Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 112 of 193
Found at i:35954972 original size:53 final size:53
Alignment explanation
Indices: 35954910--35955018 Score: 209
Period size: 53 Copynumber: 2.1 Consensus size: 53
35954900 GGAGATCCAT
*
35954910 TATCTCAATGCATGTTTGTTTTATGTATGGAGCGCCTTGTAAACTTTAAATTA
1 TATCTCAATGAATGTTTGTTTTATGTATGGAGCGCCTTGTAAACTTTAAATTA
35954963 TATCTCAATGAATGTTTGTTTTATGTATGGAGCGCCTTGTAAACTTTAAATTA
1 TATCTCAATGAATGTTTGTTTTATGTATGGAGCGCCTTGTAAACTTTAAATTA
35955016 TAT
1 TAT
35955019 AGGATTTTTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.44
Consensus pattern (53 bp):
TATCTCAATGAATGTTTGTTTTATGTATGGAGCGCCTTGTAAACTTTAAATTA
Found at i:35961717 original size:5 final size:5
Alignment explanation
Indices: 35961707--35961733 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
35961697 AGGGAGACAA
35961707 GAGGG GAGGG GAGGG GAGGG GAGGG GA
1 GAGGG GAGGG GAGGG GAGGG GAGGG GA
35961734 AGAGAAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.78, T:0.00
Consensus pattern (5 bp):
GAGGG
Found at i:35966054 original size:3 final size:3
Alignment explanation
Indices: 35966046--35966073 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
35966036 GGAGCCAAAT
35966046 GTG GTG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG G
35966074 ATGCTGTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GTG
Found at i:35967712 original size:15 final size:14
Alignment explanation
Indices: 35967692--35967725 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
35967682 ATTTAATAGT
35967692 TAATTTATAATCTAA
1 TAATTTAT-ATCTAA
*
35967707 TAATTTATATTTAA
1 TAATTTATATCTAA
35967721 TAATT
1 TAATT
35967726 AAATTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATTTATATCTAA
Found at i:35977384 original size:20 final size:20
Alignment explanation
Indices: 35977359--35977408 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
35977349 TTTATGGTTC
*
35977359 AAGGTTTGAGGTTTA-ATTTT
1 AAGGTTTGAGATTTAGA-TTT
*
35977379 AAGGTTTAAGATTTAGATTT
1 AAGGTTTGAGATTTAGATTT
*
35977399 GAGGTTTGAG
1 AAGGTTTGAG
35977409 TTTCAAGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (20 bp):
AAGGTTTGAGATTTAGATTT
Found at i:35984919 original size:11 final size:11
Alignment explanation
Indices: 35984879--35984920 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
35984869 TATTTATGAA
35984879 TAAATATTAA-
1 TAAATATTAAT
*
35984889 T-AATATTATT
1 TAAATATTAAT
35984899 TAAATA-TAAT
1 TAAATATTAAT
35984909 TAAATATTAAT
1 TAAATATTAAT
35984920 T
1 T
35984921 TTTTTTCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 7 0.26
10 11 0.41
11 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAAATATTAAT
Found at i:35985349 original size:28 final size:28
Alignment explanation
Indices: 35985298--35985357 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
35985288 ACTCTTTTAT
35985298 TTATATAAACAAAATAATAAATATATAA
1 TTATATAAACAAAATAATAAATATATAA
* * *
35985326 TTATAT-AATAAAATATATATATATATCA
1 TTATATAAACAAAATA-ATAAATATATAA
35985354 TTAT
1 TTAT
35985358 GTTAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (28 bp):
TTATATAAACAAAATAATAAATATATAA
Found at i:35985431 original size:27 final size:29
Alignment explanation
Indices: 35985373--35985429 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
35985363 AAATATTTTT
* *
35985373 AATTAATAACTTTTTTATTTATATAAATA
1 AATTAATAACTTATATATTTATATAAATA
35985402 AATTAATAA-TTATATA-TTATAT-AATA
1 AATTAATAACTTATATATTTATATAAATA
35985428 AA
1 AA
35985430 ATATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.23
27 6 0.23
28 5 0.19
29 9 0.35
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
AATTAATAACTTATATATTTATATAAATA
Found at i:35985442 original size:93 final size:94
Alignment explanation
Indices: 35985275--35985467 Score: 266
Period size: 93 Copynumber: 2.1 Consensus size: 94
35985265 TTAATTAATC
35985275 TTTTAAATTAATAACTCTTTTATTTATATAAACAAAATAATAAATATATAATTATATAATAAAAT
1 TTTTAAATTAATAACTCTTTTATTTATATAAACAAAATAATAAATATATAATTATATAATAAAAT
*
35985340 ATATATATA-TATCATTATGTTAAA-AATA
66 ATATATATATTACCATTATGTTAAATAA-A
* * * * *
35985368 TTTTTAATTAATAACTTTTTTATTTATATAAATAAATTAATAATTATAT-ATTATATAATAAAAT
1 TTTTAAATTAATAACTCTTTTATTTATATAAACAAAATAATAAATATATAATTATATAATAAAAT
* *
35985432 ATTTTTTATATTTACCATTATGTTAAATAAA
66 A-TATATATA-TTACCATTATGTTAAATAAA
35985463 TTTTA
1 TTTTA
35985468 TTTTTTAAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
92 16 0.18
93 50 0.57
95 19 0.22
96 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (94 bp):
TTTTAAATTAATAACTCTTTTATTTATATAAACAAAATAATAAATATATAATTATATAATAAAAT
ATATATATATTACCATTATGTTAAATAAA
Found at i:35989906 original size:3 final size:3
Alignment explanation
Indices: 35989900--35989937 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
35989890 GATAATAAAG
35989900 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT T
35989938 CATCTATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:35990177 original size:14 final size:14
Alignment explanation
Indices: 35990153--35990208 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
35990143 TATCTTTAAT
*
35990153 CTTGAATCTCGAAC
1 CTTGAACCTCGAAC
*
35990167 CTCGAACCTCGAAC
1 CTTGAACCTCGAAC
* ** *
35990181 TTTGAACCTTAAAT
1 CTTGAACCTCGAAC
35990195 CTTGAACCTCGAAC
1 CTTGAACCTCGAAC
35990209 TCCAAACCTT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.27
Consensus pattern (14 bp):
CTTGAACCTCGAAC
Found at i:35991247 original size:9 final size:9
Alignment explanation
Indices: 35991173--35991283 Score: 64
Period size: 9 Copynumber: 11.9 Consensus size: 9
35991163 CTAATATTTA
35991173 TATATTTTT
1 TATATTTTT
35991182 TA-ATTTTT
1 TATATTTTT
* *
35991190 TGTATTTAT
1 TATATTTTT
* *
35991199 TAGAATATTTG
1 TA-TAT-TTTT
* *
35991210 TAGAGTTTT
1 TATATTTTT
*
35991219 TATATGGTTT
1 TATAT-TTTT
*
35991229 TATGAATTTT
1 TAT-ATTTTT
35991239 TATA-TTTT
1 TATATTTTT
35991247 TATATTTTT
1 TATATTTTT
35991256 TATAATTTATT
1 TAT-ATTT-TT
*
35991267 TAGATTTTT
1 TATATTTTT
*
35991276 TGTATTTT
1 TATATTTT
35991284 AATTAAGTTT
Statistics
Matches: 77, Mismatches: 17, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
8 15 0.19
9 30 0.39
10 23 0.30
11 9 0.12
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (9 bp):
TATATTTTT
Found at i:35991268 original size:28 final size:28
Alignment explanation
Indices: 35991205--35991275 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
35991195 TTATTAGAAT
*
35991205 ATTTGTAGAGTTTTTATATGGTTTTATGA
1 ATTTTTAGA-TTTTTATATGGTTTTATGA
* *
35991234 ATTTTTATATTTTTATAT-TTTTTAT-A
1 ATTTTTAGATTTTTATATGGTTTTATGA
35991260 ATTTATTTAGATTTTT
1 A-TT-TTTAGATTTTT
35991276 TGTATTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.06
27 8 0.22
28 19 0.53
29 7 0.19
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (28 bp):
ATTTTTAGATTTTTATATGGTTTTATGA
Found at i:35998285 original size:46 final size:46
Alignment explanation
Indices: 35998218--35998307 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
35998208 AAACATAAAC
* *
35998218 ACAAAATTCTCTAAAAGTGTTATAAGTTCTAATCTCTAATGAGTGT
1 ACAAAATTCTCCAAAAGTGTTATAAGTTCTAATATCTAATGAGTGT
* *
35998264 ACAAAATTCTCCAAAAGTGTTATGAGTTCTAATATTTAATGAGT
1 ACAAAATTCTCCAAAAGTGTTATAAGTTCTAATATCTAATGAGT
35998308 ATATTTTCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (46 bp):
ACAAAATTCTCCAAAAGTGTTATAAGTTCTAATATCTAATGAGTGT
Found at i:35998651 original size:18 final size:18
Alignment explanation
Indices: 35998615--35998649 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35998605 TAGCGAACAC
*
35998615 ATATAAATATAAATATTT
1 ATATAAATACAAATATTT
35998633 ATATAAATAC-AATATTT
1 ATATAAATACAAATATTT
35998650 TAACAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAAATACAAATATTT
Found at i:36000436 original size:25 final size:26
Alignment explanation
Indices: 36000406--36000465 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
36000396 ATAGCCATGA
36000406 AAATAAAAAAATATG-AAATAAGAAT
1 AAATAAAAAAATATGCAAATAAGAAT
* * *
36000431 AAAT-AAAAATTATGCAAGTATGAAT
1 AAATAAAAAAATATGCAAATAAGAAT
*
36000456 AAATATAAAA
1 AAATAAAAAA
36000466 TATTAAACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 9 0.31
25 16 0.55
26 4 0.14
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (26 bp):
AAATAAAAAAATATGCAAATAAGAAT
Found at i:36001245 original size:51 final size:51
Alignment explanation
Indices: 36001140--36001245 Score: 115
Period size: 51 Copynumber: 2.1 Consensus size: 51
36001130 TTCTTTTTTT
** * *
36001140 AAAAAATCACTAATTTACTTAAAAATCCAAACTTTATATTTTAAATAATTA
1 AAAAAATCAAAAATTTACTTAAAAATCCAAACTTTATATTTAAAATAATAA
* ** * *
36001191 AAAAAATCAAAAATTTATTTAAAAATTTAAACTTT-TCTTTAAAATGACTAA
1 AAAAAATCAAAAATTTACTTAAAAATCCAAACTTTATATTTAAAAT-AATAA
36001242 AAAA
1 AAAA
36001246 TAGACTTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
50 8 0.18
51 37 0.82
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.36
Consensus pattern (51 bp):
AAAAAATCAAAAATTTACTTAAAAATCCAAACTTTATATTTAAAATAATAA
Found at i:36001335 original size:143 final size:142
Alignment explanation
Indices: 36001042--36001497 Score: 481
Period size: 143 Copynumber: 3.1 Consensus size: 142
36001032 AATAGTTTAA
* * *
36001042 AAAAAAATCAAAACTTTGTTTAAAAATTTAAATTTTTTCTTTAAAATCACTAAAAAAAAAATTTT
1 AAAAAAATCAAAACTTTGTTTAAAAATTTAAA-TTTTTCTTTAAAATGACTAAAAAATAGA--TT
* ** * * *
36001107 TTATTTTTTAAAAAATCTAAACTTTCTTTTTTTAAAAAATCACTAATTTACTTAAAAATCCAAAC
63 TTATTTTTT-AAAAATATAAACTTT-TTTTAAT-GAAAATCACTATTTTATTTAAAAATCCAAAC
**
36001172 TTTATATTTTAAATAATT
125 TTTATATTCAAAATAATT
* * *
36001190 AAAAAAATCAAAAATTTATTTAAAAATTTAAACTTTTCTTTAAAATGACTAAAAAATAGACTTTT
1 AAAAAAATCAAAACTTTGTTTAAAAATTTAAATTTTTCTTTAAAATGACTAAAAAATAGA-TTTT
* * *
36001255 ATTTTTTAAACATATAAACTTTTTTTAATGAAAATTACCATTTTATTTAAAAATCCAAA-TATT-
65 ATTTTTTAAAAATATAAACTTTTTTTAATGAAAATCACTATTTTATTTAAAAATCCAAACT-TTA
*
36001318 TATGTCAAAATAGTT
129 TAT-TCAAAATAATT
*
36001333 -AAAAAATCAAATCTTTGTTTAAAAATTTAAAATTTTTCTTTAAAATGACTAAAAAATAGA-TTT
1 AAAAAAATCAAAACTTTGTTTAAAAATTT-AAATTTTTCTTTAAAATGACTAAAAAATAGATTTT
* **
36001396 ATATTTTTAAAAATATAAATTTTCTCTTTTTTAAAGAAAATCACTATTTTATTTAAAAATTTAAA
65 AT-TTTTTAAAAATATAAA----CT-TTTTTTAATGAAAATCACTATTTTATTTAAAAATCCAAA
* **
36001461 CTTT-TATTTCGAAATTGTTT
124 CTTTATA-TTC-AAAATAATT
*
36001481 AAAATAATCAAAACTTT
1 AAAAAAATCAAAACTTT
36001498 TTCCAAGATC
Statistics
Matches: 261, Mismatches: 34, Indels: 25
0.82 0.11 0.08
Matches are distributed among these distances:
141 5 0.02
142 44 0.17
143 65 0.25
144 5 0.02
145 13 0.05
146 13 0.05
147 64 0.25
148 38 0.15
149 14 0.05
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (142 bp):
AAAAAAATCAAAACTTTGTTTAAAAATTTAAATTTTTCTTTAAAATGACTAAAAAATAGATTTTA
TTTTTTAAAAATATAAACTTTTTTTAATGAAAATCACTATTTTATTTAAAAATCCAAACTTTATA
TTCAAAATAATT
Found at i:36003653 original size:42 final size:40
Alignment explanation
Indices: 36003593--36003689 Score: 115
Period size: 42 Copynumber: 2.4 Consensus size: 40
36003583 TATATTGTTG
* * * * *
36003593 TTTTGGTGCTGTTTTTTACTGTTTTGGTTTTATTTTTTGCT
1 TTTTTGTGTTGTTTTTTACTGTTTTGATGTT-TTTTTTACT
36003634 ATTTTTGTGTTGTTTTTTACTGTTTTGATGTTTTTTTTACT
1 -TTTTTGTGTTGTTTTTTACTGTTTTGATGTTTTTTTTACT
*
36003675 GTTTTG-GTTGTTTTT
1 TTTTTGTGTTGTTTTT
36003690 GTCGTGTTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
39 9 0.18
40 5 0.10
41 8 0.16
42 27 0.55
ACGTcount: A:0.06, C:0.05, G:0.19, T:0.70
Consensus pattern (40 bp):
TTTTTGTGTTGTTTTTTACTGTTTTGATGTTTTTTTTACT
Found at i:36003659 original size:20 final size:20
Alignment explanation
Indices: 36003591--36003689 Score: 103
Period size: 21 Copynumber: 4.8 Consensus size: 20
36003581 ATTATATTGT
*
36003591 TGTTTTGGTGCTGTTTTTTAC
1 TGTTTT-GTGTTGTTTTTTAC
* * *
36003612 TGTTTTGGTTTTATTTTTTGC
1 TGTTTT-GTGTTGTTTTTTAC
*
36003633 TATTTTTGTGTTGTTTTTTAC
1 T-GTTTTGTGTTGTTTTTTAC
36003654 TGTTTTGATGTT-TTTTTTAC
1 TGTTTTG-TGTTGTTTTTTAC
36003674 TGTTTTG-GTTGTTTTT
1 TGTTTTGTGTTGTTTTT
36003690 GTCGTGTTGT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
18 3 0.05
19 5 0.08
20 20 0.30
21 34 0.52
22 4 0.06
ACGTcount: A:0.06, C:0.05, G:0.19, T:0.70
Consensus pattern (20 bp):
TGTTTTGTGTTGTTTTTTAC
Found at i:36003688 original size:18 final size:19
Alignment explanation
Indices: 36003636--36003689 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
36003626 TTTTTGCTAT
36003636 TTTTGTGTTGTTTTTTACTG
1 TTTTGTGTTG-TTTTTACTG
*
36003656 TTTTGATGTTTTTTTTACTG
1 TTTTG-TGTTGTTTTTACTG
36003676 TTTTG-GTTGTTTTT
1 TTTTGTGTTGTTTTT
36003690 GTCGTGTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.26
20 19 0.61
21 4 0.13
ACGTcount: A:0.06, C:0.04, G:0.19, T:0.72
Consensus pattern (19 bp):
TTTTGTGTTGTTTTTACTG
Found at i:36003714 original size:12 final size:12
Alignment explanation
Indices: 36003694--36003801 Score: 80
Period size: 12 Copynumber: 9.3 Consensus size: 12
36003684 GTTTTTGTCG
*
36003694 TGTTGTTTTTAT
1 TGTTATTTTTAT
*
36003706 TGTTATTTTTGT
1 TGTTATTTTTAT
* *
36003718 TGCTATTTTTGT
1 TGTTATTTTTAT
*
36003730 TGTTATTTTT-G
1 TGTTATTTTTAT
*
36003741 TGTT-TTTTTAA
1 TGTTATTTTTAT
* **
36003752 TGTT-GTTTTGC
1 TGTTATTTTTAT
36003763 TGTTATTTTTAT
1 TGTTATTTTTAT
* *
36003775 TGCTA-TTTGAT
1 TGTTATTTTTAT
*
36003786 TGTTATTTTTGT
1 TGTTATTTTTAT
36003798 TGTT
1 TGTT
36003802 TGGATGTTAT
Statistics
Matches: 76, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
10 5 0.07
11 25 0.33
12 46 0.61
ACGTcount: A:0.10, C:0.03, G:0.17, T:0.70
Consensus pattern (12 bp):
TGTTATTTTTAT
Found at i:36003731 original size:33 final size:32
Alignment explanation
Indices: 36003694--36003802 Score: 80
Period size: 35 Copynumber: 3.2 Consensus size: 32
36003684 GTTTTTGTCG
36003694 TGTTGTTTTTATTGTTATTTTTGTTGCTATTTT
1 TGTTGTTTTTATTGTTATTTTTGTTG-TATTTT
* * *
36003727 TGTTGTTATTTTTGTGTTTTTTTAATGTTGT-TTTGC
1 TGTTGTT-TTTAT-TGTTATTTT--TGTTGTATTT-T
* *
36003763 TGTTATTTTTATTGCTA--TTTGATTGTTATTTT
1 TGTTGTTTTTATTGTTATTTTTG-TTG-TATTTT
36003795 TGTTGTTT
1 TGTTGTTT
36003803 GGATGTTATT
Statistics
Matches: 59, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
30 2 0.03
31 3 0.05
32 10 0.17
33 10 0.17
34 7 0.12
35 15 0.25
36 7 0.12
37 5 0.08
ACGTcount: A:0.10, C:0.03, G:0.17, T:0.71
Consensus pattern (32 bp):
TGTTGTTTTTATTGTTATTTTTGTTGTATTTT
Found at i:36003809 original size:20 final size:20
Alignment explanation
Indices: 36003752--36003814 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
36003742 GTTTTTTTAA
*
36003752 TGTTGTTTTGCTGTTATTTT
1 TGTTGTTTTGATGTTATTTT
*
36003772 TATTGCTATTTGATTGTTATTTT
1 TGTTG-T-TTTGA-TGTTATTTT
*
36003795 TGTTGTTTGGATGTTATTTT
1 TGTTGTTTTGATGTTATTTT
36003815 ATGCGTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 13 0.36
21 5 0.14
22 5 0.14
23 13 0.36
ACGTcount: A:0.11, C:0.03, G:0.19, T:0.67
Consensus pattern (20 bp):
TGTTGTTTTGATGTTATTTT
Found at i:36003977 original size:28 final size:28
Alignment explanation
Indices: 36003924--36003978 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
36003914 TAATATAAAA
*
36003924 TTTTTAATGTCTTTTAAATTTATTTTAT
1 TTTTTAATGTCTTTTAAATATATTTTAT
* *
36003952 TTTTTAATGTTTGTTTTAATAT-TTTTA
1 TTTTTAATGTCT-TTTAAATATATTTTA
36003979 AGTGTATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (28 bp):
TTTTTAATGTCTTTTAAATATATTTTAT
Found at i:36004282 original size:13 final size:14
Alignment explanation
Indices: 36004256--36004284 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
36004246 CATGTATCTC
36004256 TTTTTAAAATATAT
1 TTTTTAAAATATAT
36004270 TTTTTAAAA-ATAT
1 TTTTTAAAATATAT
36004283 TT
1 TT
36004285 ACTATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTTAAAATATAT
Found at i:36011301 original size:34 final size:33
Alignment explanation
Indices: 36011236--36011301 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
36011226 TATAATAATT
* * *
36011236 TTAAAATATGAAATTTATTTTAAATTTATTTAC
1 TTAAAATATAAAATTTATTTTAAAATGATTTAC
*
36011269 TTAAATTATAAAACTTTATTTTAAAATGATTTA
1 TTAAAATATAAAA-TTTATTTTAAAATGATTTA
36011302 TAATCATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 11 0.39
34 17 0.61
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (33 bp):
TTAAAATATAAAATTTATTTTAAAATGATTTAC
Found at i:36011578 original size:20 final size:20
Alignment explanation
Indices: 36011553--36011594 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
36011543 ATCAATAAAA
36011553 AATGAAAATTATAAAAATTT
1 AATGAAAATTATAAAAATTT
36011573 AATGAAAATTATAAAAATTT
1 AATGAAAATTATAAAAATTT
36011593 AA
1 AA
36011595 AAAAATCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AATGAAAATTATAAAAATTT
Found at i:36012311 original size:18 final size:19
Alignment explanation
Indices: 36012274--36012313 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
36012264 TTTATATATA
36012274 TACTTTTTTAAATAATTTT
1 TACTTTTTTAAATAATTTT
36012293 TACTTTTTTAAATAATTTT
1 TACTTTTTTAAATAATTTT
36012312 TA
1 TA
36012314 TAGTTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TACTTTTTTAAATAATTTT
Found at i:36012312 original size:20 final size:20
Alignment explanation
Indices: 36012274--36012334 Score: 74
Period size: 19 Copynumber: 3.1 Consensus size: 20
36012264 TTTATATATA
36012274 TACTTTTTTAAATAA-TTTT
1 TACTTTTTTAAATAATTTTT
36012293 TACTTTTTTAAATAATTTTT
1 TACTTTTTTAAATAATTTTT
* *
36012313 ATAGTTTTTTGAAT--TTTTT
1 -TACTTTTTTAAATAATTTTT
36012332 TAC
1 TAC
36012335 AAAATAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.05
19 20 0.54
20 4 0.11
21 11 0.30
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TACTTTTTTAAATAATTTTT
Found at i:36016226 original size:21 final size:22
Alignment explanation
Indices: 36016182--36016232 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
36016172 GGTGATGTCA
*
36016182 CGATACCCGTAAGTGGATATCG
1 CGATACCCGGAAGTGGATATCG
*
36016204 CGATACTCGGAAGTGGA-ATCG
1 CGATACCCGGAAGTGGATATCG
36016225 CGATACCC
1 CGATACCC
36016233 AAAGAGGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.20
Consensus pattern (22 bp):
CGATACCCGGAAGTGGATATCG
Found at i:36018335 original size:83 final size:82
Alignment explanation
Indices: 36018189--36018354 Score: 305
Period size: 83 Copynumber: 2.0 Consensus size: 82
36018179 TCCCTTCCCG
36018189 ACGAAGAGTAAGTTAGCAATCTTGTTGATAAAAAAGGGGGAGAATGAGAGTAATGGGGAGTTATC
1 ACGAAGAGTAAGTTAGCAATCTTGTTGATAAAAAAGGGGGAGAATGAGAGTAATGGGGAGTTATC
36018254 GATGATATAGGAATTCA
66 GATGATATAGGAATTCA
36018271 ACGAAGAGTAAGTTAGCAATCTTGTTGATAAAAAAAGGGGGAGAATGAGAGTAATGGGGAGTTAT
1 ACGAAGAGTAAGTTAGCAATCTTGTTGAT-AAAAAAGGGGGAGAATGAGAGTAATGGGGAGTTAT
* *
36018336 CGATGTTATGGGAATTCA
65 CGATGATATAGGAATTCA
36018354 A
1 A
36018355 ATTTTGTTAC
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
82 29 0.36
83 52 0.64
ACGTcount: A:0.39, C:0.06, G:0.31, T:0.25
Consensus pattern (82 bp):
ACGAAGAGTAAGTTAGCAATCTTGTTGATAAAAAAGGGGGAGAATGAGAGTAATGGGGAGTTATC
GATGATATAGGAATTCA
Found at i:36019780 original size:19 final size:18
Alignment explanation
Indices: 36019734--36019780 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
36019724 CGGAATGATA
**
36019734 AGCATACTGGCTCGTTTG
1 AGCATACTGGCTCGTAAG
36019752 AGCATACTGGCTCGTAAG
1 AGCATACTGGCTCGTAAG
36019770 AGCATTACTGG
1 AGCA-TACTGG
36019781 ATCGCAAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (18 bp):
AGCATACTGGCTCGTAAG
Found at i:36026607 original size:78 final size:77
Alignment explanation
Indices: 36026478--36026633 Score: 228
Period size: 78 Copynumber: 2.0 Consensus size: 77
36026468 ATGGAAATAT
36026478 AATAATTTGTTGATTTAGATCACGAGCGAATGCGAAGTAGATCGCGAAAAAGAGAAAATGACAGA
1 AATAATTTGTTGATTTAGATCACGAGCGAATGCG-AGTAGATCGCGAAAAAGAGAAAATGACAGA
36026543 GTAATCCTTAGAG
65 GTAATCCTTAGAG
* *
36026556 AATAATTTGTTGATTTAGATCACGAGCG-A-GTG-GTAGATCGCGAAGAAAAAAGAGAAAATGAT
1 AATAATTTGTTGATTTAGATCACGAGCGAATGCGAGTAGATCGC---G-AAAAAGAGAAAATGAC
36026618 AGAGTAATCCTTAGAG
62 AGAGTAATCCTTAGAG
36026634 TTTCCTTTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
74 9 0.12
76 2 0.03
77 2 0.03
78 59 0.82
ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24
Consensus pattern (77 bp):
AATAATTTGTTGATTTAGATCACGAGCGAATGCGAGTAGATCGCGAAAAAGAGAAAATGACAGAG
TAATCCTTAGAG
Found at i:36026802 original size:35 final size:36
Alignment explanation
Indices: 36026756--36026841 Score: 129
Period size: 35 Copynumber: 2.4 Consensus size: 36
36026746 CAGAAAGATA
* * *
36026756 AGCATACTGGCTTGTTTGAGCATATTGGCTCATT-G
1 AGCATACTGGCTCGTTTGAGCAAACTGGCTCATTAG
36026791 AGCATACTGGCTCGTTTGAGCAAACTGGCTCATTAG
1 AGCATACTGGCTCGTTTGAGCAAACTGGCTCATTAG
*
36026827 AGCATATTGGCTCGT
1 AGCATACTGGCTCGT
36026842 AAGAGTTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 31 0.67
36 15 0.33
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (36 bp):
AGCATACTGGCTCGTTTGAGCAAACTGGCTCATTAG
Found at i:36026821 original size:18 final size:18
Alignment explanation
Indices: 36026756--36026841 Score: 102
Period size: 18 Copynumber: 4.8 Consensus size: 18
36026746 CAGAAAGATA
*
36026756 AGCATACTGGCTTGTTTG
1 AGCATACTGGCTCGTTTG
* *
36026774 AGCATATTGGCTC-ATTG
1 AGCATACTGGCTCGTTTG
36026791 AGCATACTGGCTCGTTTG
1 AGCATACTGGCTCGTTTG
* * *
36026809 AGCAAACTGGCTCATTAG
1 AGCATACTGGCTCGTTTG
*
36026827 AGCATATTGGCTCGT
1 AGCATACTGGCTCGT
36026842 AAGAGTTAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
17 15 0.27
18 41 0.73
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (18 bp):
AGCATACTGGCTCGTTTG
Found at i:36032567 original size:19 final size:19
Alignment explanation
Indices: 36032532--36032573 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
36032522 ATTAAAGTAT
*
36032532 TTTTAAATAATATAATTTA
1 TTTTAAATAATATAATTGA
*
36032551 TTTTAAATATTGA-AATTGA
1 TTTTAAATAAT-ATAATTGA
36032570 TTTT
1 TTTT
36032574 GTTATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTAAATAATATAATTGA
Found at i:36038474 original size:7 final size:7
Alignment explanation
Indices: 36038463--36038500 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
36038453 ATGAACTCTT
*
36038463 ATTCACT
1 ATTCACC
36038470 ATTCACC
1 ATTCACC
36038477 ATTCACC
1 ATTCACC
*
36038484 ATTCATC
1 ATTCACC
36038491 ATTCACC
1 ATTCACC
36038498 ATT
1 ATT
36038501 ATGAGGTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (7 bp):
ATTCACC
Found at i:36038824 original size:14 final size:14
Alignment explanation
Indices: 36038805--36038856 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
36038795 AATCAGACTC
36038805 AAATTAAAATCTAA
1 AAATTAAAATCTAA
* *
36038819 AAATTAATATTTAA
1 AAATTAAAATCTAA
36038833 CTCAAATTAAAATCTAA
1 ---AAATTAAAATCTAA
36038850 AAATTAA
1 AAATTAA
36038857 TATTTAATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 19 0.61
17 12 0.39
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTAAAATCTAA
Found at i:36038839 original size:31 final size:31
Alignment explanation
Indices: 36038801--36038863 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
36038791 AATTAATCAG
36038801 ACTCAAATTAAAATCTAAAAATTAATATTTA
1 ACTCAAATTAAAATCTAAAAATTAATATTTA
36038832 ACTCAAATTAAAATCTAAAAATTAATATTTA
1 ACTCAAATTAAAATCTAAAAATTAATATTTA
36038863 A
1 A
36038864 TTGAGATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.35
Consensus pattern (31 bp):
ACTCAAATTAAAATCTAAAAATTAATATTTA
Found at i:36038841 original size:17 final size:14
Alignment explanation
Indices: 36038805--36038863 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
36038795 AATCAGACTC
* *
36038805 AAATTAAAATCTAA
1 AAATTAATATTTAA
36038819 AAATTAATATTTAA
1 AAATTAATATTTAA
* *
36038833 CTCAAATTAAAATCTAA
1 ---AAATTAATATTTAA
36038850 AAATTAATATTTAA
1 AAATTAATATTTAA
36038864 TTGAGATGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
14 24 0.67
17 12 0.33
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATTAATATTTAA
Found at i:36044737 original size:6 final size:6
Alignment explanation
Indices: 36044719--36044796 Score: 81
Period size: 6 Copynumber: 13.0 Consensus size: 6
36044709 TTAAATTGAT
*
36044719 TTTAAA TTT--A TTTAAA TTTAAA TTTAAA TTTAATTA TTTAAA TTT-AC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A TTTAAA TTTAAA
* *
36044766 CTTAAA TTTAAA TTTAAA TTAAAA TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
36044797 ACAAATTTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
4 4 0.07
5 3 0.05
6 44 0.73
7 3 0.05
8 6 0.10
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:36044787 original size:17 final size:17
Alignment explanation
Indices: 36044699--36044788 Score: 83
Period size: 17 Copynumber: 5.1 Consensus size: 17
36044689 TTTTTGTTTT
* *
36044699 AATTTAGAAGTTAAATTG
1 AATTTA-AATTTAAATTA
* *
36044717 ATTTTAAATTT-ATTTA
1 AATTTAAATTTAAATTA
36044733 AATTTAAATTTAAATTTA
1 AATTTAAATTTAAA-TTA
**
36044751 ATTATTTAAATTTACCTTA
1 A--ATTTAAATTTAAATTA
36044770 AATTTAAATTTAAATTA
1 AATTTAAATTTAAATTA
36044787 AA
1 AA
36044789 ATTATAAAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
16 13 0.22
17 21 0.36
18 9 0.16
19 4 0.07
20 11 0.19
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (17 bp):
AATTTAAATTTAAATTA
Found at i:36046756 original size:29 final size:27
Alignment explanation
Indices: 36046681--36047091 Score: 168
Period size: 29 Copynumber: 14.0 Consensus size: 27
36046671 GTTTATAGGT
* *
36046681 CCCCAAACAGTCCAAAAATTGCATTTTGA
1 CCCCAAAC-TTCCAAAAATTCCATTTT-A
* **
36046710 CCCCAAAATTTTAGAAAATTCCATTTTGA
1 CCCCAAACTTCCA-AAAATTCCATTTT-A
36046739 CCCCGAAACTTCCAAAAATTACCATTTTA
1 CCCC-AAACTTCCAAAAATT-CCATTTTA
*
36046768 CCCCTTCAAACTTTCC-AAAATTCTATTTTTA
1 -CCC--CAAAC-TTCCAAAAATTCCA-TTTTA
* * *
36046799 ACCCTAATTTCACCAAAAATTACCATTTTA
1 CCCCAAACTT--CCAAAAATT-CCATTTTA
*
36046829 CCCTCGAACTTTCC-AAAATTCCATTTTTAA
1 CCC-CAAAC-TTCCAAAAATTCCA-TTTT-A
*
36046859 CCCCAAAACTTTCAAAAATTACCATTTTA
1 CCCC-AAACTTCCAAAAATT-CCATTTTA
*
36046888 CCCCCAAACTCTCC-AAAATTCTATTTTTA
1 -CCCCAAACT-TCCAAAAATTCCA-TTTTA
* * *
36046917 ACCCTAATTTCACCAAAAATTACCATTTTA
1 CCCCAAACTT--CCAAAAATT-CCATTTTA
* *
36046947 CCCCCAAAATTTCC-AAAATTCAATTTTTAA
1 -CCCC-AAACTTCCAAAAATTCCA-TTTT-A
* * *
36046977 TCCCGATA-TCACCAAAAATTACCATTTTA
1 -CCCCAAACT-TCCAAAAATT-CCATTTTA
36047006 CCCCTAAACTTTCC-AAAATTCCATTTTTA
1 CCCC-AAAC-TTCCAAAAATTCCA-TTTTA
* ** * *
36047035 ACCCTGATTTCACCAAAATTACCATTTTA
1 CCCCAAACTTC-CAAAAATT-CCATTTTA
* * *
36047064 CCCCTAAATTTTTCTAAAATTCCATTTT
1 CCCC-AAA-CTTCCAAAAATTCCATTTT
36047092 CGACCTCGAT
Statistics
Matches: 296, Mismatches: 44, Indels: 84
0.70 0.10 0.20
Matches are distributed among these distances:
27 6 0.02
28 27 0.09
29 119 0.40
30 98 0.33
31 34 0.11
32 12 0.04
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (27 bp):
CCCCAAACTTCCAAAAATTCCATTTTA
Found at i:36046856 original size:59 final size:58
Alignment explanation
Indices: 36046750--36047128 Score: 428
Period size: 59 Copynumber: 6.4 Consensus size: 58
36046740 CCCGAAACTT
*
36046750 CCAAAAATTACCATTTTACCCCTTCAAACTTTCCAAAATTCTATTTTTAACCCTAATTTCA
1 CCAAAAATTACCATTTTA-CCC--CAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCA
* *
36046811 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCAAAACTTT--
1 CCAAAAATTACCATTTTACCC-CAAACTTTCCAAAATTCCATTTTTAA-CCC-TAA-TTTCA
* *
36046871 -CAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTCTATTTTTAACCCTAATTTCA
1 CCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCA
* * * *
36046929 CCAAAAATTACCATTTTACCCCCAAAATTTCCAAAATTCAATTTTTAATCCC-GATATCA
1 CCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAA-CCCTAATTTCA
*
36046988 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCC-AAACTTTCCAAAATTCCATTTTTAACCCTAATTTCA
* * ** *
36047047 CC-AAAATTACCATTTTACCCCTAAATTTTTCTAAAATTCCATTTTCGA-CCTCGATTTCA
1 CCAAAAATTACCATTTTACCCC-AAA-CTTTCCAAAATTCCATTTTTAACCCT-AATTTCA
* *
36047106 CTAAAAAATTACCATTTTGCCCC
1 C-CAAAAATTACCATTTTACCCC
36047129 CAGGTATCCA
Statistics
Matches: 283, Mismatches: 21, Indels: 28
0.85 0.06 0.08
Matches are distributed among these distances:
56 3 0.01
57 2 0.01
58 36 0.13
59 189 0.67
60 12 0.04
61 38 0.13
62 3 0.01
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCA
Found at i:36046930 original size:118 final size:118
Alignment explanation
Indices: 36046692--36047091 Score: 531
Period size: 118 Copynumber: 3.4 Consensus size: 118
36046682 CCCAAACAGT
* ** *
36046692 CCAAAAATT-GCATTTTGA-CCCCAAAATTTTAGAAAATTCCA-TTTTGACCCCGAAACTTCCAA
1 CCAAAAATTACCATTTT-ACCCCCAAAA-TTTCCAAAATTCCATTTTTAACCCCGAAACTTCCAA
36046754 AAATTACCATTTTACCCCTTCAAACTTTCCAAAATTCTATTTTTAACCCTAATTTCA
64 AAATTACCATTTTACCCC--CAAACTTTCCAAAATTCTATTTTTAACCCTAATTTCA
* * * * *
36046811 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCAAAACTTTCAAAA
1 CCAAAAATTACCATTTTACCCCCAAAATTTCCAAAATTCCATTTTTAACCCCGAAACTTCCAAAA
*
36046876 ATTACCATTTTACCCCCAAACTCTCCAAAATTCTATTTTTAACCCTAATTTCA
66 ATTACCATTTTACCCCCAAACTTTCCAAAATTCTATTTTTAACCCTAATTTCA
* * * *
36046929 CCAAAAATTACCATTTTACCCCCAAAATTTCCAAAATTCAATTTTTAATCCCGATA-TCACCAAA
1 CCAAAAATTACCATTTTACCCCCAAAATTTCCAAAATTCCATTTTTAACCCCGAAACT-TCCAAA
* * *
36046993 AATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCA
65 AATTACCATTTTACCCCCAAACTTTCCAAAATTCTATTTTTAACCCTAATTTCA
* * *
36047047 CC-AAAATTACCATTTTACCCCTAAATTTTTCTAAAATTCCATTTT
1 CCAAAAATTACCATTTTACCCCCAAA-ATTTCCAAAATTCCATTTT
36047092 CGACCTCGAT
Statistics
Matches: 249, Mismatches: 27, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
117 23 0.09
118 157 0.63
119 22 0.09
120 47 0.19
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (118 bp):
CCAAAAATTACCATTTTACCCCCAAAATTTCCAAAATTCCATTTTTAACCCCGAAACTTCCAAAA
ATTACCATTTTACCCCCAAACTTTCCAAAATTCTATTTTTAACCCTAATTTCA
Found at i:36046993 original size:177 final size:176
Alignment explanation
Indices: 36046750--36047130 Score: 484
Period size: 177 Copynumber: 2.1 Consensus size: 176
36046740 CCCGAAACTT
* * *
36046750 CCAAAAATTACCATTTTACCCCTTCAAACTTTCCAAAATTCTATTTTTAACCCTAATTTCACCAA
1 CCAAAAATTACCATTTTACCCC--CAAAATTTCCAAAATTCAATTTTTAACCCTAATATCACCAA
*
36046815 AAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCCCAAAACTTTCA-AAAAT
64 AAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAA-CCC-AAA-TTTCACAAAAT
* *
36046878 TACCATTTTACCCCCAAA-CTCTCCAAAATTCTATTTTTAACC-CTAATTTCA
125 TACCATTTTACCCCCAAATCTCTCCAAAATTCCATTTTCAACCTC-AATTTCA
*
36046929 CCAAAAATTACCATTTTACCCCCAAAATTTCCAAAATTCAATTTTTAATCCC-GATATCACCAAA
1 CCAAAAATTACCATTTTACCCCCAAAATTTCCAAAATTCAATTTTTAA-CCCTAATATCACCAAA
**
36046993 AATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACCAAAATTACC
65 AATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCAAATTTCA-CAAAATTACC
* * * * * *
36047058 ATTTTACCCCTAAATTTTTCTAAAATTCCATTTTCGACCTCGATTTCA
129 ATTTTACCCCCAAATCTCTCCAAAATTCCATTTTCAACCTCAATTTCA
* *
36047106 CTAAAAAATTACCATTTTGCCCCCA
1 C-CAAAAATTACCATTTTACCCCCA
36047131 GGTATCCAAA
Statistics
Matches: 178, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
174 5 0.03
175 1 0.01
176 25 0.14
177 96 0.54
178 29 0.16
179 22 0.12
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.35
Consensus pattern (176 bp):
CCAAAAATTACCATTTTACCCCCAAAATTTCCAAAATTCAATTTTTAACCCTAATATCACCAAAA
ATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCAAATTTCACAAAATTACCAT
TTTACCCCCAAATCTCTCCAAAATTCCATTTTCAACCTCAATTTCA
Found at i:36047109 original size:29 final size:28
Alignment explanation
Indices: 36047020--36047111 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 28
36047010 TAAACTTTCC
* *
36047020 AAAATTCCATTTTTAACC-CTGATTTCACC
1 AAAATTCCA-TTTTCACCTC-GATTTCACT
* ** **
36047049 AAAATTACCATTTTACCCCTAAATTTTTCT
1 AAAATT-CCATTTT-CACCTCGATTTCACT
36047079 AAAATTCCATTTTCGACCTCGATTTCACT
1 AAAATTCCATTTTC-ACCTCGATTTCACT
36047108 AAAA
1 AAAA
36047112 AATTACCATT
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
28 1 0.02
29 30 0.64
30 16 0.34
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (28 bp):
AAAATTCCATTTTCACCTCGATTTCACT
Found at i:36047139 original size:118 final size:117
Alignment explanation
Indices: 36046692--36047141 Score: 457
Period size: 118 Copynumber: 3.8 Consensus size: 117
36046682 CCCAAACAGT
* ** * *
36046692 CCAAAAATT-GCATTTTGACCCC-AAAATTTTAGAAAATTCCATTTTGACCCCGA-A--ACTTCC
1 CCAAAAATTACCATTTT-ACCCCTAAAA-TTTCCAAAATTCCATTTTTAACCCGATATCAC-T-C
* *
36046752 AAAAATTACCATTTTACCCCTTCAAACTTTCCAAAATTCTATTTTTAACCCTAATTTCA
62 AAAAATTACCATTTTACCCC--C-AACTATCCAAAATTCCATTTTTAACCCTAATTTCA
* * * * * **
36046811 CCAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCCCAAAACTTTCAAA
1 CCAAAAATTACCATTTTACCCCT-AAAATTTCCAAAATTCCATTTTTAACCCGATATCACTCAAA
* *
36046875 AATTACCATTTTACCCCCAAACTCTCCAAAATTCTATTTTTAACCCTAATTTCA
65 AATTACCATTTTACCCCC-AACTATCCAAAATTCCATTTTTAACCCTAATTTCA
* *
36046929 CCAAAAATTACCATTTTACCCCCAAAATTTCCAAAATTCAATTTTTAATCCCGATATCAC-CAAA
1 CCAAAAATTACCATTTTACCCCTAAAATTTCCAAAATTCCATTTTTAA-CCCGATATCACTCAAA
* * *
36046993 AATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCA
65 AATTACCATTTTACCCC-CAACTATCCAAAATTCCATTTTTAACCCTAATTTCA
* * ** * *
36047047 CC-AAAATTACCATTTTACCCCTAAATTTTTCTAAAATTCCATTTTCGACCTCGATTTCACTAAA
1 CCAAAAATTACCATTTTACCCCTAAA-ATTTCCAAAATTCCATTTTTAACC-CGATATCACTCAA
* **
36047111 AAATTACCATTTTGCCCCCAGGTATCCAAAA
64 AAATTACCATTTTACCCCCAACTATCCAAAA
36047142 GTCCCGTTTT
Statistics
Matches: 282, Mismatches: 37, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
117 24 0.09
118 168 0.60
119 59 0.21
120 30 0.11
121 1 0.00
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (117 bp):
CCAAAAATTACCATTTTACCCCTAAAATTTCCAAAATTCCATTTTTAACCCGATATCACTCAAAA
ATTACCATTTTACCCCCAACTATCCAAAATTCCATTTTTAACCCTAATTTCA
Found at i:36051731 original size:24 final size:24
Alignment explanation
Indices: 36051685--36051731 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
36051675 CACGATTTAG
* *
36051685 TATTTATTAGCCTAATATATTTGA
1 TATTTATTAGCATAAAATATTTGA
* *
36051709 TATTTATTAGTATAAAATCTTTG
1 TATTTATTAGCATAAAATATTTG
36051732 TTATATCATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (24 bp):
TATTTATTAGCATAAAATATTTGA
Found at i:36057346 original size:45 final size:44
Alignment explanation
Indices: 36057292--36057418 Score: 127
Period size: 45 Copynumber: 2.8 Consensus size: 44
36057282 GAATATGCTT
36057292 TATCCATGAAGT-TTCTTCTATGAATTCGCATGTATGAG-TC-TACTA
1 TATCCATGAA-TATTCTTCTATGAATT-GCATGTATGAGTTCGT-C-A
* *
36057337 TATCTATGAATCA-TCTTCTATGAATATGGATGTATGAGTTCGTCA
1 TATCCATGAAT-ATTCTTCTATGAAT-TGCATGTATGAGTTCGTCA
* *
36057382 TATCCATGAATATTCTTCTACGAGTTTGCATGTATGA
1 TATCCATGAATATTCTTCTATGA-ATTGCATGTATGA
36057419 ATCTGCATAT
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
44 2 0.03
45 61 0.88
46 5 0.07
47 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40
Consensus pattern (44 bp):
TATCCATGAATATTCTTCTATGAATTGCATGTATGAGTTCGTCA
Found at i:36060454 original size:20 final size:20
Alignment explanation
Indices: 36060412--36060454 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
36060402 ACTTTCAGAA
* *
36060412 TTAAGCTTAATTAACCTCTT
1 TTAACCTTAATTAACCTCAT
36060432 TTAACCTTAATTAATCCT-AT
1 TTAACCTTAATTAA-CCTCAT
36060452 TTA
1 TTA
36060455 TATTCAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.33, C:0.19, G:0.02, T:0.47
Consensus pattern (20 bp):
TTAACCTTAATTAACCTCAT
Found at i:36065106 original size:21 final size:21
Alignment explanation
Indices: 36065082--36065135 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
36065072 AGAGTTTTTA
*
36065082 GTATCAGTAGAAGTA-AGACTT
1 GTATCAGTAGAAG-AGACACTT
*
36065103 GTATCGGTAGAAGAGACACTT
1 GTATCAGTAGAAGAGACACTT
*
36065124 GTAACAGTAGAA
1 GTATCAGTAGAA
36065136 CTATCACTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (21 bp):
GTATCAGTAGAAGAGACACTT
Found at i:36067448 original size:161 final size:162
Alignment explanation
Indices: 36067183--36067501 Score: 480
Period size: 161 Copynumber: 2.0 Consensus size: 162
36067173 CCCACCATTA
* * **
36067183 TCTTGATCTCGTCATTCAACTCGTATTCAAAACGGATACACATAGCCTCATTTGTTGGCACAATC
1 TCTTGATCTCGTCATTCAACTCGTATTCAAAACGGACACACATAGCCTCATCTGTCAGCACAATC
* * * *
36067248 TCCTGGGCATATTTGCTGAGATGTACAAACTCCCGTTCATAGTCTACCACCGTCTTG-TTCCTTG
66 TCCTGGCCATATTTACTGAGATGTACAAACTCCCGTTCATAGTCTACCACCATCTTGTTTCCCTG
36067312 TATTAACTCTAAGAATTATTTCTTCTTTCTGT
131 TATTAACTCTAAGAATTATTTCTTCTTTCTGT
*
36067344 TCTTGATCTCGTCATTCAAC-CTGTATTCAAAACGGACACACATAGCCTCATCTGTCAGCATAAT
1 TCTTGATCTCGTCATTCAACTC-GTATTCAAAACGGACACACATAGCCTCATCTGTCAGCACAAT
* * * *
36067408 CTCCTTGCCATATTTACTGAGATGTACAAACTCCCGTTCATATTCTGCCACTATCTTGTTTCCCT
65 CTCCTGGCCATATTTACTGAGATGTACAAACTCCCGTTCATAGTCTACCACCATCTTGTTTCCCT
* *
36067473 GTCTTAACTCTAAGAATTCTTTCTTCTTT
130 GTATTAACTCTAAGAATTATTTCTTCTTT
36067502 TTGTCTAGGT
Statistics
Matches: 141, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
160 1 0.01
161 108 0.77
162 32 0.23
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (162 bp):
TCTTGATCTCGTCATTCAACTCGTATTCAAAACGGACACACATAGCCTCATCTGTCAGCACAATC
TCCTGGCCATATTTACTGAGATGTACAAACTCCCGTTCATAGTCTACCACCATCTTGTTTCCCTG
TATTAACTCTAAGAATTATTTCTTCTTTCTGT
Found at i:36070346 original size:20 final size:20
Alignment explanation
Indices: 36070304--36070345 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
36070294 ACTTTCACAA
* *
36070304 TTAAGCTTAATTAACCTATT
1 TTAACCTTAATTAACCCATT
36070324 TTAACCTTAATTAATCCCATT
1 TTAACCTTAATTAA-CCCATT
36070345 T
1 T
36070346 ATATTCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.33, C:0.19, G:0.02, T:0.45
Consensus pattern (20 bp):
TTAACCTTAATTAACCCATT
Found at i:36071935 original size:16 final size:16
Alignment explanation
Indices: 36071916--36071946 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36071906 TGTTAATGAT
36071916 TTTGTTATTTACTTTC
1 TTTGTTATTTACTTTC
*
36071932 TTTGTTTTTTACTTT
1 TTTGTTATTTACTTT
36071947 ACCTTTTTAT
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:0.10, C:0.10, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTGTTATTTACTTTC
Found at i:36072881 original size:19 final size:17
Alignment explanation
Indices: 36072825--36072881 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 17
36072815 ATTATTGTTG
36072825 AAAATATATTTTTGCAAA
1 AAAATATATTTTTG-AAA
* *
36072843 AAAAAAGTATTTTCTTAAA
1 AAAATA-TATTTT-TGAAA
36072862 AAAATATATATTTATGAAA
1 AAAATATAT-TTT-TGAAA
36072881 A
1 A
36072882 TAAGGCATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 8 0.26
19 22 0.71
20 1 0.03
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.37
Consensus pattern (17 bp):
AAAATATATTTTTGAAA
Found at i:36074656 original size:76 final size:77
Alignment explanation
Indices: 36074482--36074657 Score: 230
Period size: 78 Copynumber: 2.3 Consensus size: 77
36074472 CAATGATGAG
* * *
36074482 CTGACGGTGACACTGTAAACATCGTAAAACTGTATCGAACTAGCAATGACACTGTAAACACTGCA
1 CTGACGGTGACACTGTAAACACCATAAAACTGTATCGAACGAGCAATGACACTGT-AACACTGCA
36074547 AACCAATACTGAA
65 AACCAATACTGAA
* * * * * *
36074560 CTGATGGCGACACTGTAAACACCATAATATTGTATCGAACCGA-CAGTGACACTGT-ACATTGCA
1 CTGACGGTGACACTGTAAACACCATAAAACTGTATCGAA-CGAGCAATGACACTGTAACACTGCA
36074623 AACCAATACTGAA
65 AACCAATACTGAA
*
36074636 CTGACGGTGACACTGCAAACAC
1 CTGACGGTGACACTGTAAACAC
36074658 TGTAATACTA
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
76 39 0.46
78 44 0.52
79 2 0.02
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (77 bp):
CTGACGGTGACACTGTAAACACCATAAAACTGTATCGAACGAGCAATGACACTGTAACACTGCAA
ACCAATACTGAA
Found at i:36074664 original size:76 final size:77
Alignment explanation
Indices: 36074482--36074666 Score: 232
Period size: 76 Copynumber: 2.4 Consensus size: 77
36074472 CAATGATGAG
* *
36074482 CTGACGGTGACACTGTAAACA-TCGTAAAACTGTATCGAACTAGCAATGACACTGTAAACACTGC
1 CTGACGGTGACACTGTAAACACT-GTAATACTGTATCGAACGAGCAATGACACTGT-AACACTGC
36074546 AAACCAATACTGAA
64 AAACCAATACTGAA
* * ** * * *
36074560 CTGATGGCGACACTGTAAACACCATAATATTGTATCGAACCGA-CAGTGACACTGT-ACATTGCA
1 CTGACGGTGACACTGTAAACACTGTAATACTGTATCGAA-CGAGCAATGACACTGTAACACTGCA
36074623 AACCAATACTGAA
65 AACCAATACTGAA
*
36074636 CTGACGGTGACACTGCAAACACTGTAATACT
1 CTGACGGTGACACTGTAAACACTGTAATACT
36074667 ATACTGAGTT
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
76 45 0.50
78 43 0.48
79 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (77 bp):
CTGACGGTGACACTGTAAACACTGTAATACTGTATCGAACGAGCAATGACACTGTAACACTGCAA
ACCAATACTGAA
Found at i:36074686 original size:76 final size:76
Alignment explanation
Indices: 36074482--36074691 Score: 197
Period size: 76 Copynumber: 2.7 Consensus size: 76
36074472 CAATGATGAG
* * * * * * **
36074482 CTGACGGTGACACTGTAAACATCGTAAAACTGTATCGAACTAGCAATGACACTGTAAACACTGCA
1 CTGACGGCGACACTGCAAACACCATAATACTATATCGAACCGGCAATGACACTGT--ACACTGCA
36074547 AACCAATACTGAA
64 AACCAATACTGAA
* * * * * * *
36074560 CTGATGGCGACACTGTAAACACCATAATATTGTATCGAACCGACAGTGACACTGTACATTGCAAA
1 CTGACGGCGACACTGCAAACACCATAATACTATATCGAACCGGCAATGACACTGTACACTGCAAA
36074625 CCAATACTGAA
66 CCAATACTGAA
* ** ***
36074636 CTGACGGTGACACTGCAAACACTGTAATACTATA-CTGAGTTGGCAATGACACTGTA
1 CTGACGGCGACACTGCAAACACCATAATACTATATC-GAACCGGCAATGACACTGTA
36074692 ACCACTACGT
Statistics
Matches: 108, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
75 1 0.01
76 62 0.57
78 45 0.42
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (76 bp):
CTGACGGCGACACTGCAAACACCATAATACTATATCGAACCGGCAATGACACTGTACACTGCAAA
CCAATACTGAA
Found at i:36074719 original size:39 final size:40
Alignment explanation
Indices: 36074676--36074754 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 40
36074666 TATACTGAGT
*
36074676 TGGCAATGACACTGTAACCACTACG-TAGCTATGTTGAAC
1 TGGCAATGACACTGTAAACACTACGATAGCTATGTTGAAC
* * * *
36074715 TGGCAGTGACACTGTAAACACTGCGATTGCTATTTTGAAC
1 TGGCAATGACACTGTAAACACTACGATAGCTATGTTGAAC
36074755 GATGGTGACA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 22 0.65
40 12 0.35
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (40 bp):
TGGCAATGACACTGTAAACACTACGATAGCTATGTTGAAC
Found at i:36077000 original size:12 final size:12
Alignment explanation
Indices: 36076983--36077007 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36076973 AACAATAATT
36076983 AAAAAAATTTAA
1 AAAAAAATTTAA
36076995 AAAAAAATTTAA
1 AAAAAAATTTAA
36077007 A
1 A
36077008 CCGCTCCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAAAATTTAA
Found at i:36078268 original size:32 final size:32
Alignment explanation
Indices: 36078231--36078327 Score: 109
Period size: 32 Copynumber: 3.2 Consensus size: 32
36078221 AAGAAAAATA
36078231 ATATTTTCTTTATTTGAATAATAATAAGAATG
1 ATATTTTCTTTATTTGAATAATAATAAGAATG
* * * *
36078263 ATA-TTT-TATA-TTG--T--TAAGAAAAATA
1 ATATTTTCTTTATTTGAATAATAATAAGAATG
36078288 ATATTTTCTTTATTTGAATAATAATAAGAATG
1 ATATTTTCTTTATTTGAATAATAATAAGAATG
36078320 ATATTTTC
1 ATATTTTC
36078328 AAGATCATCA
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
25 11 0.22
26 3 0.06
27 4 0.08
28 3 0.06
29 3 0.06
30 4 0.08
31 3 0.06
32 19 0.38
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (32 bp):
ATATTTTCTTTATTTGAATAATAATAAGAATG
Found at i:36078281 original size:57 final size:57
Alignment explanation
Indices: 36078212--36078326 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
36078202 AATATCATTA
36078212 TATATTGTTAAGAAAAATAATATTTTCTTTATTTGAATAATAATAAGAATGATATTT
1 TATATTGTTAAGAAAAATAATATTTTCTTTATTTGAATAATAATAAGAATGATATTT
36078269 TATATTGTTAAGAAAAATAATATTTTCTTTATTTGAATAATAATAAGAATGATATTT
1 TATATTGTTAAGAAAAATAATATTTTCTTTATTTGAATAATAATAAGAATGATATTT
36078326 T
1 T
36078327 CAAGATCATC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (57 bp):
TATATTGTTAAGAAAAATAATATTTTCTTTATTTGAATAATAATAAGAATGATATTT
Found at i:36089062 original size:15 final size:16
Alignment explanation
Indices: 36089033--36089069 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
36089023 AATAAAAATA
36089033 TTTTTTTTAATTTTTC
1 TTTTTTTTAATTTTTC
36089049 TATTTTTTT-A-TTTTC
1 T-TTTTTTTAATTTTTC
36089064 TTTTTT
1 TTTTTT
36089070 CTCAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.25
15 6 0.30
16 2 0.10
17 7 0.35
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTAATTTTTC
Found at i:36102741 original size:7 final size:7
Alignment explanation
Indices: 36102731--36102792 Score: 65
Period size: 7 Copynumber: 9.1 Consensus size: 7
36102721 CAACAATCAA
36102731 GTCAACG
1 GTCAACG
36102738 GTCAACG
1 GTCAACG
* *
36102745 ATGAACG
1 GTCAACG
*
36102752 ATCAACG
1 GTCAACG
*
36102759 GTCAATG
1 GTCAACG
36102766 GTCAACG
1 GTCAACG
*
36102773 ATCAACG
1 GTCAACG
36102780 GTCAA--
1 GTCAACG
36102785 GTCAACG
1 GTCAACG
36102792 G
1 G
36102793 ATTGGTTCAG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
5 5 0.11
7 40 0.89
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:36102758 original size:21 final size:21
Alignment explanation
Indices: 36102719--36102791 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
36102709 AACCCAAAAA
*
36102719 GTCAACAATCAA-G-TCAACG
1 GTCAACGATCAACGATCAACG
*
36102738 GTCAACGATGAACGATCAACG
1 GTCAACGATCAACGATCAACG
* *
36102759 GTCAATGGTCAACGATCAACG
1 GTCAACGATCAACGATCAACG
36102780 GTCAA-G-TCAACG
1 GTCAACGATCAACG
36102792 GATTGGTTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 16 0.34
20 2 0.04
21 29 0.62
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (21 bp):
GTCAACGATCAACGATCAACG
Found at i:36102770 original size:14 final size:14
Alignment explanation
Indices: 36102732--36102792 Score: 72
Period size: 14 Copynumber: 4.5 Consensus size: 14
36102722 AACAATCAAG
36102732 TCAACGGTCAACGA
1 TCAACGGTCAACGA
* * *
36102746 TGAACGATCAACGG
1 TCAACGGTCAACGA
*
36102760 TCAATGGTCAACGA
1 TCAACGGTCAACGA
36102774 TCAACGGTCAA-G-
1 TCAACGGTCAACGA
36102786 TCAACGG
1 TCAACGG
36102793 ATTGGTTCAG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
12 7 0.18
13 1 0.03
14 31 0.79
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.16
Consensus pattern (14 bp):
TCAACGGTCAACGA
Found at i:36103540 original size:29 final size:29
Alignment explanation
Indices: 36103494--36103558 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
36103484 AAAAGGGTTT
* *
36103494 TTAAAGAAAATTAGGGTTTTTAAATTGTCC
1 TTAAA-AAAATTAAGGTTTCTAAATTGTCC
*
36103524 TTAAAAAAATTAAGGTTTCTAAATTGTTC
1 TTAAAAAAATTAAGGTTTCTAAATTGTCC
36103553 TTAAAA
1 TTAAAA
36103559 CTTCACTCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (29 bp):
TTAAAAAAATTAAGGTTTCTAAATTGTCC
Found at i:36110524 original size:30 final size:30
Alignment explanation
Indices: 36110484--36110624 Score: 155
Period size: 30 Copynumber: 4.7 Consensus size: 30
36110474 TCCAGGTAGT
*
36110484 CCCT-AAAC-TTTCCTAAAATCACATTTTAA
1 CCCTCAAACTTTTCC-AAAATTACATTTTAA
* * *
36110513 CCCCCAAACTTTTTCAAAATTACATTTT-G
1 CCCTCAAACTTTTCCAAAATTACATTTTAA
*
36110542 CCCATCAAACTTTTCCAAAATTACATTTTTA
1 CCC-TCAAACTTTTCCAAAATTACATTTTAA
*
36110573 CCCTTAAACTTTTCCAAAATTACATTTTAA
1 CCCTCAAACTTTTCCAAAATTACATTTTAA
* *
36110603 -TCTCTAAACTTGTCCAAAATTA
1 CCCTC-AAACTTTTCCAAAATTA
36110625 TGATTTCACC
Statistics
Matches: 95, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.08
30 80 0.84
31 7 0.07
ACGTcount: A:0.35, C:0.26, G:0.01, T:0.38
Consensus pattern (30 bp):
CCCTCAAACTTTTCCAAAATTACATTTTAA
Found at i:36110659 original size:29 final size:29
Alignment explanation
Indices: 36110618--36110688 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
36110608 AAACTTGTCC
36110618 AAAATTA-TGATTTCACCTCCGAAC-ATCTA
1 AAAATTACT-ATTTCACCTCCGAACAATC-A
**
36110647 AAAATTACTATTTTGCCTCCGAACAATCA
1 AAAATTACTATTTCACCTCCGAACAATCA
*
36110676 AAAATTACCATTT
1 AAAATTACTATTT
36110689 TACCCCTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 33 0.89
30 4 0.11
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAATTACTATTTCACCTCCGAACAATCA
Found at i:36110689 original size:29 final size:29
Alignment explanation
Indices: 36110633--36110689 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
36110623 TATGATTTCA
*
36110633 CCTCCGAACATCTAAAAATTACTATTTTG
1 CCTCCGAACATCTAAAAATTACCATTTTG
36110662 CCTCCGAACAATC-AAAAATTACCATTTT
1 CCTCCGAAC-ATCTAAAAATTACCATTTT
36110690 ACCCCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (29 bp):
CCTCCGAACATCTAAAAATTACCATTTTG
Found at i:36110706 original size:29 final size:31
Alignment explanation
Indices: 36110674--36110789 Score: 91
Period size: 29 Copynumber: 3.9 Consensus size: 31
36110664 TCCGAACAAT
36110674 CAAAAATTACCATTTT-ACCCCTAAA-TTTC
1 CAAAAATTACCATTTTAACCCCTAAATTTTC
* *
36110703 CAAAAATCA-CATTTTCAACCTC-AAATTTTC
1 CAAAAATTACCATTTT-AACCCCTAAATTTTC
* ** *
36110733 CAAAAGTT-TGATTTTAATCCC-AAATTTTC
1 CAAAAATTACCATTTTAACCCCTAAATTTTC
* * * *
36110762 CAAAAATTTCAATTTTGACCCCCAAATT
1 CAAAAATTACCATTTTAACCCCTAAATT
36110790 CCTCAAAAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
28 6 0.09
29 30 0.43
30 28 0.41
31 5 0.07
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (31 bp):
CAAAAATTACCATTTTAACCCCTAAATTTTC
Found at i:36119379 original size:18 final size:20
Alignment explanation
Indices: 36119356--36119399 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
36119346 TATTTTATAA
36119356 TATTA-TATAATAA-AATAT
1 TATTATTATAATAATAATAT
*
36119374 TATTATTTATTATAATAATAT
1 TATTA-TTATAATAATAATAT
36119395 TATTA
1 TATTA
36119400 ATTAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
20 7 0.32
21 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTATTATAATAATAATAT
Found at i:36119403 original size:18 final size:18
Alignment explanation
Indices: 36119352--36119404 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
36119342 CTTATATTTT
36119352 ATAATATTATATAA-TAAA
1 ATAATATTAT-TAATTAAA
* * *
36119370 ATATTATTATTTATTATA
1 ATAATATTATTAATTAAA
36119388 ATAATATTATTAATTAA
1 ATAATATTATTAATTAA
36119405 TATATCTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAATATTATTAATTAAA
Found at i:36119408 original size:21 final size:20
Alignment explanation
Indices: 36119365--36119408 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
36119355 ATATTATATA
* *
36119365 ATAAAATATTATTATTTATT
1 ATAAAATATTATTAATTAAT
36119385 ATAATAATATTATTAATTAAT
1 ATAA-AATATTATTAATTAAT
36119406 ATA
1 ATA
36119409 TCTTTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAAATATTATTAATTAAT
Found at i:36123114 original size:39 final size:39
Alignment explanation
Indices: 36123011--36123100 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 39
36123001 AAAAGAGTTG
* *
36123011 GATCTCATTATATTA-CTCGAGAATCTGCAACAAAGGCTA
1 GATCTCATTATATCACCT-AAGAATCTGCAACAAAGGCTA
*
36123050 GATCTCATTATATCACCTAAGAATCTGCAACAAATGCTA
1 GATCTCATTATATCACCTAAGAATCTGCAACAAAGGCTA
*
36123089 GATCTCGTTATA
1 GATCTCATTATA
36123101 ATTTACAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 44 0.96
40 2 0.04
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (39 bp):
GATCTCATTATATCACCTAAGAATCTGCAACAAAGGCTA
Found at i:36124434 original size:13 final size:13
Alignment explanation
Indices: 36124416--36124442 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
36124406 AATGGGACTC
36124416 TAGAACCACATTT
1 TAGAACCACATTT
36124429 TAGAACCACATTT
1 TAGAACCACATTT
36124442 T
1 T
36124443 TTGGTACCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (13 bp):
TAGAACCACATTT
Found at i:36129700 original size:12 final size:12
Alignment explanation
Indices: 36129674--36129706 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
36129664 TTCGTATAAC
36129674 GTTCGTTTA--T
1 GTTCGTTTATTT
36129684 GTTCGTTTATTT
1 GTTCGTTTATTT
36129696 GTTCGTTTATT
1 GTTCGTTTATT
36129707 AAGCTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.43
12 12 0.57
ACGTcount: A:0.09, C:0.09, G:0.18, T:0.64
Consensus pattern (12 bp):
GTTCGTTTATTT
Found at i:36129838 original size:12 final size:12
Alignment explanation
Indices: 36129803--36129838 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
36129793 ATTCACGAAC
*
36129803 AAGCTCGTTTAA
1 AAGCTCGTTTAT
*
36129815 AAGCTCATTTAT
1 AAGCTCGTTTAT
36129827 AAGCTCGTTTAT
1 AAGCTCGTTTAT
36129839 TGACTCGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:36132227 original size:30 final size:28
Alignment explanation
Indices: 36132193--36132249 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
36132183 AATTAACTTT
36132193 TAATATTTTTTGAATTTTTTA-AAAATTTTA
1 TAATATTTTTT--A-TTTTTACAAAATTTTA
36132223 TAATATTTTTTATTTTTACAAAATTTT
1 TAATATTTTTTATTTTTACAAAATTTT
36132250 TAAATAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 6 0.23
28 9 0.35
30 11 0.42
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (28 bp):
TAATATTTTTTATTTTTACAAAATTTTA
Found at i:36132255 original size:28 final size:28
Alignment explanation
Indices: 36132190--36132255 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 28
36132180 ATTAATTAAC
36132190 TTTT-AATATTTTTTGAATTTTTTAAAAA
1 TTTTAAATATTTTTT-AATTTTTTAAAAA
36132218 TTTTATAATATTTTTT-A-TTTTTACAAAA
1 TTTTA-AATATTTTTTAATTTTTTA-AAAA
36132246 TTTTTAAATA
1 -TTTTAAATA
36132256 ATTTAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
27 6 0.18
28 13 0.38
29 5 0.15
30 10 0.29
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTAAATATTTTTTAATTTTTTAAAAA
Found at i:36132521 original size:15 final size:16
Alignment explanation
Indices: 36132501--36132530 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36132491 CTAAATAAAT
36132501 TTTG-AAATATCTATA
1 TTTGAAAATATCTATA
36132516 TTTGAAAATATCTAT
1 TTTGAAAATATCTAT
36132531 TGGTCTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (16 bp):
TTTGAAAATATCTATA
Found at i:36137350 original size:28 final size:29
Alignment explanation
Indices: 36137309--36137366 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
36137299 TGGGCTTGGA
*
36137309 AACCAAATTAAGTCCTTTTGGAATCTTTT
1 AACCAAATTAAGTCCTTTCGGAATCTTTT
36137338 AACC-AATTAAGTCCTTTCGGAATCTTTT
1 AACCAAATTAAGTCCTTTCGGAATCTTTT
36137366 A
1 A
36137367 CTTAGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (29 bp):
AACCAAATTAAGTCCTTTCGGAATCTTTT
Found at i:36141440 original size:23 final size:20
Alignment explanation
Indices: 36141399--36141442 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 20
36141389 GGTAGTGGGA
36141399 ATTTATTTTATTTTTATTTG
1 ATTTATTTTATTTTTATTTG
36141419 ATTTGATTTTATTATTTTATTTG
1 ATTT-ATTTTA-T-TTTTATTTG
36141442 A
1 A
36141443 AATTATCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 6 0.29
22 1 0.05
23 10 0.48
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (20 bp):
ATTTATTTTATTTTTATTTG
Found at i:36142986 original size:33 final size:33
Alignment explanation
Indices: 36142949--36143028 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
36142939 TTTTTGGCAT
*
36142949 TATGACATT-TGATATGATATATGTTCTTAAAAA
1 TATGATATTCTGATATGATATATGTT-TTAAAAA
* * * *
36142982 TATGATATTCTAATCTGGTATATGTTTTGAAAA
1 TATGATATTCTGATATGATATATGTTTTAAAAA
36143015 TATGATATTCTGAT
1 TATGATATTCTGAT
36143029 TTGACGTATG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
33 27 0.68
34 13 0.32
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (33 bp):
TATGATATTCTGATATGATATATGTTTTAAAAA
Found at i:36143039 original size:33 final size:33
Alignment explanation
Indices: 36142967--36143041 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
36142957 TTGATATGAT
**
36142967 ATATGTTCTTAAAAATATGATATTCTAATCTGGT
1 ATATGTT-TTAAAAATATGATATTCTAATCTGAC
* * *
36143001 ATATGTTTTGAAAATATGATATTCTGATTTGAC
1 ATATGTTTTAAAAATATGATATTCTAATCTGAC
*
36143034 GTATGTTT
1 ATATGTTT
36143042 CTGGTAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
33 28 0.80
34 7 0.20
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.47
Consensus pattern (33 bp):
ATATGTTTTAAAAATATGATATTCTAATCTGAC
Found at i:36146444 original size:97 final size:96
Alignment explanation
Indices: 36146244--36146446 Score: 275
Period size: 97 Copynumber: 2.1 Consensus size: 96
36146234 AATCATATTT
* * *
36146244 AATAAATAATAAATTAATTTAGGTAACTTTATTAAATATGATGGATTAGATTTAGTATTTTTATA
1 AATAAATAATAAATTAATTTAGATAACTTTATTAAATATAATGGATCAGATTTAGTATTTTTATA
* *
36146309 GTAAATGTTTTTTTTTCATAAATGATTGATTG
66 GTAAATATTTTTTTAT-ATAAATGATTGATTG
* * * *
36146341 AATAAATAATAGATTAATTTAGATAACTTTATTAAATATAATTGATCGGATTTAGTATTTTTATG
1 AATAAATAATAAATTAATTTAGATAACTTTATTAAATATAATGGATCAGATTTAGTATTTTTATA
36146406 GTAAATATTTTTTCTAT-TAAAT-AGTTGATTG
66 GTAAATATTTTTT-TATATAAATGA-TTGATTG
36146437 AATTAAATAA
1 AA-TAAATAA
36146447 AAAAAATTAA
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
95 1 0.01
96 14 0.15
97 77 0.82
98 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.46
Consensus pattern (96 bp):
AATAAATAATAAATTAATTTAGATAACTTTATTAAATATAATGGATCAGATTTAGTATTTTTATA
GTAAATATTTTTTTATATAAATGATTGATTG
Found at i:36146526 original size:15 final size:16
Alignment explanation
Indices: 36146499--36146532 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
36146489 AATCAATCTA
36146499 TTTTCTTTAAATATTT
1 TTTTCTTTAAATATTT
36146515 TTTTCTTT-AATATTT
1 TTTTCTTTAAATATTT
36146530 TTT
1 TTT
36146533 AAAAACCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTCTTTAAATATTT
Found at i:36152440 original size:10 final size:10
Alignment explanation
Indices: 36152425--36152515 Score: 54
Period size: 10 Copynumber: 9.7 Consensus size: 10
36152415 CAAGGCATTG
36152425 TTTTTAATAA
1 TTTTTAATAA
**
36152435 TTTTTAATTT
1 TTTTTAATAA
36152445 TTTTTAATAA
1 TTTTTAATAA
36152455 -TTTT-AT-A
1 TTTTTAATAA
*
36152462 TTCTT-ATAA
1 TTTTTAATAA
* *
36152471 TTCTT-ATTA
1 TTTTTAATAA
36152480 TTTTTAAATAA
1 TTTTT-AATAA
36152491 -TTTT-AT-A
1 TTTTTAATAA
*
36152498 TTTTTCTATAA
1 TTTTT-AATAA
36152509 TTTTTAA
1 TTTTTAA
36152516 AAAATTATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
7 2 0.03
8 13 0.20
9 17 0.27
10 23 0.36
11 9 0.14
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:36152484 original size:36 final size:36
Alignment explanation
Indices: 36152431--36152499 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
36152421 ATTGTTTTTA
* *
36152431 ATAATTTTTAATTTTTTTTAATAATTTTATATTCTT
1 ATAATTCTTAATTTTTTTAAATAATTTTATATTCTT
36152467 ATAATTCTT-ATTATTTTTAAATAATTTTATATT
1 ATAATTCTTAATT-TTTTTAAATAATTTTATATT
36152500 TTTCTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 3 0.10
36 27 0.90
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (36 bp):
ATAATTCTTAATTTTTTTAAATAATTTTATATTCTT
Found at i:36152490 original size:20 final size:17
Alignment explanation
Indices: 36152425--36152512 Score: 79
Period size: 18 Copynumber: 4.8 Consensus size: 17
36152415 CAAGGCATTG
*
36152425 TTTTTAATAATTTTTAATTT
1 TTTTTAATAA-TTTT-A-TA
36152445 TTTTTAATAATTTTATA
1 TTTTTAATAATTTTATA
*
36152462 TTCTT-ATAATTCTTATTA
1 TTTTTAATAATT-TTA-TA
36152480 TTTTTAAATAATTTTATA
1 TTTTT-AATAATTTTATA
*
36152498 TTTTTCTATAATTTT
1 TTTTT-AATAATTTT
36152513 TAAAAAATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
16 6 0.10
17 8 0.14
18 22 0.37
19 7 0.12
20 16 0.27
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTAATAATTTTATA
Found at i:36152537 original size:13 final size:12
Alignment explanation
Indices: 36152507--36152539 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
36152497 ATTTTTCTAT
36152507 AATT-TTTAAAA
1 AATTATTTAAAA
36152518 AATTATTTAAAA
1 AATTATTTAAAA
36152530 AATATATTTA
1 AAT-TATTTA
36152540 GGATGAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 10 0.50
13 6 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AATTATTTAAAA
Found at i:36153213 original size:18 final size:20
Alignment explanation
Indices: 36153190--36153231 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
36153180 AAGACTTTAT
36153190 TTTAATTT-ATT-TATACAA
1 TTTAATTTAATTGTATACAA
*
36153208 TTTAATTTAATTGTATACAC
1 TTTAATTTAATTGTATACAA
36153228 TTTA
1 TTTA
36153232 TTACATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 3 0.14
20 10 0.48
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTAATTTAATTGTATACAA
Found at i:36153459 original size:15 final size:16
Alignment explanation
Indices: 36153433--36153464 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
36153423 AAAATTTACT
36153433 CATGATTGGATTTGAA
1 CATGATTGGATTTGAA
36153449 CATGA-TGGATTTGAA
1 CATGATTGGATTTGAA
36153464 C
1 C
36153465 TATGCTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.34
Consensus pattern (16 bp):
CATGATTGGATTTGAA
Found at i:36164285 original size:59 final size:59
Alignment explanation
Indices: 36164148--36164369 Score: 225
Period size: 59 Copynumber: 3.8 Consensus size: 59
36164138 TTGGATTTTT
* * * * * * *
36164148 GAGGGCAAAATGGTAA-TTTTGGAAAAATTTG-GGATGAAAAATGACATTTTAGATA-TTT
1 GAGGGTAAAATGGTAATTTTTGGTAAAA-TCGAGG-TCAAAAATGAAATTTTAGAAAGTTC
* * * * ** *
36164206 GGGGGTAAAATGGTACTTTTTGGTGACATCGAGGTTTAAAATGAAATTTTAGAGAGTTC
1 GAGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATGAAATTTTAGAAAGTTC
* * * *
36164265 GAGTGTAAAACGGTAATTTTTGGTAAAATCGAGGTCAAAAATGGAATTTTAGAAAGTTT
1 GAGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATGAAATTTTAGAAAGTTC
* *
36164324 GAGGGTAAAATAGTAATTTTTGGTAAAATCGAGGTCAAAAACGAAA
1 GAGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATGAAA
36164370 ACTTTGGAAG
Statistics
Matches: 133, Mismatches: 28, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
58 32 0.24
59 101 0.76
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.31
Consensus pattern (59 bp):
GAGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATGAAATTTTAGAAAGTTC
Found at i:36164313 original size:30 final size:31
Alignment explanation
Indices: 36164279--36164364 Score: 83
Period size: 29 Copynumber: 2.9 Consensus size: 31
36164269 GTAAAACGGT
36164279 AATTTTTGGTAAAATCGAGGTCAAAAAT-GG
1 AATTTTTGGTAAAATCGAGGTCAAAAATAGG
* * * *
36164309 AA-TTTTAG-AAAGTTTGAGGGT--AAAATAGT
1 AATTTTTGGTAAA-ATCGA-GGTCAAAAATAGG
36164338 AATTTTTGGTAAAATCGAGGTCAAAAA
1 AATTTTTGGTAAAATCGAGGTCAAAAA
36164365 CGAAAACTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
28 8 0.19
29 14 0.33
30 13 0.31
31 7 0.17
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.31
Consensus pattern (31 bp):
AATTTTTGGTAAAATCGAGGTCAAAAATAGG
Found at i:36166325 original size:11 final size:11
Alignment explanation
Indices: 36166305--36166386 Score: 80
Period size: 11 Copynumber: 7.5 Consensus size: 11
36166295 TTAATACTAT
36166305 TTTAAATTAAA
1 TTTAAATTAAA
36166316 -TTAAATTTAAA
1 TTTAAA-TTAAA
36166327 TTTAAATTTAAA
1 TTTAAA-TTAAA
* *
36166339 CTTAAAGTAAA
1 TTTAAATTAAA
*
36166350 TTTAAATTTAA
1 TTTAAATTAAA
36166361 -TTAAA-TAAA
1 TTTAAATTAAA
* *
36166370 TTTAAAATCAA
1 TTTAAATTAAA
36166381 TTTAAA
1 TTTAAA
36166387 CCTCAATTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 3 0.05
10 15 0.25
11 26 0.43
12 16 0.27
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:36166327 original size:6 final size:6
Alignment explanation
Indices: 36166305--36166375 Score: 75
Period size: 6 Copynumber: 13.0 Consensus size: 6
36166295 TTAATACTAT
* *
36166305 TTTAAA -TTAAA -TTAAA TTTAAA TTTAAA TTTAAA CTTAAA -GTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
36166350 TTTAAA TTT-AA -TTAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
36166376 ATCAATTTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
4 6 0.11
5 18 0.32
6 33 0.58
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:36166335 original size:29 final size:29
Alignment explanation
Indices: 36166305--36166360 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
36166295 TTAATACTAT
*
36166305 TTTAAA-TTAAATTAAATTTAAATTTAAA
1 TTTAAACTTAAAGTAAATTTAAATTTAAA
36166333 TTTAAACTTAAAGTAAATTTAAATTTAA
1 TTTAAACTTAAAGTAAATTTAAATTTAA
36166361 TTAAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
TTTAAACTTAAAGTAAATTTAAATTTAAA
Found at i:36166382 original size:20 final size:21
Alignment explanation
Indices: 36166340--36166382 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
36166330 AAATTTAAAC
* *
36166340 TTAAAGTAAATTTAAATTTAA
1 TTAAAGTAAATTTAAAATCAA
36166361 TTAAA-TAAATTTAAAATCAA
1 TTAAAGTAAATTTAAAATCAA
36166381 TT
1 TT
36166383 TAAACCTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAAAGTAAATTTAAAATCAA
Found at i:36166781 original size:14 final size:14
Alignment explanation
Indices: 36166740--36166783 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
36166730 AATGTAATCC
*
36166740 ATTTATTTAATTTT
1 ATTTATTTTATTTT
*
36166754 ATTAATTTCT-TTTT
1 ATTTATTT-TATTTT
36166768 ATTTATTTTATTTT
1 ATTTATTTTATTTT
36166782 AT
1 AT
36166784 ACGTAATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 1 0.04
14 24 0.96
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTATTTTATTTT
Found at i:36175618 original size:18 final size:18
Alignment explanation
Indices: 36175589--36175638 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
36175579 TTTATTCCAC
36175589 AAAAATAGTTTTTT-AAT
1 AAAAATAGTTTTTTAAAT
36175606 AAAAATAGTTTTTTAAAT
1 AAAAATAGTTTTTTAAAT
36175624 AAAAATAGTTTTTTA
1 AAAAATAGTTTTTTA
36175639 TGCTTCTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 14 0.44
18 18 0.56
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
AAAAATAGTTTTTTAAAT
Found at i:36177527 original size:30 final size:27
Alignment explanation
Indices: 36177493--36177561 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 27
36177483 AACGAAAATG
36177493 GACTAAAAAAACAATCTTGATTAGTTG-GAT
1 GACTAAAAAAACAA--TTGA-TAGTTGAG-T
*
36177523 GACTAAATTAAAAGAATTGATAGTTGAGT
1 GACTAAA--AAAACAATTGATAGTTGAGT
36177552 GACTAAAAAA
1 GACTAAAAAA
36177562 GAAACGGGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
27 3 0.09
29 14 0.40
30 12 0.34
32 6 0.17
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (27 bp):
GACTAAAAAAACAATTGATAGTTGAGT
Found at i:36178345 original size:4 final size:4
Alignment explanation
Indices: 36178338--36178424 Score: 90
Period size: 4 Copynumber: 22.2 Consensus size: 4
36178328 GCGGAAGAAG
*
36178338 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG- AAG- AAGG
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
* * * * *
36178384 AAGG AAGG AAGA AAG- AAGG AAGA AGGA GAGGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA -AAGA AAGA AAGA A
36178425 GAATGAGAGA
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
3 9 0.12
4 63 0.83
5 4 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:36178396 original size:42 final size:45
Alignment explanation
Indices: 36178332--36178436 Score: 117
Period size: 42 Copynumber: 2.4 Consensus size: 45
36178322 CAAACGGCGG
36178332 AAGAAGAAGAAAGAAAGAAAGAAAG-A-AAGAAAGA-AAGAAAGA
1 AAGAAGAAGAAAGAAAGAAAGAAAGAAGAAGAAAGAGAAGAAAGA
* * * * *
36178374 AAGAAGAAGGAAGGAAGGAAGAAAGAAGGAAGAAGGAGAGGAAAGA
1 AAGAAGAAGAAAGAAAGAAAGAAAGAA-GAAGAAAGAGAAGAAAGA
*
36178420 AAGAAGAATGAGAGAAA
1 AAGAAGAA-GAAAGAAA
36178437 TGTAGTGTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
42 22 0.44
43 1 0.02
45 7 0.14
46 15 0.30
47 5 0.10
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (45 bp):
AAGAAGAAGAAAGAAAGAAAGAAAGAAGAAGAAAGAGAAGAAAGA
Found at i:36181513 original size:8 final size:7
Alignment explanation
Indices: 36181411--36181541 Score: 74
Period size: 7 Copynumber: 18.9 Consensus size: 7
36181401 GATTTAAGGT
*
36181411 GGTTTAT
1 GGTTTAA
*
36181418 GGTTTAT
1 GGTTTAA
36181425 GGTTTAA
1 GGTTTAA
36181432 GG-TTAA
1 GGTTTAA
*
36181438 GGGTTT-T
1 -GGTTTAA
36181445 GAGTTTAA
1 G-GTTTAA
*
36181453 AGTTT-A
1 GGTTTAA
* * *
36181459 GGGTCAG
1 GGTTTAA
36181466 GGTTTAA
1 GGTTTAA
36181473 GGTTTAAA
1 GGTTT-AA
*
36181481 GTTTTAA
1 GGTTTAA
*
36181488 -ATTTAA
1 GGTTTAA
36181494 GG-TTAA
1 GGTTTAA
36181500 GGTTTAA
1 GGTTTAA
36181507 GGGTTTAA
1 -GGTTTAA
* *
36181515 AGTGTAA
1 GGTTTAA
36181522 GGTTTAA
1 GGTTTAA
* *
36181529 GATTTAG
1 GGTTTAA
36181536 GGTTTA
1 GGTTTA
36181542 TAAGTATGAA
Statistics
Matches: 94, Mismatches: 21, Indels: 18
0.71 0.16 0.14
Matches are distributed among these distances:
6 19 0.20
7 60 0.64
8 15 0.16
ACGTcount: A:0.27, C:0.01, G:0.29, T:0.43
Consensus pattern (7 bp):
GGTTTAA
Found at i:36181523 original size:22 final size:21
Alignment explanation
Indices: 36181489--36181529 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
36181479 AAGTTTTAAA
*
36181489 TTTAAGGTTAAGGTTTAAGGG
1 TTTAAAGTTAAGGTTTAAGGG
36181510 TTTAAAGTGTAAGGTTTAAG
1 TTTAAAGT-TAAGGTTTAAG
36181530 ATTTAGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (21 bp):
TTTAAAGTTAAGGTTTAAGGG
Found at i:36181528 original size:35 final size:35
Alignment explanation
Indices: 36181412--36181529 Score: 107
Period size: 35 Copynumber: 3.4 Consensus size: 35
36181402 ATTTAAGGTG
* * **
36181412 GTTTATGGTTTATGGTTTAAGG-TTAAGGGTTTTGA
1 GTTTAAGGTTTAAGG-TTAAGGTTTAAGGGTTTAAA
* * * *
36181447 GTTTAAAGTTTAGGGTCAGGGTTTAA-GGTTTAAA
1 GTTTAAGGTTTAAGGTTAAGGTTTAAGGGTTTAAA
*
36181481 GTTTTAA-ATTTAAGGTTAAGGTTTAAGGGTTTAAA
1 G-TTTAAGGTTTAAGGTTAAGGTTTAAGGGTTTAAA
*
36181516 GTGTAAGGTTTAAG
1 GTTTAAGGTTTAAG
36181530 ATTTAGGGTT
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
34 30 0.45
35 36 0.55
ACGTcount: A:0.28, C:0.01, G:0.29, T:0.42
Consensus pattern (35 bp):
GTTTAAGGTTTAAGGTTAAGGTTTAAGGGTTTAAA
Found at i:36181851 original size:45 final size:44
Alignment explanation
Indices: 36181787--36181876 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 44
36181777 AGGAGGAGTA
* * *
36181787 GAGTATTGCAGTGGCTCGTCAAACTGAGGTTGATATCCTTGGCTT
1 GAGTATTGCAGTGGCTCGTCAAACCGAGGCTGATAT-CATGGCTT
**
36181832 GAGTATTGTGGTGGCTCGTCAAACCGAGGCTGATATCATGGCTT
1 GAGTATTGCAGTGGCTCGTCAAACCGAGGCTGATATCATGGCTT
36181876 G
1 G
36181877 CTTGATGAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 8 0.20
45 32 0.80
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (44 bp):
GAGTATTGCAGTGGCTCGTCAAACCGAGGCTGATATCATGGCTT
Found at i:36183735 original size:30 final size:30
Alignment explanation
Indices: 36183691--36183785 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
36183681 CCAAAATGGG
36183691 TTATTTACTAAAATGGTACAAAATAAATAT
1 TTATTTACTAAAATGGTACAAAATAAATAT
* * * * *
36183721 TTATATACCAAAATGGTATC--TACACATCA-
1 TTATTTACTAAAATGGTA-CAAAATAAAT-AT
36183750 TTATTTACTAAAATGGTACAAAATAAATAT
1 TTATTTACTAAAATGGTACAAAATAAATAT
36183780 TTATTT
1 TTATTT
36183786 TGTACTAAAC
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
28 1 0.02
29 21 0.42
30 27 0.54
31 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (30 bp):
TTATTTACTAAAATGGTACAAAATAAATAT
Found at i:36183878 original size:13 final size:13
Alignment explanation
Indices: 36183862--36183897 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
36183852 ATATTTTAAA
36183862 TTTTATATTAATT
1 TTTTATATTAATT
* *
36183875 TTTTTTATAAATT
1 TTTTATATTAATT
36183888 TTTTATATTA
1 TTTTATATTA
36183898 TTATATAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTATATTAATT
Found at i:36190176 original size:25 final size:24
Alignment explanation
Indices: 36190132--36190187 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
36190122 TTTTATATAA
36190132 TTTTAAAAAATTATAAAAAATGTTT
1 TTTTAAAAAATTATAAAAAAT-TTT
* **
36190157 TTTTATAAAATTATTTAAAATTTT
1 TTTTAAAAAATTATAAAAAATTTT
*
36190181 ATTTAAA
1 TTTTAAA
36190188 TTATTGGTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTAAAAAATTATAAAAAATTTT
Found at i:36191042 original size:17 final size:19
Alignment explanation
Indices: 36191006--36191043 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
36190996 TAGATTATAG
36191006 TAATTTTATATTATTAATTA
1 TAATTTTATA-TATTAATTA
36191026 TAATTTTATA-A-TAATTA
1 TAATTTTATATATTAATTA
36191043 T
1 T
36191044 CTAAAGGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
20 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TAATTTTATATATTAATTA
Found at i:36194702 original size:42 final size:42
Alignment explanation
Indices: 36194656--36194740 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
36194646 TTATAAATTG
36194656 GTGTTAGAATTGAAAAATAAGAAGTCCTAAATAAACTATAGT
1 GTGTTAGAATTGAAAAATAAGAAGTCCTAAATAAACTATAGT
* *
36194698 GTGTTAGAATTTAAAAATAGGAAGTCCTAAATAAACTATAGT
1 GTGTTAGAATTGAAAAATAAGAAGTCCTAAATAAACTATAGT
36194740 G
1 G
36194741 AAAACGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (42 bp):
GTGTTAGAATTGAAAAATAAGAAGTCCTAAATAAACTATAGT
Found at i:36194750 original size:42 final size:42
Alignment explanation
Indices: 36194661--36194757 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 42
36194651 AATTGGTGTT
* ***
36194661 AGAATTGAAAAATAAGAAGTCCTAAATAAACTATAGTGTGTT
1 AGAATTTAAAAATAAGAAGTCCTAAATAAACTATAGTGTAAA
*
36194703 AGAATTTAAAAATAGGAAGTCCTAAATAAACTATAGTG-AAA
1 AGAATTTAAAAATAAGAAGTCCTAAATAAACTATAGTGTAAA
36194744 ACGAA-TTAAAAATA
1 A-GAATTTAAAAATA
36194758 TGAGTTCTAG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 10 0.20
42 39 0.80
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (42 bp):
AGAATTTAAAAATAAGAAGTCCTAAATAAACTATAGTGTAAA
Found at i:36198609 original size:3 final size:3
Alignment explanation
Indices: 36198603--36198643 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
36198593 TTTTTGTTAT
* *
36198603 TTA TTA TTA TTA TTA TTA TTA ATA TTA TAA TTA TTTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA T
36198644 AAAACGTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:36199304 original size:6 final size:6
Alignment explanation
Indices: 36199285--36199340 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
36199275 GGACATTTAG
* * *
36199285 TAAATT TAAA-- TAAATT TAAACT TAAA-A TAAATT TAAATT TAAA-A
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
36199329 TAAATT TAAATT
1 TAAATT TAAATT
36199341 CTGTTTGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.10
5 8 0.20
6 29 0.71
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:36199339 original size:17 final size:17
Alignment explanation
Indices: 36199285--36199340 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
36199275 GGACATTTAG
36199285 TAAATTT-AAATAAATT
1 TAAATTTAAAATAAATT
*
36199301 TAAACTTAAAATAAATT
1 TAAATTTAAAATAAATT
36199318 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
36199335 TAAATT
1 TAAATT
36199341 CTGTTTGGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
16 6 0.16
17 31 0.84
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:36206168 original size:14 final size:14
Alignment explanation
Indices: 36206151--36206177 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36206141 TCTTAAAATA
36206151 TATATGTATGTATG
1 TATATGTATGTATG
36206165 TATATGTATGTAT
1 TATATGTATGTAT
36206178 CAAAGAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.52
Consensus pattern (14 bp):
TATATGTATGTATG
Done.