Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, 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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 1 of 22
Found at i:3176 original size:21 final size:21
Alignment explanation
Indices: 3152--3222 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
3142 TTTAAAATGC
* *
3152 AAAAAAATCTTTCAAAATCCT
1 AAAAAAATCTTTAAAAAACCT
*
3173 AAAAAAA-GTTTAAAAAACCT
1 AAAAAAATCTTTAAAAAACCT
*
3193 -TAAAAATCTTTAAAAAAACCTT
1 AAAAAAATCTTT-AAAAAACC-T
3215 AAAAAAAT
1 AAAAAAAT
3223 TAAAAAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
19 5 0.12
20 13 0.32
21 15 0.38
22 1 0.03
23 6 0.15
ACGTcount: A:0.61, C:0.13, G:0.01, T:0.25
Consensus pattern (21 bp):
AAAAAAATCTTTAAAAAACCT
Found at i:3228 original size:21 final size:21
Alignment explanation
Indices: 3184--3229 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3174 AAAAAAGTTT
** *
3184 AAAAAACCTTAAAAATCTTTA
1 AAAAAACCTTAAAAAAATTAA
3205 AAAAAACCTTAAAAAAATTAA
1 AAAAAACCTTAAAAAAATTAA
3226 AAAA
1 AAAA
3230 CATTAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAAACCTTAAAAAAATTAA
Found at i:3322 original size:11 final size:9
Alignment explanation
Indices: 3185--3376 Score: 70
Period size: 9 Copynumber: 20.0 Consensus size: 9
3175 AAAAAGTTTA
*
3185 AAAAACCTT
1 AAAAATCTT
3194 AAAAATCTTT
1 AAAAATC-TT
*
3204 AAAAAAACCTT
1 --AAAAATCTT
**
3215 AAAAAAATT
1 AAAAATCTT
*
3224 AAAAAACATT
1 AAAAATC-TT
*
3234 AAAATTTCTT
1 AAAA-ATCTT
*
3244 TAAAATCTAT
1 AAAAATCT-T
3254 AAAAATCATTT
1 AAAAATC--TT
*
3265 AAAAA-CTAC
1 AAAAATCT-T
*
3274 AAAAACCTT
1 AAAAATCTT
3283 -AAAATCCTT
1 AAAAAT-CTT
*
3292 ---AACCTT
1 AAAAATCTT
3298 AAAAATACTT
1 AAAAAT-CTT
3308 AAAAATCATT
1 AAAAATC-TT
3318 AAAAATCCCTT
1 AAAAAT--CTT
3329 AAAAATCTT
1 AAAAATCTT
*
3338 AAAAATCCCTC
1 AAAAAT--CTT
**
3349 AAAAGCCTT
1 AAAAATCTT
*
3358 AAAAAACTTT
1 AAAAATC-TT
3368 AAAAATCTT
1 AAAAATCTT
3377 TCAAATTTCA
Statistics
Matches: 140, Mismatches: 22, Indels: 42
0.69 0.11 0.21
Matches are distributed among these distances:
6 3 0.02
7 2 0.01
8 5 0.04
9 51 0.36
10 48 0.34
11 23 0.16
12 8 0.06
ACGTcount: A:0.55, C:0.16, G:0.01, T:0.29
Consensus pattern (9 bp):
AAAAATCTT
Found at i:3377 original size:10 final size:10
Alignment explanation
Indices: 3133--3845 Score: 144
Period size: 10 Copynumber: 73.4 Consensus size: 10
3123 CCCCGAACCA
3133 TAAAAATCCT
1 TAAAAATCCT
* * *
3143 TTAAAATGCA
1 TAAAAATCCT
* *
3153 AAAAAATCTT
1 TAAAAATCCT
*
3163 TCAAAATCCT
1 TAAAAATCCT
* ***
3173 AAAAAAAGTT
1 TAAAAATCCT
*
3183 TAAAAAACCT
1 TAAAAATCCT
*
3193 TAAAAATCTT
1 TAAAAATCCT
*
3203 TAAAAAAACCT
1 T-AAAAATCCT
**
3214 TAAAAA-AAT
1 TAAAAATCCT
* *
3223 TAAAAAACAT
1 TAAAAATCCT
* *
3233 TAAAATTTCT
1 TAAAAATCCT
*
3243 TTAAAAT-CT
1 TAAAAATCCT
*
3252 ATAAAAATCATT
1 -TAAAAATC-CT
3264 TAAAAA--C-
1 TAAAAATCCT
*
3271 TACAAAAACCT
1 TA-AAAATCCT
3282 T-AAAATCCT
1 TAAAAATCCT
3291 T---AA-CCT
1 TAAAAATCCT
*
3297 TAAAAATACT
1 TAAAAATCCT
*
3307 TAAAAATCAT
1 TAAAAATCCT
3317 TAAAAATCCCT
1 TAAAAAT-CCT
3328 TAAAAAT-CT
1 TAAAAATCCT
*
3337 TAAAAATCCC
1 TAAAAATCCT
* *
3347 TCAAAAGCCT
1 TAAAAATCCT
* *
3357 TAAAAAACTT
1 TAAAAATCCT
*
3367 TAAAAATCTT
1 TAAAAATCCT
** *
3377 TCAAATTTCAT
1 T-AAAAATCCT
*
3388 AAAAAAT--T
1 TAAAAATCCT
* *
3396 ACAAAAAACCT
1 -TAAAAATCCT
3407 T-AAAATCCT
1 TAAAAATCCT
*
3416 T----AGCCT
1 TAAAAATCCT
3422 TAATAAA-CCT
1 TAA-AAATCCT
*
3432 TAAAAAGCCTTT
1 TAAAAATCC--T
*
3444 TAAAAA--CA
1 TAAAAATCCT
3452 TAAAAA-CTCT
1 TAAAAATC-CT
*
3462 TAAAAAT-AT
1 TAAAAATCCT
3471 ATAAAAA-CCT
1 -TAAAAATCCT
* *
3481 TAAAAGTCTT
1 TAAAAATCCT
* *
3491 TTAAAATCTT
1 TAAAAATCCT
* *
3501 TAAAAAACCC
1 TAAAAATCCT
*
3511 TAAAAATTCT
1 TAAAAATCCT
*
3521 T--AAA-GCT
1 TAAAAATCCT
* *
3528 TCAAAATTCT
1 TAAAAATCCT
*
3538 TAAAAAAACCT
1 T-AAAAATCCT
*
3549 T--AAATCTT
1 TAAAAATCCT
* *
3557 TAAAATTGCAT
1 TAAAAAT-CCT
*
3568 TAAAAAATCTT
1 T-AAAAATCCT
*
3579 TAAAAGTCCT
1 TAAAAATCCT
* *
3589 TGAGAATCCT
1 TAAAAATCCT
*
3599 TAAAAATTCTT
1 TAAAAA-TCCT
* **
3610 TAAAATTCAAA
1 TAAAAATC-CT
* * *
3621 AAAAAAACTT
1 TAAAAATCCT
*
3631 TAAAAATCTT
1 TAAAAATCCT
3641 TAAAAA--CT
1 TAAAAATCCT
* *
3649 ATAAAAAACCA
1 -TAAAAATCCT
3660 T-AAAATCCT
1 TAAAAATCCT
*
3669 T---AA-CTT
1 TAAAAATCCT
3675 TAAAAATCCT
1 TAAAAATCCT
**
3685 TAAAAATATT
1 TAAAAATCCT
*
3695 TTAAAATCCT
1 TAAAAATCCT
*
3705 TAAATATCCT
1 TAAAAATCCT
*** *
3715 TAAGTCTCTT
1 TAAAAATCCT
3725 TAAAAAT--T
1 TAAAAATCCT
*
3733 ATAAAAATCAT
1 -TAAAAATCCT
*
3744 TCAAAATCCT
1 TAAAAATCCT
*
3754 TAAAAATCCC
1 TAAAAATCCT
* *
3764 TAAGAATCTT
1 TAAAAATCCT
*
3774 TAAAAATCTT
1 TAAAAATCCT
3784 TAAAAATCCT
1 TAAAAATCCT
3794 TGAAAAA--CT
1 T-AAAAATCCT
*
3803 ATAAAAA-GCT
1 -TAAAAATCCT
*
3813 TTAAAAT-CT
1 TAAAAATCCT
*
3822 ATAAAAA-GCT
1 -TAAAAATCCT
*
3832 TTAAAATCCT
1 TAAAAATCCT
3842 TAAA
1 TAAA
3846 CTTAAAAGTT
Statistics
Matches: 507, Mismatches: 136, Indels: 120
0.66 0.18 0.16
Matches are distributed among these distances:
6 12 0.02
7 9 0.02
8 22 0.04
9 94 0.19
10 292 0.58
11 65 0.13
12 13 0.03
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (10 bp):
TAAAAATCCT
Found at i:3467 original size:19 final size:19
Alignment explanation
Indices: 3445--3485 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3435 AAAGCCTTTT
3445 AAAA-ACATAAAAACTCTTA
1 AAAATACATAAAAAC-CTTA
*
3464 AAAATATATAAAAACCTTA
1 AAAATACATAAAAACCTTA
3483 AAA
1 AAA
3486 GTCTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAATACATAAAAACCTTA
Found at i:3494 original size:125 final size:121
Alignment explanation
Indices: 3265--3501 Score: 264
Period size: 125 Copynumber: 1.9 Consensus size: 121
3255 AAAATCATTT
* *
3265 AAAAACTACAAAAACCTTAAAATCCTTAACCTTAAAAATACTTAAAAATCATTAAAAATCCCTTA
1 AAAAACTACAAAAACCTTAAAATCCTTAACCTTAAAAATACTTAAAAACCATTAAAAA--CCATA
* * *
3330 AAAATCTTAAAAATCCCTCAAAAGCCTTAAAAAACTTTAAAAATCTTTCAAATTTCATA
64 AAAATCTTAAAAATACATCAAAAACCTTAAAAAACTTT-AAAATCTTTCAAATTTCATA
* * * *
3389 AAAAATTACAAAAAACCTTAAAATCCTTAGCCTTAATAAA-CCTTAAAAAGCCTTTTAAAAA-CA
1 AAAAACTAC-AAAAACCTTAAAATCCTTAACCTTAA-AAATACTTAAAAA-CC-ATTAAAAACCA
* **
3452 TAAAAACTCTTAAAAATATAT-AAAAACCTTAAAAGTCTTTTAAAATCTTT
62 TAAAAA-TCTTAAAAATACATCAAAAACCTTAAAAAAC-TTTAAAATCTTT
3502 AAAAAACCCT
Statistics
Matches: 95, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
124 37 0.39
125 47 0.49
126 4 0.04
127 7 0.07
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.29
Consensus pattern (121 bp):
AAAAACTACAAAAACCTTAAAATCCTTAACCTTAAAAATACTTAAAAACCATTAAAAACCATAAA
AATCTTAAAAATACATCAAAAACCTTAAAAAACTTTAAAATCTTTCAAATTTCATA
Found at i:3544 original size:28 final size:30
Alignment explanation
Indices: 3512--3582 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 30
3502 AAAAAACCCT
*
3512 AAAAATTCTTAAAGCTTCAAAATT-C-TTA
1 AAAAATCCTTAAAGCTTCAAAATTGCATTA
* * *
3540 AAAAAACCTTAAATCTTTAAAATTGCATTA
1 AAAAATCCTTAAAGCTTCAAAATTGCATTA
*
3570 AAAAATCTTTAAA
1 AAAAATCCTTAAA
3583 AGTCCTTGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 20 0.57
29 1 0.03
30 14 0.40
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAAATCCTTAAAGCTTCAAAATTGCATTA
Found at i:3647 original size:19 final size:19
Alignment explanation
Indices: 3623--3837 Score: 80
Period size: 19 Copynumber: 11.2 Consensus size: 19
3613 AATTCAAAAA
3623 AAAAACTTTAAAAATCTTT
1 AAAAACTTTAAAAATCTTT
* * **
3642 AAAAACTATAAAAAACCAT
1 AAAAACTTTAAAAATCTTT
* *
3661 AAAATCCTT---AA-CTTT
1 AAAAACTTTAAAAATCTTT
* *
3676 AAAAATCCTTAAAAATATTTT
1 AAAAA-CTTTAAAAAT-CTTT
* * * *
3697 AAAATCCTTAAATATCCTT
1 AAAAACTTTAAAAATCTTT
*** *
3716 AAGTCTCTTTAAAAAT-TAT
1 AA-AAACTTTAAAAATCTTT
* * *
3735 AAAAATCATTCAAAATCCTT
1 AAAAA-CTTTAAAAATCTTT
** *
3755 AAAAATCCCTAAGAATCTTT
1 AAAAA-CTTTAAAAATCTTT
*
3775 AAAAATCTTTAAAAATCCTTG
1 AAAAA-CTTTAAAAAT-CTTT
* *
3796 AAAAACTATAAAAAGCTTT
1 AAAAACTTTAAAAATCTTT
* * *
3815 AAAATCTATAAAAAGCTTT
1 AAAAACTTTAAAAATCTTT
3834 AAAA
1 AAAA
3838 TCCTTAAACT
Statistics
Matches: 145, Mismatches: 41, Indels: 20
0.70 0.20 0.10
Matches are distributed among these distances:
15 6 0.04
16 6 0.04
19 63 0.43
20 55 0.38
21 15 0.10
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAACTTTAAAAATCTTT
Found at i:3845 original size:19 final size:19
Alignment explanation
Indices: 3771--3839 Score: 84
Period size: 19 Copynumber: 3.5 Consensus size: 19
3761 CCCTAAGAAT
* *
3771 CTTTAAAAATCTTTAAAAATC
1 CTTT-AAAATCTATAAAAA-G
* *
3792 CTTGAAAAACTATAAAAAG
1 CTTTAAAATCTATAAAAAG
3811 CTTTAAAATCTATAAAAAG
1 CTTTAAAATCTATAAAAAG
3830 CTTTAAAATC
1 CTTTAAAATC
3840 CTTAAACTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 27 0.64
20 12 0.29
21 3 0.07
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (19 bp):
CTTTAAAATCTATAAAAAG
Found at i:6047 original size:2 final size:2
Alignment explanation
Indices: 6040--6087 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
6030 AGAAGATGGA
6040 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
6082 AT AT AT
1 AT AT AT
6088 GTTGACTGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9401 original size:22 final size:21
Alignment explanation
Indices: 9373--9429 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
9363 ACTTAATCAC
9373 TACGTGACTGATTTCAATG-CAT
1 TACGTGACTGATTT-AA-GACAT
* *
9395 TACGTGACTGGTTTTAGACAT
1 TACGTGACTGATTTAAGACAT
*
9416 TATGTGACTGATTT
1 TACGTGACTGATTT
9430 TTAGGCATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 16 0.53
22 13 0.43
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (21 bp):
TACGTGACTGATTTAAGACAT
Found at i:9438 original size:22 final size:22
Alignment explanation
Indices: 9373--9454 Score: 85
Period size: 22 Copynumber: 3.8 Consensus size: 22
9363 ACTTAATCAC
** *
9373 TACGTGACTGATTTCAATGCAT
1 TACGTGACTGATTTTTAGGCAT
* *
9395 TACGTGACTG-GTTTTAGACAT
1 TACGTGACTGATTTTTAGGCAT
*
9416 TATGTGACTGATTTTTAGGCAT
1 TACGTGACTGATTTTTAGGCAT
* *
9438 TGCATGACTGATTTTTA
1 TACGTGACTGATTTTTA
9455 AGTAATACCT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
21 15 0.31
22 33 0.69
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.41
Consensus pattern (22 bp):
TACGTGACTGATTTTTAGGCAT
Found at i:9524 original size:23 final size:22
Alignment explanation
Indices: 9473--9547 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
9463 CTAAGTCACA
* * *
9473 CAATGCCTTACTAACTAGTCATG
1 CAATGCC-TACCAACTAGTTACG
*
9496 CGATGCCTTACCAAC-AGGTTACG
1 CAATGCC-TACCAACTA-GTTACG
*
9519 CAATGCCTATCAACTAGTTACG
1 CAATGCCTACCAACTAGTTACG
*
9541 TAATGCC
1 CAATGCC
9548 ATTTTAACCA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
22 19 0.44
23 24 0.56
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (22 bp):
CAATGCCTACCAACTAGTTACG
Found at i:9582 original size:22 final size:22
Alignment explanation
Indices: 9557--9628 Score: 99
Period size: 22 Copynumber: 3.3 Consensus size: 22
9547 CATTTTAACC
9557 AGTCATGCAATACTTAAAAACT
1 AGTCATGCAATACTTAAAAACT
* * *
9579 AGTCACGAAATACTTAAAAATT
1 AGTCATGCAATACTTAAAAACT
* *
9601 AGTCATGCGATACTTAAATACT
1 AGTCATGCAATACTTAAAAACT
9623 AGTCAT
1 AGTCAT
9629 AAAATGCCCA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (22 bp):
AGTCATGCAATACTTAAAAACT
Found at i:9691 original size:22 final size:22
Alignment explanation
Indices: 9665--9707 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
9655 GTCCAAAGTC
* *
9665 AGTCATGCAATGCTTAAAAACT
1 AGTCACGCAATGCCTAAAAACT
*
9687 AGTCACGTAATGCCTAAAAAC
1 AGTCACGCAATGCCTAAAAAC
9708 CATAAAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (22 bp):
AGTCACGCAATGCCTAAAAACT
Found at i:10618 original size:17 final size:17
Alignment explanation
Indices: 10598--10634 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
10588 CTTTCTTTCC
10598 CTTTCCTCTTTTCTTCT
1 CTTTCCTCTTTTCTTCT
*
10615 CTTTTCTCTTTTCTTCT
1 CTTTCCTCTTTTCTTCT
10632 CTT
1 CTT
10635 CTCCCTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
CTTTCCTCTTTTCTTCT
Found at i:13192 original size:18 final size:18
Alignment explanation
Indices: 13166--13200 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13156 AATAAGATTC
*
13166 AAATATTTTACTTGAAGT
1 AAATATTTTAATTGAAGT
*
13184 AAATGTTTTAATTGAAG
1 AAATATTTTAATTGAAG
13201 ATGAGGATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (18 bp):
AAATATTTTAATTGAAGT
Found at i:13348 original size:27 final size:28
Alignment explanation
Indices: 13296--13355 Score: 104
Period size: 27 Copynumber: 2.2 Consensus size: 28
13286 AGGTGGAAAC
13296 TTTATTTATATTTAATGTAACTTATTTG
1 TTTATTTATATTTAATGTAACTTATTTG
*
13324 TTTATTTATATTT-ATGTAATTTATTTG
1 TTTATTTATATTTAATGTAACTTATTTG
13351 TTTAT
1 TTTAT
13356 AATATGTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 18 0.58
28 13 0.42
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.65
Consensus pattern (28 bp):
TTTATTTATATTTAATGTAACTTATTTG
Found at i:23309 original size:28 final size:27
Alignment explanation
Indices: 23249--23301 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
23239 ATGCATTAAA
* * *
23249 GTGTAATAAAATGTTTTTGAATATGAC
1 GTGTAACAAAATATTTTTCAATATGAC
23276 GTGTAACAATAATATTTTTCAATATG
1 GTGTAACAA-AATATTTTTCAATATG
23302 GTGTGTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.42
Consensus pattern (27 bp):
GTGTAACAAAATATTTTTCAATATGAC
Found at i:23458 original size:22 final size:22
Alignment explanation
Indices: 23433--23485 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
23423 TAATCATGGT
23433 GTGTAACATGTTTGTACATGAC
1 GTGTAACATGTTTGTACATGAC
23455 GTGTAACATGTTTGTACATGAC
1 GTGTAACATGTTTGTACATGAC
23477 GTGTAACAT
1 GTGTAACAT
23486 CTTAATCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (22 bp):
GTGTAACATGTTTGTACATGAC
Found at i:23509 original size:65 final size:68
Alignment explanation
Indices: 23405--23554 Score: 180
Period size: 65 Copynumber: 2.2 Consensus size: 68
23395 ATTTTTTTTA
* * *
23405 ACATGACGTGTAACAACCTAATCATGGTGTGTAACATG-TTTGTACATGACGTGT-A-ACATGTT
1 ACATGACGTGTAACATCCTAATCAAGGTGTATAACATGTTTTGTACATGACGTGTCACACATGTT
23467 TGT
66 TGT
* * * * *
23470 ACATGACGTGTAACATCTTAATCAAGGTGTATCACATGTTTTTGTACATGATGTGTCACATATTT
1 ACATGACGTGTAACATCCTAATCAAGGTGTATAACATG-TTTTGTACATGACGTGTCACACATGT
23535 TTGT
65 TTGT
* *
23539 ACATGATGTGTCACAT
1 ACATGACGTGTAACAT
23555 GTTTTTGTAC
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
65 33 0.46
67 15 0.21
68 1 0.01
69 22 0.31
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (68 bp):
ACATGACGTGTAACATCCTAATCAAGGTGTATAACATGTTTTGTACATGACGTGTCACACATGTT
TGT
Found at i:23530 original size:24 final size:24
Alignment explanation
Indices: 23501--23566 Score: 123
Period size: 24 Copynumber: 2.8 Consensus size: 24
23491 TCAAGGTGTA
23501 TCACATGTTTTTGTACATGATGTG
1 TCACATGTTTTTGTACATGATGTG
*
23525 TCACATATTTTTGTACATGATGTG
1 TCACATGTTTTTGTACATGATGTG
23549 TCACATGTTTTTGTACAT
1 TCACATGTTTTTGTACAT
23567 AACATATAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.47
Consensus pattern (24 bp):
TCACATGTTTTTGTACATGATGTG
Found at i:23566 original size:12 final size:12
Alignment explanation
Indices: 23503--23566 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
23493 AAGGTGTATC
23503 ACATGTTTTTGT
1 ACATGTTTTTGT
* *
23515 ACATG-ATGTGT
1 ACATGTTTTTGT
*
23526 CACATATTTTTGT
1 -ACATGTTTTTGT
* *
23539 ACATG-ATGTGT
1 ACATGTTTTTGT
23550 CACATGTTTTTGT
1 -ACATGTTTTTGT
23563 ACAT
1 ACAT
23567 AACATATAAC
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
11 8 0.21
12 22 0.58
13 8 0.21
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (12 bp):
ACATGTTTTTGT
Found at i:25218 original size:2 final size:2
Alignment explanation
Indices: 25211--25259 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
25201 TCAAGTCCAC
25211 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
25253 GAT AT AT
1 -AT AT AT
25260 CAATTGGAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30991 original size:6 final size:6
Alignment explanation
Indices: 30980--31008 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
30970 TTGGCAAAGT
30980 GATGAG GATGAG GATGAG GATGAG GATGA
1 GATGAG GATGAG GATGAG GATGAG GATGA
31009 TAGGGCAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.48, T:0.17
Consensus pattern (6 bp):
GATGAG
Found at i:41860 original size:4 final size:4
Alignment explanation
Indices: 41851--41885 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
41841 CGCTACTATT
*
41851 TTTC TTTC TTTC TTTC TTTC TCTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
41886 TTAGGTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:44666 original size:2 final size:2
Alignment explanation
Indices: 44659--44715 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
44649 GGGCAGTTGA
*
44659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
* *
44701 AT AG AT AG AT AT AT A
1 AT AT AT AT AT AT AT A
44716 AACTCTGCTG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:50450 original size:22 final size:19
Alignment explanation
Indices: 50425--50464 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
50415 TTAAATTTTG
50425 TAATATTGATTTATAAATTAAT
1 TAATATT-A-TTAT-AATTAAT
50447 TAATATTATTATAATTAA
1 TAATATTATTATAATTAA
50465 AAAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 1 0.06
22 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TAATATTATTATAATTAAT
Found at i:55737 original size:29 final size:29
Alignment explanation
Indices: 55704--55761 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
55694 TAAACTTTAT
55704 TTTCAAAACTTAAAGCTATACGGAGTTGA
1 TTTCAAAACTTAAAGCTATACGGAGTTGA
*
55733 TTTCAAAACTTAAAGCTATATGGAGTTGA
1 TTTCAAAACTTAAAGCTATACGGAGTTGA
55762 ATTGGGCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (29 bp):
TTTCAAAACTTAAAGCTATACGGAGTTGA
Found at i:56403 original size:13 final size:13
Alignment explanation
Indices: 56385--56409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56375 AATTAATCAA
56385 AAAATATTTAAAT
1 AAAATATTTAAAT
56398 AAAATATTTAAA
1 AAAATATTTAAA
56410 AACTTAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATATTTAAAT
Found at i:61817 original size:2 final size:2
Alignment explanation
Indices: 61812--61836 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61802 GTAACCTAAA
61812 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
61837 ATATATATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:61841 original size:2 final size:2
Alignment explanation
Indices: 61836--61883 Score: 87
Period size: 2 Copynumber: 23.5 Consensus size: 2
61826 TCTCTCTCTC
61836 TA TA TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61879 TA TA T
1 TA TA T
61884 GTGTGTGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61888 original size:2 final size:2
Alignment explanation
Indices: 61883--61927 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
61873 TATATATATA
61883 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
61924 TG TG
1 TG TG
61928 GACAATAGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
TG
Found at i:62963 original size:2 final size:2
Alignment explanation
Indices: 62956--62995 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
62946 TCAATCTTTG
* *
62956 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT 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
62996 CTAACTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68279 original size:6 final size:6
Alignment explanation
Indices: 68265--68294 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
68255 TATGGTATTC
*
68265 CAGGAG CAGGGG CAGGGG CAGGGG CAGGGG
1 CAGGGG CAGGGG CAGGGG CAGGGG CAGGGG
68295 TTGAACTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.17, G:0.63, T:0.00
Consensus pattern (6 bp):
CAGGGG
Found at i:90376 original size:2 final size:2
Alignment explanation
Indices: 90371--90396 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
90361 CTCCTTTAAT
90371 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
90397 AACTCTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:91590 original size:16 final size:16
Alignment explanation
Indices: 91569--91608 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
91559 ATTTTTGGTT
* *
91569 TATAATTTAATTTTAA
1 TATAATTTAAATATAA
*
91585 TATAATATAAATATAA
1 TATAATTTAAATATAA
91601 TATAATTT
1 TATAATTT
91609 TATTATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATAATTTAAATATAA
Found at i:91884 original size:21 final size:23
Alignment explanation
Indices: 91839--91889 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
91829 CTCGTATCAC
91839 AAAATTTATTTATAAAATTATAT
1 AAAATTTATTTATAAAATTATAT
91862 AAAATTTA-TT-T-AAATTATGAT
1 AAAATTTATTTATAAAATTAT-AT
91883 AAAATTT
1 AAAATTT
91890 TACACGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.26
21 10 0.37
22 2 0.07
23 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATTTATTTATAAAATTATAT
Found at i:98800 original size:37 final size:37
Alignment explanation
Indices: 98750--98820 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
98740 TCATCCATCC
*
98750 CTAATTCAAATTTTATTCTGCAGCTCGCAAAAAATCT
1 CTAATTCAAATTTTATTCTCCAGCTCGCAAAAAATCT
98787 CTAATTCAAATTTTATTCTCCAGCTCGCAAAAAA
1 CTAATTCAAATTTTATTCTCCAGCTCGCAAAAAA
98821 ACTCCATCCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.34
Consensus pattern (37 bp):
CTAATTCAAATTTTATTCTCCAGCTCGCAAAAAATCT
Found at i:127723 original size:6 final size:6
Alignment explanation
Indices: 127712--127743 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
127702 GTGCATACAG
127712 TACTGC TACTGC TACTGC TACTGC TACTGC TA
1 TACTGC TACTGC TACTGC TACTGC TACTGC TA
127744 TATGATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (6 bp):
TACTGC
Found at i:128999 original size:2 final size:2
Alignment explanation
Indices: 128992--129031 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
128982 TTAATTGGTA
*
128992 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
129032 TCAAGATTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:130725 original size:2 final size:2
Alignment explanation
Indices: 130718--130745 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
130708 TAATATTGGA
130718 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
130746 CTCTTTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:145609 original size:7 final size:7
Alignment explanation
Indices: 145597--145634 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
145587 GGAAAGGAGC
145597 ATTGCTG
1 ATTGCTG
145604 ATTGCTG
1 ATTGCTG
145611 ATTGCTG
1 ATTGCTG
145618 ATTGCTG
1 ATTGCTG
145625 ATTGCTG
1 ATTGCTG
145632 ATT
1 ATT
145635 AGAATTCGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.13, G:0.26, T:0.45
Consensus pattern (7 bp):
ATTGCTG
Found at i:157517 original size:7 final size:7
Alignment explanation
Indices: 157505--157534 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
157495 GAATTCATTT
157505 TTGATGA
1 TTGATGA
157512 TTGATGA
1 TTGATGA
157519 TTGATGA
1 TTGATGA
157526 TTGATGA
1 TTGATGA
157533 TT
1 TT
157535 CACCCAGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (7 bp):
TTGATGA
Found at i:178398 original size:32 final size:31
Alignment explanation
Indices: 178362--178426 Score: 121
Period size: 32 Copynumber: 2.1 Consensus size: 31
178352 ACCAGATAAC
178362 ACTAGAAAGTGCTCTTTGAGAAGCAAGATGAA
1 ACTAGAAAGTGCTCTTTGAGAAGCAAGA-GAA
178394 ACTAGAAAGTGCTCTTTGAGAAGCAAGAGAA
1 ACTAGAAAGTGCTCTTTGAGAAGCAAGAGAA
178425 AC
1 AC
178427 AATATTCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 5 0.15
32 28 0.85
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.20
Consensus pattern (31 bp):
ACTAGAAAGTGCTCTTTGAGAAGCAAGAGAA
Found at i:181931 original size:23 final size:23
Alignment explanation
Indices: 181905--181954 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
181895 TAAAAATATA
*
181905 AATTTTAT-AAATTATATTATTAT
1 AATTTTATAAAATAATATT-TTAT
181928 AATTTTATAAAATAATATTTTAT
1 AATTTTATAAAATAATATTTTAT
181951 AATT
1 AATT
181955 AAATGATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTTTATAAAATAATATTTTAT
Found at i:189152 original size:2 final size:2
Alignment explanation
Indices: 189145--189176 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
189135 TTGTCTCCTA
189145 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
189177 TTGCACTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:193790 original size:29 final size:29
Alignment explanation
Indices: 193758--193818 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
193748 GATCTTAAAA
*
193758 TATTTA-ATTAATTATATCATA-TTTATATT
1 TATTTATA-TAATTAT-TAATATTTTATATT
193787 TATTTATATAATTATTAATATTTTATATT
1 TATTTATATAATTATTAATATTTTATATT
193816 TAT
1 TAT
193819 ATGTTACAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 4 0.14
29 24 0.83
30 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
TATTTATATAATTATTAATATTTTATATT
Found at i:193795 original size:21 final size:21
Alignment explanation
Indices: 193756--193809 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
193746 AAGATCTTAA
193756 AATATTTA-A-TTAATTATAT
1 AATATTTATATTTAATTATAT
* *
193775 CATATTTATATTTATTTATAT
1 AATATTTATATTTAATTATAT
*
193796 AATTATTAATATTT
1 AA-TATTTATATTT
193810 TATATTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 7 0.25
20 1 0.04
21 10 0.36
22 10 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
AATATTTATATTTAATTATAT
Found at i:199504 original size:7 final size:7
Alignment explanation
Indices: 199492--199522 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
199482 AATTTGTTGG
199492 ATTCAGA
1 ATTCAGA
199499 ATTCAGA
1 ATTCAGA
199506 ATTCAGA
1 ATTCAGA
199513 ATTCAGA
1 ATTCAGA
199520 ATT
1 ATT
199523 TCAGTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (7 bp):
ATTCAGA
Found at i:214503 original size:2 final size:2
Alignment explanation
Indices: 214496--214531 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
214486 TAAACAGCAC
214496 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
214532 ATCTTAGTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:215933 original size:2 final size:2
Alignment explanation
Indices: 215926--215954 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
215916 CGTGTGGGTT
215926 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
215955 CGAAGGAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:221939 original size:21 final size:20
Alignment explanation
Indices: 221898--221940 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
221888 TATATATTGT
*
221898 TTGCTTGTTTAAAACATTAA
1 TTGCTTGTTTAAAACAATAA
221918 TTGCTTGCTTTAACAA-AATAA
1 TTGCTTG-TTTAA-AACAATAA
221939 TT
1 TT
221941 ATCAAAAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 11 0.55
22 2 0.10
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (20 bp):
TTGCTTGTTTAAAACAATAA
Found at i:227388 original size:2 final size:2
Alignment explanation
Indices: 227381--227413 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
227371 TCAATTCAGA
227381 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
227414 GCTAGCTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:253462 original size:2 final size:2
Alignment explanation
Indices: 253457--253483 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
253447 CTCTCTAAGA
253457 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
253484 GAAATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:273547 original size:6 final size:7
Alignment explanation
Indices: 273530--273556 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
273520 AGAGAAATTA
273530 AAAAAAG
1 AAAAAAG
273537 AAAAAAG
1 AAAAAAG
273544 AAAAAAG
1 AAAAAAG
273551 AAAAAA
1 AAAAAA
273557 TGGAATTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:276336 original size:118 final size:117
Alignment explanation
Indices: 276117--276336 Score: 377
Period size: 118 Copynumber: 1.9 Consensus size: 117
276107 TTGTAAAATG
*
276117 TAATATGCAATCTACTCTTATAGCTCCACGACCACCATGTGTTTTCTGCCGTAGTCAATATTTTT
1 TAATATGCAATCTACTCTTATAGCTCCACGACCACCATGTGTTTTCTGCCCTAGTCAATATTTTT
* * *
276182 CTGGTGGGTTTTTACATGGTCATGTGTCACGATTTTACATGGTCCATGACCC
66 CTGATAGGTTTTTACATAGTCATGTGTCACGATTTTACATGGTCCATGACCC
*
276234 TAATATGCAATCTACTCTTATAGCTCCACGACCACCATGTGTTTTTTTGCCCTAGTCAATATTTT
1 TAATATGCAATCTACTCTTATAGCTCCACGACCACCATGTG-TTTTCTGCCCTAGTCAATATTTT
*
276299 TCTGATAGGTTTTTACGTAGTCATGTGTCACGATTTTA
65 TCTGATAGGTTTTTACATAGTCATGTGTCACGATTTTA
276337 TAAAAAAGTT
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
117 41 0.43
118 55 0.57
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (117 bp):
TAATATGCAATCTACTCTTATAGCTCCACGACCACCATGTGTTTTCTGCCCTAGTCAATATTTTT
CTGATAGGTTTTTACATAGTCATGTGTCACGATTTTACATGGTCCATGACCC
Found at i:277741 original size:2 final size:2
Alignment explanation
Indices: 277734--277758 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
277724 ATTTTTGGAA
277734 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
277759 GTAACTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:304684 original size:23 final size:23
Alignment explanation
Indices: 304658--304703 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
304648 GCTTTCCGGG
* *
304658 GAAAATGCTTTAGGGTTAGATTT
1 GAAAATGCTTGAGGGCTAGATTT
304681 GAAAATGCTTGAGGGCTAGATTT
1 GAAAATGCTTGAGGGCTAGATTT
304704 ATTGTAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (23 bp):
GAAAATGCTTGAGGGCTAGATTT
Found at i:314118 original size:26 final size:23
Alignment explanation
Indices: 314070--314116 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
314060 TCTTTGAAGG
314070 AAGCAGCATTGCTAGAGTAAATA
1 AAGCAGCATTGCTAGAGTAAATA
314093 AAGCAGCATTGCTAGAGTAAATA
1 AAGCAGCATTGCTAGAGTAAATA
314116 A
1 A
314117 TATGGTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (23 bp):
AAGCAGCATTGCTAGAGTAAATA
Found at i:327207 original size:33 final size:33
Alignment explanation
Indices: 327170--327240 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
327160 ATTATGTCAA
* *
327170 ATTAACATATCACGTCATCATCAGTTATGATAT
1 ATTAACATATCACATCATCATCAATTATGATAT
* * *
327203 ATTAACATGTCATATTATCATCAATTATGATAT
1 ATTAACATATCACATCATCATCAATTATGATAT
*
327236 TTTAA
1 ATTAA
327241 TATGTTATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (33 bp):
ATTAACATATCACATCATCATCAATTATGATAT
Found at i:327957 original size:29 final size:30
Alignment explanation
Indices: 327880--327986 Score: 108
Period size: 30 Copynumber: 3.6 Consensus size: 30
327870 ATAAGAGCTC
* * * ** *
327880 ATTTGACTCGAAATAAAAGTACAAAAGTTT
1 ATTTGGCTCAAAATAAAAATACAATGGCTT
** *
327910 ATTTAACTCAAAATAAAAATACAATGGTTT
1 ATTTGGCTCAAAATAAAAATACAATGGCTT
*
327940 A-TTGGCTCAAAATAAAAATATAATGGCTT
1 ATTTGGCTCAAAATAAAAATACAATGGCTT
*
327969 ATTTGGTTCAAAATAAAA
1 ATTTGGCTCAAAATAAAA
327987 TTATAAAGAC
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
29 25 0.38
30 41 0.62
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (30 bp):
ATTTGGCTCAAAATAAAAATACAATGGCTT
Found at i:327992 original size:30 final size:29
Alignment explanation
Indices: 327916--327992 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
327906 GTTTATTTAA
* *
327916 CTCAAAATAAAAATACAATGGTTTATTGG
1 CTCAAAATAAAAATATAATGGCTTATTGG
327945 CTCAAAATAAAAATATAATGGCTTATTTGG
1 CTCAAAATAAAAATATAATGGCTTA-TTGG
* *
327975 TTCAAAATAAAATTATAA
1 CTCAAAATAAAAATATAA
327993 AGACTTAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 23 0.53
30 20 0.47
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.32
Consensus pattern (29 bp):
CTCAAAATAAAAATATAATGGCTTATTGG
Found at i:331417 original size:9 final size:8
Alignment explanation
Indices: 331397--331431 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
331387 TATCAAATGC
*
331397 TTTTTATA
1 TTTTTGTA
331405 TTTTTGTA
1 TTTTTGTA
331413 TTTTTGTA
1 TTTTTGTA
331421 TTTTTG-A
1 TTTTTGTA
331428 TTTT
1 TTTT
331432 AATTTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 5 0.19
8 21 0.81
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (8 bp):
TTTTTGTA
Found at i:334586 original size:30 final size:29
Alignment explanation
Indices: 334550--334656 Score: 102
Period size: 30 Copynumber: 3.8 Consensus size: 29
334540 TTAATATTAT
334550 AATTAAAATAAATATATAATATAGAATAAA
1 AATTAAAATAAATATATAATATAG-ATAAA
*
334580 AATTAAAATAAA-A-A-AA-ATATA-AAA
1 AATTAAAATAAATATATAATATAGATAAA
**
334604 AATT--AATATTTATATAATATAGATAAAA
1 AATTAAAATAAATATATAATATAGAT-AAA
334632 CAATTAAAATAAAATATATAATATA
1 -AATTAAAAT-AAATATATAATATA
334657 AAAAATATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
22 4 0.07
23 1 0.02
24 8 0.13
25 3 0.05
26 7 0.11
27 2 0.03
28 4 0.07
29 5 0.08
30 12 0.20
31 3 0.05
32 12 0.20
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (29 bp):
AATTAAAATAAATATATAATATAGATAAA
Found at i:334664 original size:52 final size:51
Alignment explanation
Indices: 334562--334667 Score: 144
Period size: 52 Copynumber: 2.0 Consensus size: 51
334552 TTAAAATAAA
334562 TATATAATATAGAATAAAAATTAAAATAAAAAAAATATAAAAAATTAATATT
1 TATATAATATAGAATAAAAATTAAAATAAAAAAAATATAAAAAA-TAATATT
334614 TATATAATATAG-ATAAAACAATTAAAATAAAATATATAATATAAAAAAT-ATATT
1 TATATAATATAGAAT-AAA-AATTAAAATAAAA-A-A-AATATAAAAAATAATATT
334668 AAAGAAATGA
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
51 2 0.04
52 15 0.31
53 13 0.27
54 6 0.12
55 2 0.04
56 11 0.22
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (51 bp):
TATATAATATAGAATAAAAATTAAAATAAAAAAAATATAAAAAATAATATT
Found at i:334689 original size:33 final size:32
Alignment explanation
Indices: 334638--334722 Score: 82
Period size: 33 Copynumber: 2.5 Consensus size: 32
334628 AAAACAATTA
*
334638 AAATAAAATATATAATATAAAAAA-TATATTAAAG
1 AAATAAAATA-A-AATATAAAAAATTATAAT-AAG
* *
334672 AAATGAAAATAAAATATATAAAATTATAATAAT
1 AAAT-AAAATAAAATATAAAAAATTATAATAAG
334705 AAATAAAAATAAATATAT
1 AAAT-AAAATAAA-ATAT
334723 GACATTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
33 24 0.55
34 14 0.32
35 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (32 bp):
AAATAAAATAAAATATAAAAAATTATAATAAG
Found at i:334775 original size:31 final size:29
Alignment explanation
Indices: 334684--335002 Score: 131
Period size: 26 Copynumber: 11.6 Consensus size: 29
334674 ATGAAAATAA
334684 AATATATAAAAT-TATA--ATA-ATAAAT
1 AATATATAAAATATATATTATATATAAAT
* * *
334709 AA-AAAT-AAATATATGA-CAT-TAAAAAT
1 AATATATAAAATATAT-ATTATATATAAAT
*
334735 -ATATTTAAAATATGATATTATATATAAATT
1 AATATATAAAATAT-ATATTATATATAAA-T
*
334765 AATATATAAAATATA-AATATAT-TAAAAT
1 AATATATAAAATATATATTATATAT-AAAT
*
334793 AA-ATAT-AAATAT-TATAATA-ATAAAT
1 AATATATAAAATATATATTATATATAAAT
* * *
334818 AA-AAATAAAATAT-TGA-CAT-TAAAAAT
1 AATATATAAAATATAT-ATTATATATAAAT
* *
334844 -ATATTTAAAATATGATATTATATAAAAATT
1 AATATATAAAATAT-ATATTATATATAAA-T
* *
334874 AATA-ATATAAATATA-AATATATTAAAAAT
1 AATATATA-AAATATATATTATA-TATAAAT
* *
334903 AAAATATAAAATAT-TATAATA-ATAAAT
1 AATATATAAAATATATATTATATATAAAT
* *
334930 AA-AAATAAAATATATGA-TAT-TAAAAAT
1 AATATATAAAATATAT-ATTATATATAAAT
* *
334957 -ATATTTAAGAA-ATGATATTATATAAAAATT
1 AATATATAA-AATAT-ATATTATATATAAA-T
*
334987 AATA-ATAAAAAATATA
1 AATATATAAAATATATA
335003 AATATATTAA
Statistics
Matches: 227, Mismatches: 28, Indels: 74
0.69 0.09 0.22
Matches are distributed among these distances:
23 4 0.02
24 6 0.03
25 14 0.06
26 54 0.24
27 35 0.15
28 19 0.08
29 50 0.22
30 21 0.09
31 24 0.11
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (29 bp):
AATATATAAAATATATATTATATATAAAT
Found at i:334785 original size:29 final size:30
Alignment explanation
Indices: 334634--334830 Score: 89
Period size: 31 Copynumber: 6.7 Consensus size: 30
334624 AGATAAAACA
* * * *
334634 ATTAAAATAAAATATATAATATAAAAAATAT
1 ATTAAAATAATATATAAAATAT-GATAATAT
*
334665 ATTAAAGA-AATGAAAATAAAATAT-ATAA-A-
1 ATTAAA-ATAAT--ATATAAAATATGATAATAT
* * * *
334694 ATTATAATAATAAATAAAA-ATAAATATATGAC
1 ATTAAAATAATATATAAAATAT-GATA-AT-AT
* *
334726 ATTAAAA-ATATATTTAAAATATGATATTAT
1 ATTAAAATA-ATATATAAAATATGATAATAT
*
334756 ATATAAATTAATATATAAAATAT-A-AATAT
1 AT-TAAAATAATATATAAAATATGATAATAT
*
334785 ATTAAAATAA-ATAT-AAATATTATAATA-
1 ATTAAAATAATATATAAAATATGATAATAT
*
334812 A-T-AAATAA-AAATAAAATAT
1 ATTAAAATAATATATAAAATAT
334831 TGACATTAAA
Statistics
Matches: 133, Mismatches: 16, Indels: 39
0.71 0.09 0.21
Matches are distributed among these distances:
25 9 0.07
26 15 0.11
27 14 0.11
28 15 0.11
29 15 0.11
30 5 0.04
31 30 0.23
32 19 0.14
33 11 0.08
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (30 bp):
ATTAAAATAATATATAAAATATGATAATAT
Found at i:334806 original size:18 final size:20
Alignment explanation
Indices: 334773--334824 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
334763 TTAATATATA
334773 AAATATAAATATATTAAAAT
1 AAATATAAATATATTAAAAT
334793 AAATATAAATAT-TATAATAAT
1 AAATATAAATATAT-TAA-AAT
*
334814 AAATAAAAATA
1 AAATATAAATA
334825 AAATATTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.52
21 13 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATAAATATATTAAAAT
Found at i:334810 original size:109 final size:110
Alignment explanation
Indices: 334677--335013 Score: 538
Period size: 109 Copynumber: 3.0 Consensus size: 110
334667 TAAAGAAATG
*
334677 AAAATAAAATATATAAAATTATAATAATAAATAAAAATAAATATATGACATTAAAAATATATTTA
1 AAAATAAAATATA-AATATTATAATAATAAATAAAAATAAATATATGACATTAAAAATATATTTA
*
334742 AAATATGATATTATATATAAATTAATATATAAAATATAAATATATT
65 AAATATGATATTATATAAAAATTAATATATAAAATATAAATATATT
334788 AAAAT-AAATATAAATATTATAATAATAAATAAAAATAAA-ATATTGACATTAAAAATATATTTA
1 AAAATAAAATATAAATATTATAATAATAAATAAAAATAAATATA-TGACATTAAAAATATATTTA
334851 AAATATGATATTATATAAAAATTAATA-ATATAAATATAAATATATT
65 AAATATGATATTATATAAAAATTAATATATA-AAATATAAATATATT
*
334897 AAAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATT
1 -AAAATAAAATAT-AAATATTATAATAATAAATAAAAAT-AAATATATGACATTAAAAATATATT
*
334962 TAAGAA-ATGATATTATATAAAAATTAATAATAAAAAATATAAATATATT
63 TAA-AATATGATATTATATAAAAATTAAT-ATATAAAATATAAATATATT
335011 AAA
1 AAA
335014 CTTATATTTT
Statistics
Matches: 212, Mismatches: 4, Indels: 18
0.91 0.02 0.08
Matches are distributed among these distances:
108 6 0.03
109 87 0.41
110 12 0.06
111 11 0.05
112 25 0.12
113 48 0.23
114 21 0.10
115 2 0.01
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.35
Consensus pattern (110 bp):
AAAATAAAATATAAATATTATAATAATAAATAAAAATAAATATATGACATTAAAAATATATTTAA
AATATGATATTATATAAAAATTAATATATAAAATATAAATATATT
Found at i:335007 original size:28 final size:29
Alignment explanation
Indices: 334791--335008 Score: 76
Period size: 30 Copynumber: 7.3 Consensus size: 29
334781 ATATATTAAA
*
334791 ATAAATATAAAT-ATT-ATAATAATAAAT
1 ATAAATATAAATAATTAATAATAAAAAAT
* * * *
334818 AAAAATA-AAAT-ATTGACATTAAAAATAT
1 ATAAATATAAATAATTAATAATAAAAA-AT
* * * * *
334846 ATTTAAAATATGATATTATATAAAAATTAATAAT
1 A--T-AAATAT-AAATAAT-TAATAATAAAAAAT
* *
334880 ATAAATATAAATATATTAAAAATAAAATAT
1 ATAAATATAAATA-ATTAATAATAAAAAAT
* *
334910 A-AAATATTATAATAATAAATAAAAATAAAAT
1 ATAAATA-TA-AATAATTAATAATAA-AAAAT
* * *
334941 ATATGATATTAAA-AA-T-ATATTTAAGAAAT
1 ATA-AATA-TAAATAATTAATA-ATAAAAAAT
*
334970 GATATTATATAAA-AATTAATAATAAAAAAT
1 -ATA-AATATAAATAATTAATAATAAAAAAT
335000 ATAAATATA
1 ATAAATATA
335009 TTAAACTTAT
Statistics
Matches: 143, Mismatches: 29, Indels: 37
0.68 0.14 0.18
Matches are distributed among these distances:
26 7 0.05
27 13 0.09
28 8 0.06
29 21 0.15
30 42 0.29
31 27 0.19
32 4 0.03
33 9 0.06
34 5 0.03
35 7 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (29 bp):
ATAAATATAAATAATTAATAATAAAAAAT
Found at i:335182 original size:15 final size:15
Alignment explanation
Indices: 335162--335202 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
335152 TTTTCCCTGT
*
335162 AATCACATTGCTTGC
1 AATCACATTACTTGC
335177 AATCACATTACTTGC
1 AATCACATTACTTGC
335192 AATCACATTAC
1 AATCACATTAC
335203 CTATAATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:335210 original size:15 final size:15
Alignment explanation
Indices: 335162--335215 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
335152 TTTTCCCTGT
* * *
335162 AATCACATTGCTTGC
1 AATCACATTACCTAC
* *
335177 AATCACATTACTTGC
1 AATCACATTACCTAC
*
335192 AATCACATTACCTAT
1 AATCACATTACCTAC
335207 AATCACATT
1 AATCACATT
335216 GCATTATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.33
Consensus pattern (15 bp):
AATCACATTACCTAC
Found at i:342727 original size:20 final size:20
Alignment explanation
Indices: 342689--342744 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
342679 ATCAAGCATC
* *
342689 AAGTTTT-TATTTAGTAGCA
1 AAGTTTTCTTTTTTGTAGCA
342708 AAGTTTTCTTTTTTGTAGCA
1 AAGTTTTCTTTTTTGTAGCA
* *
342728 AATTTTTCTTTATTGTA
1 AAGTTTTCTTTTTTGTA
342745 ACAATGTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 7 0.22
20 25 0.78
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.55
Consensus pattern (20 bp):
AAGTTTTCTTTTTTGTAGCA
Found at i:346715 original size:58 final size:58
Alignment explanation
Indices: 346625--346734 Score: 157
Period size: 58 Copynumber: 1.9 Consensus size: 58
346615 CAACATTGTT
346625 CAAAATTAAAAAATCTTTCAAAAATCCATGAACAAATAACTAACATCAATCAAAAACC
1 CAAAATTAAAAAATCTTTCAAAAATCCATGAACAAATAACTAACATCAATCAAAAACC
* * * * * * *
346683 CAAAATTCAAGAATTTTTCAAAAATCTATGAACTAGTAACTAATATCAATCA
1 CAAAATTAAAAAATCTTTCAAAAATCCATGAACAAATAACTAACATCAATCA
346735 TACGACTGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 45 1.00
ACGTcount: A:0.53, C:0.18, G:0.04, T:0.25
Consensus pattern (58 bp):
CAAAATTAAAAAATCTTTCAAAAATCCATGAACAAATAACTAACATCAATCAAAAACC
Found at i:347479 original size:16 final size:16
Alignment explanation
Indices: 347458--347490 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
347448 ATATTATAAG
347458 TACAAATAGCAAAGTT
1 TACAAATAGCAAAGTT
*
347474 TACAAATAGCTAAGTT
1 TACAAATAGCAAAGTT
347490 T
1 T
347491 TTGTGTAAAG
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:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (16 bp):
TACAAATAGCAAAGTT
Found at i:361808 original size:21 final size:20
Alignment explanation
Indices: 361784--361822 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
361774 CTTGAAAAAT
361784 AAATTCTGATCATTAGAAACA
1 AAATT-TGATCATTAGAAACA
* *
361805 AAATTTGGTCGTTAGAAA
1 AAATTTGATCATTAGAAA
361823 TAGTTTTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (20 bp):
AAATTTGATCATTAGAAACA
Found at i:369787 original size:12 final size:12
Alignment explanation
Indices: 369770--369795 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
369760 TCAATAGCAA
369770 ATGCTTTTGCTT
1 ATGCTTTTGCTT
369782 ATGCTTTTGCTT
1 ATGCTTTTGCTT
369794 AT
1 AT
369796 ACTTGAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.58
Consensus pattern (12 bp):
ATGCTTTTGCTT
Found at i:371994 original size:22 final size:24
Alignment explanation
Indices: 371967--372013 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
371957 ATTTTTATCT
371967 AAAAGATGTATTTT-G-TAAAATG
1 AAAAGATGTATTTTAGATAAAATG
*
371989 AAAAGATGTCTTTTAGATAAAATG
1 AAAAGATGTATTTTAGATAAAATG
372013 A
1 A
372014 TGAAAGAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
23 1 0.05
24 8 0.36
ACGTcount: A:0.47, C:0.02, G:0.17, T:0.34
Consensus pattern (24 bp):
AAAAGATGTATTTTAGATAAAATG
Found at i:372599 original size:27 final size:26
Alignment explanation
Indices: 372565--372623 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 26
372555 AATTTATTTT
372565 ATTTTTATATTTT-TATTTTTAATATA
1 ATTTTTATATTTTATA-TTTTAATATA
*
372591 ATTTCTTATATTTTATATTTTAATTTA
1 ATTT-TTATATTTTATATTTTAATATA
372618 ATTTTT
1 ATTTTT
372624 TTAAAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 6 0.20
27 22 0.73
28 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (26 bp):
ATTTTTATATTTTATATTTTAATATA
Found at i:372608 original size:19 final size:18
Alignment explanation
Indices: 372503--372608 Score: 55
Period size: 17 Copynumber: 5.9 Consensus size: 18
372493 TTATTTTTTT
372503 ATTTTTA-ATTTTTATATA
1 ATTTTTATA-TTTTATATA
* *
372521 A-TATTAT-TATTTAAATA
1 ATTTTTATAT-TTTATATA
* * *
372538 CATTTTTA-ATATCATGTA
1 -ATTTTTATATTTTATATA
*
372556 ATTTATTTTATTTT-TAT-
1 ATTT-TTATATTTTATATA
372573 ATTTTTAT-TTTTAATATA
1 ATTTTTATATTTT-ATATA
372591 ATTTCTTATATTTTATAT
1 ATTT-TTATATTTTATAT
372609 TTTAATTTAA
Statistics
Matches: 64, Mismatches: 12, Indels: 23
0.65 0.12 0.23
Matches are distributed among these distances:
15 4 0.06
16 4 0.06
17 22 0.34
18 14 0.22
19 16 0.25
20 4 0.06
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (18 bp):
ATTTTTATATTTTATATA
Found at i:372802 original size:20 final size:22
Alignment explanation
Indices: 372753--372803 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
372743 AATATCTTAT
372753 TTTTTAAAAT--TTTAATTAAA
1 TTTTTAAAATAATTTAATTAAA
*
372773 ATTTT-AAATAATTT-ATT-AA
1 TTTTTAAAATAATTTAATTAAA
372792 TTTTTAAAATAA
1 TTTTTAAAATAA
372804 ACATTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 10 0.38
20 13 0.50
21 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTTAAAATAATTTAATTAAA
Found at i:373072 original size:13 final size:12
Alignment explanation
Indices: 373050--373098 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
373040 AATATTTTTT
373050 AAAAATTAATAA
1 AAAAATTAATAA
373062 AAAAA-T-ATAA
1 AAAAATTAATAA
* * *
373072 TAATATT-TTAA
1 AAAAATTAATAA
373083 AAAAATTAATAA
1 AAAAATTAATAA
373095 AAAA
1 AAAA
373099 TATTTTAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
10 7 0.24
11 10 0.34
12 12 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAAATTAATAA
Found at i:373087 original size:24 final size:24
Alignment explanation
Indices: 373055--373106 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
373045 TTTTTAAAAA
* *
373055 TTAATAAAA-AAATATAATAATATT
1 TTAAAAAAATAAATA-AAAAATATT
*
373079 TTAAAAAAATTAATAAAAAATATT
1 TTAAAAAAATAAATAAAAAATATT
373103 TTAA
1 TTAA
373107 TTTTTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TTAAAAAAATAAATAAAAAATATT
Found at i:373101 original size:32 final size:33
Alignment explanation
Indices: 373026--373098 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
373016 CATCCGTCTT
**
373026 TAAAAAAATATAATAATATTTTTTAAAAATTAA
1 TAAAAAAATATAATAATATTTTAAAAAAATTAA
373059 TAAAAAAATATAATAATATTTTAAAAAAATTAA
1 TAAAAAAATATAATAATATTTTAAAAAAATTAA
373092 TAAAAAA
1 TAAAAAA
373099 TATTTTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (33 bp):
TAAAAAAATATAATAATATTTTAAAAAAATTAA
Found at i:373134 original size:22 final size:20
Alignment explanation
Indices: 373099--373142 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
373089 TAATAAAAAA
*
373099 TATTTTAATTTTTATATTATT
1 TATTTTAATATTTATATT-TT
373120 TATTTATAATATTTATATTTT
1 TATTT-TAATATTTATATTTT
373141 TA
1 TA
373143 AATAAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTTTAATATTTATATTTT
Found at i:374236 original size:69 final size:68
Alignment explanation
Indices: 374100--374253 Score: 172
Period size: 69 Copynumber: 2.2 Consensus size: 68
374090 AGTTATAGAT
374100 AAAAAGAATAAAAAGG-TTTAGTATACATATAAAAAAGAAAAAAAGAAAGAAAGAAAAAATTTCA
1 AAAAAGAAT-AAAAGGATTTAGTATACATATAAAAAAG-AAAAAAGAAAGAAAGAAAAAATTTCA
374164 AAATA
64 AAATA
** * *
374169 AAAAAGAATAAAAGGATTTAGTATA-ATTATAATGAAG-AAAAAGAAGGAAAGAAATTTAA-TTC
1 AAAAAGAATAAAAGGATTTAGTATACA-TATAAAAAAGAAAAAAGAAAGAAAGAAA--AAATTTC
*
374231 TAAAATC
63 -AAAATA
*
374238 AAAAAGCATAAAAGGA
1 AAAAAGAATAAAAGGA
374254 AGAATGACAA
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
67 16 0.22
68 10 0.14
69 48 0.65
ACGTcount: A:0.64, C:0.03, G:0.14, T:0.19
Consensus pattern (68 bp):
AAAAAGAATAAAAGGATTTAGTATACATATAAAAAAGAAAAAAGAAAGAAAGAAAAAATTTCAAA
ATA
Found at i:374427 original size:15 final size:14
Alignment explanation
Indices: 374394--374428 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
374384 TAAAAGGGTA
374394 AAAAGAAAAAAAAT
1 AAAAGAAAAAAAAT
*
374408 AAAAGAATAAAGAAT
1 AAAAGAA-AAAAAAT
374423 AAAAGA
1 AAAAGA
374429 GTTTAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (14 bp):
AAAAGAAAAAAAAT
Found at i:378675 original size:27 final size:29
Alignment explanation
Indices: 378645--378709 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
378635 TCCTTCTAAA
*
378645 TGTTTTTT-CTTATATTTTTC-TTATACT
1 TGTTTTTTACTTATATTTTTCATAATACT
*
378672 TGTTCTTTTAGTTATATTTTTCATAATACT
1 TGTT-TTTTACTTATATTTTTCATAATACT
378702 T-TTTTTTA
1 TGTTTTTTA
378710 TTTTAGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 4 0.12
28 9 0.27
29 13 0.39
30 7 0.21
ACGTcount: A:0.18, C:0.09, G:0.05, T:0.68
Consensus pattern (29 bp):
TGTTTTTTACTTATATTTTTCATAATACT
Found at i:389866 original size:5 final size:5
Alignment explanation
Indices: 389856--389890 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
389846 CTTTATCTTC
*
389856 AAAAG AAAAG AAAAG AAAAG AAAGG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
389891 GGAAATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:396825 original size:2 final size:2
Alignment explanation
Indices: 396818--396854 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
396808 ATTTAATTCT
396818 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
396855 TCTTCTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:398888 original size:22 final size:22
Alignment explanation
Indices: 398863--398988 Score: 80
Period size: 22 Copynumber: 5.8 Consensus size: 22
398853 TTTGGTGATA
398863 TTTAGGCATTACGTGACTAATT
1 TTTAGGCATTACGTGACTAATT
* * * *
398885 TTTAAGTATTGCGTGACTTACTT
1 TTTAGGCATTACGTGAC-TAATT
* *
398908 TGTA--CATTACGTGACTTA-T
1 TTTAGGCATTACGTGACTAATT
* *
398927 TTTAAGCATTACGTGACTTATT
1 TTTAGGCATTACGTGACTAATT
** *
398949 TTTAGATATTGA-GTAACTAATT
1 TTTAGGCATT-ACGTGACTAATT
** *
398971 GGTAGGCATTGCGTGACT
1 TTTAGGCATTACGTGACT
398989 TGTTAGCAAG
Statistics
Matches: 77, Mismatches: 21, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
19 4 0.05
20 1 0.01
21 23 0.30
22 41 0.53
23 8 0.10
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (22 bp):
TTTAGGCATTACGTGACTAATT
Found at i:398922 original size:21 final size:21
Alignment explanation
Indices: 398863--398950 Score: 99
Period size: 21 Copynumber: 4.1 Consensus size: 21
398853 TTTGGTGATA
* *
398863 TTTAGGCATTACGTGACTAATT
1 TTTAAGCATTACGTGACTTA-T
* *
398885 TTTAAGTATTGCGTGACTTACT
1 TTTAAGCATTACGTGACTTA-T
398907 TTGT-A-CATTACGTGACTTAT
1 TT-TAAGCATTACGTGACTTAT
398927 TTTAAGCATTACGTGACTTAT
1 TTTAAGCATTACGTGACTTAT
398948 TTT
1 TTT
398951 TAGATATTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.02
20 4 0.07
21 30 0.54
22 20 0.36
23 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (21 bp):
TTTAAGCATTACGTGACTTAT
Found at i:399565 original size:58 final size:58
Alignment explanation
Indices: 399495--399608 Score: 176
Period size: 58 Copynumber: 2.0 Consensus size: 58
399485 TCCCTTCTCC
* *
399495 CTGAGCCGTTGAAACCATTACTAAAAAGTATCCAGTTACCACATTCATCATGCTGCTT
1 CTGAGCCGTTGAAAACATCACTAAAAAGTATCCAGTTACCACATTCATCATGCTGCTT
* *
399553 CTGAGCTC-TTGAAAACATCACTAGAAAGTATCTAGTTACCACATTCATCATGCTGC
1 CTGAGC-CGTTGAAAACATCACTAAAAAGTATCCAGTTACCACATTCATCATGCTGC
399609 CTGCAATCAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 50 0.98
59 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (58 bp):
CTGAGCCGTTGAAAACATCACTAAAAAGTATCCAGTTACCACATTCATCATGCTGCTT
Found at i:411947 original size:3 final size:3
Alignment explanation
Indices: 411933--411965 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
411923 TTGATAACAT
*
411933 TGA TGT TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
411966 AAACATGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:429269 original size:7 final size:7
Alignment explanation
Indices: 429259--429292 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
429249 AGATGCCAGA
*
429259 TGACAGG
1 TGACAGT
429266 TGACAGT
1 TGACAGT
429273 TGACAGT
1 TGACAGT
429280 TGACAGT
1 TGACAGT
429287 TGACAG
1 TGACAG
429293 AGCAAATTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (7 bp):
TGACAGT
Found at i:437408 original size:3 final size:3
Alignment explanation
Indices: 437400--437432 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
437390 TGGAAGCGGG
*
437400 GGA GGA GGA GGA GGA GGA GGA GGA GGA AGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
437433 CATGGCGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:454015 original size:24 final size:23
Alignment explanation
Indices: 453984--454030 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
453974 CCCATTCTCA
453984 TGCTGCTTTTGAATCAGATTTTG
1 TGCTGCTTTTGAATCAGATTTTG
* *
454007 TGCTAGCTTTTGACTCTGATTTTG
1 TGCT-GCTTTTGAATCAGATTTTG
454031 AGTCCCCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.49
Consensus pattern (23 bp):
TGCTGCTTTTGAATCAGATTTTG
Found at i:476892 original size:32 final size:32
Alignment explanation
Indices: 476856--476920 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
476846 ACGAGACAGT
*
476856 GCGCCATATCGCTTTGTCTGGTTAGAAAATGA
1 GCGCCATATAGCTTTGTCTGGTTAGAAAATGA
476888 GCGCCATATAGCTTTGTCTGGTTAGAAAATGA
1 GCGCCATATAGCTTTGTCTGGTTAGAAAATGA
476920 G
1 G
476921 AAAACTTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (32 bp):
GCGCCATATAGCTTTGTCTGGTTAGAAAATGA
Found at i:489032 original size:29 final size:27
Alignment explanation
Indices: 488988--489088 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 27
488978 TATTTAAAAA
* *
488988 AATTTAAATAAGTTTTTGTATTTTTATT
1 AATTTAATTAAATTTTT-TATTTTTATT
489016 AATTTTAATTAAATTTTTATATTTTTATTTT
1 AA-TTTAATTAAATTTTT-TATTTTTA--TT
* * *
489047 AAATTAAATAAAATTTTATTATTAATTATT
1 -AATTTAATTAAATTTT-TTATT-TTTATT
489077 AATTTAATTAAA
1 AATTTAATTAAA
489089 ATATTATAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
28 2 0.03
29 31 0.53
30 2 0.03
31 18 0.31
32 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
AATTTAATTAAATTTTTTATTTTTATT
Found at i:489089 original size:30 final size:30
Alignment explanation
Indices: 489011--489102 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
489001 TTTTGTATTT
* * *
489011 TTATTAATTTTAATTAAATTTTTATATTTTTA
1 TTATTAA-TTTAATTAAAATTTTAT-TATTAA
* *
489043 TT-TTAAATTAAATAAAATTTTATTATTAA
1 TTATTAATTTAATTAAAATTTTATTATTAA
* *
489072 TTATTAATTTAATTAAAATATTATAATTAA
1 TTATTAATTTAATTAAAATTTTATTATTAA
489102 T
1 T
489103 AATAATATAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
29 6 0.12
30 38 0.76
31 4 0.08
32 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TTATTAATTTAATTAAAATTTTATTATTAA
Found at i:489101 original size:18 final size:20
Alignment explanation
Indices: 489080--489132 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 20
489070 AATTATTAAT
*
489080 TTAATTAA-AATATTATA-A
1 TTAATTAATAATATAATATA
489098 TTAA-TAATAATATAATATA
1 TTAATTAATAATATAATATA
489117 TTAATT--TAATATAATA
1 TTAATTAATAATATAATA
489133 ATATGATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 3 0.10
18 22 0.71
19 5 0.16
20 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATTAATAATATAATATA
Found at i:489114 original size:23 final size:23
Alignment explanation
Indices: 489069--489132 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 23
489059 ATTTTATTAT
*
489069 TAAT-TATTAATTTAAT-TAAAA
1 TAATATATTAATTTAATATAATA
489090 T-AT-TA-TAA-TTAATAATAATA
1 TAATATATTAATTTAAT-ATAATA
489110 TAATATATTAATTTAATATAATA
1 TAATATATTAATTTAATATAATA
489133 ATATGATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
18 5 0.14
19 3 0.08
20 9 0.25
21 3 0.08
22 2 0.06
23 9 0.25
24 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATATATTAATTTAATATAATA
Found at i:489170 original size:8 final size:7
Alignment explanation
Indices: 489152--489185 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
489142 TTTGACATGT
489152 AAATATA
1 AAATATA
489159 AAATATTA
1 AAATA-TA
489167 AAATAT-
1 AAATATA
489173 AAATATA
1 AAATATA
489180 AAATAT
1 AAATAT
489186 TATTTAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAATATA
Found at i:489183 original size:13 final size:15
Alignment explanation
Indices: 489152--489185 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
489142 TTTGACATGT
489152 AAATATAAAATATTA
1 AAATATAAAATATTA
489167 AAATAT-AAATA-TA
1 AAATATAAAATATTA
489180 AAATAT
1 AAATAT
489186 TATTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 5 0.26
15 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATATAAAATATTA
Found at i:490522 original size:30 final size:30
Alignment explanation
Indices: 490486--490584 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 30
490476 AATTATTAGT
** * *
490486 TATAAAAATTTATTTGATTCGAAATAAAAA
1 TATAAAAATTTAAATAATTCAAAATAAAAA
*
490516 TAT-AAAATTTAAATAATTTAAAATAAAAA
1 TATAAAAATTTAAATAATTCAAAATAAAAA
* *
490545 TATAAAAATTT-AATCAAAT-ATAATAAAAA
1 TATAAAAATTTAAAT-AATTCAAAATAAAAA
490574 -ATAAAAATTTA
1 TATAAAAATTTA
490585 TTTAAACTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
28 10 0.17
29 36 0.61
30 13 0.22
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (30 bp):
TATAAAAATTTAAATAATTCAAAATAAAAA
Found at i:490569 original size:29 final size:29
Alignment explanation
Indices: 490507--490584 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
490497 ATTTGATTCG
*
490507 AAATAAAAATAT-AAAATTTAAATAATTTA
1 AAATAAAAATATAAAAATTT-AATAATATA
490536 AAATAAAAATATAAAAATTTAATCAA-ATA
1 AAATAAAAATATAAAAATTTAAT-AATATA
*
490565 TAATAAAAA-ATAAAAATTTA
1 AAATAAAAATATAAAAATTTA
490585 TTTAAACTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
28 11 0.24
29 25 0.56
30 9 0.20
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (29 bp):
AAATAAAAATATAAAAATTTAATAATATA
Found at i:491835 original size:11 final size:11
Alignment explanation
Indices: 491819--491848 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
491809 TTTTATATCT
*
491819 ATATAACATTA
1 ATATAAAATTA
491830 ATATAAAATTA
1 ATATAAAATTA
491841 ATATAAAA
1 ATATAAAA
491849 ATAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAAAATTA
Found at i:491913 original size:23 final size:23
Alignment explanation
Indices: 491855--491920 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
491845 AAAAATAAAA
*
491855 AATATT-A-CATAATCATATTATT
1 AATATTAATCATAAT-ATATTAAT
*
491877 AATATTAATTATAATATATTAAT
1 AATATTAATCATAATATATTAAT
*
491900 -ATATTATATCATAATAAATTA
1 AATATTA-ATCATAATATATTA
491921 TGATATCACA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 12 0.32
23 20 0.54
24 5 0.14
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (23 bp):
AATATTAATCATAATATATTAAT
Found at i:508849 original size:2 final size:2
Alignment explanation
Indices: 508842--508872 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
508832 ATAGATAAAT
508842 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
508873 CATACTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:524518 original size:97 final size:92
Alignment explanation
Indices: 524327--524554 Score: 262
Period size: 97 Copynumber: 2.4 Consensus size: 92
524317 CCTCACTACT
* * * *
524327 TTCC-CCCTCCCGAGTCTCGATCTGATTCTCCCCCCCCACCCGAGTCCGCCGACCTAACGAATTC
1 TTCCACCCTCCCGAGTCCCGACCTGATTCTCCCCCCCCACCCGAGTCCACCGACCTAACAAATTC
* *
524391 TCCTCCCCTCCAGCGAGTCCGACCTGA
66 CCCTCCCCTCCAGCGAGTCCGACCTAA
* *
524418 TTCCACCCTTCCCGAGTCCCGACCTGATTCTCTCCCCCCTGCCCACCGAGTCCACCGACTTAA-A
1 TTCCACCC-TCCCGAGTCCCGACCTGATTCTC-CCCCCC--CAC-CCGAGTCCACCGACCTAACA
*
524482 AATTCCCCTTCCCTCCAGCGAGTCTCGACCTAA
61 AATTCCCCTCCCCTCCAGCGAGTC-CGACCTAA
* * *
524515 TTCCACCCCCCACGAGTCCGGACCTGATTCCCGCCCCCCC
1 TTCCACCCTCC-CGAGTCCCGACCTGATTCTC-CCCCCCC
524555 CCCCCCCTAG
Statistics
Matches: 116, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
91 4 0.03
92 3 0.03
93 21 0.18
94 6 0.05
95 1 0.01
96 26 0.22
97 55 0.47
ACGTcount: A:0.16, C:0.49, G:0.14, T:0.21
Consensus pattern (92 bp):
TTCCACCCTCCCGAGTCCCGACCTGATTCTCCCCCCCCACCCGAGTCCACCGACCTAACAAATTC
CCCTCCCCTCCAGCGAGTCCGACCTAA
Found at i:524573 original size:97 final size:96
Alignment explanation
Indices: 524356--524622 Score: 283
Period size: 97 Copynumber: 2.8 Consensus size: 96
524346 ATCTGATTCT
* * * *
524356 CCCCCCCCACCCGAGTCCGCCGACCTAACGAATTCTCCTCCCCTCCAGCGAGTC-CGACCTGATT
1 CCCCCCCCCCCCGAGTCCGCCGA-CTAA-AAATTCCCCTCCCCTCCAGCGAGTCTCGACCTAATT
* * *
524420 CCACCCTTCCCGAGTCCCGACCTGATTCTCTCC
64 CCACCCTCCCCGAGTCCCGACCTGATTCCCGCC
** * * *
524453 CCCCTGCCCACCGAGTCCACCGACTTAAAAATTCCCCTTCCCTCCAGCGAGTCTCGACCTAATTC
1 CCCCCCCCCCCCGAGTCCGCCGAC-TAAAAATTCCCCTCCCCTCCAGCGAGTCTCGACCTAATTC
*
524518 CACCC-CCCACGAGTCCGGACCTGATTCCCGCC
65 CACCCTCCC-CGAGTCCCGACCTGATTCCCGCC
* * * *
524550 CCCCCCCCCCCCTAGTTCGCCGAC-ACAAAATTCCCC-CCCCTCCCA-CGAGTCTCGACATGATT
1 CCCCCCCCCCCCGAGTCCGCCGACTA-AAAATTCCCCTCCCCT-CCAGCGAGTCTCGACCTAATT
*
524612 CCCCCCTCCCC
64 CCACCCTCCCC
524623 ACACCCGAGT
Statistics
Matches: 141, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
95 26 0.18
96 41 0.29
97 74 0.52
ACGTcount: A:0.17, C:0.51, G:0.13, T:0.18
Consensus pattern (96 bp):
CCCCCCCCCCCCGAGTCCGCCGACTAAAAATTCCCCTCCCCTCCAGCGAGTCTCGACCTAATTCC
ACCCTCCCCGAGTCCCGACCTGATTCCCGCC
Found at i:559913 original size:2 final size:2
Alignment explanation
Indices: 559900--559932 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
559890 ATTTTACTAT
559900 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
559933 AGAAAAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:573780 original size:2 final size:2
Alignment explanation
Indices: 573773--573808 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
573763 AACCTAAGTC
*
573773 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
573809 GCTATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:578751 original size:2 final size:2
Alignment explanation
Indices: 578746--578776 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
578736 AGTCTCTCTC
578746 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
578777 TTGTGGAGAG
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:600860 original size:17 final size:18
Alignment explanation
Indices: 600827--600860 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
600817 TCTTTTGATT
*
600827 TTTTTAATTTTTATACAG
1 TTTTTAATTTCTATACAG
600845 TTTTTAATTTCT-TACA
1 TTTTTAATTTCTATACA
600861 AATTATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTTAATTTCTATACAG
Found at i:601252 original size:24 final size:22
Alignment explanation
Indices: 601225--601273 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
601215 GACAAATAGT
*
601225 AATTAATTTATTATTAATTATAAA
1 AATTAATTTATT-TTAA-AATAAA
*
601249 AATTTATTTATTTTAAAATAAA
1 AATTAATTTATTTTAAAATAAA
601271 AAT
1 AAT
601274 ATAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 8 0.35
23 4 0.17
24 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTAATTTATTTTAAAATAAA
Found at i:601851 original size:21 final size:22
Alignment explanation
Indices: 601796--601855 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
601786 TTAATATTTT
*
601796 AATTAATAATAA-TTAATCATAA
1 AATTAATAA-AATTTAATAATAA
* **
601818 AATTTATTTAATTTAA-AATAA
1 AATTAATAAAATTTAATAATAA
601839 AATTAATAAAATTTAAT
1 AATTAATAAAATTTAAT
601856 TAAATGTACT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTAATAAAATTTAATAATAA
Found at i:607796 original size:15 final size:15
Alignment explanation
Indices: 607776--607805 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
607766 CTCAATCGAC
607776 GACGACGAAGAAGAA
1 GACGACGAAGAAGAA
*
607791 GACGACGACGAAGAA
1 GACGACGAAGAAGAA
607806 TGCGAGCGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.33, T:0.00
Consensus pattern (15 bp):
GACGACGAAGAAGAA
Done.