Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3685
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: 104426
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4407 original size:15 final size:15
Alignment explanation
Indices: 4387--4429 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
4377 TATTAGAAAT
4387 AAATAGATATTATAA
1 AAATAGATATTATAA
4402 AAATAGA-A--AT--
1 AAATAGATATTATAA
4412 AAATAGATATTATAA
1 AAATAGATATTATAA
4427 AAA
1 AAA
4430 GAAACTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 10
0.70 0.00 0.30
Matches are distributed among these distances:
10 7 0.30
11 1 0.04
12 2 0.09
13 2 0.09
14 1 0.04
15 10 0.43
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (15 bp):
AAATAGATATTATAA
Found at i:4408 original size:25 final size:25
Alignment explanation
Indices: 4380--4429 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
4370 AAATATTTAT
4380 TAGAAATAAATAGATATTATAAAAA
1 TAGAAATAAATAGATATTATAAAAA
4405 TAGAAATAAATAGATATTATAAAAA
1 TAGAAATAAATAGATATTATAAAAA
4430 GAAACTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (25 bp):
TAGAAATAAATAGATATTATAAAAA
Found at i:5201 original size:12 final size:12
Alignment explanation
Indices: 5184--5212 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5174 TATGTATAAT
5184 AATTGAATTAGA
1 AATTGAATTAGA
5196 AATTGAATTAGA
1 AATTGAATTAGA
5208 AATTG
1 AATTG
5213 TATAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (12 bp):
AATTGAATTAGA
Found at i:10139 original size:31 final size:32
Alignment explanation
Indices: 10074--10148 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
10064 ATGAAAAATT
*
10074 ATTAAATTAATAATTGATTTTAATTATACTTAA
1 ATTAAATTATTAATT-ATTTTAATTATACTTAA
*
10107 ATTAAATTATTAATT-TTTCTATTTA-ACTTAA
1 ATTAAATTATTAATTATTT-TAATTATACTTAA
10138 ATTAAA-TATTA
1 ATTAAATTATTA
10149 TAATAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 5 0.13
31 15 0.38
32 5 0.13
33 14 0.36
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (32 bp):
ATTAAATTATTAATTATTTTAATTATACTTAA
Found at i:10158 original size:7 final size:7
Alignment explanation
Indices: 10148--10404 Score: 121
Period size: 7 Copynumber: 35.9 Consensus size: 7
10138 ATTAAATATT
10148 ATAATAA
1 ATAATAA
10155 ATAATAA
1 ATAATAA
**
10162 ATTCTAA
1 ATAATAA
10169 ATATACTAA
1 ATA-A-TAA
10178 AT-ATAA
1 ATAATAA
10184 ATAATAA
1 ATAATAA
*
10191 CTAA-ATA
1 ATAATA-A
10198 ATAACTAA
1 ATAA-TAA
*
10206 AT-AGAA
1 ATAATAA
*
10212 ATAAAAA
1 ATAATAA
10219 ATAGAAATAA
1 AT---AATAA
10229 A-AATAA
1 ATAATAA
10235 ATAATAA
1 ATAATAA
*
10242 CTAAATAA
1 AT-AATAA
10250 ATAATAA
1 ATAATAA
* *
10257 CTAAATAG
1 AT-AATAA
10265 A-AATAA
1 ATAATAA
*
10271 A-AATAT
1 ATAATAA
10277 ATAATATA
1 ATAATA-A
10285 TATAA-AA
1 -ATAATAA
10292 ATATATATA
1 ATA-ATA-A
10301 ATAAT-A
1 ATAATAA
10307 ATATATAA
1 ATA-ATAA
*
10315 ATTATAA
1 ATAATAA
10322 AT-ATAA
1 ATAATAA
10328 A-AAT-A
1 ATAATAA
10333 ATATATAA
1 ATA-ATAA
*
10341 ATTATAA
1 ATAATAA
10348 ATAGATAA
1 ATA-ATAA
10356 TATAAT-A
1 -ATAATAA
10363 ATAGATAA
1 ATA-ATAA
10371 TATAAT-A
1 -ATAATAA
10378 ATAGATAGA
1 ATA-ATA-A
10387 ATAAT-A
1 ATAATAA
10393 A-AATAA
1 ATAATAA
10399 ATAATA
1 ATAATA
10405 TAGAAATATA
Statistics
Matches: 195, Mismatches: 20, Indels: 70
0.68 0.07 0.25
Matches are distributed among these distances:
5 5 0.03
6 51 0.26
7 76 0.39
8 34 0.17
9 24 0.12
10 5 0.03
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (7 bp):
ATAATAA
Found at i:10226 original size:6 final size:6
Alignment explanation
Indices: 10176--10333 Score: 64
Period size: 6 Copynumber: 24.0 Consensus size: 6
10166 TAAATATACT
* * * *
10176 AAATAT AAATAA TAACTAA ATAATAA CTAAATAG AAATAAA AAATAG AAATAA
1 AAATAA AAATAA -AAATAA A-AATAA --AAATAA AAAT-AA AAATAA AAATAA
*
10229 AAATAA ATAATAA CTAAATAA ATAATAA CTAAATAG AAATAA AAATATA
1 AAATAA A-AATAA --AAATAA A-AATAA --AAATAA AAATAA AAATA-A
* * * * * * * * *
10278 TAATAT ATATAA AAATAT ATATAA TAATAA TATATAA ATTATAA ATATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA -AAATAA A-AATAA AAATAA
10328 AAATAA
1 AAATAA
10334 TATATAAATT
Statistics
Matches: 115, Mismatches: 23, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
6 60 0.52
7 39 0.34
8 13 0.11
9 3 0.03
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.28
Consensus pattern (6 bp):
AAATAA
Found at i:10226 original size:19 final size:19
Alignment explanation
Indices: 10204--10294 Score: 74
Period size: 19 Copynumber: 4.6 Consensus size: 19
10194 AATAATAACT
*
10204 AAATAGAAATAAAAAATAG
1 AAATAAAAATAAAAAATAG
* *
10223 AAATAAAAATAAATAATAACT
1 AAATAAAAATAAAAAAT-A-G
*
10244 AAATAAATAATAACTAAATAG
1 AAATAAA-AATAA-AAAATAG
* * *
10265 AAATAAAAATATATAATAT
1 AAATAAAAATAAAAAATAG
*
10284 ATATAAAAATA
1 AAATAAAAATA
10295 TATATAATAA
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
19 29 0.51
20 5 0.09
21 14 0.25
22 6 0.11
23 3 0.05
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.24
Consensus pattern (19 bp):
AAATAAAAATAAAAAATAG
Found at i:10263 original size:11 final size:11
Alignment explanation
Indices: 10181--10249 Score: 67
Period size: 11 Copynumber: 6.6 Consensus size: 11
10171 ATACTAAATA
10181 TAAATAATAAC
1 TAAATAATAAC
10192 TAAATAATAAC
1 TAAATAATAAC
10203 TAAATAGA-AA-
1 TAAATA-ATAAC
*
10213 TAAAAAAT-A-
1 TAAATAATAAC
* *
10222 GAAATAA-AAA
1 TAAATAATAAC
10232 TAAATAATAAC
1 TAAATAATAAC
10243 TAAATAA
1 TAAATAA
10250 ATAATAACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
9 8 0.17
10 11 0.23
11 28 0.58
12 1 0.02
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.23
Consensus pattern (11 bp):
TAAATAATAAC
Found at i:10290 original size:55 final size:54
Alignment explanation
Indices: 10183--10363 Score: 176
Period size: 55 Copynumber: 3.4 Consensus size: 54
10173 ACTAAATATA
* * *
10183 AATAATAACTAAATAATAACTAAATAGAAATAAAAA-ATAGAAATAAAAATAAAT
1 AATAATAAATAAATAATAACTAAATAGAAATAAAAATATA-AAATATATATAAAT
*
10237 AATAACTAAATAAATAATAACTAAATAGAAATAAAAATATATAATATATATAAA-
1 AATAA-TAAATAAATAATAACTAAATAGAAATAAAAATATAAAATATATATAAAT
* * * *
10291 AAT-ATATAT-AATAATAA-TATATA-AATTATAAATATAAAAATAATATATAAAT
1 AATAATAAATAAATAATAACTAAATAGAAATAAAAATAT-AAAAT-ATATATAAAT
* *
10343 TATAAATAGATAATATAATAA
1 AAT-AATAAATAA-ATAATAA
10364 TAGATAATAT
Statistics
Matches: 107, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
49 10 0.09
50 9 0.08
51 17 0.16
52 6 0.06
53 1 0.01
54 13 0.12
55 41 0.38
56 10 0.09
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (54 bp):
AATAATAAATAAATAATAACTAAATAGAAATAAAAATATAAAATATATATAAAT
Found at i:10295 original size:19 final size:19
Alignment explanation
Indices: 10267--10362 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 19
10257 CTAAATAGAA
10267 ATAAAAATATATAATATAT
1 ATAAAAATATATAATATAT
10286 ATAAAAATATATATAATAATAAT
1 AT-AAAA-ATATATAAT-AT-AT
*
10309 ATATAAAT-TATAA-ATAT
1 ATAAAAATATATAATATAT
*
10326 AAAAATAATATATAA-AT-T
1 ATAAA-AATATATAATATAT
10344 ATAAATAGATAATATAATA
1 ATAAA-A-AT-ATATAATA
10363 ATAGATAATA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
17 5 0.08
18 12 0.19
19 11 0.17
20 15 0.23
21 12 0.19
22 5 0.08
23 4 0.06
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (19 bp):
ATAAAAATATATAATATAT
Found at i:10315 original size:80 final size:83
Alignment explanation
Indices: 10228--10404 Score: 197
Period size: 80 Copynumber: 2.2 Consensus size: 83
10218 AATAGAAATA
*
10228 AAAATAAATAATAACTA-AATAAATAATA-ACTAAA-TAGAAATA-AAAATAT-ATAAT-AT-AT
1 AAAATAAATAATAAATATAA-AAATAATATA-TAAATTAGAAATAGAAAATATAATAATAATAAT
* *
10286 ATAAAAATATATATAATAAT
64 ATAAAAATAGATAGAATAAT
* * *
10306 AATATATAAATTATAAATATAAAAATAATATATAAATTATAAATAGATAATATAATAATAGATAA
1 AA-A-ATAAATAATAAATATAAAAATAATATATAAATTAGAAATAGAAAATATAATAATA-ATAA
*
10371 TATAATAATAGATAGAATAAT
63 TATAAAAATAGATAGAATAAT
10392 AAAATAAATAATA
1 AAAATAAATAATA
10405 TAGAAATATA
Statistics
Matches: 81, Mismatches: 8, Indels: 14
0.79 0.08 0.14
Matches are distributed among these distances:
78 2 0.02
79 1 0.01
80 24 0.30
81 10 0.12
82 6 0.07
83 5 0.06
84 9 0.11
85 3 0.04
86 21 0.26
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (83 bp):
AAAATAAATAATAAATATAAAAATAATATATAAATTAGAAATAGAAAATATAATAATAATAATAT
AAAAATAGATAGAATAAT
Found at i:10332 original size:26 final size:26
Alignment explanation
Indices: 10282--10350 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
10272 AATATATAAT
* * *
10282 ATATATAAA-AATATATATAATAATA
1 ATATATAAATTATAAATATAAAAATA
10307 ATATATAAATTATAAATATAAAAATA
1 ATATATAAATTATAAATATAAAAATA
10333 ATATATAAATTATAAATA
1 ATATATAAATTATAAATA
10351 GATAATATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 9 0.22
26 31 0.77
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATATAAATTATAAATATAAAAATA
Found at i:10337 original size:51 final size:48
Alignment explanation
Indices: 10225--10355 Score: 117
Period size: 48 Copynumber: 2.6 Consensus size: 48
10215 AAAAATAGAA
10225 ATAAAAATAA-ATAATAACTAAATAAATAATAACTAAATAGAAATAAAAAT
1 ATAAAAATAATAT-ATAA--AAATAAATAATAACTAAATAGAAATAAAAAT
* * *
10275 AT-ATAAT-ATATATAAAAATATATATAATAA-TAATATATAAATTATAAAT
1 ATAAAAATAATATATAAAAATA-A-ATAATAACTAA-ATAGAAA-TAAAAAT
*
10324 ATAAAAATAATATATAAATTATAAATAGATAA
1 ATAAAAATAATATATAAA-AATAAATA-ATAA
10356 TATAATAATA
Statistics
Matches: 67, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
46 5 0.07
47 4 0.06
48 18 0.27
49 14 0.21
50 9 0.13
51 14 0.21
52 3 0.04
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (48 bp):
ATAAAAATAATATATAAAAATAAATAATAACTAAATAGAAATAAAAAT
Found at i:10355 original size:15 final size:14
Alignment explanation
Indices: 10231--10408 Score: 117
Period size: 15 Copynumber: 13.1 Consensus size: 14
10221 AGAAATAAAA
*
10231 ATAAATAATAACTAA
1 ATAAATAATAA-TAG
*
10246 ATAAATAATAACTAA
1 ATAAATAATAA-TAG
* *
10261 ATAGA-AATAA-AA
1 ATAAATAATAATAG
* *
10273 ATATATAAT-ATAT
1 ATAAATAATAATAG
*
10286 ATAAA-AAT-ATAT
1 ATAAATAATAATAG
*
10298 AT-AATAATAATAT
1 ATAAATAATAATAG
* *
10311 ATAAATTATAA-AT
1 ATAAATAATAATAG
*
10324 ATAAA-AATAATAT
1 ATAAATAATAATAG
*
10337 ATAAATTATAAATAG
1 ATAAATAAT-AATAG
10352 ATAATATAATAATAG
1 ATAA-ATAATAATAG
10367 ATAATATAATAATAG
1 ATAA-ATAATAATAG
10382 ATAGAATAATAA-A-
1 ATA-AATAATAATAG
10395 ATAAATAAT-ATAG
1 ATAAATAATAATAG
10408 A
1 A
10409 AATATAGATT
Statistics
Matches: 142, Mismatches: 9, Indels: 26
0.80 0.05 0.15
Matches are distributed among these distances:
11 3 0.02
12 30 0.21
13 32 0.23
14 15 0.11
15 57 0.40
16 5 0.04
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (14 bp):
ATAAATAATAATAG
Found at i:10363 original size:8 final size:8
Alignment explanation
Indices: 10230--10451 Score: 79
Period size: 8 Copynumber: 28.2 Consensus size: 8
10220 TAGAAATAAA
10230 AATAA-AT
1 AATAATAT
10237 AATAACTA-
1 AATAA-TAT
10245 AATAA-AT
1 AATAATAT
10252 AATAACTA-
1 AATAA-TAT
*
10260 AATAGAAAT
1 AATA-ATAT
*
10269 AAAAATAT
1 AATAATAT
10277 -ATAATAT
1 AATAATAT
10284 ATATAA-A-
1 A-ATAATAT
10291 AATATATAT
1 AATA-ATAT
10300 AATAATAAT
1 AATAAT-AT
10309 ATATAA-AT
1 A-ATAATAT
*
10317 TATAA-AT
1 AATAATAT
10324 -ATAA-A-
1 AATAATAT
10329 AATAATAT
1 AATAATAT
10337 -ATAA-AT
1 AATAATAT
*
10343 TATAA-AT
1 AATAATAT
10350 AGATAATAT
1 A-ATAATAT
10359 AATAATA-
1 AATAATAT
*
10366 GATAATAT
1 AATAATAT
10374 AATAATA-
1 AATAATAT
*
10381 GATAGA-AT
1 AATA-ATAT
*
10389 AATAAAAT
1 AATAATAT
10397 AAATAATAT
1 -AATAATAT
10406 AGA-AATAT
1 A-ATAATAT
*
10414 AGAT-TTAT
1 A-ATAATAT
10422 AAATCGAAATAT
1 -AAT---AATAT
*
10434 ATTAATAT
1 AATAATAT
10442 AATAATAT
1 AATAATAT
10450 AA
1 AA
10452 ATATTATTAA
Statistics
Matches: 168, Mismatches: 15, Indels: 63
0.68 0.06 0.26
Matches are distributed among these distances:
6 15 0.09
7 46 0.27
8 69 0.41
9 29 0.17
10 4 0.02
11 2 0.01
12 3 0.02
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (8 bp):
AATAATAT
Found at i:10375 original size:48 final size:50
Alignment explanation
Indices: 10225--10380 Score: 116
Period size: 48 Copynumber: 3.2 Consensus size: 50
10215 AAAAATAGAA
* * *
10225 ATAAAAATAAATAATAACTAAATA-A-ATAATAACTAA-ATAGAAAT-AAAAAT
1 ATAAAAATATAT-ATAA--AAATATATATAATAA-TAATATATAAATGATAAAT
* *
10275 AT-ATAATATATATAAAAATATATATAATAATAATATATAAATTATAAAT
1 ATAAAAATATATATAAAAATATATATAATAATAATATATAAATGATAAAT
*
10324 ATAAAAATA-ATATATAAAT-TATA-AATAGATAATATA-ATAATAGAT-AAT
1 ATAAAAATATATATAAAAATATATATAATA-ATAATATATA-AAT-GATAAAT
*
10372 ATAATAATA
1 ATAAAAATA
10381 GATAGAATAA
Statistics
Matches: 90, Mismatches: 8, Indels: 18
0.78 0.07 0.16
Matches are distributed among these distances:
46 5 0.06
47 9 0.10
48 44 0.49
49 25 0.28
50 7 0.08
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (50 bp):
ATAAAAATATATATAAAAATATATATAATAATAATATATAAATGATAAAT
Found at i:10411 original size:15 final size:14
Alignment explanation
Indices: 10211--10412 Score: 75
Period size: 15 Copynumber: 13.8 Consensus size: 14
10201 ACTAAATAGA
* *
10211 AATAAAAAATAGA-
1 AATATAAAATAAAT
10224 AATA-AAAATAAAT
1 AATATAAAATAAAT
10237 AATA-ACTAAATAAAT
1 AATATA--AAATAAAT
*
10252 AATA-ACTAAATAGA-
1 AATATA--AAATAAAT
*
10266 AATA-AAAATATAT
1 AATATAAAATAAAT
10279 AATATATATAA-AAAT
1 AATATA-A-AATAAAT
10294 ATATATAATAAT-AAT
1 A-ATATAA-AATAAAT
10309 -ATATAAATTATAAAT
1 AATATAAA--ATAAAT
10324 -ATA-AAAATAATAT
1 AATATAAAATAA-AT
* *
10337 ATAAATTATAAATAGAT
1 A-ATA-TA-AAATAAAT
*
10354 AATATAATAATAGAT
1 AATATAA-AATAAAT
*
10369 AATATAATAATAGATAG
1 AATATAA-AATA-A-AT
10386 AATAATAAAATAAAT
1 AAT-ATAAAATAAAT
10401 AATATAGAAATA
1 AATATA-AAATA
10413 TAGATTTATA
Statistics
Matches: 156, Mismatches: 10, Indels: 44
0.74 0.05 0.21
Matches are distributed among these distances:
12 18 0.12
13 21 0.13
14 15 0.10
15 71 0.46
16 10 0.06
17 12 0.08
18 9 0.06
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (14 bp):
AATATAAAATAAAT
Found at i:10459 original size:23 final size:23
Alignment explanation
Indices: 10428--10511 Score: 64
Period size: 26 Copynumber: 3.6 Consensus size: 23
10418 TTATAAATCG
10428 AAATA-TATTAATATAATAATAT
1 AAATATTATTAATATAATAATAT
* *
10450 AAATATTATTAATTACTTAATATTCT
1 AAATATTATTAA-TA--TAATAATAT
* * *
10476 GAATATTAATAACA-AATAATAT
1 AAATATTATTAATATAATAATAT
*
10498 AAATTAATATTAAT
1 AAA-TATTATTAAT
10512 TGCTAATAAC
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
22 13 0.28
23 13 0.28
24 2 0.04
25 1 0.02
26 17 0.37
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.42
Consensus pattern (23 bp):
AAATATTATTAATATAATAATAT
Found at i:16178 original size:15 final size:15
Alignment explanation
Indices: 16160--16190 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16150 ATCTCTCATC
16160 TATCTATCTATTTTT
1 TATCTATCTATTTTT
16175 TATCTATCTATTTTT
1 TATCTATCTATTTTT
16190 T
1 T
16191 CTTTAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (15 bp):
TATCTATCTATTTTT
Found at i:16892 original size:16 final size:17
Alignment explanation
Indices: 16865--16898 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
16855 AAATGGATTT
16865 AATAGAAATTAAATAGA
1 AATAGAAATTAAATAGA
16882 AATAG-AATTAAATAGA
1 AATAGAAATTAAATAGA
16898 A
1 A
16899 TTCTCTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (17 bp):
AATAGAAATTAAATAGA
Found at i:17828 original size:15 final size:15
Alignment explanation
Indices: 17799--17860 Score: 54
Period size: 16 Copynumber: 4.0 Consensus size: 15
17789 GTAGAAAGCC
* *
17799 TATTTTTTTTTCTAG
1 TATTTTATTTACTAG
17814 TATTTTATTTACTAG
1 TATTTTATTTACTAG
**
17829 CGTGTTTATTTACTAGCG
1 TAT-TTTATTTACTA--G
17847 TA-TTTATTTACTAG
1 TATTTTATTTACTAG
17861 CGTATTTGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
14 1 0.03
15 14 0.37
16 22 0.58
18 1 0.03
ACGTcount: A:0.21, C:0.10, G:0.11, T:0.58
Consensus pattern (15 bp):
TATTTTATTTACTAG
Found at i:17838 original size:16 final size:16
Alignment explanation
Indices: 17817--17867 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
17807 TTTCTAGTAT
*
17817 TTTATTTACTAGCGTG
1 TTTATTTACTAGCGTA
17833 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
17849 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
17865 TTT
1 TTT
17868 GCTCTTTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.53
Consensus pattern (16 bp):
TTTATTTACTAGCGTA
Found at i:19218 original size:13 final size:14
Alignment explanation
Indices: 19185--19218 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19175 GCCCGGAGGC
*
19185 TAAAGAAAAAGTGA
1 TAAAAAAAAAGTGA
19199 TAAAAAAAAAGTGA
1 TAAAAAAAAAGTGA
19213 TGAAAA
1 T-AAAA
19219 GTTTTCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (14 bp):
TAAAAAAAAAGTGA
Found at i:20539 original size:8 final size:8
Alignment explanation
Indices: 20489--20628 Score: 70
Period size: 8 Copynumber: 16.9 Consensus size: 8
20479 AAAAATAGAA
20489 ATAAATAT
1 ATAAATAT
*
20497 ATATATAAT
1 ATAAAT-AT
20506 AATAATATAT
1 -ATAA-ATAT
* *
20516 AAAAAGAAT
1 ATAAA-TAT
*
20525 ATTAATAT
1 ATAAATAT
20533 ATAAATAT
1 ATAAATAT
*
20541 AAAAATAT
1 ATAAATAT
20549 ATAAAATAT
1 AT-AAATAT
*
20558 TTAGAATAT
1 ATA-AATAT
*
20567 ATATAATAAA
1 ATA-AAT-AT
*
20577 ATAGATAT
1 ATAAATAT
*
20585 ATAGATAT
1 ATAAATAT
*
20593 ATAAATAA
1 ATAAATAT
**
20601 ATTGA-AT
1 ATAAATAT
20608 AT-AATAT
1 ATAAATAT
*
20615 -TAAATAG
1 ATAAATAT
20622 ATAAATA
1 ATAAATA
20629 AATTAAACCA
Statistics
Matches: 99, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
6 2 0.02
7 9 0.09
8 48 0.48
9 29 0.29
10 9 0.09
11 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (8 bp):
ATAAATAT
Found at i:20578 original size:32 final size:33
Alignment explanation
Indices: 20495--20579 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 33
20485 AGAAATAAAT
20495 ATATATATAATAATAATATATAAAAAGAATATTA
1 ATATATATAATAA-AATATATAAAAAGAATATTA
* *
20529 ATATATA-AATATAAAAATAT-ATAA-AATATTTAGA
1 ATATATATAATA-AAATATATAAAAAGAATA-TT--A
20563 ATATATATAATAAAATA
1 ATATATATAATAAAATA
20580 GATATATAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
31 4 0.09
32 5 0.12
33 10 0.23
34 20 0.47
35 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (33 bp):
ATATATATAATAAAATATATAAAAAGAATATTA
Found at i:20609 original size:25 final size:24
Alignment explanation
Indices: 20525--20610 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 24
20515 TAAAAAGAAT
* * *
20525 ATTAATATATAAATATAAAAATAT
1 ATTAATATATAGATATATAAATAA
* *
20549 ATAAAATATTTAGAATATATATAATAA
1 AT-TAATATATAG-ATATATA-AATAA
*
20576 AATAGATATATAGATATATAAATAA
1 ATTA-ATATATAGATATATAAATAA
20601 ATTGAATATA
1 ATT-AATATA
20611 ATATTAAATA
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
24 2 0.04
25 19 0.40
26 15 0.31
27 12 0.25
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (24 bp):
ATTAATATATAGATATATAAATAA
Found at i:21026 original size:13 final size:13
Alignment explanation
Indices: 21008--21035 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20998 GTTATTCATA
21008 ATTAATATGAATT
1 ATTAATATGAATT
21021 ATTAATATGAATT
1 ATTAATATGAATT
21034 AT
1 AT
21036 AGACTCGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (13 bp):
ATTAATATGAATT
Found at i:21217 original size:19 final size:21
Alignment explanation
Indices: 21189--21238 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
21179 AAATTAAAAT
21189 TTTATATATATA-TTTAT-TA
1 TTTATATATATATTTTATATA
*
21208 TTTATCTATATATTTTATATA
1 TTTATATATATATTTTATATA
21229 TTTA-ATATAT
1 TTTATATATAT
21239 TTAATATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 10 0.37
21 6 0.22
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATATATATATTTTATATA
Found at i:21237 original size:11 final size:9
Alignment explanation
Indices: 21214--21256 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
21204 ATTATTTATC
21214 TATATATTT
1 TATATATTT
21223 TATATATTT
1 TATATATTT
*
21232 AATATATTT
1 TATATATTT
* *
21241 AATATCTTT
1 TATATATTT
*
21250 TTTATAT
1 TATATAT
21257 CTTAGTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (9 bp):
TATATATTT
Found at i:21330 original size:17 final size:17
Alignment explanation
Indices: 21308--21346 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
21298 CTGACTCCAT
*
21308 TTTTAT-TTTCTAGTTTA
1 TTTTATATTT-TAGTATA
21325 TTTTATATTTTAGTATA
1 TTTTATATTTTAGTATA
21342 TTTTA
1 TTTTA
21347 CATCTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (17 bp):
TTTTATATTTTAGTATA
Found at i:21442 original size:31 final size:31
Alignment explanation
Indices: 21407--21466 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
21397 CGATCGATTT
*
21407 AATAGATTTAATATAGATTCAATTTATTTTG
1 AATAGATTTAATATAGATTAAATTTATTTTG
21438 AATAGATTTAATATAGATTAAATTTATTT
1 AATAGATTTAATATAGATTAAATTTATTT
21467 CTATTTAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (31 bp):
AATAGATTTAATATAGATTAAATTTATTTTG
Found at i:21543 original size:15 final size:17
Alignment explanation
Indices: 21513--21544 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
21503 GTCAAAATCT
21513 TTTTATGCAGTTATATA
1 TTTTATGCAGTTATATA
21530 TTTTATG-A-TTATATA
1 TTTTATGCAGTTATATA
21545 AATGAAACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.56
Consensus pattern (17 bp):
TTTTATGCAGTTATATA
Found at i:22193 original size:18 final size:18
Alignment explanation
Indices: 22166--22208 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
22156 CGCATAAAAA
* *
22166 GAAAGCAAATAAATAAAC
1 GAAAGAAAATAAACAAAC
*
22184 GAAAGAAAATAAACAAAT
1 GAAAGAAAATAAACAAAC
22202 GAAAGAA
1 GAAAGAA
22209 GGGGGAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (18 bp):
GAAAGAAAATAAACAAAC
Found at i:26952 original size:15 final size:15
Alignment explanation
Indices: 26932--26962 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
26922 GACGGTTCCG
26932 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
26947 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
26962 T
1 T
26963 ACTGATACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
TGTGCTCTGATTCAT
Found at i:30417 original size:20 final size:19
Alignment explanation
Indices: 30387--30470 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 19
30377 GATGTTAGAA
30387 TATTAATTCTATTATATATT
1 TATT-ATTCTATTATATATT
30407 TATCTATTCTATTATATA--
1 TAT-TATTCTATTATATATT
*
30425 TA-TATTCTAATATATATT
1 TATTATTCTATTATATATT
30443 AGTATTATT-T-TTATATTATT
1 --TATTATTCTATTATA-TATT
30463 TATCTATT
1 TAT-TATT
30471 TCTTATCTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
16 13 0.24
18 5 0.09
19 8 0.15
20 23 0.43
21 5 0.09
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (19 bp):
TATTATTCTATTATATATT
Found at i:30432 original size:16 final size:17
Alignment explanation
Indices: 30392--30441 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 17
30382 TAGAATATTA
30392 ATTCTATTATATATTTATCT
1 ATTCTATTATATA--TA-CT
30412 ATTCTATTATATATA-T
1 ATTCTATTATATATACT
*
30428 ATTCTAATATATAT
1 ATTCTATTATATAT
30442 TAGTATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 14 0.48
18 2 0.07
20 13 0.45
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTCTATTATATATACT
Found at i:35067 original size:17 final size:17
Alignment explanation
Indices: 35045--35078 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35035 ATAGATTCGC
*
35045 TTAGATATACTTAGTAT
1 TTAGATATAATTAGTAT
35062 TTAGATATAATTAGTAT
1 TTAGATATAATTAGTAT
35079 AATATACGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
TTAGATATAATTAGTAT
Found at i:42341 original size:13 final size:13
Alignment explanation
Indices: 42310--42343 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
42300 TTTTAATTTC
42310 AATTT-ATTTAAT
1 AATTTAATTTAAT
42322 AATTTTAATTTAAT
1 AA-TTTAATTTAAT
42336 AATTTAAT
1 AATTTAAT
42344 CCAAGGAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 9 0.45
14 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTAATTTAAT
Found at i:44108 original size:24 final size:23
Alignment explanation
Indices: 44052--44108 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
44042 ATTTTCTTTC
44052 TATAT-TATTAATATTATTTATT
1 TATATATATTAATATTATTTATT
*
44074 TAAATATTATTAATA-TATTTAAATT
1 TATATA-TATTAATATTATTT--ATT
44099 TATATATATT
1 TATATATATT
44109 TTAATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 4 0.14
23 5 0.17
24 12 0.41
25 8 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATATATATTAATATTATTTATT
Found at i:44118 original size:15 final size:15
Alignment explanation
Indices: 44082--44120 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
44072 TTTAAATATT
44082 ATTA-ATATATTTAA
1 ATTATATATATTTAA
*
44096 ATTTATATATATTTTA
1 A-TTATATATATTTAA
44112 ATTATATAT
1 ATTATATAT
44121 TGAAATGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 11 0.50
16 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTATATATATTTAA
Found at i:44340 original size:21 final size:21
Alignment explanation
Indices: 44300--44338 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
44290 AAATCATGGA
44300 TAAATCCAAGCGACTCTTTCT
1 TAAATCCAAGCGACTCTTTCT
44321 TAAATCCAAGCGA-TCTTT
1 TAAATCCAAGCGACTCTTT
44339 TCGTAGGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (21 bp):
TAAATCCAAGCGACTCTTTCT
Found at i:46875 original size:12 final size:12
Alignment explanation
Indices: 46858--46882 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46848 ATTTTATAAC
46858 ATAAATATTGTT
1 ATAAATATTGTT
46870 ATAAATATTGTT
1 ATAAATATTGTT
46882 A
1 A
46883 ATAGCCTCTG
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAATATTGTT
Found at i:58644 original size:13 final size:15
Alignment explanation
Indices: 58618--58657 Score: 66
Period size: 13 Copynumber: 2.8 Consensus size: 15
58608 CCTTAATTTA
58618 TTAATATTTATTAAT
1 TTAATATTTATTAAT
58633 TTAAT-TTT-TTAAT
1 TTAATATTTATTAAT
58646 TTAATATTTATT
1 TTAATATTTATT
58658 TAATAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.43
14 6 0.26
15 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTAATATTTATTAAT
Found at i:61432 original size:14 final size:14
Alignment explanation
Indices: 61413--61441 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
61403 ACAGATGGAT
61413 TCGTATAATTCTTA
1 TCGTATAATTCTTA
61427 TCGTATAATTCTTA
1 TCGTATAATTCTTA
61441 T
1 T
61442 ATATATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TCGTATAATTCTTA
Found at i:65665 original size:20 final size:21
Alignment explanation
Indices: 65599--65667 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
65589 TCACTTCGTT
65599 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
65620 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
* * *
65641 TCTTTTTGTCTAACTCACTTC
1 TCTTTTTGTCCAAGTTACTTC
65662 -CTTTTT
1 TCTTTTT
65668 TCTTTGTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.12, C:0.25, G:0.09, T:0.55
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:68060 original size:18 final size:18
Alignment explanation
Indices: 68027--68120 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
68017 AAGGTTTTCT
68027 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
68042 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
*
68060 TATTGATGCTAGTGACGA
1 TATTGATGATAGTGACGA
* *
68078 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
*
68096 TATTGATGATAGTGACGC
1 TATTGATGATAGTGACGA
68114 TATTGAT
1 TATTGAT
68121 CGTGACCTTG
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:76396 original size:14 final size:14
Alignment explanation
Indices: 76377--76404 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
76367 TATATTAGTA
76377 TTTTCTATTCTATT
1 TTTTCTATTCTATT
76391 TTTTCTATTCTATT
1 TTTTCTATTCTATT
76405 AGTATTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:76412 original size:6 final size:6
Alignment explanation
Indices: 76401--76474 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
76391 TTTTCTATTC
*
76401 TATTAG TATTAGAG TATTAG -ATTAG TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATT--AG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
76448 TATTAG --TTAG -ATTAG -ATTAG TATTAG T
1 TATTAG TATTAG TATTAG TATTAG TATTAG T
76475 TAGTGATCCC
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
4 4 0.07
5 23 0.39
6 26 0.44
8 6 0.10
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (6 bp):
TATTAG
Found at i:76427 original size:11 final size:11
Alignment explanation
Indices: 76402--76478 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
76392 TTTCTATTCT
76402 ATTAGTATTAG
1 ATTAGTATTAG
76413 ---AGTATTAG
1 ATTAGTATTAG
**
76421 ATTAGTATTCT
1 ATTAGTATTAG
76432 ATTAGTATTAG
1 ATTAGTATTAG
76443 ATTAGTATTAG
1 ATTAGTATTAG
76454 -TTAG-ATTAG
1 ATTAGTATTAG
76463 ATTAGTATTAG
1 ATTAGTATTAG
76474 -TTAGT
1 ATTAGT
76479 GATCCCGGCT
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 8 0.14
9 5 0.09
10 13 0.23
11 31 0.54
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:76432 original size:30 final size:30
Alignment explanation
Indices: 76396--76474 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
76386 CTATTTTTTC
76396 TATTCTATTAGTATTAG-AGTATTAGATTAG
1 TATTCTATTAGTATTAGTAGTATTAG-TTAG
76426 TATTCTATTAGTATTAGATTAGTATTAGTTAG
1 TATTCTATTAGTATTAG--TAGTATTAGTTAG
**
76458 -ATTAGATTAGTATTAGT
1 TATTCTATTAGTATTAGT
76475 TAGTGATCCC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 1 0.02
30 17 0.39
31 14 0.32
32 4 0.09
33 8 0.18
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (30 bp):
TATTCTATTAGTATTAGTAGTATTAGTTAG
Found at i:76446 original size:5 final size:5
Alignment explanation
Indices: 76416--76477 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
76406 GTATTAGAGT
**
76416 ATTAG ATTAG TATTCT ATTAG TATTAG ATTAG TATTAG -TTAG ATTAG
1 ATTAG ATTAG -ATTAG ATTAG -ATTAG ATTAG -ATTAG ATTAG ATTAG
76463 ATTAG TATTAG -TTAG
1 ATTAG -ATTAG ATTAG
76478 TGATCCCGGC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 8 0.17
5 22 0.46
6 18 0.38
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.47
Consensus pattern (5 bp):
ATTAG
Found at i:76463 original size:20 final size:21
Alignment explanation
Indices: 76402--76478 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
76392 TTTCTATTCT
76402 ATTAGTATTAG--AGTATTAG
1 ATTAGTATTAGTTAGTATTAG
76421 ATTAGTATTCTA-TTAGTATTAG
1 ATTAGTA-T-TAGTTAGTATTAG
76443 ATTAGTATTAGTTAG-ATTAG
1 ATTAGTATTAGTTAGTATTAG
76463 ATTAGTATTAGTTAGT
1 ATTAGTATTAGTTAGT
76479 GATCCCGGCT
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.13
20 23 0.44
21 7 0.13
22 15 0.29
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (21 bp):
ATTAGTATTAGTTAGTATTAG
Found at i:80939 original size:37 final size:37
Alignment explanation
Indices: 80877--81019 Score: 175
Period size: 36 Copynumber: 3.9 Consensus size: 37
80867 ATAAAGTATG
*
80877 GTTTTAATTAATAATAAAACAAAATAGTATGAGAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGTATG-GAAGTA
80915 GTTTTAATTAACAA-AAAACAAAATAGTATGGGGAA-TA
1 GTTTTAATTAACAATAAAACAAAATAGTAT--GGAAGTA
* *
80952 GTTTTAATTAACAATAAAACAAAATAGCATGGGAGT-
1 GTTTTAATTAACAATAAAACAAAATAGTATGGAAGTA
* * * *
80988 GTTTTGATTAATAATAAAACAAAGTAGCATGG
1 GTTTTAATTAACAATAAAACAAAATAGTATGG
81020 GGGAGTGGAA
Statistics
Matches: 95, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
36 32 0.34
37 32 0.34
38 30 0.32
39 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (37 bp):
GTTTTAATTAACAATAAAACAAAATAGTATGGAAGTA
Found at i:81004 original size:36 final size:37
Alignment explanation
Indices: 80877--81020 Score: 184
Period size: 37 Copynumber: 3.9 Consensus size: 37
80867 ATAAAGTATG
* * *
80877 GTTTTAATTAATAATAAAACAAAATAGTATGAGAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGCATG-GGAGTA
* *
80915 GTTTTAATTAACAA-AAAACAAAATAGTATGGGGAATA
1 GTTTTAATTAACAATAAAACAAAATAGCAT-GGGAGTA
80952 GTTTTAATTAACAATAAAACAAAATAGCATGGGAGT-
1 GTTTTAATTAACAATAAAACAAAATAGCATGGGAGTA
* * *
80988 GTTTTGATTAATAATAAAACAAAGTAGCATGGG
1 GTTTTAATTAACAATAAAACAAAATAGCATGGG
81021 GGAGTGGAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
36 30 0.31
37 38 0.40
38 28 0.29
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.29
Consensus pattern (37 bp):
GTTTTAATTAACAATAAAACAAAATAGCATGGGAGTA
Found at i:81023 original size:75 final size:75
Alignment explanation
Indices: 80877--81021 Score: 204
Period size: 75 Copynumber: 1.9 Consensus size: 75
80867 ATAAAGTATG
* * *
80877 GTTTTAATTAATAATAAAACAAAATAGTATGAGAAGTAGTTTTAATTAACAAAAAACAAAATAGT
1 GTTTTAATTAACAATAAAACAAAATAGCATGAGAAGTAGTTTTAATTAACAAAAAACAAAATAGC
80942 ATGGGGAATA
66 ATGGGGAATA
* * * *
80952 GTTTTAATTAACAATAAAACAAAATAGCATG-GGAGT-GTTTTGATTAATAATAAAACAAAGTAG
1 GTTTTAATTAACAATAAAACAAAATAGCATGAGAAGTAGTTTTAATTAACAA-AAAACAAAATAG
81015 CATGGGG
65 CATGGGG
81022 GAGTGGAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
73 12 0.19
74 21 0.34
75 29 0.47
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (75 bp):
GTTTTAATTAACAATAAAACAAAATAGCATGAGAAGTAGTTTTAATTAACAAAAAACAAAATAGC
ATGGGGAATA
Found at i:81552 original size:24 final size:22
Alignment explanation
Indices: 81525--81571 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
81515 TGTATATACC
*
81525 ATGTAAATATTTTAATATTATATT
1 ATGTAAACATTTT-ATA-TATATT
*
81549 ATGTATACATTTTATATATATT
1 ATGTAAACATTTTATATATATT
81571 A
1 A
81572 ATATTGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 3 0.14
24 11 0.52
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (22 bp):
ATGTAAACATTTTATATATATT
Found at i:85416 original size:15 final size:15
Alignment explanation
Indices: 85380--85429 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
85370 CGATATTCTT
85380 TTTGCAT-TCATACA
1 TTTGCATCTCATACA
85394 TTTGCATCTCATAACA
1 TTTGCATCTCAT-ACA
*
85410 TTT-CATCACAT-CA
1 TTTGCATCTCATACA
85423 TTTGCAT
1 TTTGCAT
85430 TCAAGGTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 11 0.34
16 6 0.19
ACGTcount: A:0.28, C:0.24, G:0.06, T:0.42
Consensus pattern (15 bp):
TTTGCATCTCATACA
Found at i:85493 original size:15 final size:15
Alignment explanation
Indices: 85473--85503 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
85463 TTTACTTTCC
85473 AGAGAGGTAGAAAAG
1 AGAGAGGTAGAAAAG
85488 AGAGAGGTAGAAAAG
1 AGAGAGGTAGAAAAG
85503 A
1 A
85504 AAATCTGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.06
Consensus pattern (15 bp):
AGAGAGGTAGAAAAG
Found at i:94089 original size:208 final size:207
Alignment explanation
Indices: 93467--94430 Score: 1231
Period size: 208 Copynumber: 4.7 Consensus size: 207
93457 CCTTCATCGG
* ** *
93467 GCAGATCTAAGATGACAGATCTTATCTCTCTGTATTCGG-GGGGAGCATATCGAAGATATAGTTG
1 GCAGATCCAAGATGACAGATCTTATCTCT-TGTATTCGGCAAGGAGCA-ATCGAAGATATAGCTG
93531 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTA-TGTCAGA
64 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
* * *
93595 GAACGAATCGAAGTTTGGCATCTTCACTTTGATGAGAGCAGACACATAGCAGATCTGACCTTCAG
129 GAACAAATCGAAGTCTGGCATCTTCACTTTGATGAGAGCAGACACATAGCAGATCTTACCTTCAG
*
93660 ATGTTTATGCTGAA
194 ATGTTTACGCTGAA
* * ** * *
93674 GCGGATCCAAGATG---G-T-TTGGCATC-CTTGTGTT-TACAAGGAACAAATCGAAGACATAGC
1 GCAGATCCAAGATGACAGATCTT---ATCTCTTGTATTCGGCAAGGAGC-AATCGAAGATATAGC
*
93732 TGATTTGGCTTTCACGTGTTTACGTTGAAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTC
62 TGATTTGGCTTTCACGTGTTTACGATG-AAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTC
93797 AGAGAACAAATCGAAGTCTGGCAT-TTCCACTTTGATG-GAAGGCAGACACATAGCAGATCTTA-
126 AGAGAACAAATCGAAGTCTGGCATCTT-CACTTTGATGAG-A-GCAGACACATAGCAGATCTTAC
93859 CTTCAGATGTTTACGCTGAA
188 CTTCAGATGTTTACGCTGAA
93879 GCAGATCCAAGATGACAGATCTTATCTCTTGTATTCGGCAAGGAGCAATCGAAGATATAGCTGAT
1 GCAGATCCAAGATGACAGATCTTATCTCTTGTATTCGGCAAGGAGCAATCGAAGATATAGCTGAT
93944 TTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGA
66 TTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGA
94009 ACAAATCGAAGTCTGGCAT-TTCCACTTTGATG-GAAGGCAGACACATAGCAGATCTTACCTTCA
131 ACAAATCGAAGTCTGGCATCTT-CACTTTGATGAG-A-GCAGACACATAGCAGATCTTACCTTCA
94072 GATGTTTACGCTGAA
193 GATGTTTACGCTGAA
* *
94087 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAACAGATCGAAGATATAGCTG
1 GCAGATCCAAGATGACAGATCTTATCTCT-TGTATTCGGCAAGGAGCA-ATCGAAGATATAGCTG
*
94152 ATTTGGCTTTCACGTGTTTTCGATGAAGCAAATCTAAGATGATTTGT-GTCTCTGTATTGTCAGA
64 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGA
* * * **
94216 GAACGAATCAAAGTTTGGCATCTTCACTTTGATGAGAGCAGACACATAGCAGATCTCGCCTTC-G
129 GAACAAATCGAAGTCTGGCATCTTCACTTTGATGAGAGCAGACACATAGCAGATCTTACCTTCAG
*
94280 AATGTTTATGCTGAA
194 -ATGTTTACGCTGAA
* ** * * ** * *
94295 GCGGATCCAAGATG---G-T-TTGGCATCCT-TATGCTTACAAGAAGCAAATCG-A-ATCATAGT
1 GCAGATCCAAGATGACAGATCTTATC-TCTTGTATTC-GGCAAGGAGC-AATCGAAGAT-ATAGC
* * * *
94352 TGATTTGGCTTTCACGTGCTTACG-TAAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA
62 TGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCA
*
94416 GGGAACAAATCGAAG
127 GAGAACAAATCGAAG
94431 AAGCAGATTT
Statistics
Matches: 679, Mismatches: 50, Indels: 61
0.86 0.06 0.08
Matches are distributed among these distances:
201 24 0.04
202 59 0.09
203 61 0.09
204 43 0.06
205 73 0.11
206 20 0.03
207 115 0.17
208 147 0.22
209 70 0.10
210 67 0.10
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (207 bp):
GCAGATCCAAGATGACAGATCTTATCTCTTGTATTCGGCAAGGAGCAATCGAAGATATAGCTGAT
TTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGA
ACAAATCGAAGTCTGGCATCTTCACTTTGATGAGAGCAGACACATAGCAGATCTTACCTTCAGAT
GTTTACGCTGAA
Found at i:94384 original size:411 final size:408
Alignment explanation
Indices: 93510--94430 Score: 1210
Period size: 411 Copynumber: 2.2 Consensus size: 408
93500 ATTCGGGGGG
93510 AGCATATCGAAGATATAGTTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATT
1 AGCA-ATCGAAGATATAGTTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATT
* *
93575 TGTCGTCTCTGTA-TGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGAGAGCAGACA
65 TGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTTCACTTTGATGAGAGCAGACA
* * *
93639 CATAGCAGATCTGACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTTGTG
130 CATAGCAGATCTGACCTTCAGATGTTTACGCTGAAGCAGATCCAAGATGGTTT-G-ATCCTTGTA
* *
93704 TTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAAGCAAATC
193 TTGACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAAGCAAATC
*
93769 TAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATTTCCACTTTGATG
258 TAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATTTCCACTTTGATG
*
93834 GAAGGCAGACACATAGCAGATCTTACTTCAGATGTTTACGCTGAAGCAGATCCAAGATGACAGAT
323 GAAGGCAGACACATAGCAGATCTGACTTCAGATGTTTACGCTGAAGCAGATCCAAGATG--AGAT
* * * * *
93899 CTTATCTCTTGTATTCGGCAAGG
386 CTTAGCTCCTGTATGCGACAAGA
*
93922 AGCAATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTT
1 AGCAATCGAAGATATAGTTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTT
93987 GTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCAT-TTCCACTTTGATG-GAAGGCAGA
66 GTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTT-CACTTTGATGAG-A-GCAGA
*
94050 CACATAGCAGATCTTACCTTCAGATGTTTACGCTGAAGCAGATCCAAGATGACAGATCTT-ATCT
128 CACATAGCAGATCTGACCTTCAGATGTTTACGCTGAAGCAGATCCAAGATG---G-T-TTGATC-
* * * * *
94114 CTCTGTATTCGGCAGGGAACAGATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTTCGATG-A
187 CT-TGTATT-GACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAA
* *
94178 AGCAAATCTAAGATGATTTGT-GTCTCTGTATTGTCAGAGAACGAATCAAAGTTTGGCATCTT-C
250 AGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCAT-TTCC
* * *
94241 ACTTTGAT-G-AGAGCAGACACATAGCAGATCTCGCCTTC-GAATGTTTATGCTGAAGCGGATCC
314 ACTTTGATGGAAG-GCAGACACATAGCAGATCT-GACTTCAG-ATGTTTACGCTGAAGCAGATCC
* *
94303 AAGATG-G-T-TTGGCATCCT-TATGCTTACAAGA
376 AAGATGAGATCTTAGC-TCCTGTATGC-GACAAGA
* *
94334 AGCAAATCG-A-ATCATAGTTGATTTGGCTTTCACGTGCTTACG-TAAAGCAAATCTAAGATGAT
1 AGC-AATCGAAGAT-ATAGTTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGAT
* * *
94396 TTGGCATCTCTGTATTGTCAGGGAACAAATCGAAG
64 TTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAG
94431 AAGCAGATTT
Statistics
Matches: 455, Mismatches: 34, Indels: 41
0.86 0.06 0.08
Matches are distributed among these distances:
411 135 0.30
412 80 0.18
413 59 0.13
414 2 0.00
415 24 0.05
416 77 0.17
417 30 0.07
418 48 0.11
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (408 bp):
AGCAATCGAAGATATAGTTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTT
GTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTTCACTTTGATGAGAGCAGACAC
ATAGCAGATCTGACCTTCAGATGTTTACGCTGAAGCAGATCCAAGATGGTTTGATCCTTGTATTG
ACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAAGCAAATCTAA
GATGATTTGTCGTCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATTTCCACTTTGATGGAA
GGCAGACACATAGCAGATCTGACTTCAGATGTTTACGCTGAAGCAGATCCAAGATGAGATCTTAG
CTCCTGTATGCGACAAGA
Found at i:95884 original size:39 final size:39
Alignment explanation
Indices: 95805--95953 Score: 189
Period size: 39 Copynumber: 3.9 Consensus size: 39
95795 ATAAAGTATG
* * *
95805 GTTTTAATTAATAATAAAACAAAAT-GTATGAGGAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGCATGGGGAAGTA
* *
95843 GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAATA
1 GTTTTAATTAACAATAAAACAAAATAGCATGGGGAAGTA
95882 GTTTTAATTAACAATAAAACAAAATAGCAT-GGG-AGT-
1 GTTTTAATTAACAATAAAACAAAATAGCATGGGGAAGTA
* * *
95918 GTTTTTGATTAATAATAAAACAAAGTAGCATGGGGA
1 G-TTTTAATTAACAATAAAACAAAATAGCATGGGGA
95954 GTGGAATCAG
Statistics
Matches: 99, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
36 1 0.01
37 28 0.28
38 30 0.30
39 40 0.40
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (39 bp):
GTTTTAATTAACAATAAAACAAAATAGCATGGGGAAGTA
Found at i:98842 original size:24 final size:22
Alignment explanation
Indices: 98815--98858 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 22
98805 GAGGGTTAGA
98815 TTTTTTTAAAATCAAGACTAATAG
1 TTTTTTT--AATCAAGACTAATAG
98839 TTTTTTTAATCAAGACTAAT
1 TTTTTTTAATCAAGACTAAT
98859 TAACATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTTTTTAATCAAGACTAATAG
Found at i:100060 original size:15 final size:15
Alignment explanation
Indices: 100040--100070 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
100030 TGACAACATT
100040 TTTAGTATTTTAAGC
1 TTTAGTATTTTAAGC
100055 TTTAGTATTTTAAGC
1 TTTAGTATTTTAAGC
100070 T
1 T
100071 ACCCTCCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (15 bp):
TTTAGTATTTTAAGC
Done.