Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008942.1 Hibiscus syriacus cultivar Beakdansim tig00112261_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: 2383254
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2220815 original size:14 final size:14
Alignment explanation
Indices: 2220779--2220886 Score: 78
Period size: 14 Copynumber: 7.8 Consensus size: 14
2220769 ATTTACGATC
2220779 TAGGGTTTAAGATT
1 TAGGGTTTAAGATT
* * *
2220793 TAAGTTTTAAGTTT
1 TAGGGTTTAAGATT
* * *
2220807 TATGGTTTATGACT
1 TAGGGTTTAAGATT
* *
2220821 TGGGGTTTATGATT
1 TAGGGTTTAAGATT
*
2220835 TATGGTTTAAGATT
1 TAGGGTTTAAGATT
2220849 TAGGGTTT-AGATAT
1 TAGGGTTTAAGAT-T
* *
2220863 T--GATGTAAGATTT
1 TAGGGTTTAAGA-TT
2220876 TAGGGTTTAAG
1 TAGGGTTTAAG
2220887 GTTTCATGGT
Statistics
Matches: 70, Mismatches: 19, Indels: 9
0.71 0.19 0.09
Matches are distributed among these distances:
12 3 0.04
13 9 0.13
14 52 0.74
15 6 0.09
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.47
Consensus pattern (14 bp):
TAGGGTTTAAGATT
Found at i:2229288 original size:17 final size:17
Alignment explanation
Indices: 2229184--2229289 Score: 77
Period size: 17 Copynumber: 6.1 Consensus size: 17
2229174 AATTAAGAGT
*
2229184 TAGTTTAATAAATGAAC
1 TAGTTTAATGAATGAAC
*
2229201 TAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
* *
2229218 TAGTTTAATTAATGGAC
1 TAGTTTAATGAATGAAC
* * *
2229235 TAACTTTATTCAATGAAC
1 T-AGTTTAATGAATGAAC
* * ** *
2229253 TTGTAATCTTGAATAAAC
1 TAGT-TTAATGAATGAAC
*
2229271 TAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
2229288 TA
1 TA
2229290 CTTAGTTAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
17 42 0.63
18 25 0.37
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:2232365 original size:22 final size:22
Alignment explanation
Indices: 2232345--2232396 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
2232335 AAAATATATT
2232345 TATTAATATTTCTAATAATATAA
1 TATT-ATATTTCTAATAATATAA
* *
2232368 TATTATATTTTTAATATTATAA
1 TATTATATTTCTAATAATATAA
*
2232390 TAATATA
1 TATTATA
2232397 AGATATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTATATTTCTAATAATATAA
Found at i:2232403 original size:32 final size:31
Alignment explanation
Indices: 2232339--2232438 Score: 114
Period size: 32 Copynumber: 3.1 Consensus size: 31
2232329 ATTTTTAAAA
*
2232339 TATATTTATTAATATTTCTAATAATAT-AATAT
1 TATATTT-TTAATA-TTATAATAATATAAATAT
2232371 TATATTTTTAATATTATAATAATATAAGATAT
1 TATATTTTTAATATTATAATAATATAA-ATAT
2232403 TATATTTTT-ATATTAATAATATATAATAAAATAT
1 TATATTTTTAATATT-ATAATA-AT-AT-AAATAT
2232437 TA
1 TA
2232439 ATAAAATTTA
Statistics
Matches: 61, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
30 11 0.18
31 12 0.20
32 26 0.43
33 2 0.03
34 8 0.13
35 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
TATATTTTTAATATTATAATAATATAAATAT
Found at i:2232440 original size:11 final size:11
Alignment explanation
Indices: 2232412--2232445 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2232402 TTATATTTTT
*
2232412 ATATTAATAAT
1 ATATTAATAAA
2232423 ATA-TAATAAA
1 ATATTAATAAA
2232433 ATATTAATAAA
1 ATATTAATAAA
2232444 AT
1 AT
2232446 TTATATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATTAATAAA
Found at i:2232487 original size:27 final size:25
Alignment explanation
Indices: 2232434--2232508 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 25
2232424 TATAATAAAA
* *
2232434 TATTAATAA-AATTTATATTATTTAT
1 TATTAATAAGAA-TAATATTATTAAT
*
2232459 TAATTCAT-AGAAATAATATTATTAAAT
1 T-ATTAATAAG-AATAATATTATT-AAT
2232486 TATTAATAATGAATAATATTATT
1 TATTAATAA-GAATAATATTATT
2232509 TATATATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
25 2 0.05
26 19 0.47
27 18 0.45
28 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (25 bp):
TATTAATAAGAATAATATTATTAAT
Found at i:2232508 original size:19 final size:19
Alignment explanation
Indices: 2232472--2232552 Score: 62
Period size: 19 Copynumber: 4.3 Consensus size: 19
2232462 TTCATAGAAA
*
2232472 TAAT-ATTATTAA-ATTAT
1 TAATAATTAATAATATTAT
*
2232489 TAATAATGAATAATATTATT
1 TAATAATTAATAATATTA-T
* * *
2232509 TATATATTTAATACTAATA-
1 TA-ATAATTAATAATATTAT
2232528 TAATAATCTAATAATATT-T
1 TAATAAT-TAATAATATTAT
2232547 TAATAA
1 TAATAA
2232553 AGATATTTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
17 4 0.08
18 10 0.20
19 20 0.41
20 3 0.06
21 12 0.24
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (19 bp):
TAATAATTAATAATATTAT
Found at i:2232527 original size:27 final size:27
Alignment explanation
Indices: 2232357--2232527 Score: 77
Period size: 27 Copynumber: 6.2 Consensus size: 27
2232347 TTAATATTTC
* *
2232357 TAATAATATAATATTATATTTTTAATATTA
1 TAATAATATTAT-TTATATATTTAATA--A
* * *
2232387 TAATAATATAAGATATTATAT-TTTTATAT
1 TAATAATAT--TAT-TTATATATTTAATAA
* * *
2232416 TAATAATATATAATAAAATA-TTAATAA
1 TAATAATAT-TATTTATATATTTAATAA
* * *
2232443 -AATTTATATTATTTAT-TAATTCATAGA
1 TAA-TAATATTATTTATATATTTAATA-A
*
2232470 -AATAATATTA-TTAAAT-TATTAATAA
1 TAATAATATTATTTATATAT-TTAATAA
*
2232495 TGAATAATATTATTTATATATTTAATAC
1 T-AATAATATTATTTATATATTTAATAA
2232523 TAATA
1 TAATA
2232528 TAATAATCTA
Statistics
Matches: 109, Mismatches: 20, Indels: 27
0.70 0.13 0.17
Matches are distributed among these distances:
25 6 0.06
26 24 0.22
27 31 0.28
28 14 0.13
29 10 0.09
30 9 0.08
31 6 0.06
32 9 0.08
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (27 bp):
TAATAATATTATTTATATATTTAATAA
Found at i:2235521 original size:17 final size:17
Alignment explanation
Indices: 2235482--2235521 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2235472 ATAATAAACT
*
2235482 TATGATAATTAAATTAT
1 TATGATAATTAAATTAA
*
2235499 TTTGATAATTAAATTAA
1 TATGATAATTAAATTAA
2235516 TATGAT
1 TATGAT
2235522 TACTTTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
TATGATAATTAAATTAA
Found at i:2235746 original size:15 final size:15
Alignment explanation
Indices: 2235706--2235746 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2235696 AAATTAAATT
* * *
2235706 TAAATATTATCTTAT
1 TAAATTTTATTTTAA
2235721 TAAATTTTATTTTAA
1 TAAATTTTATTTTAA
2235736 TAAATTTTATT
1 TAAATTTTATT
2235747 AATTAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
TAAATTTTATTTTAA
Found at i:2236845 original size:14 final size:17
Alignment explanation
Indices: 2236782--2236844 Score: 99
Period size: 17 Copynumber: 3.5 Consensus size: 17
2236772 TACAAAATAT
2236782 TAATACTAATAATTATTA
1 TAATA-TAATAATTATTA
2236800 TAATTTATAATAATTATTA
1 TAA--TATAATAATTATTA
2236819 TAATATAATAATTATTA
1 TAATATAATAATTATTA
2236836 TAATATAAT
1 TAATATAAT
2236845 TTTTTATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
17 23 0.53
18 3 0.07
19 15 0.35
20 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATATAATAATTATTA
Found at i:2236972 original size:35 final size:33
Alignment explanation
Indices: 2236960--2237035 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
2236950 TCAACTTTAG
*
2236960 TATATATATAGTTCGTATGTAAACTATATAGTT
1 TATATATATAGTTCATATGTAAACTATATAGTT
2236993 TATATATATAGTTCATATGTAAAC--TATAGTT
1 TATATATATAGTTCATATGTAAACTATATAGTT
*
2237024 CATATATATAGT
1 TATATATATAGT
2237036 ATATAAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 18 0.44
33 23 0.56
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.45
Consensus pattern (33 bp):
TATATATATAGTTCATATGTAAACTATATAGTT
Found at i:2237002 original size:13 final size:13
Alignment explanation
Indices: 2236984--2237069 Score: 55
Period size: 13 Copynumber: 6.2 Consensus size: 13
2236974 GTATGTAAAC
2236984 TATATAGTTTATA
1 TATATAGTTTATA
2236997 TATATAGTTCATATGTA
1 TATATAGTT--TA--TA
* *
2237014 AACTATAGTTCATA
1 TA-TATAGTTTATA
*
2237028 TATATAGTATATA
1 TATATAGTTTATA
* **
2237041 AATATAAATTATA
1 TATATAGTTTATA
*
2237054 GTATGTAGTTTATA
1 -TATATAGTTTATA
2237068 TA
1 TA
2237070 AATATAAATA
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
13 29 0.54
14 12 0.22
15 2 0.04
16 1 0.02
17 3 0.06
18 7 0.13
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:2237038 original size:18 final size:17
Alignment explanation
Indices: 2236993--2237038 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2236983 CTATATAGTT
2236993 TATATATATAGTTCATA
1 TATATATATAGTTCATA
* *
2237010 TGTAAACTATAGTTCATA
1 TATATA-TATAGTTCATA
2237028 TATATAGTATA
1 TATATA-TATA
2237039 TAAATATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (17 bp):
TATATATATAGTTCATA
Found at i:2237126 original size:42 final size:42
Alignment explanation
Indices: 2237079--2237176 Score: 178
Period size: 42 Copynumber: 2.3 Consensus size: 42
2237069 AAATATAAAT
2237079 ATAAACCCTAAACCCTAAACCCAACCTACTAAATCATGATCC
1 ATAAACCCTAAACCCTAAACCCAACCTACTAAATCATGATCC
*
2237121 ATAAACCCTAAACCCTAAACCTAACCTACTAAATCATGATCC
1 ATAAACCCTAAACCCTAAACCCAACCTACTAAATCATGATCC
*
2237163 CTAAACCCTAAACC
1 ATAAACCCTAAACC
2237177 ATATATTATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.43, C:0.36, G:0.02, T:0.19
Consensus pattern (42 bp):
ATAAACCCTAAACCCTAAACCCAACCTACTAAATCATGATCC
Found at i:2238457 original size:2 final size:2
Alignment explanation
Indices: 2238450--2238621 Score: 57
Period size: 2 Copynumber: 81.0 Consensus size: 2
2238440 ACATATAGTT
* * *
2238450 TA TA TA TA -A TA TA GA TA TA TA AA CTA TA TA GT- TCA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA T-A TA TA TA
* *
2238491 AA T- TA TA CTA TA TA GTA TA TA TA GTT TA TA TA TA TA -A TA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
2238532 TA GTA TA TA AA TA TA AA CTA TA GCA TA TA TA TA TA CA TG TCA TA
1 TA -TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA T-A TA
* * *
2238576 TG TA AA CTA TA TA GTA TA TA AA TA TCA -A CTA TA GTA TA TA TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA T-A TA -TA TA -TA TA TA TA TA
2238620 TA
1 TA
2238622 GGTCATATGT
Statistics
Matches: 124, Mismatches: 26, Indels: 40
0.65 0.14 0.21
Matches are distributed among these distances:
1 5 0.04
2 99 0.80
3 20 0.16
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (2 bp):
TA
Found at i:2238513 original size:9 final size:9
Alignment explanation
Indices: 2238442--2238540 Score: 54
Period size: 9 Copynumber: 11.3 Consensus size: 9
2238432 TGTTTTCAAC
*
2238442 ATATAGTTT
1 ATATAGTAT
2238451 ATATA-TA-
1 ATATAGTAT
2238458 ATATAG-AT
1 ATATAGTAT
*
2238466 ATATA-AACT
1 ATATAGTA-T
2238475 ATATAGT-T
1 ATATAGTAT
*
2238483 CATAT-GTAA
1 -ATATAGTAT
2238492 AT-TA-TACT
1 ATATAGTA-T
2238500 ATATAGTAT
1 ATATAGTAT
2238509 ATATAGTTTAT
1 ATATAG--TAT
2238520 ATATA-TAAT
1 ATATAGT-AT
2238529 ATATAGTAT
1 ATATAGTAT
2238538 ATA
1 ATA
2238541 AATATAAACT
Statistics
Matches: 71, Mismatches: 4, Indels: 30
0.68 0.04 0.29
Matches are distributed among these distances:
7 9 0.13
8 15 0.21
9 36 0.51
10 3 0.04
11 8 0.11
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.44
Consensus pattern (9 bp):
ATATAGTAT
Found at i:2238524 original size:20 final size:20
Alignment explanation
Indices: 2238494--2238566 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
2238484 ATATGTAAAT
2238494 TATACTATATAGT-ATATATAG
1 TATA-TATATA-TAATATATAG
*
2238515 TTTATATATATAATATATAG
1 TATATATATATAATATATAG
*
2238535 TATATAAATATAA-ACTATAG
1 TATATATATATAATA-TATAG
*
2238555 CATATATATATA
1 TATATATATATA
2238567 CATGTCATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 40 0.89
21 3 0.07
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (20 bp):
TATATATATATAATATATAG
Found at i:2238553 original size:29 final size:29
Alignment explanation
Indices: 2238450--2238566 Score: 84
Period size: 29 Copynumber: 4.1 Consensus size: 29
2238440 ACATATAGTT
*
2238450 TATATATAATATAGATATATAAACTATATAG
1 TATATATAATATAAATATAT-AA-TATATAG
* * *
2238481 T-T-CAT-ATGTAAAT-TATACTATATAG
1 TATATATAATATAAATATATAATATATAG
* * *
2238506 TATATATAGTTTATATATATAATATATAG
1 TATATATAATATAAATATATAATATATAG
**
2238535 TATATA-AATATAAACTATAGCATATATA-
1 TATATATAATATAAA-TATATAATATATAG
2238563 TATA
1 TATA
2238567 CATGTCATAT
Statistics
Matches: 67, Mismatches: 14, Indels: 13
0.71 0.15 0.14
Matches are distributed among these distances:
25 8 0.12
26 2 0.03
27 5 0.07
28 20 0.30
29 30 0.45
30 1 0.01
31 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (29 bp):
TATATATAATATAAATATATAATATATAG
Found at i:2238617 original size:53 final size:54
Alignment explanation
Indices: 2238528--2238654 Score: 193
Period size: 53 Copynumber: 2.4 Consensus size: 54
2238518 ATATATATAA
*
2238528 TATATAGTATATAAATATAAACTATAGCATATATATATACATGTCATATGTAAAC
1 TATATAGTATATAAATATAAACTATAG-ATATATATATACAGGTCATATGTAAAC
* *
2238583 TATATAGTATATAAATATCAACTATAG-TATATATATATAGGTCATATGTAAAC
1 TATATAGTATATAAATATAAACTATAGATATATATATACAGGTCATATGTAAAC
* *
2238636 TATATAGTTTATATATATA
1 TATATAGTATATAAATATA
2238655 TAGTTCATAG
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
53 40 0.61
55 26 0.39
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (54 bp):
TATATAGTATATAAATATAAACTATAGATATATATATACAGGTCATATGTAAAC
Found at i:2238639 original size:20 final size:19
Alignment explanation
Indices: 2238616--2238712 Score: 55
Period size: 20 Copynumber: 5.2 Consensus size: 19
2238606 ATAGTATATA
2238616 TATATAGGTCATATGTAAAC
1 TATATAGGT-ATATGTAAAC
* *
2238636 TATATA-GT-T-TATATA-
1 TATATAGGTATATGTAAAC
* *
2238651 TATATAGTTCATAGGTAAAC
1 TATATAGGT-ATATGTAAAC
2238671 TATAGTTA-GTATA--TAAAC
1 TATA--TAGGTATATGTAAAC
*
2238689 TATATAGTTTATATGTAAAC
1 TATATAG-GTATATGTAAAC
2238709 TATA
1 TATA
2238713 GTTCATATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 22
0.66 0.09 0.25
Matches are distributed among these distances:
15 6 0.10
16 7 0.12
17 1 0.02
18 14 0.24
19 5 0.09
20 22 0.38
21 1 0.02
22 2 0.03
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.41
Consensus pattern (19 bp):
TATATAGGTATATGTAAAC
Found at i:2238653 original size:128 final size:126
Alignment explanation
Indices: 2238508--2238780 Score: 315
Period size: 128 Copynumber: 2.1 Consensus size: 126
2238498 CTATATAGTA
*
2238508 TATATAGTTTATATATATAATA-T-ATAGTATATAAATATAAACTATAGCATATATA-TATACA-
1 TATATAGTTTATATATAT-ATAGTCATAG-ATA-AAATAT--ACT-TAGCATATAAACTATACAG
2238569 TGTCATATGTAAACTATA-T-AGTATATAAATATCAACTATAGTATATATATATAGGTCATATGT
60 T-TCATATGTAAACTATAGTCA-TATATAAATATCAACTATAGTATATATATATAGGTCATATGT
2238632 AAAC
123 AAAC
* * * * * *
2238636 TATATAGTTTATATATATATAGTTCATAGGTAAACTATAGTTAGTATATAAACTATATAGTTTAT
1 TATATAGTTTATATATATATAG-TCATAGATAAAATATACTTAGCATATAAACTATACAGTTCAT
* * * *
2238701 ATGTAAACTATAGTTCATATATAAATATCAACTTTAGTATATATATATAGTTCTTCTGTAAAC
65 ATGTAAACTATAG-TCATATATAAATATCAACTATAGTATATATATATAGGTCATATGTAAAC
2238764 TATATAGTTTATATATA
1 TATATAGTTTATATATA
2238781 GAGAAAATCG
Statistics
Matches: 126, Mismatches: 11, Indels: 16
0.82 0.07 0.10
Matches are distributed among these distances:
125 9 0.07
126 22 0.17
127 4 0.03
128 83 0.66
129 4 0.03
130 4 0.03
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (126 bp):
TATATAGTTTATATATATATAGTCATAGATAAAATATACTTAGCATATAAACTATACAGTTCATA
TGTAAACTATAGTCATATATAAATATCAACTATAGTATATATATATAGGTCATATGTAAAC
Found at i:2238656 original size:35 final size:36
Alignment explanation
Indices: 2238610--2238714 Score: 140
Period size: 35 Copynumber: 2.9 Consensus size: 36
2238600 TCAACTATAG
* *
2238610 TATATATATATAGGTCATATGTAAACTATA-TAGTT
1 TATATATATATAGTTCATATGTAAACTATAGTAGTA
*
2238645 TATATATATATAGTTCATAGGTAAACTATAGTTAGTA
1 TATATATATATAGTTCATATGTAAACTATAG-TAGTA
* *
2238682 TATAAACTATATAGTTTATATGTAAACTATAGT
1 TATATA-TATATAGTTCATATGTAAACTATAGT
2238715 TCATATATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 28 0.46
37 10 0.16
38 23 0.38
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (36 bp):
TATATATATATAGTTCATATGTAAACTATAGTAGTA
Found at i:2238676 original size:18 final size:18
Alignment explanation
Indices: 2238618--2238725 Score: 80
Period size: 18 Copynumber: 5.9 Consensus size: 18
2238608 AGTATATATA
*
2238618 TATAGGTCATATGTAAAC
1 TATAGTTCATATGTAAAC
* *
2238636 TATATAGTT--TATATATA-
1 --TATAGTTCATATGTAAAC
*
2238653 TATAGTTCATAGGTAAAC
1 TATAGTTCATATGTAAAC
*
2238671 TATAGTT-AGTATATAAAC
1 TATAGTTCA-TATGTAAAC
*
2238689 TATATAGTTTATATGTAAAC
1 --TATAGTTCATATGTAAAC
*
2238709 TATAGTTCATATATAAA
1 TATAGTTCATATGTAAA
2238726 TATCAACTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
15 7 0.10
17 6 0.09
18 35 0.50
20 21 0.30
21 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:2238887 original size:19 final size:20
Alignment explanation
Indices: 2238863--2238913 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2238853 AATGACCAAT
2238863 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
2238882 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
2238902 AAAATCGCAACG
1 AAAATCGCAACG
2238914 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:2238907 original size:20 final size:20
Alignment explanation
Indices: 2238863--2239120 Score: 117
Period size: 20 Copynumber: 12.6 Consensus size: 20
2238853 AATGACCAAT
* *
2238863 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
2238882 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
2238902 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
2238922 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
2238942 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
2238963 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
2238986 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
2239006 TGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
2239026 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
2239046 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
2239069 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
2239089 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
2239109 AGAATCGCAACG
1 AAAATCGCAACG
2239121 TTAAAAAGAA
Statistics
Matches: 186, Mismatches: 41, Indels: 23
0.74 0.16 0.09
Matches are distributed among these distances:
19 17 0.09
20 126 0.68
21 14 0.08
23 29 0.16
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:2239134 original size:20 final size:20
Alignment explanation
Indices: 2239111--2239150 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2239101 CGATTGAGAG
*
2239111 AATCGCAACGTTAAAAAGAA
1 AATCGCAACGGTAAAAAGAA
*
2239131 AATCGCAACGGTCAAAAGAA
1 AATCGCAACGGTAAAAAGAA
2239151 TAGTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGGTAAAAAGAA
Found at i:2239137 original size:83 final size:83
Alignment explanation
Indices: 2238967--2239140 Score: 231
Period size: 83 Copynumber: 2.1 Consensus size: 83
2238957 GCTTCCAAGT
* ** * *
2238967 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
* *** * *
2239032 GCAATGCGATTGAGAGAG
66 GCAACGCGAAAAAGAAAA
2239050 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
**
2239115 GCAACGTTAAAAAGAAAA
66 GCAACGCGAAAAAGAAAA
2239133 TCGCAACG
1 TCGCAACG
2239141 GTCAAAAGAA
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
GCAACGCGAAAAAGAAAA
Found at i:2239239 original size:6 final size:6
Alignment explanation
Indices: 2239228--2239343 Score: 225
Period size: 6 Copynumber: 19.5 Consensus size: 6
2239218 GACACGTATT
2239228 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2239276 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2239324 ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
2239344 CGAGACGAGA
Statistics
Matches: 110, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.05
6 105 0.95
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2240053 original size:6 final size:6
Alignment explanation
Indices: 2240032--2240086 Score: 96
Period size: 6 Copynumber: 9.5 Consensus size: 6
2240022 TCTCGTCTCG
2240032 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2240078 GGTCGT GGT
1 GGTCGT GGT
2240087 AATACGTGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.20
6 39 0.80
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:2240189 original size:20 final size:20
Alignment explanation
Indices: 2240164--2240207 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2240154 TTTTTAACTA
*
2240164 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
2240184 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
2240204 TTCT
1 TTCT
2240208 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:2240217 original size:20 final size:20
Alignment explanation
Indices: 2240194--2240491 Score: 143
Period size: 20 Copynumber: 14.6 Consensus size: 20
2240184 TTCTTTTTAA
2240194 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
2240214 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
2240234 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
2240254 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * * *
2240274 CATTGCGAATCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
2240294 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
2240317 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
2240337 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
2240357 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
2240380 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
2240401 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
2240419 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
2240441 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
2240461 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
2240480 CGTTGCGATTTT
1 CGTTGCGATTTT
2240492 ATTGGTCATT
Statistics
Matches: 225, Mismatches: 42, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 160 0.71
21 14 0.06
22 5 0.02
23 27 0.12
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:2240240 original size:40 final size:40
Alignment explanation
Indices: 2240196--2240366 Score: 216
Period size: 40 Copynumber: 4.2 Consensus size: 40
2240186 CTTTTTAACG
* * *
2240196 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* *
2240236 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* * *
2240276 TTGCGAATCTCTCAGTCGCATTGCGATTCTCTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCATTGCGATTCTC-TC--AATCGCA
* **
2240319 TTGCGACTCTCTCAATCGCATTGCGATTCAATCAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
2240359 TTGCGATT
1 TTGCGATT
2240367 TTCTTCTAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
40 78 0.68
41 2 0.02
42 2 0.02
43 32 0.28
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.35
Consensus pattern (40 bp):
TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
Found at i:2240344 original size:63 final size:63
Alignment explanation
Indices: 2240194--2240387 Score: 259
Period size: 63 Copynumber: 3.1 Consensus size: 63
2240184 TTCTTTTTAA
* * * *
2240194 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTC-TC--AGTCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTTCTAAATCG
* * * *
2240254 CATTGCGATTCTCTCAGTCGCATTGCGAATCTCTCAGTCGCATTGCGATTCTCTTCTAAATCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTTCTAAATCG
* ** *
2240317 CGTTGCGACTCTCTCAATCGCATTGCGATTCAATCAATCGCATTGCGATTTTCTTCTAAATCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTTCTAAATCG
2240380 CGTTGCGA
1 CGTTGCGA
2240388 ACTTGGAAGC
Statistics
Matches: 115, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
60 46 0.40
61 2 0.02
63 67 0.58
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (63 bp):
CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTTCTAAATCG
Found at i:2240481 original size:19 final size:20
Alignment explanation
Indices: 2240441--2240491 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2240431 TTCTTTTTAA
*
2240441 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
2240461 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
2240480 CGTTGCGATTTT
1 CGTTGCGATTTT
2240492 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:2240614 original size:31 final size:32
Alignment explanation
Indices: 2240576--2240670 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 32
2240566 ATTTTCTCTT
*
2240576 ATATATATAGT-TCAT-ATGTAAACTATAGTTC
1 ATATATATAGTAT-ATAATATAAACTATAGTTC
*
2240607 ATATATATAGTATATAAATATAAACTATAGTTT
1 ATATATATAGTATAT-AATATAAACTATAGTTC
* *
2240640 ATATAAATAGTATATAAATATAAATTATAGT
1 ATATATATAGTATAT-AATATAAACTATAGT
2240671 ATGTAGTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
31 13 0.23
32 1 0.02
33 43 0.75
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.41
Consensus pattern (32 bp):
ATATATATAGTATATAATATAAACTATAGTTC
Found at i:2240620 original size:18 final size:17
Alignment explanation
Indices: 2240575--2240620 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2240565 GATTTTCTCT
2240575 TATATATATAGTTCATA
1 TATATATATAGTTCATA
* *
2240592 TGTAAACTATAGTTCATA
1 TATATA-TATAGTTCATA
2240610 TATATAGTATA
1 TATATA-TATA
2240621 TAAATATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (17 bp):
TATATATATAGTTCATA
Found at i:2240631 original size:33 final size:33
Alignment explanation
Indices: 2240594--2240670 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
2240584 AGTTCATATG
*
2240594 TAAACTATAGTTCATATATATAGTATATAAATA
1 TAAACTATAGTTCATATAAATAGTATATAAATA
*
2240627 TAAACTATAGTTTATATAAATAGTATATAAATA
1 TAAACTATAGTTCATATAAATAGTATATAAATA
*
2240660 TAAATTATAGT
1 TAAACTATAGT
2240671 ATGTAGTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.40
Consensus pattern (33 bp):
TAAACTATAGTTCATATAAATAGTATATAAATA
Found at i:2240635 original size:20 final size:19
Alignment explanation
Indices: 2240611--2240672 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
2240601 TAGTTCATAT
2240611 ATATAGTATATAAATATAA
1 ATATAGTATATAAATATAA
2240630 ACTATAGT-T-T--ATAT-A
1 A-TATAGTATATAAATATAA
2240645 A-ATAGTATATAAATATAA
1 ATATAGTATATAAATATAA
2240663 ATTATAGTAT
1 A-TATAGTAT
2240673 GTAGTTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 15
0.70 0.00 0.30
Matches are distributed among these distances:
13 5 0.14
14 1 0.03
15 3 0.09
16 4 0.11
17 4 0.11
18 3 0.09
19 2 0.06
20 13 0.37
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (19 bp):
ATATAGTATATAAATATAA
Found at i:2240725 original size:21 final size:21
Alignment explanation
Indices: 2240701--2240758 Score: 98
Period size: 21 Copynumber: 2.7 Consensus size: 21
2240691 AATATACACT
2240701 CTAAACCCTAATACTTAAACC
1 CTAAACCCTAATACTTAAACC
2240722 CTAAACCCTAATACTTAAACC
1 CTAAACCCTAATACTTAAACC
*
2240743 CTAAACCATATATACT
1 CTAAACCCTA-ATACT
2240759 ATATATATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 30 0.86
22 5 0.14
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (21 bp):
CTAAACCCTAATACTTAAACC
Found at i:2240805 original size:22 final size:22
Alignment explanation
Indices: 2240751--2240807 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
2240741 CCCTAAACCA
* *
2240751 TATATACTATATATATAAAAAC
1 TATATAATTTATATATAAAAAC
*
2240773 TATATAGTTTATAT-TAATAAAC
1 TATATAATTTATATATAA-AAAC
2240795 TATATAATTTATA
1 TATATAATTTATA
2240808 CAATATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (22 bp):
TATATAATTTATATATAAAAAC
Found at i:2240836 original size:17 final size:17
Alignment explanation
Indices: 2240798--2240848 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
2240788 AATAAACTAT
*
2240798 ATAATTTATACAATATAT
1 ATAATTTATA-AATATAC
*
2240816 ATAATTTATAATTATAC
1 ATAATTTATAAATATAC
*
2240833 ATAATATATAAATATA
1 ATAATTTATAAATATA
2240849 AATTGTATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 19 0.66
18 10 0.34
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATTTATAAATATAC
Found at i:2240839 original size:24 final size:25
Alignment explanation
Indices: 2240797--2240843 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
2240787 TAATAAACTA
2240797 TATAATTTATACAATATATATAATT
1 TATAATTTATACAATATATATAATT
2240822 TATAA-TTATAC-ATAATATATAA
1 TATAATTTATACAAT-ATATATAA
2240844 ATATAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 2 0.10
24 14 0.67
25 5 0.24
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
TATAATTTATACAATATATATAATT
Found at i:2240852 original size:24 final size:23
Alignment explanation
Indices: 2240796--2240852 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
2240786 TTAATAAACT
*
2240796 ATATAATTTATACAATATATATA
1 ATATAAATTATACAATATATATA
*
2240819 ATTTATAATTATAC-ATAATATATAA
1 ATATA-AATTATACAAT-ATATAT-A
2240844 ATATAAATT
1 ATATAAATT
2240853 GTATAGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 6 0.21
24 17 0.61
25 5 0.18
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATAAATTATACAATATATATA
Found at i:2240889 original size:13 final size:11
Alignment explanation
Indices: 2240854--2240891 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
2240844 ATATAAATTG
*
2240854 TATAGTTTATA
1 TATAATTTATA
*
2240865 TATAATTCATA
1 TATAATTTATA
2240876 TATAATTTATA
1 TATAATTTATA
2240887 TATAA
1 TATAA
2240892 ACTATGTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
TATAATTTATA
Found at i:2240966 original size:2 final size:2
Alignment explanation
Indices: 2240959--2241074 Score: 94
Period size: 2 Copynumber: 57.0 Consensus size: 2
2240949 TTATACATGG
* *
2240959 TA TA TA TA GTT TA TA CA TA -A 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
* * *
2241001 TA TA TA TA TA TA GTT TA TA TA TA TA -A TA CA TA TA CTT 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
* * *
2241044 TA AA CTA TA TA GTT TA TA T- TA CA TA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
2241075 AAATGAATGC
Statistics
Matches: 90, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
1 3 0.03
2 82 0.91
3 5 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2240968 original size:20 final size:20
Alignment explanation
Indices: 2240936--2241004 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
2240926 TATAAACTAT
2240936 ATAGTAT-TATAGTTTATAC
1 ATAGTATATATAGTTTATAC
*
2240955 ATGGTATATATAGTTTATAC
1 ATAGTATATATAGTTTATAC
* * *
2240975 ATAATATATATA-TATATAT
1 ATAGTATATATAGTTTATAC
2240994 ATA-TATATATA
1 ATAGTATATATA
2241005 TATATATAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
18 8 0.18
19 14 0.32
20 22 0.50
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (20 bp):
ATAGTATATATAGTTTATAC
Found at i:2241374 original size:14 final size:14
Alignment explanation
Indices: 2241355--2241383 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2241345 TTAGTTTATT
2241355 TAATTTTTTATTTG
1 TAATTTTTTATTTG
2241369 TAATTTTTTATTTG
1 TAATTTTTTATTTG
2241383 T
1 T
2241384 TCAATTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (14 bp):
TAATTTTTTATTTG
Found at i:2241664 original size:216 final size:216
Alignment explanation
Indices: 2241131--2242056 Score: 1519
Period size: 216 Copynumber: 4.3 Consensus size: 216
2241121 CCATTTTGTA
* * *
2241131 TTGTTTAATTTATTTAAATTTTTATTTGTCATTTCATATTTGTTCAATTTAGACCTCTACATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTT
* *
2241196 ATTTGCATATGAAATTGACCCATACTTATTACTTATTTCTATTTATTAATTGGCCCATAACTTTT
66 ATTTGCATATGAAATTGACCCATACTTATTACTTAATTCTATTTTTTAATTGGCCCATAACTTTT
* * *
2241261 TAAATGAGTATAATTTAGTACATTTTTGTATTAATTTCAAC-CTCAAAATTTAAAATTATTTCGA
131 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACAC-CACAATTTAAAATTATTTCGA
2241325 TTTGATCCCT--T---T-TGTG
195 TTTGATCCCTCATCAATGTGTG
* * ** *
2241341 TTGTTTAGTTTATTTAATTTTTTATTTGTAATTTTTTATTTGTTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTT
* * *
2241406 ATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTT
66 ATTTGCATATGAAATTGACCCATACTTATTACTTAATTCTATTTTTTAATTGGCCCATAACTTTT
2241471 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACACCACAATTTAAAATTATTTCGAT
131 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACACCACAATTTAAAATTATTTCGAT
2241536 TTGATCCCTCATCAATGTGTG
196 TTGATCCCTCATCAATGTGTG
*
2241557 TTGTTTAATTAATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTT
* *
2241622 ATTTGCATATGAAATTGATCCATACTTTTTACTTAATTCTATTTTTTAATTGGCCCATAACTTTT
66 ATTTGCATATGAAATTGACCCATACTTATTACTTAATTCTATTTTTTAATTGGCCCATAACTTTT
2241687 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACACCACAATTTAAAATTATTTCGAT
131 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACACCACAATTTAAAATTATTTCGAT
2241752 TTGATCCCTCATCAATGTGTG
196 TTGATCCCTCATCAATGTGTG
*
2241773 TTGTTTAATTAATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTT
* *
2241838 ATTTGCATATGAAATTGATCCATACTTTTTACTTAATTCTATTTTTTAATTGGCCCATAACTTTT
66 ATTTGCATATGAAATTGACCCATACTTATTACTTAATTCTATTTTTTAATTGGCCCATAACTTTT
* * *
2241903 TAAATGGGTATAATTTAGTA-TTTTTTTTATTAATTTCAACATCACAATTTAAAATTATTTTGAT
131 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACACCACAATTTAAAATTATTTCGAT
2241967 TTGATCCCTCATCAATGTGTG
196 TTGATCCCTCATCAATGTGTG
* * *
2241988 TTGTTTAATTTATTTAAATTTTTATTTGCAATTTCATATTTGTTCAATTTAATTCT-TAAATTTG
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTT-
2242052 TATTT
65 TATTT
2242057 TTCATAAAAT
Statistics
Matches: 676, Mismatches: 32, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
210 188 0.28
211 1 0.00
212 1 0.00
214 7 0.01
215 120 0.18
216 359 0.53
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (216 bp):
TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTT
ATTTGCATATGAAATTGACCCATACTTATTACTTAATTCTATTTTTTAATTGGCCCATAACTTTT
TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACACCACAATTTAAAATTATTTCGAT
TTGATCCCTCATCAATGTGTG
Found at i:2244891 original size:15 final size:17
Alignment explanation
Indices: 2244866--2244899 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2244856 TAAAGGTCCT
2244866 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
2244882 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
2244898 AA
1 AA
2244900 CATGTCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:2251210 original size:20 final size:22
Alignment explanation
Indices: 2251185--2251227 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
2251175 AATTTCCAGC
2251185 TGTGAGAGACA-TT-GTTTACA
1 TGTGAGAGACATTTAGTTTACA
2251205 TGTGAGAGACATTTAGTTTACA
1 TGTGAGAGACATTTAGTTTACA
2251227 T
1 T
2251228 AATATAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.52
21 2 0.10
22 8 0.38
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.37
Consensus pattern (22 bp):
TGTGAGAGACATTTAGTTTACA
Found at i:2255517 original size:2 final size:2
Alignment explanation
Indices: 2255510--2255592 Score: 157
Period size: 2 Copynumber: 41.0 Consensus size: 2
2255500 CTATGAACAA
2255510 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
2255552 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
2255593 GAACAACTGA
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 78 0.98
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2256671 original size:22 final size:21
Alignment explanation
Indices: 2256646--2256978 Score: 83
Period size: 21 Copynumber: 15.8 Consensus size: 21
2256636 AAAAATAAAT
*
2256646 TAATTAATATTTAAATATTTAA
1 TAATTAATA-TAAAATATTTAA
* *
2256668 TAATTATTATAAAATATTT-T
1 TAATTAATATAAAATATTTAA
* * *
2256688 TACTATTATATATATACTA-TAATA
1 TA--ATTA-ATATAAAATATTTA-A
* *
2256712 TATATATAATATATAATATATAA
1 TA-AT-TAATATAAAATATTTAA
* *
2256735 T-ATATAATATATAATATATAA
1 TAAT-TAATATAAAATATTTAA
* *
2256756 T-ATATAATATATAATATATAA
1 TAAT-TAATATAAAATATTTAA
* *
2256777 T-ATATAATATATAATATATAA
1 TAAT-TAATATAAAATATTTAA
* *
2256798 T-ATATAATATATAATATATAA
1 TAAT-TAATATAAAATATTTAA
* *
2256819 T-ATATAATATATAATATATAA
1 TAAT-TAATATAAAATATTTAA
* *
2256840 T-ATATAATATATAATATATAA
1 TAAT-TAATATAAAATATTTAA
* *
2256861 T-A-TATATATAATATAATATATA
1 TAATTA-ATATAAAAT-ATTTA-A
2256883 TAAATATAATAT-AAATA--TAA
1 T-AAT-TAATATAAAATATTTAA
* *
2256903 T-ATATAATATATAATATATAA
1 TAAT-TAATATAAAATATTTAA
*
2256924 T-A-TAATAT---ATATATAA
1 TAATTAATATAAAATATTTAA
* *
2256940 TAATATAATATATAATATATAA
1 TAAT-TAATATAAAATATTTAA
* * *
2256962 TATTTACTATATAATAT
1 TAATTAATATAAAATAT
2256979 AATGTATAGT
Statistics
Matches: 271, Mismatches: 17, Indels: 47
0.81 0.05 0.14
Matches are distributed among these distances:
16 9 0.03
17 1 0.00
18 9 0.03
19 18 0.07
20 11 0.04
21 160 0.59
22 26 0.10
23 22 0.08
24 9 0.03
25 4 0.01
26 2 0.01
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATTAATATAAAATATTTAA
Found at i:2256715 original size:7 final size:7
Alignment explanation
Indices: 2256697--2257131 Score: 488
Period size: 7 Copynumber: 61.9 Consensus size: 7
2256687 TTACTATTAT
2256697 ATATATA
1 ATATATA
*
2256704 CTATAATA
1 ATAT-ATA
2256712 TATATATA
1 -ATATATA
2256720 ATATATA
1 ATATATA
2256727 ATATATA
1 ATATATA
2256734 ATATATA
1 ATATATA
2256741 ATATATA
1 ATATATA
2256748 ATATATA
1 ATATATA
2256755 ATATATA
1 ATATATA
2256762 ATATATA
1 ATATATA
2256769 ATATATA
1 ATATATA
2256776 ATATATA
1 ATATATA
2256783 ATATATA
1 ATATATA
2256790 ATATATA
1 ATATATA
2256797 ATATATA
1 ATATATA
2256804 ATATATA
1 ATATATA
2256811 ATATATA
1 ATATATA
2256818 ATATATA
1 ATATATA
2256825 ATATATA
1 ATATATA
2256832 ATATATA
1 ATATATA
2256839 ATATATA
1 ATATATA
2256846 ATATATA
1 ATATATA
2256853 ATATATA
1 ATATATA
2256860 ATATATA
1 ATATATA
2256867 TATAATATA
1 -AT-ATATA
2256876 ATATAT-
1 ATATATA
*
2256882 ATAAAT-
1 ATATATA
2256888 ATAATATA
1 AT-ATATA
2256896 A-ATATA
1 ATATATA
2256902 ATATATA
1 ATATATA
2256909 ATATATA
1 ATATATA
2256916 ATATATA
1 ATATATA
2256923 ATATAATA
1 ATAT-ATA
2256931 TATATATA
1 -ATATATA
2256939 ATAATATA
1 AT-ATATA
2256947 ATATATA
1 ATATATA
2256954 ATATATA
1 ATATATA
*
2256961 ATATTTA
1 ATATATA
*
2256968 CTATAT-
1 ATATATA
2256974 A-ATATA
1 ATATATA
*
2256980 ATGTATA
1 ATATATA
*
2256987 GTATAATA
1 ATAT-ATA
2256995 ATATATA
1 ATATATA
*
2257002 CA-ACAT-
1 -ATATATA
2257008 ATATGAT-
1 ATAT-ATA
*
2257015 ATATAAA
1 ATATATA
2257022 ATATATA
1 ATATATA
2257029 ATATA-A
1 ATATATA
2257035 A-ATATA
1 ATATATA
*
2257041 AAATATA
1 ATATATA
2257048 ATATA-A
1 ATATATA
2257054 TATGATATAA
1 -AT-ATAT-A
2257064 TATAATATA
1 -AT-ATATA
*
2257073 ATATACA
1 ATATATA
*
2257080 ATATGTA
1 ATATATA
2257087 ATATAT-
1 ATATATA
2257093 A-ATATA
1 ATATATA
2257099 ATATA-A
1 ATATATA
2257105 CATATAT-
1 -ATATATA
*
2257112 CTAATATA
1 AT-ATATA
2257120 ATATAT-
1 ATATATA
2257126 ATATAT
1 ATATAT
2257132 TACAGATATA
Statistics
Matches: 375, Mismatches: 24, Indels: 59
0.82 0.05 0.13
Matches are distributed among these distances:
5 12 0.03
6 31 0.08
7 274 0.73
8 37 0.10
9 13 0.03
10 8 0.02
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (7 bp):
ATATATA
Found at i:2257431 original size:19 final size:18
Alignment explanation
Indices: 2257409--2257467 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
2257399 CGACTCGATC
2257409 AACTCGACTCAACTTGGTT
1 AACTC-ACTCAACTTGGTT
* * *
2257428 AACTCAAATCAGCTCGGTT
1 AACTC-ACTCAACTTGGTT
*
2257447 AACTCAGCTCGACTTGGTT
1 AACTCA-CTCAACTTGGTT
2257466 AA
1 AA
2257468 TGGCTCGGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
18 1 0.03
19 30 0.97
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (18 bp):
AACTCACTCAACTTGGTT
Found at i:2259336 original size:22 final size:22
Alignment explanation
Indices: 2259288--2259347 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
2259278 AATGCAAAAA
* *
2259288 TAGTATCAATACCAT--AATAG
1 TAGTATCGATACCATGGTATAG
2259308 -AGTATCGATACCATGGTATAG
1 TAGTATCGATACCATGGTATAG
2259329 TAGTATCGATACCATGGTA
1 TAGTATCGATACCATGGTA
2259348 GGGGTATCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.37
21 4 0.11
22 18 0.51
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (22 bp):
TAGTATCGATACCATGGTATAG
Found at i:2259356 original size:20 final size:21
Alignment explanation
Indices: 2259289--2259360 Score: 78
Period size: 22 Copynumber: 3.5 Consensus size: 21
2259279 ATGCAAAAAT
* *
2259289 AGTATCAATACCAT-AATA-G
1 AGTATCGATACCATGGATAGG
*
2259308 AGTATCGATACCATGGTATAGT
1 AGTATCGATACCATGG-ATAGG
2259330 AGTATCGATACCATGG-TAGG
1 AGTATCGATACCATGGATAGG
*
2259350 GGTATCGATAC
1 AGTATCGATAC
2259361 TGAGGAGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.29
20 13 0.29
21 3 0.07
22 16 0.36
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (21 bp):
AGTATCGATACCATGGATAGG
Found at i:2259772 original size:55 final size:55
Alignment explanation
Indices: 2259703--2260294 Score: 747
Period size: 55 Copynumber: 10.7 Consensus size: 55
2259693 GTGCAGAAAG
** ** *
2259703 TTAAGAAATTCATAATTTGTTCATGAATTTCCGTATGGGCACTTTATGTGTAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
* *
2259758 TTAAGAAATTCATAATAAGTGGATGAATTTTCGTATGGGCACTATATGTGCAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
* * *
2259813 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGTGCACTATATGTGTAAAT
1 TTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
*
2259868 TTAAGAAATTCATATTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
*
2259923 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
* * * *
2259978 TTAAGAAATTCATACTAAGTGGATGAATTTCTGAATGTGCACTATATGTGTAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
* ** * *
2260033 TTAAGAAATTTATTCTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAATC
1 TTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
* * *
2260088 TAAAGAAATTCATACTAAGTGGATGAATTTCCGTATGAGCACTATATGTGTAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
** * * * *
2260143 TTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGGCACTCTGTGTGCAAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTATATGTG-TAAAC
** * * * * * * * *
2260199 -TAAGAAATTCATAATAAGTTTATAAATTTTTCGTATTGACATTGTGTGTGCAAAAC
1 TTAAGAAATTCATAATAAGTGGATGAA-TTTCCGTATGGGCACTATATGTG-TAAAC
** * *
2260255 -TAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCA
1 TTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCA
2260295 TGCAACTTAA
Statistics
Matches: 484, Mismatches: 51, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
55 431 0.89
56 53 0.11
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (55 bp):
TTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
Found at i:2260546 original size:30 final size:31
Alignment explanation
Indices: 2260484--2260551 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
2260474 TTATTTACGA
*
2260484 CATTTAGGTGCAACTCATATACTATGCTTTTT
1 CATTTAGGTGCAACTCA-ATACTATGCATTTT
*
2260516 CATTTAGGTGCAACTC-ATGCTATGCATTTT
1 CATTTAGGTGCAACTCAATACTATGCATTTT
2260546 CATTTA
1 CATTTA
2260552 ACATATATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 18 0.53
32 16 0.47
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (31 bp):
CATTTAGGTGCAACTCAATACTATGCATTTT
Found at i:2265931 original size:55 final size:55
Alignment explanation
Indices: 2265837--2266482 Score: 741
Period size: 55 Copynumber: 11.8 Consensus size: 55
2265827 GTGCAAAAAG
** ** * *
2265837 TTAAGAAATTCATAATTTGTTTTATGAATTTTCGTATGGGCACTTTATTTGTAAAC
1 TTAAGAAATTCATAATAAG-TGGATGAATTTTCGTATGGGCACTATATGTGTAAAC
*
2265893 TTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTTCGTATGGGCACTATATGTGTAAAC
* * * * *
2265948 TTAAGAAATCCATACTAAGTGGATGAATTTCCGTATGGACACTATATGTTTAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTTCGTATGGGCACTATATGTGTAAAC
*
2266003 TTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGTAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTTCGTATGGGCACTATATGTGTAAAC
*
2266058 TT-AGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGTAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTTCGTATGGGCACTATATGTGTAAAC
* * *
2266112 TTAAGAAACTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGTAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTTCGTATGGGCACTATATGTGTAAAC
* * *
2266167 ATAAGAAATTCATACTAAGTGGATGAATTTTCGTATGTGCACTATATGTGTAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTTCGTATGGGCACTATATGTGTAAAC
** * * * * * *
2266222 TTAAGAAATTCATAATAAGTTTATGAA-TTTCTGTATAGGCATTGTGTATGCAAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTTC-GTATGGGCACTATATGTG-TAAAC
*
2266278 -T-A-AAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGTAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTTCGTATGGGCACTATATGTGTAAAC
** * * * * *
2266330 TTAAGAAATTCATAATAAGTTTATGAATTTAT-GTATAGGCATTGTGTGTGCAAAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTT-TCGTATGGGCACTATATGTG-TAAAC
* ** * * * * * *
2266386 -TAAGAAATTCGTAATAAGTTTATGAATTTCCGTATTGACACTGTGTGTG-CAAC
1 TTAAGAAATTCATAATAAGTGGATGAATTTTCGTATGGGCACTATATGTGTAAAC
* ** * *
2266439 TTAAGAAATTCATAATGAGTTTATGAATTTCCGTATCGGCACTA
1 TTAAGAAATTCATAATAAGTGGATGAATTTTCGTATGGGCACTA
2266483 AGTGTGCAAC
Statistics
Matches: 519, Mismatches: 60, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
52 4 0.01
53 36 0.07
54 102 0.20
55 351 0.68
56 26 0.05
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (55 bp):
TTAAGAAATTCATAATAAGTGGATGAATTTTCGTATGGGCACTATATGTGTAAAC
Found at i:2266132 original size:164 final size:165
Alignment explanation
Indices: 2265860--2266482 Score: 783
Period size: 164 Copynumber: 3.8 Consensus size: 165
2265850 AATTTGTTTT
* *
2265860 ATGAATTTTCGTATGGGCACTTTATTTGTAAACTTAAGAAATTCATAATAAGTGGATGAATTTCC
1 ATGAATTTTCGTATGGGCACTATATGTGTAAACTTAAGAAATTCATAATAAGTGGATGAATTTCC
* *
2265925 GTATGGGCACTATATGTGTAAACTTAAGAAATCCATACTAAGTGGATGAATTTCCGTATGGACAC
66 GTATGGGCACTATATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCAC
*
2265990 TATATGTTTAAACTTAAGAAATTCATACTAAGTGG
131 TATATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
2266025 ATGAATTTTCGTATGGGCACTATATGTGTAAACTT-AGAAATTCATACTAAGTGGATGAATTTTC
1 ATGAATTTTCGTATGGGCACTATATGTGTAAACTTAAGAAATTCATAATAAGTGGATGAATTTCC
* *
2266089 GTATGGGCACTATATGTGTAAACTTAAGAAACTCATACTAAGTGGATGAATTTTCGTATGGGCAC
66 GTATGGGCACTATATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCAC
* *
2266154 TTTATGTGTAAACATAAGAAATTCATACTAAGTGG
131 TATATGTGTAAACTTAAGAAATTCATACTAAGTGG
* ** *
2266189 ATGAATTTTCGTATGTGCACTATATGTGTAAACTTAAGAAATTCATAATAAGTTTATGAATTTCT
1 ATGAATTTTCGTATGGGCACTATATGTGTAAACTTAAGAAATTCATAATAAGTGGATGAATTTCC
* * * * * * *
2266254 GTATAGGCATTGTGTATGCAAAAC-T-A-AAATTCATACTAAGTGGATGAATTTTCGTATGGGCA
66 GTATGGGCACTATATGTG-TAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCA
* **
2266316 CTATATGTGTAAACTTAAGAAATTCATAATAAGTTT
130 CTATATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * * * * * **
2266352 ATGAATTTAT-GTATAGGCATTGTGTGTGCAAAAC-TAAGAAATTCGTAATAAGTTTATGAATTT
1 ATGAATTT-TCGTATGGGCACTATATGTG-TAAACTTAAGAAATTCATAATAAGTGGATGAATTT
* * * * * * * ** *
2266415 CCGTATTGACACTGTGTGTG-CAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATCGGC
64 CCGTATGGGCACTATATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGC
2266479 ACTA
129 ACTA
2266483 AGTGTGCAAC
Statistics
Matches: 403, Mismatches: 48, Indels: 15
0.86 0.10 0.03
Matches are distributed among these distances:
161 3 0.01
162 1 0.00
163 131 0.33
164 193 0.48
165 71 0.18
166 4 0.01
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (165 bp):
ATGAATTTTCGTATGGGCACTATATGTGTAAACTTAAGAAATTCATAATAAGTGGATGAATTTCC
GTATGGGCACTATATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCAC
TATATGTGTAAACTTAAGAAATTCATACTAAGTGG
Found at i:2266539 original size:54 final size:54
Alignment explanation
Indices: 2266383--2266539 Score: 138
Period size: 54 Copynumber: 2.9 Consensus size: 54
2266373 GTGTGTGCAA
* * * ** * **
2266383 AACT-AAGAAATTCGTAATAAGTTTATGAATTTCCGTATTGACACTGTGTGTGC
1 AACTCAAGAAATTCATAATGAGATTATGAATAACCGTATCGACACTAAGTGTGC
* * ** *
2266436 AACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATCGGCACTAAGTGTGC
1 AACTCAAGAAATTCATAATGAGATTATGAATAACCGTATCGACACTAAGTGTGC
* * * *
2266490 AACTCACAG-AATTTATAATGAGATTATGAATAACTGTGTCGACATTAAGT
1 AACTCA-AGAAATTCATAATGAGATTATGAATAACCGTATCGACACTAAGT
2266540 ACGCATCCCA
Statistics
Matches: 87, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
53 4 0.05
54 81 0.93
55 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (54 bp):
AACTCAAGAAATTCATAATGAGATTATGAATAACCGTATCGACACTAAGTGTGC
Found at i:2268137 original size:24 final size:24
Alignment explanation
Indices: 2268109--2268193 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
2268099 GAATATTTTA
* *
2268109 TCTGATTTCCGATTTGAATTCTGT
1 TCTGATTTCCGATCTGAATTATGT
* *
2268133 TCTGA-TTCCTGACCTGGATTATGT
1 TCTGATTTCC-GATCTGAATTATGT
* *
2268157 TCTGATATCTGATCTGAATTATGT
1 TCTGATTTCCGATCTGAATTATGT
* *
2268181 TTTGTTTTCCGAT
1 TCTGATTTCCGAT
2268194 ATCTCCATTT
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
23 4 0.09
24 41 0.87
25 2 0.04
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (24 bp):
TCTGATTTCCGATCTGAATTATGT
Found at i:2268328 original size:54 final size:54
Alignment explanation
Indices: 2268246--2268351 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
2268236 TGGAGGGTTT
*
2268246 ATATCTGTAGGTTCCTCGGCTTTGTGCTCAGGGCCCTACTATTATACAGGGGTG
1 ATATCTGCAGGTTCCTCGGCTTTGTGCTCAGGGCCCTACTATTATACAGGGGTG
* * *
2268300 ATATCTGCAGGTTCCTCGGCTTTGTGCTCAGGGCCTTACTGTTGTACAGGGG
1 ATATCTGCAGGTTCCTCGGCTTTGTGCTCAGGGCCCTACTATTATACAGGGG
2268352 GTGTATGGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.15, C:0.23, G:0.29, T:0.33
Consensus pattern (54 bp):
ATATCTGCAGGTTCCTCGGCTTTGTGCTCAGGGCCCTACTATTATACAGGGGTG
Found at i:2270361 original size:13 final size:14
Alignment explanation
Indices: 2270328--2270368 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
2270318 TTGACTAATT
*
2270328 TTTGACCCAACCCG
1 TTTGACCCGACCCG
*
2270342 TTTGACCCGACTCG
1 TTTGACCCGACCCG
2270356 -TTGACCCGACCCG
1 TTTGACCCGACCCG
2270369 ACCTGACCCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.17, C:0.41, G:0.20, T:0.22
Consensus pattern (14 bp):
TTTGACCCGACCCG
Found at i:2272806 original size:55 final size:55
Alignment explanation
Indices: 2272738--2272841 Score: 154
Period size: 55 Copynumber: 1.9 Consensus size: 55
2272728 TGGAGGGTTT
* * *
2272738 ATATCTGCAGGTTCCTTAGCTTTGTCCTCAGGGCCTTACTGTTGTGCAGGGGGTG
1 ATATCTACAGGTTCATCAGCTTTGTCCTCAGGGCCTTACTGTTGTGCAGGGGGTG
* * *
2272793 ATATCTACAGGTTCATCGGCTTTGTGCTCAGGGTCTTACTGTTGTGCAG
1 ATATCTACAGGTTCATCAGCTTTGTCCTCAGGGCCTTACTGTTGTGCAG
2272842 CGAGTGTATG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.36
Consensus pattern (55 bp):
ATATCTACAGGTTCATCAGCTTTGTCCTCAGGGCCTTACTGTTGTGCAGGGGGTG
Found at i:2274852 original size:17 final size:17
Alignment explanation
Indices: 2274830--2274862 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2274820 CGACCCGTTA
*
2274830 ACTGTTGACCGTTGACC
1 ACTGTTGACCATTGACC
2274847 ACTGTTGACCATTGAC
1 ACTGTTGACCATTGAC
2274863 TTTGACCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.30
Consensus pattern (17 bp):
ACTGTTGACCATTGACC
Found at i:2277304 original size:24 final size:25
Alignment explanation
Indices: 2277265--2277320 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
2277255 ATTTTCTATT
2277265 TGAATT-TTTTCCTGATACCTGACC
1 TGAATTATTTTCCTGATACCTGACC
* * *
2277289 TGGATTATTTT-CTGATATCTGATC
1 TGAATTATTTTCCTGATACCTGACC
2277313 TGAATTAT
1 TGAATTAT
2277321 GTTTTGTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.46
Consensus pattern (25 bp):
TGAATTATTTTCCTGATACCTGACC
Found at i:2281918 original size:24 final size:23
Alignment explanation
Indices: 2281847--2281918 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
2281837 GAATATTTTA
2281847 TCTGATTTTCGAT-TGAATTCTGT
1 TCTGATTTT-GATCTGAATTCTGT
* * *
2281870 TCTGATTCCTGACCTGGATTCTGT
1 TCTGATT-TTGATCTGAATTCTGT
*
2281894 TCTGATATTTGATCTGAATTATGT
1 TCTGAT-TTTGATCTGAATTCTGT
2281918 T
1 T
2281919 TTGTTTTCTG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
23 9 0.23
24 29 0.74
25 1 0.03
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.49
Consensus pattern (23 bp):
TCTGATTTTGATCTGAATTCTGT
Found at i:2286624 original size:24 final size:24
Alignment explanation
Indices: 2286554--2286612 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
2286544 ATTTTCGATT
* * *
2286554 TGAATTCTATTCTGAT-TCCTGACC
1 TGAATTATGTTCTGATAT-CTGATC
*
2286578 TGGATTATGTTCTGATATCTGATC
1 TGAATTATGTTCTGATATCTGATC
2286602 TGAATTATGTT
1 TGAATTATGTT
2286613 TTGTTTTCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (24 bp):
TGAATTATGTTCTGATATCTGATC
Found at i:2286721 original size:55 final size:55
Alignment explanation
Indices: 2286677--2286786 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
2286667 TGGAGGGTTT
*
2286677 ATATCTGCAGGTTCCTCGGCTTTGTGCTCAGGGCCTTACTATTATGCAGGGGGTG
1 ATATCTGCAGGTTCCTCAGCTTTGTGCTCAGGGCCTTACTATTATGCAGGGGGTG
* *
2286732 ATATCTGCAGGTTCCTCAGCTTTGTGCTCAGGGCCTTACTGTTGTGCAGGGGGTG
1 ATATCTGCAGGTTCCTCAGCTTTGTGCTCAGGGCCTTACTATTATGCAGGGGGTG
2286787 TATAGTTATG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.14, C:0.22, G:0.32, T:0.33
Consensus pattern (55 bp):
ATATCTGCAGGTTCCTCAGCTTTGTGCTCAGGGCCTTACTATTATGCAGGGGGTG
Found at i:2290980 original size:55 final size:54
Alignment explanation
Indices: 2290892--2291000 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 54
2290882 TTGAGGGTTT
* *
2290892 ATATCTGTAGGTTCCTCGGCTTTGTGCTCAGGGCCTTACTGTTGTGCAGGGGGTG
1 ATATCTGTAGGTTCATCGGCTTTGTGCTCAGGGCCTTAC-CTTGTGCAGGGGGTG
*
2290947 ATATCTGTAGGTTCATCGGCTTTGTGCTTAGGGCCTTACCTTGTGCAGGGGGTG
1 ATATCTGTAGGTTCATCGGCTTTGTGCTCAGGGCCTTACCTTGTGCAGGGGGTG
2291001 TATGGTTATG
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 14 0.27
55 37 0.73
ACGTcount: A:0.12, C:0.19, G:0.34, T:0.35
Consensus pattern (54 bp):
ATATCTGTAGGTTCATCGGCTTTGTGCTCAGGGCCTTACCTTGTGCAGGGGGTG
Found at i:2294635 original size:20 final size:21
Alignment explanation
Indices: 2294607--2294647 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2294597 CGAAATTCAG
* *
2294607 AAACGTCTAAATTACTCTGGA
1 AAACGTCTAAAGTACCCTGGA
2294628 AAAC-TCTAAAGTACCCTGGA
1 AAACGTCTAAAGTACCCTGGA
2294648 TAGACTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (21 bp):
AAACGTCTAAAGTACCCTGGA
Found at i:2295327 original size:24 final size:23
Alignment explanation
Indices: 2295255--2295327 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
2295245 GAATATTTTA
* * *
2295255 TCTGATTTCCGATTTGAATTCTAT
1 TCTGA-TTCTGATCTGAATTCTGT
* *
2295279 TCTGATTCCTGACCTGGATTCTGT
1 TCTGATT-CTGATCTGAATTCTGT
*
2295303 TCTGATATCTGATCTGAATTATGT
1 TCTGAT-TCTGATCTGAATTCTGT
2295327 T
1 T
2295328 TTGTTTTCTG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
23 2 0.05
24 36 0.92
25 1 0.03
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.47
Consensus pattern (23 bp):
TCTGATTCTGATCTGAATTCTGT
Found at i:2297161 original size:21 final size:20
Alignment explanation
Indices: 2297137--2297194 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
2297127 ACTTTCAATC
2297137 TATTTAACTC-CAATTTCCTTT
1 TATTTAACTCTCAATTT-C-TT
*
2297158 TATTT-GCTCTCAATTTCTT
1 TATTTAACTCTCAATTTCTT
2297177 T-TTTAACTCTC-ATTTCTT
1 TATTTAACTCTCAATTTCTT
2297195 CTTTTTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 10 0.30
19 8 0.24
20 4 0.12
21 11 0.33
ACGTcount: A:0.19, C:0.22, G:0.02, T:0.57
Consensus pattern (20 bp):
TATTTAACTCTCAATTTCTT
Found at i:2297188 original size:19 final size:19
Alignment explanation
Indices: 2297139--2297199 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
2297129 TTTCAATCTA
2297139 TTTAACTC-CAATTTCCTTT
1 TTTAACTCTCAATTT-CTTT
**
2297158 TATTTGCTCTCAATTTCTTT
1 T-TTAACTCTCAATTTCTTT
2297178 TTTAACTCTC-ATTTCTTCT
1 TTTAACTCTCAATTTCTT-T
2297197 TTT
1 TTT
2297200 TCTTTGCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 7 0.20
19 12 0.34
20 10 0.29
21 6 0.17
ACGTcount: A:0.16, C:0.23, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTAACTCTCAATTTCTTT
Found at i:2298518 original size:16 final size:16
Alignment explanation
Indices: 2298497--2298530 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2298487 CGCTATAAAA
2298497 AAAGGAAATGGATGAT
1 AAAGGAAATGGATGAT
2298513 AAAGGAAATGGATGAT
1 AAAGGAAATGGATGAT
2298529 AA
1 AA
2298531 CTACAAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.29, T:0.18
Consensus pattern (16 bp):
AAAGGAAATGGATGAT
Found at i:2299550 original size:17 final size:17
Alignment explanation
Indices: 2299521--2299574 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
2299511 AATTAAGATT
2299521 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
2299538 TATTTTGATAAATGAAT
1 TAGTTTAATAAATGAAC
*
2299555 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
2299572 TAG
1 TAG
2299575 ATGCATGAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.41
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:2299586 original size:34 final size:34
Alignment explanation
Indices: 2299520--2299587 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
2299510 CAATTAAGAT
**
2299520 TTAGTTTAATAAATGAACTATTTTGATAAATGAA
1 TTAGTTTAATAAATGAACTATGATGATAAATGAA
* *
2299554 TTAGTTTAATTAATGAACTA-GATGCATGAATGAA
1 TTAGTTTAATAAATGAACTATGATG-ATAAATGAA
2299588 GTAAAATGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 2 0.07
34 27 0.93
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (34 bp):
TTAGTTTAATAAATGAACTATGATGATAAATGAA
Found at i:2306209 original size:16 final size:16
Alignment explanation
Indices: 2306188--2306229 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
2306178 AAGTAAGAGA
*
2306188 ATAAAAGGTTATCATC
1 ATAAAAGGTTATCACC
2306204 ATAAAAGGTTATCACC
1 ATAAAAGGTTATCACC
2306220 ATAAAAGGTT
1 ATAAAAGGTT
2306230 CTAGTGAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (16 bp):
ATAAAAGGTTATCACC
Found at i:2306749 original size:20 final size:20
Alignment explanation
Indices: 2306724--2306761 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2306714 TACGTTGGGC
2306724 TATGAATCTGAAACATGAGT
1 TATGAATCTGAAACATGAGT
*
2306744 TATGAATCTGAAATATGA
1 TATGAATCTGAAACATGA
2306762 AAGTACATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (20 bp):
TATGAATCTGAAACATGAGT
Found at i:2317309 original size:21 final size:21
Alignment explanation
Indices: 2317292--2317331 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2317282 GAGTCTGACC
2317292 TGGCTACGGTGGCATCTGAAA
1 TGGCTACGGTGGCATCTGAAA
* *
2317313 TGGCTATGGTGCCATCTGA
1 TGGCTACGGTGGCATCTGA
2317332 TACGACTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.28
Consensus pattern (21 bp):
TGGCTACGGTGGCATCTGAAA
Found at i:2319320 original size:63 final size:63
Alignment explanation
Indices: 2319237--2319398 Score: 236
Period size: 63 Copynumber: 2.6 Consensus size: 63
2319227 AGATGTGTGG
* *
2319237 TAATTAATGTGGGAGACGGAC-AGTTGTAGAATTAAAGGAAAAACGCATAGTAGAGACGAATGA
1 TAATCAATGTGGGAGACGGACGA-TTATAGAATTAAAGGAAAAACGCATAGTAGAGACGAATGA
* * *
2319300 TAATCAATGTGGGAGACGGACGATTATGGAATTAAAGGAAAAGCGCATAGTAGAGACGAGTGA
1 TAATCAATGTGGGAGACGGACGATTATAGAATTAAAGGAAAAACGCATAGTAGAGACGAATGA
* * *
2319363 TAATCAATGTGGTAGACGAACGATTATGGAATTAAA
1 TAATCAATGTGGGAGACGGACGATTATAGAATTAAA
2319399 AAGAAAGGTG
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
63 90 0.99
64 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.28, T:0.22
Consensus pattern (63 bp):
TAATCAATGTGGGAGACGGACGATTATAGAATTAAAGGAAAAACGCATAGTAGAGACGAATGA
Found at i:2320490 original size:43 final size:43
Alignment explanation
Indices: 2320424--2320507 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
2320414 ACTACCTGAG
*
2320424 ACTGGTGAATGTACTTTTAATATGGAGTTATTAATTGCATCTT
1 ACTGGTGAATGTACTTTGAATATGGAGTTATTAATTGCATCTT
* **
2320467 ACTGGT-AACTGTACTTTGCATATGGAGTTATTGGTTGCATC
1 ACTGGTGAA-TGTACTTTGAATATGGAGTTATTAATTGCATC
2320508 CTCTTCATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 2 0.06
43 34 0.94
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (43 bp):
ACTGGTGAATGTACTTTGAATATGGAGTTATTAATTGCATCTT
Found at i:2324975 original size:3 final size:3
Alignment explanation
Indices: 2324967--2324991 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2324957 GATTGCGTCA
2324967 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
2324992 TTATTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2331950 original size:30 final size:30
Alignment explanation
Indices: 2331914--2331975 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
2331904 ATGCATGAGA
2331914 GTATGAATGTATGAATGTATGCGTGAGTTG
1 GTATGAATGTATGAATGTATGCGTGAGTTG
2331944 GTATGAATGTATGAATGTATGCGTGAGTTG
1 GTATGAATGTATGAATGTATGCGTGAGTTG
2331974 GT
1 GT
2331976 TAGTGGCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.03, G:0.34, T:0.37
Consensus pattern (30 bp):
GTATGAATGTATGAATGTATGCGTGAGTTG
Found at i:2338244 original size:16 final size:17
Alignment explanation
Indices: 2338223--2338263 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
2338213 CCACCGCTTT
2338223 AGGGGAATTAAATAA-C-
1 AGGGGAATTAAA-AAGCA
2338239 AGGGGAATTAAAAAGCA
1 AGGGGAATTAAAAAGCA
2338256 AGGGGAAT
1 AGGGGAAT
2338264 GTAGTAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 13 0.57
17 8 0.35
ACGTcount: A:0.49, C:0.05, G:0.32, T:0.15
Consensus pattern (17 bp):
AGGGGAATTAAAAAGCA
Found at i:2339465 original size:19 final size:18
Alignment explanation
Indices: 2339421--2339461 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
2339411 TTATTACTGC
*
2339421 TATCCTTTTTTGCAAGTG
1 TATCCTTTTTTGAAAGTG
2339439 TATCCTTTTTTGAAAGTG
1 TATCCTTTTTTGAAAGTG
2339457 TATCC
1 TATCC
2339462 CTTTCTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.49
Consensus pattern (18 bp):
TATCCTTTTTTGAAAGTG
Found at i:2349478 original size:2 final size:2
Alignment explanation
Indices: 2349471--2349521 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2349461 GACTGTCTCG
2349471 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
2349513 AT AT AT AT A
1 AT AT AT AT A
2349522 ATAATTTAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2350695 original size:65 final size:65
Alignment explanation
Indices: 2350625--2350755 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
2350615 TCTGTAGCAA
2350625 AAAAATTGTAATTATACTTAATGAACAAAGTTAAGAGATTTAGGAGAGAAAAAGAAGAGGGGAAG
1 AAAAATTGTAATTATACTTAATGAACAAAGTTAAGAGATTTAGGAGAGAAAAAGAAGAGGGGAAG
* *
2350690 AAAAATTGTAATTGTACTTGATGAACAAAGTTAAGAGATTTAGGAGAGAAAAAGAAGAGGGGAAG
1 AAAAATTGTAATTATACTTAATGAACAAAGTTAAGAGATTTAGGAGAGAAAAAGAAGAGGGGAAG
2350755 A
1 A
2350756 GATTGTTTGT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.50, C:0.03, G:0.26, T:0.21
Consensus pattern (65 bp):
AAAAATTGTAATTATACTTAATGAACAAAGTTAAGAGATTTAGGAGAGAAAAAGAAGAGGGGAAG
Found at i:2352252 original size:21 final size:20
Alignment explanation
Indices: 2352206--2352252 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2352196 ATGAATGTAG
2352206 ATGT-TTTTAATGAATATTC
1 ATGTCTTTTAATGAATATTC
*
2352225 GTGTCTTTTAATGGAAT-TTC
1 ATGTCTTTTAAT-GAATATTC
2352245 ATGCTCTT
1 ATG-TCTT
2352253 AGCCAAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.13
20 12 0.52
21 8 0.35
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (20 bp):
ATGTCTTTTAATGAATATTC
Found at i:2367216 original size:23 final size:22
Alignment explanation
Indices: 2367186--2367262 Score: 93
Period size: 23 Copynumber: 3.5 Consensus size: 22
2367176 ACACTAGACA
*
2367186 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATACA-CCCTTGAAT
* *
2367209 GTGCATCGATACACCATT-AAG
1 GTGCATCGATACACCCTTGAAT
*
2367230 GTGCACCGATACACTCCTTGAAT
1 GTGCATCGATACAC-CCTTGAAT
2367253 GTGCATCGAT
1 GTGCATCGAT
2367263 GAACAATGCT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
21 15 0.33
22 7 0.16
23 23 0.51
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (22 bp):
GTGCATCGATACACCCTTGAAT
Found at i:2369487 original size:22 final size:22
Alignment explanation
Indices: 2369459--2369501 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2369449 AAGGGGGAGT
2369459 ATATAGTAAGGGGGAGTAATTA
1 ATATAGTAAGGGGGAGTAATTA
*
2369481 ATATAGTAAGTGGGAGTAATT
1 ATATAGTAAGGGGGAGTAATT
2369502 TTTTCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (22 bp):
ATATAGTAAGGGGGAGTAATTA
Found at i:2369942 original size:34 final size:34
Alignment explanation
Indices: 2369867--2369942 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
2369857 ATGATGCATT
* *
2369867 GATGCACACCTATTTCGAATGCATTTTGTGTACC
1 GATGCACACCCATTTCGAATACATTTTGTGTACC
* * *
2369901 AAGGCACACCCATTTCGAATACATTTTTTGTACC
1 GATGCACACCCATTTCGAATACATTTTGTGTACC
2369935 GATGCACA
1 GATGCACA
2369943 AGCCATGCAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (34 bp):
GATGCACACCCATTTCGAATACATTTTGTGTACC
Found at i:2369991 original size:65 final size:65
Alignment explanation
Indices: 2369915--2370071 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 65
2369905 CACACCCATT
* * * * *
2369915 TCGAATACATTTTTTGTACCGATGCACA-AGCCATGCATCGATGTACTCTTGAATATTTTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAGA-CCATGCATCAATGCACTCCTGAATATTTTGAAAC
2369979 A
65 A
** *
2369980 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCAATGCACTCCTGGCTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCAATGCACTCCTGAATATTTTGAAACA
* * *
2370045 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
2370072 CCCTAGTGTA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
65 79 0.99
66 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCAATGCACTCCTGAATATTTTGAAACA
Found at i:2373932 original size:37 final size:38
Alignment explanation
Indices: 2373870--2373941 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
2373860 TATAATGTAG
*
2373870 TTTTTGAAAATATTTTTTGAAAGCATATAACATATAAC
1 TTTTAGAAAATATTTTTTGAAAGCATATAACATATAAC
* *
2373908 TTTTAGAAAATGTTTTTT-AAAGCATATAATATAT
1 TTTTAGAAAATATTTTTTGAAAGCATATAACATAT
2373942 GGTTTTTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 15 0.48
38 16 0.52
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (38 bp):
TTTTAGAAAATATTTTTTGAAAGCATATAACATATAAC
Found at i:2374040 original size:23 final size:23
Alignment explanation
Indices: 2374009--2374068 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 23
2373999 GAAAACATTT
* *
2374009 TTTTGAAAACATATAATGTCTAG
1 TTTTGAAAACATATAATATATAG
*
2374032 TTTTAAAAACGTATATAATATATAG
1 TTTTGAAAAC--ATATAATATATAG
2374057 TTTTGAAAACAT
1 TTTTGAAAACAT
2374069 TTTTGAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 11 0.35
25 20 0.65
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (23 bp):
TTTTGAAAACATATAATATATAG
Found at i:2374115 original size:71 final size:70
Alignment explanation
Indices: 2374031--2374169 Score: 235
Period size: 71 Copynumber: 2.0 Consensus size: 70
2374021 ATAATGTCTA
*
2374031 GTTTTAAAAACGTATATAATATATAGTTTTGAAAACATTTTTGAAAACGTATA-ATATATGGTTT
1 GTTTTAAAAACGTATATAATATATAGTTTTGAAAACA-TTTTGAAAACGTATATA-ATATAGTTT
2374095 TGAAAGC
64 TGAAAGC
*
2374102 GTTTTAAAAACGTATATAATATATAGTTTTGAAAAGATTTTGAAAACGTATATAATATAGTTTTG
1 GTTTTAAAAACGTATATAATATATAGTTTTGAAAACATTTTGAAAACGTATATAATATAGTTTTG
2374167 AAA
66 AAA
2374170 ACATATATAT
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
70 28 0.43
71 37 0.57
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.40
Consensus pattern (70 bp):
GTTTTAAAAACGTATATAATATATAGTTTTGAAAACATTTTGAAAACGTATATAATATAGTTTTG
AAAGC
Found at i:2374169 original size:23 final size:21
Alignment explanation
Indices: 2374138--2374186 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 21
2374128 TTTTGAAAAG
*
2374138 ATTTTGAAAACGTATATAATAT
1 ATTTTGAAAACATATAT-ATAT
2374160 AGTTTTGAAAACATATATATAT
1 A-TTTTGAAAACATATATATAT
2374182 ATTTT
1 ATTTT
2374187 AAATGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 6 0.24
23 15 0.60
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (21 bp):
ATTTTGAAAACATATATATAT
Found at i:2374170 original size:34 final size:36
Alignment explanation
Indices: 2374032--2374170 Score: 180
Period size: 36 Copynumber: 3.9 Consensus size: 36
2374022 TAATGTCTAG
*
2374032 TTTTAAAAACGTATATAATATATAGTTTTGAAAACA
1 TTTTAAAAACGTATATAATATATAGTTTTGAAAAGA
* * *
2374068 TTTTTGAAAACG--TATAATATATGGTTTTG-AAAGCG
1 -TTTTAAAAACGTATATAATATATAGTTTTGAAAAG-A
2374103 TTTTAAAAACGTATATAATATATAGTTTTGAAAAGA
1 TTTTAAAAACGTATATAATATATAGTTTTGAAAAGA
*
2374139 TTTTGAAAACGTATAT-A-ATATAGTTTTGAAAA
1 TTTTAAAAACGTATATAATATATAGTTTTGAAAA
2374171 CATATATATA
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
34 28 0.31
35 17 0.19
36 31 0.34
37 14 0.16
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTTAAAAACGTATATAATATATAGTTTTGAAAAGA
Found at i:2374276 original size:17 final size:16
Alignment explanation
Indices: 2374234--2374300 Score: 63
Period size: 15 Copynumber: 4.3 Consensus size: 16
2374224 ATAAACTTAC
2374234 ATATTATA-TAATTAT
1 ATATTATATTAATTAT
2374249 ATATT-TCATTACATTAT
1 ATATTAT-ATTA-ATTAT
2374266 ATATTATATTAA-TAT
1 ATATTATATTAATTAT
*
2374281 -TATTTATATTTATT-T
1 ATA-TTATATTAATTAT
2374296 ATATT
1 ATATT
2374301 TTTTTGTATA
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
14 3 0.07
15 20 0.45
16 6 0.14
17 14 0.32
18 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTATATTAATTAT
Found at i:2374295 original size:10 final size:10
Alignment explanation
Indices: 2374265--2374334 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
2374255 CATTACATTA
2374265 TATATTATATT
1 TATATT-TATT
*
2374276 AATA-TTATT
1 TATATTTATT
2374285 TATATTTATT
1 TATATTTATT
2374295 TATATTT-TT
1 TATATTTATT
* *
2374304 T-TGTATA-T
1 TATATTTATT
*
2374312 TATGTTTA-T
1 TATATTTATT
2374321 TATTATTTATT
1 TA-TATTTATT
2374332 TAT
1 TAT
2374335 TTTTTCAGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
8 5 0.10
9 18 0.38
10 19 0.40
11 6 0.12
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (10 bp):
TATATTTATT
Found at i:2374311 original size:37 final size:36
Alignment explanation
Indices: 2374270--2374339 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
2374260 CATTATATAT
2374270 TATATTA-ATATTATT-TATATTTATTTATATTTTTTTG
1 TATATTATAT-TTATTAT-TATTTATTTAT-TTTTTTTG
*
2374307 TATATTATGTTTATTATTATTTATTTATTTTTT
1 TATATTATATTTATTATTATTTATTTATTTTTT
2374340 CAGGTCCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
36 5 0.17
37 23 0.77
38 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (36 bp):
TATATTATATTTATTATTATTTATTTATTTTTTTTG
Found at i:2376230 original size:16 final size:16
Alignment explanation
Indices: 2376209--2376239 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2376199 TATTATTTAT
2376209 AAACTATATAATATGC
1 AAACTATATAATATGC
2376225 AAACTATATAATATG
1 AAACTATATAATATG
2376240 TAACACACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (16 bp):
AAACTATATAATATGC
Found at i:2376344 original size:20 final size:20
Alignment explanation
Indices: 2376298--2376335 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2376288 TAATATGAAT
2376298 TAAAATATGCCATGCAATAC
1 TAAAATATGCCATGCAATAC
2376318 TAAAATATGCCATGCAAT
1 TAAAATATGCCATGCAAT
2376336 TATTTAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (20 bp):
TAAAATATGCCATGCAATAC
Found at i:2377722 original size:41 final size:41
Alignment explanation
Indices: 2377677--2377767 Score: 102
Period size: 41 Copynumber: 2.2 Consensus size: 41
2377667 TCCTCATATA
*
2377677 TTCTCTAAAGC-AATCTTCA-GGTTTTCACTTTAGA-TTTTCTT
1 TTCTCTAAAGCGAAT-TT-ATGGTTTTCACTTT-GACATTTCTT
2377718 TTCTC-AAAGCGTAATTTATGGTTTTCACTTTGACATTTCTT
1 TTCTCTAAAGCG-AATTTATGGTTTTCACTTTGACATTTCTT
2377759 TTCT-TAAAG
1 TTCTCTAAAG
2377768 TGCCTTTGGG
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
40 8 0.18
41 33 0.75
42 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.48
Consensus pattern (41 bp):
TTCTCTAAAGCGAATTTATGGTTTTCACTTTGACATTTCTT
Found at i:2377836 original size:25 final size:25
Alignment explanation
Indices: 2377802--2377851 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2377792 CTTTCTTCTA
*
2377802 TTTTCCCTTTTT-TTGTTTTTTTGTT
1 TTTTCCCTTTTTCTT-TCTTTTTGTT
*
2377827 TTTTCTCTTTTTCTTTCTTTTTGTT
1 TTTTCCCTTTTTCTTTCTTTTTGTT
2377852 ATTCTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (25 bp):
TTTTCCCTTTTTCTTTCTTTTTGTT
Found at i:2377867 original size:24 final size:25
Alignment explanation
Indices: 2377819--2377865 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
2377809 TTTTTTTGTT
*
2377819 TTTTTGTTTTTTCTCTTTTTCTTTC
1 TTTTTGTTTATTCTCTTTTTCTTTC
2377844 TTTTTG-TTATTCT-TTTTTCTTT
1 TTTTTGTTTATTCTCTTTTTCTTT
2377866 TCAAAACTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 6 0.29
25 6 0.29
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (25 bp):
TTTTTGTTTATTCTCTTTTTCTTTC
Found at i:2378552 original size:28 final size:25
Alignment explanation
Indices: 2378521--2378603 Score: 69
Period size: 28 Copynumber: 3.0 Consensus size: 25
2378511 TCTTGAACCC
2378521 TCTTTCATTTCTCTTTTTTATTTTTCTT
1 TCTTTC-TTT-TCTTTTTT-TTTTTCTT
2378549 TCTTT-TTTGTCTTTTTCTTTTTTTCTAT
1 TCTTTCTTT-TC-TTTT-TTTTTTTCT-T
*
2378577 TCTTTTCGTTTTCTTTTATTTTTTCTT
1 TC-TTTC-TTTTCTTTTTTTTTTTCTT
2378604 CTTCAAGCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
26 5 0.11
27 12 0.26
28 18 0.38
29 7 0.15
30 2 0.04
31 3 0.06
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (25 bp):
TCTTTCTTTTCTTTTTTTTTTTCTT
Found at i:2378582 original size:19 final size:19
Alignment explanation
Indices: 2378523--2378572 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2378513 TTGAACCCTC
*
2378523 TTTCATTTCTCTTTTT-TATT
1 TTTC-TTTCT-TTTTTGTCTT
2378543 TTTCTTTCTTTTTTGTCTT
1 TTTCTTTCTTTTTTGTCTT
2378562 TTTCTTT-TTTT
1 TTTCTTTCTTTT
2378573 CTATTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 9 0.32
19 15 0.54
20 4 0.14
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTCTTTCTTTTTTGTCTT
Done.