Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 35
Found at i:2067836 original size:38 final size:36
Alignment explanation
Indices: 2067760--2067918 Score: 124
Period size: 38 Copynumber: 4.1 Consensus size: 36
2067750 ATTTAAACTA
* *
2067760 TATATATTATATA-ATTTATACATAGTA-TATATAATT
1 TATA-ATTATATATATTTATATATA-AACTATATAATT
*
2067796 TATAGTTATATATAGTTTATATTATAAACTATATAATT
1 TATAATTATATATA-TTTATA-TATAAACTATATAATT
* * *
2067834 TATAATTATACATAATATATAAATATAAGCTATATATATTT
1 TATAATTAT--AT-ATATTTATATATAAACTATATA-A-TT
*
2067875 AAATATAATTCATATATATTTATAGATAAACTATATAATT
1 ---TATAATT-ATATATATTTATATATAAACTATATAATT
2067915 TATA
1 TATA
2067919 TTAATAAACT
Statistics
Matches: 99, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
35 7 0.07
36 5 0.05
37 11 0.11
38 20 0.20
39 12 0.12
40 9 0.09
41 6 0.06
42 18 0.18
43 2 0.02
44 7 0.07
45 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (36 bp):
TATAATTATATATATTTATATATAAACTATATAATT
Found at i:2068008 original size:2 final size:2
Alignment explanation
Indices: 2068003--2068072 Score: 63
Period size: 2 Copynumber: 34.5 Consensus size: 2
2067993 TTTCTACATA
* * *
2068003 AT AT AT AT AT AGT TT AT AT AT AGT AC AT A- AT A- AT AT AA AT AT
1 AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
2068045 AA ACT AT AT AT AT AT AT AT AT AT AT AT A
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT A
2068073 CTTATAAACT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
1 2 0.04
2 49 0.89
3 4 0.07
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2068022 original size:11 final size:11
Alignment explanation
Indices: 2067984--2068026 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2067974 TTATACATGG
2067984 TATATATAGTT
1 TATATATAGTT
* * * *
2067995 TCTACATAATA
1 TATATATAGTT
2068006 TATATATAGTT
1 TATATATAGTT
2068017 TATATATAGT
1 TATATATAGT
2068027 ACATAATAAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.49
Consensus pattern (11 bp):
TATATATAGTT
Found at i:2068108 original size:51 final size:52
Alignment explanation
Indices: 2068051--2068164 Score: 149
Period size: 51 Copynumber: 2.2 Consensus size: 52
2068041 ATATAAACTA
* *
2068051 TATATATATATATATATATATACTTATAAACTTTAGTCTTTATAATTATACTT
1 TATATATATATATAT-TATATACTTATAAACTTTAATCTTTATAACTATACTT
* * * * *
2068104 TATATGT-TTTATATTATGTGCTTATATACTTTAATCTTTATAACTATACTT
1 TATATATATATATATTATATACTTATAAACTTTAATCTTTATAACTATACTT
2068155 TATATATATA
1 TATATATATA
2068165 GTGTTTCTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
51 38 0.75
52 7 0.14
53 6 0.12
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.53
Consensus pattern (52 bp):
TATATATATATATATTATATACTTATAAACTTTAATCTTTATAACTATACTT
Found at i:2068196 original size:16 final size:15
Alignment explanation
Indices: 2068176--2068362 Score: 90
Period size: 15 Copynumber: 12.1 Consensus size: 15
2068166 TGTTTCTATT
2068176 TTATATTATTATATA
1 TTATATTATTATATA
2068191 TGTATATTATTATATA
1 T-TATATTATTATATA
2068207 TTATATGTATATTATATA
1 TTATA--T-TATTATATA
* *
2068225 TAATATAATTATACT-
1 TTATATTATTATA-TA
*
2068240 TTATATATATATACATA
1 TTATAT-TAT-TATATA
*
2068257 CTTATACTT-TT-TATT
1 -TTATA-TTATTATATA
2068272 TTATATGTA-TATATA
1 TTATAT-TATTATATA
2068287 CTT-TATATACTTATATA
1 -TTATAT-TA-TTATATA
*
2068304 TTTTA-TATTATATA
1 TTATATTATTATATA
*
2068318 CTTATA-TACTT-TAGTCT
1 -TTATATTA-TTATA-T-A
2068335 TTATATTATTAT-TA
1 TTATATTATTATATA
2068349 TTATA-TA-TATATA
1 TTATATTATTATATA
2068362 T
1 T
2068363 AATTTATAGT
Statistics
Matches: 136, Mismatches: 12, Indels: 50
0.69 0.06 0.25
Matches are distributed among these distances:
12 3 0.02
13 6 0.04
14 19 0.14
15 37 0.27
16 35 0.26
17 16 0.12
18 19 0.14
19 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (15 bp):
TTATATTATTATATA
Found at i:2068201 original size:26 final size:26
Alignment explanation
Indices: 2068154--2068317 Score: 74
Period size: 26 Copynumber: 6.3 Consensus size: 26
2068144 TAACTATACT
* * * *
2068154 TTATATATATAGTGTTTCTATTTTATA
1 TTATATATATATTATAT-TATTATATA
2068181 TTAT-TATATATGTATATTATTATATA
1 TTATATATATAT-TATATTATTATATA
* *
2068207 TTATATGTATATTATA-TATAATATAA
1 TTATATATATATTATATTATTATAT-A
* *
2068233 TTATACTTTATA-TATA-TA-TACATA
1 TTATA-TATATATTATATTATTATATA
* * *
2068257 CTTATACTTTTTATTTTA-TATGTATATA
1 -TTATA-TATATATTATATTAT-TATATA
* *
2068285 -TACTTTATATACTTATA-TATTTTATA
1 TTA-TATATATA-TTATATTATTATATA
2068311 TTATATA
1 TTATATA
2068318 CTTATATACT
Statistics
Matches: 108, Mismatches: 18, Indels: 23
0.72 0.12 0.15
Matches are distributed among these distances:
24 1 0.01
25 21 0.19
26 53 0.49
27 28 0.26
28 5 0.05
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (26 bp):
TTATATATATATTATATTATTATATA
Found at i:2068211 original size:21 final size:21
Alignment explanation
Indices: 2068179--2068252 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 21
2068169 TTCTATTTTA
2068179 TATTAT-TA-TATATGTATAT
1 TATTATATATTATATGTATAT
2068198 TATTATATATTATATGTATAT
1 TATTATATATTATATGTATAT
* *
2068219 TA-TATATAATATAAT-TATAC
1 TATTATATATTAT-ATGTATAT
2068239 T-TTATATATATATA
1 TATTATATAT-TATA
2068253 CATACTTATA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
19 6 0.13
20 23 0.49
21 18 0.38
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTATATATTATATGTATAT
Found at i:2068266 original size:25 final size:24
Alignment explanation
Indices: 2068219--2068266 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
2068209 ATATGTATAT
*
2068219 TATATATAATATAATTATACTTTA
1 TATATATAACATAATTATACTTTA
*
2068243 TATATATATACATACTTATACTTT
1 TATATATA-ACATAATTATACTTT
2068267 TTATTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (24 bp):
TATATATAACATAATTATACTTTA
Found at i:2068293 original size:17 final size:16
Alignment explanation
Indices: 2068175--2068317 Score: 63
Period size: 17 Copynumber: 8.8 Consensus size: 16
2068165 GTGTTTCTAT
2068175 TTTATATTATTATATA-
1 TTTATATTA-TATATAC
*
2068191 TGTATATTAT-TATA-
1 TTTATATTATATATAC
2068205 TATTATATGTATAT-TA-
1 T-TTATAT-TATATATAC
* *
2068221 TATATAATATAATTATAC
1 TTTATATTAT-A-TATAC
2068239 TTTATA-TATATATAC
1 TTTATATTATATATAC
*
2068254 ATACTTATACTT-T-T-TAT
1 -T--TTATA-TTATATATAC
2068271 TTTATATGTATATATAC
1 TTTATAT-TATATATAC
*
2068288 TTTATA-TACTTATATAT
1 TTTATATTA--TATATAC
2068305 TTTATATTATATA
1 TTTATATTATATA
2068318 CTTATATACT
Statistics
Matches: 100, Mismatches: 8, Indels: 38
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.01
14 14 0.14
15 19 0.19
16 23 0.23
17 28 0.28
18 13 0.13
19 1 0.01
20 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTATATTATATATAC
Found at i:2068317 original size:22 final size:22
Alignment explanation
Indices: 2068289--2068380 Score: 82
Period size: 22 Copynumber: 4.1 Consensus size: 22
2068279 TATATATACT
2068289 TTATATACTTATATATTTTATA
1 TTATATACTTATATATTTTATA
* *
2068311 TTATATACTTATATACTTTAGTC
1 TTATATACTTATATATTTTA-TA
*
2068334 TT-TATA-TTATTATTATTATATA
1 TTATATACTTA-TA-TATTTTATA
* *
2068356 TATATATAATT-TATAGTTTATA
1 T-TATATACTTATATATTTTATA
2068378 TTA
1 TTA
2068381 ATAAAGTATA
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
21 5 0.09
22 35 0.61
23 11 0.19
24 4 0.07
25 2 0.04
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (22 bp):
TTATATACTTATATATTTTATA
Found at i:2068351 original size:38 final size:39
Alignment explanation
Indices: 2068175--2068370 Score: 137
Period size: 39 Copynumber: 5.2 Consensus size: 39
2068165 GTGTTTCTAT
*
2068175 TTTATATTA-TTATATA-TGTATATTAT-TATATAT-TA-
1 TTTATA-TACTTATATATTTTATATTATATATATATATAC
* * ** *
2068210 TATGTATA-TTATATATAATATAATTATACTTTATATATA-
1 TTTATATACTTATATATTTTAT-ATTATA-TATATATATAC
* * * *
2068249 TATACATACTTATACT-TTTTATTTTATATGTATATATAC
1 TTTATATACTTATA-TATTTTATATTATATATATATATAC
2068288 TTTATATACTTATATATTTTATATTATATACT-TATATAC
1 TTTATATACTTATATATTTTATATTATATA-TATATATAC
* *
2068327 TTTA-GT-CTT-TATATTATTATTATTATATATATATATAA
1 TTTATATACTTATATATT-TTA-TATTATATATATATATAC
2068365 TTTATA
1 TTTATA
2068371 GTTTATATTA
Statistics
Matches: 129, Mismatches: 18, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
34 9 0.07
35 7 0.05
36 11 0.09
37 7 0.05
38 36 0.28
39 48 0.37
40 10 0.08
41 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (39 bp):
TTTATATACTTATATATTTTATATTATATATATATATAC
Found at i:2068376 original size:38 final size:37
Alignment explanation
Indices: 2068267--2068380 Score: 117
Period size: 38 Copynumber: 3.0 Consensus size: 37
2068257 CTTATACTTT
*
2068267 TTATT-TTATATGTATATATACTTTATATACTTATA-TA
1 TTATTATTATATATATATATACTTTATAT--TTATATTA
* *
2068304 TTTTATATTATATACT-TATATACTTTAGTCTTTATATTA
1 TTAT-TATTATATA-TATATATACTTTA-TATTTATATTA
*
2068343 TTATTATTATATATATATATAATTTATAGTTTATATTA
1 TTATTATTATATATATATATACTTTATA-TTTATATTA
2068381 ATAAAGTATA
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
37 5 0.08
38 34 0.53
39 22 0.34
40 3 0.05
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (37 bp):
TTATTATTATATATATATATACTTTATATTTATATTA
Found at i:2068481 original size:9 final size:10
Alignment explanation
Indices: 2068387--2068502 Score: 55
Period size: 9 Copynumber: 11.5 Consensus size: 10
2068377 ATTAATAAAG
2068387 TATATAATT-
1 TATATAATTA
* *
2068396 TATA-CATCA
1 TATATAATTA
2068405 TATAT-ATTA
1 TATATAATTA
*
2068414 TTTATAATTA
1 TATATAATTA
*
2068424 TACATAATATA
1 TATATAAT-TA
* *
2068435 TAAATATAAGATG
1 T--ATATAA-TTA
*
2068448 TATATATTTA
1 TATATAATTA
*
2068458 AATATAATTCA
1 TATATAATT-A
2068469 TATATAATTTA
1 TATATAA-TTA
2068480 TATATAA--A
1 TATATAATTA
2068488 CTATATAATT-
1 -TATATAATTA
2068498 TATAT
1 TATAT
2068503 TAATAAACTA
Statistics
Matches: 80, Mismatches: 15, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
8 3 0.04
9 27 0.34
10 18 0.22
11 23 0.29
12 2 0.03
13 7 0.09
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (10 bp):
TATATAATTA
Found at i:2068484 original size:22 final size:22
Alignment explanation
Indices: 2068352--2068527 Score: 104
Period size: 22 Copynumber: 8.4 Consensus size: 22
2068342 ATTATTATTA
* *
2068352 TATATATATATA-ATTTATAGTT
1 TATATATA-ATACATATATAATT
*
2068374 TATAT-TAATAAAGTATATAATT
1 TATATATAATACA-TATATAATT
* * *
2068396 TATACATCAT--ATATATTATT
1 TATATATAATACATATATAATT
* *
2068416 TATA-ATTATACATA-AT-ATA
1 TATATATAATACATATATAATT
* * **
2068435 TAAATATAAGATGTATAT-ATT
1 TATATATAATACATATATAATT
* *
2068456 TAAATATAATTCATATATAATT
1 TATATATAATACATATATAATT
2068478 TATATATAA-AC-TATATAATT
1 TATATATAATACATATATAATT
* *
2068498 TATAT-TAATAAACTATATAGTT
1 TATATATAATACA-TATATAATT
2068520 TATATATA
1 TATATATA
2068528 TAATTTTTAT
Statistics
Matches: 121, Mismatches: 21, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
19 12 0.10
20 38 0.31
21 26 0.21
22 40 0.33
23 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (22 bp):
TATATATAATACATATATAATT
Found at i:2068492 original size:20 final size:20
Alignment explanation
Indices: 2068469--2068565 Score: 106
Period size: 22 Copynumber: 4.7 Consensus size: 20
2068459 ATATAATTCA
2068469 TATATAATTTATATATAAAC
1 TATATAATTTATATATAAAC
2068489 TATATAATTTATATTAATAAAC
1 TATATAATTTATA-T-ATAAAC
* *
2068511 TATATAGTTTATATATATAATT
1 TATATAATTTATATATA-AA-C
*
2068533 TTTATACA-TTATATATAAAC
1 TATATA-ATTTATATATAAAC
*
2068553 TATATAGTTTATA
1 TATATAATTTATA
2068566 CCTAGTATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
20 26 0.41
21 6 0.09
22 32 0.50
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.48
Consensus pattern (20 bp):
TATATAATTTATATATAAAC
Found at i:2068524 original size:42 final size:42
Alignment explanation
Indices: 2068469--2068565 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 42
2068459 ATATAATTCA
*
2068469 TATATAATTTATATATA-AA-CTATATA-ATTTATATTAATAAAC
1 TATATAGTTTATATATATAATCTATATACA-TTATA-T-ATAAAC
* *
2068511 TATATAGTTTATATATATAATTTTTATACATTATATATAAAC
1 TATATAGTTTATATATATAATCTATATACATTATATATAAAC
2068553 TATATAGTTTATA
1 TATATAGTTTATA
2068566 CCTAGTATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
42 35 0.71
43 3 0.06
44 10 0.20
45 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.48
Consensus pattern (42 bp):
TATATAGTTTATATATATAATCTATATACATTATATATAAAC
Found at i:2068549 original size:2 final size:2
Alignment explanation
Indices: 2068177--2068529 Score: 63
Period size: 2 Copynumber: 186.0 Consensus size: 2
2068167 GTTTCTATTT
* *
2068177 TA TA T- TA T- TA TA TA TG TA TA T- TA T- TA TA TA T- TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2068214 TA TA T- TA TA TA TA -A TA TA -A T- TA TA CTT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * * *
2068253 CA TA CT- TA TA CTT TT TA T- TT TA TA TG TA TA TA TA CTT TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
2068294 TA CT- TA TA TA T- TT TA TA T- TA TA TA CT- TA TA TA CTT TA GTC
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA -TA
* *
2068334 TT TA TA T- TA T- TA T- TA T- TA TA TA TA TA TA TA -A TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
2068371 GTT TA TA T- TA -A TA AA GTA TA TA -A TT TA TA CA TCA TA TA TA
1 -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T-A TA TA TA
* * * * *
2068411 T- TA TT TA TA -A T- TA TA CA TA -A TA TA TA AA TA TA -A GA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
2068448 TA TA TA TT TA AA TA TA -A T- TCA TA TA TA -A TT TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
* * *
2068488 CTA TA TA -A TT TA TA T- TA -A TA AA CTA TA TA GTT TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
2068528 TA
1 TA
2068530 ATTTTTATAC
Statistics
Matches: 248, Mismatches: 54, Indels: 98
0.62 0.14 0.25
Matches are distributed among these distances:
1 34 0.14
2 198 0.80
3 16 0.06
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2071460 original size:3 final size:3
Alignment explanation
Indices: 2071452--2071480 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2071442 TTATCTTTAT
2071452 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2071481 TCAGGTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2075820 original size:19 final size:19
Alignment explanation
Indices: 2075792--2075879 Score: 70
Period size: 23 Copynumber: 4.3 Consensus size: 19
2075782 AAAACCAAAA
* *
2075792 CCCC-AGGGGGTATCGTTT
1 CCCCTAGGGGGAATCGGTT
2075810 CCCCTAGGGGGAATCGGTT
1 CCCCTAGGGGGAATCGGTT
*
2075829 CCCCTTCAAAGGGAGAATCGGTT
1 CCCC-T---AGGGGGAATCGGTT
2075852 CCCCTTCAAAGGGGGAATCGGTT
1 CCCC-T---AGGGGGAATCGGTT
2075875 CCCCT
1 CCCCT
2075880 TGAAGGGGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
18 4 0.07
19 16 0.26
20 1 0.02
22 1 0.02
23 39 0.64
ACGTcount: A:0.18, C:0.30, G:0.30, T:0.23
Consensus pattern (19 bp):
CCCCTAGGGGGAATCGGTT
Found at i:2075888 original size:22 final size:23
Alignment explanation
Indices: 2075815--2075899 Score: 127
Period size: 23 Copynumber: 3.7 Consensus size: 23
2075805 CGTTTCCCCT
2075815 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
2075838 AGGGAGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
2075861 AGGGGGAATCGGTTCCCCTT-GA
1 AGGGGGAATCGGTTCCCCTTCAA
* *
2075883 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
2075900 TCTGCCCTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 16 0.28
23 41 0.72
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.22
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:2081433 original size:11 final size:11
Alignment explanation
Indices: 2081399--2081434 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
2081389 GTTTGATGCT
2081399 TTCTCT-TTGA
1 TTCTCTCTTGA
*
2081409 TTATCTCTTGA
1 TTCTCTCTTGA
2081420 TTCTCTCTTGA
1 TTCTCTCTTGA
2081431 TTCT
1 TTCT
2081435 AGTTGCTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.11, C:0.22, G:0.08, T:0.58
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:2095200 original size:91 final size:92
Alignment explanation
Indices: 2095097--2095276 Score: 299
Period size: 92 Copynumber: 2.0 Consensus size: 92
2095087 TCGACCATAC
2095097 TTTTTCCATCTGTTTGCTACTACTTGTTTTTCC-TTTGTGAATACCATTAGACAAGAATCTTAGG
1 TTTTTCCATCTGTTTGCTACTACTTGTTTTTCCTTTTGTGAATACCATTAGACAAGAATCTTAGG
* * *
2095161 ACTAGTTAGTGATAGCTAGTTCTATCT
66 AATAGTTAGTGACACCTAGTTCTATCT
* *
2095188 TTTTTTCATCTGTTTGCTACTACTTGTTTTTCCTTTTGTTAATACCATTAGACAAGAATCTTAGG
1 TTTTTCCATCTGTTTGCTACTACTTGTTTTTCCTTTTGTGAATACCATTAGACAAGAATCTTAGG
*
2095253 AATTGTTAGTGACACCTAGTTCTA
66 AATAGTTAGTGACACCTAGTTCTA
2095277 GCTATAGCAA
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 32 0.39
92 50 0.61
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.45
Consensus pattern (92 bp):
TTTTTCCATCTGTTTGCTACTACTTGTTTTTCCTTTTGTGAATACCATTAGACAAGAATCTTAGG
AATAGTTAGTGACACCTAGTTCTATCT
Found at i:2099341 original size:21 final size:22
Alignment explanation
Indices: 2099306--2099362 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
2099296 TTTAATTTCA
*
2099306 TTTTTATTCTATGTT-TTTACT
1 TTTTTATTATATGTTATTTACT
* *
2099327 TTTTTATTATTTGTTAGTTTATT
1 TTTTTATTATATGTTA-TTTACT
2099350 TTTTTAATTATAT
1 TTTTT-ATTATAT
2099363 TCATTAATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 13 0.45
23 10 0.34
24 6 0.21
ACGTcount: A:0.19, C:0.04, G:0.05, T:0.72
Consensus pattern (22 bp):
TTTTTATTATATGTTATTTACT
Found at i:2119197 original size:18 final size:18
Alignment explanation
Indices: 2119170--2119204 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2119160 GAGGATGAGA
2119170 AGAATAAGAAGAAGAATG
1 AGAATAAGAAGAAGAATG
*
2119188 AGAATGAGAAGAAGAAT
1 AGAATAAGAAGAAGAAT
2119205 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.11
Consensus pattern (18 bp):
AGAATAAGAAGAAGAATG
Found at i:2119779 original size:157 final size:157
Alignment explanation
Indices: 2119502--2119806 Score: 547
Period size: 157 Copynumber: 1.9 Consensus size: 157
2119492 CCTATTGTGT
2119502 CCTTCACCTCTGTAGTGGACACATAGCTTCAGTAGACCTTGCTCTCTCTAATGGTCATCCATATT
1 CCTTCACCTCTGTAGTGGACACATAGCTTCAGTAGACCTTGCTCTCTCTAATGGTCATCCATATT
* *
2119567 AGTATGGATTTAACTAGATTCAGGACAACCGCTCAACTTTCCTTTTTAATTACGGATTGGGCAAC
66 AGTATGAATTTAACTAGATTCAGGACAACCGCTCAACTTTCCTTTGTAATTACGGATTGGGCAAC
*
2119632 CATTCTTCAGAGACAGTACTATTCTAG
131 CATTATTCAGAGACAGTACTATTCTAG
* *
2119659 CCTTCACCTCTGTAGTGGCCACATAGCTTCGGTAGACCTTGCTCTCTCTAATGGTCATCCATATT
1 CCTTCACCTCTGTAGTGGACACATAGCTTCAGTAGACCTTGCTCTCTCTAATGGTCATCCATATT
*
2119724 AGTATGAATTTAACTAGATTCAGGACAACTGCTCAACTTTCCTTTGTAATTACGGATTGGGCAAC
66 AGTATGAATTTAACTAGATTCAGGACAACCGCTCAACTTTCCTTTGTAATTACGGATTGGGCAAC
*
2119789 CATTATTCAGAGATAGTA
131 CATTATTCAGAGACAGTA
2119807 GGTGGCTAAT
Statistics
Matches: 141, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 141 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (157 bp):
CCTTCACCTCTGTAGTGGACACATAGCTTCAGTAGACCTTGCTCTCTCTAATGGTCATCCATATT
AGTATGAATTTAACTAGATTCAGGACAACCGCTCAACTTTCCTTTGTAATTACGGATTGGGCAAC
CATTATTCAGAGACAGTACTATTCTAG
Found at i:2124512 original size:20 final size:20
Alignment explanation
Indices: 2124487--2124531 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
2124477 GATGCATTTT
2124487 TTGTTTACAAATGTCGTTAA
1 TTGTTTACAAATGTCGTTAA
2124507 TTGTTTACAAATGTCGTTAA
1 TTGTTTACAAATGTCGTTAA
2124527 TTGTT
1 TTGTT
2124532 GCGGCACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.49
Consensus pattern (20 bp):
TTGTTTACAAATGTCGTTAA
Found at i:2129523 original size:23 final size:23
Alignment explanation
Indices: 2129497--2129564 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
2129487 CACCATAGCT
* *
2129497 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACTGAAGTGCCA
*
2129520 CGTAGAATTGCACTGAAGTGCCA
1 CGTAGAAATGCACTGAAGTGCCA
2129543 CGTAGAAATGCACTGAAGTGCC
1 CGTAGAAATGCACTGAAGTGCC
2129565 TTATAAGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACTGAAGTGCCA
Found at i:2135436 original size:10 final size:10
Alignment explanation
Indices: 2135423--2135487 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
2135413 TTTTTTGAAA
2135423 TTTTTGGCTT
1 TTTTTGGCTT
2135433 TTTTT---TT
1 TTTTTGGCTT
*
2135440 TTTTTGGTTT
1 TTTTTGGCTT
2135450 TTTTTGGCTT
1 TTTTTGGCTT
**
2135460 TTTTTCTTCTTT
1 TTTTT-GGC-TT
*
2135472 TTTTTGCCTT
1 TTTTTGGCTT
2135482 TTTTTG
1 TTTTTG
2135488 AAAAAAATAG
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
7 7 0.16
10 29 0.64
11 2 0.04
12 7 0.16
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.78
Consensus pattern (10 bp):
TTTTTGGCTT
Found at i:2135437 original size:11 final size:11
Alignment explanation
Indices: 2135437--2135486 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
2135427 TGGCTTTTTT
2135437 TTTTTTTTGG-
1 TTTTTTTTGGC
2135447 TTTTTTTTGGC
1 TTTTTTTTGGC
*
2135458 TTTTTTTCT-TC
1 TTTTTTT-TGGC
*
2135469 TTTTTTTTGCC
1 TTTTTTTTGGC
2135480 TTTTTTT
1 TTTTTTT
2135487 GAAAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 11 0.31
11 23 0.66
12 1 0.03
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGGC
Found at i:2135443 original size:17 final size:16
Alignment explanation
Indices: 2135423--2135454 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
2135413 TTTTTTGAAA
2135423 TTTTTGGCTTTTTTTTT
1 TTTTTGG-TTTTTTTTT
2135440 TTTTTGGTTTTTTTT
1 TTTTTGGTTTTTTTT
2135455 GGCTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.84
Consensus pattern (16 bp):
TTTTTGGTTTTTTTTT
Found at i:2136997 original size:21 final size:22
Alignment explanation
Indices: 2136947--2137008 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
2136937 ATACTACCCT
*
2136947 TAGGGTACTGATACCTCTATGC
1 TAGGGTACCGATACCTCTATGC
*
2136969 TAGGGTACCGATACGTCTATGC
1 TAGGGTACCGATACCTCTATGC
2136991 T-GGGTACCGATACC-CTAT
1 TAGGGTACCGATACCTCTAT
2137009 CCAGGTACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 4 0.11
21 12 0.32
22 21 0.57
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (22 bp):
TAGGGTACCGATACCTCTATGC
Found at i:2137093 original size:22 final size:22
Alignment explanation
Indices: 2137047--2137121 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
2137037 AAGTTCTCAG
*
2137047 GGTATCGATA-CCCTCCCCATA-
1 GGTATCGATACCCCT-TCCATAT
2137068 GGTATCGATACCCCTTCCATAT
1 GGTATCGATACCCCTTCCATAT
*
2137090 GGTATTGATACCCCTTCCATAT
1 GGTATCGATACCCCTTCCATAT
2137112 GGTATCGATA
1 GGTATCGATA
2137122 TTGTTCATAC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
21 15 0.31
22 34 0.69
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (22 bp):
GGTATCGATACCCCTTCCATAT
Found at i:2140083 original size:25 final size:23
Alignment explanation
Indices: 2140055--2140127 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 23
2140045 GGAAAAAATG
2140055 AATAAATGAAAAAATGAAGAAT-AAA
1 AATAAAT-AAAAAAT-AA-AATGAAA
*
2140080 AATAAGTAAAAAAAATAAAATGAAA
1 AATAA--ATAAAAAATAAAATGAAA
2140105 AATAAATAAATAAAT-AAATGAAA
1 AATAAATAAA-AAATAAAATGAAA
2140128 TATTAATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
23 12 0.29
24 7 0.17
25 15 0.36
26 7 0.17
27 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (23 bp):
AATAAATAAAAAATAAAATGAAA
Found at i:2140111 original size:16 final size:15
Alignment explanation
Indices: 2140047--2140115 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
2140037 TGTCAGAGGG
*
2140047 AAAAAATGAATAAATG
1 AAAAAATGAA-AAATA
*
2140063 AAAAAATGAAGAATA
1 AAAAAATGAAAAATA
2140078 AAAATAA-GTAAAAA-A
1 AAAA-AATG-AAAAATA
2140093 AATAAAATGAAAAATA
1 AA-AAAATGAAAAATA
*
2140109 AATAAAT
1 AAAAAAT
2140116 AAATAAATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
15 22 0.50
16 22 0.50
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (15 bp):
AAAAAATGAAAAATA
Found at i:2140214 original size:16 final size:17
Alignment explanation
Indices: 2140185--2140219 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
2140175 TCATAACAAT
2140185 AATAATAGTAATATAAA
1 AATAATAGTAATATAAA
2140202 AATAATA-TAATATAAA
1 AATAATAGTAATATAAA
2140218 AA
1 AA
2140220 AAAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AATAATAGTAATATAAA
Found at i:2140441 original size:19 final size:19
Alignment explanation
Indices: 2140410--2140447 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2140400 AAAAAAAAGT
*
2140410 ATATATATATAAATAATAA
1 ATATATATATAAAAAATAA
2140429 ATATAGTAT-TAAAAAATAA
1 ATATA-TATATAAAAAATAA
2140448 CCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATATATATAAAAAATAA
Found at i:2140488 original size:23 final size:24
Alignment explanation
Indices: 2140457--2140505 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
2140447 ACCAAATGAA
2140457 TATAAATAAATAA-AAAATATA-TG
1 TATAAAT-AATAATAAAATATAGTG
* *
2140480 TATAGATAATAATAATATATAGTG
1 TATAAATAATAATAAAATATAGTG
2140504 TA
1 TA
2140506 AAAAAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (24 bp):
TATAAATAATAATAAAATATAGTG
Found at i:2141009 original size:37 final size:37
Alignment explanation
Indices: 2140968--2141072 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
2140958 GTGCTTGTGG
* * *
2140968 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
2141005 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
2141042 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
2141073 GACGAAAAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:2143178 original size:14 final size:14
Alignment explanation
Indices: 2143159--2143190 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2143149 TATTTTGATA
*
2143159 AAAATTAAGATATT
1 AAAATTAAAATATT
2143173 AAAATTAAAATATT
1 AAAATTAAAATATT
2143187 AAAA
1 AAAA
2143191 AAAGAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
AAAATTAAAATATT
Found at i:2143653 original size:26 final size:24
Alignment explanation
Indices: 2143605--2143662 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
2143595 CTGATGGAAT
*
2143605 TCAATTCCATCAAATGAGGGAAAG
1 TCAATTCCATCAAATGAAGGAAAG
* * *
2143629 TGAATTCCATCCAAAATGAATGAAAT
1 TCAATTCCAT-C-AAATGAAGGAAAG
2143655 TCAATTCC
1 TCAATTCC
2143663 CTTGTTGGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 9 0.33
25 1 0.04
26 17 0.63
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (24 bp):
TCAATTCCATCAAATGAAGGAAAG
Found at i:2144038 original size:38 final size:38
Alignment explanation
Indices: 2143973--2144059 Score: 131
Period size: 38 Copynumber: 2.3 Consensus size: 38
2143963 TTTATTTTAT
2143973 TCGGGTCGGG-TTTTTTAAGTGTAATATTCGGGTCGAG
1 TCGGGTCGGGTTTTTTTAAGTGTAATATTCGGGTCGAG
* *
2144010 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGGTCGGGTTTTTTTAAGTGTAATATTCGGGTCGAG
* *
2144048 TCGAGTTGGGTT
1 TCGGGTCGGGTT
2144060 CGGGTTTAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
37 10 0.22
38 35 0.78
ACGTcount: A:0.13, C:0.10, G:0.38, T:0.39
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTAATATTCGGGTCGAG
Found at i:2144167 original size:63 final size:64
Alignment explanation
Indices: 2144043--2144167 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 64
2144033 GATATTCGGG
* * * *
2144043 TCGGGTCGAGTTGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCAACCCGAAAATATATATAAT
1 TCGGGTCGAGTCGGGTTCGGGTTTAGGGTGAAAAAAACCAGACCAACCCGAAAAAAAATATAAT
* * **
2144107 TCGGGTCGGGTCGGG-TCGGGTTTAGGGTGAAAAAAATCAGACTGACCCGAAAAAAAATATA
1 TCGGGTCGAGTCGGGTTCGGGTTTAGGGTGAAAAAAACCAGACCAACCCGAAAAAAAATATA
2144168 TAATTTTACC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
63 40 0.75
64 13 0.25
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.22
Consensus pattern (64 bp):
TCGGGTCGAGTCGGGTTCGGGTTTAGGGTGAAAAAAACCAGACCAACCCGAAAAAAAATATAAT
Found at i:2144739 original size:18 final size:16
Alignment explanation
Indices: 2144702--2144747 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2144692 ATATGGAATT
2144702 AGATTCCAATTCCTAC
1 AGATTCCAATTCCTAC
*
2144718 AGATTTCAATTCCTTCAC
1 AGATTCCAATTCC-T-AC
*
2144736 AGATTCTAATTC
1 AGATTCCAATTC
2144748 TCTCATAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 12 0.48
17 1 0.04
18 12 0.48
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (16 bp):
AGATTCCAATTCCTAC
Found at i:2146010 original size:113 final size:111
Alignment explanation
Indices: 2145805--2146010 Score: 254
Period size: 113 Copynumber: 1.8 Consensus size: 111
2145795 TCACCTCAGT
* *
2145805 AAAAAAATCAACTATAAAGTTGAGTGAGAAAATTAAAATTTTTGAAAGTACGTTGAATAAAATAT
1 AAAAAAATCAACCATAAAGTTGAGTGAGAAAATTAAAATTTTTGAAAGTACGGTGAATAAAATAT
* * *
2145870 GAATCATATGAAAGTTCAATTATCAAATGTATAACAATAGAGTGAC
66 GAATCAGATGAAAGTACAATTACCAAATGTATAACAATAGAGTGAC
* * * *
2145916 AAAAAAATTCAATCCATAAAGTTGAGTTAGCAAATTAAACA-TTTTGAAAGTATGGTGAGTAAAA
1 AAAAAAA-TCAA-CCATAAAGTTGAGTGAGAAAATTAAA-ATTTTTGAAAGTACGGTGAATAAAA
** *
2145980 TA-GAAATTGGATGAAAGTACAGTTACCAAAT
63 TATG-AATCAGATGAAAGTACAATTACCAAAT
2146011 TTGTAATTTA
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
111 7 0.09
112 5 0.06
113 66 0.84
114 1 0.01
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.28
Consensus pattern (111 bp):
AAAAAAATCAACCATAAAGTTGAGTGAGAAAATTAAAATTTTTGAAAGTACGGTGAATAAAATAT
GAATCAGATGAAAGTACAATTACCAAATGTATAACAATAGAGTGAC
Found at i:2151785 original size:10 final size:10
Alignment explanation
Indices: 2151770--2151830 Score: 63
Period size: 10 Copynumber: 6.1 Consensus size: 10
2151760 CAATAGTTTG
2151770 TGCTTGATAT
1 TGCTTGATAT
2151780 TGCTTGAT-T
1 TGCTTGATAT
* *
2151789 CTGTTTTATAT
1 -TGCTTGATAT
*
2151800 TGTTTGAT-T
1 TGCTTGATAT
2151809 CTGCTTGATAT
1 -TGCTTGATAT
2151820 TGCTTGATAT
1 TGCTTGATAT
2151830 T
1 T
2151831 TGTAAGGGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
9 2 0.05
10 39 0.91
11 2 0.05
ACGTcount: A:0.16, C:0.10, G:0.18, T:0.56
Consensus pattern (10 bp):
TGCTTGATAT
Found at i:2151801 original size:20 final size:20
Alignment explanation
Indices: 2151770--2151827 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
2151760 CAATAGTTTG
2151770 TGCTTGATATTGCTTGATTC
1 TGCTTGATATTGCTTGATTC
* * *
2151790 TGTTTTATATTGTTTGATTC
1 TGCTTGATATTGCTTGATTC
2151810 TGCTTGATATTGCTTGAT
1 TGCTTGATATTGCTTGAT
2151828 ATTTGTAAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.16, C:0.10, G:0.19, T:0.55
Consensus pattern (20 bp):
TGCTTGATATTGCTTGATTC
Found at i:2151949 original size:23 final size:23
Alignment explanation
Indices: 2151923--2152045 Score: 228
Period size: 23 Copynumber: 5.3 Consensus size: 23
2151913 CTGAATGCAA
* *
2151923 GATGCTTGCTGAATTGATTCAAT
1 GATGCTTGCTGAATTGATACAGT
2151946 GATGCTTGCTGAATTGATACAGT
1 GATGCTTGCTGAATTGATACAGT
2151969 GATGCTTGCTGAATTGATACAGT
1 GATGCTTGCTGAATTGATACAGT
2151992 GATGCTTGCTGAATTGATACAGT
1 GATGCTTGCTGAATTGATACAGT
2152015 GATGCTTGCTGAATTGATACAGT
1 GATGCTTGCTGAATTGATACAGT
2152038 GATGCTTG
1 GATGCTTG
2152046 TTGGTTACTG
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 98 1.00
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (23 bp):
GATGCTTGCTGAATTGATACAGT
Found at i:2152709 original size:38 final size:38
Alignment explanation
Indices: 2152666--2152747 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
2152656 ATTATAAATA
2152666 AAATTTATAATATA-AGAAGTATAATTAATATAAAAACC
1 AAATTTATAATATACA-AAGTATAATTAATATAAAAACC
* * *
2152704 AAATTTATAATATACAAATTATAATTAATATAAGAACT
1 AAATTTATAATATACAAAGTATAATTAATATAAAAACC
2152742 AAATTT
1 AAATTT
2152748 CAAAAAGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 39 0.98
39 1 0.03
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (38 bp):
AAATTTATAATATACAAAGTATAATTAATATAAAAACC
Found at i:2152856 original size:16 final size:16
Alignment explanation
Indices: 2152835--2152867 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2152825 TATTACTTAT
2152835 AAGTCAAGTAAATATC
1 AAGTCAAGTAAATATC
*
2152851 AAGTCAGGTAAATATC
1 AAGTCAAGTAAATATC
2152867 A
1 A
2152868 GATCTGTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (16 bp):
AAGTCAAGTAAATATC
Found at i:2153477 original size:39 final size:39
Alignment explanation
Indices: 2153423--2153506 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
2153413 TTTTATGGCT
*
2153423 AACCTTACTCAATTGAGTTAACTCACTACATAACCCAAC
1 AACCTCACTCAATTGAGTTAACTCACTACATAACCCAAC
*
2153462 AACCTCACTCAATTGAGTTAACTCACTACATAACCTAAC
1 AACCTCACTCAATTGAGTTAACTCACTACATAACCCAAC
2153501 AACCTC
1 AACCTC
2153507 TTTTACTTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.38, C:0.32, G:0.05, T:0.25
Consensus pattern (39 bp):
AACCTCACTCAATTGAGTTAACTCACTACATAACCCAAC
Found at i:2154646 original size:24 final size:24
Alignment explanation
Indices: 2154619--2154678 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
2154609 CTAGCTATAA
*
2154619 ACTCACCTAGTTAGCTACCAAGAC
1 ACTCACCTAGCTAGCTACCAAGAC
2154643 ACTCACCTAGCTAGCTACCAAGAC
1 ACTCACCTAGCTAGCTACCAAGAC
2154667 ACTCACCTAGCT
1 ACTCACCTAGCT
2154679 TACCTTGAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.32, C:0.37, G:0.12, T:0.20
Consensus pattern (24 bp):
ACTCACCTAGCTAGCTACCAAGAC
Found at i:2174697 original size:64 final size:63
Alignment explanation
Indices: 2174623--2174743 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 63
2174613 ATTGTTTAAG
* * * * * *
2174623 GTGTATCGATGCACATGAAGTGTATCGCTGCACTCCTTTAAAATAAAAACATTGAATGCAATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATGCAATCA
* *
2174687 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATG
2174744 GAATTTATGC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 16 0.33
64 33 0.67
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATGCAATCA
Found at i:2175450 original size:2 final size:2
Alignment explanation
Indices: 2175443--2175481 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2175433 TAGCGTAAAC
*
2175443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2175482 GGTAAATTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2176410 original size:23 final size:23
Alignment explanation
Indices: 2176376--2176428 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
2176366 TATGGAACTT
*
2176376 CGGTGCATTTCTACGCGGCACTA
1 CGGTGCAATTCTACGCGGCACTA
* * *
2176399 CGGTGCAATTCTATGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTA
2176422 CGGTGCA
1 CGGTGCA
2176429 TTTATACGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.28
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTA
Found at i:2179046 original size:64 final size:63
Alignment explanation
Indices: 2178971--2179091 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 63
2178961 ATTGTTCAAG
* * * *
2178971 GTGTATCGATGCACATGAAGTGTAACGATGCACTCCTTTAAAATAAAAACATCGAATGCAATCA
1 GTGTATCGATGCACAAGAAGTGCAACGATGCACCCCCTT-AAATAAAAACATCGAATGCAATCA
* * *
2179035 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCAACGATGCACCCCCTTAAATAAAAACATCGAATG
2179092 GAATTTATGC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 17 0.34
64 33 0.66
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCAACGATGCACCCCCTTAAATAAAAACATCGAATGCAATCA
Found at i:2179110 original size:63 final size:64
Alignment explanation
Indices: 2178977--2179132 Score: 165
Period size: 63 Copynumber: 2.5 Consensus size: 64
2178967 CAAGGTGTAT
* * * * * * * *
2178977 CGATGCACATGAAGTGTAACGATGCACTCCTTTAAAATAAAAACATCGAATGCAATCAGTGTAT
1 CGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCAATCAGTGCAC
* * *
2179041 CGATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATACAAACATCGAATGGAATTTA-TGCAC
1 CGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCAA-TCAGTGCAC
*
2179104 CGATGCA-TAGATAGTGCATCGATGCACCC
1 CGATGCACAAG-TAGTGCATCGATGCACCC
2179133 GTCAAGGGAT
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
62 2 0.03
63 47 0.60
64 29 0.37
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (64 bp):
CGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCAATCAGTGCAC
Found at i:2179821 original size:28 final size:25
Alignment explanation
Indices: 2179772--2179831 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
2179762 TTGCGTAAAC
*
2179772 TATATATATATATATAATAATTATA
1 TATATATATATATATAATAATTAGA
**
2179797 TTATATATATATATATGGGTAAATTAGA
1 -TATATATATATATAT-AAT-AATTAGA
2179825 TATATAT
1 TATATAT
2179832 GATTTAAGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 15 0.52
27 8 0.28
28 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (25 bp):
TATATATATATATATAATAATTAGA
Found at i:2179831 original size:2 final size:2
Alignment explanation
Indices: 2179772--2179812 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
2179762 TTGCGTAAAC
2179772 TA TA TA TA TA TA TA TA -A TA -A T- TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2179810 TA T
1 TA T
2179813 GGGTAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 4 0.11
2 31 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2180719 original size:23 final size:23
Alignment explanation
Indices: 2180651--2180719 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
2180641 CAAACTTATA
2180651 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
2180674 CGGCAATAT-GCTGCAATTCTACG
1 TGGCACT-TCGGTGCATTTCTACG
*
2180697 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
2180720 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
22 1 0.03
23 33 0.94
24 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:2183348 original size:137 final size:135
Alignment explanation
Indices: 2183082--2183400 Score: 397
Period size: 137 Copynumber: 2.3 Consensus size: 135
2183072 GGCGAGTCAT
* * * * * *
2183082 TCTAGGCTACGACATGTATTATTGTGGTCCGAATAAAATTCTAATTGGTAATTATTAACTTCTAA
1 TCTAGGGTATGACATGCATTATTGTGGTCAG-ATAAAATTCTAACTGGTAATTACTAACTTCTAA
* * * *
2183147 TTTTTAATACAAATTTACTAACCGCTAATCCTAATATATTCGAATTAATTTATGACCTTGTGGTG
65 TTTTTAATACAAATGTACTAACAGCTAACCCTAATATATTCGAATTAATTTACGACCTTGTGGTG
2183212 A-CTCGC
130 ACCT-GC
* * *
2183218 TCTAGGGTATGACATGCATTAATGTGGTCTAGATAAAATTCTAACTGTTAATTACTAACTTTTAA
1 TCTAGGGTATGACATGCATTATTGTGGTC-AGATAAAATTCTAACTGGTAATTACTAACTTCTAA
* * *
2183283 TTTTTTAATACTAATGTACTAACAGGTAACCCTAATATATTCGAGTTAATTTACGACCTTGTGGT
65 -TTTTTAATACAAATGTACTAACAGCTAACCCTAATATATTCGAATTAATTTACGACCTTGTGGT
2183348 GACCTGC
129 GACCTGC
*** * *
2183355 TCTAGGGTATGACCCACGTTATTATGGTCCAGATAAAATTCTAACT
1 TCTAGGGTATGACATGCATTATTGTGGT-CAGATAAAATTCTAACT
2183401 TACTAACTTT
Statistics
Matches: 157, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
136 54 0.34
137 100 0.64
138 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (135 bp):
TCTAGGGTATGACATGCATTATTGTGGTCAGATAAAATTCTAACTGGTAATTACTAACTTCTAAT
TTTTAATACAAATGTACTAACAGCTAACCCTAATATATTCGAATTAATTTACGACCTTGTGGTGA
CCTGC
Found at i:2189242 original size:17 final size:17
Alignment explanation
Indices: 2189220--2189254 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2189210 TAGTTTGTTT
*
2189220 TTTTTTTCCTTTCTCTG
1 TTTTTTTCCTGTCTCTG
*
2189237 TTTTTTTTCTGTCTCTG
1 TTTTTTTCCTGTCTCTG
2189254 T
1 T
2189255 CTCTAGTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.09, T:0.71
Consensus pattern (17 bp):
TTTTTTTCCTGTCTCTG
Found at i:2189257 original size:23 final size:20
Alignment explanation
Indices: 2189215--2189284 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 20
2189205 TGGTATAGTT
*
2189215 TGTTTTTTTTTTCCTTTCTC
1 TGTTTTTTTTTTCCTGTCTC
2189235 TG--TTTTTTTT-CTGTCTC
1 TGTTTTTTTTTTCCTGTCTC
* * **
2189252 TGTCTCTAGTTT-CTGTCTC
1 TGTTTTTTTTTTCCTGTCTC
2189271 TGCTTTTTTTTTTC
1 TG-TTTTTTTTTTC
2189285 ATTTTTTTCG
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
17 8 0.21
18 8 0.21
19 14 0.37
20 8 0.21
ACGTcount: A:0.01, C:0.20, G:0.10, T:0.69
Consensus pattern (20 bp):
TGTTTTTTTTTTCCTGTCTC
Found at i:2189737 original size:3 final size:3
Alignment explanation
Indices: 2189724--2189794 Score: 96
Period size: 3 Copynumber: 24.7 Consensus size: 3
2189714 AATATATATT
2189724 TAA TAA T-A TAA TAA TAA T-A TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2189769 T-A TAC TAAA TAA TAA TAA TAA TAA TA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TA
2189795 TGGATAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
2 8 0.13
3 51 0.84
4 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2189747 original size:30 final size:29
Alignment explanation
Indices: 2189717--2189794 Score: 110
Period size: 27 Copynumber: 2.8 Consensus size: 29
2189707 TTTATTTAAT
*
2189717 ATATATTTAATAAT-ATAATAATAATATA
1 ATATATATAATAATAATAATAATAATATA
2189745 ATATA-ATAATAATAATAATAATAATATA
1 ATATATATAATAATAATAATAATAATATA
*
2189773 CTA-A-ATAATAATAATAATAATA
1 ATATATATAATAATAATAATAATA
2189795 TGGATAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 26 0.55
28 21 0.45
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (29 bp):
ATATATATAATAATAATAATAATAATATA
Found at i:2190689 original size:111 final size:113
Alignment explanation
Indices: 2190103--2190732 Score: 1043
Period size: 112 Copynumber: 5.7 Consensus size: 113
2190093 TGATAGTATC
* *
2190103 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
** * * *
2190167 TCATTATGAACCTTCTCTGGCAA-AATAATCCATCAATTGATGAATTC
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
* *
2190214 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--ATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
2190277 TCATTCATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTT
66 TCATT-ATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
2190326 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
2190391 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATG--TTT
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
2190437 AAACAAAAAGTTGAACAAG---TTCTC-TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
2190498 TCATTCATGAACTTTCTCTGGCAATG-TGATCCATCAAATGATGAATTT
66 TCATT-ATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
2190546 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
2190611 TCATTATG-ACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
2190658 AAAC-AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
2190722 TCATTATGAAC
66 TCATTATGAAC
2190733 TTATGGCAAT
Statistics
Matches: 490, Mismatches: 15, Indels: 27
0.92 0.03 0.05
Matches are distributed among these distances:
107 59 0.12
108 24 0.05
109 22 0.04
110 16 0.03
111 125 0.26
112 150 0.31
113 78 0.16
114 16 0.03
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (113 bp):
AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
Found at i:2192441 original size:19 final size:18
Alignment explanation
Indices: 2192401--2192445 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 18
2192391 AATAGAAAAG
2192401 AATAAATTGAATTTCCAAA
1 AATAAATTGAA-TTCCAAA
2192420 AATAAATTGAA-TCC--A
1 AATAAATTGAATTCCAAA
2192435 AATAAATTGAA
1 AATAAATTGAA
2192446 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 12 0.46
17 3 0.12
19 11 0.42
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.29
Consensus pattern (18 bp):
AATAAATTGAATTCCAAA
Found at i:2192794 original size:15 final size:15
Alignment explanation
Indices: 2192768--2192815 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
2192758 CACCTTGACC
*
2192768 CTCTTTCTTTTTCTT
1 CTCTTTTTTTTTCTT
*
2192783 CTCTTTTTTTTTATTTT
1 CTC-TTTTTTTT-TCTT
*
2192800 CTATTTTTTTTTCTT
1 CTCTTTTTTTTTCTT
2192815 C
1 C
2192816 AAGCATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 7 0.26
16 15 0.56
17 5 0.19
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (15 bp):
CTCTTTTTTTTTCTT
Found at i:2203430 original size:13 final size:15
Alignment explanation
Indices: 2203408--2203444 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2203398 TTTGACATAA
2203408 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
2203420 AAATAAAATACTTGC
1 AAATAAAATACTTGC
2203435 AAATAAAATA
1 AAATAAAATA
2203445 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:2203483 original size:18 final size:17
Alignment explanation
Indices: 2203435--2203485 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
2203425 AAATACTTGC
*
2203435 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
2203453 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
2203471 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
2203486 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:2203981 original size:15 final size:16
Alignment explanation
Indices: 2203952--2203983 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2203942 TTTTTAATCT
2203952 TATTATTTCAAAAATA
1 TATTATTTCAAAAATA
2203968 TATTATTT-AAAAATA
1 TATTATTTCAAAAATA
2203983 T
1 T
2203984 CTGAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTATTTCAAAAATA
Found at i:2205069 original size:19 final size:18
Alignment explanation
Indices: 2205045--2205112 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 18
2205035 TGGTATAGTT
*
2205045 TGTTTTTTTTTCCTTTCTC
1 TGTTTTTTTTT-CTGTCTC
2205064 TGTTTTTTTTTCTGTCTC
1 TGTTTTTTTTTCTGTCTC
* **
2205082 TGTCTCTAGTTTCTGTCTC
1 TGT-TTTTTTTTCTGTCTC
2205101 TGCTTTTTTTTT
1 TG-TTTTTTTTT
2205113 TCTTTTTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 9 0.22
19 30 0.75
20 1 0.03
ACGTcount: A:0.01, C:0.19, G:0.10, T:0.69
Consensus pattern (18 bp):
TGTTTTTTTTTCTGTCTC
Found at i:2205071 original size:18 final size:18
Alignment explanation
Indices: 2205048--2205111 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
2205038 TATAGTTTGT
*
2205048 TTTTTTTTCCTTTCTCTG
1 TTTTTTTTCCTGTCTCTG
*
2205066 TTTTTTTTTCTGTCTCTG
1 TTTTTTTTCCTGTCTCTG
**
2205084 TCTCTAGTTT-CTGTCTCTG
1 T-T-TTTTTTCCTGTCTCTG
2205103 CTTTTTTTT
1 -TTTTTTTT
2205112 TTCTTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 21 0.57
19 11 0.30
20 5 0.14
ACGTcount: A:0.02, C:0.20, G:0.09, T:0.69
Consensus pattern (18 bp):
TTTTTTTTCCTGTCTCTG
Found at i:2205563 original size:3 final size:3
Alignment explanation
Indices: 2205555--2205640 Score: 142
Period size: 3 Copynumber: 29.7 Consensus size: 3
2205545 TTAATATATT
2205555 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2205601 TAA TAA -AA TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2205641 TGGATAAAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
2 6 0.08
3 72 0.92
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2206892 original size:29 final size:29
Alignment explanation
Indices: 2206797--2206879 Score: 157
Period size: 29 Copynumber: 2.8 Consensus size: 29
2206787 ATAAAAAAAA
2206797 TTAATTGATTTAATTTTTTAATTTAAAAGC
1 TTAATTGATTT-ATTTTTTAATTTAAAAGC
2206827 TTAATTGATTTATTTTTTAATTTAAAAGC
1 TTAATTGATTTATTTTTTAATTTAAAAGC
2206856 TTAATTGATTTATTTTTTAATTTA
1 TTAATTGATTTATTTTTTAATTTA
2206880 TATAACTACT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 42 0.79
30 11 0.21
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (29 bp):
TTAATTGATTTATTTTTTAATTTAAAAGC
Found at i:2209127 original size:87 final size:89
Alignment explanation
Indices: 2208981--2209159 Score: 263
Period size: 87 Copynumber: 2.0 Consensus size: 89
2208971 ACGTGACTTG
* * *
2208981 TGTCATATACATTGTCATCACTTATATACATGTACCATATGTAAAATCATTACTTATGTACAA-T
1 TGTCATATACAATGTCATCACTTATATACATGTAACATATGTAAAATCATCACTTATGTACAATT
2209045 TT-TAAAAAGAAAATGGGCTATTT
66 TTATAAAAAGAAAATGGGCTATTT
* * * *
2209068 TGTCATATACAATGTCATCACTTATGTACATGTAACATATGTCATATCATCACTTATGTATAATT
1 TGTCATATACAATGTCATCACTTATATACATGTAACATATGTAAAATCATCACTTATGTACAATT
*
2209133 TTAATAAAAATAAAATGGGCTATTT
66 TT-ATAAAAAGAAAATGGGCTATTT
2209158 TG
1 TG
2209160 ATCGTCAGTC
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
87 56 0.69
88 3 0.04
90 22 0.27
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (89 bp):
TGTCATATACAATGTCATCACTTATATACATGTAACATATGTAAAATCATCACTTATGTACAATT
TTATAAAAAGAAAATGGGCTATTT
Found at i:2210382 original size:18 final size:18
Alignment explanation
Indices: 2210359--2210393 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2210349 TTTTTATTTT
2210359 TATTTTCTACTGATAATC
1 TATTTTCTACTGATAATC
*
2210377 TATTTTCTATTGATAAT
1 TATTTTCTACTGATAAT
2210394 TTATATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (18 bp):
TATTTTCTACTGATAATC
Found at i:2210476 original size:88 final size:88
Alignment explanation
Indices: 2210327--2210502 Score: 280
Period size: 88 Copynumber: 2.0 Consensus size: 88
2210317 CTGAAAATTC
* * * * * *
2210327 AAAATTATCATATATTTTACATTTTTTATTTTTATTTTCTACTGATAATCTATTTTCTATTGATA
1 AAAATTATCATATATTTTAAATATTTTACTTGTATTATCTACTGATAATCCATTTTCTATTGATA
*
2210392 ATTTATATTTTAAATTTTATAAT
66 AATTATATTTTAAATTTTATAAT
*
2210415 AAAATTATCATATATTTTAAATATTTTACTTGTATTATCTACTGATAATCCGTTTTCTATTGATA
1 AAAATTATCATATATTTTAAATATTTTACTTGTATTATCTACTGATAATCCATTTTCTATTGATA
2210480 AATTATATTTTAAATTTTATAAT
66 AATTATATTTTAAATTTTATAAT
2210503 CCGTCCCTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (88 bp):
AAAATTATCATATATTTTAAATATTTTACTTGTATTATCTACTGATAATCCATTTTCTATTGATA
AATTATATTTTAAATTTTATAAT
Found at i:2215030 original size:5 final size:5
Alignment explanation
Indices: 2215016--2215053 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
2215006 AGTGCTTCAA
*
2215016 CTTTT C-TTT CTTTT CTTTT CTTTT CTTTT -TCTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
2215054 TGAGTGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 7 0.24
5 22 0.76
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
CTTTT
Found at i:2215081 original size:23 final size:23
Alignment explanation
Indices: 2215043--2215094 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
2215033 TTCTTTTCTT
2215043 TTTCTTCTTTTTGAGTGCTTTCAA
1 TTTCTTCTTTTTGAGTGCTTT-AA
*
2215067 TTTCTTC-TTTTGAGTGCTTTGA
1 TTTCTTCTTTTTGAGTGCTTTAA
2215089 TTTCTT
1 TTTCTT
2215095 TACTGGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 7 0.26
23 13 0.48
24 7 0.26
ACGTcount: A:0.10, C:0.15, G:0.13, T:0.62
Consensus pattern (23 bp):
TTTCTTCTTTTTGAGTGCTTTAA
Found at i:2215980 original size:10 final size:12
Alignment explanation
Indices: 2215955--2215984 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2215945 ACAAGCAACT
2215955 AGAATCAAAGAG
1 AGAATCAAAGAG
2215967 AGAATCAAAGAG
1 AGAATCAAAGAG
2215979 A-AATCA
1 AGAATCA
2215985 TCAAACCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.60, C:0.10, G:0.20, T:0.10
Consensus pattern (12 bp):
AGAATCAAAGAG
Found at i:2221528 original size:23 final size:23
Alignment explanation
Indices: 2221502--2221547 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2221492 CGATACCACC
2221502 TTGAAGGGGAACTGATTCCCCCT
1 TTGAAGGGGAACTGATTCCCCCT
*
2221525 TTGAAGGGTAACTGATTCCCCCT
1 TTGAAGGGGAACTGATTCCCCCT
2221548 AGGGGAATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (23 bp):
TTGAAGGGGAACTGATTCCCCCT
Found at i:2224674 original size:47 final size:48
Alignment explanation
Indices: 2224598--2224729 Score: 164
Period size: 47 Copynumber: 2.7 Consensus size: 48
2224588 CTAAATTTAT
*
2224598 TCATTCTTGAGTGTTCTTTTCTTTGTTCTAGAATTG-TGCAAACAATC-TA
1 TCATTCGTGAGTGTTCTTTTCTTTGTTCTAGAATTGTTG--AA-AATCGTA
*
2224647 -CCTT-GTGAGTGTTCTTTTCTTTGTTCTAGAATTTGTTGAAAATCGTA
1 TCATTCGTGAGTGTTCTTTTCTTTGTTCTAGAA-TTGTTGAAAATCGTA
*
2224694 TTCATTCTTGAGTGTTCTTTTCTTTGTTCTAGAATT
1 -TCATTCGTGAGTGTTCTTTTCTTTGTTCTAGAATT
2224730 TTTTGATACT
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
46 4 0.05
47 30 0.41
48 6 0.08
49 7 0.10
50 26 0.36
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (48 bp):
TCATTCGTGAGTGTTCTTTTCTTTGTTCTAGAATTGTTGAAAATCGTA
Found at i:2224727 original size:50 final size:50
Alignment explanation
Indices: 2224595--2224735 Score: 186
Period size: 50 Copynumber: 2.9 Consensus size: 50
2224585 GTACTAAATT
2224595 TATTCATTCTTGAGTGTTCTTTTCTTTGTTCTAGAA-TTG-TGCAAACAATC
1 TATTCATTCTTGAGTGTTCTTTTCTTTGTTCTAGAATTTGTTG--AACAATC
* *
2224645 TA--CCTT-GTGAGTGTTCTTTTCTTTGTTCTAGAATTTGTTGAA-AATC
1 TATTCATTCTTGAGTGTTCTTTTCTTTGTTCTAGAATTTGTTGAACAATC
*
2224691 GTATTCATTCTTGAGTGTTCTTTTCTTTGTTCTAGAATTTTTTGA
1 -TATTCATTCTTGAGTGTTCTTTTCTTTGTTCTAGAATTTGTTGA
2224736 TACTTTGCAC
Statistics
Matches: 80, Mismatches: 5, Indels: 12
0.82 0.05 0.12
Matches are distributed among these distances:
46 4 0.05
47 30 0.38
48 6 0.08
49 5 0.06
50 35 0.44
ACGTcount: A:0.19, C:0.13, G:0.16, T:0.52
Consensus pattern (50 bp):
TATTCATTCTTGAGTGTTCTTTTCTTTGTTCTAGAATTTGTTGAACAATC
Found at i:2227170 original size:65 final size:64
Alignment explanation
Indices: 2227086--2227265 Score: 234
Period size: 65 Copynumber: 2.8 Consensus size: 64
2227076 TGAATAAATT
* * *
2227086 AAACATCGAATGCAGTTTATGCATCGATGCACTCTCCGTGCATCGATGCACTCAGGTTTTAATAA
1 AAACATCGAATGCATTTTATGCATCGATGCACACTCCGTGCATCGATGCACTCAGG-CTTAATAA
* * * * * *
2227151 AAACATCGAATGTATTTTATGCATCGATGCACACACCATGCATCGATGCACTTAGGCTTATTCA
1 AAACATCGAATGCATTTTATGCATCGATGCACACTCCGTGCATCGATGCACTCAGGCTTAATAA
* ** *
2227215 AAACATCGAATGCATTTTATGCATAGATGCACACTTAGTGCACCGATGCAC
1 AAACATCGAATGCATTTTATGCATCGATGCACACTCCGTGCATCGATGCAC
2227266 ACTTAGTGCA
Statistics
Matches: 99, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
64 49 0.49
65 50 0.51
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (64 bp):
AAACATCGAATGCATTTTATGCATCGATGCACACTCCGTGCATCGATGCACTCAGGCTTAATAA
Found at i:2227262 original size:19 final size:19
Alignment explanation
Indices: 2227240--2227284 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
2227230 TTTATGCATA
2227240 GATGCACACTTAGTGCACC
1 GATGCACACTTAGTGCACC
2227259 GATGCACACTTAGTGCACC
1 GATGCACACTTAGTGCACC
2227278 GATGCAC
1 GATGCAC
2227285 TCAGTTCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (19 bp):
GATGCACACTTAGTGCACC
Found at i:2227262 original size:64 final size:65
Alignment explanation
Indices: 2227086--2227265 Score: 229
Period size: 64 Copynumber: 2.8 Consensus size: 65
2227076 TGAATAAATT
* * * *
2227086 AAACATCGAATGCAGTTTATGCATCGATGCACTCTCCGTGCATCGATGCACTCAGGTTTTAATAA
1 AAACATCGAATGCATTTTATGCATCGATGCACACTCAGTGCATCGATGCACTCAGGTCTTAATAA
* * * * *
2227151 AAACATCGAATGTATTTTATGCATCGATGCACACACCA-TGCATCGATGCACTTAGG-CTTATTC
1 AAACATCGAATGCATTTTATGCATCGATGCACAC-TCAGTGCATCGATGCACTCAGGTCTTAATA
2227214 A
65 A
* * *
2227215 AAACATCGAATGCATTTTATGCATAGATGCACACTTAGTGCACCGATGCAC
1 AAACATCGAATGCATTTTATGCATCGATGCACACTCAGTGCATCGATGCAC
2227266 ACTTAGTGCA
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
63 1 0.01
64 49 0.49
65 48 0.48
66 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (65 bp):
AAACATCGAATGCATTTTATGCATCGATGCACACTCAGTGCATCGATGCACTCAGGTCTTAATAA
Found at i:2229614 original size:90 final size:90
Alignment explanation
Indices: 2229493--2229759 Score: 471
Period size: 90 Copynumber: 3.0 Consensus size: 90
2229483 TAATCCCGAA
* * *
2229493 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCATAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
2229558 TAGGGTAACTTAGATATAAAATGAT
66 TAGGGTAACTTAGATATAAAATGAT
2229583 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
2229648 TAGGGTAACTTAGATATAAAATGAT
66 TAGGGTAACTTAGATATAAAATGAT
*
2229673 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATTAAAAACCCTAATATGA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAA-TAAAATCCCTAATATGA
* *
2229738 TTAGGGTAACTTGGCTATAAAA
65 TTAGGGTAACTTAGATATAAAA
2229760 GGGTGTGTTA
Statistics
Matches: 170, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
90 134 0.79
91 36 0.21
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
TAGGGTAACTTAGATATAAAATGAT
Found at i:2238690 original size:36 final size:36
Alignment explanation
Indices: 2238650--2238754 Score: 135
Period size: 36 Copynumber: 2.9 Consensus size: 36
2238640 TTTGTCTTGG
2238650 AAAAACAAAATTTTGTCTCACTTGAGACAATTTTCT
1 AAAAACAAAATTTTGTCTCACTTGAGACAATTTTCT
2238686 AAAAAC-AAATTTTGTCTCACTTGAGACAA-TTTCT
1 AAAAACAAAATTTTGTCTCACTTGAGACAATTTTCT
* * * *
2238720 ATCAAAA-AAAATTTCGTCTTACTTGACACATTTTT
1 A--AAAACAAAATTTTGTCTCACTTGAGACAATTTT
2238755 TCTTTAAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
34 6 0.10
35 23 0.38
36 29 0.48
37 3 0.05
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (36 bp):
AAAAACAAAATTTTGTCTCACTTGAGACAATTTTCT
Found at i:2238913 original size:66 final size:66
Alignment explanation
Indices: 2238804--2238959 Score: 185
Period size: 66 Copynumber: 2.4 Consensus size: 66
2238794 AAAATTTATA
* * *
2238804 ATCTTTGAGTATGTTTCTCTTGAAACAAGTTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACC
1 ATCTTTGAGTATGTTTCTCTTGAAAAAAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACACC
2238869 C
66 C
* **
2238870 ATCTTTGAG-ATCGCTTTC-CTTGAAAAAAATTTTGTCTCTCTTGAGACAACTTCTCTTG-AAGT
1 ATCTTTGAGTAT-G-TTTCTCTTGAAAAAAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACA
**
2238932 GTC
64 CCC
2238935 ATCTTTGAGTCA-GTTTCTCTTGAAA
1 ATCTTTGAGT-ATGTTTCTCTTGAAA
2238960 CCATTATCCC
Statistics
Matches: 77, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
64 4 0.05
65 22 0.29
66 46 0.60
67 5 0.06
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (66 bp):
ATCTTTGAGTATGTTTCTCTTGAAAAAAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACACC
C
Found at i:2239212 original size:131 final size:131
Alignment explanation
Indices: 2238967--2239308 Score: 400
Period size: 131 Copynumber: 2.6 Consensus size: 131
2238957 AAACCATTAT
* ** * *
2238967 CCCTAAAGATGGTCTGTCATTCTCATCACGTGGGAACCGTGTCATCC-CCGACAATACCTCCTCA
1 CCCTAAAGATGGCCTACCATCCTCATCACGTAGGAACCGTGTCATCCACCGACAATACCTCCTCA
* *** *
2239031 TCACGTAAGAGTTGTGTCACCCCTAGATAACCAGCCATCCTTATCACGTAGGAA-TCGTGTTATC
66 TCACGTAGGAGCCATGTCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAACT-GTGTTATC
2239095 AC
130 AC
* *
2239097 CCCTAAAGATGGCCTACCATCCTCATCACGTAGGAACCGTATCATCCACCGACAAGACCTCCTCA
1 CCCTAAAGATGGCCTACCATCCTCATCACGTAGGAACCGTGTCATCCACCGACAATACCTCCTCA
* * * *
2239162 TCACGTAGGAGCCATGTCACCCCTAGATAACCAGTCGTCCTCGTCGCGTAGGAACTGTGTTATCA
66 TCACGTAGGAGCCATGTCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAACTGTGTTATCA
2239227 C
131 C
* * * ** * * *
2239228 CATTTCCTAAAGATGGCCAAGCCGTCCTCATCACGTAAGAACAATGTCATCCACCAACCATATCT
1 C----CCTAAAGATGGCCTA-CCATCCTCATCACGTAGGAACCGTGTCATCCACCGACAATACCT
2239293 CCTCATCACGTAGGAG
61 CCTCATCACGTAGGAG
2239309 TCGTGTTACC
Statistics
Matches: 179, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
130 41 0.23
131 72 0.40
132 1 0.01
135 14 0.08
136 51 0.28
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.23
Consensus pattern (131 bp):
CCCTAAAGATGGCCTACCATCCTCATCACGTAGGAACCGTGTCATCCACCGACAATACCTCCTCA
TCACGTAGGAGCCATGTCACCCCTAGATAACCAGCCATCCTCATCACGTAGGAACTGTGTTATCA
C
Found at i:2239468 original size:3 final size:3
Alignment explanation
Indices: 2239460--2239506 Score: 67
Period size: 3 Copynumber: 15.0 Consensus size: 3
2239450 AATATTATAT
*
2239460 TTA TTA TTA TTA TCA TTA TTA TTA TATA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA
2239507 CATATCTTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 35 0.88
4 4 0.10
5 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2239500 original size:23 final size:23
Alignment explanation
Indices: 2239466--2239511 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2239456 ATATTTATTA
*
2239466 TTATTATCATTATTATTATATAT
1 TTATTATCATTATTATTACATAT
*
2239489 TTATTATTATTATTATTACATAT
1 TTATTATCATTATTATTACATAT
2239512 CTTACATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATTATCATTATTATTACATAT
Found at i:2241152 original size:30 final size:30
Alignment explanation
Indices: 2241083--2241295 Score: 250
Period size: 30 Copynumber: 7.1 Consensus size: 30
2241073 TCATCCCTCG
* *
2241083 AATTTCTATTTTTGCTATTTTAGTCCTATA
1 AATTTCTGTTTTTGCTATTTTAGTCCTTTA
* * **
2241113 AGTTTTATGTTTTTATTATTTTAGTCCTTTA
1 A-ATTTCTGTTTTTGCTATTTTAGTCCTTTA
* *
2241144 AATTTATGTTTTTGCTATTTTAGTCTTTTA
1 AATTTCTGTTTTTGCTATTTTAGTCCTTTA
* *
2241174 AGTTTCTATTATTT-CTATTTTAGTCCTTTA
1 AATTTCTGTT-TTTGCTATTTTAGTCCTTTA
* *
2241204 AATTTCTGTTTTTTCTATTTTAGACCTTTA
1 AATTTCTGTTTTTGCTATTTTAGTCCTTTA
* *
2241234 AGTTTTTGTTTTTGCTATTTTAGTCCTTT-
1 AATTTCTGTTTTTGCTATTTTAGTCCTTTA
* *
2241263 AATTTCTTTTTTTGCTATTTTGGTCCTTTA
1 AATTTCTGTTTTTGCTATTTTAGTCCTTTA
2241293 AAT
1 AAT
2241296 AGAATATGAT
Statistics
Matches: 154, Mismatches: 25, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
29 28 0.18
30 99 0.64
31 27 0.18
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.62
Consensus pattern (30 bp):
AATTTCTGTTTTTGCTATTTTAGTCCTTTA
Found at i:2241244 original size:90 final size:89
Alignment explanation
Indices: 2241083--2241295 Score: 295
Period size: 90 Copynumber: 2.4 Consensus size: 89
2241073 TCATCCCTCG
* * *
2241083 AATTTCTATTTTTGCTATTTTAGTCCTATAAGTTTTATGTTTTTATTATTTTAGTCCTTTAAATT
1 AATTTCTATTTTTGCTATTTTAGTCCTTTAA-ATTTATGTTTTTATTATTTTAGACCTTTAAATT
*
2241148 TATGTTTTTGCTATTTTAGTCTTTT
65 TATGTTTTTGCTATTTTAGTCCTTT
* *
2241173 AAGTTTCTATTATTT-CTATTTTAGTCCTTTAAATTTCTGTTTTT-TCTATTTTAGACCTTTAAG
1 AA-TTTCTATT-TTTGCTATTTTAGTCCTTTAAATTTATGTTTTTAT-TATTTTAGACCTTTAAA
*
2241236 TTTTTGTTTTTGCTATTTTAGTCCTTT
63 TTTATGTTTTTGCTATTTTAGTCCTTT
* *
2241263 AATTTCTTTTTTTGCTATTTTGGTCCTTTAAAT
1 AATTTCTATTTTTGCTATTTTAGTCCTTTAAAT
2241296 AGAATATGAT
Statistics
Matches: 110, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
88 3 0.03
89 26 0.24
90 54 0.49
91 24 0.22
92 3 0.03
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.62
Consensus pattern (89 bp):
AATTTCTATTTTTGCTATTTTAGTCCTTTAAATTTATGTTTTTATTATTTTAGACCTTTAAATTT
ATGTTTTTGCTATTTTAGTCCTTT
Found at i:2242012 original size:16 final size:17
Alignment explanation
Indices: 2241978--2242016 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
2241968 CCCATACTAT
2241978 TTTTATCTTAAAAAATGA
1 TTTT-TCTTAAAAAATGA
*
2241996 TTTTTCTT-AAAATTGA
1 TTTTTCTTAAAAAATGA
2242012 TTTTT
1 TTTTT
2242017 AAAAGACGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 4 0.20
18 4 0.20
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (17 bp):
TTTTTCTTAAAAAATGA
Found at i:2242738 original size:15 final size:15
Alignment explanation
Indices: 2242718--2242747 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2242708 TATAAAACAT
2242718 TATTAAAATTTTAAA
1 TATTAAAATTTTAAA
*
2242733 TATTAATATTTTAAA
1 TATTAAAATTTTAAA
2242748 GAATTTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAAAATTTTAAA
Found at i:2244939 original size:2 final size:2
Alignment explanation
Indices: 2244932--2244962 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2244922 TGAAGATCGT
2244932 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2244963 TCAATCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2262536 original size:2 final size:2
Alignment explanation
Indices: 2262529--2262554 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2262519 CTACTAAATA
2262529 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2262555 TTTACATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2262697 original size:30 final size:30
Alignment explanation
Indices: 2262661--2262721 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2262651 ATGTATGAGT
*
2262661 TAAAATAGATTACTGTGAAGAATTAATCTA
1 TAAAATAGATTACCGTGAAGAATTAATCTA
2262691 TAAAATAGATTACCGTGAAGAATTAATCTA
1 TAAAATAGATTACCGTGAAGAATTAATCTA
2262721 T
1 T
2262722 CTTTGAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (30 bp):
TAAAATAGATTACCGTGAAGAATTAATCTA
Found at i:2263551 original size:40 final size:38
Alignment explanation
Indices: 2263449--2263555 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 38
2263439 CATAATCCTC
*
2263449 AAATTATTTCAC-TCTAACATTCTAAAATCCTAATTTCTT
1 AAATTATTTCACAT-TAACATTCT-AAATTCTAATTTCTT
* * *
2263488 AAATT-TTGACACAATAGCATTCTAAATTCTAAATTTTCTT
1 AAATTATT-TCACATTAACATTCTAAATTCT-AA-TTTCTT
*
2263528 AAATTATTTCACATTAACGTTCTAAATT
1 AAATTATTTCACATTAACATTCTAAATT
2263556 ATTTTTAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
38 8 0.15
39 18 0.33
40 27 0.49
41 2 0.04
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (38 bp):
AAATTATTTCACATTAACATTCTAAATTCTAATTTCTT
Found at i:2263821 original size:21 final size:22
Alignment explanation
Indices: 2263797--2263855 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
2263787 TAATTATATA
2263797 TATATTAACTTAAAATAT-TTT
1 TATATTAACTTAAAATATATTT
*
2263818 TATATCAACTTATTAAATATATTT
1 TATATTAACTTA--AAATATATTT
2263842 TATTATTAACTTAA
1 TA-TATTAACTTAA
2263856 TTTAAAGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 11 0.34
23 7 0.22
24 5 0.16
25 9 0.28
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTAACTTAAAATATATTT
Found at i:2263847 original size:27 final size:26
Alignment explanation
Indices: 2263801--2263872 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 26
2263791 TATATATATA
* *
2263801 TTAACTTAAAATATTTT-TATATCAAC
1 TTAATTTAAAATATTTTAT-TATTAAC
2263827 TT-A-TTAAATATATTTTATTATTAAC
1 TTAATTTAAA-ATATTTTATTATTAAC
*
2263852 TTAATTTAAAGATATGTTATT
1 TTAATTTAAA-ATATTTTATT
2263873 TTCATTTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 5 0.13
25 16 0.41
26 4 0.10
27 14 0.36
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (26 bp):
TTAATTTAAAATATTTTATTATTAAC
Found at i:2263852 original size:25 final size:25
Alignment explanation
Indices: 2263799--2263872 Score: 75
Period size: 27 Copynumber: 3.0 Consensus size: 25
2263789 ATTATATATA
2263799 TATTAACTTA--AAATAT-TTTTA-
1 TATTAACTTATTAAATATATTTTAT
*
2263820 TATCAACTTATTAAATATATTTTAT
1 TATTAACTTATTAAATATATTTTAT
* *
2263845 TATTAACTTAATTTAAAGATATGTTAT
1 TATTAACTT-A-TTAAATATATTTTAT
2263872 T
1 T
2263873 TTCATTTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
21 9 0.21
23 6 0.14
24 5 0.12
25 8 0.19
26 1 0.02
27 14 0.33
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (25 bp):
TATTAACTTATTAAATATATTTTAT
Found at i:2265599 original size:14 final size:14
Alignment explanation
Indices: 2265576--2265609 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2265566 TTTACCATTG
2265576 ATTTTTATTTATTT
1 ATTTTTATTTATTT
2265590 -TTTTTGATTTATTT
1 ATTTTT-ATTTATTT
2265604 ATTTTT
1 ATTTTT
2265610 TTAAACATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.28
14 8 0.44
15 5 0.28
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (14 bp):
ATTTTTATTTATTT
Found at i:2267449 original size:2 final size:2
Alignment explanation
Indices: 2267442--2267480 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2267432 GGTGTTAGCT
2267442 TA TA TA TA TA T- TA TA TA TA TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2267481 GTTTTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2267460 original size:13 final size:13
Alignment explanation
Indices: 2267441--2267480 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
2267431 AGGTGTTAGC
2267441 TTATATATATAT-
1 TTATATATATATA
2267453 TATATATATATATA
1 T-TATATATATATA
2267467 TTATATATATATA
1 TTATATATATATA
2267480 T
1 T
2267481 GTTTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATATATATATA
Found at i:2267462 original size:15 final size:15
Alignment explanation
Indices: 2267442--2267480 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
2267432 GGTGTTAGCT
2267442 TATATATATATTATA
1 TATATATATATTATA
2267457 TATATATATATTATA
1 TATATATATATTATA
2267472 TATATATAT
1 TATATATAT
2267481 GTTTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATATATATTATA
Found at i:2270867 original size:16 final size:16
Alignment explanation
Indices: 2270842--2270872 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2270832 ATTATTTAAT
*
2270842 ATATATTTTTTAAAAC
1 ATATAGTTTTTAAAAC
2270858 ATATAGTTTTTAAAA
1 ATATAGTTTTTAAAA
2270873 ACATGTTTAA
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:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
ATATAGTTTTTAAAAC
Found at i:2270873 original size:17 final size:16
Alignment explanation
Indices: 2270842--2270876 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2270832 ATTATTTAAT
*
2270842 ATATATTTTTTAAAAC
1 ATATATTTTTAAAAAC
2270858 ATATAGTTTTTAAAAAC
1 ATATA-TTTTTAAAAAC
2270875 AT
1 AT
2270877 GTTTAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (16 bp):
ATATATTTTTAAAAAC
Found at i:2271064 original size:33 final size:33
Alignment explanation
Indices: 2271027--2271127 Score: 92
Period size: 33 Copynumber: 3.2 Consensus size: 33
2271017 GATGTCCAAA
2271027 GTCCAAAATTCCAGTGGCCCAACTCCAATCAAG
1 GTCCAAAATTCCAGTGGCCCAACTCCAATCAAG
* * **
2271060 GTCCAAAAATCCAAAAT-G---ATGTCC-A--AA-
1 GTCCAAAATTCC--AGTGGCCCAACTCCAATCAAG
2271087 GTCCAAAATTCCAGTGGCCCAACTCCAATCAAG
1 GTCCAAAATTCCAGTGGCCCAACTCCAATCAAG
2271120 GTCCAAAA
1 GTCCAAAA
2271128 CACATGCCCG
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
25 2 0.04
26 1 0.02
27 11 0.22
28 2 0.04
29 4 0.08
30 2 0.04
31 4 0.08
32 2 0.04
33 19 0.38
34 1 0.02
35 2 0.04
ACGTcount: A:0.39, C:0.30, G:0.14, T:0.18
Consensus pattern (33 bp):
GTCCAAAATTCCAGTGGCCCAACTCCAATCAAG
Found at i:2271094 original size:60 final size:60
Alignment explanation
Indices: 2271006--2271127 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
2270996 TTTATTTTCC
2271006 AAATCCAAAATGATGTCCAAAGTCCAAAATTCCAGTGGCCCAACTCCAATCAAGGTCCAA
1 AAATCCAAAATGATGTCCAAAGTCCAAAATTCCAGTGGCCCAACTCCAATCAAGGTCCAA
2271066 AAATCCAAAATGATGTCCAAAGTCCAAAATTCCAGTGGCCCAACTCCAATCAAGGTCCAA
1 AAATCCAAAATGATGTCCAAAGTCCAAAATTCCAGTGGCCCAACTCCAATCAAGGTCCAA
2271126 AA
1 AA
2271128 CACATGCCCG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.18
Consensus pattern (60 bp):
AAATCCAAAATGATGTCCAAAGTCCAAAATTCCAGTGGCCCAACTCCAATCAAGGTCCAA
Found at i:2272694 original size:71 final size:71
Alignment explanation
Indices: 2272578--2272722 Score: 281
Period size: 71 Copynumber: 2.0 Consensus size: 71
2272568 AACGTAATTT
*
2272578 CGAGACCACTCGAAGGACGATTACGACAACTTTGTGACTCTGCTATGGACAGTAAGAGAGTCAAT
1 CGAGACCACTCGAAGGACGATTACGACAACTTTGCGACTCTGCTATGGACAGTAAGAGAGTCAAT
2272643 GATTCC
66 GATTCC
2272649 CGAGACCACTCGAAGGACGATTACGACAACTTTGCGACTCTGCTATGGACAGTAAGAGAGTCAAT
1 CGAGACCACTCGAAGGACGATTACGACAACTTTGCGACTCTGCTATGGACAGTAAGAGAGTCAAT
2272714 GATTCC
66 GATTCC
2272720 CGA
1 CGA
2272723 TTTTCTTCAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.21
Consensus pattern (71 bp):
CGAGACCACTCGAAGGACGATTACGACAACTTTGCGACTCTGCTATGGACAGTAAGAGAGTCAAT
GATTCC
Found at i:2284700 original size:39 final size:40
Alignment explanation
Indices: 2284627--2284720 Score: 127
Period size: 39 Copynumber: 2.3 Consensus size: 40
2284617 TTTTCACCCT
* *
2284627 AAACCCGACCCGACCCGACCCGAACAATACA-TTTTAAAA
1 AAACCCGACCCGACCCGACCCGAACAAGAAATTTTTAAAA
**
2284666 AAACCCGACCCGACCCGACCCGAACCCGAAATTTTTTTAAAA
1 AAACCCGACCCGACCCGACCCGAACAAGAAA--TTTTTAAAA
2284708 AAACCCGACCCGA
1 AAACCCGACCCGA
2284721 TCGGGTCGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
39 27 0.56
42 21 0.44
ACGTcount: A:0.38, C:0.37, G:0.12, T:0.13
Consensus pattern (40 bp):
AAACCCGACCCGACCCGACCCGAACAAGAAATTTTTAAAA
Found at i:2292680 original size:16 final size:17
Alignment explanation
Indices: 2292659--2292697 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2292649 TAATATATCT
*
2292659 TATATAATTTT-TAAAA
1 TATATAATTTTAAAAAA
*
2292675 TATATAGTTTTAAAAAA
1 TATATAATTTTAAAAAA
2292692 TATATA
1 TATATA
2292698 TATTATCCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TATATAATTTTAAAAAA
Found at i:2299954 original size:209 final size:208
Alignment explanation
Indices: 2299549--2299955 Score: 636
Period size: 207 Copynumber: 2.0 Consensus size: 208
2299539 CAGATTCCTT
* * **
2299549 TTATGCTATTGATATTTCGAATTTGAAATTCGTCACTTTCATGGAACTTTTTCCCCAAAGCAGGA
1 TTATGCTACTGATATTTCGAATTCGAAATTCGTCACTTTCATGGAACTTTTTCCCCAAAGCAAAA
* * * * *
2299614 CTTTTCAGAGTTGTCATTCCAGGGTCTTCAAGATTCATTGGGGAAAGGTTGATGACAATGTTGTA
66 CGTTTCAGAGTTGTCATTCCAGGGTCTACAAGATTCACTAGGGAAAGGTTGATGAAAATGTTGTA
* * * *
2299679 CCTAAGAGAATGTACTAAAAGTTTCTACCTCAGTCCATGAACTAACTAAAGATGATTGGGATTGG
131 CCTAAGAAAATGTACTAAAAGTTTCAACCTCAGTCCATGAACTAACCAAAGATGATTGGAATTGG
2299744 TATCAATGTTCCA
196 TATCAATGTTCCA
* **
2299757 TTATGCTACTGATATTTCGAATTCGAAATTCGTCACTTTCATGG-ATTTTTTTTCCAAAGCAAAA
1 TTATGCTACTGATATTTCGAATTCGAAATTCGTCACTTTCATGGAACTTTTTCCCCAAAGCAAAA
2299821 CGTTTCAGAGTTGTCATTCCAGGGTCTACAAGATTCACTAGGGAAAGGTTGATGAAAATGTTGTG
66 CGTTTCAGAGTTGTCATTCCAGGGTCTACAAGATTCACTAGGGAAAGGTTGATGAAAATG-T-TG
*
2299886 TACCTAAGAAAATGTATTAAAAGTTTCAACCTCAGTCCATGAACTAACCAAAGATGATTGGAATT
129 TACCTAAGAAAATGTACTAAAAGTTTCAACCTCAGTCCATGAACTAACCAAAGATGATTGGAATT
2299951 GGTAT
194 GGTAT
2299956 TAAGTTGTAA
Statistics
Matches: 180, Mismatches: 17, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
207 70 0.39
208 43 0.24
209 67 0.37
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (208 bp):
TTATGCTACTGATATTTCGAATTCGAAATTCGTCACTTTCATGGAACTTTTTCCCCAAAGCAAAA
CGTTTCAGAGTTGTCATTCCAGGGTCTACAAGATTCACTAGGGAAAGGTTGATGAAAATGTTGTA
CCTAAGAAAATGTACTAAAAGTTTCAACCTCAGTCCATGAACTAACCAAAGATGATTGGAATTGG
TATCAATGTTCCA
Found at i:2300929 original size:6 final size:6
Alignment explanation
Indices: 2300920--2300992 Score: 128
Period size: 6 Copynumber: 11.8 Consensus size: 6
2300910 TTCCATTTCT
2300920 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
2300968 CTCTCTC TCTCTCC CTCTCC CTCTC
1 CTCTC-C -CTCTCC CTCTCC CTCTC
2300993 TCTCACATCC
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
6 58 0.89
7 2 0.03
8 5 0.08
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
CTCTCC
Found at i:2302577 original size:14 final size:14
Alignment explanation
Indices: 2302560--2302593 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2302550 TGTTTTACTG
2302560 AAAATGTTTTTCGA
1 AAAATGTTTTTCGA
* *
2302574 AAAATATTTTTCGT
1 AAAATGTTTTTCGA
2302588 AAAATG
1 AAAATG
2302594 AATTACATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (14 bp):
AAAATGTTTTTCGA
Found at i:2302791 original size:22 final size:22
Alignment explanation
Indices: 2302744--2302795 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2302734 ATCATAAAAC
* *
2302744 TTAATATT-ATTTTTTTAAATA
1 TTAATATTAAGTTTTATAAATA
* *
2302765 ATAATATTAAGTTTTATATATA
1 TTAATATTAAGTTTTATAAATA
2302787 TTAATATTA
1 TTAATATTA
2302796 TATATATTAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAATATTAAGTTTTATAAATA
Found at i:2302798 original size:15 final size:16
Alignment explanation
Indices: 2302768--2302804 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2302758 TTAAATAATA
*
2302768 ATATTAAGTTTTATAT
1 ATATTAAGTATTATAT
2302784 ATATTAA-TATTATAT
1 ATATTAAGTATTATAT
2302799 ATATTA
1 ATATTA
2302805 CTTTTTAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATATTAAGTATTATAT
Found at i:2302817 original size:23 final size:22
Alignment explanation
Indices: 2302787--2302829 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
2302777 TTTATATATA
2302787 TTAATATTATATATATTACTTT
1 TTAATATTATATATATTACTTT
2302809 TTAACTATTATATATATTACT
1 TTAA-TATTATATATATTACT
2302830 ATTATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATATTATATATATTACTTT
Done.