Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 24
Found at i:4102163 original size:65 final size:64
Alignment explanation
Indices: 4101965--4102192 Score: 215
Period size: 65 Copynumber: 3.5 Consensus size: 64
4101955 TCAAAGATAG
* * * * * * *
4101965 TTTTATTTCAAGAGAAATAAACTCAAAGATTTTGTATTTCTAGAGAAACTGCCTCAATGGAGACA
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATTTT-T-TTTCAAAAGAAATTGTCTCAA--GAGACA
4102030 AAA
62 AAA
* * * * * * * *
4102033 -TTTGTTTTAATAGAAACGATCTCAAAGGTGGATATTTTCAAAAGAAATTGTCTCGAGAGACAAA
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT--TTTTTTTCAAAAGAAATTGTCTCAAGAGACAAA
4102097 A
64 A
* * *
4102098 TTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTTCAAAAGAAATTGTCTTTAAGAGATAAAA
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTTCAAAAGAAATTGTC-TCAAGAGACAAAA
*
4102163 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
4102193 AGATTACATC
Statistics
Matches: 129, Mismatches: 27, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
64 19 0.15
65 47 0.36
66 23 0.18
67 38 0.29
68 1 0.01
69 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (64 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTTCAAAAGAAATTGTCTCAAGAGACAAAA
Found at i:4102305 original size:120 final size:119
Alignment explanation
Indices: 4102089--4102316 Score: 289
Period size: 120 Copynumber: 1.9 Consensus size: 119
4102079 ATTGTCTCGA
** * *
4102089 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTTCAAAAGAAATTGTCTTTAA
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTAGTTTTCAAAAGAAACTGTCTTCAA
* *
4102154 GAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATAGATTACATCTTAAGT
66 GAGAGAAAAATTTGTTTCAAAAGAAACAGACTCAAAGAT-GATTACATCTTAAGT
* * * **
4102209 GAGACCAAA-TTTGTTTCAAAGGAAACAATCTCAAAGGTTGAGTTTTCATTAGAAACTGTC-TCA
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATT-AGTTTTCAAAAGAAACTGTCTTCA
* * *
4102272 AGAGAGACAAAATTTGTTTTAATAGAAATAGACTCAAAGATGATT
65 AGAGAGA-AAAATTTGTTTCAAAAGAAACAGACTCAAAGATGATT
4102317 TTGTTAAAAG
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
119 40 0.43
120 52 0.57
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (119 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTAGTTTTCAAAAGAAACTGTCTTCAA
GAGAGAAAAATTTGTTTCAAAAGAAACAGACTCAAAGATGATTACATCTTAAGT
Found at i:4103129 original size:35 final size:35
Alignment explanation
Indices: 4103034--4103137 Score: 127
Period size: 35 Copynumber: 2.9 Consensus size: 35
4103024 GTATCTCAAA
* **
4103034 AGAAAATTGTCTCAAGTGAGATGAAATTTGTTTTG
1 AGAAAATTGTCTCAAGCGAGACAAAATTTGTTTTG
* * *
4103069 AAAGAAATTGTCTCAAGCGAAACAAAATTTGTTTTT
1 AGA-AAATTGTCTCAAGCGAGACAAAATTTGTTTTG
* *
4103105 AGAAAACTATCTCAAGCGAGACAAAATTTGTTT
1 AGAAAATTGTCTCAAGCGAGACAAAATTTGTTT
4103138 AAAAATTCTC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 29 0.50
36 29 0.50
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (35 bp):
AGAAAATTGTCTCAAGCGAGACAAAATTTGTTTTG
Found at i:4103487 original size:4 final size:4
Alignment explanation
Indices: 4103478--4106389 Score: 5529
Period size: 4 Copynumber: 736.8 Consensus size: 4
4103468 TTTATATATC
4103478 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4103526 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4103574 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4103622 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4103670 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4103716 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4103764 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4103811 ATGT -TGT ATGT ATGT ATGT ATGT ATG- ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4103857 ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATG- -TGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4103901 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4103949 ATGT ATGT ATGT -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4103996 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104044 ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104090 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104138 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104186 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104234 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104282 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104330 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104378 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104425 A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104471 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104519 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104567 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
4104615 ATGGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT CTGT ATGT
1 AT-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104664 ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104711 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104759 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
4104807 ATGT ATGT CTGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104855 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104903 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104951 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4104999 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT -TGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105046 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105094 A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105141 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105189 ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105235 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105282 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105330 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105378 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105426 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105474 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105522 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105570 ATGTT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATG-T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105619 ATGT ATGT ATGT ATGT ATGT -TGT ATGT ATGT A--T ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105664 ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105711 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105759 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105807 ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105853 ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105899 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105947 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4105995 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4106043 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG-
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4106090 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4106138 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4106184 ATGT ATGT ATGT ATGT AT-T ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4106231 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4106279 A-GT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATG- -TGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4106323 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4106371 ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATG
4106390 CTTTTCTCGA
Statistics
Matches: 2865, Mismatches: 4, Indels: 78
0.97 0.00 0.03
Matches are distributed among these distances:
2 22 0.01
3 45 0.02
4 2790 0.97
5 8 0.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:4106459 original size:41 final size:41
Alignment explanation
Indices: 4106402--4106485 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
4106392 TTTCTCGATC
*
4106402 TGGAAGGAGAATTGTTGCGAGAGCAGTCTTCACTCTATCAT
1 TGGAAGGAGAATTGTTGCGAGAGCAGTCTTCACTCTATAAT
4106443 TGGAAGGAGAATTGTTGCGAGAGCAGTCTTCACTCTATAAT
1 TGGAAGGAGAATTGTTGCGAGAGCAGTCTTCACTCTATAAT
4106484 TG
1 TG
4106486 ATTCAGTTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (41 bp):
TGGAAGGAGAATTGTTGCGAGAGCAGTCTTCACTCTATAAT
Found at i:4107784 original size:26 final size:26
Alignment explanation
Indices: 4107755--4107813 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
4107745 CTTTTCTTTG
4107755 TTTTT-TT-CTTTTTTTGCACTTTGTT
1 TTTTTGTTGCTTTTTTT-CACTTTGTT
*
4107780 TTTTTGTTGCTTTTTTTCTCTTTGTT
1 TTTTTGTTGCTTTTTTTCACTTTGTT
*
4107806 TTTATGTT
1 TTTTTGTT
4107814 CTCTTCGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 17 0.57
27 8 0.27
ACGTcount: A:0.03, C:0.10, G:0.10, T:0.76
Consensus pattern (26 bp):
TTTTTGTTGCTTTTTTTCACTTTGTT
Found at i:4114510 original size:15 final size:15
Alignment explanation
Indices: 4114490--4114533 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
4114480 TGCAAACATG
4114490 TAATAA-AAAAATTAA
1 TAATAATAAAAATT-A
*
4114505 TAATAATAATAATTA
1 TAATAATAAAAATTA
4114520 TAATAATAAAAATT
1 TAATAATAAAAATT
4114534 TTAAAAAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATAATAAAAATTA
Found at i:4116512 original size:15 final size:15
Alignment explanation
Indices: 4116489--4116520 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4116479 ATTATTATGA
*
4116489 CAAATTTAATTTTGT
1 CAAAATTAATTTTGT
4116504 CAAAATTAATTTTGT
1 CAAAATTAATTTTGT
4116519 CA
1 CA
4116521 TTATCAGTAG
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:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (15 bp):
CAAAATTAATTTTGT
Found at i:4117650 original size:420 final size:416
Alignment explanation
Indices: 4117017--4117816 Score: 1158
Period size: 420 Copynumber: 1.9 Consensus size: 416
4117007 ATGTTTTAAT
* * * **
4117017 TATAGTGACAAAATATATTGTCACAAATATTTCCCTCCATATTTTTATGCGCCAAAAATGTCATA
1 TATAGTAACAAAATATATTGTCACAAAAATTTCCCTCCATATTTTTATGCGCAAAAAAAATCATA
* * *
4117082 TAGTGACAAATTTTGTAACTATAAGTGTTAATAATTATTAAAAAAAATATTGTAATAAAAAATAA
66 TAGTAACAAATTTTGTAACTATAAGTGTTAATAATTATTAAAAAAAACATTGTAACAAAAAATAA
* * * *
4117147 TGCTATTCACGTTTTTGTGACAAATTATATTTGTAGTTATAAATTTTAGCTATAGTGATAGCATA
131 TGCTATTCACGTTTTTGTGACAAATTATATGTGTAGTTATAAATTTTAACTATAGAGATAACATA
* * *
4117212 TATTGTCATAACTATTTTTTCTCAAC-TTTTTTGTTTC-AAAATTTATATTGACAATTTTTATAA
196 TATTGTCATAAATA-TTTTTCTCAACTTTTTTTATTTCAAAAATTTATATTGACAAGTTTTATAA
4117275 TTATAATTTATAGTTATTGTTATAG-AAAAAATTATCACATCAAATAATAAAATTCAAAATTTTT
260 TTATAATTTATAGTTATT-TTATAGAAAAAAATTATCACATCAAATAATAAAATTC-AAATTTTT
4117339 TATAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCAGAACATT
323 TATAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCAGAACATT
4117404 TCTCCCTATTTTTAGTGTCAAAATTGTTA
388 TCTCCCTATTTTTAGTGTCAAAATTGTTA
* * * * *
4117433 TATAGTAACAAAATATATTGTCATAAAAATTTTCCTCTATATTTTTTTGTGCAAAAAAAAAATCA
1 TATAGTAACAAAATATATTGTCACAAAAATTTCCCTCCATATTTTTATGCGC--AAAAAAAATCA
* * * *
4117498 TATAGTAAC-AATTTTCGTAACTATAAGTGTTTATAATTATTACGAAATAACATTGTCACAAAAA
64 TATAGTAACAAATTTT-GTAACTATAAGTGTTAATAATTATTA-AAAAAAACATTGTAACAAAAA
* * *
4117562 ATAATGGTATTCACATTTTTTGTGACAAATTATATGTGTAGTTATAAATTTTAATTATAGAGATA
127 ATAATGCTATTCAC-GTTTTTGTGACAAATTATATGTGTAGTTATAAATTTTAACTATAGAGATA
* * * * *
4117627 ACATGTTTTGTGATAAATATTTTTCTCCACTTTTTTTATTTCAAAAATTTATATTGATAAGTTTT
191 ACATATATTGTCATAAATATTTTTCTCAACTTTTTTTATTTCAAAAATTTATATTGACAAGTTTT
* * * *
4117692 GTAATTATAATTTATAGTTATTTTATAGAAAAAAATTATCACATTAGATAATAAAATTCAAGTTT
256 ATAATTATAATTTATAGTTATTTTATAGAAAAAAATTATCACATCAAATAATAAAATTCAAATTT
* *
4117757 TTTGTAATAAATTATTTTTGTAGTTATATATTTTAATCATTATGAAAAATTATACTATCA
321 TTTATAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCA
4117817 ACAAAAATAA
Statistics
Matches: 338, Mismatches: 38, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
416 45 0.13
417 6 0.02
418 41 0.12
419 39 0.12
420 138 0.41
421 69 0.20
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (416 bp):
TATAGTAACAAAATATATTGTCACAAAAATTTCCCTCCATATTTTTATGCGCAAAAAAAATCATA
TAGTAACAAATTTTGTAACTATAAGTGTTAATAATTATTAAAAAAAACATTGTAACAAAAAATAA
TGCTATTCACGTTTTTGTGACAAATTATATGTGTAGTTATAAATTTTAACTATAGAGATAACATA
TATTGTCATAAATATTTTTCTCAACTTTTTTTATTTCAAAAATTTATATTGACAAGTTTTATAAT
TATAATTTATAGTTATTTTATAGAAAAAAATTATCACATCAAATAATAAAATTCAAATTTTTTAT
AATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCAGAACATTTCT
CCCTATTTTTAGTGTCAAAATTGTTA
Found at i:4118347 original size:29 final size:29
Alignment explanation
Indices: 4118305--4118373 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
4118295 ATTCTACTTC
4118305 ACTCTCAACCCAACCTAAAAAACTAATAT
1 ACTCTCAACCCAACCTAAAAAACTAATAT
4118334 ACTCTCAACCCAACCTAAAAAACTAATAT
1 ACTCTCAACCCAACCTAAAAAACTAATAT
4118363 ACTCTCAACCC
1 ACTCTCAACCC
4118374 CTCTCACGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (29 bp):
ACTCTCAACCCAACCTAAAAAACTAATAT
Found at i:4119969 original size:32 final size:32
Alignment explanation
Indices: 4119932--4120014 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 32
4119922 AACAAATTAA
*
4119932 ATTTAGTTAAAATAAAATATTATATCAAAACT
1 ATTTAGTTAAAATAAAAAATTATATCAAAACT
*
4119964 ATTTAGTTAAAATAAAAAATTATATCAAAATT
1 ATTTAGTTAAAATAAAAAATTATATCAAAACT
* *
4119996 ATGTAGTCAAAATAAAAAA
1 ATTTAGTTAAAATAAAAAA
4120015 AAATTGACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (32 bp):
ATTTAGTTAAAATAAAAAATTATATCAAAACT
Found at i:4120140 original size:98 final size:96
Alignment explanation
Indices: 4120023--4120347 Score: 234
Period size: 98 Copynumber: 3.3 Consensus size: 96
4120013 AAAAATTGAC
* *
4120023 AAATTTTTTAATCAAAATAATAATTTATAACAAATATTAATTTCTCAATATAAAAAAATGTGACA
1 AAATTATTTAATCAAAATAATAATTTATAACAAATATTAATTTCTCAATAT-AAAATATGTGACA
4120088 AGTAATATTCTTTCACAATAACAAATTGTAACA
65 A-TAATATTCTTTCACAATAACAAATTGTAACA
* * * * ** * **
4120121 AAATGATTTAGTCACAATAACACGTTAACTTTA-ATCAAAATAAAAAGTTATGTCAA-AT-TTAT
1 AAATTATTTAATCAAAAT-A-A---TAA-TTTATAAC-AAATATTAA-TT-TCTCAATATAAAAT
* * * * * *
4120183 TTCT-TC-ATAATATT-TTGTCAAAATAGA-AAATTGTGAGA
57 ATGTGACAATAATATTCTT-TCACAATA-ACAAATTGTAACA
* * * *
4120221 AATTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTTATTATGAAAATATGTGACA
1 AAATTATTTAATCAAAATAATAATTTATAACAAATATTAATTTCTCAATAT-AAAATATGTGAC-
4120286 AATAATATTCTTTCACAATAACAAATTGTAAC-
64 AATAATATTCTTTCACAATAACAAATTGTAACA
* * * *
4120318 AAATTATTTAGTCACAATAAAAAATTATAA
1 AAATTATTTAATCAAAATAATAATTTATAA
4120348 AAAAAAATAT
Statistics
Matches: 166, Mismatches: 41, Indels: 41
0.67 0.17 0.17
Matches are distributed among these distances:
92 3 0.02
93 4 0.02
94 11 0.07
95 8 0.05
96 1 0.01
97 26 0.16
98 38 0.23
99 6 0.04
100 38 0.23
101 2 0.01
102 1 0.01
103 8 0.05
104 11 0.07
105 4 0.02
106 5 0.03
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (96 bp):
AAATTATTTAATCAAAATAATAATTTATAACAAATATTAATTTCTCAATATAAAATATGTGACAA
TAATATTCTTTCACAATAACAAATTGTAACA
Found at i:4129340 original size:24 final size:24
Alignment explanation
Indices: 4129311--4129360 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4129301 TGGTGGTTGA
4129311 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAACTTTATT
* *
4129335 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTGAACTTTATT
4129359 TT
1 TT
4129361 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAACTTTATT
Found at i:4136253 original size:19 final size:21
Alignment explanation
Indices: 4136216--4136258 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
4136206 TAACTTTTTG
*
4136216 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
4136236 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
4136256 TTT
1 TTT
4136259 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:4139499 original size:24 final size:24
Alignment explanation
Indices: 4139472--4139521 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4139462 TGGTGGTTGA
*
4139472 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTCAACTTTATT
*
4139496 TTTAATGGTGTATTCAATTTTATT
1 TTTAATGGTGTATTCAACTTTATT
4139520 TT
1 TT
4139522 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.04, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTCAACTTTATT
Found at i:4142379 original size:28 final size:30
Alignment explanation
Indices: 4142328--4142390 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 30
4142318 AACTGCACAA
* **
4142328 AAATTATTAAATAAAATA-TTAAAAAT-TT
1 AAATAATTAAATAAAATACAAAAAAATATT
4142356 AAATAATTAAATAAAATACAAAAAAATATT
1 AAATAATTAAATAAAATACAAAAAAATATT
4142386 AAATA
1 AAATA
4142391 TAATAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 17 0.57
29 6 0.20
30 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (30 bp):
AAATAATTAAATAAAATACAAAAAAATATT
Found at i:4142865 original size:21 final size:21
Alignment explanation
Indices: 4142839--4142888 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
4142829 ACCGTGGAGA
4142839 AGCCAATGCTAAATAGTGTCT
1 AGCCAATGCTAAATAGTGTCT
4142860 AGCCAATGCTAAATAGTGTCT
1 AGCCAATGCTAAATAGTGTCT
4142881 AGCCAATG
1 AGCCAATG
4142889 AAAATCGGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (21 bp):
AGCCAATGCTAAATAGTGTCT
Found at i:4144554 original size:17 final size:17
Alignment explanation
Indices: 4144506--4144554 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 17
4144496 AAATTTAAAT
*
4144506 AAATAATAATTATATAA
1 AAATAATATTTATATAA
* *
4144523 ATATTAT-TTTA-ATAA
1 AAATAATATTTATATAA
4144538 AAATAATATTTATATAA
1 AAATAATATTTATATAA
4144555 TTATATTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
15 9 0.36
16 7 0.28
17 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAATATTTATATAA
Found at i:4144576 original size:32 final size:32
Alignment explanation
Indices: 4144506--4144578 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
4144496 AAATTTAAAT
*
4144506 AAATAATAATTATATAAATATTATTTTAATAA
1 AAATAATAATTATATAAATATTATTATAATAA
* *
4144538 AAATAATATTTATATAATTA-TATTA-ATATAA
1 AAATAATAATTATATAAATATTATTATA-ATAA
4144569 AATATAATAA
1 AA-ATAATAA
4144579 CTGAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
30 1 0.03
31 10 0.29
32 24 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
AAATAATAATTATATAAATATTATTATAATAA
Found at i:4145254 original size:20 final size:21
Alignment explanation
Indices: 4145229--4145270 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4145219 AAACTATGTG
4145229 GTTGAA-GAGG-GTTCTTTGGT
1 GTTGAAGGAGGCG-TCTTTGGT
4145249 GTTGAAGGAGGCGTCTTTGGT
1 GTTGAAGGAGGCGTCTTTGGT
4145270 G
1 G
4145271 ACTCAGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 13 0.65
22 1 0.05
ACGTcount: A:0.14, C:0.07, G:0.43, T:0.36
Consensus pattern (21 bp):
GTTGAAGGAGGCGTCTTTGGT
Found at i:4151331 original size:17 final size:17
Alignment explanation
Indices: 4151297--4151355 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
4151287 TAACATGAAG
*
4151297 ATAAAAAGATAAAGAAA
1 ATAAAAAGATAAAAAAA
*
4151314 ATAAAAAGAAATAAAAAA
1 ATAAAAAGATA-AAAAAA
*
4151332 AT-ACAA-ATAAAAATGAA
1 ATAAAAAGATAAAAA--AA
4151349 ATAAAAA
1 ATAAAAA
4151356 TGAAAACATA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
15 4 0.12
16 2 0.06
17 17 0.52
18 10 0.30
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.14
Consensus pattern (17 bp):
ATAAAAAGATAAAAAAA
Found at i:4151356 original size:17 final size:19
Alignment explanation
Indices: 4151311--4151371 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 19
4151301 AAAGATAAAG
*
4151311 AAAATAAAAA-GAAATA-AA
1 AAAATAAAAATGAAA-ACAT
*
4151329 AAAATACAAAT-AAAA-AT
1 AAAATAAAAATGAAAACAT
*
4151346 GAAATAAAAATGAAAACAT
1 AAAATAAAAATGAAAACAT
4151365 AAAATAA
1 AAAATAA
4151372 TAATTAAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 11 0.31
18 16 0.46
19 8 0.23
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAATAAAAATGAAAACAT
Found at i:4153935 original size:24 final size:20
Alignment explanation
Indices: 4153908--4153965 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
4153898 GCATGGGTAG
4153908 TGCATCGATACACATGTTAAAGAA
1 TGCATCGATACAC-TG-T--AGAA
*
4153932 TGCATCGATGCACTGTAGAA
1 TGCATCGATACACTGTAGAA
*
4153952 TGCATCGATGCACT
1 TGCATCGATACACT
4153966 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 18 0.55
22 1 0.03
23 2 0.06
24 12 0.36
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCATCGATACACTGTAGAA
Found at i:4153953 original size:20 final size:20
Alignment explanation
Indices: 4153928--4153965 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4153918 CACATGTTAA
4153928 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
4153948 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
4153966 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:4154800 original size:31 final size:31
Alignment explanation
Indices: 4154738--4154802 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
4154728 AGAGTCGAGG
* *
4154738 GTTTACCTATGTCTTTCGAGACATATGGACA
1 GTTTACCTAGGTCTTTCGAGACATATAGACA
* *
4154769 GTTTACCTAGGT-TCTTCGGGACCTATAGACA
1 GTTTACCTAGGTCT-TTCGAGACATATAGACA
4154800 GTT
1 GTT
4154803 GCCGAGGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATAGACA
Found at i:4154822 original size:30 final size:29
Alignment explanation
Indices: 4154788--4154851 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
4154778 GGTTCTTCGG
*
4154788 GACCTATAGACAGTTGCCGAGGTTCTTTAT
1 GACCTATAGACAGTTGCCG-GGGTCTTTAT
* * * *
4154818 GACCTATGGATAGTTGTCGGGGTCTTTGT
1 GACCTATAGACAGTTGCCGGGGTCTTTAT
4154847 GACCT
1 GACCT
4154852 CTGGATAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (29 bp):
GACCTATAGACAGTTGCCGGGGTCTTTAT
Found at i:4158710 original size:31 final size:31
Alignment explanation
Indices: 4158675--4158740 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
4158665 AAGAGTCGAG
*
4158675 AGTTTACCTA-TTTCTTTCGAGACATATGGAC
1 AGTTTACCTAGGTTC-TTCGAGACATATGGAC
* *
4158706 AGTTTACCTAGGTTCTTCGGGACCTATGGAC
1 AGTTTACCTAGGTTCTTCGAGACATATGGAC
4158737 AGTT
1 AGTT
4158741 GTCGAGGTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (31 bp):
AGTTTACCTAGGTTCTTCGAGACATATGGAC
Found at i:4158760 original size:30 final size:29
Alignment explanation
Indices: 4158726--4158794 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
4158716 GGTTCTTCGG
* *
4158726 GACCTATGGACAGTTGTCGAGGTTCTTTAT
1 GACCTCTGGACAGTTGTCG-GGGTCTTTAT
* * *
4158756 GACCTCTAGATAGTTGTCGGGGTCTTTGT
1 GACCTCTGGACAGTTGTCGGGGTCTTTAT
4158785 GACCTCTGGA
1 GACCTCTGGA
4158795 TAGGTCCTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (29 bp):
GACCTCTGGACAGTTGTCGGGGTCTTTAT
Found at i:4158790 original size:29 final size:30
Alignment explanation
Indices: 4158737--4158797 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
4158727 ACCTATGGAC
*
4158737 AGTTGTCGAGGTTCTTTATGACCTCTAGAT
1 AGTTGTCGAGGGTCTTTATGACCTCTAGAT
* *
4158767 AGTTGTCG-GGGTCTTTGTGACCTCTGGAT
1 AGTTGTCGAGGGTCTTTATGACCTCTAGAT
4158796 AG
1 AG
4158798 GTCCTTCGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.16, C:0.16, G:0.30, T:0.38
Consensus pattern (30 bp):
AGTTGTCGAGGGTCTTTATGACCTCTAGAT
Found at i:4159788 original size:183 final size:184
Alignment explanation
Indices: 4159480--4159847 Score: 729
Period size: 183 Copynumber: 2.0 Consensus size: 184
4159470 TCTGTAAATG
4159480 TTTTGAATAAGTTATATGTATAAAAAATTTAAATTACTCACTATTTTATACAAGTAAATGTTTTG
1 TTTTGAATAAGTTATATGTATAAAAAATTTAAATTACTCACTATTTTATACAAGTAAATGTTTTG
4159545 AAAAGTCAATGTGACACCTCGGACTCGGATACGGGTTGGGGTGTTACAGTTGAAATCCGATATTA
66 AAAAGTCAATGTGACACCTCGGACTCGGATACGGGTTGGGGTGTTACAGTTGAAATCCGATATTA
4159610 A-ACCAATTTGTTGATTTGGATTGAATCACGAAATAACTCCCTCATCGTGAGGT
131 AGACCAATTTGTTGATTTGGATTGAATCACGAAATAACTCCCTCATCGTGAGGT
4159663 TTTTGAATAAGTTATATGTATAAAAAATTTAAATTACTCACTATTTTATACAAGTAAATGTTTTG
1 TTTTGAATAAGTTATATGTATAAAAAATTTAAATTACTCACTATTTTATACAAGTAAATGTTTTG
4159728 AAAAGTCAATGTGACACCTCGGACTCGGATACGGGTTGGGGTGTTACAGTTGAAATCCGATATTA
66 AAAAGTCAATGTGACACCTCGGACTCGGATACGGGTTGGGGTGTTACAGTTGAAATCCGATATTA
4159793 AGACCAATTTGTTGATTTGGATTGAATCACGAAATAACTCCCTCATCGTGAGGT
131 AGACCAATTTGTTGATTTGGATTGAATCACGAAATAACTCCCTCATCGTGAGGT
4159847 T
1 T
4159848 GAGTCAAACT
Statistics
Matches: 184, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
183 131 0.71
184 53 0.29
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (184 bp):
TTTTGAATAAGTTATATGTATAAAAAATTTAAATTACTCACTATTTTATACAAGTAAATGTTTTG
AAAAGTCAATGTGACACCTCGGACTCGGATACGGGTTGGGGTGTTACAGTTGAAATCCGATATTA
AGACCAATTTGTTGATTTGGATTGAATCACGAAATAACTCCCTCATCGTGAGGT
Found at i:4172138 original size:17 final size:17
Alignment explanation
Indices: 4172116--4172174 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
4172106 CAATATGAAG
4172116 ATAAAAAGATAAAGAAA
1 ATAAAAAGATAAAGAAA
4172133 ATAAAAAGGAATAAA-AAA
1 ATAAAAA-G-ATAAAGAAA
*
4172151 ATACAAATA-AAAAAG-AA
1 ATA-AAA-AGATAAAGAAA
4172168 ATAAAAA
1 ATAAAAA
4172175 TAAAAATGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
15 1 0.03
16 3 0.08
17 16 0.44
18 7 0.19
19 8 0.22
20 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (17 bp):
ATAAAAAGATAAAGAAA
Found at i:4172175 original size:17 final size:17
Alignment explanation
Indices: 4172126--4172185 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
4172116 ATAAAAAGAT
*
4172126 AAAGAAAATAAAAAGGAATA
1 AAAG-AAATAAAAA-TAA-A
*
4172146 AAA-AAATACAAATAAA
1 AAAGAAATAAAAATAAA
4172162 AAAGAAATAAAAATAAA
1 AAAGAAATAAAAATAAA
*
4172179 AATGAAA
1 AAAGAAA
4172186 ACATAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 4 0.11
17 20 0.57
18 8 0.23
20 3 0.09
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (17 bp):
AAAGAAATAAAAATAAA
Found at i:4172186 original size:7 final size:6
Alignment explanation
Indices: 4172147--4172193 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
4172137 AAAGGAATAA
* *
4172147 AAAAAT ACAAAT AAAAA- AGAAAT AAAAAT AAAAAT GAAAACAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAA-AT AAAA
4172194 TAATAACTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
5 4 0.12
6 20 0.59
7 8 0.24
8 2 0.06
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:4172186 original size:24 final size:24
Alignment explanation
Indices: 4172130--4172186 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
4172120 AAAGATAAAG
*
4172130 AAAATAAAAAGGAATAAAAAAATA
1 AAAATAAAAAAGAATAAAAAAATA
* *
4172154 CAAATAAAAAAGAA-ATAAAAATA
1 AAAATAAAAAAGAATAAAAAAATA
*
4172177 AAAATGAAAA
1 AAAATAAAAA
4172187 CATAAAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (24 bp):
AAAATAAAAAAGAATAAAAAAATA
Found at i:4172465 original size:12 final size:12
Alignment explanation
Indices: 4172450--4172518 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 12
4172440 ACAAATATAT
4172450 AAAATAATAATAA
1 AAAATAATAAT-A
*
4172463 AAAACAATAATA
1 AAAATAATAATA
*
4172475 AAAACAA-AATA
1 AAAATAATAATA
4172486 AAAA-ACATAATTA
1 AAAATA-ATAA-TA
*
4172499 AATATAGATAATA
1 AAAATA-ATAATA
4172512 ATAAATA
1 A-AAATA
4172519 TGCTATTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
10 1 0.02
11 9 0.19
12 10 0.21
13 18 0.38
14 9 0.19
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.22
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:4172471 original size:13 final size:13
Alignment explanation
Indices: 4172450--4172496 Score: 64
Period size: 12 Copynumber: 3.8 Consensus size: 13
4172440 ACAAATATAT
*
4172450 AAAATAATAATAA
1 AAAACAATAATAA
4172463 AAAACAATAAT-A
1 AAAACAATAATAA
4172475 AAAACAA-AATAA
1 AAAACAATAATAA
4172487 AAAAC-ATAAT
1 AAAACAATAAT
4172497 TAAATATAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
11 4 0.13
12 17 0.55
13 10 0.32
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAACAATAATAA
Found at i:4172475 original size:24 final size:25
Alignment explanation
Indices: 4172443--4172512 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
4172433 TATATATACA
4172443 AATATATAAAATA-ATAATAAAAAAC
1 AATA-ATAAAATACATAATAAAAAAC
*
4172468 AATAATAAAA-ACAAAATAAAAAAC
1 AATAATAAAATACATAATAAAAAAC
*
4172492 -ATAATTAAATATAGATAATAA
1 AATAA-TAAA-ATACATAATAA
4172513 TAAATATGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.13
24 21 0.55
25 5 0.13
26 7 0.18
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.23
Consensus pattern (25 bp):
AATAATAAAATACATAATAAAAAAC
Found at i:4172489 original size:11 final size:12
Alignment explanation
Indices: 4172450--4172489 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 12
4172440 ACAAATATAT
*
4172450 AAAATAATAATAA
1 AAAACAATAAT-A
4172463 AAAACAATAATA
1 AAAACAATAATA
4172475 AAAACAA-AATA
1 AAAACAATAATA
4172486 AAAA
1 AAAA
4172490 ACATAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 8 0.31
12 8 0.31
13 10 0.38
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAACAATAATA
Found at i:4173506 original size:17 final size:17
Alignment explanation
Indices: 4173484--4173516 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4173474 GAACCGGTCC
4173484 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
4173501 GACCCGACCCGACCGT
1 GACCCGACCCGACCGT
4173517 AAACCGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.48, G:0.24, T:0.09
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:4173585 original size:29 final size:29
Alignment explanation
Indices: 4173527--4173588 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
4173517 AAACCGTTAA
**
4173527 TATTCTGGGAATTAATTCGATTTTGGTGC
1 TATTCTGGGAATTAATTCGATAATGGTGC
4173556 TATTCTGGGAATTAATTCGA-AATGGATGC
1 TATTCTGGGAATTAATTCGATAATGG-TGC
4173585 TATT
1 TATT
4173589 TTGGTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (29 bp):
TATTCTGGGAATTAATTCGATAATGGTGC
Found at i:4173722 original size:29 final size:29
Alignment explanation
Indices: 4173624--4173723 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 29
4173614 GGTTATATTG
* * *
4173624 AATTAATTCG-AAAG-ATGTTATTTTGGG
1 AATTAATTTGAAAAGTATGCTATTTTGGT
** *
4173651 AATTAATTCAAAAAGTGTGCTATTTTGGT
1 AATTAATTTGAAAAGTATGCTATTTTGGT
4173680 AATTAATTTGAAAAGTATGCTATTTTGGT
1 AATTAATTTGAAAAGTATGCTATTTTGGT
* * *
4173709 TATTATTTTTAAAAG
1 AATTAATTTGAAAAG
4173724 GGGTGTTATT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
27 9 0.15
28 4 0.07
29 48 0.79
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (29 bp):
AATTAATTTGAAAAGTATGCTATTTTGGT
Found at i:4174462 original size:24 final size:24
Alignment explanation
Indices: 4174435--4174495 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
4174425 TACCTGATTG
4174435 TTGACCTGGATTCAAATATGATAC
1 TTGACCTGGATTCAAATATGATAC
* ***
4174459 TTGACCTGAATTTTTATATGATAC
1 TTGACCTGGATTCAAATATGATAC
*
4174483 TTGACATGGATTC
1 TTGACCTGGATTC
4174496 TGATTTGTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (24 bp):
TTGACCTGGATTCAAATATGATAC
Found at i:4178078 original size:13 final size:14
Alignment explanation
Indices: 4178060--4178090 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4178050 AATTCTCATA
4178060 TATTTTA-AATTTT
1 TATTTTATAATTTT
4178073 TATTTTATAATTTT
1 TATTTTATAATTTT
4178087 TATT
1 TATT
4178091 AATAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTTATAATTTT
Found at i:4178354 original size:22 final size:24
Alignment explanation
Indices: 4178314--4178366 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
4178304 TGAGTCGAGT
*
4178314 AATAAAAGTTTCAATATTTTT-TA
1 AATAAAAGTTTAAATATTTTTGTA
*
4178337 AATAAAA-TTTAAATATTTTTGTG
1 AATAAAAGTTTAAATATTTTTGTA
4178360 AATAAAA
1 AATAAAA
4178367 AATATTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (24 bp):
AATAAAAGTTTAAATATTTTTGTA
Found at i:4182993 original size:24 final size:24
Alignment explanation
Indices: 4182953--4183053 Score: 112
Period size: 24 Copynumber: 4.2 Consensus size: 24
4182943 TGATTCACAT
* * *
4182953 GTTTATCGACTCATTTATAAGTTC
1 GTTTATCTACTCGTTTATAAGCTC
* * *
4182977 GTTTATCTACTTGTTTATAAACTA
1 GTTTATCTACTCGTTTATAAGCTC
* *
4183001 GTTTATCTACTCGTCTATAAGTTC
1 GTTTATCTACTCGTTTATAAGCTC
* *
4183025 ATTTATCTACTCATTTATAAGCTC
1 GTTTATCTACTCGTTTATAAGCTC
4183049 GTTTA
1 GTTTA
4183054 CTCGATTCTC
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.48
Consensus pattern (24 bp):
GTTTATCTACTCGTTTATAAGCTC
Found at i:4183020 original size:48 final size:48
Alignment explanation
Indices: 4182953--4183058 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 48
4182943 TGATTCACAT
* * **
4182953 GTTTATCGACTCATTTATAAGTTCGTTTATCTACTTGTTTATAAACTA
1 GTTTATCGACTCATCTATAAGTTCATTTATCTACTCATTTATAAACTA
* * * *
4183001 GTTTATCTACTCGTCTATAAGTTCATTTATCTACTCATTTATAAGCTC
1 GTTTATCGACTCATCTATAAGTTCATTTATCTACTCATTTATAAACTA
4183049 GTTTACTCGA
1 GTTTA-TCGA
4183059 TTCTCTTTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
48 45 0.94
49 3 0.06
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.46
Consensus pattern (48 bp):
GTTTATCGACTCATCTATAAGTTCATTTATCTACTCATTTATAAACTA
Found at i:4183284 original size:23 final size:23
Alignment explanation
Indices: 4183258--4183301 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4183248 TTAACACAAA
*
4183258 CATGTACATGAACATTAAACGGT
1 CATGTACATGAACACTAAACGGT
* *
4183281 CATGTTCTTGAACACTAAACG
1 CATGTACATGAACACTAAACG
4183302 AACGAACACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (23 bp):
CATGTACATGAACACTAAACGGT
Found at i:4184857 original size:22 final size:22
Alignment explanation
Indices: 4184826--4184876 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
4184816 GCCACGACTG
*
4184826 ATCAAGATGACACTTATTTGTT
1 ATCATGATGACACTTATTTGTT
*
4184848 ATTATGATGACACTTATTTGTT
1 ATCATGATGACACTTATTTGTT
4184870 ATCATGA
1 ATCATGA
4184877 CGATCTTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (22 bp):
ATCATGATGACACTTATTTGTT
Found at i:4185834 original size:2 final size:2
Alignment explanation
Indices: 4185827--4185861 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4185817 AATCACTTGG
4185827 AT 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 AT A
4185862 ATTCTATAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4186877 original size:2 final size:2
Alignment explanation
Indices: 4186863--4186916 Score: 92
Period size: 2 Copynumber: 27.0 Consensus size: 2
4186853 TAACAAATAC
4186863 AT AT AT ACT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4186905 AT AT AT AT AT AT
1 AT AT AT AT AT AT
4186917 GTTTAGCATT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4189658 original size:23 final size:21
Alignment explanation
Indices: 4189614--4189661 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
4189604 ACTGGTATAG
*
4189614 TTTACCTTTTATTTTAAATAA
1 TTTACCTTTAATTTTAAATAA
*
4189635 TTTACCTTTAAATATTTAATTAA
1 TTTACCTTT-AAT-TTTAAATAA
4189658 TTTA
1 TTTA
4189662 TAATTATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 2 0.09
23 12 0.52
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTACCTTTAATTTTAAATAA
Found at i:4189998 original size:6 final size:7
Alignment explanation
Indices: 4189978--4190003 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4189968 TTAATTTATT
4189978 AATAAAA
1 AATAAAA
4189985 AATAAAA
1 AATAAAA
4189992 AATAAAA
1 AATAAAA
4189999 AATAA
1 AATAA
4190004 TACGTTAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AATAAAA
Found at i:4190035 original size:18 final size:19
Alignment explanation
Indices: 4190017--4190072 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 19
4190007 GTTAACTAAT
4190017 ATATTATTTTTAATAAATA
1 ATATTATTTTTAATAAATA
* * *
4190036 ATAAAATATTATTAATTAATA
1 AT--ATTATTTTTAATAAATA
4190057 ATATTA-TTTTAATAAA
1 ATATTATTTTTAATAAA
4190073 AAACTCAACC
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 8 0.28
19 5 0.17
21 16 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATTATTTTTAATAAATA
Found at i:4190067 original size:39 final size:39
Alignment explanation
Indices: 4189991--4190072 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
4189981 AAAAAATAAA
4189991 AAATAAAAAATAATACGTTAACTAATATATTATTTTTAAT
1 AAATAAAAAATAATAC-TTAACTAATATATTATTTTTAAT
* *
4190031 AAATAATAAAATATTA-TTAATTAATAATATTA-TTTTAAT
1 AAATAA-AAAATAATACTTAACTAAT-ATATTATTTTTAAT
4190070 AAA
1 AAA
4190073 AAACTCAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
39 18 0.47
40 12 0.32
41 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (39 bp):
AAATAAAAAATAATACTTAACTAATATATTATTTTTAAT
Found at i:4191065 original size:2 final size:2
Alignment explanation
Indices: 4191058--4191086 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4191048 ATATCCAAAT
4191058 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4191087 GTTAGTGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4191371 original size:59 final size:59
Alignment explanation
Indices: 4191298--4191418 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
4191288 AATAGATGGA
* * *
4191298 TAAGTGTCTTATCGAACCCTCATAGTTGCAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCGAACCCTCATAGTCGCAATGAAAAGACAAACTCGATAATATGGCTC
*
4191357 TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGACAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCGAACCCTCATAGTCGCAATGAAAAGACAAACTCGATAATATGGCTC
4191416 TAA
1 TAA
4191419 ACAACCCTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (59 bp):
TAAGTGTCCTATCGAACCCTCATAGTCGCAATGAAAAGACAAACTCGATAATATGGCTC
Found at i:4197370 original size:13 final size:12
Alignment explanation
Indices: 4197354--4197393 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
4197344 CAATTTTTGA
4197354 TTTTTTTGGTATT
1 TTTTTTTGGT-TT
4197367 TTTTTTTGGTTT
1 TTTTTTTGGTTT
4197379 TTTATTTT-GTTT
1 TTT-TTTTGGTTT
4197391 TTT
1 TTT
4197394 AAAAAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.05, C:0.00, G:0.12, T:0.82
Consensus pattern (12 bp):
TTTTTTTGGTTT
Found at i:4197476 original size:10 final size:11
Alignment explanation
Indices: 4197461--4197489 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
4197451 AACTTGAAAC
4197461 GATACCAAT-T
1 GATACCAATCT
4197471 GATACCAATCT
1 GATACCAATCT
4197482 GATACCAA
1 GATACCAA
4197490 GAATCAGCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (11 bp):
GATACCAATCT
Found at i:4197780 original size:59 final size:59
Alignment explanation
Indices: 4197688--4197808 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 59
4197678 AATAGATGGA
4197688 TAAGTGTCCTATCAAACCCTCACAGACCCAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCAAACCCTCACAGACCCAATGAAAAGGCAAACTCGATAATATGGCTC
* * * * * *
4197747 TAAGTGTCCTATCGAACCCTCATAGTCGCAATGAAAAGGCAAACTTGATAATATGGTTC
1 TAAGTGTCCTATCAAACCCTCACAGACCCAATGAAAAGGCAAACTCGATAATATGGCTC
4197806 TAA
1 TAA
4197809 CCAACCCTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (59 bp):
TAAGTGTCCTATCAAACCCTCACAGACCCAATGAAAAGGCAAACTCGATAATATGGCTC
Found at i:4199291 original size:24 final size:25
Alignment explanation
Indices: 4199251--4199297 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
4199241 AACTCAAAAA
4199251 AAAATTAGAAGCTCGATTGAAGCCT
1 AAAATTAGAAGCTCGATTGAAGCCT
*
4199276 AAAATTCG-AGCTCGATTGAAGC
1 AAAATTAGAAGCTCGATTGAAGC
4199298 GAAAGAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (25 bp):
AAAATTAGAAGCTCGATTGAAGCCT
Found at i:4200011 original size:6 final size:6
Alignment explanation
Indices: 4200000--4200033 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
4199990 AAAAAAAGCT
* *
4200000 GAAAGA GAAAGA GAAAGA GAAAAA GAAAAA GAAA
1 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GAAA
4200034 AAGGAAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:4200017 original size:12 final size:12
Alignment explanation
Indices: 4200000--4200036 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
4199990 AAAAAAAGCT
*
4200000 GAAAGAGAAAGA
1 GAAAGAGAAAAA
4200012 GAAAGAGAAAAA
1 GAAAGAGAAAAA
*
4200024 GAAAAAGAAAAA
1 GAAAGAGAAAAA
4200036 G
1 G
4200037 GAAATCCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAAGAGAAAAA
Found at i:4200254 original size:30 final size:30
Alignment explanation
Indices: 4200204--4200292 Score: 71
Period size: 30 Copynumber: 3.0 Consensus size: 30
4200194 CGACCCGATA
4200204 AATATTAA-AAATAATT-ATTTATATATATAT
1 AATATTAATAAAT--TTAATTTATATATATAT
* *
4200234 AATATTAATAAATTTAATTTA-A-ATAAAA
1 AATATTAATAAATTTAATTTATATATATAT
* * *
4200262 AATATATATTTAATTTAA-ATATATATATAT
1 AATAT-TAATAAATTTAATTTATATATATAT
4200292 A
1 A
4200293 CCCGGCCCGA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
28 11 0.23
29 14 0.30
30 18 0.38
31 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
AATATTAATAAATTTAATTTATATATATAT
Found at i:4200259 original size:24 final size:26
Alignment explanation
Indices: 4200232--4200292 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 26
4200222 TTATATATAT
*
4200232 ATAATATTAATA-A-ATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
4200256 ATAA-A-AAATATATATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
*
4200280 AT-ATATATATATA
1 ATAATATAAATATA
4200293 CCCGGCCCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 4 0.13
23 3 0.10
24 18 0.58
25 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATATAAATATATATTTAATTTAA
Found at i:4200274 original size:19 final size:19
Alignment explanation
Indices: 4200250--4200289 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4200240 AATAAATTTA
4200250 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
4200269 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
4200288 AT
1 AT
4200290 ATACCCGGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:4200348 original size:12 final size:12
Alignment explanation
Indices: 4200290--4200351 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
4200280 ATATATATAT
*
4200290 ATACCCGGCCCG
1 ATACCCGGCCCA
*
4200302 ATTCCCGGCCCA
1 ATACCCGGCCCA
* *
4200314 ATA-CTGACCCA
1 ATACCCGGCCCA
* **
4200325 ATACTCTACCCA
1 ATACCCGGCCCA
4200337 ATACCCGGCCCA
1 ATACCCGGCCCA
4200349 ATA
1 ATA
4200352 TCCGTTTAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
11 9 0.24
12 29 0.76
ACGTcount: A:0.27, C:0.44, G:0.13, T:0.16
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:4211546 original size:16 final size:16
Alignment explanation
Indices: 4211525--4211555 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4211515 ACCAGGTTCA
*
4211525 ACTAGGGAATGACATG
1 ACTAGGGAACGACATG
4211541 ACTAGGGAACGACAT
1 ACTAGGGAACGACAT
4211556 ATGAATTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.16, G:0.29, T:0.16
Consensus pattern (16 bp):
ACTAGGGAACGACATG
Found at i:4214690 original size:4 final size:4
Alignment explanation
Indices: 4214681--4214707 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4214671 TTCAACTATG
4214681 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
4214708 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:4215124 original size:15 final size:15
Alignment explanation
Indices: 4215102--4215143 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
4215092 AAAATTAAAA
4215102 TATATATATATAATAT
1 TATATATATATAAT-T
*
4215118 T-TATATATTTAATT
1 TATATATATATAATT
*
4215132 TAAATATATATA
1 TATATATATATA
4215144 CCCGACCCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 2 0.09
15 19 0.86
16 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:4225718 original size:15 final size:15
Alignment explanation
Indices: 4225698--4225727 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4225688 AGTTATTTTG
4225698 TTATATATATATATA
1 TTATATATATATATA
*
4225713 TTATATGTATATATA
1 TTATATATATATATA
4225728 GTAATATAGT
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:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATATATATATATA
Found at i:4225816 original size:26 final size:25
Alignment explanation
Indices: 4225787--4225841 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 25
4225777 CTGGTTTTCA
* *
4225787 AAAATTTATATATTATATAGTTTTTG
1 AAAATATATATAATATATAG-TTTTG
4225813 AAAATATATATAATATATAGTTTTG
1 AAAATATATATAATATATAGTTTTG
4225838 AAAA
1 AAAA
4225842 CATTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (25 bp):
AAAATATATATAATATATAGTTTTG
Found at i:4225854 original size:36 final size:34
Alignment explanation
Indices: 4225807--4226189 Score: 323
Period size: 34 Copynumber: 10.8 Consensus size: 34
4225797 TATTATATAG
4225807 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
1 TTTTT-AAAA-ATATATAATATATAGTTTT-AAAACA
*
4225844 TTTTTAAAATATTTATATATTATATAGTTTTTAAAACA
1 TTTTTAAAA-A--TATATAATATATAG-TTTTAAAACA
*
4225882 -TTTTAAAAATAAATATAATATATAGTTTTTAAACA
1 TTTTTAAAAAT--ATATAATATATAGTTTTAAAACA
* * *
4225917 TTTTTGAAAAAAAAAATATTATATAGTTTTAAAACA
1 TTTTT--AAAAATATATAATATATAGTTTTAAAACA
* *
4225953 -TTTTGAAAATATATAATATATAGTTTTTAAAGCA
1 TTTTTAAAAATATATAATATATAG-TTTTAAAACA
* *
4225987 TTTTGAAAACATATATATATTATATAGTTTTTAAAAAAACC
1 TTTTTAAAA-ATATATA-A-TATATAG-TTTT---AAAACA
* * *
4226028 TTTTGAAAAACATATAATATATAATTTTAAAATCA
1 TTTTTAAAAATATATAATATATAGTTTTAAAA-CA
* *
4226063 -TTTTGAAAACATATAATATATAGTTTTAAAAACA
1 TTTTTAAAAATATATAATATATAGTTTT-AAAACA
* * *
4226097 TTTTTGAAAA-CTAT-ATA-AT--TTTGAAAACA
1 TTTTTAAAAATATATAATATATAGTTTTAAAACA
* *
4226126 TTTTTAAAAAATATATAATATATAATTTTAAAATA
1 TTTTT-AAAAATATATAATATATAGTTTTAAAACA
*
4226161 TTTTTAAAAATATATATTATATAGATTTT
1 TTTTTAAAAATATATAATATATAG-TTTT
4226190 TGGAAAATAT
Statistics
Matches: 290, Mismatches: 30, Indels: 54
0.78 0.08 0.14
Matches are distributed among these distances:
29 11 0.04
30 7 0.02
31 3 0.01
32 5 0.02
33 20 0.07
34 60 0.21
35 50 0.17
36 50 0.17
37 18 0.06
38 42 0.14
39 5 0.02
40 6 0.02
41 13 0.04
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.44
Consensus pattern (34 bp):
TTTTTAAAAATATATAATATATAGTTTTAAAACA
Found at i:4225855 original size:25 final size:26
Alignment explanation
Indices: 4225801--4225855 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
4225791 TTTATATATT
* *
4225801 ATATAGTTTTTGAAAATATATATAAT
1 ATATAGTTTTTGAAAACATATATAAA
* *
4225827 ATATAG-TTTTGAAAACATTTTTAAA
1 ATATAGTTTTTGAAAACATATATAAA
4225852 ATAT
1 ATAT
4225856 TTATATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (26 bp):
ATATAGTTTTTGAAAACATATATAAA
Found at i:4226112 original size:29 final size:29
Alignment explanation
Indices: 4226043--4226144 Score: 114
Period size: 29 Copynumber: 3.3 Consensus size: 29
4226033 AAAAACATAT
* *
4226043 AATATATAATTTTAAAATCATTTTGAAAA
1 AATATATAATTTTAAAAACATTTTTAAAA
*
4226072 CATATAATATATAGTTTTAAAAACATTTTTGAAA
1 -A-AT-ATATA-A-TTTTAAAAACATTTTTAAAA
* *
4226106 ACTATATAATTTTGAAAACATTTTTAAAA
1 AATATATAATTTTAAAAACATTTTTAAAA
4226135 AATATATAAT
1 AATATATAAT
4226145 ATATAATTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
29 27 0.44
30 2 0.03
31 7 0.11
32 6 0.10
33 2 0.03
34 17 0.28
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (29 bp):
AATATATAATTTTAAAAACATTTTTAAAA
Found at i:4226128 original size:63 final size:63
Alignment explanation
Indices: 4226043--4226176 Score: 175
Period size: 63 Copynumber: 2.1 Consensus size: 63
4226033 AAAAACATAT
* *
4226043 AATATATAATTTTAAAATCA-TTTT-GAAAACATATAATATATAGTTTTAAAAACATTTTTGAAA
1 AATATATAATTTTAAAATCATTTTTAAAAAACATATAATATATAATTTT-AAAACATTTTT-AAA
* * *
4226106 ACTATATAATTTTGAAAA-CATTTTTAAAAAATATATAATATATAATTTTAAAATATTTTTAAA
1 AATATATAATTTT-AAAATCATTTTTAAAAAACATATAATATATAATTTTAAAACATTTTTAAA
4226169 AATATATA
1 AATATATA
4226177 TTATATAGAT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
63 24 0.39
64 18 0.29
65 20 0.32
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (63 bp):
AATATATAATTTTAAAATCATTTTTAAAAAACATATAATATATAATTTTAAAACATTTTTAAA
Found at i:4226236 original size:9 final size:9
Alignment explanation
Indices: 4226224--4226248 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4226214 TTATTTTAAT
4226224 TTATTTACC
1 TTATTTACC
4226233 TTATTTACC
1 TTATTTACC
4226242 TTATTTA
1 TTATTTA
4226249 TTTATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (9 bp):
TTATTTACC
Found at i:4226249 original size:4 final size:4
Alignment explanation
Indices: 4226197--4226270 Score: 64
Period size: 4 Copynumber: 18.0 Consensus size: 4
4226187 TTTTGGAAAA
* *
4226197 TATT T-TT TAGTT TA-T T-TT TATTT TAATT TATT TACCT TATT TACCT
1 TATT TATT TA-TT TATT TATT TA-TT T-ATT TATT TA-TT TATT TA-TT
4226243 TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT
4226271 ATTACTTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
3 7 0.12
4 34 0.59
5 16 0.28
6 1 0.02
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:4227825 original size:2 final size:2
Alignment explanation
Indices: 4227818--4227843 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4227808 TAGAATGCTG
4227818 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
4227844 TATGTATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4228568 original size:22 final size:21
Alignment explanation
Indices: 4228521--4228577 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 21
4228511 GGTCTATACA
*
4228521 GTCCTTCGGGACAACTCATAG
1 GTCCTTCGGGACAACTCACAG
* *
4228542 GTCCTTTGGGACATATTCACAG
1 GTCCTTCGGGACA-ACTCACAG
4228564 GTCCTTCGGGACAA
1 GTCCTTCGGGACAA
4228578 AATTTCATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (21 bp):
GTCCTTCGGGACAACTCACAG
Found at i:4229395 original size:12 final size:12
Alignment explanation
Indices: 4229375--4229420 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
4229365 TTTAACATTC
*
4229375 GGTATTGTTCAT
1 GGTACTGTTCAT
4229387 GGTACTGTTCAT
1 GGTACTGTTCAT
* *
4229399 --TACTATTCAA
1 GGTACTGTTCAT
4229409 GGTACTGTTCAT
1 GGTACTGTTCAT
4229421 ACCATATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
10 8 0.30
12 19 0.70
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (12 bp):
GGTACTGTTCAT
Found at i:4233250 original size:22 final size:20
Alignment explanation
Indices: 4233225--4233270 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
4233215 TCATGATGAG
4233225 ATATGGAAGATAAAGATGGTTT
1 ATATGG-AGAT-AAGATGGTTT
* *
4233247 ATATGGATATAAGTTGGTTT
1 ATATGGAGATAAGATGGTTT
4233267 ATAT
1 ATAT
4233271 AAAGGTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 3 0.14
22 6 0.27
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
ATATGGAGATAAGATGGTTT
Found at i:4234172 original size:24 final size:24
Alignment explanation
Indices: 4234145--4234194 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
4234135 ATAAAGAACC
4234145 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
4234169 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
4234193 AA
1 AA
4234195 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:4239813 original size:24 final size:24
Alignment explanation
Indices: 4239786--4239835 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
4239776 TTAAAGAACC
4239786 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
4239810 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
4239834 AA
1 AA
4239836 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:4240762 original size:2 final size:2
Alignment explanation
Indices: 4240755--4240800 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4240745 TAGAATGTTG
4240755 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
4240797 AT AT
1 AT AT
4240801 TATGTATGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4241222 original size:16 final size:16
Alignment explanation
Indices: 4241201--4241235 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
4241191 ATAAAATGAC
*
4241201 ATGTATATGTGAATAT
1 ATGTATATGAGAATAT
4241217 ATGTATATGAGAATAT
1 ATGTATATGAGAATAT
4241233 ATG
1 ATG
4241236 CCTATGTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (16 bp):
ATGTATATGAGAATAT
Found at i:4241538 original size:21 final size:22
Alignment explanation
Indices: 4241509--4241563 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
4241499 GGGTCTACGC
*
4241509 GGTCCTTCGGGACA-ACTCATA
1 GGTCCTTCGGGACATACTCACA
* *
4241530 GGTCATTCGGGACATATTCACA
1 GGTCCTTCGGGACATACTCACA
4241552 GGTCCTTCGGGA
1 GGTCCTTCGGGA
4241564 TATAATTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (22 bp):
GGTCCTTCGGGACATACTCACA
Found at i:4242361 original size:35 final size:39
Alignment explanation
Indices: 4242321--4242463 Score: 100
Period size: 41 Copynumber: 3.7 Consensus size: 39
4242311 TCTTCTCTAT
*
4242321 TTTTCTTTATTTTTTATTTCCA-TTA-TATTTATT-TTA
1 TTTTCTTTATTTTTTATTTCCATTTATTATATATTATTA
* * **
4242357 -TTTCTCTATTTTTTGTTTTTATTTATTGTATATATTATTA
1 TTTTCTTTATTTTTTATTTCCATTTA-T-TATATATTATTA
* * * * * *
4242397 TTTTCTTTATTTTTTATTTTCTTTGTTTTTTATTTCTTTTA
1 TTTTCTTTATTTTTTATTTCCATT-TATTATATAT-TATTA
4242438 TTTTCTTTATTCTTTT-TTTCC-TTTAT
1 TTTTCTTTATT-TTTTATTTCCATTTAT
4242464 CATTTTTTCT
Statistics
Matches: 83, Mismatches: 15, Indels: 15
0.73 0.13 0.13
Matches are distributed among these distances:
35 17 0.20
36 3 0.04
39 9 0.11
40 10 0.12
41 39 0.47
42 5 0.06
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (39 bp):
TTTTCTTTATTTTTTATTTCCATTTATTATATATTATTA
Found at i:4242413 original size:16 final size:16
Alignment explanation
Indices: 4242321--4242441 Score: 73
Period size: 16 Copynumber: 6.8 Consensus size: 16
4242311 TCTTCTCTAT
4242321 TTTTCTTTATTTTTTA
1 TTTTCTTTATTTTTTA
*
4242337 TTTCCATTATATTTATTTTA
1 TTTTC-TT-TA-TT-TTTTA
* *
4242357 TTTCTCTATTTTTTGTTTT
1 TTT-TCT-TTATTT-TTTA
*
4242376 TATTTATTGTATATATTATTA
1 T-TTTCTT-TAT-T-TT-TTA
4242397 TTTTCTTTATTTTTTA
1 TTTTCTTTATTTTTTA
*
4242413 TTTTCTTTGTTTTTTA
1 TTTTCTTTATTTTTTA
4242429 -TTTCTTTTATTTT
1 TTTTC-TTTATTTT
4242442 CTTTATTCTT
Statistics
Matches: 82, Mismatches: 10, Indels: 26
0.69 0.08 0.22
Matches are distributed among these distances:
15 4 0.05
16 29 0.35
17 4 0.05
18 5 0.06
19 15 0.18
20 19 0.23
21 6 0.07
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTTCTTTATTTTTTA
Found at i:4242436 original size:25 final size:25
Alignment explanation
Indices: 4242408--4242463 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
4242398 TTTCTTTATT
*
4242408 TTTTATTTTCTTTGTT-TTTTATTTC
1 TTTTATTTTCTTTATTCTTTT-TTTC
4242433 TTTTATTTTCTTTATTCTTTTTTTC
1 TTTTATTTTCTTTATTCTTTTTTTC
*
4242458 CTTTAT
1 TTTTAT
4242464 CATTTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.79
Consensus pattern (25 bp):
TTTTATTTTCTTTATTCTTTTTTTC
Found at i:4242463 original size:16 final size:16
Alignment explanation
Indices: 4242425--4242472 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
4242415 TTCTTTGTTT
*
4242425 TTTATTTCTTTTATTTTC
1 TTTA-TTCTTTT-TTTCC
4242443 TTTATTCTTTTTTTCC
1 TTTATTCTTTTTTTCC
*
4242459 TTTA-TCATTTTTTC
1 TTTATTCTTTTTTTC
4242473 TCTATTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 9 0.32
16 8 0.29
17 7 0.25
18 4 0.14
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTATTCTTTTTTTCC
Found at i:4242482 original size:16 final size:16
Alignment explanation
Indices: 4242438--4242487 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
4242428 ATTTCTTTTA
* *
4242438 TTTTCTTTA-TTCTTT
1 TTTTCTCTATTTCATT
4242453 TTTTC-CT-TTATCATT
1 TTTTCTCTATT-TCATT
4242468 TTTTCTCTATTTCATT
1 TTTTCTCTATTTCATT
4242484 TTTT
1 TTTT
4242488 ATTTCGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 2 0.07
15 14 0.48
16 11 0.38
17 2 0.07
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTCTCTATTTCATT
Found at i:4242486 original size:17 final size:17
Alignment explanation
Indices: 4242427--4242487 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 17
4242417 CTTTGTTTTT
* *
4242427 TATTTCTTTTATTTTCTT
1 TATTTCATTT-TTTTCTC
4242445 TA-TTC-TTTTTTTC-C
1 TATTTCATTTTTTTCTC
4242459 T-TTATCA-TTTTTTCTC
1 TATT-TCATTTTTTTCTC
4242475 TATTTCATTTTTT
1 TATTTCATTTTTT
4242488 ATTTCGTTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
14 2 0.06
15 14 0.39
16 8 0.22
17 10 0.28
18 2 0.06
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTCATTTTTTTCTC
Found at i:4247755 original size:72 final size:72
Alignment explanation
Indices: 4247603--4247742 Score: 176
Period size: 72 Copynumber: 1.9 Consensus size: 72
4247593 GAGATTGCTT
* * *
4247603 TTCTTAAAAC-AGACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTTCATTCAA
1 TTCTTAAAACAAGACTTTGTCTCGCTTGAGACCGTTTTACTCGAAAGAAGATTTATTTCACTCAA
*
4247667 TATTGTTT
66 TA-TGTTG
*
4247675 TTCTTAAAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATTTTAC
1 TTCTTAAAACAAGACTTTGTCTCGCTTGAGACCGTTTT-ACTCGAAAGAA-G-ATTT-ATTTCAC
4247739 TCAA
62 TCAA
4247743 GTCTGTTTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
72 31 0.53
73 14 0.24
74 1 0.02
75 4 0.07
76 9 0.15
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (72 bp):
TTCTTAAAACAAGACTTTGTCTCGCTTGAGACCGTTTTACTCGAAAGAAGATTTATTTCACTCAA
TATGTTG
Found at i:4247823 original size:20 final size:20
Alignment explanation
Indices: 4247761--4247823 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
4247751 TAAAAGAATA
4247761 TTTTATCTCGCTTGAGATAG
1 TTTTATCTCGCTTGAGATAG
* ** *
4247781 -TTTCTCTCGAAAT-A-AAAG
1 TTTTATCTCG-CTTGAGATAG
4247799 ATTTTATCTCGCTTGAGATAG
1 -TTTTATCTCGCTTGAGATAG
4247820 TTTT
1 TTTT
4247824 CCTCGAAACA
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
18 3 0.10
19 10 0.33
20 14 0.47
21 3 0.10
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.44
Consensus pattern (20 bp):
TTTTATCTCGCTTGAGATAG
Found at i:4247902 original size:39 final size:39
Alignment explanation
Indices: 4247757--4247948 Score: 208
Period size: 39 Copynumber: 5.0 Consensus size: 39
4247747 GTTTTAAAAG
* *
4247757 AATATTTTATCTCGCTTGAGATAGTTTCTCTCGAAATAA
1 AATATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* * *
4247796 AAGATTTTATCTCGCTTGAGATAGTTTTCCTCGAAACAG
1 AATATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* * *
4247835 AAGATTTTGTCTCGCTTGAGATGGTTTCCCTCGAAACAA
1 AATATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* * *
4247874 AATATTTTATCTCGCTAGAGACAGTTTCCCTTG-AA-AA
1 AATATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
** * * * * *
4247911 TTTTTTTTATCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACA
4247949 TAAACATTGA
Statistics
Matches: 130, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
37 29 0.22
38 4 0.03
39 97 0.75
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (39 bp):
AATATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
Found at i:4248011 original size:36 final size:36
Alignment explanation
Indices: 4247964--4248049 Score: 127
Period size: 36 Copynumber: 2.4 Consensus size: 36
4247954 ATTGAAAACA
** * *
4247964 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
4248000 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
4248036 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
4248050 TAAACTTTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:4248073 original size:29 final size:31
Alignment explanation
Indices: 4248027--4248109 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
4248017 TTTGTCTCCC
* * * *
4248027 TTGAGACAGTTTCTCTTGAAACA-TAAA-CT
1 TTGAAACAGTTTCCCTTGAAACACAAAATAT
4248056 TTGAAA-ACGTTTCCCTTGAAACACAAAATAT
1 TTGAAACA-GTTTCCCTTGAAACACAAAATAT
*
4248087 TTGAATCAGTTTCCCTTGAAACA
1 TTGAAACAGTTTCCCTTGAAACA
4248110 AATTTTGTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.02
29 19 0.42
30 3 0.07
31 21 0.47
32 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (31 bp):
TTGAAACAGTTTCCCTTGAAACACAAAATAT
Found at i:4248212 original size:96 final size:96
Alignment explanation
Indices: 4247915--4248204 Score: 393
Period size: 96 Copynumber: 3.0 Consensus size: 96
4247905 TGAAAATTTT
* *
4247915 TTTTATCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACATTTCCCTTGAAA--AA
**** *
4247980 TTTTGTCTCTCTTGAGAT-AGTTTCCCTTGAAACAAA
64 --TAAAATAT-TTGA-ATCAGTTTCCCTTGAAACAAA
* * *
4248016 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACGTTTCCCTTGAAACACA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACATTTCCCTTGAAAAATA
4248081 AAATATTTGAATCAGTTTCCCTTGAAACAAA
66 AAATATTTGAATCAGTTTCCCTTGAAACAAA
* * *
4248112 TTTTGTCTCCCTTGAGACAATTTCTCTTGAAATATAAACTTTGAAAACATTTCCATTGAAAAATA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACATTTCCCTTGAAAAATA
*
4248177 AAATATTTGAATCAGTTCCCCTTGAAAC
66 AAATATTTGAATCAGTTTCCCTTGAAAC
4248205 GAGTTTTGAG
Statistics
Matches: 171, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
95 2 0.01
96 108 0.63
97 2 0.01
99 1 0.01
101 58 0.34
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (96 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACATTTCCCTTGAAAAATA
AAATATTTGAATCAGTTTCCCTTGAAACAAA
Found at i:4248313 original size:65 final size:67
Alignment explanation
Indices: 4248210--4248362 Score: 197
Period size: 65 Copynumber: 2.3 Consensus size: 67
4248200 GAAACGAGTT
* * * *
4248210 TTGAGACAGTTTCCCTTG-AAACACCCACATTTGAGATTGTTTCCC-TTAAA-ACATGTT-GTCT
1 TTGAGACAATTTCCCTTGAAAACACCAACATTTGAGATTGTTTCCCATGAAACAAAT-TTCGTCT
*
4248271 CTC
65 CGC
* *
4248274 TTGAGACAATTTCTCTTGAAAACACCAACCTTTGAGATTGTTTCCCATGAAACAAATTTCGTCTC
1 TTGAGACAATTTCCCTTGAAAACACCAACATTTGAGATTGTTTCCCATGAAACAAATTTCGTCTC
4248339 GC
66 GC
4248341 TTGAGACAATTTTCCCTTGAAA
1 TTGAGACAA-TTTCCCTTGAAA
4248363 CAAGAAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
64 16 0.21
65 25 0.33
66 6 0.08
67 18 0.24
68 11 0.14
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.35
Consensus pattern (67 bp):
TTGAGACAATTTCCCTTGAAAACACCAACATTTGAGATTGTTTCCCATGAAACAAATTTCGTCTC
GC
Found at i:4249298 original size:18 final size:17
Alignment explanation
Indices: 4249270--4249305 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
4249260 TTTTTTTTTG
4249270 TTTTATATATATATATA
1 TTTTATATATATATATA
*
4249287 TTTTATTATATATGTATA
1 TTTTA-TATATATATATA
4249305 T
1 T
4249306 ATAGTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTATATATATATATA
Found at i:4249316 original size:20 final size:20
Alignment explanation
Indices: 4249273--4249316 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
4249263 TTTTTTGTTT
** *
4249273 TATATATATATATATTTTAT
1 TATATATATATATATAGTAA
*
4249293 TATATATGTATATATAGTAA
1 TATATATATATATATAGTAA
4249313 TATA
1 TATA
4249317 GTTTTTGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (20 bp):
TATATATATATATATAGTAA
Found at i:4249482 original size:11 final size:11
Alignment explanation
Indices: 4249436--4249485 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
4249426 TATAGTTTCG
*
4249436 AAAACATTTTG
1 AAAACATTTTT
*
4249447 AAAACATTTAT
1 AAAACATTTTT
*
4249458 ATATACAGTTTTT
1 A-AAACA-TTTTT
4249471 AAAACATTTTT
1 AAAACATTTTT
4249482 AAAA
1 AAAA
4249486 ATAAATATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
11 19 0.59
12 8 0.25
13 5 0.16
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (11 bp):
AAAACATTTTT
Found at i:4249505 original size:37 final size:37
Alignment explanation
Indices: 4249312--4249791 Score: 182
Period size: 36 Copynumber: 13.3 Consensus size: 37
4249302 ATATATAGTA
* *
4249312 ATATAGTTTTTGAAAACGTTTTT-AACA-AAATATAAT
1 ATATAGTTTTT-AAAACATTTTTAAAAATAAATATAAT
* * * ** ** *
4249348 ATATAATTTTCAGAAAACGGTTTTCGAAAATTTATATATT
1 ATATAGTTTT--TAAAAC-ATTTTTAAAAATAAATATAAT
*
4249388 ATATAGTTTTTGAAAACATTTTT-AAAATATATATAAT
1 ATATAGTTTTT-AAAACATTTTTAAAAATAAATATAAT
** * *
4249425 ATATAGTTTCGAAAACATTTTGAAAACAT--TTAT-AT
1 ATATAGTTTTTAAAACATTTTTAAAA-ATAAATATAAT
*
4249460 ATACAGTTTTTAAAACATTTTTAAAAATAAATATAAT
1 ATATAGTTTTTAAAACATTTTTAAAAATAAATATAAT
4249497 ATATAGTTTTT-AAACATTTTTCAATATATATATATATATATAT
1 ATATAGTTTTTAAAACATTTTT-AA-A-A-ATA-A-ATATA-AT
* *
4249540 ATTATAGTTTTTAAAAGA-TTTTGAAAAT--ATAT-A-
1 A-TATAGTTTTTAAAACATTTTTAAAAATAAATATAAT
* * *
4249573 ATATA-----TAAAGCATTTTGAAAACATATATATATAT
1 ATATAGTTTTTAAAACATTTTTAAAA-ATAAATATA-AT
* * * *
4249607 ATTATAGTTTTTAAAAAAAACTTTTGAAAATCAATCAT-AT
1 A-TATAGTTTTT--AAAACATTTTTAAAAATAAAT-ATAAT
* * *
4249647 ATA-A--TTTTAAAATTATTTTGAAAACT---TATAAT
1 ATATAGTTTTTAAAA-CATTTTTAAAAATAAATATAAT
* * * *
4249679 ATATAGTTTTAAAAATATTTTT---GA-AAA-CT-AT
1 ATATAGTTTTTAAAACATTTTTAAAAATAAATATAAT
* *
4249710 ATA-A-TTTTGAAAACATTTTTAAAAATATATATAAT
1 ATATAGTTTTTAAAACATTTTTAAAAATAAATATAAT
* * * *
4249745 ATATA-ATTTTAAAATATTTTTAAAAA-ATATATATT
1 ATATAGTTTTTAAAACATTTTTAAAAATAAATATAAT
4249780 ATATAGATTTTT
1 ATATAG-TTTTT
4249792 TGAAAAATAT
Statistics
Matches: 335, Mismatches: 56, Indels: 105
0.68 0.11 0.21
Matches are distributed among these distances:
27 5 0.01
28 6 0.02
29 16 0.05
30 1 0.00
31 11 0.03
32 12 0.04
33 5 0.01
34 15 0.04
35 61 0.18
36 62 0.19
37 47 0.14
38 13 0.04
39 11 0.03
40 24 0.07
41 6 0.02
42 18 0.05
43 4 0.01
44 14 0.04
45 4 0.01
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.44
Consensus pattern (37 bp):
ATATAGTTTTTAAAACATTTTTAAAAATAAATATAAT
Found at i:4249540 original size:46 final size:43
Alignment explanation
Indices: 4249455--4249579 Score: 122
Period size: 44 Copynumber: 3.0 Consensus size: 43
4249445 TGAAAACATT
* * *
4249455 TATATA-TACAGTTTTTAAAACATTTT-TAAA-A-ATAA-ATA
1 TATATATTATAGTTTTTAAAAGATTTTCAAAATATATAATATA
* *
4249493 TA-ATA-TATAGTTTTTAAACA-TTTTTCAATATATATATATATA
1 TATATATTATAGTTTTTAAA-AGATTTTCAAAATATATA-ATATA
*
4249535 TATATATTATAGTTTTTAAAAGATTTTGAAAATATATAATATA
1 TATATATTATAGTTTTTAAAAGATTTTCAAAATATATAATATA
4249578 TA
1 TA
4249580 AAGCATTTTG
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
37 19 0.27
38 5 0.07
39 1 0.01
40 3 0.04
41 1 0.01
42 5 0.07
43 11 0.15
44 26 0.37
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (43 bp):
TATATATTATAGTTTTTAAAAGATTTTCAAAATATATAATATA
Found at i:4249546 original size:44 final size:40
Alignment explanation
Indices: 4249380--4249579 Score: 135
Period size: 37 Copynumber: 5.2 Consensus size: 40
4249370 TTCGAAAATT
4249380 TATATAT-TATATAGTTTTTGAAAACATTTTT-AA-A-AT-A
1 TATATATATATATAGTTTTT--AAACATTTTTAAATATATAA
** * *
4249417 TATATA-ATATATAGTTTCGAAAACA-TTTTGAA-A-A-CA
1 TATATATATATATAGTTT-TTAAACATTTTTAAATATATAA
*
4249453 T-T-TATATATACAGTTTTTAAAACATTTTTAAA-A-ATAA
1 TATATATATATATAGTTTTT-AAACATTTTTAAATATATAA
4249490 -ATATA-ATATATAGTTTTTAAACATTTTTCAATATATATATA
1 TATATATATATATAGTTTTTAAACATTTTT-AA-ATATATA-A
* *
4249531 TATATATATATTATAGTTTTTAAAAGATTTTGAAAATATATAA
1 TATATATATA-TATAGTTTTT-AAACATTTT-TAAATATATAA
4249574 TATATA
1 TATATA
4249580 AAGCATTTTG
Statistics
Matches: 133, Mismatches: 10, Indels: 34
0.75 0.06 0.19
Matches are distributed among these distances:
34 2 0.02
35 20 0.15
36 29 0.22
37 32 0.24
38 3 0.02
39 1 0.01
40 3 0.02
41 1 0.01
42 5 0.04
43 10 0.08
44 17 0.13
45 10 0.08
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (40 bp):
TATATATATATATAGTTTTTAAACATTTTTAAATATATAA
Found at i:4249581 original size:27 final size:29
Alignment explanation
Indices: 4249551--4249607 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 29
4249541 TTATAGTTTT
*
4249551 TAAAAG-ATTTTGAAAATATATA-ATATA
1 TAAAAGCATTTTGAAAACATATATATATA
4249578 T-AAAGCATTTTGAAAACATATATATATA
1 TAAAAGCATTTTGAAAACATATATATATA
4249606 TA
1 TA
4249608 TTATAGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 4 0.15
27 16 0.62
28 6 0.23
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.37
Consensus pattern (29 bp):
TAAAAGCATTTTGAAAACATATATATATA
Found at i:4249683 original size:36 final size:36
Alignment explanation
Indices: 4249585--4249790 Score: 130
Period size: 35 Copynumber: 5.8 Consensus size: 36
4249575 ATATAAAGCA
* *
4249585 TTTTGAAAACATATATATATATATTATAGTTTTTAAAAAAAAC
1 TTTTGAAAAC-TATATA-ATATA-TA-A--TTTT-AAAAATAT
* *
4249628 TTTTGAAAA-TCA-ATCATATATAATTTTAAAATTA-
1 TTTTGAAAACT-ATATAATATATAATTTTAAAAATAT
*
4249662 TTTTGAAAACT-TATAATATATAGTTTTAAAAATAT
1 TTTTGAAAACTATATAATATATAATTTTAAAAATAT
* *
4249697 TTTTGAAAAC-------TATATAATTTTGAAAACAT
1 TTTTGAAAACTATATAATATATAATTTTAAAAATAT
* *
4249726 TTTTAAAAATATATATAATATATAATTTT-AAAATAT
1 TTTTGAAAA-CTATATAATATATAATTTTAAAAATAT
* * *
4249762 TTTTAAAAAATATATATTATATAGATTTT
1 TTTTGAAAACTATATAATATATA-ATTTT
4249791 TTGAAAAATA
Statistics
Matches: 137, Mismatches: 13, Indels: 33
0.75 0.07 0.18
Matches are distributed among these distances:
29 24 0.18
34 28 0.20
35 29 0.21
36 24 0.18
37 11 0.08
38 1 0.01
39 2 0.01
40 5 0.04
41 3 0.02
42 1 0.01
43 9 0.07
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTTGAAAACTATATAATATATAATTTTAAAAATAT
Found at i:4249738 original size:28 final size:29
Alignment explanation
Indices: 4249676--4249740 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
4249666 GAAAACTTAT
* *
4249676 AATATATAGTTTTAAAAATATTTTTGAAA
1 AATATATAATTTTAAAAACATTTTTGAAA
* *
4249705 ACTATATAATTTTGAAAACATTTTT-AAA
1 AATATATAATTTTAAAAACATTTTTGAAA
4249733 AATATATA
1 AATATATA
4249741 TAATATATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (29 bp):
AATATATAATTTTAAAAACATTTTTGAAA
Found at i:4250915 original size:2 final size:2
Alignment explanation
Indices: 4250903--4250945 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
4250893 TTATTTTTAT
*
4250903 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4250945 T
1 T
4250946 TATGTTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4251009 original size:30 final size:30
Alignment explanation
Indices: 4250973--4251036 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
4250963 ATCTTCATCC
*
4250973 TTTTTACCTTT-TATA-TTTATTTTATCTTTT
1 TTTTTA-CTTTATATATTTTATTTTAT-TTTA
*
4251003 TTTTTACTTTATTTATTTTATTTTATTTTA
1 TTTTTACTTTATATATTTTATTTTATTTTA
4251033 TTTT
1 TTTT
4251037 ATGTTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.13
30 16 0.53
31 10 0.33
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTTTACTTTATATATTTTATTTTATTTTA
Found at i:4251013 original size:5 final size:5
Alignment explanation
Indices: 4250981--4251265 Score: 89
Period size: 5 Copynumber: 55.8 Consensus size: 5
4250971 CCTTTTTACC
* *
4250981 TTTTA TATTTA TTTTA TCTTTTT TTTTA CTTTA -TTTA TTTTA TTTTA
1 TTTTA T-TTTA TTTTA --TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * *
4251028 TTTTA TTTTA TGTTA -TTTA -TTTA TTATG TTTTA TTTATACA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT-T--A TTTTA
* **
4251074 TTATA TGCATA TTTCTA --TTA TTTTA TTTCT- TTTTA -TTTA TTTCT-
1 TTTTA T-TTTA TTT-TA TTTTA TTTTA TTT-TA TTTTA TTTTA TTT-TA
* * *
4251118 TCTCTC TTTT- TCTTTA -TTT- TTTTA TTTT- CTTTA TATTTA TTTTA
1 T-TTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA
* * * * *
4251162 TTTCTC TATT- TTTTA TTTTA TTCTTG TTTT- TATTTA TTCTA -TATA
1 TTT-TA TTTTA TTTTA TTTTA TT-TTA TTTTA T-TTTA TTTTA TTTTA
* * *
4251207 TTATTA TTATTA TTATTA TTTGTT TTTTA -TTTC TTTTA TTTTCT TTATTA
1 TT-TTA TT-TTA TT-TTA TTT-TA TTTTA TTTTA TTTTA TTTT-A TT-TTA
4251257 TTTTA TTTT
1 TTTTA TTTT
4251266 CCTTTCTTTC
Statistics
Matches: 215, Mismatches: 30, Indels: 70
0.68 0.10 0.22
Matches are distributed among these distances:
3 2 0.01
4 37 0.17
5 112 0.52
6 53 0.25
7 7 0.03
8 4 0.02
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:4251147 original size:17 final size:17
Alignment explanation
Indices: 4251125--4251266 Score: 73
Period size: 17 Copynumber: 8.3 Consensus size: 17
4251115 TCTTCTCTCT
4251125 TTTTCTTTATTTTTTTA
1 TTTTCTTTATTTTTTTA
4251142 TTTTCTTTATATTTATTT-
1 TTTTCTTTAT-TTT-TTTA
*
4251160 TATTTCTCTA-TTTTTTA
1 T-TTTCTTTATTTTTTTA
* *
4251177 TTTTATTCT-TGTTTTTA
1 TTTTCTT-TATTTTTTTA
* * *
4251194 TTTATTCTATATATTATTA
1 -TT-TTCTTTATTTTTTTA
* *
4251213 TTATT-ATTA-TTATTT-
1 TT-TTCTTTATTTTTTTA
*
4251228 GTTT-TTTATTTCTTTTA
1 TTTTCTTTATTT-TTTTA
*
4251245 TTTTCTTTATTATTTTA
1 TTTTCTTTATTTTTTTA
4251262 TTTTC
1 TTTTC
4251267 CTTTCTTTCT
Statistics
Matches: 94, Mismatches: 18, Indels: 26
0.68 0.13 0.19
Matches are distributed among these distances:
14 5 0.05
15 3 0.03
16 13 0.14
17 36 0.38
18 18 0.19
19 19 0.20
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (17 bp):
TTTTCTTTATTTTTTTA
Found at i:4251149 original size:44 final size:42
Alignment explanation
Indices: 4251089--4251180 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 42
4251079 TGCATATTTC
* * *
4251089 TATTATTTTATTTCTTTTTATTTATTTCT-TCTCTCTTTTTCTT
1 TATTTTTTTATTTCTTTATATTTATTT-TATCTCTCTATTT-TT
*
4251132 TATTTTTTTATTTTCTTTATATTTATTTTATTTCTCTATTTTT
1 TATTTTTTTA-TTTCTTTATATTTATTTTATCTCTCTATTTTT
4251175 TATTTT
1 TATTTT
4251181 ATTCTTGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 18 0.42
44 25 0.58
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (42 bp):
TATTTTTTTATTTCTTTATATTTATTTTATCTCTCTATTTTT
Found at i:4251195 original size:52 final size:48
Alignment explanation
Indices: 4251130--4251265 Score: 130
Period size: 52 Copynumber: 2.6 Consensus size: 48
4251120 TCTCTTTTTC
* *
4251130 TTTATTTTTTTATTTTCTTTATATTTATTTTATTTCTCTATTTTTTATTT
1 TTTATTTTTTTATTTTCTTTATATTTATTTTA-TTAT-TATTATTTATTT
* * *
4251180 TATTCTTGTTTTTATTTAT-TCTATATATTATTATTATTATTATTATTTGTTT
1 T-TTATT-TTTTTATTT-TCTTTATAT-TTATT-TTATTATTATTATTTATTT
4251232 TTTATTTCTTTTATTTTCTTTATTATTTTATTTT
1 TTTATTT-TTTTATTTTCTTTA-TA-TTTATTTT
4251266 CCTTTCTTTC
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
50 3 0.04
51 21 0.30
52 33 0.47
53 10 0.14
54 3 0.04
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.75
Consensus pattern (48 bp):
TTTATTTTTTTATTTTCTTTATATTTATTTTATTATTATTATTTATTT
Found at i:4251287 original size:23 final size:22
Alignment explanation
Indices: 4251233--4251288 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
4251223 TATTTGTTTT
**
4251233 TTATTTC-TTTTATTTTCTTTA
1 TTATTTCATTTTCCTTTCTTTA
* *
4251254 TTATTTTATTTTCCTTTCTTTC
1 TTATTTCATTTTCCTTTCTTTA
4251276 TCTATTTCATTTT
1 T-TATTTCATTTT
4251289 TTATTTCGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 6 0.21
22 12 0.43
23 10 0.36
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.73
Consensus pattern (22 bp):
TTATTTCATTTTCCTTTCTTTA
Found at i:4251847 original size:15 final size:16
Alignment explanation
Indices: 4251827--4251857 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4251817 AGTTTGAGTC
4251827 AAACTCAAAA-ATTTT
1 AAACTCAAAATATTTT
4251842 AAACTCAAAATATTTT
1 AAACTCAAAATATTTT
4251858 TTAACTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (16 bp):
AAACTCAAAATATTTT
Found at i:4255286 original size:15 final size:15
Alignment explanation
Indices: 4255266--4255296 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4255256 AGATTTTGCG
4255266 ACATCAAGAGTAGGA
1 ACATCAAGAGTAGGA
*
4255281 ACATCAGGAGTAGGA
1 ACATCAAGAGTAGGA
4255296 A
1 A
4255297 GGACATTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.13, G:0.29, T:0.13
Consensus pattern (15 bp):
ACATCAAGAGTAGGA
Found at i:4256296 original size:2 final size:2
Alignment explanation
Indices: 4256289--4256340 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
4256279 TTTACCTCAT
4256289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4256331 TA TA TA TA TA
1 TA TA TA TA TA
4256341 ACCCCGAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4257900 original size:2 final size:2
Alignment explanation
Indices: 4257893--4257927 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
4257883 TTTTGAAATA
4257893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
4257928 TTAATTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4265320 original size:13 final size:13
Alignment explanation
Indices: 4265302--4265332 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4265292 CCTTAAAAGC
*
4265302 ATATTTTATTTAT
1 ATATTTTAATTAT
4265315 ATATTTTAATTAT
1 ATATTTTAATTAT
4265328 ATATT
1 ATATT
4265333 CATCCTCACT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATATTTTAATTAT
Done.