 -TTGAGAGAATTTTTGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
*
39871033 ATTGA
1 TTTGA
39871038 TATTGAATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
21 4 0.09
22 38 0.83
23 4 0.09
ACGTcount: A:0.37, C:0.01, G:0.28, T:0.34
Consensus pattern (22 bp):
TTTGAGAGAATTTTTGAAGGAA
Found at i:39881000 original size:47 final size:46
Alignment explanation
Indices: 39880949--39881050 Score: 134
Period size: 47 Copynumber: 2.2 Consensus size: 46
39880939 GTGGTTTAAC
* * *
39880949 CACATATCTGTTTTGGCAGT-TTGACTTCAATTATAGTGGCTCGACCA
1 CACATATCTGTTCTGGCA-TCTTAACTGCAA-TATAGTGGCTCGACCA
*
39880996 CACATATCTGTTCTGGCATCTTAACTGCAATATAGTGGCTTGACCA
1 CACATATCTGTTCTGGCATCTTAACTGCAATATAGTGGCTCGACCA
*
39881042 CATATATCT
1 CACATATCT
39881051 AATCTGACAG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
46 24 0.49
47 25 0.51
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (46 bp):
CACATATCTGTTCTGGCATCTTAACTGCAATATAGTGGCTCGACCA
Found at i:39881043 original size:46 final size:47
Alignment explanation
Indices: 39880949--39881067 Score: 143
Period size: 46 Copynumber: 2.6 Consensus size: 47
39880939 GTGGTTTAAC
* * *
39880949 CACATATCTGTTTTGGCAGTTTGACTTCAATTATAGTGGCTCGACCA
1 CACATATCTGTTCTGGCAGTTTAACTGCAATTATAGTGGCTCGACCA
*
39880996 CACATATCTGTTCTGGCA-TCTTAACTGCAA-TATAGTGGCTTGACCA
1 CACATATCTGTTCTGGCAGT-TTAACTGCAATTATAGTGGCTCGACCA
* ** *
39881042 CATATATCTAATCTGACAGTTTAACT
1 CACATATCTGTTCTGGCAGTTTAACT
39881068 TCAACTCTGG
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
46 36 0.58
47 26 0.42
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (47 bp):
CACATATCTGTTCTGGCAGTTTAACTGCAATTATAGTGGCTCGACCA
Found at i:39882179 original size:3 final size:3
Alignment explanation
Indices: 39882173--39882207 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
39882163 ATGTTGTTTG
39882173 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
39882208 AGTTTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39882446 original size:2 final size:2
Alignment explanation
Indices: 39882439--39882469 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39882429 NNNNNNNNNN
39882439 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 T
39882470 TAATTTTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39885881 original size:18 final size:18
Alignment explanation
Indices: 39885860--39885904 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
39885850 ATAATCTTCC
39885860 CAAATACCATAACATCAT
1 CAAATACCATAACATCAT
39885878 CAAATACCATAACATCAT
1 CAAATACCATAACATCAT
*
39885896 AAAATACCA
1 CAAATACCA
39885905 GAATTTCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (18 bp):
CAAATACCATAACATCAT
Found at i:39891248 original size:9 final size:9
Alignment explanation
Indices: 39891226--39891268 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
39891216 CCAAAATATT
39891226 AATTAATT-
1 AATTAATTA
39891234 AATTAATTA
1 AATTAATTA
*
39891243 AATTAATTG
1 AATTAATTA
* *
39891252 ACTTAACTA
1 AATTAATTA
39891261 AATTAATT
1 AATTAATT
39891269 TCTCAATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (9 bp):
AATTAATTA
Found at i:39891248 original size:17 final size:17
Alignment explanation
Indices: 39891226--39891282 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
39891216 CCAAAATATT
*
39891226 AATTAATTAATTAATTA
1 AATTAATTACTTAATTA
*
39891243 AATTAATTGACTTAACTA
1 AATTAATT-ACTTAATTA
* *
39891261 AATTAATTTCTCAATTA
1 AATTAATTACTTAATTA
39891278 AATTA
1 AATTA
39891283 TTTTTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 19 0.56
18 15 0.44
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTAATTACTTAATTA
Found at i:39891262 original size:18 final size:17
Alignment explanation
Indices: 39891226--39891268 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
39891216 CCAAAATATT
*
39891226 AATTAATTAATTAATTA
1 AATTAATTAATTAACTA
*
39891243 AATTAATTGACTTAACTA
1 AATTAATT-AATTAACTA
39891261 AATTAATT
1 AATTAATT
39891269 TCTCAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTAATTAATTAACTA
Found at i:39891515 original size:14 final size:15
Alignment explanation
Indices: 39891491--39891519 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39891481 TTTTTCTGTG
39891491 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
39891506 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
39891520 AGTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:39891757 original size:28 final size:28
Alignment explanation
Indices: 39891711--39891767 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
39891701 TATAGTTTTT
39891711 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
*
39891739 ATAATATATTATAAA-GTTATTATAATAA
1 ATAATA-ATTATAAAGGTTATAATAATAA
39891767 A
1 A
39891768 AACAAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATAATTATAAAGGTTATAATAATAA
Found at i:39892746 original size:21 final size:22
Alignment explanation
Indices: 39892720--39892762 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
39892710 CAGTTGAATT
39892720 TAAAGTTATGAAT-TAT-ATATA
1 TAAAGTT-TGAATGTATGATATA
39892741 TAAAGTTTGAATGTATGATATA
1 TAAAGTTTGAATGTATGATATA
39892763 AGTTCTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (22 bp):
TAAAGTTTGAATGTATGATATA
Found at i:39892761 original size:20 final size:21
Alignment explanation
Indices: 39892720--39892763 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
39892710 CAGTTGAATT
*
39892720 TAAAGTTATGAATTATATATA
1 TAAAGTTATGAATTATAGATA
39892741 TAAAGTT-TGAATGTAT-GATA
1 TAAAGTTATGAAT-TATAGATA
39892761 TAA
1 TAA
39892764 GTTCTTTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (21 bp):
TAAAGTTATGAATTATAGATA
Found at i:39893210 original size:41 final size:41
Alignment explanation
Indices: 39893153--39893308 Score: 165
Period size: 41 Copynumber: 3.8 Consensus size: 41
39893143 TTTGAGATTT
* * *
39893153 TCAGGCTTAATGCCTAGCAGGCTTGATGTCGGTGAATTACA
1 TCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTATA
*
39893194 TCAGGCTTTATGCCTAGCAGGC-TCAGTGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTGA-TGCCGGTGAATTATA
* * * *
39893235 TCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGC-TTGATGCCGGTGAATTATA
* * * *
39893276 TC-GGCTTTGTGCCTAGCAGACTTTATGTCGGTG
1 TCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTG
39893309 TTTTATACAA
Statistics
Matches: 96, Mismatches: 15, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
39 2 0.02
40 24 0.25
41 69 0.72
43 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.32
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTATA
Found at i:39903740 original size:17 final size:17
Alignment explanation
Indices: 39903684--39903741 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
39903674 CTTAATCACT
* *
39903684 TTAATATTAAATTAATA
1 TTAATATTATATTAAAA
* *
39903701 -TAATATT-TATCAAGA
1 TTAATATTATATTAAAA
*
39903716 TAAATATTATATTAAAA
1 TTAATATTATATTAAAA
39903733 TTAATATTA
1 TTAATATTA
39903742 AATCTTATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 5 0.16
16 13 0.41
17 14 0.44
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TTAATATTATATTAAAA
Found at i:39905453 original size:14 final size:15
Alignment explanation
Indices: 39905420--39905451 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39905410 TATGCATGCA
*
39905420 AAATATAAAAGACAT
1 AAATAAAAAAGACAT
39905435 AAATAAAAAAGACAT
1 AAATAAAAAAGACAT
39905450 AA
1 AA
39905452 TAGTGAAATG
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:0.72, C:0.06, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATAAAAAAGACAT
Found at i:39909791 original size:24 final size:24
Alignment explanation
Indices: 39909749--39909800 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
39909739 AATCAAAGTC
** *
39909749 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
39909773 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
39909797 AAAT
1 AAAT
39909801 CTTCTCGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:39914037 original size:24 final size:24
Alignment explanation
Indices: 39913995--39914046 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
39913985 AATCAAAGTC
** *
39913995 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
39914019 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
39914043 AAAT
1 AAAT
39914047 CATCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:39915611 original size:20 final size:20
Alignment explanation
Indices: 39915586--39915625 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39915576 TTAGAATTTA
39915586 AAATAATAAATTAATAACAC
1 AAATAATAAATTAATAACAC
39915606 AAATAATAAATTAATAACAC
1 AAATAATAAATTAATAACAC
39915626 GTACCTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAATAAATTAATAACAC
Found at i:39916222 original size:39 final size:39
Alignment explanation
Indices: 39916173--39916251 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
39916163 GCACTGGCAA
* * * *
39916173 TCATTGAATTTATACCAAAGGCCTATCCATCATAATATG
1 TCATAGAATTTATAACAAAGGCCCATCCATCATAACATG
* *
39916212 TCATAGAATTTATAACATAGGCCCATGCATCATAACATG
1 TCATAGAATTTATAACAAAGGCCCATCCATCATAACATG
39916251 T
1 T
39916252 TTGCATTTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (39 bp):
TCATAGAATTTATAACAAAGGCCCATCCATCATAACATG
Found at i:39917860 original size:204 final size:205
Alignment explanation
Indices: 39917486--39917894 Score: 784
Period size: 204 Copynumber: 2.0 Consensus size: 205
39917476 AAAATCATTT
39917486 TATTTTTGTATTTTAATTTTATTTCTTATAATTTGGTCCTCTCCAAAATAAATAATTATACCTAA
1 TATTTTTGTATTTTAATTTTATTTCTTATAATTTGGTCCTCTCCAAAATAAATAATTATACCTAA
39917551 ATATCCATATGAATCTATTACTTTTTTTAACTTATTTATTAATTCTATTTAAACTAATATTTAAA
66 ATATCCATATGAATCTATTACTTTTTTTAACTTATTTATTAATTCTATTTAAACTAATATTTAAA
* *
39917616 TATATCAAATGGTTTAGATTAAATTTTTTTAAATATAAAAGTATTAATTAATTGTATAAAATTTT
131 TATATCAAATGGTTTAGATTAAATTTTTTTAAATATAAAAGCATTAATTAATTGTATAAAATTTA
39917681 ATCATTTAAC
196 ATCATTTAAC
39917691 TATTTTTGTATTTTAATTTTATTTCTTATAATTTGGTCCTCTCCAAAATAAATAATTATACCTAA
1 TATTTTTGTATTTTAATTTTATTTCTTATAATTTGGTCCTCTCCAAAATAAATAATTATACCTAA
39917756 ATATCCATATGAATCTATTA-TTTTTTTAACTTATTTATTAATTCTATTTAAACTAATATTTAAA
66 ATATCCATATGAATCTATTACTTTTTTTAACTTATTTATTAATTCTATTTAAACTAATATTTAAA
*
39917820 TATATCAAATGGTTTAGATTAAATTTTTTTAAATATAAAAGCATTATTTAATTGTATAAAATTTA
131 TATATCAAATGGTTTAGATTAAATTTTTTTAAATATAAAAGCATTAATTAATTGTATAAAATTTA
39917885 ATCATTTAAC
196 ATCATTTAAC
39917895 CAATCTCAAG
Statistics
Matches: 201, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
204 116 0.58
205 85 0.42
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (205 bp):
TATTTTTGTATTTTAATTTTATTTCTTATAATTTGGTCCTCTCCAAAATAAATAATTATACCTAA
ATATCCATATGAATCTATTACTTTTTTTAACTTATTTATTAATTCTATTTAAACTAATATTTAAA
TATATCAAATGGTTTAGATTAAATTTTTTTAAATATAAAAGCATTAATTAATTGTATAAAATTTA
ATCATTTAAC
Found at i:39918126 original size:15 final size:14
Alignment explanation
Indices: 39918108--39918188 Score: 65
Period size: 14 Copynumber: 5.6 Consensus size: 14
39918098 CCGGCCCCTA
39918108 AATCCCTAAACTTT
1 AATCCCTAAACTTT
39918122 AAATCCCT-AACTCTT
1 -AATCCCTAAACT-TT
* ** *
39918137 AACCCCTAATGTCT
1 AATCCCTAAACTTT
39918151 AATCCCTAAACCTTT
1 AATCCCTAAA-CTTT
* *
39918166 AACCCCTAAACCTT
1 AATCCCTAAACTTT
*
39918180 AAACCCTAA
1 AATCCCTAA
39918189 CCCTTAAACC
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
14 30 0.58
15 22 0.42
ACGTcount: A:0.36, C:0.35, G:0.01, T:0.28
Consensus pattern (14 bp):
AATCCCTAAACTTT
Found at i:39918144 original size:29 final size:28
Alignment explanation
Indices: 39918111--39918195 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 28
39918101 GCCCCTAAAT
39918111 CCCTAAACTTTAAATCCCTAACTCTTAAC
1 CCCTAAACTTTAAATCCCTAAC-CTTAAC
** *
39918140 CCCTAATGTCT-AATCCCTAAACCTTTAAC
1 CCCTAAACTTTAAATCCCT-AACC-TTAAC
*
39918169 CCCTAAACCTTAAA-CCCTAACCCTTAA
1 CCCTAAACTTTAAATCCCTAA-CCTTAA
39918196 ACCATAATCC
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
28 14 0.31
29 29 0.64
30 2 0.04
ACGTcount: A:0.34, C:0.36, G:0.01, T:0.28
Consensus pattern (28 bp):
CCCTAAACTTTAAATCCCTAACCTTAAC
Found at i:39918159 original size:7 final size:7
Alignment explanation
Indices: 39918149--39918252 Score: 66
Period size: 7 Copynumber: 14.6 Consensus size: 7
39918139 CCCCTAATGT
39918149 CTAATCC
1 CTAATCC
*
39918156 CTAAACC
1 CTAATCC
* *
39918163 TTTAACCC
1 -CTAATCC
*
39918171 CTAAACC
1 CTAATCC
* *
39918178 TTAAACC
1 CTAATCC
39918185 CTAA-CC
1 CTAATCC
*
39918191 CTTAAACC
1 C-TAATCC
*
39918199 ATAATCC
1 CTAATCC
39918206 CTAATCC
1 CTAATCC
*
39918213 ATAATCC
1 CTAATCC
39918220 CTAATCC
1 CTAATCC
*
39918227 ATAATCC
1 CTAATCC
39918234 CTATATCC
1 CTA-ATCC
* *
39918242 ATACTCC
1 CTAATCC
39918249 CTAA
1 CTAA
39918253 ACCTTAAAAT
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
6 3 0.04
7 59 0.79
8 13 0.17
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.27
Consensus pattern (7 bp):
CTAATCC
Found at i:39918214 original size:14 final size:14
Alignment explanation
Indices: 39918197--39918252 Score: 94
Period size: 14 Copynumber: 3.9 Consensus size: 14
39918187 AACCCTTAAA
39918197 CCATAATCCCTAAT
1 CCATAATCCCTAAT
39918211 CCATAATCCCTAAT
1 CCATAATCCCTAAT
39918225 CCATAATCCCTATAT
1 CCATAATCCCTA-AT
*
39918240 CCATACTCCCTAA
1 CCATAATCCCTAA
39918253 ACCTTAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
14 27 0.68
15 13 0.32
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.29
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:39918221 original size:29 final size:29
Alignment explanation
Indices: 39918193--39918255 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
39918183 CCCTAACCCT
39918193 TAAACCATAATCCCTA-ATCCATAATCCC
1 TAAACCATAATCCCTATATCCATAATCCC
* *
39918221 TAATCCATAATCCCTATATCCATACTCCC
1 TAAACCATAATCCCTATATCCATAATCCC
39918250 TAAACC
1 TAAACC
39918256 TTAAAATATG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (29 bp):
TAAACCATAATCCCTATATCCATAATCCC
Found at i:39918483 original size:14 final size:14
Alignment explanation
Indices: 39918466--39918521 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
39918456 CCCCTAATGT
*
39918466 CTAACCCCTAAACC
1 CTAACCCTTAAACC
* *
39918480 CTAACCCATAACCC
1 CTAACCCTTAAACC
*
39918494 CTAAACCTTAAATCC
1 CTAACCCTTAAA-CC
39918509 C-AACCCTTAAACC
1 CTAACCCTTAAACC
39918522 GTAATCCATA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
13 2 0.06
14 30 0.86
15 3 0.09
ACGTcount: A:0.38, C:0.45, G:0.00, T:0.18
Consensus pattern (14 bp):
CTAACCCTTAAACC
Found at i:39918551 original size:15 final size:15
Alignment explanation
Indices: 39918531--39918562 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39918521 CGTAATCCAT
39918531 AATCCATAATCCCTA
1 AATCCATAATCCCTA
*
39918546 AATCCATACTCCCTA
1 AATCCATAATCCCTA
39918561 AA
1 AA
39918563 CCTCAAAATA
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:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (15 bp):
AATCCATAATCCCTA
Found at i:39919001 original size:42 final size:42
Alignment explanation
Indices: 39918914--39919055 Score: 146
Period size: 42 Copynumber: 3.5 Consensus size: 42
39918904 AAATATTTTT
* * * * **
39918914 AGCGGCGCTTTTTC-AAAAACGCCGCTAAAGACACCAACATT
1 AGCGGCGCTTTTCCAAAAAAAGCCGCTAAAGACCCCAGCAAC
* **
39918955 AGCGGCGCTTATCCAAAAAAAGCCGCTAAATCCCCCAGCAAC
1 AGCGGCGCTTTTCCAAAAAAAGCCGCTAAAGACCCCAGCAAC
* * **
39918997 AGCGGCGCTTTTTC--AAAACGCCGCTAAAGACCCCAGCATT
1 AGCGGCGCTTTTCCAAAAAAAGCCGCTAAAGACCCCAGCAAC
39919037 AGCGGCGCTTTTCCAAAAA
1 AGCGGCGCTTTTCCAAAAA
39919056 CGCCACTAAA
Statistics
Matches: 81, Mismatches: 17, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
40 34 0.42
41 12 0.15
42 35 0.43
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (42 bp):
AGCGGCGCTTTTCCAAAAAAAGCCGCTAAAGACCCCAGCAAC
Found at i:39919031 original size:40 final size:41
Alignment explanation
Indices: 39918912--39919070 Score: 196
Period size: 40 Copynumber: 3.9 Consensus size: 41
39918902 TAAAATATTT
* * *
39918912 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACACCAACA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGCA
* * **
39918953 TTAGCGGCGCTTATCCAAAAAAAGCCGCTAAATCCCCCAGCA
1 TTAGCGGCGCTTTTCC-AAAAACGCCGCTAAAGACCCCAGCA
** *
39918995 ACAGCGGCGCTTTTTC-AAAACGCCGCTAAAGACCCCAGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGCA
*
39919035 TTAGCGGCGCTTTTCCAAAAACGCCACTAAAG-CCCC
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCC
39919071 GAAAGGTAGG
Statistics
Matches: 98, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
40 38 0.39
41 28 0.29
42 32 0.33
ACGTcount: A:0.31, C:0.33, G:0.18, T:0.18
Consensus pattern (41 bp):
TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCCAGCA
Found at i:39919159 original size:40 final size:41
Alignment explanation
Indices: 39919114--39919239 Score: 168
Period size: 40 Copynumber: 3.1 Consensus size: 41
39919104 TTTTTGCAAA
*
39919114 GTTTTTCCTAAAAATGCCGCTAATGCTC-ATTTTTAACGGC
1 GTTTTTCCTAAAAATGCCGCTAATGCTCGATTTTTAGCGGC
* * *
39919154 GTTTTT-CTAAAAACGCCGCTAATGCTCGATCTTTAGCAGC
1 GTTTTTCCTAAAAATGCCGCTAATGCTCGATTTTTAGCGGC
* * *
39919194 GATTTTCGT-AAAGTGCCGCTAATGCTCGATTTTTAGCGGC
1 GTTTTTCCTAAAAATGCCGCTAATGCTCGATTTTTAGCGGC
39919234 GTTTTT
1 GTTTTT
39919240 TGTCCAAACG
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 20 0.27
40 52 0.71
41 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (41 bp):
GTTTTTCCTAAAAATGCCGCTAATGCTCGATTTTTAGCGGC
Found at i:39922107 original size:52 final size:52
Alignment explanation
Indices: 39921992--39922108 Score: 123
Period size: 52 Copynumber: 2.2 Consensus size: 52
39921982 CTTTGGAGAC
* * * * *
39921992 CTTTTATTTTGTTGTCAACTTTCAAGACTACTATGTGCTGCCTTGGACACTT
1 CTTTTCTTTTGTTGCCAACTTTAAAGACTACTATGTGCTACCTTGAACACTT
*
39922044 CTTTTCTTTTGTTGCCAACTTTAAA-AGCTA-TCATGTGCTACCTTGAAGACTT
1 CTTTTCTTTTGTTGCCAACTTTAAAGA-CTACT-ATGTGCTACCTTGAACACTT
*
39922096 -TTTTTTGTTTGTT
1 CTTTTCT-TTTGTT
39922109 TAAGCATGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
51 7 0.13
52 48 0.87
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (52 bp):
CTTTTCTTTTGTTGCCAACTTTAAAGACTACTATGTGCTACCTTGAACACTT
Found at i:39922169 original size:26 final size:26
Alignment explanation
Indices: 39922138--39922193 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
39922128 TTAACTATAT
39922138 TTTTAATGTAGTGTTTGTTATTATG-G
1 TTTTAATGTAGTG-TTGTTATTATGTG
* *
39922164 TTTTAATTTAGTGTTGTTATTGTGTG
1 TTTTAATGTAGTGTTGTTATTATGTG
39922190 TTTT
1 TTTT
39922194 TTTTCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.16, C:0.00, G:0.21, T:0.62
Consensus pattern (26 bp):
TTTTAATGTAGTGTTGTTATTATGTG
Found at i:39924489 original size:5 final size:5
Alignment explanation
Indices: 39924479--39924505 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
39924469 TTAATGATGC
39924479 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
39924506 CTTGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:39924686 original size:9 final size:9
Alignment explanation
Indices: 39924667--39924697 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
39924657 TTGTTATGTG
39924667 TTATT-TTA
1 TTATTGTTA
39924675 TTATTGTTA
1 TTATTGTTA
39924684 TTATTGTTA
1 TTATTGTTA
39924693 TTATT
1 TTATT
39924698 CATTGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (9 bp):
TTATTGTTA
Found at i:39924704 original size:13 final size:12
Alignment explanation
Indices: 39924660--39924710 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
39924650 TACTGTCTTG
39924660 TTATGTGTTATT-
1 TTAT-TGTTATTA
* *
39924672 TTATTATTGTTA
1 TTATTGTTATTA
39924684 TTATTGTTATTA
1 TTATTGTTATTA
39924696 TTCATTGTTATTA
1 TT-ATTGTTATTA
39924709 TT
1 TT
39924711 TATTCTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 5 0.15
12 16 0.48
13 12 0.36
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.67
Consensus pattern (12 bp):
TTATTGTTATTA
Found at i:39926382 original size:29 final size:30
Alignment explanation
Indices: 39926350--39926408 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
39926340 GATAAAAAAT
39926350 AAAAAATAAAATCAATTGAGCC-TTCATGA
1 AAAAAATAAAATCAATTGAGCCTTTCATGA
* * *
39926379 AAAAAGTACATTCAATTGAGCCTTTCATGA
1 AAAAAATAAAATCAATTGAGCCTTTCATGA
39926409 TTCAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (30 bp):
AAAAAATAAAATCAATTGAGCCTTTCATGA
Found at i:39927144 original size:30 final size:31
Alignment explanation
Indices: 39927108--39927169 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
39927098 TGATTTCAAT
39927108 TCAGTCACTCAA-ATT-TCGAAAAATAACAAA
1 TCAGTCACT-AACATTATCGAAAAATAACAAA
* *
39927138 TCAGTCACTAACATTATTGAAAAATGACAAA
1 TCAGTCACTAACATTATCGAAAAATAACAAA
39927169 T
1 T
39927170 TAGTTACCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 2 0.07
30 12 0.43
31 14 0.50
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.26
Consensus pattern (31 bp):
TCAGTCACTAACATTATCGAAAAATAACAAA
Found at i:39927237 original size:21 final size:21
Alignment explanation
Indices: 39927211--39927252 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
39927201 TTAACGGGAC
39927211 AGCTGATGTGGCCAGTTAACT
1 AGCTGATGTGGCCAGTTAACT
*
39927232 AGCTGATGTGGCTAGTTAACT
1 AGCTGATGTGGCCAGTTAACT
39927253 TGCCATGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.31
Consensus pattern (21 bp):
AGCTGATGTGGCCAGTTAACT
Found at i:39927344 original size:28 final size:31
Alignment explanation
Indices: 39927313--39927373 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
39927303 CCTTTTCTAT
39927313 TTTTTA-ATAAAT-GACCCAATAT-TTT-TAC
1 TTTTTACATAAATAG-CCCAATATGTTTATAC
39927341 TTTTTACATAAATAGCCCAATATGTTTATAC
1 TTTTTACATAAATAGCCCAATATGTTTATAC
39927372 TT
1 TT
39927374 ATTCTTCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 6 0.21
29 14 0.48
30 4 0.14
31 5 0.17
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (31 bp):
TTTTTACATAAATAGCCCAATATGTTTATAC
Found at i:39927814 original size:3 final size:3
Alignment explanation
Indices: 39927808--39927841 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
39927798 TTAACAAAAA
39927808 AAG AAG AAG AAG AA- AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
39927842 ATGGAGATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39927825 original size:14 final size:14
Alignment explanation
Indices: 39927806--39927841 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
39927796 AGTTAACAAA
39927806 AAAAGAAGAAGAAG
1 AAAAGAAGAAGAAG
39927820 AAAAGAAGAAGAAG
1 AAAAGAAGAAGAAG
39927834 AAGAAGAA
1 AA-AAGAA
39927842 ATGGAGATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAGAAG
Found at i:39927828 original size:17 final size:17
Alignment explanation
Indices: 39927803--39927838 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
39927793 GTTAGTTAAC
39927803 AAAAAAAGAAGAAGAAG
1 AAAAAAAGAAGAAGAAG
*
39927820 AAAAGAAGAAGAAGAAG
1 AAAAAAAGAAGAAGAAG
39927837 AA
1 AA
39927839 GAAATGGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAGAAGAAG
Found at i:39928011 original size:3 final size:3
Alignment explanation
Indices: 39928003--39928033 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
39927993 TTCTAGAAAT
39928003 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
39928034 ACTGCCTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:39944122 original size:21 final size:20
Alignment explanation
Indices: 39944071--39944122 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
39944061 GGTTGGATTT
39944071 TATATATTTA-AAATTTATAA
1 TATAT-TTTATAAATTTATAA
* *
39944091 TATAATGTATAATATTTATAA
1 TATATTTTATAA-ATTTATAA
39944112 TATATTTTATA
1 TATATTTTATA
39944123 TGCATTCGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 6 0.23
21 17 0.65
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATATTTTATAAATTTATAA
Found at i:39947112 original size:11 final size:11
Alignment explanation
Indices: 39947098--39947141 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
39947088 TTTATATTTT
*
39947098 ATTTTTTTATG
1 ATTTTTTTATA
39947109 ATTTTTTTATA
1 ATTTTTTTATA
39947120 ATTTATAATTTATA
1 ATTT-T--TTTATA
39947134 ATTTTTTT
1 ATTTTTTT
39947142 CTATACTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
11 17 0.59
12 1 0.03
13 1 0.03
14 10 0.34
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (11 bp):
ATTTTTTTATA
Found at i:39948315 original size:9 final size:9
Alignment explanation
Indices: 39948301--39948331 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39948291 GTTAAACGAA
39948301 TCGAGTTAT
1 TCGAGTTAT
*
39948310 TCGAGTTAA
1 TCGAGTTAT
39948319 TCGAGTTAT
1 TCGAGTTAT
39948328 TCGA
1 TCGA
39948332 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:39948981 original size:5 final size:5
Alignment explanation
Indices: 39948971--39948996 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39948961 CTCGAAAATT
39948971 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
39948997 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:39953787 original size:29 final size:28
Alignment explanation
Indices: 39953737--39953793 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
39953727 ATTTAAAGCA
** *
39953737 TTTATTTATACTTTAAGTAAATTATATT
1 TTTATTTATACTTTAAAAAAATCATATT
*
39953765 TTTATTTATTATTTTAAAAAAATCATATT
1 TTTATTTA-TACTTTAAAAAAATCATATT
39953794 AGATAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTATTTATACTTTAAAAAAATCATATT
Found at i:39956863 original size:14 final size:14
Alignment explanation
Indices: 39956838--39956873 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39956828 AGGAGTATTA
*
39956838 TTATTATTTTCTTT
1 TTATTTTTTTCTTT
*
39956852 TTCTTTTTTTCTTT
1 TTATTTTTTTCTTT
39956866 TTATTTTT
1 TTATTTTT
39956874 CAAACTAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.83
Consensus pattern (14 bp):
TTATTTTTTTCTTT
Found at i:39957302 original size:5 final size:5
Alignment explanation
Indices: 39957292--39957325 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
39957282 GTCTACCTGC
39957292 AAATA AAATA AAATA GAAA-A AAATA AAATA AAAT
1 AAATA AAATA AAATA -AAATA AAATA AAATA AAAT
39957326 GTGTAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 3 0.11
5 21 0.78
6 3 0.11
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:39970356 original size:22 final size:22
Alignment explanation
Indices: 39970323--39970364 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
39970313 AGTTAAAAAT
39970323 TATTATTATTAAATAATTATAC
1 TATTATTATTAAATAATTATAC
39970345 TATT-TTATTTAAATAATTAT
1 TATTATTA-TTAAATAATTAT
39970365 CGCATTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTATTATTAAATAATTATAC
Found at i:39977369 original size:16 final size:16
Alignment explanation
Indices: 39977348--39977382 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
39977338 GAAAAAAAAA
39977348 ATGTTAGTAGTATATT
1 ATGTTAGTAGTATATT
39977364 ATGTTAGTAGTATATT
1 ATGTTAGTAGTATATT
39977380 ATG
1 ATG
39977383 AGGAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (16 bp):
ATGTTAGTAGTATATT
Found at i:39980636 original size:18 final size:18
Alignment explanation
Indices: 39980602--39980642 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
39980592 TAATTGATAT
**
39980602 GGAGGATATATTTGAGGA
1 GGAGGATATATGAGAGGA
*
39980620 GGAGGATATATGAGAGGT
1 GGAGGATATATGAGAGGA
39980638 GGAGG
1 GGAGG
39980643 TGGGTGATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.46, T:0.22
Consensus pattern (18 bp):
GGAGGATATATGAGAGGA
Found at i:39981589 original size:14 final size:14
Alignment explanation
Indices: 39981566--39981603 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
39981556 AAAATGTACA
39981566 ATAT-AATTAAATT
1 ATATAAATTAAATT
39981579 ATATAAATTAAATT
1 ATATAAATTAAATT
*
39981593 ATATAATTTAA
1 ATATAAATTAA
39981604 TTAACTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATAAATTAAATT
Found at i:39984399 original size:16 final size:16
Alignment explanation
Indices: 39984380--39984412 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39984370 TTTAAATCTT
*
39984380 ATTATTTTAAAATAAA
1 ATTATTTAAAAATAAA
39984396 ATTATTTAAAAATAAA
1 ATTATTTAAAAATAAA
39984412 A
1 A
39984413 AATATCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTATTTAAAAATAAA
Found at i:40001642 original size:2 final size:2
Alignment explanation
Indices: 40001523--40001626 Score: 120
Period size: 2 Copynumber: 51.5 Consensus size: 2
40001513 NNNNNNNACT
*
40001523 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
40001565 TC TC AC TC AC TC TC TC TC TC TC TC ATC TC TT TC TAA T- TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC T-C TC TC TC TC
* *
40001608 TC TC TC TT TC CC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
40001627 TTTCTTTCGT
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
1 1 0.01
2 82 0.95
3 3 0.03
ACGTcount: A:0.05, C:0.47, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:40003735 original size:43 final size:43
Alignment explanation
Indices: 40003682--40003968 Score: 303
Period size: 43 Copynumber: 6.7 Consensus size: 43
40003672 GTTTTTAGAA
*
40003682 ACAAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCT
1 ACAAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCC
* * *
40003725 ACAAACGCCGCTAAAGACCAATACCTTTACCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCC
* * * * *
40003768 AAAAACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCC
* * *
40003811 ACAAACGCTGCTAAAGACCATGACCTTTAACGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCC
* **
40003854 ACAAACGCCGCTAAAGAACATGACCTTTAGA-GGCGCTTTTTGTC
1 ACAAACGCCGCTAAAGAACAAGACCTTTA-ACGGCGC-TTTTCCC
* * * * * * *
40003898 ACCAACGCTGCTATAGATCAA-ACCTTTAGCGGCGCTTCTCGC
1 ACAAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCC
* *
40003940 AAAAACGCCACTAAA-AACATA-ACCTTTAA
1 ACAAACGCCGCTAAAGAACA-AGACCTTTAA
40003969 AAAAATTTAT
Statistics
Matches: 207, Mismatches: 33, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
41 3 0.01
42 22 0.11
43 160 0.77
44 22 0.11
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCC
Done.