Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002086.1 Hibiscus syriacus cultivar Beakdansim tig00004258_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: 473624
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 3
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--2599 Score: 4227
Period size: 2 Copynumber: 1347.0 Consensus size: 2
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
43 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT TT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
85 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GG GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
* *
127 GT GT GT TT GT GT GT GT GT GT GG GT GT GT GT G- GT GT GT G- GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
167 GT -T GT GT GT -T GT G- GT GT GT GT GT GT GT G- GT GT TT GT G-
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
204 GT GT GT GT GT G- GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
245 GT GT GT GG GT GT GT GT GT GT GT GT G- GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
286 GT GT GT GT GT GT GT G- GT GT GT GT GT GT GT GT GT GT GT GG GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
327 GG GT GT GT GT GT G- GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
368 GT GT GT GT GT G- GT GT GT GT GT GT -T GT GT GT G- GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
* * *
407 GT GT GT GG GT GT GT GT GT GT G- GT GT G- GT GT TT TT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
447 GT G- GT GT GT -T GT GT G- GT GT GT -T GT GT GT G- GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
484 GT GT GT GT GT G- GT GT GT GT GT GT -T GT GT GT GT G- GT GT TT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
523 GT GT GT GT GT GT GT GT GT GT GT GT -T G- GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
563 GT GT GT GT GT -T GT GT GT -T GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
603 GT G- GT G- GT GT GT -T GT GT GT GT GT GT TT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
642 GT GT GT GT GT GT GT GT GG GT GT GT GT GT G- GT GT GT G- GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
682 GT GT GT TT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
724 GT GT GT GG GT GT GT GT GT G- GT G- GT GT GT GT GT -T GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
763 GT GT TT GT GT GT GT -T GT G- GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
803 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G- GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
844 G- GT GT GT GT GT -T GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
884 GT GT GT GT -T GT GT GT GT GT GT GT GT G- GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
924 GT GT GT GT GT GT GT GT GT GT GT G- GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
965 GT GT GG GT GT GT GT GT GT GT GT GT GT GT GT GT G- GT G- GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1005 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1047 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G- GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1088 GT GT GT GT GT -T GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
1129 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GG GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
1171 GT GT GG GT GT GT GT GT GT GT GT GT GT GT GT GT GT G- GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
1212 GT GT GT GT GT GT GT GT G- GT GT GT GT GT TT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1253 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1295 GT GT GT G- GT GT GT G- GT GT GT GT GT GT G- GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1334 GT GT GT GT GT GT GT GT G- GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
* *
1375 -T GT GT GT GT GT GT TT GT GT GT GT GT GG GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1416 -T G- GT GT GT GT GT -T GT GT GT GT GT GT GT GT G- GT G- GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
1453 GT GT GT GT G- GT GT GG GT GT GT GT GT GT GT GT GT G- GT -T GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
* *
1492 GT GT GT TT GT GT GT GG GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1534 G- GT GT GT GT GT GT GT GT GT GT GT G- GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1574 GT GT GT GT GT GT GT GT GT GT GT G- GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
1615 GT GT GT GG GT GT GT GT GT G- GT G- GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1655 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1697 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1739 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G- GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
1780 GT GT G- GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GG GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
1821 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G- GT GG GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1862 GT G- GT GT GT GT GT GT GT GT GT GT GT GT GT G- GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1902 GT GT GT GT GT G- GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1943 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1985 GT GT GT GT GT GT GT GT GT GT GT GT GT G- GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
2026 GT GT GT G- GT GT GT GG GT GT GT GT -T GT GT GT GT GT G- GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2065 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2107 GT GT GT GT GT GT GT GT GT GT GT GT G- GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2148 GT GT GT GT GT GT GT GT GT GT GT GT GT -T GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
2189 GT GT GT GT GG GT GT G- GT GT GT GT GT GT GT -T GT GT GT GT G-
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2228 GT GT GT GT G- GT GT GT GT GT GT G- GT GT GT G- GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
2267 GT GT GT GT GT GT GT GT G- GT GG GT GT GT GT GT G- GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2307 GT GT GT GT GT GT GT GT GT GT GT G- GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2348 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2390 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2432 GT GT GT GT GT GT GT GT GT GT GT GT -T GT GT GT GT GT G- GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2472 GT GT GT GT GT GT GT GT GT GT GT G- GT GT G- GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
2512 -T GT GT GT GT GT G- GT GT GT TT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
2552 GT GT GG GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2594 GT GT GT
1 GT GT GT
2600 ATGCGTGCAA
Statistics
Matches: 2436, Mismatches: 66, Indels: 190
0.90 0.02 0.07
Matches are distributed among these distances:
1 95 0.04
2 2341 0.96
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:9316 original size:20 final size:20
Alignment explanation
Indices: 9271--9340 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
9261 TTTAAATTAT
9271 AAATA-TAAAATT-AT-TCAA
1 AAATATTAAAATTAATAT-AA
*
9289 ATATATTAAAATTAATATAA
1 AAATATTAAAATTAATATAA
* * *
9309 AAATATTAAAAATAAAAAACA
1 AAATATTAAAATTAATATA-A
9330 AAATATTAAAA
1 AAATATTAAAA
9341 AATGAATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
18 4 0.09
19 7 0.16
20 19 0.44
21 13 0.30
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATATTAAAATTAATATAA
Found at i:9332 original size:21 final size:21
Alignment explanation
Indices: 9286--9341 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
9276 TAAAATTATT
* * *
9286 CAAATATATTAAAATTAATATA
1 CAAA-ATATTAAAAATAAAAAA
9308 -AAAATATTAAAAATAAAAAA
1 CAAAATATTAAAAATAAAAAA
9328 CAAAATATTAAAAA
1 CAAAATATTAAAAA
9342 ATGAATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
CAAAATATTAAAAATAAAAAA
Found at i:9388 original size:2 final size:2
Alignment explanation
Indices: 9381--9419 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
9371 TTATAAAAAT
*
9381 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9420 GTGTGTGTGT
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:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9551 original size:27 final size:26
Alignment explanation
Indices: 9495--9551 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
9485 ACACAATTTA
* * *
9495 AATTGATCGAGACTTATAATTTTTGT
1 AATTAATCGAAACTTATAATTTTTCT
*
9521 -ATTAATCGAAACTTATTATATTTTCT
1 AATTAATCGAAACTTATAAT-TTTTCT
9547 AATTA
1 AATTA
9552 TCTTTTTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 16 0.64
26 5 0.20
27 4 0.16
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (26 bp):
AATTAATCGAAACTTATAATTTTTCT
Found at i:9737 original size:2 final size:2
Alignment explanation
Indices: 9730--9793 Score: 87
Period size: 2 Copynumber: 32.0 Consensus size: 2
9720 GATGATATGC
*
9730 AT AT AT AT CAT AT GA- AT AT AT -T AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9772 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
9794 TTTTTTAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 2 0.04
2 51 0.91
3 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9926 original size:22 final size:21
Alignment explanation
Indices: 9899--9952 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
9889 TATATTCAAT
9899 TTTTTTAATAATTTAATTTTT-A
1 TTTTTTAATAA-TT-ATTTTTAA
9921 TTTTTTAATAATTATTTTTAA
1 TTTTTTAATAATTATTTTTAA
9942 TTTTTTGAATA
1 TTTTTT-AATA
9953 TTTGAATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.20
21 9 0.30
22 15 0.50
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTTAATAATTATTTTTAA
Found at i:10829 original size:12 final size:13
Alignment explanation
Indices: 10804--10836 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
10794 ATAATATACT
10804 AAATATTATAAAA
1 AAATATTATAAAA
10817 AAATATTAT-AAA
1 AAATATTATAAAA
10829 AAATATTA
1 AAATATTA
10837 AATTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATATTATAAAA
Found at i:12646 original size:22 final size:20
Alignment explanation
Indices: 12585--12647 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
12575 ATTCTTCTAC
12585 TTTATTTATTTTATCATTA-TT
1 TTTATTTA-TTT-TCATTATTT
* *
12606 TTTATTT-TATTCAATATTT
1 TTTATTTATTTTCATTATTT
12625 ATTTATTTATTTTCATTGATTT
1 -TTTATTTATTTTCATT-ATTT
12647 T
1 T
12648 AAACCCCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 5 0.15
19 4 0.12
20 7 0.21
21 14 0.41
22 4 0.12
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTATTTATTTTCATTATTT
Found at i:15811 original size:2 final size:2
Alignment explanation
Indices: 15804--15861 Score: 56
Period size: 2 Copynumber: 32.0 Consensus size: 2
15794 CCGCCCCGAT
*
15804 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT 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 TA
*
15843 TT TA TA T- TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
15862 ATACAAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
1 6 0.12
2 42 0.88
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:17508 original size:15 final size:17
Alignment explanation
Indices: 17483--17514 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
17473 AAGGCCTTAG
17483 ATAACTAATAAA-TAAA
1 ATAACTAATAAACTAAA
17499 ATAA-TAATAAACTAAA
1 ATAACTAATAAACTAAA
17515 CATGTCTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAACTAATAAACTAAA
Found at i:21145 original size:31 final size:31
Alignment explanation
Indices: 21107--21205 Score: 180
Period size: 31 Copynumber: 3.2 Consensus size: 31
21097 CGATGACCAC
*
21107 ATCTTAATTAAATAAAAACAAAAGTGATCAT
1 ATCTTAATTAAATAAAAACGAAAGTGATCAT
21138 ATCTTAATTAAATAAAAACGAAAGTGATCAT
1 ATCTTAATTAAATAAAAACGAAAGTGATCAT
*
21169 ATCTTAATTAAATAAAAACGAAAGTGACCAT
1 ATCTTAATTAAATAAAAACGAAAGTGATCAT
21200 ATCTTA
1 ATCTTA
21206 TGTTTTCTGA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.52, C:0.11, G:0.08, T:0.29
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACGAAAGTGATCAT
Found at i:24217 original size:20 final size:20
Alignment explanation
Indices: 24189--24240 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
24179 ATGTGTACGT
*
24189 AGTACCGATACTGTTCTTAC
1 AGTATCGATACTGTTCTTAC
*
24209 AGTATCGATATTGTTCTTAC
1 AGTATCGATACTGTTCTTAC
24229 AGTATCGATACT
1 AGTATCGATACT
24241 AAATGAACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (20 bp):
AGTATCGATACTGTTCTTAC
Found at i:28284 original size:32 final size:32
Alignment explanation
Indices: 28243--28436 Score: 219
Period size: 32 Copynumber: 5.8 Consensus size: 32
28233 TAGGTTACAA
* *
28243 CCATATTTTAGGTTGGAACTTGTTTTAAATAC
1 CCATATTTTAAGTTGGAACTTGTTTTAGATAC
* *
28275 CCATATTTTAAGTTGGAACTTGTTTTTAGGTTGCAA
1 CCATATTTTAAGTTGGAACTTG-TTTTA-GAT--AC
*
28311 GCATATTTT-AGTTTGGAACTTGTTTTAGATAC
1 CCATATTTTAAG-TTGGAACTTGTTTTAGATAC
* *
28343 CCATATTTTAAGTTGGAACTTGTTTTTAGGTTGCAA
1 CCATATTTTAAGTTGGAACTTG-TTTTA-GAT--AC
*
28379 CCATATTTTAAGTTGGAACTTGTCTTAGATAC
1 CCATATTTTAAGTTGGAACTTGTTTTAGATAC
*
28411 CCATATTTTAAGTTAGAACTTGTTTT
1 CCATATTTTAAGTTGGAACTTGTTTT
28437 TAGGTTGGAA
Statistics
Matches: 137, Mismatches: 15, Indels: 20
0.80 0.09 0.12
Matches are distributed among these distances:
32 65 0.47
33 12 0.09
34 7 0.05
35 11 0.08
36 42 0.31
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (32 bp):
CCATATTTTAAGTTGGAACTTGTTTTAGATAC
Found at i:28299 original size:68 final size:68
Alignment explanation
Indices: 28223--28443 Score: 379
Period size: 68 Copynumber: 3.2 Consensus size: 68
28213 AGTTAGAAAC
* *
28223 AACTTGTTTTTAGGTTACAACCATATTTTAGGTTGGAACTTGTTTTAAATACCCATATTTTAAGT
1 AACTTGTTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTGTTTTAGATACCCATATTTTAAGT
28288 TGG
66 TGG
* *
28291 AACTTGTTTTTAGGTTGCAAGCATATTTTAGTTTGGAACTTGTTTTAGATACCCATATTTTAAGT
1 AACTTGTTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTGTTTTAGATACCCATATTTTAAGT
28356 TGG
66 TGG
* *
28359 AACTTGTTTTTAGGTTGCAACCATATTTTAAGTTGGAACTTGTCTTAGATACCCATATTTTAAGT
1 AACTTGTTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTGTTTTAGATACCCATATTTTAAGT
*
28424 TAG
66 TGG
28427 AACTTGTTTTTAGGTTG
1 AACTTGTTTTTAGGTTG
28444 GAACTTGTTT
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 144 1.00
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (68 bp):
AACTTGTTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTGTTTTAGATACCCATATTTTAAGT
TGG
Found at i:28338 original size:17 final size:17
Alignment explanation
Indices: 28280--28460 Score: 59
Period size: 18 Copynumber: 10.6 Consensus size: 17
28270 AATACCCATA
*
28280 TTTTAAGTTGGAACTTG
1 TTTTAGGTTGGAACTTG
* * *
28297 TTTTTAGGTTGCAAGCATA
1 -TTTTAGGTTGGAA-CTTG
*
28316 TTTTAGTTTGGAACTTG
1 TTTTAGGTTGGAACTTG
* * * *
28333 TTTTA-GAT--ACCCATA
1 TTTTAGGTTGGA-ACTTG
*
28348 TTTTAAGTTGGAACTTG
1 TTTTAGGTTGGAACTTG
* * *
28365 TTTTTAGGTTGCAACCATA
1 -TTTTAGGTTGGAA-CTTG
*
28384 TTTTAAGTTGGAACTTG
1 TTTTAGGTTGGAACTTG
* * * * *
28401 TCTTA-GAT--ACCCATA
1 TTTTAGGTTGGA-ACTTG
* *
28416 TTTTAAGTTAGAACTTG
1 TTTTAGGTTGGAACTTG
28433 TTTTTAGGTTGGAACTTG
1 -TTTTAGGTTGGAACTTG
*
28451 TTTTAAGTTG
1 TTTTAGGTTG
28461 TAACCATATT
Statistics
Matches: 113, Mismatches: 38, Indels: 25
0.64 0.22 0.14
Matches are distributed among these distances:
14 2 0.02
15 13 0.12
16 7 0.06
17 26 0.23
18 61 0.54
19 4 0.04
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.46
Consensus pattern (17 bp):
TTTTAGGTTGGAACTTG
Found at i:28447 original size:18 final size:18
Alignment explanation
Indices: 28416--28459 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
28406 GATACCCATA
28416 TTTTAAGTTAGAACTTGT
1 TTTTAAGTTAGAACTTGT
* *
28434 TTTTAGGTTGGAACTTG-
1 TTTTAAGTTAGAACTTGT
28451 TTTTAAGTT
1 TTTTAAGTT
28460 GTAACCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.52
Consensus pattern (18 bp):
TTTTAAGTTAGAACTTGT
Found at i:28921 original size:40 final size:39
Alignment explanation
Indices: 28808--28930 Score: 106
Period size: 40 Copynumber: 3.1 Consensus size: 39
28798 GAAGTGGTAA
* *
28808 ACATCTAAATATGAAAGTGATGATGTATTGTACGAGATAC
1 ACATCTAAATATGAAAGTGGTGAT-TATTGTACGGGATAC
* * * * * * *
28848 ACACCCAACTACAAGCAAGATGGTG--TATCGTACGGGGTAC
1 ACATCTAA--ATATGAAAG-TGGTGATTATTGTACGGGATAC
28888 ACATCTAAATATGAAAGTGGTGATATATTGTACGGGATAC
1 ACATCTAAATATGAAAGTGGTGAT-TATTGTACGGGATAC
28928 ACA
1 ACA
28931 CCCAATTATA
Statistics
Matches: 61, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
37 5 0.08
38 6 0.10
40 40 0.66
42 6 0.10
43 4 0.07
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.25
Consensus pattern (39 bp):
ACATCTAAATATGAAAGTGGTGATTATTGTACGGGATAC
Found at i:28950 original size:40 final size:40
Alignment explanation
Indices: 28828--28968 Score: 122
Period size: 40 Copynumber: 3.5 Consensus size: 40
28818 ATGAAAGTGA
* * * * * *
28828 TGATGTATTGTACGAGATACACACCCAACTACAAGCAAGA
1 TGATGTATCGTACGGGATACACACCCAAATATAAACAAGG
* * * * **
28868 TGGTGTATCGTACGGGGTACACATCTAAATATGAAA-GTGG
1 TGATGTATCGTACGGGATACACACCCAAATAT-AAACAAGG
* * *
28908 TGATATATTGTACGGGATACACACCCAATTATAAACAAGG
1 TGATGTATCGTACGGGATACACACCCAAATATAAACAAGG
*
28948 TGATGTATCGTACGGGGTACA
1 TGATGTATCGTACGGGATACA
28969 TGCCTAAGTT
Statistics
Matches: 75, Mismatches: 24, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
39 3 0.04
40 70 0.93
41 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (40 bp):
TGATGTATCGTACGGGATACACACCCAAATATAAACAAGG
Found at i:28967 original size:80 final size:80
Alignment explanation
Indices: 28771--28968 Score: 254
Period size: 80 Copynumber: 2.5 Consensus size: 80
28761 GAGGTACAAC
* * * * * * *
28771 CCCAATTACAAGA-AAGATGATGTATTGGAAGTGGTAAACATCTAAATATGAAAGTGATGATGTA
1 CCCAACTACAA-ACAAGATGATGTATCGTACGGGGTACACATCTAAATATGAAAGTGATGATATA
28835 TTGTACGAGATACACA
65 TTGTACGAGATACACA
* * *
28851 CCCAACTACAAGCAAGATGGTGTATCGTACGGGGTACACATCTAAATATGAAAGTGGTGATATAT
1 CCCAACTACAAACAAGATGATGTATCGTACGGGGTACACATCTAAATATGAAAGTGATGATATAT
*
28916 TGTACGGGATACACA
66 TGTACGAGATACACA
* * *
28931 CCCAATTATAAACAAGGTGATGTATCGTACGGGGTACA
1 CCCAACTACAAACAAGATGATGTATCGTACGGGGTACA
28969 TGCCTAAGTT
Statistics
Matches: 101, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 101 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (80 bp):
CCCAACTACAAACAAGATGATGTATCGTACGGGGTACACATCTAAATATGAAAGTGATGATATAT
TGTACGAGATACACA
Found at i:28996 original size:80 final size:79
Alignment explanation
Indices: 28833--28996 Score: 177
Period size: 80 Copynumber: 2.1 Consensus size: 79
28823 AGTGATGATG
* * *
28833 TATTGTACGAGATACACACCCAACTACAAGCAAGATGGTGTATCGTACGGGGTACACATCTAAAT
1 TATTGTACGAGATACACACCCAACTACAAACAAGATGATGTATCGTACGGGGTACACACCTAAAT
* * *
28898 ATGAAAGTGGTGATA
66 ATG-AAGTAGCGAAA
* * * * **
28913 TATTGTACGGGATACACACCCAATTATAAACAAGGTGATGTATCGTACGGGGTACATGCCTAAGT
1 TATTGTACGAGATACACACCCAACTACAAACAAGATGATGTATCGTACGGGGTACACACCTAA--
*
28978 TTATG-AGTAGCGAAA
64 ATATGAAGTAGCGAAA
28993 TATT
1 TATT
28997 ATATTTTTAT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
80 65 0.94
82 4 0.06
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (79 bp):
TATTGTACGAGATACACACCCAACTACAAACAAGATGATGTATCGTACGGGGTACACACCTAAAT
ATGAAGTAGCGAAA
Found at i:29801 original size:14 final size:14
Alignment explanation
Indices: 29768--29803 Score: 51
Period size: 11 Copynumber: 2.8 Consensus size: 14
29758 CACTTTCAAC
29768 TATTGCAAATTAGG
1 TATTGCAAATTAGG
29782 ---TGCAAATTAGG
1 TATTGCAAATTAGG
29793 TATTGCAAATT
1 TATTGCAAATT
29804 TACTAACAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 6
0.76 0.00 0.24
Matches are distributed among these distances:
11 11 0.58
14 8 0.42
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (14 bp):
TATTGCAAATTAGG
Found at i:33943 original size:21 final size:21
Alignment explanation
Indices: 33874--34010 Score: 99
Period size: 20 Copynumber: 6.8 Consensus size: 21
33864 GCATCTAAGT
33874 TTTG-AAATTCGCAACGCGAA
1 TTTGTAAATTCGCAACGCGAA
* * *
33894 TTTCT--TTTCCGCAACGCGAT
1 TTTGTAAATT-CGCAACGCGAA
** *
33914 TTTCCAAATTCGTAACGCGAA
1 TTTGTAAATTCGCAACGCGAA
* *
33935 TATGTAAA-TCGCAATGCGAA
1 TTTGTAAATTCGCAACGCGAA
*
33955 TTTGT-AATTCGCAACACAGAA
1 TTTGTAAATTCGCAACGC-GAA
* * *
33976 TTTGTAAA-TCGAAATGTGAA
1 TTTGTAAATTCGCAACGCGAA
33996 TTTGT-AATTCGCAAC
1 TTTGTAAATTCGCAAC
34011 AAAGAAGTCA
Statistics
Matches: 88, Mismatches: 21, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
19 6 0.07
20 51 0.58
21 27 0.31
22 4 0.05
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (21 bp):
TTTGTAAATTCGCAACGCGAA
Found at i:33982 original size:41 final size:41
Alignment explanation
Indices: 33932--34016 Score: 134
Period size: 41 Copynumber: 2.1 Consensus size: 41
33922 TTCGTAACGC
* *
33932 GAATATGTAAATCGCAATGCGAATTTGTAATTCGCAACACA
1 GAATATGTAAATCGAAATGCGAATTTGTAATTCGCAACAAA
* *
33973 GAATTTGTAAATCGAAATGTGAATTTGTAATTCGCAACAAA
1 GAATATGTAAATCGAAATGCGAATTTGTAATTCGCAACAAA
34014 GAA
1 GAA
34017 GTCAAATTCG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (41 bp):
GAATATGTAAATCGAAATGCGAATTTGTAATTCGCAACAAA
Found at i:35375 original size:21 final size:21
Alignment explanation
Indices: 35351--35398 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
35341 ACCTATTTCT
*
35351 GAGGACATAATATTATTGGTA
1 GAGGACATAACATTATTGGTA
*
35372 GAGGACTTAACATTATTGGTA
1 GAGGACATAACATTATTGGTA
35393 GAGGAC
1 GAGGAC
35399 CTAAATGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.29
Consensus pattern (21 bp):
GAGGACATAACATTATTGGTA
Found at i:36096 original size:21 final size:21
Alignment explanation
Indices: 36072--36117 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
36062 GGGGAGTTAT
* *
36072 GTGATGAGGTCAGTGCTTTGC
1 GTGATGAGGTCAGTACTTTAC
*
36093 GTGATGAGGTCGGTACTTTAC
1 GTGATGAGGTCAGTACTTTAC
36114 GTGA
1 GTGA
36118 CGACAATGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.13, G:0.37, T:0.33
Consensus pattern (21 bp):
GTGATGAGGTCAGTACTTTAC
Found at i:36176 original size:63 final size:63
Alignment explanation
Indices: 36070--36191 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 63
36060 TAGGGGAGTT
* * * *
36070 ATGTGATGAGGTCAGTGCTTTGCGTGATGAGGTCGGTACTTTACGTGACGACAATGGTGCATA
1 ATGTGATGAGGTCAGTGCTTTACGTGATGAGGTAGATACTTTACGCGACGACAATGGTGCATA
* * *
36133 ATGTGATGAGGT-A-TGGTCTTTACGTGGTGAGGTAGATATTTTACGCGATGACAATGGTG
1 ATGTGATGAGGTCAGT-G-CTTTACGTGATGAGGTAGATACTTTACGCGACGACAATGGTG
36192 TTTTACGTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
61 1 0.02
62 2 0.04
63 47 0.94
ACGTcount: A:0.23, C:0.11, G:0.34, T:0.32
Consensus pattern (63 bp):
ATGTGATGAGGTCAGTGCTTTACGTGATGAGGTAGATACTTTACGCGACGACAATGGTGCATA
Found at i:36183 original size:42 final size:43
Alignment explanation
Indices: 36137--36229 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 43
36127 TGCATAATGT
* *
36137 GATGAGGTATGGT-CTTTACGTGGTGAGGTAGATATTTTACGC
1 GATGAGGTATGGTGCTTTACGTGGTGAGATAGATACTTTACGC
** * ** *
36179 GATGA-CAATGGTGTTTTACGTGGTGAGATATCTACTTTACGT
1 GATGAGGTATGGTGCTTTACGTGGTGAGATAGATACTTTACGC
36221 GATGAGGTA
1 GATGAGGTA
36230 GCCGCTCTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
41 5 0.13
42 33 0.85
43 1 0.03
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.35
Consensus pattern (43 bp):
GATGAGGTATGGTGCTTTACGTGGTGAGATAGATACTTTACGC
Found at i:36556 original size:21 final size:22
Alignment explanation
Indices: 36524--36642 Score: 140
Period size: 21 Copynumber: 5.6 Consensus size: 22
36514 GATTCACTTG
*
36524 TCATCATTCAAGAGGCCCCTCC
1 TCATCGTTCAAGAGGCCCCTCC
*
36546 T-ATTGTTCAAGAGGCCCCT-C
1 TCATCGTTCAAGAGGCCCCTCC
36566 TCATCGTTCAAGAGGCCCCTCC
1 TCATCGTTCAAGAGGCCCCTCC
* *
36588 -CACCGTTCAAGTGGCCCCT-C
1 TCATCGTTCAAGAGGCCCCTCC
* *
36608 TCATCGTTTAAGAGGTCCCTCC
1 TCATCGTTCAAGAGGCCCCTCC
*
36630 -CACCGTTCAAGAG
1 TCATCGTTCAAGAG
36643 CCCGATTCAC
Statistics
Matches: 82, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
20 3 0.04
21 76 0.93
22 3 0.04
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.24
Consensus pattern (22 bp):
TCATCGTTCAAGAGGCCCCTCC
Found at i:36576 original size:42 final size:42
Alignment explanation
Indices: 36524--36642 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
36514 GATTCACTTG
* * **
36524 TCATCATTCAAGAGGCCCCTCCTATTGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
*
36566 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGTGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
* *
36608 TCATCGTTTAAGAGGTCCCTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAG
36643 CCCGATTCAC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:39679 original size:28 final size:28
Alignment explanation
Indices: 39639--39695 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
39629 ACAGTATCCC
39639 ATTGTTAACATCCATGGCTACTACTAAT
1 ATTGTTAACATCCATGGCTACTACTAAT
39667 ATTGTTAACATCCATGGCTACTACTAAT
1 ATTGTTAACATCCATGGCTACTACTAAT
39695 A
1 A
39696 AGTTTACTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (28 bp):
ATTGTTAACATCCATGGCTACTACTAAT
Found at i:40789 original size:24 final size:24
Alignment explanation
Indices: 40755--40808 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
40745 CTGAAACATC
40755 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
40779 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
40803 ATCAAA
1 ATCAAA
40809 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:40822 original size:24 final size:24
Alignment explanation
Indices: 40755--40822 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
40745 CTGAAACATC
* * *
40755 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
40779 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
40803 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
40823 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:40955 original size:12 final size:12
Alignment explanation
Indices: 40934--40967 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40924 GGTTGTGGGT
*
40934 TTTGAGATTGTG
1 TTTGATATTGTG
40946 TTTGATATTGTG
1 TTTGATATTGTG
*
40958 TTTGGTATTG
1 TTTGATATTG
40968 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:41762 original size:20 final size:20
Alignment explanation
Indices: 41737--41805 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
41727 CAAAATATTT
41737 GTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
*
41757 GTGTTGTG-AATTCGAAAA-TC
1 GTGTTGCGAAATT--AAAATTC
* **
41777 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAATTAAAATTC
41797 GTGTTGCGA
1 GTGTTGCGA
41806 TTTAGAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 8 0.21
20 25 0.64
21 6 0.15
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:41786 original size:40 final size:40
Alignment explanation
Indices: 41739--41947 Score: 137
Period size: 40 Copynumber: 5.2 Consensus size: 40
41729 AAATATTTGT
*
41739 GTTGCGAAATTAAAATTCGTGTTGTGAATTCGAAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
** * * * **
41779 GTTGCGAAAACAAAATTCGTGTTGCGATTTAGAAAAACTT
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
* ** *
41819 GTTACGAAAAGGAAACTT-GTGTTGCGAATTC-AGAAATCGA
1 GTTGCG-AAATTAAAATTCGTGTTGCGAATTCGA-AAATCGA
* *
41859 GTTGCG-AATTGAAATTCTGTGTTGCGAATTTGGAAAATC-A
1 GTTGCGAAATTAAAATTC-GTGTTGCGAA-TTCGAAAATCGA
* *
41899 CGTTGCGAGAA--AGAAATTCGCGTTGCG-ATTGCAGAAACT-GA
1 -GTTGCGA-AATTA-AAATTCGTGTTGCGAATT-C-GAAAATCGA
41940 GTTGCGAA
1 GTTGCGAA
41948 TTTAGAAACT
Statistics
Matches: 129, Mismatches: 27, Indels: 27
0.70 0.15 0.15
Matches are distributed among these distances:
38 6 0.05
39 4 0.03
40 76 0.59
41 34 0.26
42 7 0.05
43 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
Found at i:41882 original size:20 final size:20
Alignment explanation
Indices: 41836--41888 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
41826 AAAGGAAACT
41836 TGTGTTGCGAATTCAGAAATC
1 TGTGTTGCGAATT-AGAAATC
*
41857 -GAGTTGCGAATT-GAAATTC
1 TGTGTTGCGAATTAGAAA-TC
41876 TGTGTTGCGAATT
1 TGTGTTGCGAATT
41889 TGGAAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 22 0.79
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.36
Consensus pattern (20 bp):
TGTGTTGCGAATTAGAAATC
Found at i:47926 original size:50 final size:51
Alignment explanation
Indices: 47850--47945 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 51
47840 TGATCCGCGC
* * *
47850 TATATGTCACGTAAGGGTATAGCGCGG-ATCAGGGGCCGCGTTATACTTGAT
1 TATATGACACGTAAGGGTATAGCGCGGTA-CAGAGGACGCGTTATACTTGAT
*
47901 TATATGACACGT-GGGGTATAGCGCGGTACAGAGGACGCGTTATAC
1 TATATGACACGTAAGGGTATAGCGCGGTACAGAGGACGCGTTATAC
47946 CTTTAATTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
50 28 0.70
51 12 0.30
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (51 bp):
TATATGACACGTAAGGGTATAGCGCGGTACAGAGGACGCGTTATACTTGAT
Found at i:48057 original size:12 final size:11
Alignment explanation
Indices: 48018--48060 Score: 56
Period size: 10 Copynumber: 4.1 Consensus size: 11
48008 TTCATCACAC
48018 CAAA-TTCTCT
1 CAAATTTCTCT
48028 CAAATTT-TCT
1 CAAATTTCTCT
48038 C-AATTTCTCT
1 CAAATTTCTCT
48048 CAAATATTCTCT
1 CAAAT-TTCTCT
48060 C
1 C
48061 TGTTTAAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 5 0.17
10 12 0.41
11 5 0.17
12 7 0.24
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (11 bp):
CAAATTTCTCT
Found at i:48137 original size:17 final size:18
Alignment explanation
Indices: 48100--48140 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
48090 ATATTATGTA
*
48100 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
48118 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
48135 TTTACT
1 TTTACT
48141 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:50944 original size:16 final size:16
Alignment explanation
Indices: 50923--50960 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
50913 GTAGTGCATC
50923 GATGCACCCGTCAAGG
1 GATGCACCCGTCAAGG
50939 GATGCACCCGTCAAGG
1 GATGCACCCGTCAAGG
50955 GATGCA
1 GATGCA
50961 TCGATACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (16 bp):
GATGCACCCGTCAAGG
Found at i:51573 original size:2 final size:2
Alignment explanation
Indices: 51566--51604 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
51556 CATGAGTTAG
51566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51605 GGAATTGGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53558 original size:30 final size:31
Alignment explanation
Indices: 53522--53596 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
53512 TAATGTATTT
* *
53522 CAGTTATTTTTATTT-ATTACCATTTAATAG
1 CAGTTATTGTAATTTGATTACCATTTAATAG
*
53552 CAGTTATTGTAATTTGATTATCATTTAATA-
1 CAGTTATTGTAATTTGATTACCATTTAATAG
53582 C--TTATTGTAAGTTTG
1 CAGTTATTGTAA-TTTG
53597 TTGTATTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
28 9 0.22
29 4 0.10
30 14 0.35
31 13 0.32
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.52
Consensus pattern (31 bp):
CAGTTATTGTAATTTGATTACCATTTAATAG
Found at i:53591 original size:28 final size:30
Alignment explanation
Indices: 53533--53596 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
53523 AGTTATTTTT
53533 ATTT-ATTACCATTTAATAGCAGTTATTGTA
1 ATTTGATTACCATTTAATAGCA-TTATTGTA
*
53563 ATTTGATTATCATTTAATA-C-TTATTGTA
1 ATTTGATTACCATTTAATAGCATTATTGTA
53591 AGTTTG
1 A-TTTG
53597 TTGTATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 9 0.29
29 4 0.13
30 5 0.16
31 13 0.42
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.50
Consensus pattern (30 bp):
ATTTGATTACCATTTAATAGCATTATTGTA
Found at i:60153 original size:47 final size:47
Alignment explanation
Indices: 60102--60195 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
60092 AGAGATTATT
60102 TTGTAATTTTTAATAGTCGAAATATTCAACAAAATAACATTATATAG
1 TTGTAATTTTTAATAGTCGAAATATTCAACAAAATAACATTATATAG
60149 TTGTAATTTTTAATAGTCGAAATATTCAACAAAATAACATTATATAG
1 TTGTAATTTTTAATAGTCGAAATATTCAACAAAATAACATTATATAG
60196 CGAGACTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (47 bp):
TTGTAATTTTTAATAGTCGAAATATTCAACAAAATAACATTATATAG
Found at i:63967 original size:2 final size:2
Alignment explanation
Indices: 63962--64055 Score: 119
Period size: 2 Copynumber: 49.5 Consensus size: 2
63952 ATTTATGTAG
*
63962 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
64003 TGA TA TA T- TA TA T- TA T- TA -A GA TA TA TA TA TA TA T- TA TA
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64041 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
64056 CATTACCTAT
Statistics
Matches: 83, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
1 6 0.07
2 75 0.90
3 2 0.02
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64160 original size:24 final size:22
Alignment explanation
Indices: 64133--64184 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 22
64123 ATATTTCCCC
*
64133 TTTATTTTATTATATTATTATTT
1 TTTATTCTATTATATTA-TATTT
*
64156 ATTTATGCTATTATATTATATTT
1 -TTTATTCTATTATATTATATTT
64179 TTTATT
1 TTTATT
64185 ATATACGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.20
23 5 0.20
24 15 0.60
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTATTCTATTATATTATATTT
Found at i:64189 original size:19 final size:18
Alignment explanation
Indices: 64137--64189 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
64127 TTCCCCTTTA
64137 TTTTATTATATTATTATTT
1 TTTTATTATA-TATTATTT
*
64156 ATTTATGCTATTATATTATATT
1 TTTTAT--TA-TATATTAT-TT
64178 TTTTATTATATA
1 TTTTATTATATA
64190 CGATATGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
19 9 0.32
20 2 0.07
21 8 0.29
22 9 0.32
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTATTATATATTATTT
Found at i:74710 original size:49 final size:50
Alignment explanation
Indices: 74632--74727 Score: 140
Period size: 49 Copynumber: 1.9 Consensus size: 50
74622 AATACTTCGC
* ** *
74632 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAA-AAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAAACGT
*
74681 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAAA
74728 GAGGGAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
49 35 0.85
50 6 0.15
ACGTcount: A:0.48, C:0.15, G:0.23, T:0.15
Consensus pattern (50 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAAACGT
Found at i:75929 original size:105 final size:105
Alignment explanation
Indices: 75462--75921 Score: 875
Period size: 105 Copynumber: 4.4 Consensus size: 105
75452 AGGTTTTACC
*
75462 CAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
75527 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
75567 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
75632 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
75672 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
75737 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
75777 CAGAGCCAATTTCGACTTCACAACGAGGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
75842 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
75882 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
75922 GAAACAACAC
Statistics
Matches: 347, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 347 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:77636 original size:2 final size:2
Alignment explanation
Indices: 77631--77679 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
77621 TGTATTTATG
*
77631 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
77673 TA TA TA T
1 TA TA TA T
77680 TCATTTTACC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:77772 original size:18 final size:18
Alignment explanation
Indices: 77749--77789 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
77739 CATTCATTAA
*
77749 TTATTTATTCCATTTTAT
1 TTATTTATCCCATTTTAT
*
77767 TTATTT-TCCCCTTTTAT
1 TTATTTATCCCATTTTAT
77784 TT-TTTA
1 TTATTTA
77790 CTATTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 3 0.15
17 11 0.55
18 6 0.30
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTATCCCATTTTAT
Found at i:77804 original size:19 final size:19
Alignment explanation
Indices: 77780--77829 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
77770 TTTTCCCCTT
77780 TTATTTTTTA-CTATTATTA
1 TTATTTTTTAGCTATTA-TA
77799 TTATTTATTTATGCTATTATA
1 TTATTT-TTTA-GCTATTATA
77820 TTATATTTTT
1 TTAT-TTTTT
77830 TATTATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.22
20 4 0.15
21 9 0.33
22 8 0.30
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (19 bp):
TTATTTTTTAGCTATTATA
Found at i:77818 original size:22 final size:22
Alignment explanation
Indices: 77790--77832 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
77780 TTATTTTTTA
77790 CTATTATTATTAT-TTATTTATG
1 CTATTA-TATTATATTATTTATG
*
77812 CTATTATATTATATTTTTTAT
1 CTATTATATTATATTATTTAT
77833 TATTGTATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (22 bp):
CTATTATATTATATTATTTATG
Found at i:77914 original size:2 final size:2
Alignment explanation
Indices: 77909--77946 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
77899 TATACTCTAC
77909 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77947 TTTATTTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83854 original size:14 final size:14
Alignment explanation
Indices: 83835--83862 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
83825 TAACAGACTT
83835 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
83849 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
83863 TGGTATCAGG
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:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:85679 original size:51 final size:51
Alignment explanation
Indices: 85620--85720 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
85610 TCAGGGGGAG
* *
85620 AGTTACAAGGAATTTCAGCCTGTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTATT
85671 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTAT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTAT
85721 CCTTTCCTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (51 bp):
AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTATT
Found at i:87967 original size:14 final size:14
Alignment explanation
Indices: 87948--87975 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
87938 TAACAGACTT
87948 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
87962 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
87976 AATATATCAT
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:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:92172 original size:38 final size:38
Alignment explanation
Indices: 92129--92208 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
92119 CAAAATTTCT
*
92129 TTTAAGAAAAATGCGTAGTT-TAATTTATCTGTCATTCC
1 TTTAAGAAAAATGCGTAGTTCTAATATATCTGTCATT-C
* * * *
92167 TTTAAGACAAATGTGTAGTTCTTATATATCTTTCATTC
1 TTTAAGAAAAATGCGTAGTTCTAATATATCTGTCATTC
92205 TTTA
1 TTTA
92209 GCCATTCTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
38 23 0.64
39 13 0.36
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.46
Consensus pattern (38 bp):
TTTAAGAAAAATGCGTAGTTCTAATATATCTGTCATTC
Found at i:95466 original size:4 final size:4
Alignment explanation
Indices: 95457--95616 Score: 320
Period size: 4 Copynumber: 40.0 Consensus size: 4
95447 TTGAATTATA
95457 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
95505 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
95553 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
95601 TATG TATG TATG TATG
1 TATG TATG TATG TATG
95617 CAGGGTTGCT
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 156 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:99786 original size:43 final size:43
Alignment explanation
Indices: 99725--99807 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
99715 TCATTTTTCA
* *
99725 ACAATATCACCATTGCAATTCAAGAGCAATACTGGCACAAAGC
1 ACAATATCACCATCGCAATTCAAGAGCAATACTAGCACAAAGC
*
99768 ACAATATCACC-TACGCAATTTAAGAGCAATACTAGCACAA
1 ACAATATCACCAT-CGCAATTCAAGAGCAATACTAGCACAA
99808 GCAGTGAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.43, C:0.25, G:0.12, T:0.19
Consensus pattern (43 bp):
ACAATATCACCATCGCAATTCAAGAGCAATACTAGCACAAAGC
Found at i:102559 original size:46 final size:46
Alignment explanation
Indices: 102503--102637 Score: 164
Period size: 46 Copynumber: 2.9 Consensus size: 46
102493 TTTTGAATAA
*
102503 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTTGAGC
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTTGAAC
* * *
102549 ATGTATGCGAAGTAGAAATCATGCGGCTAGGTTTATTTTTCTCGAAC
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTT-TTGAAC
* * * * * *
102596 AAGCATGCGAATTAGATATCATGCAGTTAGGATT-TTTTTTTG
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTTG
102638 TGAATGACAA
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
45 2 0.03
46 43 0.57
47 31 0.41
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (46 bp):
ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTTGAAC
Found at i:107314 original size:125 final size:125
Alignment explanation
Indices: 107061--107288 Score: 289
Period size: 125 Copynumber: 1.8 Consensus size: 125
107051 GAATACCCAC
** * * * *
107061 ATTGGGGCATGACTGAACCCCAATCATTTTGAGATGACATGATTCGGACGAAGAAGGCATTGAGA
1 ATTGGGGCATGACTGAACCCCAATCATGATGAAATGACAAGATTCAGACCAAGAAGGCATTGAGA
* ** *
107126 ATAAGCCTTACAATTTGAGGTTTTGGGGCATTTTGAAGACCCGTACCAGTAAAAGATAAT
66 ATAAGCCTTACAACTTGAAATGTTGGGGCATTTTGAAGACCCGTACCAGTAAAAGATAAT
* *
107186 ATTGGGGCATGAGTGAA-CCCACATCATGATGAAATGACAAGATTCAGACCAAG-AGGACGTTGA
1 ATTGGGGCATGACTGAACCCCA-ATCATGATGAAATGACAAGATTCAGACCAAGAAGG-CATTGA
* * *
107249 GAGTGAGTCTTACAACTTGAAATGTTGGGGCATTTTGAAG
64 GAATAAGCCTTACAACTTGAAATGTTGGGGCATTTTGAAG
107289 GCTTGTTCCA
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
124 7 0.08
125 79 0.92
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.25
Consensus pattern (125 bp):
ATTGGGGCATGACTGAACCCCAATCATGATGAAATGACAAGATTCAGACCAAGAAGGCATTGAGA
ATAAGCCTTACAACTTGAAATGTTGGGGCATTTTGAAGACCCGTACCAGTAAAAGATAAT
Found at i:108553 original size:37 final size:37
Alignment explanation
Indices: 108478--108579 Score: 109
Period size: 37 Copynumber: 2.8 Consensus size: 37
108468 AAAGACAAGT
* *** *
108478 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTGAGC
1 CTTCACTAAAGAGTAGTGAAGCAAATCCAAGCTAAGC
108515 CTTCACTAAAGAGTAGTGAAGCAAA-CCAAAGCTAAGC
1 CTTCACTAAAGAGTAGTGAAGCAAATCC-AAGCTAAGC
* *
108552 CTTCA-TCGAAGAGTAGTGAAGCATATCC
1 CTTCACT-AAAGAGTAGTGAAGCAAATCC
108580 TTTTTAAACC
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
36 3 0.05
37 50 0.91
38 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (37 bp):
CTTCACTAAAGAGTAGTGAAGCAAATCCAAGCTAAGC
Found at i:109616 original size:54 final size:54
Alignment explanation
Indices: 108979--109600 Score: 1005
Period size: 54 Copynumber: 11.6 Consensus size: 54
108969 GTAGTAAAGC
* * * *
108979 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGATAAAGAGGGAGCGAACCCGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
* * * *
109033 AGAAGAAGATATTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCTGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
*
109087 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCTGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
109141 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
109195 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAG-AA-AGGGAGCGAACCTGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
*
109247 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCTGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
*
109301 AGAAGAATATGTTTGAGTTTCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
* * * *
109355 AGAAGAATATGTTTGAGTTTCATACTCCCTAGAGAAATAGGGAGCAAACCTATA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
*
109409 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCAGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
* * *
109463 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
* * *
109517 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
* **
109571 AGAAGAAGATGTTCAAGTTCCATACTCCCT
1 AGAAGAATATGTTTGAGTTCCATACTCCCT
109601 GAACGAATAA
Statistics
Matches: 541, Mismatches: 25, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
52 50 0.09
53 4 0.01
54 487 0.90
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
Found at i:109713 original size:51 final size:52
Alignment explanation
Indices: 109592--109736 Score: 175
Period size: 51 Copynumber: 2.8 Consensus size: 52
109582 TTCAAGTTCC
* * * * *
109592 ATACTCCCTGAACGAATAAGGAGCGGACTCGTTTGTTGAAGATTGTTCGAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTG-AG--TGATCGAGTCCT
* *
109647 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAG-GATCGAGTCTT
1 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAGTGATCGAGTCCT
* *
109698 ATACTCTCTGAAGGAATAGTGAGCGGACCCGTTTGTTGA
1 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGA
109737 AGATTGTTTG
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
51 45 0.56
54 2 0.03
55 33 0.41
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (52 bp):
ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAGTGATCGAGTCCT
Found at i:109724 original size:106 final size:106
Alignment explanation
Indices: 109592--109785 Score: 275
Period size: 106 Copynumber: 1.8 Consensus size: 106
109582 TTCAAGTTCC
*
109592 ATACTCCCTGAACGAATAAGGAGCGGACTCGTTTGTTGAAGATTGTTCGAGTCCTATACT-CTCT
1 ATACTCCCTGAACGAATAAGGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTCCTATACTCCT-T
* * *
109656 GAAGGAATAGGGAGCGGACACGTTTATTGAGGATCGAGTCTT
65 AAAAGAATAGGGAGCAGACACGTTTATTGAGGATCGAGTCTT
* * * *
109698 ATACTCTCTGAAGGAAT-AGTGAGCGGACCCGTTTGTTGAAGATTGTTTGAGTCTTATACTCCTT
1 ATACTCCCTGAACGAATAAG-GAGCGGACCCGTTTGTTGAAGATTGTTCGAGTCCTATACTCCTT
*
109762 AAAAGAATAGGGAGCAGACCCGTT
65 AAAAGAATAGGGAGCAGACACGTT
109786 ATTCGAAGAT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
105 2 0.03
106 73 0.95
107 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (106 bp):
ATACTCCCTGAACGAATAAGGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTCCTATACTCCTTA
AAAGAATAGGGAGCAGACACGTTTATTGAGGATCGAGTCTT
Found at i:109770 original size:55 final size:55
Alignment explanation
Indices: 109592--109785 Score: 227
Period size: 55 Copynumber: 3.6 Consensus size: 55
109582 TTCAAGTTCC
* * * * *
109592 ATACTCCCTGAACGAATAAGGAGCGGACTCGTTTGTTGAAGATTGTTCGAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTCTT
* * *
109647 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTG-AG---GATCGAGTCTT
1 ATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTCTT
* *
109698 ATACTCTCTGAAGGAATAGTGAGCGGACCCGTTTGTTGAAGATTGTTTGAGTCTT
1 ATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTCTT
* * *
109753 ATACTC-CTTAAAAGAATAGGGAGCAGACCCGTT
1 ATACTCTC-TGAAGGAATAGGGAGCGGACCCGTT
109786 ATTCGAAGAT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
51 44 0.37
52 2 0.02
54 3 0.03
55 69 0.58
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (55 bp):
ATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTCTT
Found at i:110392 original size:43 final size:43
Alignment explanation
Indices: 110331--110413 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
110321 TCATTTTTCA
* *
110331 ACAATATCACCATTGCAATTCAAGAGCAATACTGGCACAAAGC
1 ACAATATCACCATCGCAATTCAAGAGCAATACTAGCACAAAGC
*
110374 ACAATATCACC-TACGCAATTTAAGAGCAATACTAGCACAA
1 ACAATATCACCAT-CGCAATTCAAGAGCAATACTAGCACAA
110414 GCAGTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.43, C:0.25, G:0.12, T:0.19
Consensus pattern (43 bp):
ACAATATCACCATCGCAATTCAAGAGCAATACTAGCACAAAGC
Found at i:114676 original size:55 final size:55
Alignment explanation
Indices: 114617--114937 Score: 257
Period size: 55 Copynumber: 5.9 Consensus size: 55
114607 ATACTTGAAA
* * *
114617 AATCTTCAA-ATAACGGGTATGCTCCCTATTCTTTCAAGGAGTATAAGACTCGAAC
1 AATCTTCAATA-AACGGGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAAC
** * * * *
114672 AATCTTCGGTAAATGTGTCTCCTCCCTATTCGTTCAGGGAGTATAAGACTCAAAC
1 AATCTTCAATAAACGGGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAAC
* *
114727 AATCTTCAATAAACGAGTCCGCTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAAC
1 AATCTTCAATAAACGGGTCTGCTCCCTATTCGTTCAGGGAGTATAAG-ACTCGAAC
* ** * *
114782 AATCTTC-ATAAAACGGGTCCGCTCTTTATTCATTC-GGAGAGTAT-AGAACTCGAAT
1 AATCTTCAAT-AAACGGGTCTGCTCCCTATTCGTTCAGG-GAGTATAAG-ACTCGAAC
* * * * ** *
114837 AATCTTC-ATAAAATGGGTCCGCTCCCTATTCATTTAGAAAGTATAGGACTCG---
1 AATCTTCAAT-AAACGGGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAAC
* * * * * *
114889 -ATCTTTAACAAACGTGTCCGCTCCCTATTCTTTCAGAGAGTATAAGACT
1 AATCTTCAATAAACGGGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACT
114938 TGATCATCAC
Statistics
Matches: 223, Mismatches: 36, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
51 39 0.17
52 1 0.00
54 6 0.03
55 174 0.78
56 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (55 bp):
AATCTTCAATAAACGGGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAAC
Found at i:116296 original size:45 final size:45
Alignment explanation
Indices: 116211--116296 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
116201 TAAACAAAAC
* * *
116211 TCAAGCCGCCCTTTGCGGGTTTTCAACTTGATACCTCCTTTGGTT
1 TCAAGACGCCCTTTGCAGGTTTTCAACTTGATACCCCCTTTGGTT
* *
116256 TCAAGACGCCCTTTTCAGGTTTTCATCTTGA-ATCCCCCTTT
1 TCAAGACGCCCTTTGCAGGTTTTCAACTTGATA-CCCCCTTT
116297 TATTTTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.15, C:0.30, G:0.16, T:0.38
Consensus pattern (45 bp):
TCAAGACGCCCTTTGCAGGTTTTCAACTTGATACCCCCTTTGGTT
Found at i:116347 original size:24 final size:24
Alignment explanation
Indices: 116302--116346 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
116292 CCTTTTATTT
116302 TTTTTCCTTTCTTTCCATTTTTAA
1 TTTTTCCTTTCTTTCCATTTTTAA
116326 TTTTTCTCTTTC-TT-CATTTTT
1 TTTTTC-CTTTCTTTCCATTTTT
116347 TCATTTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 8 0.40
25 5 0.25
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTTCCTTTCTTTCCATTTTTAA
Found at i:116386 original size:9 final size:8
Alignment explanation
Indices: 116374--116490 Score: 94
Period size: 9 Copynumber: 13.6 Consensus size: 8
116364 ATTTTCCTAT
116374 TTTTTTCA
1 TTTTTTCA
*
116382 CTTTTTCA
1 TTTTTTCA
*
116390 -TTTTTCT
1 TTTTTTCA
116397 TTATTTTCA
1 TT-TTTTCA
116406 TTTTTTCA
1 TTTTTTCA
116414 TTTTTTTCA
1 -TTTTTTCA
116423 TTTTACTTTTCA
1 --TT--TTTTCA
*
116435 TCATTTTCA
1 T-TTTTTCA
116444 TTTTTTTCA
1 -TTTTTTCA
116453 TTTTTTCA
1 TTTTTTCA
116461 TTTTTTTCA
1 -TTTTTTCA
116470 TTTTCTTC-
1 TTTT-TTCA
*
116478 TTTTTTCC
1 TTTTTTCA
116486 TTTTT
1 TTTTT
116491 CTTTTCTTTT
Statistics
Matches: 93, Mismatches: 5, Indels: 22
0.77 0.04 0.18
Matches are distributed among these distances:
7 9 0.10
8 35 0.38
9 38 0.41
10 5 0.05
12 6 0.06
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:116410 original size:32 final size:31
Alignment explanation
Indices: 116300--116495 Score: 134
Period size: 33 Copynumber: 6.1 Consensus size: 31
116290 CCCCTTTTAT
* *
116300 TTTTTTTCCTTTCTTTCCA-TTTTTAATTTTTC
1 TTTTTTTCATTT-TTT-CATTTTTTCATTTTTC
* * *
116332 TCTTTCTTCATTTTTTCA--TTTTCCTATTTCC
1 T-TTTTTTCATTTTTTCATTTTTTCAT-TTTTC
* * *
116363 TATTTTCCTATTTTTTTCACTTTTTCATTTTTC
1 TTTTTTTC-A-TTTTTTCATTTTTTCATTTTTC
*
116396 TTTATTTTCATTTTTTCATTTTTTTCATTTTAC
1 TTT-TTTTCATTTTTTCA-TTTTTTCATTTTTC
**
116429 TTTTCATCA--TTTTCATTTTTTTCATTTTTTC
1 TTTTTTTCATTTTTTCA-TTTTTTCA-TTTTTC
*
116460 ATTTTTTTCATTTTCTTC-TTTTTTCCTTTTTC
1 -TTTTTTTCATTTT-TTCATTTTTTCATTTTTC
116492 TTTT
1 TTTT
116496 CTTTTCTCTT
Statistics
Matches: 131, Mismatches: 20, Indels: 27
0.74 0.11 0.15
Matches are distributed among these distances:
30 24 0.18
31 17 0.13
32 37 0.28
33 38 0.29
34 12 0.09
35 3 0.02
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (31 bp):
TTTTTTTCATTTTTTCATTTTTTCATTTTTC
Found at i:116433 original size:64 final size:62
Alignment explanation
Indices: 116303--116496 Score: 159
Period size: 64 Copynumber: 3.1 Consensus size: 62
116293 CTTTTATTTT
* * * * **
116303 TTTTCCT-TTCTTTCCATTTTTAATTTTTCTCTTTCTTCATTTTTTCATTTTCCT-ATTTCCTA-
1 TTTTCCTATTATTTTCATTTTTCATTTTTCT-TTTTTTCATTTTTTCATTTTTTTCATTT--TAC
*
116365 TTTTCCTATTTTTTTCACTTTTTCATTTTTCTTTATTTTCATTTTTTCATTTTTTTCATTTTAC
1 TTTTCCTATTATTTTCA-TTTTTCATTTTTCTTT-TTTTCATTTTTTCATTTTTTTCATTTTAC
* *
116429 TTTT-C-ATCATTTTCATTTTTTTCATTTTTTCATTTTTTTCATTTTCTTC--TTTTTTCCTTTT
1 TTTTCCTATTATTTTCA--TTTTTCA-TTTTTC-TTTTTTTCATTTT-TTCATTTTTTTCATTTT
*
116490 TC
61 AC
116492 TTTTC
1 TTTTC
116497 TTTTCTCTTT
Statistics
Matches: 111, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
62 15 0.14
63 35 0.32
64 51 0.46
65 10 0.09
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.71
Consensus pattern (62 bp):
TTTTCCTATTATTTTCATTTTTCATTTTTCTTTTTTTCATTTTTTCATTTTTTTCATTTTAC
Found at i:116452 original size:47 final size:45
Alignment explanation
Indices: 116384--116473 Score: 146
Period size: 47 Copynumber: 2.0 Consensus size: 45
116374 TTTTTTCACT
116384 TTTTCATTTTTCTTTATTTTCATTTTTTCATTTTTTTCATTTTAC
1 TTTTCATTTTTCTTTATTTTCATTTTTTCATTTTTTTCATTTTAC
116429 TTTTCATCATTTTCATTT-TTTTCATTTTTTCATTTTTTTCATTTT
1 TTTTCAT--TTTTC-TTTATTTTCATTTTTTCATTTTTTTCATTTT
116474 CTTCTTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
45 7 0.17
47 32 0.76
48 3 0.07
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (45 bp):
TTTTCATTTTTCTTTATTTTCATTTTTTCATTTTTTTCATTTTAC
Found at i:116500 original size:17 final size:18
Alignment explanation
Indices: 116444--116508 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 18
116434 ATCATTTTCA
*
116444 TTTTTT-TCATTTT-TTC
1 TTTTTTCTCTTTTTCTTC
*
116460 ATTTTTT-TCATTTTCTTC
1 -TTTTTTCTCTTTTTCTTC
116478 TTTTTTC-CTTTTTCTT-
1 TTTTTTCTCTTTTTCTTC
116494 TTCTTTTCTCTTTTT
1 TT-TTTTCTCTTTTT
116509 TTCATTTCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
16 2 0.05
17 32 0.74
18 9 0.21
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTCTCTTTTTCTTC
Found at i:116510 original size:27 final size:29
Alignment explanation
Indices: 116408--116521 Score: 89
Period size: 27 Copynumber: 4.1 Consensus size: 29
116398 TATTTTCATT
* * * * *
116408 TTTTCATTTTTTTCATTTTACTTTTCATC
1 TTTTCATTTTCTTCTTTTTTCATTTCTTC
*
116437 ATTTTCATTTTTTTCATTTTTTCA--T-TT-
1 -TTTTCATTTTCTTC-TTTTTTCATTTCTTC
*
116464 TTTTCATTTTCTTCTTTTTTCCTTT-TTC
1 TTTTCATTTTCTTCTTTTTTCATTTCTTC
116492 TTTTC-TTTTC-TCTTTTTTTCATTTCTTC
1 TTTTCATTTTCTTC-TTTTTTCATTTCTTC
116520 TT
1 TT
116522 CAACCGAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
25 7 0.10
26 15 0.21
27 18 0.25
28 11 0.15
29 1 0.01
30 14 0.20
31 5 0.07
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (29 bp):
TTTTCATTTTCTTCTTTTTTCATTTCTTC
Found at i:116511 original size:10 final size:9
Alignment explanation
Indices: 116390--116510 Score: 52
Period size: 9 Copynumber: 13.4 Consensus size: 9
116380 CACTTTTTCA
116390 TTTTTCTTT
1 TTTTTCTTT
* *
116399 ATTTTC-AT
1 TTTTTCTTT
*
116407 TTTTTCATT
1 TTTTTCTTT
116416 TTTTTCATTT
1 TTTTTC-TTT
* *
116426 TACTTTTCATC
1 T--TTTTCTTT
* *
116437 ATTTTCATT
1 TTTTTCTTT
*
116446 TTTTTC-AT
1 TTTTTCTTT
*
116454 TTTTTCATT
1 TTTTTCTTT
*
116463 TTTTTCATT
1 TTTTTCTTT
*
116472 TTCTTC-TT
1 TTTTTCTTT
*
116480 TTTTCCTTT
1 TTTTTCTTT
*
116489 TTCTTT-TCT
1 TT-TTTCTTT
*
116498 TTTCTCTTT
1 TTTTTCTTT
116507 TTTT
1 TTTT
116511 CATTTCTTCT
Statistics
Matches: 84, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
8 21 0.25
9 52 0.62
10 5 0.06
11 1 0.01
12 5 0.06
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:126231 original size:45 final size:45
Alignment explanation
Indices: 126164--126297 Score: 196
Period size: 45 Copynumber: 2.9 Consensus size: 45
126154 CCATGCTTTG
* *
126164 TTATTCACAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC
1 TTATTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
*
126211 TTATTCAAAAAATAAACCTAACCGCGTGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
* * *
126256 TTGTTCGAAAAATAAACTTAACCGCATGATATCTAGTTCGCA
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCA
126298 AGCATTTATT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 65 0.81
46 8 0.10
47 7 0.09
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.29
Consensus pattern (45 bp):
TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
Found at i:133170 original size:22 final size:22
Alignment explanation
Indices: 133115--133182 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
133105 TTTTTCTGTA
*
133115 ATCTTCATTTCTTCTCTTCTTACG
1 ATCTCCATTTCTT-TCTTC-TACG
**
133139 AAATCC-TTTCTTTCTTCTACG
1 ATCTCCATTTCTTTCTTCTACG
*
133160 ATCTCCATTTCTCTCTTCT-CG
1 ATCTCCATTTCTTTCTTCTACG
133181 AT
1 AT
133183 TAAAACTCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
21 12 0.32
22 16 0.43
23 6 0.16
24 3 0.08
ACGTcount: A:0.15, C:0.31, G:0.04, T:0.50
Consensus pattern (22 bp):
ATCTCCATTTCTTTCTTCTACG
Found at i:134443 original size:15 final size:15
Alignment explanation
Indices: 134423--134453 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
134413 TTAGAATGGC
134423 TCAAATGTAAATTTA
1 TCAAATGTAAATTTA
134438 TCAAATGTAAATTTA
1 TCAAATGTAAATTTA
134453 T
1 T
134454 AATTTAGGAA
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:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (15 bp):
TCAAATGTAAATTTA
Found at i:152811 original size:31 final size:31
Alignment explanation
Indices: 152776--152852 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
152766 TGTTTGAAAA
* * * *
152776 GTAACAAATTGATGAATAATATTATCGATTT
1 GTAACAAAATGATCAATAACATTACCGATTT
* * *
152807 GTAACAAAATGGTCACTAACGTTACCGATTT
1 GTAACAAAATGATCAATAACATTACCGATTT
152838 GTAACAAAATGATCA
1 GTAACAAAATGATCA
152853 CCCTACCGCC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (31 bp):
GTAACAAAATGATCAATAACATTACCGATTT
Found at i:154310 original size:31 final size:31
Alignment explanation
Indices: 154252--154312 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
154242 GGTAGGGTGA
**
154252 TCATTTTGTTACAAATCGTTAACGTTAGTGG
1 TCATTTTGTTACAAATCAATAACGTTAGTGG
* *
154283 TCATTTTGTTATAAATCAATAATGTTAGTG
1 TCATTTTGTTACAAATCAATAACGTTAGTG
154313 ACCAATTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (31 bp):
TCATTTTGTTACAAATCAATAACGTTAGTGG
Found at i:155347 original size:33 final size:33
Alignment explanation
Indices: 155299--155385 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
155289 TTAAAAAAAT
*
155299 TTCGGGATCGAGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGG-TCGGGTCGGGTTTTTTTAAGTGTGATA
*
155333 TTCGGGTCGGGTCGGATTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
*
155366 TTCGGGTCAGGTTCGGGTTT
1 TTCGGGTC-GGGTCGGGTTT
155386 AGGGTGAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 33 0.69
34 15 0.31
ACGTcount: A:0.14, C:0.10, G:0.34, T:0.41
Consensus pattern (33 bp):
TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
Found at i:156045 original size:18 final size:18
Alignment explanation
Indices: 155963--156045 Score: 82
Period size: 18 Copynumber: 4.7 Consensus size: 18
155953 AAACAGGTTT
155963 CAGATTCTAATTCC-T-A
1 CAGATTCTAATTCCTTCA
* * *
155979 CATATTCCAATTTCTTCA
1 CAGATTCTAATTCCTTCA
* *
155997 CAGATT-TGAATTTCTTTA
1 CAGATTCT-AATTCCTTCA
156015 CAGATTCTAATTCCTTCA
1 CAGATTCTAATTCCTTCA
*
156033 CATATTCTAATTC
1 CAGATTCTAATTC
156046 TCTCATAAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
16 11 0.20
17 1 0.02
18 41 0.76
19 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.43
Consensus pattern (18 bp):
CAGATTCTAATTCCTTCA
Found at i:156388 original size:21 final size:21
Alignment explanation
Indices: 156355--156399 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
156345 GTTTTGACTA
*
156355 TCGCATTGTGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
156376 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
156397 TCG
1 TCG
156400 TAATGCGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:156458 original size:21 final size:21
Alignment explanation
Indices: 156401--156532 Score: 180
Period size: 21 Copynumber: 6.4 Consensus size: 21
156391 CCTAATTCGT
*
156401 AATGCGAA-TACGTAAATCGC
1 AATGCGAATTACGAAAATCGC
* *
156421 AACGCG-ATTACGTAAATCGC
1 AATGCGAATTACGAAAATCGC
*
156441 AATGCGAATTAGGAAAATCGC
1 AATGCGAATTACGAAAATCGC
*
156462 AATGCGAATTAGGAAAATCGC
1 AATGCGAATTACGAAAATCGC
*
156483 AATGCGAATTAGGAAAATCGC
1 AATGCGAATTACGAAAATCGC
*
156504 AATGCGAA-TACGTAAATCGC
1 AATGCGAATTACGAAAATCGC
156524 AATGCGAAT
1 AATGCGAAT
156533 CTGACTATCG
Statistics
Matches: 103, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
19 1 0.01
20 40 0.39
21 62 0.60
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (21 bp):
AATGCGAATTACGAAAATCGC
Found at i:157223 original size:20 final size:20
Alignment explanation
Indices: 157166--157228 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
157156 TCGCGTTGCG
**
157166 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATTTTC
*
157186 ATT-TCCTCGTTGCAATTTTC
1 ATTCT-CTCGTTGCGATTTTC
157206 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
157226 ATT
1 ATT
157229 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.48
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:159112 original size:94 final size:93
Alignment explanation
Indices: 158923--159298 Score: 580
Period size: 94 Copynumber: 4.1 Consensus size: 93
158913 TAGATTGCTT
* * * *
158923 AGTAAATTTATTCGGTTGCTGCCAATACTACTAAAC--TGT-TT-ATTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
158984 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTATCTTTTGGTTGA
159013 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
159078 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTATCTTTTGGTTG-A
* *
159107 AGTAAATTTGTTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
159172 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTATCTTTTGGTTG-A
* * * * *
159201 AGTAAATTTTTTCGTTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
159266 ATTTGTCTTTGTTTTATCTTTTGGTTGA
66 ATTTGTCTTTGTTTTATCTTTTGGTTGA
159294 AGTAA
1 AGTAA
159299 TGTAATCCAT
Statistics
Matches: 268, Mismatches: 13, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
90 34 0.13
92 3 0.01
93 28 0.10
94 203 0.76
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTATCTTTTGGTTGA
Found at i:159414 original size:20 final size:19
Alignment explanation
Indices: 159387--159477 Score: 102
Period size: 19 Copynumber: 5.0 Consensus size: 19
159377 TCTTTTGGTT
*
159387 GAAATGAAAATTGCAACGA
1 GAAATGAAAATCGCAACGA
*
159406 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
*
159426 GAAACGAAAATCGCAAC--
1 GAAATGAAAATCGCAACGA
*
159443 G--A-GAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
159459 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
159478 CAAAATCGCA
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
14 12 0.19
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 29 0.47
20 17 0.27
ACGTcount: A:0.49, C:0.19, G:0.22, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:159435 original size:39 final size:35
Alignment explanation
Indices: 159387--159510 Score: 130
Period size: 33 Copynumber: 3.5 Consensus size: 35
159377 TCTTTTGGTT
*
159387 GAAATGAAAATTGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-GAAAATCGCAACGC
*
159426 GAAACGAAAATCGCAAC--GAGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAAAATCGCAACGC
*
159459 GAAATGAAAATCGCAAC--GACAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAAAATCGCAACGC
**
159492 GAAACCAAAAATCGCAACG
1 GAAA-TGAAAATCGCAACG
159511 CAAAACTATA
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
33 49 0.64
34 12 0.16
35 1 0.01
39 15 0.19
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.09
Consensus pattern (35 bp):
GAAATGAAAATCGCAACGAGAGAAAATCGCAACGC
Found at i:159436 original size:19 final size:19
Alignment explanation
Indices: 159387--159516 Score: 109
Period size: 20 Copynumber: 7.3 Consensus size: 19
159377 TCTTTTGGTT
* * *
159387 GAAATGAAAATTGCAACGA
1 GAAACGAAAATCGCAACGC
*
159406 GAGAATGAAAATCGCAACGC
1 GA-AACGAAAATCGCAACGC
159426 GAAACGAAAATCGCAA--C
1 GAAACGAAAATCGCAACGC
159443 G--A-GAAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
159459 GAAATGAAAATCGCAA--C
1 GAAACGAAAATCGCAACGC
159476 G--AC-AAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
159492 GAAACCAAAAATCGCAACGC
1 GAAA-CGAAAATCGCAACGC
*
159512 AAAAC
1 GAAAC
159517 TATAATCGCG
Statistics
Matches: 94, Mismatches: 5, Indels: 24
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.22
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 28 0.30
20 33 0.35
ACGTcount: A:0.50, C:0.22, G:0.19, T:0.08
Consensus pattern (19 bp):
GAAACGAAAATCGCAACGC
Found at i:159448 original size:14 final size:14
Alignment explanation
Indices: 159431--159495 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 14
159421 AACGCGAAAC
159431 GAAAATCGCAACGA
1 GAAAATCGCAACGA
159445 GAAAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
159463 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
159478 CAAAATCGCAACGC
1 GAAAATCGCAACGA
159492 GAAA
1 GAAA
159496 CCAAAAATCG
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 26 0.60
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 11 0.26
ACGTcount: A:0.49, C:0.23, G:0.20, T:0.08
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:159515 original size:33 final size:33
Alignment explanation
Indices: 159413--159515 Score: 163
Period size: 33 Copynumber: 3.1 Consensus size: 33
159403 CGAGAGAATG
*
159413 AAAATCGCAACGCGAAACGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
*
159446 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
*
159479 AAAATCGCAACGCGAAACCAAAAATCGCAACG-C
1 AAAATCGCAACGCGAAA-CGAAAATCGCAACGAC
159512 AAAA
1 AAAA
159516 CTATAATCGC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
33 53 0.82
34 12 0.18
ACGTcount: A:0.50, C:0.25, G:0.17, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACGAAAATCGCAACGAC
Found at i:159562 original size:19 final size:19
Alignment explanation
Indices: 159540--159629 Score: 91
Period size: 19 Copynumber: 4.9 Consensus size: 19
159530 TGATTTTTGG
159540 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
159559 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
159575 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
**
159592 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
*
159611 TTTTTCACGTTGCGATTTT
1 --TTTCGCGTTGCGATTTT
159630 AAGTTCCATT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.18
16 3 0.05
17 3 0.05
19 27 0.47
21 14 0.25
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:161537 original size:14 final size:14
Alignment explanation
Indices: 161518--161553 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
161508 ATTGTTTAAT
161518 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
161532 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
161546 TGATTTGT
1 TGATTTGT
161554 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:161685 original size:19 final size:19
Alignment explanation
Indices: 161663--161758 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
161653 AATGACTATT
*
161663 GCAATGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
161682 GCAA--CG--A-GAGAATC
1 GCAACGCGAAATGAAAATC
161696 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
161715 GCAA--CG--A-CAAAATC
1 GCAACGCGAAATGAAAATC
161729 GCAACGCGAAACT-AAAATC
1 GCAACGCGAAA-TGAAAATC
161748 GCAACGCGAAA
1 GCAACGCGAAA
161759 CTAAATTCGC
Statistics
Matches: 63, Mismatches: 3, Indels: 22
0.72 0.03 0.25
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:161710 original size:33 final size:33
Alignment explanation
Indices: 161663--161753 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
161653 AATGACTATT
* * *
161663 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
1 GCAACGCGAAATGAAAATCGCAACGACAAAATC
161696 GCAACGCGAAATGAAAATCGCAACGACAAAATC
1 GCAACGCGAAATGAAAATCGCAACGACAAAATC
161729 GCAACGCGAAACT-AAAATCGCAACG
1 GCAACGCGAAA-TGAAAATCGCAACG
161754 CGAAACTAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.98
34 1 0.02
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (33 bp):
GCAACGCGAAATGAAAATCGCAACGACAAAATC
Found at i:161775 original size:19 final size:19
Alignment explanation
Indices: 161692--161769 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 19
161682 GCAACGAGAG
161692 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
161711 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
161725 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
161744 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
161763 ATTCGCA
1 AATCGCA
161770 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 35 0.67
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:161786 original size:19 final size:19
Alignment explanation
Indices: 161764--161914 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
161754 CGAAACTAAA
161764 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
161783 TTCGCTTTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
161799 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
161816 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
161832 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
161849 TTCTCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
161865 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* **
161882 TTCACATTGCGATAGTCAT
1 TTCGCATTGCGATTTTCAT
*
161901 TTCCGCGTTGCGAT
1 TT-CGCATTGCGAT
161915 AGACATTAAG
Statistics
Matches: 100, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
14 18 0.18
16 19 0.19
17 18 0.18
19 36 0.36
20 9 0.09
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:161812 original size:33 final size:33
Alignment explanation
Indices: 161770--161894 Score: 214
Period size: 33 Copynumber: 3.8 Consensus size: 33
161760 TAAATTCGCA
* *
161770 TTGCGATTTTCATTTCGCTTTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
161803 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
161836 TTGCGATTTTCATTTCTCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
161869 TTGCGATTTTCATTTCACATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
161895 AGTCATTTCC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:161841 original size:14 final size:14
Alignment explanation
Indices: 161789--161876 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
161779 TCATTTCGCT
*
161789 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
161803 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
161820 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
161836 TTGCGATTTTCATTTCTCA
1 TTGCGA--TTC---TCTCG
161855 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
161869 TTGCGATT
1 TTGCGATT
161877 TTCATTTCAC
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 24 0.41
16 10 0.17
17 9 0.15
19 16 0.27
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:161960 original size:20 final size:20
Alignment explanation
Indices: 161888--161960 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
161878 TCATTTCACA
**
161888 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCATG
* ***
161908 TTGCGATAGACATTAAGATG
1 TTGCGATAGTCATTTCCATG
161928 ATTGCGA-ACGTCATTTCCATG
1 -TTGCGATA-GTCATTTCCATG
161949 TTGCGATAGTCA
1 TTGCGATAGTCA
161961 AATGAATGCC
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCATG
Found at i:165388 original size:21 final size:21
Alignment explanation
Indices: 165334--165409 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
165324 GCGATTTACT
* *
165334 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
165354 AAATCG-AAGTGCGAATTAGGA
1 AAATCGCAA-TGCGAATTAGGA
* * *
165375 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
*
165396 AAATTGCAATGCGA
1 AAATCGCAATGCGA
165410 TAGTCAGAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.04
20 10 0.22
21 32 0.70
22 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:169052 original size:18 final size:20
Alignment explanation
Indices: 169010--169052 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
169000 TTTGGTTCAC
* *
169010 GGAAGGTAAGATTATCACTG
1 GGAATGTAAGATTATCACAG
169030 GGAATGTAAGATTA-C-CAG
1 GGAATGTAAGATTATCACAG
169048 GGAAT
1 GGAAT
169053 ACGATTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
20 13 0.62
ACGTcount: A:0.37, C:0.09, G:0.30, T:0.23
Consensus pattern (20 bp):
GGAATGTAAGATTATCACAG
Found at i:172087 original size:18 final size:18
Alignment explanation
Indices: 172064--172098 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
172054 ATTTTTATTG
172064 AATAAAAATAATATTTTT
1 AATAAAAATAATATTTTT
* *
172082 AATAAATATATTATTTT
1 AATAAAAATAATATTTT
172099 AGGTCGGATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAAAAATAATATTTTT
Found at i:177183 original size:39 final size:36
Alignment explanation
Indices: 177075--177195 Score: 154
Period size: 36 Copynumber: 3.3 Consensus size: 36
177065 TGGTAAATAG
*
177075 ATCATGCATATAATCATTAGTAGCAAGCACATGTAT
1 ATCATGCATATAATCATCAGTAGCAAGCACATGTAT
* *
177111 ATCATGCATATAATCATCAATTGCAAG-AGCATGTAT
1 ATCATGCATATAATCATCAGTAGCAAGCA-CATGTAT
* *
177147 ATAATGCATATAATGATCATCAGTAGCCAGCACATGTAT
1 ATCATGCATAT-A--ATCATCAGTAGCAAGCACATGTAT
177186 ATCATGCATA
1 ATCATGCATA
177196 GGAACATTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
35 1 0.01
36 41 0.57
37 1 0.01
39 28 0.39
40 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (36 bp):
ATCATGCATATAATCATCAGTAGCAAGCACATGTAT
Found at i:178362 original size:107 final size:107
Alignment explanation
Indices: 178176--178389 Score: 419
Period size: 107 Copynumber: 2.0 Consensus size: 107
178166 CTCCATATTC
178176 AATACTACATAGCATGATCTCAAATTAACATACATCATTATAGGACCAATACACACATCTCATTT
1 AATACTACATAGCATGATCTCAAATTAACATACATCATTATAGGACCAATACACACATCTCATTT
178241 TATGAAGCATACTCAATAAACACTCACTCTATTCGATCATAT
66 TATGAAGCATACTCAATAAACACTCACTCTATTCGATCATAT
*
178283 AATACTACATAGCATGATCTCAAATTAACATACATCATTATAGGACTAATACACACATCTCATTT
1 AATACTACATAGCATGATCTCAAATTAACATACATCATTATAGGACCAATACACACATCTCATTT
178348 TATGAAGCATACTCAATAAACACTCACTCTATTCGATCATAT
66 TATGAAGCATACTCAATAAACACTCACTCTATTCGATCATAT
178390 GCTTTTCTTA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 106 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (107 bp):
AATACTACATAGCATGATCTCAAATTAACATACATCATTATAGGACCAATACACACATCTCATTT
TATGAAGCATACTCAATAAACACTCACTCTATTCGATCATAT
Found at i:179993 original size:3 final size:3
Alignment explanation
Indices: 179987--180027 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
179977 TCTTCTTCTT
179987 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
180028 TCTTCTTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CTC
Found at i:182307 original size:31 final size:31
Alignment explanation
Indices: 182269--182424 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
182259 CCCGAAGGAC
* * *
182269 CAGTCCATA-GATCTCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
182300 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
182331 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
182362 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
182393 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
182424 C
1 C
182425 CCTCGACTCT
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:184409 original size:2 final size:2
Alignment explanation
Indices: 184402--184427 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
184392 ATGTAATTTA
184402 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
184428 TACTCGACCA
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:188392 original size:11 final size:11
Alignment explanation
Indices: 188376--188410 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
188366 CTCAATTATT
188376 TATTTAAATTA
1 TATTTAAATTA
188387 TATTTAATATTA
1 TATTTAA-ATTA
*
188399 TATTTTAATTA
1 TATTTAAATTA
188410 T
1 T
188411 CATCTTCCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTAAATTA
Found at i:188400 original size:12 final size:12
Alignment explanation
Indices: 188372--188403 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
188362 ATCACTCAAT
188372 TATT-TATTTAA
1 TATTATATTTAA
188383 -ATTATATTTAA
1 TATTATATTTAA
188394 TATTATATTT
1 TATTATATTT
188404 TAATTATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.16
11 7 0.37
12 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTATATTTAA
Found at i:188936 original size:18 final size:17
Alignment explanation
Indices: 188913--188950 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
188903 TTTTTATTAG
*
188913 GTTAAATTATTTAAAACT
1 GTTAAAATATTTAAAA-T
188931 GTTAAAATATTTAAAAT
1 GTTAAAATATTTAAAAT
188948 GTT
1 GTT
188951 TTATTCATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (17 bp):
GTTAAAATATTTAAAAT
Found at i:190041 original size:19 final size:19
Alignment explanation
Indices: 190017--190055 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
190007 TTTGGATACG
190017 AATATCGAAACTCCCAGAA
1 AATATCGAAACTCCCAGAA
190036 AATATCGAAACTCCCAGAA
1 AATATCGAAACTCCCAGAA
190055 A
1 A
190056 GTATTAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (19 bp):
AATATCGAAACTCCCAGAA
Found at i:190065 original size:19 final size:19
Alignment explanation
Indices: 190017--190066 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
190007 TTTGGATACG
*
190017 AATATCGAAACTCCCAGAA
1 AATATCAAAACTCCCAGAA
*
190036 AATATCGAAACTCCCAGAA
1 AATATCAAAACTCCCAGAA
* *
190055 AGTATTAAAACT
1 AATATCAAAACT
190067 AGATAGAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.48, C:0.22, G:0.10, T:0.20
Consensus pattern (19 bp):
AATATCAAAACTCCCAGAA
Found at i:201774 original size:6 final size:6
Alignment explanation
Indices: 201765--201795 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
201755 TTGGTTCCTA
*
201765 GCTTTA GCTTTG GCTTTG GCTTTG GCTTTG G
1 GCTTTG GCTTTG GCTTTG GCTTTG GCTTTG G
201796 ATTGTACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.16, G:0.32, T:0.48
Consensus pattern (6 bp):
GCTTTG
Found at i:202535 original size:2 final size:2
Alignment explanation
Indices: 202528--202579 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
202518 AAATTTATTA
202528 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
202570 AT AT AT AT AT
1 AT AT AT AT AT
202580 GGATAATTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:206519 original size:18 final size:19
Alignment explanation
Indices: 206498--206544 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
206488 GTAAAAAGAT
*
206498 ATTAAAAT-AATAAAAGTG
1 ATTAAAATAAATAAAAGTA
206516 ATT-AAATAAATAAAAGTA
1 ATTAAAATAAATAAAAGTA
*
206534 ATTAAAGTAAA
1 ATTAAAATAAA
206545 AATAAGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 15 0.60
19 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (19 bp):
ATTAAAATAAATAAAAGTA
Done.