Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 32 of 193
Found at i:10077379 original size:15 final size:15
Alignment explanation
Indices: 10077359--10077388 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10077349 AACTTAAAGT
10077359 GGTGATAGTAAGATA
1 GGTGATAGTAAGATA
10077374 GGTGATAGTAAGATA
1 GGTGATAGTAAGATA
10077389 TATTGTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (15 bp):
GGTGATAGTAAGATA
Found at i:10079011 original size:16 final size:16
Alignment explanation
Indices: 10078990--10079022 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
10078980 ATGTTTGTTT
10078990 CATTATCTTCCTTTGA
1 CATTATCTTCCTTTGA
10079006 CATTATCTTCCTTTGA
1 CATTATCTTCCTTTGA
10079022 C
1 C
10079023 TTTTGTGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.27, G:0.06, T:0.48
Consensus pattern (16 bp):
CATTATCTTCCTTTGA
Found at i:10085319 original size:22 final size:22
Alignment explanation
Indices: 10085289--10085336 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
10085279 CGAATGTAAC
*
10085289 ATCAAAAACTAGTATATATGAA
1 ATCAAAAACTAGTATATATAAA
*
10085311 ATCACAAACTAGTATATATAAA
1 ATCAAAAACTAGTATATATAAA
10085333 ATCA
1 ATCA
10085337 GAGTTTGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.27
Consensus pattern (22 bp):
ATCAAAAACTAGTATATATAAA
Found at i:10087848 original size:32 final size:29
Alignment explanation
Indices: 10087781--10087850 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 29
10087771 TAACTTATAT
*
10087781 TTAAAAATAAAAATTATAAATAAAAAATT
1 TTAAAAATAAAAATTATAAATAAAAAATC
**
10087810 TCTAAAAATACAAAATATATATGTAAAAAAATC
1 T-TAAAAATA-AAAAT-TATAAAT-AAAAAATC
10087843 TTAAAAAT
1 TTAAAAAT
10087851 TTACGAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 1 0.03
30 8 0.24
31 5 0.15
32 12 0.35
33 8 0.24
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30
Consensus pattern (29 bp):
TTAAAAATAAAAATTATAAATAAAAAATC
Found at i:10092467 original size:17 final size:17
Alignment explanation
Indices: 10092445--10092483 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
10092435 GGTGGAGAAT
* *
10092445 TTGTTCGTTGAGAGTTC
1 TTGTTCGTAGAGAATTC
10092462 TTGTTCGTAGAGAATTC
1 TTGTTCGTAGAGAATTC
10092479 TTGTT
1 TTGTT
10092484 AAGGTGGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
TTGTTCGTAGAGAATTC
Found at i:10094295 original size:16 final size:15
Alignment explanation
Indices: 10094265--10094298 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
10094255 AAGGAAAGGA
*
10094265 AAATGAAAAATAAAT
1 AAATAAAAAATAAAT
10094280 AAATAAAAAGATAAAT
1 AAATAAAAA-ATAAAT
10094296 AAA
1 AAA
10094299 AGATTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (15 bp):
AAATAAAAAATAAAT
Found at i:10095837 original size:118 final size:117
Alignment explanation
Indices: 10095613--10095848 Score: 454
Period size: 118 Copynumber: 2.0 Consensus size: 117
10095603 CTGACTTTAG
10095613 CTGGCACTTGTAAATTCCATAGTTTTTTATAAAAAGTTCGAGCACTGGTCTGTATATTAATAGGA
1 CTGGCACTTGTAAATTCCATAGTTTTTTATAAAAAGTTCGAGCACTGGTCTGTATATTAATAGGA
*
10095678 TTGGCAACACCTCTTTGTAATAGTTTATAAAAGCTTCTCATTGAGAAGACCT
66 TTAGCAACACCTCTTTGTAATAGTTTATAAAAGCTTCTCATTGAGAAGACCT
10095730 CTGGCACTTGTAAATTCCATAGTTTTTTATAAAAAGTTCGAGCACTGGTCTGTATAATTAATAGG
1 CTGGCACTTGTAAATTCCATAGTTTTTTATAAAAAGTTCGAGCACTGGTCTGTAT-ATTAATAGG
10095795 ATTAGCAACACCTCTTTGTAATAGTTTATAAAAGCTTCTCATTGAGAAGACCT
65 ATTAGCAACACCTCTTTGTAATAGTTTATAAAAGCTTCTCATTGAGAAGACCT
10095848 C
1 C
10095849 AGAAAGTTCC
Statistics
Matches: 117, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
117 55 0.47
118 62 0.53
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (117 bp):
CTGGCACTTGTAAATTCCATAGTTTTTTATAAAAAGTTCGAGCACTGGTCTGTATATTAATAGGA
TTAGCAACACCTCTTTGTAATAGTTTATAAAAGCTTCTCATTGAGAAGACCT
Found at i:10100563 original size:2 final size:2
Alignment explanation
Indices: 10100556--10100586 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10100546 TTCTAAACAT
10100556 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10100587 TTAAATTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10104265 original size:3 final size:3
Alignment explanation
Indices: 10104257--10104285 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10104247 CAGAAAAAGA
10104257 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
10104286 ATTACTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10109405 original size:8 final size:9
Alignment explanation
Indices: 10109392--10109592 Score: 120
Period size: 9 Copynumber: 21.1 Consensus size: 9
10109382 ATAAAAAAAG
10109392 TAAAAATTA
1 TAAAAATTA
10109401 TAAAAATTA
1 TAAAAATTA
10109410 TAAAAATTA
1 TAAAAATTA
**
10109419 TTAAATTTTAA
1 -TAAAAATT-A
10109430 TAAAAA-TA
1 TAAAAATTA
*
10109438 TAGAAAATATT
1 TA-AAAAT-TA
10109449 TAAAAATTAGA
1 TAAAAATT--A
*
10109460 AAAAAATTA
1 TAAAAATTA
*
10109469 TAAAAATCA
1 TAAAAATTA
*
10109478 TTAAAAAATA
1 -TAAAAATTA
10109488 T-AAAATATA
1 TAAAAAT-TA
*
10109497 TAAAAATATG
1 TAAAAAT-TA
10109507 TAAAAATTA
1 TAAAAATTA
*
10109516 T-AAAATTT
1 TAAAAATTA
*
10109524 TATAAAATTG
1 TA-AAAATTA
10109534 TAAGAAAATTA
1 T-A-AAAATTA
* *
10109545 TAAAAAATG
1 TAAAAATTA
*
10109554 TAAAGAAATA
1 TAAA-AATTA
** *
10109564 TAAATTTTG
1 TAAAAATTA
10109573 TAAAAAATTA
1 T-AAAAATTA
10109583 TAAAAATTA
1 TAAAAATTA
10109592 T
1 T
10109593 CATACTAAAA
Statistics
Matches: 149, Mismatches: 28, Indels: 30
0.72 0.14 0.14
Matches are distributed among these distances:
8 14 0.09
9 58 0.39
10 58 0.39
11 19 0.13
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:10109406 original size:19 final size:18
Alignment explanation
Indices: 10109375--10109520 Score: 91
Period size: 18 Copynumber: 7.7 Consensus size: 18
10109365 GATATGTGGA
*
10109375 AAAAATGATAAAAA-AAGT
1 AAAAATTATAAAAATAA-T
*
10109393 AAAAATTATAAAAATTAT
1 AAAAATTATAAAAATAAT
**
10109411 AAAAATTATTAAATTTTAAT
1 AAAAATTA-TAAA-AATAAT
*
10109431 AAAAA-TATAGAAAATATTT
1 AAAAATTATA-AAAATA-AT
* *
10109450 AAAAATTAGAAAAAAATTAT
1 AAAAATT--ATAAAAATAAT
* *
10109470 AAAAATCATTAAAA-AAT
1 AAAAATTATAAAAATAAT
*
10109487 ATAAAATATATAAAAATATGT
1 A-AAAAT-TATAAAAATA-AT
10109508 AAAAATTATAAAA
1 AAAAATTATAAAA
10109521 TTTTATAAAA
Statistics
Matches: 98, Mismatches: 18, Indels: 23
0.71 0.13 0.17
Matches are distributed among these distances:
17 3 0.03
18 36 0.37
19 28 0.29
20 22 0.22
21 7 0.07
22 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAAATTATAAAAATAAT
Found at i:10109423 original size:10 final size:10
Alignment explanation
Indices: 10109392--10109552 Score: 78
Period size: 10 Copynumber: 16.7 Consensus size: 10
10109382 ATAAAAAAAG
10109392 TAAAAATTA-
1 TAAAAATTAT
10109401 TAAAAATTA-
1 TAAAAATTAT
10109410 TAAAAATTAT
1 TAAAAATTAT
** *
10109420 TAAATTTTAA
1 TAAAAATTAT
10109430 TAAAAA-TA-
1 TAAAAATTAT
10109438 TAGAAAA-TATT
1 TA-AAAATTA-T
*
10109449 TAAAAATTAGA
1 TAAAAATTA-T
*
10109460 AAAAAATTA-
1 TAAAAATTAT
*
10109469 TAAAAATCAT
1 TAAAAATTAT
*
10109479 TAAAAAATA-
1 TAAAAATTAT
10109488 T-AAAA-TAT
1 TAAAAATTAT
10109496 ATAAAAA-TAT
1 -TAAAAATTAT
10109506 GTAAAAATTA-
1 -TAAAAATTAT
10109516 T-AAAATT-T
1 TAAAAATTAT
*
10109524 TATAAAATTGT
1 TA-AAAATTAT
*
10109535 AAGAAAATTAT
1 TA-AAAATTAT
*
10109546 AAAAAAT
1 TAAAAAT
10109553 GTAAAGAAAT
Statistics
Matches: 122, Mismatches: 16, Indels: 27
0.74 0.10 0.16
Matches are distributed among these distances:
7 2 0.02
8 13 0.11
9 36 0.30
10 46 0.38
11 25 0.20
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:10109485 original size:31 final size:28
Alignment explanation
Indices: 10109374--10109589 Score: 127
Period size: 28 Copynumber: 7.6 Consensus size: 28
10109364 TGATATGTGG
* * *
10109374 AAAAAATGATAAAAAAAGTAAAAATT-A
1 AAAAAATTATAAAAATATTAAAAATTAA
* **
10109401 TAAAAATTATAAAAATTATTAAATTTTAA
1 AAAAAATTATAAAAA-TATTAAAAATTAA
*
10109430 TAAAAA-TATAGAAAATATTTAAAAATTAGA
1 AAAAAATTATA-AAAATA-TTAAAAATTA-A
* *
10109460 AAAAAATTATAAAAATCATTAAAAAATAT
1 AAAAAATTATAAAAAT-ATTAAAAATTAA
* *
10109489 AAAATA-TATAAAAATATGTAAAAATTAT
1 AAAAAATTATAAAAATAT-TAAAAATTAA
** * * * *
10109517 AAAATTTTATAAAATTGTAAGAAAATTAT
1 AAAAAATTATAAAAATATTA-AAAATTAA
** **
10109546 AAAAAATGTA-AAGAAATA-TAAATTTTGT
1 AAAAAAT-TATAA-AAATATTAAAAATTAA
10109574 AAAAAATTATAAAAAT
1 AAAAAATTATAAAAAT
10109590 TATCATACTA
Statistics
Matches: 151, Mismatches: 25, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
27 21 0.14
28 51 0.34
29 49 0.32
30 25 0.17
31 5 0.03
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (28 bp):
AAAAAATTATAAAAATATTAAAAATTAA
Found at i:10109529 original size:19 final size:19
Alignment explanation
Indices: 10109392--10109592 Score: 119
Period size: 19 Copynumber: 10.5 Consensus size: 19
10109382 ATAAAAAAAG
10109392 TAAAAATTATAAAA-ATTA
1 TAAAAATTATAAAATATTA
* *
10109410 TAAAAATTATTAAATTTTAA
1 TAAAAATTATAAAATATT-A
*
10109430 TAAAAATATAGAAAATATT-
1 TAAAAAT-TATAAAATATTA
* *
10109449 TAAAAATTAGAAAAAAATTA
1 TAAAAATTA-TAAAATATTA
* *
10109469 TAAAAATCATTAAAA-AATA
1 TAAAAATTA-TAAAATATTA
*
10109488 T-AAAATATATAAAA-ATATG
1 TAAAAAT-TATAAAATAT-TA
*
10109507 TAAAAATTATAAAATTTTA
1 TAAAAATTATAAAATATTA
* *
10109526 T-AAAATTGTAAGAAAATTA
1 TAAAAATTATAA-AATATTA
* * *
10109545 TAAAAAATGTAAAGA-AATA
1 TAAAAATTATAAA-ATATTA
** * *
10109564 TAAATTTTGTAAAAAATTA
1 TAAAAATTATAAAATATTA
10109583 TAAAAATTAT
1 TAAAAATTAT
10109593 CATACTAAAA
Statistics
Matches: 142, Mismatches: 28, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
18 36 0.25
19 62 0.44
20 36 0.25
21 8 0.06
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
TAAAAATTATAAAATATTA
Found at i:10109543 original size:21 final size:21
Alignment explanation
Indices: 10109517--10109561 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
10109507 TAAAAATTAT
* *
10109517 AAAATTTTATAAAATTGT-AAG
1 AAAATTATA-AAAAATGTAAAG
10109538 AAAATTATAAAAAATGTAAAG
1 AAAATTATAAAAAATGTAAAG
10109559 AAA
1 AAA
10109562 TATAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (21 bp):
AAAATTATAAAAAATGTAAAG
Found at i:10109577 original size:76 final size:75
Alignment explanation
Indices: 10109429--10109592 Score: 183
Period size: 76 Copynumber: 2.1 Consensus size: 75
10109419 TTAAATTTTA
*
10109429 ATAAAAATATAGAAAATATTTAAAAATTAGAAAAAAATTATAAAAATCATTAAAAAATATAAAAT
1 ATAAAAAT-TATAAAATATTTAAAAATTAGAAAAAAATTATAAAAA-CATTAAAAAATATAAAAT
10109494 ATAT-AAAAATAT
64 ATATAAAAAAT-T
* *
10109506 GTAAAAATTATAAAAT-TTTATAAAATT-GTAAGAAAATTATAAAAA-ATGTAAAGAAATATAAA
1 ATAAAAATTATAAAATATTTA-AAAATTAG-AAAAAAATTATAAAAACAT-TAAA-AAATATAAA
* * *
10109568 TTTTGTAAAAAATT
62 ATATATAAAAAATT
10109582 ATAAAAATTAT
1 ATAAAAATTAT
10109593 CATACTAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
74 2 0.03
75 9 0.12
76 51 0.68
77 13 0.17
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.32
Consensus pattern (75 bp):
ATAAAAATTATAAAATATTTAAAAATTAGAAAAAAATTATAAAAACATTAAAAAATATAAAATAT
ATAAAAAATT
Found at i:10109780 original size:19 final size:19
Alignment explanation
Indices: 10109756--10109868 Score: 83
Period size: 19 Copynumber: 5.9 Consensus size: 19
10109746 GGGTCATACA
10109756 TTTTATAATTTTTTATTAT
1 TTTTATAATTTTTTATTAT
**
10109775 TTTTATAAAATTTTA-TAT
1 TTTTATAATTTTTTATTAT
*
10109793 ATTTTAT-ATTTTTTA-CAGT
1 -TTTTATAATTTTTTATTA-T
* *
10109812 TTTTATATTTTTTTCTTAT
1 TTTTATAATTTTTTATTAT
* *
10109831 TTTTAATAAATTTTAAGTT-T
1 TTTT-ATAATTTTTTA-TTAT
10109851 TTTTAT-ATATTTTTATTA
1 TTTTATAAT-TTTTTATTA
10109869 ATACTTAATA
Statistics
Matches: 72, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
18 19 0.26
19 38 0.53
20 13 0.18
21 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTATAATTTTTTATTAT
Found at i:10109790 original size:29 final size:30
Alignment explanation
Indices: 10109755--10109866 Score: 101
Period size: 29 Copynumber: 3.9 Consensus size: 30
10109745 AGGGTCATAC
10109755 ATTTTATAATTTTTTATTATTTTTATA-AA
1 ATTTTATAATTTTTTATTATTTTTATACAA
* *
10109784 ATTTTAT-ATATTTTA-TATTTTT-TACAG
1 ATTTTATAATTTTTTATTATTTTTATACAA
* * * *
10109811 TTTTTATATTTTTTTCTTATTTTTA-ATAA
1 ATTTTATAATTTTTTATTATTTTTATACAA
*
10109840 ATTTTA-AGTTTTTTTATATATTTTTAT
1 ATTTTATA-ATTTTTTAT-TATTTTTAT
10109867 TAATACTTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
26 2 0.03
27 14 0.21
28 13 0.20
29 29 0.44
30 8 0.12
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (30 bp):
ATTTTATAATTTTTTATTATTTTTATACAA
Found at i:10109833 original size:18 final size:18
Alignment explanation
Indices: 10109755--10109921 Score: 67
Period size: 19 Copynumber: 8.8 Consensus size: 18
10109745 AGGGTCATAC
10109755 ATTTTATAATTTTTTATT
1 ATTTTATAATTTTTTATT
**
10109773 ATTTTTATAAAATTTTATAT
1 A-TTTTATAATTTTTTAT-T
*
10109793 ATTTTAT-ATTTTTTA-C
1 ATTTTATAATTTTTTATT
* *
10109809 AGTTTTTATATTTTTTTCTT
1 A--TTTTATAATTTTTTATT
* *
10109829 ATTTTTAATAAATTTTAAGTT
1 A-TTTT-ATAATTTTTTA-TT
*
10109850 TTTTTAT-ATATTTTTATT
1 ATTTTATAAT-TTTTTATT
* *
10109868 AATACTTAATAA-TTTTTATA
1 -AT--TTTATAATTTTTTATT
*
10109888 ACTTTTATTGA-TTTTTATT
1 A-TTTTA-TAATTTTTTATT
10109907 -TTTTATATATTTTTT
1 ATTTTATA-ATTTTTT
10109922 TGCACATGTC
Statistics
Matches: 110, Mismatches: 22, Indels: 34
0.66 0.13 0.20
Matches are distributed among these distances:
16 2 0.02
17 6 0.05
18 24 0.22
19 49 0.45
20 22 0.20
21 6 0.05
22 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTTATAATTTTTTATT
Found at i:10109863 original size:10 final size:10
Alignment explanation
Indices: 10109756--10109920 Score: 72
Period size: 10 Copynumber: 17.4 Consensus size: 10
10109746 GGGTCATACA
10109756 TTTTATA-AT
1 TTTTATATAT
10109765 TTTT-TATTAT
1 TTTTATA-TAT
* *
10109775 TTTTATAAAA
1 TTTTATATAT
10109785 TTTTATATA-
1 TTTTATATAT
10109794 TTTTATAT-T
1 TTTTATATAT
* *
10109803 TTTTACA-GT
1 TTTTATATAT
*
10109812 TTTTATATTT
1 TTTTATATAT
*
10109822 TTTTCT-TAT
1 TTTTATATAT
*
10109831 TTTTA-ATAAA
1 TTTTATAT-AT
*
10109841 TTTTA-AGTTT
1 TTTTATA-TAT
10109851 TTTTATATAT
1 TTTTATATAT
10109861 TTTTAT-TAAT
1 TTTTATAT-AT
**
10109871 ACTTA-ATAAT
1 TTTTATAT-AT
*
10109881 TTTTATA-AC
1 TTTTATATAT
10109890 TTTTAT-TGA-
1 TTTTATAT-AT
10109899 TTTT-TAT-T
1 TTTTATATAT
10109907 TTTTATATAT
1 TTTTATATAT
10109917 TTTT
1 TTTT
10109921 TTGCACATGT
Statistics
Matches: 119, Mismatches: 18, Indels: 37
0.68 0.10 0.21
Matches are distributed among these distances:
8 7 0.06
9 48 0.40
10 59 0.50
11 5 0.04
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTATATAT
Found at i:10110129 original size:83 final size:83
Alignment explanation
Indices: 10110040--10110222 Score: 219
Period size: 86 Copynumber: 2.2 Consensus size: 83
10110030 TTGACAATTC
* * * *
10110040 AAGTACTCAATTGGGTGCAAAAAAAATTAGGAGATTAA-TTTTTTTTTAAGTTTGA-GA-GTCTT
1 AAGTACTTAATTGAGTG-AAAAAAAA-CAGGAGATTAATTTTTTTTTTAA-TTTGAGGATATCTT
*
10110102 TTTGATGTATTTTGAAAGTTT
63 TTTGATATATTTTGAAAGTTT
* *
10110123 AAGTACTTAATTGAGTGAAAAAAAACAGGAGCTTAATTGTTTTTTTTTTAATTTGAGGATATTTT
1 AAGTACTTAATTGAGTGAAAAAAAACAGGAGATTAA---TTTTTTTTTTAATTTGAGGATATCTT
*
10110188 TTTTATATATTTTGAAAGTTT
63 TTTGATATATTTTGAAAGTTT
10110209 AAGTACTTAATTGA
1 AAGTACTTAATTGA
10110223 ATACAAAAAG
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
81 9 0.10
82 8 0.09
83 15 0.17
84 5 0.06
85 13 0.15
86 36 0.42
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (83 bp):
AAGTACTTAATTGAGTGAAAAAAAACAGGAGATTAATTTTTTTTTTAATTTGAGGATATCTTTTT
GATATATTTTGAAAGTTT
Found at i:10110254 original size:86 final size:85
Alignment explanation
Indices: 10110079--10110255 Score: 207
Period size: 86 Copynumber: 2.1 Consensus size: 85
10110069 GGAGATTAAT
* * *
10110079 TTTTTTTTAAGTTTGAGAGTCTTTTTGATGTATTTTGAAAGTTTAAGTACTTAATTGAGTGAAAA
1 TTTTTTTTAAGTTTGAGAATCTTTTTGATATATTTTGAAAGTTTAAGTACTTAATTGAATGAAAA
* **
10110144 AAAACAGGAGCTTAATTGTT
66 AAAACAGGAACTTAATTGAC
* *
10110164 TTTTTTTTAA-TTTGAGGATATTTTTTTTATATATTTTGAAAGTTTAAGTACTTAATTGAAT-AC
1 TTTTTTTTAAGTTTGA-GA-ATCTTTTTGATATATTTTGAAAGTTTAAGTACTTAATTGAATGA-
* *
10110227 AAAAAGAATAGGAATTTAATT-AC
63 AAAAA-AACAGGAACTTAATTGAC
10110250 TTTTTT
1 TTTTTT
10110256 GAAAAAATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
84 5 0.06
85 13 0.17
86 48 0.62
87 12 0.15
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (85 bp):
TTTTTTTTAAGTTTGAGAATCTTTTTGATATATTTTGAAAGTTTAAGTACTTAATTGAATGAAAA
AAAACAGGAACTTAATTGAC
Found at i:10112363 original size:16 final size:16
Alignment explanation
Indices: 10112341--10112379 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
10112331 TATCTCTATC
*
10112341 ATATTTATTTATAATAT
1 ATATTTATAT-TAATAT
10112358 -TATTTATATTAATAT
1 ATATTTATATTAATAT
10112373 ATATTTA
1 ATATTTA
10112380 ATAGCTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATTTATATTAATAT
Found at i:10118335 original size:19 final size:20
Alignment explanation
Indices: 10118298--10118335 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
10118288 ACCACATAGC
*
10118298 ATGTTTTGATCAATGAAAAA
1 ATGTTGTGATCAATGAAAAA
*
10118318 ATGTTGTGA-CAATTAAAA
1 ATGTTGTGATCAATGAAAA
10118336 TAAAAACATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (20 bp):
ATGTTGTGATCAATGAAAAA
Found at i:10120210 original size:24 final size:24
Alignment explanation
Indices: 10120183--10120261 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 24
10120173 TGGTTGAAGG
* *
10120183 TTTAACATAGTTGAGGGTTTAGTA
1 TTTAGCATAGTTAAGGGTTTAGTA
*
10120207 TTTAGCATGGTTTAA-GGTTTAGTA
1 TTTAGCATAG-TTAAGGGTTTAGTA
*
10120231 TTTAGCA-CGATTAAGGGTTTAGTA
1 TTTAGCATAG-TTAAGGGTTTAGTA
10120255 TTTAGCA
1 TTTAGCA
10120262 GGATTAAGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 5 0.10
24 40 0.83
25 3 0.06
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (24 bp):
TTTAGCATAGTTAAGGGTTTAGTA
Found at i:10120266 original size:24 final size:24
Alignment explanation
Indices: 10120196--10120269 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
10120186 AACATAGTTG
*
10120196 AGGGTTTAGTATTTAGCATGGTTTA
1 AGGGTTTAGTATTTAGCA-GGATTA
*
10120221 A-GGTTTAGTATTTAGCACGATTA
1 AGGGTTTAGTATTTAGCAGGATTA
10120244 AGGGTTTAGTATTTAGCAGGATTA
1 AGGGTTTAGTATTTAGCAGGATTA
10120268 AG
1 AG
10120270 AGCTTAGGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.11
24 39 0.87
25 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.27, T:0.39
Consensus pattern (24 bp):
AGGGTTTAGTATTTAGCAGGATTA
Found at i:10120582 original size:14 final size:13
Alignment explanation
Indices: 10120550--10120583 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
10120540 TATTAAGAAT
10120550 AAATTTTTTAATA
1 AAATTTTTTAATA
*
10120563 ATATTTTTTAATGA
1 AAATTTTTTAAT-A
10120577 AAATTTT
1 AAATTTT
10120584 AATATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
AAATTTTTTAATA
Found at i:10127979 original size:29 final size:29
Alignment explanation
Indices: 10127940--10128014 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
10127930 AAATAATTTT
10127940 AAAATTATTAAAATTAGTTTTT-AAAATAA
1 AAAATTATTAAAATTA-TTTTTCAAAATAA
10127969 AAAATTATTAAAATTATTTTTCAAAATAA
1 AAAATTATTAAAATTATTTTTCAAAATAA
10127998 AAAATTATTAAAATTAT
1 AAAATTATTAAAATTAT
10128015 CGTCATCCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 5 0.11
29 40 0.89
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (29 bp):
AAAATTATTAAAATTATTTTTCAAAATAA
Found at i:10132125 original size:27 final size:27
Alignment explanation
Indices: 10132072--10132131 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
10132062 GTGCACTGTA
*
10132072 CTTGAAATTCGAGTTTAGATCTGCTTC
1 CTTGAAATTCGAGTTTAGACCTGCTTC
* *
10132099 CTTGAAATTCCGTGTTT-GACCTTCTTC
1 CTTGAAATT-CGAGTTTAGACCTGCTTC
*
10132126 TTTGAA
1 CTTGAA
10132132 CCTCCCAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (27 bp):
CTTGAAATTCGAGTTTAGACCTGCTTC
Found at i:10137156 original size:166 final size:166
Alignment explanation
Indices: 10136876--10137210 Score: 598
Period size: 166 Copynumber: 2.0 Consensus size: 166
10136866 TGAAGTTGAG
10136876 TAAGGAAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTTATTTCAGATGACTTC
1 TAAGGAAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTTATTTCAGATGACTTC
* * *
10136941 GAGGATCTTATGACTCTGTTGTGTTCTTCTTTTAGGAAATCTTTCAGCATTTTTATGTAATCATT
66 GAGGATCTTATGACTCTGTTCTGTTCTTCCTTTAGGAAATCTTTCAGCATTTTCATGTAATCATT
* *
10137006 GCGATTGTTTAGTTGTCTTCCCTAATTTCTTTTAAT
131 GCGATTGTCTAGTTGTCTTCCCTAATTTCCTTTAAT
* * *
10137042 TAAGGCAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAACTCTTTATTTCAGATGACTTT
1 TAAGGAAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTTATTTCAGATGACTTC
10137107 GAGGATCTTATGACTCTGTTCTGTTCTTCCTTTAGGAAATCTTTCAGCATTTTCATGTAATCATT
66 GAGGATCTTATGACTCTGTTCTGTTCTTCCTTTAGGAAATCTTTCAGCATTTTCATGTAATCATT
10137172 GCGATTGTCTAGTTGTCTTCCCTAATTTCCTTTAAT
131 GCGATTGTCTAGTTGTCTTCCCTAATTTCCTTTAAT
10137208 TAA
1 TAA
10137211 TTTTTCCTCG
Statistics
Matches: 161, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
166 161 1.00
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (166 bp):
TAAGGAAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTTATTTCAGATGACTTC
GAGGATCTTATGACTCTGTTCTGTTCTTCCTTTAGGAAATCTTTCAGCATTTTCATGTAATCATT
GCGATTGTCTAGTTGTCTTCCCTAATTTCCTTTAAT
Found at i:10142962 original size:21 final size:21
Alignment explanation
Indices: 10142932--10142989 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
10142922 TTTTTTCGAA
*
10142932 TCGAGTCGAGTGAAATGAAAT
1 TCGAGACGAGTGAAATGAAAT
10142953 TCGAGACGAGTGAAATGAAAT
1 TCGAGACGAGTGAAATGAAAT
*
10142974 TCAAGACGAGTGAAAT
1 TCGAGACGAGTGAAAT
10142990 TGTTCGAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (21 bp):
TCGAGACGAGTGAAATGAAAT
Found at i:10147162 original size:3 final size:3
Alignment explanation
Indices: 10147156--10147207 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
10147146 GATAGTGGTG
10147156 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
10147204 GAA G
1 GAA G
10147208 TTTCATCTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:10151638 original size:18 final size:17
Alignment explanation
Indices: 10151608--10151642 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
10151598 AAATTTAATA
10151608 ATTTTTATAATTTTTTG
1 ATTTTTATAATTTTTTG
*
10151625 ATTTATTATTATTTTTTG
1 ATTT-TTATAATTTTTTG
10151643 TCTCATGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
ATTTTTATAATTTTTTG
Found at i:10154192 original size:29 final size:29
Alignment explanation
Indices: 10154146--10154206 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
10154136 TGAAAAAAAA
* *
10154146 TTTCTTCTCTCAACTTCTCCCATCATCTT
1 TTTCTTCTCTCAACTTCTCCCAACATATT
* **
10154175 TTTCTTCTCTTATTTTCTCCCAACATATT
1 TTTCTTCTCTCAACTTCTCCCAACATATT
10154204 TTT
1 TTT
10154207 TTTTCACTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTCTTCTCTCAACTTCTCCCAACATATT
Found at i:10154220 original size:30 final size:29
Alignment explanation
Indices: 10154146--10154222 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
10154136 TGAAAAAAAA
* ** *
10154146 TTTCTTCTCTCAACTTCTCCCATCATCTT
1 TTTCTTCACTCATTTTCTCCCAACATCTT
* * *
10154175 TTTCTTCTCTTATTTTCTCCCAACATATTT
1 TTTCTTCACTCATTTTCTCCCAACAT-CTT
*
10154205 TTTTTTCACTCATTTTCT
1 TTTCTTCACTCATTTTCT
10154223 TTCCAACACA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 22 0.56
30 17 0.44
ACGTcount: A:0.14, C:0.30, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTCTTCACTCATTTTCTCCCAACATCTT
Found at i:10154963 original size:24 final size:24
Alignment explanation
Indices: 10154935--10154980 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
10154925 AAAAGCTTTA
10154935 TTTTT-TTAATTCTATATTAAAATG
1 TTTTTCTTAATTCTAT-TTAAAATG
* *
10154959 TTTTTCTTTATTTTATTTAAAA
1 TTTTTCTTAATTCTATTTAAAA
10154981 AATTGGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTTCTTAATTCTATTTAAAATG
Found at i:10155903 original size:2 final size:2
Alignment explanation
Indices: 10155896--10155924 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10155886 AAATATAGTG
10155896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10155925 TACAACCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10163698 original size:19 final size:19
Alignment explanation
Indices: 10163671--10163710 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
10163661 GAAACCTTTG
10163671 ATTTATCAATTTCATTCTC
1 ATTTATCAATTTCATTCTC
*
10163690 ATTTCTCAATTTCATTCTC
1 ATTTATCAATTTCATTCTC
10163709 AT
1 AT
10163711 ATCACTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTATCAATTTCATTCTC
Found at i:10164099 original size:12 final size:12
Alignment explanation
Indices: 10164049--10164103 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
10164039 TAATAGGGAT
10164049 TTTCAATTT-AC
1 TTTCAATTTCAC
*
10164060 TATTC-ATATCAC
1 T-TTCAATTTCAC
* *
10164072 TTTCAATTCCAA
1 TTTCAATTTCAC
*
10164084 TTTCACTTTCAC
1 TTTCAATTTCAC
10164096 TTTCAATT
1 TTTCAATT
10164104 CTGATCACAA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
11 7 0.21
12 26 0.79
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.49
Consensus pattern (12 bp):
TTTCAATTTCAC
Found at i:10164839 original size:14 final size:14
Alignment explanation
Indices: 10164820--10164846 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10164810 CTTTTTCTTT
10164820 TTCCTTCCCTTTTC
1 TTCCTTCCCTTTTC
10164834 TTCCTTCCCTTTT
1 TTCCTTCCCTTTT
10164847 TCGTTTGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (14 bp):
TTCCTTCCCTTTTC
Found at i:10165643 original size:20 final size:20
Alignment explanation
Indices: 10165620--10165705 Score: 82
Period size: 20 Copynumber: 4.0 Consensus size: 20
10165610 AAGACGAATA
* *
10165620 AAAAATAACATCTAAACAAC
1 AAAAATAACAGCAAAACAAC
10165640 AAAAATAACAGCAAAACAAC
1 AAAAATAACAGCAAAACAAC
* **
10165660 ACAAATAGCAACAAAAACAACAAC
1 A-AAA-A-TAACAGCAA-AACAAC
10165684 AAAAATAACAGCAAAAACAAC
1 AAAAATAACAGC-AAAACAAC
10165705 A
1 A
10165706 CTAAAACAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
20 19 0.36
21 14 0.26
22 4 0.08
23 9 0.17
24 7 0.13
ACGTcount: A:0.69, C:0.21, G:0.03, T:0.07
Consensus pattern (20 bp):
AAAAATAACAGCAAAACAAC
Found at i:10165654 original size:12 final size:12
Alignment explanation
Indices: 10165634--10165705 Score: 62
Period size: 12 Copynumber: 6.3 Consensus size: 12
10165624 ATAACATCTA
*
10165634 AACAACAAAAAT
1 AACAACAAAAAC
*
10165646 AACAGC-AAAAC
1 AACAACAAAAAC
*
10165657 AAC-AC--AAAT
1 AACAACAAAAAC
*
10165666 AGCAACAAAAAC
1 AACAACAAAAAC
*
10165678 AACAACAAAAAT
1 AACAACAAAAAC
*
10165690 AACAGCAAAAAC
1 AACAACAAAAAC
10165702 AACA
1 AACA
10165706 CTAAAACAGT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
9 5 0.11
10 3 0.06
11 7 0.15
12 32 0.68
ACGTcount: A:0.69, C:0.22, G:0.04, T:0.04
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:10165711 original size:12 final size:11
Alignment explanation
Indices: 10165638--10165713 Score: 59
Period size: 12 Copynumber: 6.8 Consensus size: 11
10165628 CATCTAAACA
*
10165638 ACAAAAATAAC
1 ACAAAAACAAC
10165649 AGC-AAAACAAC
1 A-CAAAAACAAC
*
10165660 ACAAATAGC-A-
1 ACAAA-AACAAC
10165670 ACAAAAACAAC
1 ACAAAAACAAC
*
10165681 AACAAAAATAAC
1 -ACAAAAACAAC
10165693 AGCAAAAACAAC
1 A-CAAAAACAAC
*
10165705 ACTAAAACA
1 ACAAAAACA
10165714 GTAAAAAAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
9 2 0.04
10 7 0.13
11 20 0.38
12 23 0.44
ACGTcount: A:0.68, C:0.22, G:0.04, T:0.05
Consensus pattern (11 bp):
ACAAAAACAAC
Found at i:10165711 original size:24 final size:23
Alignment explanation
Indices: 10165638--10165711 Score: 91
Period size: 24 Copynumber: 3.3 Consensus size: 23
10165628 CATCTAAACA
10165638 ACAAAAATAACAGC-AAAACAAC
1 ACAAAAATAACAGCAAAAACAAC
* *
10165660 AC--AAATAGCAACAAAAACAAC
1 ACAAAAATAACAGCAAAAACAAC
10165681 AACAAAAATAACAGCAAAAACAAC
1 -ACAAAAATAACAGCAAAAACAAC
*
10165705 ACTAAAA
1 ACAAAAA
10165712 CAGTAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 8 0.19
21 8 0.19
22 4 0.09
23 6 0.14
24 17 0.40
ACGTcount: A:0.69, C:0.22, G:0.04, T:0.05
Consensus pattern (23 bp):
ACAAAAATAACAGCAAAAACAAC
Found at i:10165764 original size:22 final size:21
Alignment explanation
Indices: 10165696--10165798 Score: 93
Period size: 21 Copynumber: 4.9 Consensus size: 21
10165686 AAATAACAGC
* *
10165696 AAAAACAACACTAAAACAGTA
1 AAAAACAGCACCAAAACAGTA
** *
10165717 AAAAA-AGCATTAAAACAGCA
1 AAAAACAGCACCAAAACAGTA
*
10165737 TCAAAACAGCAACCAAAA-AGTGA
1 -AAAAACAGC-ACCAAAACAGT-A
*
10165760 AAAAAAAGCACCAAAACAGTA
1 AAAAACAGCACCAAAACAGTA
*
10165781 AAAAACAACACCAAAACA
1 AAAAACAGCACCAAAACA
10165799 ACAATATAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
20 12 0.18
21 33 0.50
22 15 0.23
23 6 0.09
ACGTcount: A:0.65, C:0.20, G:0.08, T:0.07
Consensus pattern (21 bp):
AAAAACAGCACCAAAACAGTA
Found at i:10169339 original size:37 final size:37
Alignment explanation
Indices: 10169289--10169373 Score: 161
Period size: 37 Copynumber: 2.3 Consensus size: 37
10169279 AAAAGAAATA
*
10169289 TAATTTAATGTAATGTAATTCATGTAGAAATAGTTTG
1 TAATTTAATGTAATGCAATTCATGTAGAAATAGTTTG
10169326 TAATTTAATGTAATGCAATTCATGTAGAAATAGTTTG
1 TAATTTAATGTAATGCAATTCATGTAGAAATAGTTTG
10169363 TAATTTAATGT
1 TAATTTAATGT
10169374 GTTAGGTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.44
Consensus pattern (37 bp):
TAATTTAATGTAATGCAATTCATGTAGAAATAGTTTG
Found at i:10170785 original size:29 final size:31
Alignment explanation
Indices: 10170731--10170795 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
10170721 TAATAAAGAT
10170731 AAAATTACACTTTAACCTCTTTAAAATAATA
1 AAAATTACACTTTAACCTCTTTAAAATAATA
* *
10170762 AAAATTA-A-TTTAATCT-TTTAAAAATTATA
1 AAAATTACACTTTAACCTCTTT-AAAATAATA
10170791 AAAAT
1 AAAAT
10170796 ATAAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 3 0.10
29 20 0.65
30 1 0.03
31 7 0.23
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.38
Consensus pattern (31 bp):
AAAATTACACTTTAACCTCTTTAAAATAATA
Found at i:10174096 original size:1 final size:1
Alignment explanation
Indices: 10174092--10174122 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
10174082 AAAAAAAAGC
10174092 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
10174123 CTGTTCTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:10181723 original size:16 final size:17
Alignment explanation
Indices: 10181702--10181737 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
10181692 CAATTCAAAA
*
10181702 AATAATAA-TATAAATT
1 AATAATAATTAGAAATT
10181718 AATAATAATTAGAAATT
1 AATAATAATTAGAAATT
10181735 AAT
1 AAT
10181738 TTATTGCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
AATAATAATTAGAAATT
Found at i:10190023 original size:27 final size:26
Alignment explanation
Indices: 10189976--10190053 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 26
10189966 TTTGGTTTTC
10189976 TTGAAAATTAAAAAACAATTTTAGAAAA
1 TTGAAAA-TAAAAAACAATTTTA-AAAA
* *
10190004 TTGAAAACAAAAAATAATTTTAAAAA
1 TTGAAAATAAAAAACAATTTTAAAAA
*
10190030 -TGAAAATAAAAAAC-ATTTAAAAAA
1 TTGAAAATAAAAAACAATTTTAAAAA
10190054 ATCAGACAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
24 9 0.20
25 12 0.27
26 4 0.09
27 13 0.29
28 7 0.16
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (26 bp):
TTGAAAATAAAAAACAATTTTAAAAA
Found at i:10190029 original size:26 final size:27
Alignment explanation
Indices: 10189976--10190044 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 27
10189966 TTTGGTTTTC
10189976 TTGAAAATTAAAAAACAATTTTAGAAAA
1 TTGAAAA-TAAAAAACAATTTTAGAAAA
* *
10190004 TTGAAAACAAAAAATAATTTTA-AAAA
1 TTGAAAATAAAAAACAATTTTAGAAAA
10190030 -TGAAAATAAAAAACA
1 TTGAAAATAAAAAACA
10190045 TTTAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 13 0.35
26 4 0.11
27 13 0.35
28 7 0.19
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (27 bp):
TTGAAAATAAAAAACAATTTTAGAAAA
Found at i:10190053 original size:25 final size:25
Alignment explanation
Indices: 10189977--10190055 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 25
10189967 TTGGTTTTCT
* *
10189977 TGAAAATTAAAAAACAATTTTAGAAAAT
1 TGAAAA-TAAAAAAC-A-TTTAAAAAAA
* * *
10190005 TGAAAACAAAAAATAATTT-TAAAAA
1 TGAAAATAAAAAA-CATTTAAAAAAA
10190030 TGAAAATAAAAAACATTTAAAAAAA
1 TGAAAATAAAAAACATTTAAAAAAA
10190055 T
1 T
10190056 CAGACAATAG
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
24 4 0.10
25 22 0.52
26 3 0.07
27 7 0.17
28 6 0.14
ACGTcount: A:0.66, C:0.04, G:0.05, T:0.25
Consensus pattern (25 bp):
TGAAAATAAAAAACATTTAAAAAAA
Found at i:10192106 original size:6 final size:6
Alignment explanation
Indices: 10192095--10192126 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
10192085 AGCACACTAT
10192095 ATATAA ATATAA ATATAA ATATAA ATATAA AT
1 ATATAA ATATAA ATATAA ATATAA ATATAA AT
10192127 TGTAATTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:10192717 original size:59 final size:58
Alignment explanation
Indices: 10192621--10192773 Score: 164
Period size: 59 Copynumber: 2.6 Consensus size: 58
10192611 TTAATATAAC
*
10192621 ATTTGGTACTTGAACTTGACACTTTTCCTAATTTGGTA-CTTAAAACTTTTTTTACCCA
1 ATTTGATACTTGAACTTGACACTTTTCCTAATTTGGTAGC-TAAAACTTTTTTTACCCA
* * * * **
10192679 ATTTGATATTTGAACTTGATAGTTTTTCTTAATTTGGTAGCTAAATTTTTTTTTACCCA
1 ATTTGATACTTGAACTTGACA-CTTTTCCTAATTTGGTAGCTAAAACTTTTTTTACCCA
* * * * *
10192738 ATTGGGTACCTAAACTTGACATGTTTTCCTAATTTG
1 ATTTGATACTTGAACTTGACA-CTTTTCCTAATTTG
10192774 ATACCCAATC
Statistics
Matches: 77, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
58 18 0.23
59 58 0.75
60 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (58 bp):
ATTTGATACTTGAACTTGACACTTTTCCTAATTTGGTAGCTAAAACTTTTTTTACCCA
Found at i:10193089 original size:93 final size:90
Alignment explanation
Indices: 10192957--10193152 Score: 270
Period size: 93 Copynumber: 2.1 Consensus size: 90
10192947 TTAAAAAAGA
* ***
10192957 TTAGGTACCAAATTAGAAAAACAAGTCAAGTTCAGGTACCAAATTGGACCCTAAAAAGTTTAAAT
1 TTAGGTACCAAATTAGAAAAAAAAGTCAAGTTCAGGTACCAAATTGGACAAAAAAAAGTTTAAAT
10193022 ACCAACA-TAAAAAAAAGTGTCAAGT
66 ACCAA-ATTAAAAAAAAGTGTCAAGT
* *
10193047 TTAGGTACTAAATTAGGAAAAAAAAATGTCAAGTT-TGAGTACCAAATTGGACAAAAAAAAGTTT
1 TTAGGTACCAAATTA-G-AAAAAAAA-GTCAAGTTCAG-GTACCAAATTGGACAAAAAAAAGTTT
*
10193111 AAATACCAAATTAAGAAAAAGTGTCAAGT
62 AAATACCAAATTAAAAAAAAGTGTCAAGT
10193140 TTAGGTACCAAAT
1 TTAGGTACCAAAT
10193153 GTTATAGTAA
Statistics
Matches: 93, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
90 14 0.15
91 1 0.01
92 9 0.10
93 69 0.74
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (90 bp):
TTAGGTACCAAATTAGAAAAAAAAGTCAAGTTCAGGTACCAAATTGGACAAAAAAAAGTTTAAAT
ACCAAATTAAAAAAAAGTGTCAAGT
Found at i:10193103 original size:35 final size:34
Alignment explanation
Indices: 10193030--10193152 Score: 104
Period size: 34 Copynumber: 3.9 Consensus size: 34
10193020 ATACCAACAT
* *
10193030 AAAAAAAAGTGTCAAGTTTAGGTACTAAATTAGG
1 AAAAAAAAATGTCAAGTTTAGGTACCAAATTAGG
10193064 AAAAAAAAATGTCAAGTTT-GAGTACCAAATT-GG
1 AAAAAAAAATGTCAAGTTTAG-GTACCAAATTAGG
* **
10193097 -ACAAAAAA----AAGTTTAAATACCAAATT---
1 AAAAAAAAATGTCAAGTTTAGGTACCAAATTAGG
* *
10193123 AAGAAAAAGTGTCAAGTTTAGGTACCAAAT
1 AAAAAAAAATGTCAAGTTTAGGTACCAAAT
10193153 GTTATAGTAA
Statistics
Matches: 73, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
27 6 0.08
28 15 0.21
31 15 0.21
32 7 0.10
33 3 0.04
34 27 0.37
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.24
Consensus pattern (34 bp):
AAAAAAAAATGTCAAGTTTAGGTACCAAATTAGG
Found at i:10196641 original size:24 final size:24
Alignment explanation
Indices: 10196573--10196647 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
10196563 ACAGACAACA
* * *
10196573 TTAGCTCTCACGAGCTTAGGATGG
1 TTAGCTCTTACGAGCCTAGAATGG
*
10196597 TTAGCTCTTACAAGTCC-AGAATGG
1 TTAGCTCTTACGAG-CCTAGAATGG
*
10196621 TTAGCTCTTACGAGCCTAGAATAG
1 TTAGCTCTTACGAGCCTAGAATGG
10196645 TTA
1 TTA
10196648 ACTAGTATAC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
23 2 0.05
24 40 0.93
25 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCTAGAATGG
Found at i:10201697 original size:18 final size:18
Alignment explanation
Indices: 10201684--10201739 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
10201674 TACGAGCCGG
*
10201684 TATGCTCAATCGAGCCAA
1 TATGCTCAAACGAGCCAA
*
10201702 TATGCTCAAACGAGCCAT
1 TATGCTCAAACGAGCCAA
*
10201720 TATGCTCAAATGAGCCAA
1 TATGCTCAAACGAGCCAA
10201738 TA
1 TA
10201740 AGCTATTCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (18 bp):
TATGCTCAAACGAGCCAA
Found at i:10203633 original size:20 final size:21
Alignment explanation
Indices: 10203586--10203636 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
10203576 TGGCTTGCTT
10203586 AAGGAACTTGGTGTTGAGCAC
1 AAGGAACTTGGTGTTGAGCAC
10203607 AAGGAACTTGGTGTTGAG-AC
1 AAGGAACTTGGTGTTGAGCAC
*
10203627 AATGAACTTG
1 AAGGAACTTG
10203637 TTATATTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.25
Consensus pattern (21 bp):
AAGGAACTTGGTGTTGAGCAC
Found at i:10206439 original size:19 final size:19
Alignment explanation
Indices: 10206415--10206457 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
10206405 AGTTGACTTT
*
10206415 AATTT-CAAAGTTTCAAAAC
1 AATTTCCAAAATTT-AAAAC
*
10206434 AATTTCCAAAATTTTAAAC
1 AATTTCCAAAATTTAAAAC
10206453 AATTT
1 AATTT
10206458 TGAAGGATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (19 bp):
AATTTCCAAAATTTAAAAC
Found at i:10207880 original size:20 final size:21
Alignment explanation
Indices: 10207857--10207907 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
10207847 AAATTATAGA
10207857 AAATTATAAAAAAT-GTAAAG
1 AAATTATAAAAAATCGTAAAG
*
10207877 AAA-TAT-AAAATTCGTAAAG
1 AAATTATAAAAAATCGTAAAG
10207896 AAATTATAAAAA
1 AAATTATAAAAA
10207908 TTATTGTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.19
19 12 0.44
20 6 0.22
21 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (21 bp):
AAATTATAAAAAATCGTAAAG
Found at i:10208123 original size:39 final size:40
Alignment explanation
Indices: 10208080--10208156 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
10208070 TTTTTATGCA
* * *
10208080 TTTTATAATTTTTAT-AAAAAATTAC-AATTTTTTATAATT
1 TTTTAAAATTGTTATAAAAAAATT-CTAATTTTTAATAATT
10208119 TTTTAAAATTGTTATAAAAAAATTCTAATTTTTAATAA
1 TTTTAAAATTGTTATAAAAAAATTCTAATTTTTAATAA
10208157 ATTTAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 14 0.42
40 19 0.58
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (40 bp):
TTTTAAAATTGTTATAAAAAAATTCTAATTTTTAATAATT
Found at i:10208168 original size:40 final size:39
Alignment explanation
Indices: 10208086--10208166 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 39
10208076 TGCATTTTAT
* * **
10208086 AATTTTTATAAAAAATTACAATTTTTTATAATTTTTTAA
1 AATTGTTATAAAAAATTACAATTTTTAATAATTTAATAA
10208125 AATTGTTATAAAAAAATT-CTAATTTTTAATAAATTTAATAA
1 AATTGTTAT-AAAAAATTAC-AATTTTTAAT-AATTTAATAA
10208166 A
1 A
10208167 TTTATTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
39 9 0.26
40 17 0.49
41 9 0.26
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (39 bp):
AATTGTTATAAAAAATTACAATTTTTAATAATTTAATAA
Found at i:10208468 original size:90 final size:85
Alignment explanation
Indices: 10208279--10208544 Score: 216
Period size: 90 Copynumber: 3.1 Consensus size: 85
10208269 TCAAAAAGCA
* * * * * *
10208279 TTTTTGATGTA-TTTGACAGTTCAAGTACCCAATTGAGTGAAAAAAATCAGGGGCTTAATTATTT
1 TTTTTGATGCATTTTGAAAGTTCAAGCACCCAATTGAGTGAAAAAAAACAAGGGATTAATTATTT
*
10208343 TCTTTTAAAGTTTGAAGGCC
66 TCTTTAAAAGTTTGAAGGCC
* *
10208363 TTTTTGATGCTTTTTGAAAGTTCAAGCACTCAATTGAGTGTAAAAAAAAGACAAGGGATTAATTG
1 TTTTTGATGCATTTTGAAAGTTCAAGCACCCAATTGAGTG--AAAAAAA-ACAAGGGATTAATT-
* ***
10208428 CTTTT-TTTGAAAAAGTTTGAAGTTT
62 ATTTTCTTT--AAAAGTTTGAAGGCC
* * * * * *
10208453 TTTTTGATGCATTTTGACAGCTT-AAGTATCCAATTGAGTACAAAATTAAAATAAGGGTTTAATT
1 TTTTTGATGCATTTTGAAAG-TTCAAGCACCCAATTGAGT-GAAAA--AAAACAAGGGATTAATT
* * *
10208517 ATTTTTTTTTAAAGTTTG-AGGAC
62 ATTTTCTTTAAAAGTTTGAAGGCC
10208540 TTTTT
1 TTTTT
10208545 ACACCCTTAA
Statistics
Matches: 144, Mismatches: 26, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
84 9 0.06
85 25 0.17
87 14 0.10
88 22 0.15
89 12 0.08
90 57 0.40
91 5 0.03
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (85 bp):
TTTTTGATGCATTTTGAAAGTTCAAGCACCCAATTGAGTGAAAAAAAACAAGGGATTAATTATTT
TCTTTAAAAGTTTGAAGGCC
Found at i:10214490 original size:4 final size:4
Alignment explanation
Indices: 10214481--10214510 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
10214471 CATCTTGGAA
10214481 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CT
10214511 GTGTCTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (4 bp):
CTAT
Found at i:10217188 original size:18 final size:17
Alignment explanation
Indices: 10217158--10217192 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
10217148 AAAGTTAGAT
10217158 AAAAATGTCGTATACAG
1 AAAAATGTCGTATACAG
*
10217175 AAAAAGTGTTGTATACAG
1 AAAAA-TGTCGTATACAG
10217193 CTACATAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (17 bp):
AAAAATGTCGTATACAG
Found at i:10227960 original size:30 final size:31
Alignment explanation
Indices: 10227924--10227983 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
10227914 TTAATAACTC
10227924 AATGACTTAAA-AAAAACTT-TTGAATAGTTG
1 AATGACTTAAATAAAAA-TTCTTGAATAGTTG
*
10227954 AATGACTTAAATGAAAATTCTTGAATAGTT
1 AATGACTTAAATAAAAATTCTTGAATAGTT
10227984 CATTGACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (31 bp):
AATGACTTAAATAAAAATTCTTGAATAGTTG
Found at i:10227991 original size:31 final size:31
Alignment explanation
Indices: 10227922--10227995 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
10227912 ATTTAATAAC
10227922 TCAATGACTTAAA-AAAAACTTTTGAATAGT
1 TCAATGACTTAAATAAAAACTTTTGAATAGT
* *
10227952 TGAATGACTTAAATGAAAA-TTCTTGAATAGT
1 TCAATGACTTAAATAAAAACTT-TTGAATAGT
*
10227983 TCATTGAC-TAAAT
1 TCAATGACTTAAAT
10227996 TGTAACTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 19 0.50
31 19 0.50
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (31 bp):
TCAATGACTTAAATAAAAACTTTTGAATAGT
Found at i:10230722 original size:17 final size:17
Alignment explanation
Indices: 10230697--10230734 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
10230687 AATTTCAATA
10230697 ATTTATAATTTTAAAAT
1 ATTTATAATTTTAAAAT
* *
10230714 ATTTTTAATTTTTAAAT
1 ATTTATAATTTTAAAAT
10230731 -TTTA
1 ATTTA
10230735 AAAAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATAATTTTAAAAT
Found at i:10230747 original size:26 final size:26
Alignment explanation
Indices: 10230667--10230752 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 26
10230657 TTTTTAAAAA
* *
10230667 TAATTTTTATACTTTTAAATAATTTCAA-
1 TAATTTTTA-AATTTTAAA-AAATT-AAT
* * *
10230695 TAATTTAT-AATTTTAAAATATT-TT
1 TAATTTTTAAATTTTAAAAAATTAAT
10230719 TAATTTTTAAATTTTAAAAAATTAAT
1 TAATTTTTAAATTTTAAAAAATTAAT
10230745 TAATTTTT
1 TAATTTTT
10230753 GATATGGTCT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
24 7 0.15
25 16 0.34
26 17 0.36
28 7 0.15
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TAATTTTTAAATTTTAAAAAATTAAT
Found at i:10233944 original size:12 final size:12
Alignment explanation
Indices: 10233927--10233951 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10233917 TGGATAAGAA
10233927 AAAAAGAGTATT
1 AAAAAGAGTATT
10233939 AAAAAGAGTATT
1 AAAAAGAGTATT
10233951 A
1 A
10233952 TTATTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (12 bp):
AAAAAGAGTATT
Found at i:10241612 original size:17 final size:16
Alignment explanation
Indices: 10241590--10241634 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
10241580 GTCACATCAT
10241590 TTTGAATCAATTTTCA-G
1 TTTGAATC-A-TTTCAGG
10241607 TTTGAATCATTTCAGG
1 TTTGAATCATTTCAGG
*
10241623 TTTGAATTATTT
1 TTTGAATCATTT
10241635 TGAGTGCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 5 0.19
16 13 0.50
17 8 0.31
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (16 bp):
TTTGAATCATTTCAGG
Found at i:10242970 original size:14 final size:14
Alignment explanation
Indices: 10242948--10243010 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
10242938 TATAAATATT
10242948 TATAAAATTAAAAA
1 TATAAAATTAAAAA
* *
10242962 TATATAATTTAAAA
1 TATAAAATTAAAAA
** *
10242976 TATAAAAGCAAATAGT
1 TATAAAATTAAA-A-A
10242992 TATAAAATATAAAAA
1 TATAAAAT-TAAAAA
10243007 TATA
1 TATA
10243011 TGTGACTTTT
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
14 20 0.56
15 5 0.14
16 8 0.22
17 3 0.08
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (14 bp):
TATAAAATTAAAAA
Found at i:10242998 original size:23 final size:23
Alignment explanation
Indices: 10242941--10243006 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 23
10242931 AAAAATATAT
* *
10242941 AAATATTTATAAAAT-TAAAAAT
1 AAATAATTATAAAATATAAAAAC
* *
10242963 ATATAATT-TAAAATATAAAAGC
1 AAATAATTATAAAATATAAAAAC
*
10242985 AAATAGTTATAAAATATAAAAA
1 AAATAATTATAAAATATAAAAA
10243007 TATATGTGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
21 6 0.17
22 17 0.49
23 12 0.34
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (23 bp):
AAATAATTATAAAATATAAAAAC
Found at i:10244979 original size:11 final size:11
Alignment explanation
Indices: 10244965--10244996 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
10244955 TCTAAAATGA
10244965 TAAATATAAAT
1 TAAATATAAAT
*
10244976 TAAATACAAAT
1 TAAATATAAAT
10244987 TAAATATAAA
1 TAAATATAAA
10244997 ATATCCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAATATAAAT
Found at i:10246256 original size:12 final size:12
Alignment explanation
Indices: 10246239--10246272 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
10246229 AGCATATTGA
10246239 TGGGCAAAATAG
1 TGGGCAAAATAG
*
10246251 TGGGCAAAATTG
1 TGGGCAAAATAG
10246263 TGGGCAAAAT
1 TGGGCAAAAT
10246273 CTTGAGAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.32, T:0.21
Consensus pattern (12 bp):
TGGGCAAAATAG
Found at i:10246590 original size:22 final size:22
Alignment explanation
Indices: 10246551--10246592 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
10246541 AGTTTCTTGA
*
10246551 AAAAATAAGAAAATAAATAAAT
1 AAAAATAAGAAAAAAAATAAAT
10246573 AAAAATAA-AAATAAAAATAA
1 AAAAATAAGAAA-AAAAATAA
10246593 TTGGGTTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (22 bp):
AAAAATAAGAAAAAAAATAAAT
Found at i:10251166 original size:143 final size:144
Alignment explanation
Indices: 10250901--10251176 Score: 328
Period size: 143 Copynumber: 1.9 Consensus size: 144
10250891 GAGACCTTTG
* *
10250901 GATACCCGACGGTAAAATAATAATTTTGGACTTTCGGGGATAAAATGGTAATTTTGAGAAAATTT
1 GATACCCGACGGTAAAATAATAATTTTGGACTTTAGGGGATAAAATGGTAATTTAGAGAAAATTT
* * * * * ****
10250966 CGGGTTAAAAATGACATTTTAGACATTTTGGGATAACATGGTAATTTTTTTTTAAATCGAGATCA
66 CGGGTTAAAAATGACATTTTAGACATATCGGAATAAAACGGTAATTTTTAGAAAAATCGAGATCA
10251031 AAACGGGGTTTTTT
131 AAACGGGGTTTTTT
**
10251045 GATACCCGA-GAGTAAAATGGTAATTTTGGACTCTTAGGGG-T-AAATGGTAATTTAG-GAAAAT
1 GATACCCGACG-GTAAAATAATAATTTTGGACT-TTAGGGGATAAAATGGTAATTTAGAGAAAA-
* * * *
10251106 TTTGGGGTTAGAAATGATATTTTAGACA-ATCGAGAATAAAACGGTAATTTTTAGAAAAATCGGG
63 TTTCGGGTTAAAAATGACATTTTAGACATATCG-GAATAAAACGGTAATTTTTAGAAAAATCGAG
10251170 ATCAAAA
127 ATCAAAA
10251177 ATAGAATTAT
Statistics
Matches: 111, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
142 7 0.06
143 69 0.62
144 29 0.26
145 6 0.05
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (144 bp):
GATACCCGACGGTAAAATAATAATTTTGGACTTTAGGGGATAAAATGGTAATTTAGAGAAAATTT
CGGGTTAAAAATGACATTTTAGACATATCGGAATAAAACGGTAATTTTTAGAAAAATCGAGATCA
AAACGGGGTTTTTT
Found at i:10251213 original size:29 final size:28
Alignment explanation
Indices: 10251173--10251272 Score: 76
Period size: 29 Copynumber: 3.5 Consensus size: 28
10251163 AATCGGGATC
*
10251173 AAAAATAG-AATTATGGAAAACTTAGGGGT
1 AAAAAT-GTAATTTTGGAAAA-TTAGGGGT
* * *
10251202 AAAAATGTAATTTTAGAAAGTTTTGGGGT
1 AAAAATGTAATTTTGGAAA-ATTAGGGGT
* * *
10251231 TAAAATATAATTTTGGAAAGATTATGGGT
1 AAAAATGTAATTTTGGAAA-ATTAGGGGT
* *
10251260 TAAAATGCAATTT
1 AAAAATGTAATTT
10251273 ACAAAAAGTT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
28 1 0.02
29 56 0.98
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (28 bp):
AAAAATGTAATTTTGGAAAATTAGGGGT
Found at i:10251293 original size:59 final size:58
Alignment explanation
Indices: 10251174--10251362 Score: 182
Period size: 59 Copynumber: 3.2 Consensus size: 58
10251164 ATCGGGATCA
* * * * * **
10251174 AAAATAGAATTATGGAAAACTTAGGGGTAAAAATGTAATTTTAGAAAGTTTTGGGGTT
1 AAAATATAATTTTGGAAAACTTAGGGGTAAAAATGCAATTTCAAAAAGTTTTAAGGTT
* *
10251232 AAAATATAATTTTGGAAAGA-TTATGGGTTAAAATGCAATTTACAAAAAGTTTTAAGGTT
1 AAAATATAATTTTGGAAA-ACTTAGGGGTAAAAATGCAATTT-CAAAAAGTTTTAAGGTT
* * ** ** ** *
10251291 AAAATATAATTTTGGAAAAGTTAAGGGGTCAAAATATAATTTTTAAAAGTTTTGGGGTC
1 AAAATATAATTTTGGAAAACTT-AGGGGTAAAAATGCAATTTCAAAAAGTTTTAAGGTT
10251350 AAAATATAATTTT
1 AAAATATAATTTT
10251363 AAAGAAGTTT
Statistics
Matches: 109, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
58 35 0.32
59 59 0.54
60 15 0.14
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (58 bp):
AAAATATAATTTTGGAAAACTTAGGGGTAAAAATGCAATTTCAAAAAGTTTTAAGGTT
Found at i:10251302 original size:30 final size:28
Alignment explanation
Indices: 10251228--10251419 Score: 102
Period size: 30 Copynumber: 6.6 Consensus size: 28
10251218 AAAGTTTTGG
*** * *
10251228 GGTTAAAATATAATTTTGGAAAGATTATG
1 GGTTAAAATATAATTTAAAAAAGTTTA-A
**
10251257 GGTTAAAATGCAATTTACAAAAAGTTTTAA
1 GGTTAAAATATAATTTA-AAAAAG-TTTAA
**
10251287 GGTTAAAATATAATTTTGGAAAAG-TTAA
1 GGTTAAAATATAA-TTTAAAAAAGTTTAA
* ** **
10251315 GGGGTCAAAATATAATTTTTAAAAGTTTTGG
1 --GGTTAAAATATAATTTAAAAAAG-TTTAA
* * *
10251346 GGTCAAAATATAATTTTAAAGAAGTTTAGG
1 GGTTAAAATATAA-TTTAAAAAAGTTTA-A
*
10251376 GGTTAAAATATAATTTAATAAA-TTTAA
1 GGTTAAAATATAATTTAAAAAAGTTTAA
**
10251403 ATTTAAAATA-AATTTAA
1 GGTTAAAATATAATTTAA
10251420 TTTTAGAATA
Statistics
Matches: 128, Mismatches: 26, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
26 7 0.05
27 8 0.06
28 8 0.06
29 45 0.35
30 52 0.41
31 8 0.06
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.37
Consensus pattern (28 bp):
GGTTAAAATATAATTTAAAAAAGTTTAA
Found at i:10251348 original size:29 final size:29
Alignment explanation
Indices: 10251197--10251391 Score: 185
Period size: 29 Copynumber: 6.6 Consensus size: 29
10251187 GGAAAACTTA
* * *
10251197 GGGGTAAAAATGTAATTTTAGAAAGTTTT
1 GGGGTTAAAATATAATTTTAAAAAGTTTT
** *
10251226 GGGGTTAAAATATAATTTTGGAAAGATTAT
1 GGGGTTAAAATATAATTTTAAAAAG-TTTT
** *
10251256 -GGGTTAAAATGCAATTTACAAAAAGTTTT
1 GGGGTTAAAATATAATTT-TAAAAAGTTTT
** * **
10251285 AAGGTTAAAATATAATTTTGGAAAAGTTAA
1 GGGGTTAAAATATAATTTT-AAAAAGTTTT
* *
10251315 GGGGTCAAAATATAATTTTTAAAAGTTTT
1 GGGGTTAAAATATAATTTTAAAAAGTTTT
* *
10251344 GGGGTCAAAATATAATTTTAAAGAAGTTTA
1 GGGGTTAAAATATAATTTTAAA-AAGTTTT
10251374 GGGGTTAAAATATAATTT
1 GGGGTTAAAATATAATTT
10251392 AATAAATTTA
Statistics
Matches: 135, Mismatches: 26, Indels: 9
0.79 0.15 0.05
Matches are distributed among these distances:
29 68 0.50
30 67 0.50
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (29 bp):
GGGGTTAAAATATAATTTTAAAAAGTTTT
Found at i:10251371 original size:59 final size:59
Alignment explanation
Indices: 10251194--10251391 Score: 208
Period size: 59 Copynumber: 3.4 Consensus size: 59
10251184 TATGGAAAAC
* *
10251194 TTAGGGGTAAAAATGTAA-TTTTAGAAAGTTTTGGGGTTAAAATATAATTTTGGAAAG-A-
1 TTAGGGGTTAAAATATAATTTTTA-AAAGTTTTGGGGTTAAAATATAATTTT-GAAAGAAG
* ** ** ** *
10251252 TTATGGGTTAAAATGCAATTTACAAAAAGTTTTAAGGTTAAAATATAATTTTGGAA-AAG
1 TTAGGGGTTAAAATATAATTT-TTAAAAGTTTTGGGGTTAAAATATAATTTTGAAAGAAG
* *
10251311 TTAAGGGGTCAAAATATAATTTTTAAAAGTTTTGGGGTCAAAATATAATTTT-AAAGAAG
1 TT-AGGGGTTAAAATATAATTTTTAAAAGTTTTGGGGTTAAAATATAATTTTGAAAGAAG
10251370 TTTAGGGGTTAAAATATAATTT
1 -TTAGGGGTTAAAATATAATTT
10251392 AATAAATTTA
Statistics
Matches: 114, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
58 21 0.18
59 75 0.66
60 18 0.16
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (59 bp):
TTAGGGGTTAAAATATAATTTTTAAAAGTTTTGGGGTTAAAATATAATTTTGAAAGAAG
Found at i:10251414 original size:17 final size:17
Alignment explanation
Indices: 10251392--10251433 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
10251382 AATATAATTT
10251392 AATAAATTTAAATTTAA
1 AATAAATTTAAATTTAA
* *
10251409 AATAAATTTAATTTTAG
1 AATAAATTTAAATTTAA
10251426 AATAAATT
1 AATAAATT
10251434 CAAAATGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:10252613 original size:100 final size:100
Alignment explanation
Indices: 10252449--10253418 Score: 1466
Period size: 100 Copynumber: 9.7 Consensus size: 100
10252439 ACGGGTTCAT
* * * * * * * *
10252449 CGTTGCGACTTAAACATTTCCCTTCA-AATCTTCGTGGTATTGGATCCGCCGTTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* *
10252513 TCCTTT-CCTTCCTGT-TTCTGAGGTACACGGTCCGC
66 T-CTTTCCCGTCGTGTCTT-TGAGGTACACGGTCCGC
* * *
10252548 CATTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCAGTACTGGATTCGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* *
10252613 TCTTTGCCGTCGTGTCTTTGAGGTATACGGTCCGC
66 TCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCGC
* *
10252648 CGTTACGACTTAGACCTTTCCCTTTAGTATCTTTGC--TA-TCGGATCCGCCATTGCGATCTTAG
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACT-GGATCCGCCATTGCGGTCTTAG
*
10252710 ATCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCAC
65 ATCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCGC
* *
10252746 CGTTGCGACTTAGGCCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTACGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* *
10252811 TCTTTCCCTTCGTGTCTTTGAGGTACACGGTCCAC
66 TCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCGC
* * * * *
10252846 CGTTGCGACTTAGACCTTTCCTTTTAGTATCTTTGCAGTACTAGATTCGCCATTGCGGTTTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
*
10252911 TCTTTCCCGTCCTGTCTTTGAGGTACACGGTCCGC
66 TCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCGC
* * * *
10252946 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTATTAGATCTGCCATTGCGGTCTTTGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
10253011 TCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCGC
66 TCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCGC
* *
10253046 CGTTGCGACTTAGACCTTTCCTTTTAGTATCTTTGCGGTACTGGATCCGCCATTGTGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
10253111 TCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCGC
66 TCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCGC
* *
10253146 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCTGCCATTGTGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
10253211 TCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCGC
66 TCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCGC
* * *
10253246 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTATTGGATCCGCTATTGTGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
*
10253311 TCTTTCCCATCGTGTCTTTGAGGTACACGGTCCGC
66 TCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCGC
* * **
10253346 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGTGGTACTGGATCTGCCATTGCTATCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
*
10253411 CCTTTCCC
66 TCTTTCCC
10253419 TTTTGTGTTT
Statistics
Matches: 800, Mismatches: 64, Indels: 13
0.91 0.07 0.01
Matches are distributed among these distances:
97 1 0.00
98 89 0.11
99 26 0.03
100 681 0.85
101 3 0.00
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.37
Consensus pattern (100 bp):
CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
TCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCGC
Found at i:10260510 original size:59 final size:58
Alignment explanation
Indices: 10260382--10260541 Score: 144
Period size: 59 Copynumber: 2.7 Consensus size: 58
10260372 TTTTAGACTT
* * * * * *
10260382 TTAGGGGTAAAATGGTAATTTTAGAAAAATTTTGGGGTTAGAAATGATATTTTAGACAA
1 TTAGGGGTAAAAAGGTAATTTTAGAAAAA-TTTAGGGTTAAAAATGAAATTATAGAAAA
* * * *
10260441 -TCGAGAGTAAAACGGTAATTTTTAGAAAAA-TTAGGGTTAAAAATGAAATTATCGAAAA
1 TTAG-GGGTAAAAAGGTAA-TTTTAGAAAAATTTAGGGTTAAAAATGAAATTATAGAAAA
* ** *
10260499 CTTAGGGGTAAAAATGTAATTTTAGAAAGTTTTGGGGTTAAAA
1 -TTAGGGGTAAAAAGGTAATTTTAGAAAAATTTAGGGTTAAAA
10260542 TATAATTTTG
Statistics
Matches: 80, Mismatches: 16, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
58 33 0.41
59 34 0.43
60 13 0.16
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.33
Consensus pattern (58 bp):
TTAGGGGTAAAAAGGTAATTTTAGAAAAATTTAGGGTTAAAAATGAAATTATAGAAAA
Found at i:10260526 original size:29 final size:29
Alignment explanation
Indices: 10260358--10260727 Score: 177
Period size: 30 Copynumber: 12.6 Consensus size: 29
10260348 GGATGCTCGA
**
10260358 GGGT-AAAATGGTAATTTTAG-ACTTTTAG
1 GGGTAAAAAT-GTAATTTTAGAAAATTTAG
*
10260386 GGGT-AAAATGGTAATTTTAGAAAAATTTTG
1 GGGTAAAAAT-GTAATTTTAG-AAAATTTAG
* * **
10260416 GGGTTAGAAATG-ATATTTTAGACAATCGA-
1 GGG-TAAAAATGTA-ATTTTAGAAAATTTAG
* ** *
10260445 GAGTAAAACGGTAATTTTTAGAAAAATTAG
1 GGGTAAAAATGTAA-TTTTAGAAAATTTAG
* * * * *
10260475 GGTTAAAAATGAAATTATCGAAAACTTAG
1 GGGTAAAAATGTAATTTTAGAAAATTTAG
* *
10260504 GGGTAAAAATGTAATTTTAGAAAGTTTTG
1 GGGTAAAAATGTAATTTTAGAAAATTTAG
* * *
10260533 GGGTTAAAATATAATTTTGGAAAAGTTTAG
1 GGGTAAAAATGTAATTTTAGAAAA-TTTAG
* * *
10260563 GGGTTAAAATGTAATTTACAGAAAGTTTTA-
1 GGGTAAAAATGTAATTT-TAGAAA-ATTTAG
* * * * *
10260593 AGGTCAAAATATAATTTTGGAAAAGTTAAG
1 GGGTAAAAATGTAATTTTAGAAAA-TTTAG
* * *
10260623 GGGTTAAAATATAATTTTCA-AATATTTTA-
1 GGGTAAAAATGTAATTTT-AGAA-AATTTAG
* * *
10260652 GGGT-TAAATATAATTTTA-AAGAAGTTTGG
1 GGGTAAAAATGTAATTTTAGAA-AA-TTTAG
* * *
10260681 GGGTTAAAATGTAAGTTTTAGAAAGTTTTG
1 GGGTAAAAATGTAA-TTTTAGAAAATTTAG
*
10260711 GGGT-AAAATATAATTTT
1 GGGTAAAAATGTAATTTT
10260728 TGGATTGCTT
Statistics
Matches: 261, Mismatches: 61, Indels: 40
0.72 0.17 0.11
Matches are distributed among these distances:
27 4 0.02
28 45 0.17
29 90 0.34
30 92 0.35
31 24 0.09
32 6 0.02
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTAGAAAATTTAG
Found at i:10260563 original size:59 final size:59
Alignment explanation
Indices: 10260500--10260727 Score: 286
Period size: 60 Copynumber: 3.9 Consensus size: 59
10260490 TATCGAAAAC
* *
10260500 TTAGGGGTAAAAATGTAATTTTAGAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGT
1 TTAGGGGTTAAAATGTAATTTTAGAAAGTTTTAGGGTTAAAATATAATTTTGGAAAAGT
* * *
10260559 TTAGGGGTTAAAATGTAATTTACAGAAAGTTTTAAGGTCAAAATATAATTTTGGAAAAGT
1 TTAGGGGTTAAAATGTAATTT-TAGAAAGTTTTAGGGTTAAAATATAATTTTGGAAAAGT
* * *
10260619 TAAGGGGTTAAAATATAATTTTCA-AATA-TTTTAGGGTT-AAATATAATTTT-AAAGAAGT
1 TTAGGGGTTAAAATGTAATTTT-AGAA-AGTTTTAGGGTTAAAATATAATTTTGGAA-AAGT
* *
10260677 TTGGGGGTTAAAATGTAAGTTTTAGAAAGTTTT-GGGGTAAAATATAATTTT
1 TTAGGGGTTAAAATGTAA-TTTTAGAAAGTTTTAGGGTTAAAATATAATTTT
10260728 TGGATTGCTT
Statistics
Matches: 146, Mismatches: 15, Indels: 16
0.82 0.08 0.09
Matches are distributed among these distances:
57 2 0.01
58 37 0.25
59 52 0.36
60 55 0.38
ACGTcount: A:0.39, C:0.01, G:0.21, T:0.38
Consensus pattern (59 bp):
TTAGGGGTTAAAATGTAATTTTAGAAAGTTTTAGGGTTAAAATATAATTTTGGAAAAGT
Found at i:10260577 original size:118 final size:115
Alignment explanation
Indices: 10260382--10260705 Score: 268
Period size: 118 Copynumber: 2.7 Consensus size: 115
10260372 TTTTAGACTT
* **
10260382 TTAGGGGTAAAATGGTAATTTTAGAAAAATTTTGGGGTTAGAAATGAT-ATTTTAGACAA-TCGA
1 TTAGGGGTAAAAT-GTAATTTTAG--AAATTTTGGGGTTA-AAAT-ATAATTTT-GAAAAGTTTA
* * *
10260445 -GAG-TAAAACGGTAATTTTTAGAAA-AATTAGGGTTAAAAATGA-AATTATCGAAAAC
60 GGGGTTAAAA-TGTAATTTTTAGAAAGAATTAAGG-TAAAAAT-ATAATTATCGAAAAC
10260500 TTAGGGGTAAAAATGTAATTTTAGAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGTTTAGGG
1 TTAGGGGT-AAAATGTAATTTTAGAAA-TTTTGGGGTTAAAATATAATTTT-GAAAAGTTTAGGG
** ** * * * *
10260565 GTTAAAATGTAATTTACAGAAAGTTTTAAGGTCAAAATATAATTTTGGAAAAG
63 GTTAAAATGTAATTTTTAGAAAGAATTAAGGTAAAAATATAATTATCGAAAAC
* * * *
10260618 TTAAGGGGTTAAAATATAATTTTCA-AATATTTTAGGGTT-AAATATAATTTTAAAGAAGTTTGG
1 TT-AGGGG-TAAAATGTAATTTT-AGAA-ATTTTGGGGTTAAAATATAATTTTGAA-AAGTTTAG
*
10260681 GGGTTAAAATGTAAGTTTTAGAAAG
61 GGGTTAAAATGTAATTTTTAGAAAG
10260706 TTTTGGGGTA
Statistics
Matches: 171, Mismatches: 22, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
115 2 0.01
116 16 0.09
117 16 0.09
118 91 0.53
119 43 0.25
120 3 0.02
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.35
Consensus pattern (115 bp):
TTAGGGGTAAAATGTAATTTTAGAAATTTTGGGGTTAAAATATAATTTTGAAAAGTTTAGGGGTT
AAAATGTAATTTTTAGAAAGAATTAAGGTAAAAATATAATTATCGAAAAC
Found at i:10260602 original size:60 final size:58
Alignment explanation
Indices: 10260500--10260727 Score: 273
Period size: 59 Copynumber: 3.9 Consensus size: 58
10260490 TATCGAAAAC
* * *
10260500 TTAGGGGTAAAAATGTAATTTTAGAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGT
1 TTAGGGGTTAAAATGTAATTTCAGAAAGTTTTAGGG-TAAAATATAATTTTGGAAAAGT
*
10260559 TTAGGGGTTAAAATGTAATTTACAGAAAGTTTTAAGGTCAAAATATAATTTTGGAAAAGT
1 TTAGGGGTTAAAATGTAATTT-CAGAAAGTTTTAGGGT-AAAATATAATTTTGGAAAAGT
* * * *
10260619 TAAGGGGTTAAAATATAATTTTCA-AATA-TTTTAGGGTTAAATATAATTTT-AAAGAAGT
1 TTAGGGGTTAAAATGTAA-TTTCAGAA-AGTTTTAGGGTAAAATATAATTTTGGAA-AAGT
* * *
10260677 TTGGGGGTTAAAATGTAAGTTTTAGAAAGTTTTGGGGTAAAATATAATTTT
1 TTAGGGGTTAAAATGTAA-TTTCAGAAAGTTTTAGGGTAAAATATAATTTT
10260728 TGGATTGCTT
Statistics
Matches: 146, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
57 2 0.01
58 36 0.25
59 53 0.36
60 52 0.36
61 3 0.02
ACGTcount: A:0.39, C:0.01, G:0.21, T:0.38
Consensus pattern (58 bp):
TTAGGGGTTAAAATGTAATTTCAGAAAGTTTTAGGGTAAAATATAATTTTGGAAAAGT
Found at i:10260728 original size:29 final size:29
Alignment explanation
Indices: 10260503--10260727 Score: 215
Period size: 30 Copynumber: 7.7 Consensus size: 29
10260493 CGAAAACTTA
* *
10260503 GGGGTAAAAATGTAATTTTAGAAAGTTTT
1 GGGGTTAAAATATAATTTTAGAAAGTTTT
* *
10260532 GGGGTTAAAATATAATTTTGGAAAAGTTTA
1 GGGGTTAAAATATAATTTTAG-AAAGTTTT
* *
10260562 GGGGTTAAAATGTAATTTACAGAAAGTTTT
1 GGGGTTAAAATATAATTT-TAGAAAGTTTT
** * * **
10260592 AAGGTCAAAATATAATTTTGGAAAAGTTAA
1 GGGGTTAAAATATAATTTTAG-AAAGTTTT
10260622 GGGGTTAAAATATAATTTTCA-AATA-TTTT
1 GGGGTTAAAATATAATTTT-AGAA-AGTTTT
* * *
10260651 AGGGTT-AAATATAATTTTAAAGAAGTTTG
1 GGGGTTAAAATATAATTTTAGA-AAGTTTT
*
10260680 GGGGTTAAAATGTAAGTTTTAGAAAGTTTT
1 GGGGTTAAAATATAA-TTTTAGAAAGTTTT
10260710 GGGG-TAAAATATAATTTT
1 GGGGTTAAAATATAATTTT
10260728 TGGATTGCTT
Statistics
Matches: 157, Mismatches: 29, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
27 1 0.01
28 18 0.11
29 46 0.29
30 85 0.54
31 7 0.04
ACGTcount: A:0.40, C:0.01, G:0.21, T:0.38
Consensus pattern (29 bp):
GGGGTTAAAATATAATTTTAGAAAGTTTT
Found at i:10262027 original size:19 final size:19
Alignment explanation
Indices: 10261983--10262019 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10261973 AAAAAGGGTT
*
10261983 ATTATTATTAATTATAATC
1 ATTATTATTAATAATAATC
*
10262002 ATTATTATTACTAATAAT
1 ATTATTATTAATAATAAT
10262020 ATTTATTAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTATTATTAATAATAATC
Found at i:10262333 original size:27 final size:25
Alignment explanation
Indices: 10262299--10262360 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 25
10262289 TTGTAATTGA
* *
10262299 ATTGATTTCTCAGAAAGGGTTCATGT
1 ATTGATTTCTC-CAAAGGGTTCATAT
*
10262325 ATTGAATTTTCTCCAAAGGGTTCGTAT
1 ATTG-A-TTTCTCCAAAGGGTTCATAT
10262352 ATTGATTTC
1 ATTGATTTC
10262361 AAGAATAGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 4 0.13
26 5 0.16
27 16 0.52
28 6 0.19
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (25 bp):
ATTGATTTCTCCAAAGGGTTCATAT
Found at i:10262767 original size:17 final size:17
Alignment explanation
Indices: 10262724--10262767 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
10262714 TTATAACAAT
*
10262724 TTTAAATTTAAATTAAA
1 TTTAAATTTAAAATAAA
**
10262741 TCCAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
10262758 TTTAATTTTA
1 TTTAAATTTA
10262768 GAACAAATTC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:10266066 original size:11 final size:11
Alignment explanation
Indices: 10266050--10266082 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
10266040 TCTAAAATGA
10266050 TAAATATAAAT
1 TAAATATAAAT
*
10266061 TAAATACAAAT
1 TAAATATAAAT
10266072 TAAATATAAAT
1 TAAATATAAAT
10266083 AATATCCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATATAAAT
Found at i:10273799 original size:3 final size:3
Alignment explanation
Indices: 10273793--10273826 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
10273783 AGTCCTGGCT
10273793 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
10273827 CGTGATTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:10273977 original size:22 final size:23
Alignment explanation
Indices: 10273943--10274007 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 23
10273933 CCTAGACTCT
* *
10273943 ATTTAGATTTATTTTAATTA-AA
1 ATTTAAATATATTTTAATTATAA
*
10273965 ATTTAAATATATTTTAATTATCA
1 ATTTAAATATATTTTAATTATAA
10273988 ATTTAATTATATATTTTAAT
1 ATTTAA--ATATATTTTAAT
10274008 AATTTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.49
23 7 0.19
25 12 0.32
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTAAATATATTTTAATTATAA
Found at i:10273994 original size:12 final size:11
Alignment explanation
Indices: 10273955--10274003 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
10273945 TTAGATTTAT
*
10273955 TTTAATTAAAA
1 TTTAATTATAA
* *
10273966 TTTAAATATAT
1 TTTAATTATAA
10273977 TTTAATTATCAA
1 TTTAATTAT-AA
10273989 TTTAATTATATA
1 TTTAATTATA-A
10274001 TTT
1 TTT
10274004 TAATAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 17 0.55
12 14 0.45
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTAATTATAA
Found at i:10275199 original size:15 final size:15
Alignment explanation
Indices: 10275181--10275212 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10275171 CTGAAAATAG
10275181 TTTTCGAAAAATGAT
1 TTTTCGAAAAATGAT
*
10275196 TTTTTGAAAAATGAT
1 TTTTCGAAAAATGAT
10275211 TT
1 TT
10275213 ACTTTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (15 bp):
TTTTCGAAAAATGAT
Found at i:10279336 original size:14 final size:14
Alignment explanation
Indices: 10279317--10279345 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10279307 CTATCATTTC
10279317 ACTATTATATTGTT
1 ACTATTATATTGTT
10279331 ACTATTATATTGTT
1 ACTATTATATTGTT
10279345 A
1 A
10279346 TTGTTTGGAT
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:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (14 bp):
ACTATTATATTGTT
Found at i:10285357 original size:57 final size:56
Alignment explanation
Indices: 10285276--10285417 Score: 187
Period size: 57 Copynumber: 2.5 Consensus size: 56
10285266 ATATTATGAT
* * *
10285276 TTTTATT-AATTCATATTTTAATAATAATTATGTCAAAATGTTATTAAATTATATACTA
1 TTTTATTAAATT-ATA-TTTAATAATAATCATGTCAAAATATGATTAAATTATATA-TA
* * * *
10285334 TTTTATTAAATTGTATTTAATAATAATCATGTTAAAATATGATTAAATTATTTATT
1 TTTTATTAAATTATATTTAATAATAATCATGTCAAAATATGATTAAATTATATATA
10285390 TTTTATTAAATTATATTTAATAATAATC
1 TTTTATTAAATTATATTTAATAATAATC
10285418 TTATTAAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
56 28 0.37
57 34 0.45
58 9 0.12
59 4 0.05
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (56 bp):
TTTTATTAAATTATATTTAATAATAATCATGTCAAAATATGATTAAATTATATATA
Found at i:10285417 original size:56 final size:57
Alignment explanation
Indices: 10285275--10285427 Score: 193
Period size: 56 Copynumber: 2.7 Consensus size: 57
10285265 TATATTATGA
* * * *
10285275 TTTTTATT-AATTCATATTTTAATAATAATTATGTCAAAATGTTATTAAATTATATACT
1 TTTTTATTAAATT-ATA-TTTAATAATAATCATGTTAAAATATGATTAAATTATATACT
* * *
10285333 ATTTTATTAAATTGTATTTAATAATAATCATGTTAAAATATGATTAAATTATTTA-T
1 TTTTTATTAAATTATATTTAATAATAATCATGTTAAAATATGATTAAATTATATACT
* *
10285389 TTTTTATTAAATTATATTTAATAATAATCTTATTAAAAT
1 TTTTTATTAAATTATATTTAATAATAATCATGTTAAAAT
10285428 TTAATAACAA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
56 36 0.43
57 34 0.41
58 9 0.11
59 4 0.05
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (57 bp):
TTTTTATTAAATTATATTTAATAATAATCATGTTAAAATATGATTAAATTATATACT
Found at i:10285629 original size:16 final size:15
Alignment explanation
Indices: 10285594--10285645 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
10285584 TGAAATACTG
*
10285594 ATTACAACCCTATTC
1 ATTACAACTCTATTC
10285609 TATTACAACTCTATTAC
1 -ATTACAACTCTATT-C
**
10285626 ATTACAGTTCTATTCC
1 ATTACAACTCTATT-C
10285642 ATTA
1 ATTA
10285646 TAGCGAACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 30 0.97
17 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (15 bp):
ATTACAACTCTATTC
Found at i:10288073 original size:22 final size:22
Alignment explanation
Indices: 10288024--10288075 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
10288014 CGTTTCGTGT
*
10288024 CCTCTGTTCAGCACTGTGTGTG
1 CCTCTGTTCAGCACTGTATGTG
* *
10288046 CTTCTGTTTAGCACT-TATGTG
1 CCTCTGTTCAGCACTGTATGTG
10288067 CCCTCTGTT
1 -CCTCTGTT
10288076 AAATTCTTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.10, C:0.27, G:0.21, T:0.42
Consensus pattern (22 bp):
CCTCTGTTCAGCACTGTATGTG
Found at i:10290204 original size:195 final size:196
Alignment explanation
Indices: 10289787--10290231 Score: 581
Period size: 195 Copynumber: 2.3 Consensus size: 196
10289777 TTCAACTTAT
* * * **
10289787 GCTGCTCATACGAGCTATCGAGGACTAGCAACATATGCGATACC-CTAGTCATCGATACGGTATC
1 GCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGATACCTC-AACCATCGATACGGTATC
*
10289851 TATGCATATAAATGTTCCCTGACAATGCTACTCACACGAGCTGTCGAGAATATGCACTTATACAT
65 TATGCATATAAATGTTCCCTAACAATGCTACTCACACGAGCTGTCGAGAATATGCACTTATACAT
* * * *
10289916 GAATCTTAGCCATCGTAGGGCATATAATCCATTCTTGGGTTTATTTCTCATTTTCTCGACCCACG
130 AAATCTTAGCCATCGCAGGGCATATAATCCATTCTTGGATTCATTTCTCATTTTCTCGACCCACG
*
10289981 AT
195 AC
* * * *
10289983 ACTACTCACACGAGTTGTCGAGGACTCGCAACATATGCGTTACCTCAACCATCGATACGGTATCT
1 GCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGATACCTCAACCATCGATACGGTATCT
* * * * * * *
10290048 GTGCTTATAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAG-ATATGCATTTATGCATA
66 ATGCATATAAATGTTCCCTAACAATGCTACTCACACGAGCTGTCGAGAATATGCACTTATACATA
* * * *
10290112 AATCTTAGCCATTGCAGGGCCTATAATCCATTCTTGGATTCATTTCTCATTTTC-CTGACTCATG
131 AATCTTAGCCATCGCAGGGCATATAATCCATTCTTGGATTCATTTCTCATTTTCTC-GACCCACG
10290176 AC
195 AC
* * * *
10290178 GCTGCTCACATGAGCTGTCAAGGACTCGTAACATATGCGATACGTCAACCATCG
1 GCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGATACCTCAACCATCG
10290232 CGTCGGTTTC
Statistics
Matches: 213, Mismatches: 34, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
194 1 0.00
195 116 0.54
196 95 0.45
197 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (196 bp):
GCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGATACCTCAACCATCGATACGGTATCT
ATGCATATAAATGTTCCCTAACAATGCTACTCACACGAGCTGTCGAGAATATGCACTTATACATA
AATCTTAGCCATCGCAGGGCATATAATCCATTCTTGGATTCATTTCTCATTTTCTCGACCCACGA
C
Found at i:10292763 original size:5 final size:5
Alignment explanation
Indices: 10292753--10292778 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
10292743 CTTTTCCCTC
10292753 AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA A
10292779 TTGGCCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:10293354 original size:28 final size:30
Alignment explanation
Indices: 10293318--10293376 Score: 95
Period size: 28 Copynumber: 2.0 Consensus size: 30
10293308 ATTAGAAATT
10293318 AAATAATATAACAATTTT-AT-ATTTTAAA
1 AAATAATATAACAATTTTAATAATTTTAAA
*
10293346 AAATAATATAATAATTTTAATAATTTTAAA
1 AAATAATATAACAATTTTAATAATTTTAAA
10293376 A
1 A
10293377 TTATTTATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 17 0.61
29 2 0.07
30 9 0.32
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (30 bp):
AAATAATATAACAATTTTAATAATTTTAAA
Found at i:10293686 original size:38 final size:38
Alignment explanation
Indices: 10293635--10293711 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
10293625 CTTTTCGTCG
10293635 TACATTTTCTTGGCAGCATAATCATAGGCCAGAGTAGC
1 TACATTTTCTTGGCAGCATAATCATAGGCCAGAGTAGC
*
10293673 TACATTTTCTTGGCAGCATCATCATAGGCCAGAGTAGC
1 TACATTTTCTTGGCAGCATAATCATAGGCCAGAGTAGC
10293711 T
1 T
10293712 TCGATAACAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (38 bp):
TACATTTTCTTGGCAGCATAATCATAGGCCAGAGTAGC
Found at i:10295505 original size:20 final size:21
Alignment explanation
Indices: 10295477--10295527 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
10295467 ATAAAATTTA
10295477 ATTAGAATATATAAAT-TATATT
1 ATTA-AATATATAAATATA-ATT
*
10295499 -TTAAATATTTAAATATAATT
1 ATTAAATATATAAATATAATT
10295519 ATTAAATAT
1 ATTAAATAT
10295528 TTGTATTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTAAATATATAAATATAATT
Found at i:10295509 original size:33 final size:35
Alignment explanation
Indices: 10295414--10295510 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 35
10295404 ATTAAAATTT
10295414 TAATATATGAAA-TATTATTTTAAATATTT--TTAAG
1 TAATATAT-AAATTA-TATTTTAAATATTTAATTAAG
* *
10295448 TAATTAATATTAATTAT-TTATAAA-ATTTAATT-AG
1 TAA-T-ATATAAATTATATTTTAAATATTTAATTAAG
10295482 -AATATATAAATTATATTTTAAATATTTAA
1 TAATATATAAATTATATTTTAAATATTTAA
10295511 ATATAATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
31 10 0.19
32 7 0.13
33 12 0.23
34 11 0.21
35 6 0.12
36 6 0.12
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (35 bp):
TAATATATAAATTATATTTTAAATATTTAATTAAG
Found at i:10295525 original size:21 final size:21
Alignment explanation
Indices: 10295477--10295529 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
10295467 ATAAAATTTA
*
10295477 ATTAGAATATATAAATTATATT
1 ATTA-AATATTTAAATTATATT
10295499 -TTAAATATTTAAA-TATAATT
1 ATTAAATATTTAAATTAT-ATT
10295519 ATTAAATATTT
1 ATTAAATATTT
10295530 GTATTTAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.11
20 12 0.43
21 13 0.46
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTAAATATTTAAATTATATT
Found at i:10295525 original size:33 final size:32
Alignment explanation
Indices: 10295429--10295525 Score: 83
Period size: 33 Copynumber: 2.9 Consensus size: 32
10295419 TATGAAATAT
*
10295429 TATTTTAAATATTTTTAAGTAATTAATATT-AATTA
1 TATTTTAAATA--TTTAAAT-A-TAATATTAAATTA
* * *
10295464 T-TTATAAA-ATTTAATTAGAATATATAAATTA
1 TATTTTAAATATTTAAATATAATAT-TAAATTA
10295495 TATTTTAAATATTTAAATATAATTATTAAAT
1 TATTTTAAATATTTAAATATAA-TATTAAAT
10295526 ATTTGTATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
29 5 0.10
30 2 0.04
31 12 0.24
32 6 0.12
33 16 0.31
34 9 0.18
35 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (32 bp):
TATTTTAAATATTTAAATATAATATTAAATTA
Found at i:10296061 original size:91 final size:91
Alignment explanation
Indices: 10295920--10296141 Score: 331
Period size: 91 Copynumber: 2.5 Consensus size: 91
10295910 CTAAACCCAT
* *
10295920 TAGAGATAAAATAATGAAGAGTACAAAAGACTGAAATAAAATTTATGGGTTTAATATTTGACAAA
1 TAGAGATAAAATAATGAAGAGTACAAAAGATTGAGATAAAATTTATGGGTTTAATATTTGACAAA
*
10295985 AGGTTGCTTAACGTATGTAAGCTTTA
66 AAGTTGCTTAACGTATGTAAGCTTTA
*
10296011 TAGAGATAAAATAATGAAGAGTACAAAATATTGAGATAAAATTTGA-GGGTTTAATATTTGACAA
1 TAGAGATAAAATAATGAAGAGTACAAAAGATTGAGATAAAATTT-ATGGGTTTAATATTTGACAA
*
10296075 AAAGTTGCTTAATGTATGTAAGCTTTA
65 AAAGTTGCTTAACGTATGTAAGCTTTA
* * * * *
10296102 TA-TGCTAAAATAATTAAGAATATAAAAGATTGAGATAAAA
1 TAGAGATAAAATAATGAAGAGTACAAAAGATTGAGATAAAA
10296142 ACTAAACACT
Statistics
Matches: 119, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
90 32 0.27
91 86 0.72
92 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (91 bp):
TAGAGATAAAATAATGAAGAGTACAAAAGATTGAGATAAAATTTATGGGTTTAATATTTGACAAA
AAGTTGCTTAACGTATGTAAGCTTTA
Found at i:10296936 original size:19 final size:20
Alignment explanation
Indices: 10296900--10296954 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
10296890 CTACCCTGAG
* *
10296900 ACTTCTACCAGTAGAACTTC
1 ACTTCTACCAATACAACTTC
10296920 ACTTC-ACCAATACAACTTC
1 ACTTCTACCAATACAACTTC
* *
10296939 AGTTCTACCTATACAA
1 ACTTCTACCAATACAA
10296955 GTACGCTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.29
Consensus pattern (20 bp):
ACTTCTACCAATACAACTTC
Found at i:10297278 original size:8 final size:8
Alignment explanation
Indices: 10297265--10297296 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
10297255 CTTGTAAGGA
10297265 TTGTTTCT
1 TTGTTTCT
10297273 TTGTTTCT
1 TTGTTTCT
*
10297281 TTGTTTGT
1 TTGTTTCT
10297289 TTGTTTCT
1 TTGTTTCT
10297297 CTTTTGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.09, G:0.16, T:0.75
Consensus pattern (8 bp):
TTGTTTCT
Found at i:10298603 original size:22 final size:21
Alignment explanation
Indices: 10298578--10298619 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
10298568 AATATCAAAA
10298578 TAAAATTAT-AAATAAACTAATT
1 TAAAATT-TCAAATAAA-TAATT
10298600 TAAAATTTCAAATAAATAAT
1 TAAAATTTCAAATAAATAAT
10298620 AACAATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAATTTCAAATAAATAATT
Found at i:10327699 original size:58 final size:57
Alignment explanation
Indices: 10327606--10327786 Score: 195
Period size: 58 Copynumber: 3.1 Consensus size: 57
10327596 AATTTGGATG
* * **
10327606 AAAAAAAGTTGAAGTCTCAATGTG-GAAACATTTGTCAAGTTTGGGATCTAACTTGGAC
1 AAAAAAAGTTCAAGTC-CAATGTGAG-AACAATTGTCAAGTTCAGGATCTAACTTGGAC
* * * *
10327664 AAAAAAAGTTTAGGTTCCAATGTGAGAACAATTGTCAAGTTCAGAACCTAACTTGGAC
1 AAAAAAAGTTCAAG-TCCAATGTGAGAACAATTGTCAAGTTCAGGATCTAACTTGGAC
* * * *
10327722 AAAAAACA-TTCATGCTCCAATGTGAGAACAATTGTTAAGTTCAGGATCTGACTTGGAT
1 AAAAAA-AGTTCAAG-TCCAATGTGAGAACAATTGTCAAGTTCAGGATCTAACTTGGAC
10327780 AAAAAAA
1 AAAAAAA
10327787 AAGATTTAAG
Statistics
Matches: 105, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
57 1 0.01
58 100 0.95
59 4 0.04
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (57 bp):
AAAAAAAGTTCAAGTCCAATGTGAGAACAATTGTCAAGTTCAGGATCTAACTTGGAC
Found at i:10328411 original size:30 final size:30
Alignment explanation
Indices: 10328371--10328428 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
10328361 TAATAAATAC
10328371 TAAAAATAAAAATATTTTAAAATTTATTTT
1 TAAAAATAAAAATATTTTAAAATTTATTTT
* * *
10328401 TAAAATTAAAATTATTTTAAACTTTATT
1 TAAAAATAAAAATATTTTAAAATTTATT
10328429 ATAATACTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAAAATAAAAATATTTTAAAATTTATTTT
Found at i:10329735 original size:12 final size:11
Alignment explanation
Indices: 10329703--10329779 Score: 52
Period size: 12 Copynumber: 7.0 Consensus size: 11
10329693 AAATACATGA
10329703 ATAATAA-AAT
1 ATAATAATAAT
* *
10329713 AAAACAATAAT
1 ATAATAATAAT
10329724 ACTAATAATAAT
1 A-TAATAATAAT
* * *
10329736 ACAAGTAGTAAC
1 ATAA-TAATAAT
*
10329748 ATAA-AAAAAT
1 ATAATAATAAT
10329758 A-AATAATAAT
1 ATAATAATAAT
10329768 AATAATAATAAT
1 -ATAATAATAAT
10329780 TAGCCCCTCA
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 7 0.14
12 26 0.53
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:10330409 original size:23 final size:23
Alignment explanation
Indices: 10330383--10330426 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
10330373 AAAATTTTAA
10330383 TTTAATCATT-TAAAAAATACACT
1 TTTAAT-ATTGTAAAAAATACACT
* *
10330406 TTTACTATTGTAAAAATTACA
1 TTTAATATTGTAAAAAATACA
10330427 ATTTAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.41
Consensus pattern (23 bp):
TTTAATATTGTAAAAAATACACT
Done.