Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold243
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: 1218968
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 59385 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:834145 original size:14 final size:14
Alignment explanation
Indices: 834126--834153 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
834116 ATGTATGATG
834126 AGCTTAATTAATAA
1 AGCTTAATTAATAA
834140 AGCTTAATTAATAA
1 AGCTTAATTAATAA
834154 TCTTCTTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
AGCTTAATTAATAA
Found at i:834438 original size:66 final size:66
Alignment explanation
Indices: 834357--834490 Score: 223
Period size: 66 Copynumber: 2.0 Consensus size: 66
834347 CATGAATATA
** * * *
834357 TAATTAAATGTATGTTTACGAGGAATATTTATGTTCAATTTATTTAATAAATGAAACTCAAAATT
1 TAATTAAATACATGTTAACAAGGAATATTTATATTCAATTTATTTAATAAATGAAACTCAAAATT
834422 T
66 T
834423 TAATTAAATACATGTTAACAAGGAATATTTATATTCAATTTATTTAATAAATGAAACTCAAAATT
1 TAATTAAATACATGTTAACAAGGAATATTTATATTCAATTTATTTAATAAATGAAACTCAAAATT
834488 T
66 T
834489 TA
1 TA
834491 CTCCATGTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (66 bp):
TAATTAAATACATGTTAACAAGGAATATTTATATTCAATTTATTTAATAAATGAAACTCAAAATT
T
Found at i:844538 original size:9 final size:9
Alignment explanation
Indices: 844524--844582 Score: 91
Period size: 9 Copynumber: 6.6 Consensus size: 9
844514 TTTGGTTAAA
844524 AATTACCCG
1 AATTACCCG
844533 AATTACCCG
1 AATTACCCG
*
844542 AATTATCCG
1 AATTACCCG
844551 AATTACCCG
1 AATTACCCG
*
844560 AATTAACCG
1 AATTACCCG
*
844569 AATTAACCG
1 AATTACCCG
844578 AATTA
1 AATTA
844583 TCAAAAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:851017 original size:10 final size:10
Alignment explanation
Indices: 851004--851051 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
850994 CCTTTTATAC
*
851004 TTTATTTAAT
1 TTTAATTAAT
851014 TTTAATTAAT
1 TTTAATTAAT
*
851024 AATTAATTAA-
1 -TTTAATTAAT
*
851034 CTTAATTAAT
1 TTTAATTAAT
851044 TTTAATTA
1 TTTAATTA
851052 TTAAACCTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTAATTAAT
Found at i:851401 original size:206 final size:206
Alignment explanation
Indices: 851047--851433 Score: 659
Period size: 206 Copynumber: 1.9 Consensus size: 206
851037 AATTAATTTT
* *
851047 AATTATTAAACCTTAAGCAAGATTAACATTTGTTAGTGGATTATAGTTAATAACCACCACAGTTT
1 AATTATTAAACCTTAAGCAAGATTAACATTTGTTAGTGGATTACACTTAATAACCACCACAGTTT
851112 GATAATATATTAGTGATTCAATTGCTCAATTGGTCCTTCAATTAATTAAAATTTCATAGTAATTA
66 GATAATATATTAGTGATTCAATTGCTCAATTGGTCCTTCAATTAATTAAAATTTCATAGTAATTA
* * *
851177 ACTTTTACCACTTTTACAATTTAGTTCTTTCACCTCAATTAGTCACTAATTTAGCAAAAATACTT
131 ACTTTCACCACTTTTACAATTTAGTCCTTACACCTCAATTAGTCACTAATTTAGCAAAAATACTT
851242 ATCCAAAATTC
196 ATCCAAAATTC
* * **
851253 AATTATTAAACCTTAAGCAAGATTAACATTTGTTAGTGGATTACACTTGATATCTGCCATCA-TT
1 AATTATTAAACCTTAAGCAAGATTAACATTTGTTAGTGGATTACACTTAATAACCACCA-CAGTT
* *
851317 TGATAATATATTAGTGGTTCAATTTCTCAATTGGTCCTTCAATTAATTAAAATTTCATAGTAATT
65 TGATAATATATTAGTGATTCAATTGCTCAATTGGTCCTTCAATTAATTAAAATTTCATAGTAATT
851382 AACTTTCACCACTTTTACAATTTAGTCCTTACACCTCAATTAGTCACTAATT
130 AACTTTCACCACTTTTACAATTTAGTCCTTACACCTCAATTAGTCACTAATT
851434 CATCAAAATT
Statistics
Matches: 169, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
206 167 0.99
207 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.40
Consensus pattern (206 bp):
AATTATTAAACCTTAAGCAAGATTAACATTTGTTAGTGGATTACACTTAATAACCACCACAGTTT
GATAATATATTAGTGATTCAATTGCTCAATTGGTCCTTCAATTAATTAAAATTTCATAGTAATTA
ACTTTCACCACTTTTACAATTTAGTCCTTACACCTCAATTAGTCACTAATTTAGCAAAAATACTT
ATCCAAAATTC
Found at i:854463 original size:13 final size:13
Alignment explanation
Indices: 854445--854469 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
854435 ATCAACATTT
854445 TAAACTTTTACCC
1 TAAACTTTTACCC
854458 TAAACTTTTACC
1 TAAACTTTTACC
854470 TTTTATTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAACTTTTACCC
Found at i:856640 original size:24 final size:24
Alignment explanation
Indices: 856607--856673 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
856597 AGTATATTGC
856607 GAACTGTATTTGCAGAAATGTTTT
1 GAACTGTATTTGCAGAAATGTTTT
* ** *
856631 GAACTATATTTGTTGACATGTTTT
1 GAACTGTATTTGCAGAAATGTTTT
* *
856655 GAATTGTATTTGCATAAAT
1 GAACTGTATTTGCAGAAAT
856674 TTTCCAAACA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (24 bp):
GAACTGTATTTGCAGAAATGTTTT
Found at i:857477 original size:13 final size:13
Alignment explanation
Indices: 857459--857485 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
857449 ATATGTGATA
857459 TGTGTGAAAATTT
1 TGTGTGAAAATTT
857472 TGTGTGAAAATTT
1 TGTGTGAAAATTT
857485 T
1 T
857486 ATCGTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:860226 original size:16 final size:17
Alignment explanation
Indices: 860205--860237 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
860195 TTGTTTTGTT
860205 ATATGTTCTG-TATATG
1 ATATGTTCTGATATATG
*
860221 ATATGTTTTGATATATG
1 ATATGTTCTGATATATG
860238 CTGGATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.27, C:0.03, G:0.18, T:0.52
Consensus pattern (17 bp):
ATATGTTCTGATATATG
Found at i:861823 original size:14 final size:15
Alignment explanation
Indices: 861804--861832 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
861794 CTTAAGAATG
861804 CTATGGCAAA-GATA
1 CTATGGCAAATGATA
861818 CTATGGCAAATGATA
1 CTATGGCAAATGATA
861833 GAAGGTCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (15 bp):
CTATGGCAAATGATA
Found at i:869356 original size:18 final size:18
Alignment explanation
Indices: 869301--869357 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
869291 TTGTTGTTTA
*
869301 ATTTTTCTTATTATTCTT
1 ATTTTTATTATTATTCTT
* * *
869319 AGTTTTATTATCATTATT
1 ATTTTTATTATTATTCTT
*
869337 ATTTTTATTCTTATTCTT
1 ATTTTTATTATTATTCTT
869355 ATT
1 ATT
869358 GTTAGTTCTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.68
Consensus pattern (18 bp):
ATTTTTATTATTATTCTT
Found at i:869447 original size:13 final size:14
Alignment explanation
Indices: 869424--869469 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
869414 TCTTTTAGTT
869424 ATTACTATTATTTTC
1 ATTA-TATTATTTTC
869439 ATT-TATTATTTT-
1 ATTATATTATTTTC
*
869451 ATTATATATATTATC
1 ATTATAT-TATTTTC
869466 ATTA
1 ATTA
869470 CTTAGCCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 3 0.11
13 12 0.44
14 5 0.19
15 7 0.26
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTATATTATTTTC
Found at i:872603 original size:45 final size:45
Alignment explanation
Indices: 872493--872710 Score: 253
Period size: 45 Copynumber: 4.9 Consensus size: 45
872483 AACGGTTACA
* ** **
872493 CGGTGG-ATCAGCACATAGC-ACCACCCTTATAATCAATTATATT
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACC
* * * ** * **
872536 CGGTGAAATTAGC-CTACAGCAACCACCTTTATTTTCAGTGGTTTC
1 CGGTGGAATCAGCAC-ATAGCAACCACCTTTATAATCAATGGTACC
* * *
872581 TGGTGGAGTCAGCACATAGCAACCACCTTTATAGTCAATGGTACC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACC
872626 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACC
*
872671 CGGTGGAATCAGTACATAGCAACCACCTTTATAATCAATG
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATG
872711 ATACTCAGTA
Statistics
Matches: 146, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
43 6 0.04
44 9 0.06
45 130 0.89
46 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACC
Found at i:872789 original size:51 final size:53
Alignment explanation
Indices: 872725--872825 Score: 134
Period size: 55 Copynumber: 1.9 Consensus size: 53
872715 TCAGTACACG
*
872725 TAGTAGCCTGCACATAGT-A-CTACACATGTGACCATTACTATCACTTTCACA
1 TAGTAGCCTGCACATAGTCAGCCACACATGTGACCATTACTATCACTTTCACA
* * *
872776 TAGTGGCCTGCACATAGTCCATGCCACACATGTGATCATTACTGTCACTT
1 TAGTAGCCTGCACATAGT-CA-GCCACACATGTGACCATTACTATCACTT
872826 CATTTGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 17 0.40
53 1 0.02
55 24 0.57
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (53 bp):
TAGTAGCCTGCACATAGTCAGCCACACATGTGACCATTACTATCACTTTCACA
Found at i:878015 original size:42 final size:43
Alignment explanation
Indices: 877951--878037 Score: 167
Period size: 42 Copynumber: 2.0 Consensus size: 43
877941 CATTTTAGGC
877951 CTAGCCGAACCATTTTCATAACTATAGTAGTCAACAACACTCA
1 CTAGCCGAACCATTTTCATAACTATAGTAGTCAACAACACTCA
877994 CTAGCCGAACC-TTTTCATAACTATAGTAGTCAACAACACTCA
1 CTAGCCGAACCATTTTCATAACTATAGTAGTCAACAACACTCA
878036 CT
1 CT
878038 TATTCACACA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 33 0.75
43 11 0.25
ACGTcount: A:0.36, C:0.29, G:0.09, T:0.26
Consensus pattern (43 bp):
CTAGCCGAACCATTTTCATAACTATAGTAGTCAACAACACTCA
Found at i:882432 original size:51 final size:51
Alignment explanation
Indices: 882374--882568 Score: 227
Period size: 51 Copynumber: 3.8 Consensus size: 51
882364 GATACCGGTT
* * ***
882374 CACATAGTAGCCTGCACATAGTACTGCACATGTGACCATCACTATCCAATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTA
* *
882425 CACATAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCTGGTG
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCTGGTA
* * *
882476 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCTGGTA
* *
882526 CACATAGTAGCCTACACATAGTATTACACACGTGACCATCACT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
882569 TTCACTTTCA
Statistics
Matches: 121, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
49 4 0.03
50 41 0.34
51 73 0.60
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTA
Found at i:882545 original size:101 final size:102
Alignment explanation
Indices: 882376--882560 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
882366 TACCGGTTCA
* * *
882376 CATAGTAGCCTGCACATAGTACTGCACATGTGACCATCACTATCCAATACACATAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCAATACACATAGTAGCCTACA
882441 CATAGTACTACACACGTGATCGAAGCTATCTGGTGCG
66 CATAGTACTACACACGTGATCGAAGCTATCTGGTGCG
***
882478 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACATAGTAGCCTAC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCAATACACATAGTAGCCTAC
*
882541 ACATAGTATTACACACGTGA
65 ACATAGTACTACACACGTGA
882561 CCATCACTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 37 0.49
102 34 0.45
103 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCAATACACATAGTAGCCTACA
CATAGTACTACACACGTGATCGAAGCTATCTGGTGCG
Found at i:882583 original size:101 final size:102
Alignment explanation
Indices: 882371--882594 Score: 249
Period size: 101 Copynumber: 2.2 Consensus size: 102
882361 AATGATACCG
* *
882371 GTTCACATAGTAGCCTGCACATAGTACTGCACATGTGACCATCACTATCCAATACACATAGTAGC
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCAATACACATAGTAGC
* * **
882436 CTGCACATAGTACTACACACGTGATCGAAGCTATCTG
66 CTACACATAGTACTACACACGTGATCCAAGCTATCAC
* * ***
882473 GTGCGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACATAGTAG
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCAATACACATAGTAG
* *
882536 CCTACACATAGTATTACACACGTGA-CCATCA-CTTTCAC
65 CCTACACATAGTACTACACACGTGATCCA--AGCTATCAC
* * *
882574 TTTCACATAGTTGCCTACACA
1 GTTCACATAGTAGCCTGCACA
882595 CAGTCCGTGC
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
100 2 0.02
101 57 0.56
102 38 0.38
103 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (102 bp):
GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCAATACACATAGTAGC
CTACACATAGTACTACACACGTGATCCAAGCTATCAC
Found at i:901823 original size:21 final size:21
Alignment explanation
Indices: 901781--901823 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
901771 CTGATTCTGG
** *
901781 TGTGGATGCATCTGCCTTTGT
1 TGTGGATGCATCTAACTGTGT
*
901802 TGTGGATGCATCTAAGTGTGT
1 TGTGGATGCATCTAACTGTGT
901823 T
1 T
901824 AATTGCAGTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.14, G:0.30, T:0.42
Consensus pattern (21 bp):
TGTGGATGCATCTAACTGTGT
Found at i:917878 original size:21 final size:21
Alignment explanation
Indices: 917834--917888 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
917824 TGAACCCTTC
*
917834 CATTTACTTAC-TTTCCATTA
1 CATTTACTTACTTTTCAATTA
*
917854 CATTTACTTACTTTTCAATTG
1 CATTTACTTACTTTTCAATTA
*
917875 CATTTACATACTTT
1 CATTTACTTACTTT
917889 AGTTTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.25, C:0.22, G:0.02, T:0.51
Consensus pattern (21 bp):
CATTTACTTACTTTTCAATTA
Found at i:921476 original size:20 final size:20
Alignment explanation
Indices: 921423--921476 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
921413 TGAATCTTTC
*
921423 CATTTACTTACTTGCCATTG
1 CATTTACTTACTTTCCATTG
* *
921443 CATTTACTTACTTTTCATTT
1 CATTTACTTACTTTCCATTG
921463 CATTTACTTACTTT
1 CATTTACTTACTTT
921477 AGCTTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.54
Consensus pattern (20 bp):
CATTTACTTACTTTCCATTG
Found at i:923954 original size:40 final size:39
Alignment explanation
Indices: 923862--923967 Score: 99
Period size: 40 Copynumber: 2.6 Consensus size: 39
923852 TGTACGGGAC
* * * *
923862 TTGCACTTCGATGCCCCTGTATACACTTTGGTGTCCCTA
1 TTGCACTTCGGTGCCCCTGTTTGCACTTTGGTGCCCCTA
*
923901 TTCGCA-TTACGGTGCCCCTGTTTGCACATTT-GTGCCCCTG
1 TT-GCACTT-CGGTGCCCCTGTTTGCAC-TTTGGTGCCCCTA
*
923941 TCTGCACTTCGGTGCCTCTGTTATGCA
1 T-TGCACTTCGGTGCCCCTGTT-TGCA
923968 TCTATGATGC
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
39 4 0.07
40 41 0.75
41 10 0.18
ACGTcount: A:0.12, C:0.31, G:0.21, T:0.36
Consensus pattern (39 bp):
TTGCACTTCGGTGCCCCTGTTTGCACTTTGGTGCCCCTA
Found at i:923955 original size:20 final size:19
Alignment explanation
Indices: 923862--923962 Score: 71
Period size: 20 Copynumber: 5.1 Consensus size: 19
923852 TGTACGGGAC
*
923862 TTGCACTTCGATGCCCCTG
1 TTGCACTTCGGTGCCCCTG
* * * *
923881 TATACACTTTGGTGTCCCTA
1 T-TGCACTTCGGTGCCCCTG
923901 TTCGCA-TTACGGTGCCCCTG
1 TT-GCACTT-CGGTGCCCCTG
*
923921 TTTGCACATT-TGTGCCCCTG
1 -TTGCAC-TTCGGTGCCCCTG
*
923941 TCTGCACTTCGGTGCCTCTG
1 T-TGCACTTCGGTGCCCCTG
923961 TT
1 TT
923963 ATGCATCTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
19 8 0.13
20 50 0.81
21 2 0.03
22 2 0.03
ACGTcount: A:0.11, C:0.32, G:0.21, T:0.37
Consensus pattern (19 bp):
TTGCACTTCGGTGCCCCTG
Found at i:927431 original size:23 final size:23
Alignment explanation
Indices: 927405--927549 Score: 218
Period size: 23 Copynumber: 6.3 Consensus size: 23
927395 ATAAGTGCCA
*
927405 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
927428 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
927451 CACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
927474 CACTGATATGTAGCTGAATCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
927497 CACTGATACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
927520 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
927543 CACTGAT
1 CACTGAT
927550 CAATAACACT
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 109 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:933009 original size:25 final size:25
Alignment explanation
Indices: 932973--933075 Score: 152
Period size: 25 Copynumber: 4.1 Consensus size: 25
932963 TAGGGTTACT
* *
932973 GATTTATGGCTCGTGAGAGCGTACC
1 GATTTATAGCTCGTGAGAGCATACC
* *
932998 AATTTATAGCTCGTGAGAGCGTACC
1 GATTTATAGCTCGTGAGAGCATACC
*
933023 GATTTATAGCTCGTGAGAGCATACT
1 GATTTATAGCTCGTGAGAGCATACC
*
933048 GGTTTATAGCTCGTGAGAGCATACC
1 GATTTATAGCTCGTGAGAGCATACC
933073 GAT
1 GAT
933076 CTTCAACTCA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 70 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (25 bp):
GATTTATAGCTCGTGAGAGCATACC
Found at i:933098 original size:50 final size:50
Alignment explanation
Indices: 932999--933121 Score: 119
Period size: 50 Copynumber: 2.5 Consensus size: 50
932989 GAGCGTACCA
* **
932999 ATTTATAGCTCGTGAGAGCGTACCGATTTATAGCTCGTGAGAGCATACTG
1 ATTTATAGCTCGTGAGAGCATACCGATTTATAGCTCGAAAGAGCATACTG
* *
933049 GTTTATAGCTCGTGAGAGCATACCGATCTTCA-A-CTC-AAATGAGCTTACTG
1 ATTTATAGCTCGTGAGAGCATACCGAT-TT-ATAGCTCGAAA-GAGCATACTG
* *
933099 ATTCACAGCTCGT-ATGAGCATAC
1 ATTTATAGCTCGTGA-GAGCATAC
933122 ATGTATATGA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
49 2 0.03
50 55 0.90
51 3 0.05
52 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (50 bp):
ATTTATAGCTCGTGAGAGCATACCGATTTATAGCTCGAAAGAGCATACTG
Found at i:939096 original size:14 final size:13
Alignment explanation
Indices: 939077--939114 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
939067 GGGACTGTAT
939077 ATGTTAATCAATTA
1 ATGTTAA-CAATTA
939091 ATGTTAA-AATTA
1 ATGTTAACAATTA
*
939103 AAGTTAACAATT
1 ATGTTAACAATT
939115 TGGTGATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 4 0.18
14 7 0.32
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (13 bp):
ATGTTAACAATTA
Found at i:941903 original size:30 final size:29
Alignment explanation
Indices: 941845--941907 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
941835 ATAAATAAAT
941845 AAATATAAATAAAAATTACTGAAATTATTA
1 AAATATAAATAAAAATTAC-GAAATTATTA
941875 AAATAT-AATAAAAATATTAC-AAAGTTATTA
1 AAATATAAAT-AAAA-ATTACGAAA-TTATTA
941905 AAA
1 AAA
941908 ATTANNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 6 0.20
30 19 0.63
31 5 0.17
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (29 bp):
AAATATAAATAAAAATTACGAAATTATTA
Found at i:943626 original size:194 final size:195
Alignment explanation
Indices: 943400--943790 Score: 775
Period size: 194 Copynumber: 2.0 Consensus size: 195
943390 AGATATAACT
943400 TATTTATGTGTCAATATTATATTTTATAAAAATAATATGTTTATTCATAAAAAAATGTTATAGCC
1 TATTTATGTGTCAATATTATATTTTATAAAAATAATATGTTTATTCATAAAAAAATGTTATAGCC
943465 TTTTTTATCTTAACTTATTTATAAAAAAAATCTAAAGTTATGAAAAAATTATATTATTTATAAGA
66 TTTTTTATCTTAACTTATTTATAAAAAAAATCTAAAGTTATGAAAAAATTATATTATTTATAAGA
943530 AATGTTATGAAAGTTGTGGACAATTTATAAAATCTTTTTTATAATAATTACATATTATAAAAAGG
131 AATGTTATGAAAGTTGTGGACAATTTATAAAATCTTTTTTATAATAATTACATATTATAAAAAGG
943595 TATTTATGTGTC-ATATTATATTTTATAAAAATAATATGTTTATTCATAAAAAAATGTTATAGCC
1 TATTTATGTGTCAATATTATATTTTATAAAAATAATATGTTTATTCATAAAAAAATGTTATAGCC
943659 TTTTTTATCTTAACTTATTTATAAAAAAAATCTAAAGTTATGAAAAAATTATATTATTTATAAGA
66 TTTTTTATCTTAACTTATTTATAAAAAAAATCTAAAGTTATGAAAAAATTATATTATTTATAAGA
943724 AATGTTATGAAAGTTGTGGACAATTTATAAAATCTTTTTTATAATAATTACATATTATAAAAAGG
131 AATGTTATGAAAGTTGTGGACAATTTATAAAATCTTTTTTATAATAATTACATATTATAAAAAGG
943789 TA
1 TA
943791 ATTAACCTAG
Statistics
Matches: 196, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
194 184 0.94
195 12 0.06
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (195 bp):
TATTTATGTGTCAATATTATATTTTATAAAAATAATATGTTTATTCATAAAAAAATGTTATAGCC
TTTTTTATCTTAACTTATTTATAAAAAAAATCTAAAGTTATGAAAAAATTATATTATTTATAAGA
AATGTTATGAAAGTTGTGGACAATTTATAAAATCTTTTTTATAATAATTACATATTATAAAAAGG
Found at i:945763 original size:18 final size:18
Alignment explanation
Indices: 945732--945779 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
945722 TGTCGTTTGT
*
945732 TTTCAAAACATTATTC-A
1 TTTCAAAACGTTATTCAA
*
945749 TTTACAAATCGTTATTCAA
1 TTT-CAAAACGTTATTCAA
945768 TTTCAAAACGTT
1 TTTCAAAACGTT
945780 TTCTTATTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (18 bp):
TTTCAAAACGTTATTCAA
Found at i:952061 original size:6 final size:6
Alignment explanation
Indices: 952050--952079 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
952040 CTATCAAAGA
*
952050 CAGTTT CAGTTT TAGTTT CAGTTT CAGTTT
1 CAGTTT CAGTTT CAGTTT CAGTTT CAGTTT
952080 AAACAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (6 bp):
CAGTTT
Found at i:952430 original size:18 final size:17
Alignment explanation
Indices: 952388--952430 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
952378 TGTCGTTCGT
952388 TTTCAAAACATTATTCA
1 TTTCAAAACATTATTCA
* *
952405 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTC-A
952424 TTTCAAA
1 TTTCAAA
952431 GTGTTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTCAAAACATTATTCA
Found at i:954283 original size:28 final size:28
Alignment explanation
Indices: 954241--954295 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
954231 GGCCAAAAGA
*
954241 GATCACTTACTAGATGAAAAAGGGCCAT
1 GATCACTTACCAGATGAAAAAGGGCCAT
954269 GATCACTTACCAGATGAAAAAGGGCCA
1 GATCACTTACCAGATGAAAAAGGGCCA
954296 CGAACGCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (28 bp):
GATCACTTACCAGATGAAAAAGGGCCAT
Found at i:956450 original size:21 final size:21
Alignment explanation
Indices: 956417--956459 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
956407 TTTTGAGTTG
* *
956417 TTTATGAAGTTGGATGATAAA
1 TTTAAGAACTTGGATGATAAA
* *
956438 TTTAAGAACTTGGTTGTTAAA
1 TTTAAGAACTTGGATGATAAA
956459 T
1 T
956460 AAGACTATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (21 bp):
TTTAAGAACTTGGATGATAAA
Found at i:957547 original size:12 final size:12
Alignment explanation
Indices: 957532--957577 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
957522 AAGATATTAG
957532 ATTAAATTTAAT
1 ATTAAATTTAAT
957544 ATTAAATATTAA-
1 ATTAAAT-TTAAT
*
957556 ATTAAATTAAAT
1 ATTAAATTTAAT
957568 ATTAAATTTA
1 ATTAAATTTA
957578 TTAAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 3 0.10
12 23 0.77
13 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
ATTAAATTTAAT
Found at i:957553 original size:24 final size:24
Alignment explanation
Indices: 957525--957574 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
957515 ATTTATCAAG
* *
957525 ATATTAGATTAAATTTAATATTAA
1 ATATTAAATTAAATTAAATATTAA
957549 ATATTAAATTAAATTAAATATTAA
1 ATATTAAATTAAATTAAATATTAA
957573 AT
1 AT
957575 TTATTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATTAAATTAAATTAAATATTAA
Found at i:958006 original size:19 final size:19
Alignment explanation
Indices: 957974--958012 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
957964 AAATATAATT
*
957974 TTAATTTTAATTAATTTGA
1 TTAATTTTAATTAACTTGA
957993 TTAA-TTTAATTTAACTTGA
1 TTAATTTTAA-TTAACTTGA
958012 T
1 T
958013 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (19 bp):
TTAATTTTAATTAACTTGA
Found at i:967955 original size:25 final size:25
Alignment explanation
Indices: 967927--967976 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
967917 CAGCTCTCAT
*
967927 GAGCATCCCGA-TATATGGCTCTTTG
1 GAGCATCCCGATTA-AAGGCTCTTTG
*
967952 GAGCTTCCCGATTAAAGGCTCTTTG
1 GAGCATCCCGATTAAAGGCTCTTTG
967977 TAAGTTTCCT
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:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (25 bp):
GAGCATCCCGATTAAAGGCTCTTTG
Found at i:967991 original size:26 final size:25
Alignment explanation
Indices: 967943--967998 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
967933 CCCGATATAT
*
967943 GGCTCTTTGGAGCTTCCCGATTAAA
1 GGCTCTTTGAAGCTTCCCGATTAAA
* * *
967968 GGCTCTTTGTAAGTTTCCTGATTAAT
1 GGCTCTTTG-AAGCTTCCCGATTAAA
967994 GGCTC
1 GGCTC
967999 ACCAGAGCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (25 bp):
GGCTCTTTGAAGCTTCCCGATTAAA
Found at i:970957 original size:39 final size:40
Alignment explanation
Indices: 970881--970957 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 40
970871 ATAAGTTGGT
** *
970881 CTGCTCACACAAGCTATCGGTCGTAACGTAGCTACATGATA
1 CTGCTCACACAAGCTATC-GAAGTAACGTAACTACATGATA
970922 CTGCTCACACAAGCTATC-AAGTAACCGTAAC-ACATG
1 CTGCTCACACAAGCTATCGAAGTAA-CGTAACTACATG
970958 CTAGAAACTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 9 0.28
40 5 0.16
41 18 0.56
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (40 bp):
CTGCTCACACAAGCTATCGAAGTAACGTAACTACATGATA
Found at i:983837 original size:9 final size:10
Alignment explanation
Indices: 983817--983845 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
983807 ATTGCGTGTT
983817 TGAATAGAAA
1 TGAATAGAAA
983827 TGAAT-GAAA
1 TGAATAGAAA
983836 TGAATAGAAA
1 TGAATAGAAA
983846 AAGAGAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:986217 original size:63 final size:64
Alignment explanation
Indices: 986131--986258 Score: 249
Period size: 63 Copynumber: 2.0 Consensus size: 64
986121 CTAAGACTAA
986131 CTTTATTTTTTCATAATTAATCCTATATTTTCATGCAAATTCCACTTTAAACTAAATTTAACTC
1 CTTTATTTTTTCATAATTAATCCTATATTTTCATGCAAATTCCACTTTAAACTAAATTTAACTC
986195 CTTT-TTTTTTCATAATTAATCCTATATTTTCATGCAAATTCCACTTTAAACTAAATTTAACTC
1 CTTTATTTTTTCATAATTAATCCTATATTTTCATGCAAATTCCACTTTAAACTAAATTTAACTC
986258 C
1 C
986259 CTAAATTTTG
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
63 60 0.94
64 4 0.06
ACGTcount: A:0.32, C:0.20, G:0.02, T:0.47
Consensus pattern (64 bp):
CTTTATTTTTTCATAATTAATCCTATATTTTCATGCAAATTCCACTTTAAACTAAATTTAACTC
Found at i:986591 original size:10 final size:10
Alignment explanation
Indices: 986572--986634 Score: 56
Period size: 10 Copynumber: 5.9 Consensus size: 10
986562 TTTATTTCTT
986572 TTTTTCTTTC
1 TTTTTCTTTC
986582 TTTTTCTTTC
1 TTTTTCTTTC
*
986592 TGTTTCGTTT-
1 TTTTTC-TTTC
*
986602 TGGTTTTGTATTCC
1 T--TTTTCT-TT-C
986616 TTTTTCTTTC
1 TTTTTCTTTC
986626 TTTTTCTTT
1 TTTTTCTTT
986635 TATTTATTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 26 0.60
11 6 0.14
12 10 0.23
14 1 0.02
ACGTcount: A:0.02, C:0.16, G:0.08, T:0.75
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:988038 original size:45 final size:45
Alignment explanation
Indices: 987879--988050 Score: 181
Period size: 44 Copynumber: 3.8 Consensus size: 45
987869 TCACATTTAA
* *
987879 TGCCATAGTATGTTTCAACTATGGTCTTGT-TCATTTTTC-GATATAG
1 TGCCATAGTATCTTTCAACTATGGTCTT-TCTCA--TTTCGGTTATAG
* * * ** *
987925 TGTCATAGTATCTTTCAACTAGGGTCTTACTCGCTTCGGTT-TAT
1 TGCCATAGTATCTTTCAACTATGGTCTTTCTCATTTCGGTTATAG
*
987969 TTCCATAGTATCTTTCAACTATGGTCTTTCTCATTTCGGTTATAG
1 TGCCATAGTATCTTTCAACTATGGTCTTTCTCATTTCGGTTATAG
* *
988014 TGCCAT-GATATCTTTCAACCATGGTCTTTCTCTTTTC
1 TGCCATAG-TATCTTTCAACTATGGTCTTTCTCATTTC
988051 TCAAGTTAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
44 41 0.39
45 36 0.35
46 27 0.26
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.45
Consensus pattern (45 bp):
TGCCATAGTATCTTTCAACTATGGTCTTTCTCATTTCGGTTATAG
Found at i:998343 original size:23 final size:23
Alignment explanation
Indices: 998316--998361 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
998306 TAATTTGTTA
998316 TATTAA-ACATATATTAACCTTAT
1 TATTAATAC-TATATTAACCTTAT
998339 TATTAATTTACTATATTAACCTT
1 TATTAA--TACTATATTAACCTT
998362 TACTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATACTATATTAACCTTAT
Found at i:999857 original size:27 final size:26
Alignment explanation
Indices: 999822--999899 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 26
999812 CAACACAATA
*
999822 CCATGTTTAACGTCCTAACGGACTACC
1 CCATGTTTAA-GTCCCAACGGACTACC
* * *
999849 CCATTTTTATATTCCCGACGGACTACC
1 CCATGTTTA-AGTCCCAACGGACTACC
* *
999876 CCATGTTTAATGTCTCGACGGACT
1 CCATGTTTAA-GTCCCAACGGACT
999900 CCAAATGTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
26 1 0.02
27 40 0.95
28 1 0.02
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (26 bp):
CCATGTTTAAGTCCCAACGGACTACC
Found at i:1003471 original size:21 final size:21
Alignment explanation
Indices: 1003445--1003490 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1003435 AAAAGAAATT
* *
1003445 TTTTTTACTGCTTTCTTGTTG
1 TTTTTTACTGCTTTATTGTTA
* *
1003466 TTTTTTATTGTTTTATTGTTA
1 TTTTTTACTGCTTTATTGTTA
1003487 TTTT
1 TTTT
1003491 CTTGTTGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.07, G:0.11, T:0.74
Consensus pattern (21 bp):
TTTTTTACTGCTTTATTGTTA
Found at i:1003495 original size:11 final size:11
Alignment explanation
Indices: 1003456--1003501 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
1003446 TTTTTACTGC
1003456 TTTCTTGTTGT
1 TTTCTTGTTGT
*
1003467 TTT-TTATTGT
1 TTTCTTGTTGT
* *
1003477 TTTATTGTTAT
1 TTTCTTGTTGT
1003488 TTTCTTGTTGT
1 TTTCTTGTTGT
1003499 TTT
1 TTT
1003502 TTTCACTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.07, C:0.04, G:0.13, T:0.76
Consensus pattern (11 bp):
TTTCTTGTTGT
Found at i:1003680 original size:16 final size:17
Alignment explanation
Indices: 1003647--1003685 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1003637 GAAACATTTG
*
1003647 TTTTAATGTTTTAGTAT
1 TTTTAATGTATTAGTAT
*
1003664 TTTTTATGTATTA-TAT
1 TTTTAATGTATTAGTAT
1003680 TTTTAA
1 TTTTAA
1003686 AAAATTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (17 bp):
TTTTAATGTATTAGTAT
Found at i:1003700 original size:12 final size:12
Alignment explanation
Indices: 1003683--1003716 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1003673 ATTATATTTT
* *
1003683 TAAAAAATTATA
1 TAAAAAATAAAA
1003695 TAAAAAATAAAA
1 TAAAAAATAAAA
1003707 TAAAAAATAA
1 TAAAAAATAA
1003717 TACGGCCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:1004054 original size:30 final size:30
Alignment explanation
Indices: 1004020--1004081 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1004010 TCATGTTTTC
1004020 TAATCACATATTATATTTTAGGGTAAATTA
1 TAATCACATATTATATTTTAGGGTAAATTA
1004050 TAATCACATATTATATTTTAGGGTAAATTA
1 TAATCACATATTATATTTTAGGGTAAATTA
1004080 TA
1 TA
1004082 CAAATGGCCA
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:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (30 bp):
TAATCACATATTATATTTTAGGGTAAATTA
Found at i:1012087 original size:22 final size:22
Alignment explanation
Indices: 1012048--1012110 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
1012038 ATAAATAATA
*
1012048 TAAATAATATT-TAAAATTTAT
1 TAAAAAATATTATAAAATTTAT
* *
1012069 TAAAAATTATTATAAAATTCA-
1 TAAAAAATATTATAAAATTTAT
*
1012090 TAAAAAAT-TTATAAAAATTAT
1 TAAAAAATATTATAAAATTTAT
1012111 CGTACCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 10 0.29
21 16 0.47
22 8 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAAAAATATTATAAAATTTAT
Found at i:1012103 original size:11 final size:11
Alignment explanation
Indices: 1012060--1012106 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
1012050 AATAATATTT
*
1012060 AAAATTTATTA
1 AAAATTTATAA
*
1012071 AAAA-TTATTAT
1 AAAATTTA-TAA
*
1012082 AAAATTCATAA
1 AAAATTTATAA
1012093 AAAATTTATAA
1 AAAATTTATAA
1012104 AAA
1 AAA
1012107 TTATCGTACC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
10 3 0.10
11 24 0.83
12 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATTTATAA
Found at i:1012290 original size:9 final size:9
Alignment explanation
Indices: 1012278--1012383 Score: 58
Period size: 9 Copynumber: 11.4 Consensus size: 9
1012268 TTAAAATGCA
1012278 TTTTATAATT
1 TTTTATAA-T
*
1012288 TTTTATGAT
1 TTTTATAAT
1012297 TTTTATAAAT
1 TTTTAT-AAT
*
1012307 TTTTACAATTT
1 TTTTATAA--T
*
1012318 TTTTCTAAT
1 TTTTATAAT
*
1012327 TTATAT-AT
1 TTTTATAAT
*
1012335 ATTTTA-AAA
1 -TTTTATAAT
*
1012344 TTTTAAAAT
1 TTTTATAAT
*
1012353 TTTTATTTAT
1 TTTTA-TAAT
1012363 TTTTAT--T
1 TTTTATAAT
1012370 TTTTATAAT
1 TTTTATAAT
1012379 GTTTT
1 -TTTT
1012384 GTCATATGTC
Statistics
Matches: 74, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
7 7 0.09
8 7 0.09
9 28 0.38
10 25 0.34
11 7 0.09
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1012293 original size:10 final size:10
Alignment explanation
Indices: 1012278--1012320 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
1012268 TTAAAATGCA
1012278 TTTTATAATT
1 TTTTATAATT
*
1012288 TTTTATGA-T
1 TTTTATAATT
*
1012297 TTTTATAAAT
1 TTTTATAATT
*
1012307 TTTTACAATT
1 TTTTATAATT
1012317 TTTT
1 TTTT
1012321 TCTAATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:1012317 original size:19 final size:19
Alignment explanation
Indices: 1012278--1012319 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1012268 TTAAAATGCA
* **
1012278 TTTTATAATTTTTTATGAT
1 TTTTATAAATTTTTACAAT
1012297 TTTTATAAATTTTTACAAT
1 TTTTATAAATTTTTACAAT
1012316 TTTT
1 TTTT
1012320 TTCTAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTATAAATTTTTACAAT
Found at i:1014875 original size:43 final size:43
Alignment explanation
Indices: 1014742--1014882 Score: 201
Period size: 43 Copynumber: 3.3 Consensus size: 43
1014732 TACAGGAGAT
* *
1014742 ACACGCCCGTGTGGCCAGGCTGTGTGTCTCACATGGCCAAGAG
1 ACACGCCCGTGTGGCCAGGCCGTGTGTCTCACAAGGCCAAGAG
* *
1014785 ACACACTCGTGTGGCCAGGCCGTGTGTCTCACAAGGCCAAGAG
1 ACACGCCCGTGTGGCCAGGCCGTGTGTCTCACAAGGCCAAGAG
* * * * *
1014828 ACACGCTCGTGTGGCTAGGCCGTGTGTGTCACACGGCTAAGAG
1 ACACGCCCGTGTGGCCAGGCCGTGTGTCTCACAAGGCCAAGAG
1014871 ACACGCCCGTGT
1 ACACGCCCGTGT
1014883 CTTAGGCAGT
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 88 1.00
ACGTcount: A:0.20, C:0.30, G:0.32, T:0.18
Consensus pattern (43 bp):
ACACGCCCGTGTGGCCAGGCCGTGTGTCTCACAAGGCCAAGAG
Found at i:1018145 original size:20 final size:20
Alignment explanation
Indices: 1018120--1018170 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1018110 GTATCGATCC
*
1018120 AGTATCGATACT-TTTCTTAA
1 AGTATCGATA-TATTTCCTAA
1018140 AGTATCGATATATTTCCTAA
1 AGTATCGATATATTTCCTAA
*
1018160 GGTATCGATAT
1 AGTATCGATAT
1018171 TCCTGCTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (20 bp):
AGTATCGATATATTTCCTAA
Found at i:1018374 original size:37 final size:38
Alignment explanation
Indices: 1018312--1018386 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
1018302 TCTACAACAA
1018312 CCACAATGGTTAAAAACCAATTAGAGGGTATAAATACC
1 CCACAATGGTTAAAAACCAATTAGAGGGTATAAATACC
1018350 CCACAATGGTT-AAAACCAATTAGAGGGTATAAATACC
1 CCACAATGGTTAAAAACCAATTAGAGGGTATAAATACC
1018387 ATTTTCCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 26 0.70
38 11 0.30
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (38 bp):
CCACAATGGTTAAAAACCAATTAGAGGGTATAAATACC
Found at i:1019702 original size:20 final size:20
Alignment explanation
Indices: 1019677--1019727 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1019667 GTATCGATCC
*
1019677 AGTATCGATACT-TTTCTTAA
1 AGTATCGATA-TATTTCCTAA
1019697 AGTATCGATATATTTCCTAA
1 AGTATCGATATATTTCCTAA
*
1019717 GGTATCGATAT
1 AGTATCGATAT
1019728 TCCTGCTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (20 bp):
AGTATCGATATATTTCCTAA
Found at i:1020269 original size:145 final size:145
Alignment explanation
Indices: 1020006--1020296 Score: 582
Period size: 145 Copynumber: 2.0 Consensus size: 145
1019996 TCTTATAAAC
1020006 GCTTGTGAGCTTTCATTGTATTCATTTGGCTCAAGTGTTTTTCTTTGTATTTGTGCTTAATTGGC
1 GCTTGTGAGCTTTCATTGTATTCATTTGGCTCAAGTGTTTTTCTTTGTATTTGTGCTTAATTGGC
1020071 AGACATCCTAATCTTGTAAGAATTGTTTCTTTGTTTGCTTATTTGTTTCTCTTTGAAAGAGGGTT
66 AGACATCCTAATCTTGTAAGAATTGTTTCTTTGTTTGCTTATTTGTTTCTCTTTGAAAGAGGGTT
1020136 TATTCTTAAGGTTTG
131 TATTCTTAAGGTTTG
1020151 GCTTGTGAGCTTTCATTGTATTCATTTGGCTCAAGTGTTTTTCTTTGTATTTGTGCTTAATTGGC
1 GCTTGTGAGCTTTCATTGTATTCATTTGGCTCAAGTGTTTTTCTTTGTATTTGTGCTTAATTGGC
1020216 AGACATCCTAATCTTGTAAGAATTGTTTCTTTGTTTGCTTATTTGTTTCTCTTTGAAAGAGGGTT
66 AGACATCCTAATCTTGTAAGAATTGTTTCTTTGTTTGCTTATTTGTTTCTCTTTGAAAGAGGGTT
1020281 TATTCTTAAGGTTTG
131 TATTCTTAAGGTTTG
1020296 G
1 G
1020297 GTAGAAACCT
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 146 1.00
ACGTcount: A:0.18, C:0.12, G:0.20, T:0.49
Consensus pattern (145 bp):
GCTTGTGAGCTTTCATTGTATTCATTTGGCTCAAGTGTTTTTCTTTGTATTTGTGCTTAATTGGC
AGACATCCTAATCTTGTAAGAATTGTTTCTTTGTTTGCTTATTTGTTTCTCTTTGAAAGAGGGTT
TATTCTTAAGGTTTG
Found at i:1021279 original size:18 final size:17
Alignment explanation
Indices: 1021256--1021293 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1021246 GGTAAGGTTA
1021256 AAATGG-TAAATAGTAAAT
1 AAATGGATAAAT--TAAAT
1021274 AAATGGATAAATTAAAT
1 AAATGGATAAATTAAAT
1021291 AAA
1 AAA
1021294 ACAAATTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (17 bp):
AAATGGATAAATTAAAT
Found at i:1025834 original size:20 final size:20
Alignment explanation
Indices: 1025809--1025859 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1025799 GTATCGATCC
*
1025809 AGTATCGATACT-TTTCTTAA
1 AGTATCGATA-TATTTCCTAA
1025829 AGTATCGATATATTTCCTAA
1 AGTATCGATATATTTCCTAA
*
1025849 GGTATCGATAT
1 AGTATCGATAT
1025860 TCCTGCTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (20 bp):
AGTATCGATATATTTCCTAA
Found at i:1030403 original size:32 final size:32
Alignment explanation
Indices: 1030363--1030439 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
1030353 TAAATGGTCT
1030363 AATT-ACCATTTAAGTCCCTTTTCCTTTATTC
1 AATTAACCATTTAAGTCCCTTTTCCTTTATTC
*
1030394 AATTAACCATTTAAGTCCCTTTTTCTTTATTC
1 AATTAACCATTTAAGTCCCTTTTCCTTTATTC
1030426 AATTAACCATTTAA
1 AATTAACCATTTAA
1030440 TCACTCAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 4 0.09
32 40 0.91
ACGTcount: A:0.29, C:0.22, G:0.03, T:0.47
Consensus pattern (32 bp):
AATTAACCATTTAAGTCCCTTTTCCTTTATTC
Found at i:1035575 original size:41 final size:41
Alignment explanation
Indices: 1035520--1035858 Score: 311
Period size: 41 Copynumber: 8.3 Consensus size: 41
1035510 GGGAACGTAG
* * * *
1035520 GTGCTATTCAGGGGTACCGAAGTACAAACAAGGGCACATAT
1 GTGCAATTTAGGGGTACCAAAGTACAAACAGGGGCACATAT
* * * * * *
1035561 GTACAATTTTGGGGTATCGAAGTACAAACAAGGGCACGTAT
1 GTGCAATTTAGGGGTACCAAAGTACAAACAGGGGCACATAT
** * * *
1035602 GTGCAATTTAAAGGTATCGAAGTACAAATAGGGGCACATAT
1 GTGCAATTTAGGGGTACCAAAGTACAAACAGGGGCACATAT
* *
1035643 GTGCAATTCAGGGGTACCAAAGTATAAACAGGGGCACATAT
1 GTGCAATTTAGGGGTACCAAAGTACAAACAGGGGCACATAT
* * ** * * **
1035684 GTGCAATTCAGGAGTATTAAAGTGCAAATAGGGGCATGTAT
1 GTGCAATTTAGGGGTACCAAAGTACAAACAGGGGCACATAT
* * * *
1035725 GTACAATTCAAGGGTACCAAAGTACAAATAGGGGCA-ATTAT
1 GTGCAATTTAGGGGTACCAAAGTACAAACAGGGGCACA-TAT
* * * * *
1035766 GTGTAATTTAGGGGTATCAAAGTAAAAATAGGGGCACGTAT
1 GTGCAATTTAGGGGTACCAAAGTACAAACAGGGGCACATAT
* * * **
1035807 GTGCAATTTAGGGGTGCCGAAGTACAAACAAGGGCATGTAT
1 GTGCAATTTAGGGGTACCAAAGTACAAACAGGGGCACATAT
1035848 GTGCAATTTAG
1 GTGCAATTTAG
1035859 TGAATAATTA
Statistics
Matches: 246, Mismatches: 50, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
41 246 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.24
Consensus pattern (41 bp):
GTGCAATTTAGGGGTACCAAAGTACAAACAGGGGCACATAT
Found at i:1035719 original size:123 final size:123
Alignment explanation
Indices: 1035520--1035855 Score: 368
Period size: 123 Copynumber: 2.7 Consensus size: 123
1035510 GGGAACGTAG
* * * * * ** * *
1035520 GTGCTATTCAGGGGTACCGAAGTACAAACAAGGGCACATATGTACAATTTTGGGGTATCGAAGTA
1 GTGCAATTCAGGGGTACCAAAGTAAAAACAGGGGCACATATGTGCAATTCAGGAGTATCAAAGTA
* * * *
1035585 CAAACAAGGGCACGTATGTGCAATTTAAAGGTATCGAAGTACAAATAGGGGCACA-TAT
66 CAAACAAGGGCACGTATGTACAATTCAAAGGTACCAAAGTACAAATAGGGGCA-ATTAT
* * *
1035643 GTGCAATTCAGGGGTACCAAAGTATAAACAGGGGCACATATGTGCAATTCAGGAGTATTAAAGTG
1 GTGCAATTCAGGGGTACCAAAGTAAAAACAGGGGCACATATGTGCAATTCAGGAGTATCAAAGTA
* * * *
1035708 CAAATAGGGGCATGTATGTACAATTCAAGGGTACCAAAGTACAAATAGGGGCAATTAT
66 CAAACAAGGGCACGTATGTACAATTCAAAGGTACCAAAGTACAAATAGGGGCAATTAT
* * * * * * * ** *
1035766 GTGTAATTTAGGGGTATCAAAGTAAAAATAGGGGCACGTATGTGCAATTTAGGGGTGCCGAAGTA
1 GTGCAATTCAGGGGTACCAAAGTAAAAACAGGGGCACATATGTGCAATTCAGGAGTATCAAAGTA
* *
1035831 CAAACAAGGGCATGTATGTGCAATT
66 CAAACAAGGGCACGTATGTACAATT
1035856 TAGTGAATAA
Statistics
Matches: 177, Mismatches: 35, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
122 1 0.01
123 176 0.99
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.24
Consensus pattern (123 bp):
GTGCAATTCAGGGGTACCAAAGTAAAAACAGGGGCACATATGTGCAATTCAGGAGTATCAAAGTA
CAAACAAGGGCACGTATGTACAATTCAAAGGTACCAAAGTACAAATAGGGGCAATTAT
Found at i:1035858 original size:82 final size:82
Alignment explanation
Indices: 1035505--1035858 Score: 359
Period size: 82 Copynumber: 4.3 Consensus size: 82
1035495 ATCAGAGTGT
* * * * * * * *
1035505 AAAC-AGGGAACGTAGGTGCTATTCAGGGGTACCGAAGTACAAACAAGGGCACATATGTACAATT
1 AAACAAGGGCACGTATGTGCAATTTAGGGGTATCAAAGTACAAATAGGGGCACATATGTACAATT
** * *
1035569 TTGGGGTATCGAAGTAC
66 CAGGGGTACCAAAGTAC
** * *
1035586 AAACAAGGGCACGTATGTGCAATTTAAAGGTATCGAAGTACAAATAGGGGCACATATGTGCAATT
1 AAACAAGGGCACGTATGTGCAATTTAGGGGTATCAAAGTACAAATAGGGGCACATATGTACAATT
*
1035651 CAGGGGTACCAAAGTAT
66 CAGGGGTACCAAAGTAC
* * * * * * **
1035668 AAACAGGGGCACATATGTGCAATTCAGGAGTATTAAAGTGCAAATAGGGGCATGTATGTACAATT
1 AAACAAGGGCACGTATGTGCAATTTAGGGGTATCAAAGTACAAATAGGGGCACATATGTACAATT
*
1035733 CAAGGGTACCAAAGTAC
66 CAGGGGTACCAAAGTAC
* * ** * * * *
1035750 AAATAGGGGCAATTATGTGTAATTTAGGGGTATCAAAGTAAAAATAGGGGCACGTATGTGCAATT
1 AAACAAGGGCACGTATGTGCAATTTAGGGGTATCAAAGTACAAATAGGGGCACATATGTACAATT
* * *
1035815 TAGGGGTGCCGAAGTAC
66 CAGGGGTACCAAAGTAC
*
1035832 AAACAAGGGCATGTATGTGCAATTTAG
1 AAACAAGGGCACGTATGTGCAATTTAG
1035859 TGAATAATTA
Statistics
Matches: 223, Mismatches: 49, Indels: 1
0.82 0.18 0.00
Matches are distributed among these distances:
81 4 0.02
82 219 0.98
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (82 bp):
AAACAAGGGCACGTATGTGCAATTTAGGGGTATCAAAGTACAAATAGGGGCACATATGTACAATT
CAGGGGTACCAAAGTAC
Found at i:1038646 original size:21 final size:21
Alignment explanation
Indices: 1038605--1038646 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1038595 TGAAAAGGAC
*
1038605 TAAATTGGAAATTAAATTAAT
1 TAAATTGGAAATTAAACTAAT
*
1038626 TAAATATGGAAA-TAAGCTAAT
1 TAAAT-TGGAAATTAAACTAAT
1038647 ATCATCTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (21 bp):
TAAATTGGAAATTAAACTAAT
Found at i:1044748 original size:24 final size:24
Alignment explanation
Indices: 1044721--1044772 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1044711 ACTCTAATCA
* *
1044721 AACCAAACCGGTTAAGTTTTCCCT
1 AACCAAACCAGTTAACTTTTCCCT
* *
1044745 AACC-AGCCATTTAACTTTTCCCT
1 AACCAAACCAGTTAACTTTTCCCT
1044768 AACCA
1 AACCA
1044773 GCTACTTAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.31, C:0.33, G:0.08, T:0.29
Consensus pattern (24 bp):
AACCAAACCAGTTAACTTTTCCCT
Found at i:1044781 original size:23 final size:23
Alignment explanation
Indices: 1044732--1044781 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1044722 ACCAAACCGG
* *
1044732 TTAAGTTTTCCCTAACCAGCCAT
1 TTAACTTTTCCCTAACCAGCCAC
*
1044755 TTAACTTTTCCCTAACCAGCTAC
1 TTAACTTTTCCCTAACCAGCCAC
1044778 TTAA
1 TTAA
1044782 GTTTCTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.36
Consensus pattern (23 bp):
TTAACTTTTCCCTAACCAGCCAC
Found at i:1053218 original size:16 final size:16
Alignment explanation
Indices: 1053197--1053228 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1053187 TGATTGAAAG
1053197 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
1053213 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
1053229 GCAACAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:1063456 original size:27 final size:27
Alignment explanation
Indices: 1063399--1063462 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
1063389 GAGTCCGTCG
* * ** *
1063399 GGACATTAAATACGGGGTAGTTTGTTG
1 GGACATTAAATACGGAGTAGTCTACTA
1063426 GGACATTAAATACGGAGTAGTCTACTA
1 GGACATTAAATACGGAGTAGTCTACTA
1063453 GGACATTAAA
1 GGACATTAAA
1063463 CATGGGGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.28
Consensus pattern (27 bp):
GGACATTAAATACGGAGTAGTCTACTA
Found at i:1072576 original size:26 final size:25
Alignment explanation
Indices: 1072544--1072616 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 25
1072534 TAAAAAATTA
1072544 AAATAAAACTTATAAAATTTTATAT
1 AAATAAAACTTATAAAATTTTATAT
* **
1072569 GAAATAAATA-TTAT--AGTAGTA-A-
1 -AAATAAA-ACTTATAAAATTTTATAT
1072591 AAATAAAACTTATAAAATTTTATAT
1 AAATAAAACTTATAAAATTTTATAT
1072616 A
1 A
1072617 TGAAATATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 13
0.65 0.11 0.24
Matches are distributed among these distances:
20 1 0.03
21 11 0.31
23 5 0.14
24 5 0.14
25 1 0.03
26 11 0.31
27 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (25 bp):
AAATAAAACTTATAAAATTTTATAT
Found at i:1074193 original size:16 final size:16
Alignment explanation
Indices: 1074093--1074202 Score: 57
Period size: 17 Copynumber: 6.7 Consensus size: 16
1074083 TATATATACC
*
1074093 TTAAAT-TATAAAAAG
1 TTAAATATATAAAAAA
* * *
1074108 TTAGAGATATAAAAAT
1 TTAAATATATAAAAAA
*
1074124 TTAAAAATTATAAAAAA
1 TTAAATA-TATAAAAAA
*
1074141 TT--ATATATAAACTTTAA
1 TTAAATATATAAA---AAA
* *
1074158 -TACATATAAGAAATAAA
1 TTAAATAT-ATAAA-AAA
1074175 TTAAATATATAAAAAA
1 TTAAATATATAAAAAA
1074191 TTATAATATATA
1 TTA-AATATATA
1074203 TTGGTATTTG
Statistics
Matches: 73, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
14 6 0.08
15 6 0.08
16 20 0.27
17 27 0.37
18 10 0.14
19 4 0.05
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (16 bp):
TTAAATATATAAAAAA
Found at i:1074549 original size:17 final size:18
Alignment explanation
Indices: 1074520--1074554 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1074510 TGCTTGGTAA
1074520 GAAAGATAAAAAAAAATT
1 GAAAGATAAAAAAAAATT
*
1074538 GAAAGA-AAAAAATAATT
1 GAAAGATAAAAAAAAATT
1074555 TTCTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (18 bp):
GAAAGATAAAAAAAAATT
Found at i:1075371 original size:20 final size:20
Alignment explanation
Indices: 1075343--1075400 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1075333 AATGAGGAGT
*
1075343 ACGAGTGTGCAATCAGGGGC
1 ACGAATGTGCAATCAGGGGC
** *
1075363 ACGAATGTGCTGTTAGGGGC
1 ACGAATGTGCAATCAGGGGC
* *
1075383 ACGAATGTACAAACAGGG
1 ACGAATGTGCAATCAGGG
1075401 ACACCGAAGT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.36, T:0.17
Consensus pattern (20 bp):
ACGAATGTGCAATCAGGGGC
Found at i:1077081 original size:25 final size:26
Alignment explanation
Indices: 1077035--1077086 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
1077025 CTAGCAAAAT
1077035 CCGAATAGACGAATGCTTCACAACTGG
1 CCGAATAGAC-AATGCTTCACAACTGG
1077062 CCGAATAGAC-ATGCTTCACAACTGG
1 CCGAATAGACAATGCTTCACAACTGG
1077087 AGAAAACACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 15 0.60
27 10 0.40
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (26 bp):
CCGAATAGACAATGCTTCACAACTGG
Found at i:1080018 original size:2 final size:2
Alignment explanation
Indices: 1080011--1080035 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1080001 GAATTTACAA
1080011 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1080036 ACAATGCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1080241 original size:23 final size:24
Alignment explanation
Indices: 1080215--1080263 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
1080205 GACTTTCCAA
1080215 TATTTGATA-CACATCTTTGACTT
1 TATTTGATACCACATCTTTGACTT
*
1080238 TATTTGATACTCATATCTTTGACTT
1 TATTTGATAC-CACATCTTTGACTT
1080263 T
1 T
1080264 TCATAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.39
25 14 0.61
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.51
Consensus pattern (24 bp):
TATTTGATACCACATCTTTGACTT
Found at i:1086530 original size:13 final size:14
Alignment explanation
Indices: 1086501--1086538 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1086491 ATTTTGTACA
1086501 AAAATATTAAATTT
1 AAAATATTAAATTT
*
1086515 AAAATATT-AGTTT
1 AAAATATTAAATTT
1086528 AAAATA-TAAAT
1 AAAATATTAAAT
1086539 CGAATTCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 1 0.05
13 12 0.57
14 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
AAAATATTAAATTT
Found at i:1086578 original size:13 final size:14
Alignment explanation
Indices: 1086547--1086588 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
1086537 ATCGAATTCG
1086547 AATTTAATATTTAA
1 AATTTAATATTTAA
1086561 AATTTAA-AGTTT-A
1 AATTTAATA-TTTAA
1086574 AATTTAATATATTAA
1 AATTTAATAT-TTAA
1086589 TTTTTAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 10 0.42
14 13 0.54
15 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
AATTTAATATTTAA
Found at i:1106909 original size:52 final size:52
Alignment explanation
Indices: 1106827--1106951 Score: 171
Period size: 52 Copynumber: 2.4 Consensus size: 52
1106817 TCCATCTTAT
* * * *
1106827 TTTCGATTTGTCAAGGATTAGATCTTATTTTTGA-TTTCTTCTATTTTTCATA
1 TTTCAATTTGTCAAGGATTATATC-TAATTTTCATTTTCTTCTATTTTTCATA
* *
1106879 TTTCAATTTATCAAGGATTATATCTAATTTTCATTTTCTTCTATTTTTCATC
1 TTTCAATTTGTCAAGGATTATATCTAATTTTCATTTTCTTCTATTTTTCATA
*
1106931 TTTCAATTTGTCAATGATTAT
1 TTTCAATTTGTCAAGGATTAT
1106952 TTCTTAGATG
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 7 0.11
52 57 0.89
ACGTcount: A:0.24, C:0.13, G:0.08, T:0.55
Consensus pattern (52 bp):
TTTCAATTTGTCAAGGATTATATCTAATTTTCATTTTCTTCTATTTTTCATA
Found at i:1106926 original size:17 final size:18
Alignment explanation
Indices: 1106901--1106934 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1106891 AAGGATTATA
1106901 TCTAATTTTCAT-TTTCT
1 TCTAATTTTCATCTTTCT
*
1106918 TCTATTTTTCATCTTTC
1 TCTAATTTTCATCTTTC
1106935 AATTTGTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.65
Consensus pattern (18 bp):
TCTAATTTTCATCTTTCT
Found at i:1116202 original size:53 final size:54
Alignment explanation
Indices: 1116122--1116226 Score: 176
Period size: 55 Copynumber: 1.9 Consensus size: 54
1116112 ACCGTTACAA
* *
1116122 TAAGTTAGCTTTTATTTAATT-AAAAAAAAACTAGTTGATTTGCTTTAAAATAG
1 TAAGTTAGCTTTTATTTAATTAAAAAAAAAACTAGCTGATTTGCTTAAAAATAG
1116175 TAAGTTAGCTTTTATTTAATTCAAAAAAAAAACTAGCTGATTTGCTTAAAAA
1 TAAGTTAGCTTTTATTTAATT-AAAAAAAAAACTAGCTGATTTGCTTAAAAA
1116227 CTTGTCTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 21 0.44
55 27 0.56
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (54 bp):
TAAGTTAGCTTTTATTTAATTAAAAAAAAAACTAGCTGATTTGCTTAAAAATAG
Found at i:1119906 original size:11 final size:11
Alignment explanation
Indices: 1119876--1119917 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
1119866 GGCCCATTTT
1119876 TATTTTAAAAA
1 TATTTTAAAAA
*
1119887 T-TTTAAAAAA
1 TATTTTAAAAA
1119897 TATTTTAAAAA
1 TATTTTAAAAA
1119908 TATTTTAAAA
1 TATTTTAAAA
1119918 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:1119965 original size:29 final size:29
Alignment explanation
Indices: 1119889--1119968 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
1119879 TTTAAAAATT
* *
1119889 TTAAAAAATATTTTAAAAA-TATTTTAAAA
1 TTAAAAAA-AATTAAAAAAGTATTTTAAAA
1119918 TT-AAAAAAATTAAAAAAAGTATTTTAAAA
1 TTAAAAAAAATT-AAAAAAGTATTTTAAAA
1119947 TTAAAAAAAATTAAAAAAGTAT
1 TTAAAAAAAATTAAAAAAGTAT
1119969 GTAAAAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 3 0.07
28 10 0.22
29 24 0.52
30 9 0.20
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
TTAAAAAAAATTAAAAAAGTATTTTAAAA
Found at i:1119975 original size:29 final size:29
Alignment explanation
Indices: 1119914--1119975 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
1119904 AAAATATTTT
* *
1119914 AAAATTAAAAAAATTAAAAAAAGTATTTT
1 AAAATTAAAAAAATTAAAAAAAGTATGTA
1119943 AAAATTAAAAAAAATT-AAAAAAGTATGTA
1 AAAATT-AAAAAAATTAAAAAAAGTATGTA
1119972 AAAA
1 AAAA
1119976 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (29 bp):
AAAATTAAAAAAATTAAAAAAAGTATGTA
Found at i:1125134 original size:31 final size:31
Alignment explanation
Indices: 1125082--1125158 Score: 127
Period size: 31 Copynumber: 2.4 Consensus size: 31
1125072 TGGAAAAGTT
*
1125082 AATATTTTTTGGTGTTTGGATGAATCTGTATAA
1 AATATTTTCT-GT-TTTGGATGAATCTGTATAA
1125115 AATATTTTCTGTTTTGGATGAATCTGTATAA
1 AATATTTTCTGTTTTGGATGAATCTGTATAA
1125146 AATATTTTCTGTT
1 AATATTTTCTGTT
1125159 ATTTGACAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
31 32 0.74
32 2 0.05
33 9 0.21
ACGTcount: A:0.27, C:0.05, G:0.17, T:0.51
Consensus pattern (31 bp):
AATATTTTCTGTTTTGGATGAATCTGTATAA
Found at i:1127427 original size:41 final size:41
Alignment explanation
Indices: 1127382--1128515 Score: 1908
Period size: 41 Copynumber: 27.7 Consensus size: 41
1127372 GGTTTTAAAA
* *
1127382 CCTAGCATGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
1127423 CCTAGCAGGCTAAGTGCCGGTGATCTGAATAAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
1127464 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
1127505 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
1127546 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
1127587 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
1127628 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
1127669 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
1127710 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
1127751 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
1127792 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
1127833 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
1127874 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
1127915 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
1127956 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
1127997 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
1128038 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
1128079 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
1128120 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
1128161 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
1128202 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
1128243 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
1128284 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
1128325 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
1128366 CCTAGCAGGCTAAGTGCCGGTGAACTGAAACAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
1128407 CCTAGCAGGCTAAGTGCCGATGATTTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
1128448 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
1128489 CCTAGCAGGCTAAGTGCCGGTGATCTG
1 CCTAGCAGGCTAAGTGCCGGTGATCTG
1128516 NNNNNNNNNN
Statistics
Matches: 1015, Mismatches: 78, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 1015 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
Found at i:1127519 original size:82 final size:82
Alignment explanation
Indices: 1127382--1128514 Score: 2140
Period size: 82 Copynumber: 13.8 Consensus size: 82
1127372 GGTTTTAAAA
* * *
1127382 CCTAGCATGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
* * *
1127447 CTGAATAAGGCTATAAG
66 CTAAATCAGGTTATAAG
1127464 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1127529 CTAAATCAGGTTATAAG
66 CTAAATCAGGTTATAAG
1127546 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1127611 CTAAATCAGGTTATAAG
66 CTAAATCAGGTTATAAG
1127628 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1127693 CTAAATCAGGTTATAAG
66 CTAAATCAGGTTATAAG
1127710 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1127775 CTAAATCAGGTTATAAG
66 CTAAATCAGGTTATAAG
1127792 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1127857 CTAAATCAGGTTATAAG
66 CTAAATCAGGTTATAAG
1127874 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1127939 CTAAATCAGGTTATAAG
66 CTAAATCAGGTTATAAG
1127956 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1128021 CTAAATCAGGTTATAAG
66 CTAAATCAGGTTATAAG
1128038 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1128103 CTAAATCAGGTTATAAG
66 CTAAATCAGGTTATAAG
1128120 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1128185 CTAAATCAGGTTATAAG
66 CTAAATCAGGTTATAAG
1128202 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1128267 CTAAATCAGGTTATAAG
66 CTAAATCAGGTTATAAG
1128284 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1128349 CTAAATCAGGTTATAAG
66 CTAAATCAGGTTATAAG
* * * *
1128366 CCTAGCAGGCTAAGTGCCGGTGAACTGAAACAGGCTATAAGCCTAGCAGGCTAAGTGCCGATGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
* * *
1128431 TTGAATCAGGCTATAAG
66 CTAAATCAGGTTATAAG
*
1128448 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
1128513 CT
66 CT
1128515 GNNNNNNNNN
Statistics
Matches: 1034, Mismatches: 17, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 1034 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (82 bp):
CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAT
CTAAATCAGGTTATAAG
Found at i:1144287 original size:14 final size:14
Alignment explanation
Indices: 1144268--1144307 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1144258 TGGTTATATA
1144268 TTTTAAAAGTTTAT
1 TTTTAAAAGTTTAT
*
1144282 TTTTAAAAGTATAT
1 TTTTAAAAGTTTAT
*
1144296 CTTTAAAAGTTT
1 TTTTAAAAGTTT
1144308 TTCTATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (14 bp):
TTTTAAAAGTTTAT
Found at i:1144321 original size:27 final size:26
Alignment explanation
Indices: 1144262--1144322 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
1144252 TTAGCTTGGT
*
1144262 TATATATTTTAAAAGTTTATTTTTAA
1 TATATATTTTAAAAGTTTATTTATAA
*
1144288 AAGTATATCTTTAAAAGTTT-TTCTATAA
1 TA-TATAT-TTTAAAAGTTTATT-TATAA
1144316 TATATAT
1 TATATAT
1144323 AATAGAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.03
27 12 0.41
28 16 0.55
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.52
Consensus pattern (26 bp):
TATATATTTTAAAAGTTTATTTATAA
Found at i:1144446 original size:18 final size:17
Alignment explanation
Indices: 1144423--1144457 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
1144413 AAGTTGAAGC
1144423 AAAATAATTATACATTTA
1 AAAATAATTATA-ATTTA
1144441 AAAATAATTATAATTTA
1 AAAATAATTATAATTTA
1144458 TTAAAAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATAATTATAATTTA
Found at i:1144607 original size:6 final size:6
Alignment explanation
Indices: 1144596--1144635 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1144586 AAAAATTAAA
* *
1144596 TATAAT TATAAT TTTAAC TATAAT TATAA- TATAAT TATAA
1 TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAA
1144636 AAAAATTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (6 bp):
TATAAT
Found at i:1144612 original size:18 final size:18
Alignment explanation
Indices: 1144591--1144625 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1144581 AAGAAAAAAA
1144591 TTAAATATAATTATAATT
1 TTAAATATAATTATAATT
*
1144609 TTAACTATAATTATAAT
1 TTAAATATAATTATAAT
1144626 ATAATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAATATAATTATAATT
Found at i:1147803 original size:41 final size:42
Alignment explanation
Indices: 1147718--1147862 Score: 159
Period size: 41 Copynumber: 3.4 Consensus size: 42
1147708 TAAGACGACT
1147718 TCTGGGACGA-TGGCATCGATATATGTGATTACGTGTAAGACCATG
1 TCTGGGAC-ATTGGCATCGATAT-T-TGATT-CGTGTAAGACCATG
*
1147763 TCTAGGACATTGGCATC-ATATTTGATTCGTGTAAGACCATG
1 TCTGGGACATTGGCATCGATATTTGATTCGTGTAAGACCATG
* ** * * *
1147804 TCTGGGACAGTGGCATCGATATGAGATAGCATGTAAGACCACG
1 TCTGGGACATTGGCATCGATATTTGAT-TCGTGTAAGACCATG
*
1147847 TCTGGGACGTTGGCAT
1 TCTGGGACATTGGCAT
1147863 TGTTCGATAT
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
41 29 0.33
42 12 0.14
43 27 0.31
44 5 0.06
45 14 0.16
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (42 bp):
TCTGGGACATTGGCATCGATATTTGATTCGTGTAAGACCATG
Found at i:1153299 original size:14 final size:16
Alignment explanation
Indices: 1153266--1153303 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1153256 TATGGTTTAT
1153266 TAATTAAGATTAAGGC
1 TAATTAAGATTAAGGC
*
1153282 TAATTTAGATT-A-GC
1 TAATTAAGATTAAGGC
1153296 TAATTAAG
1 TAATTAAG
1153304 TAAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 10 0.50
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (16 bp):
TAATTAAGATTAAGGC
Found at i:1157217 original size:16 final size:16
Alignment explanation
Indices: 1157193--1157223 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1157183 TAGTTCATAC
*
1157193 AATATTTATGTGTTTA
1 AATAATTATGTGTTTA
1157209 AATAATTATGTGTTT
1 AATAATTATGTGTTT
1157224 GATTAGTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (16 bp):
AATAATTATGTGTTTA
Found at i:1159007 original size:70 final size:70
Alignment explanation
Indices: 1158858--1159100 Score: 326
Period size: 70 Copynumber: 3.5 Consensus size: 70
1158848 GATGTTTAAG
* * *
1158858 GTGTAAGAACATAGCTCGACTATGGCAACATGAAGAGTCTAG-CAGGATGTTAAAACATGGGGAA
1 GTGTAAGACCATAGCTCAACTATGGCAACATGAAGAGTCT-GCCAAGATGTT-AAACATGGGGAA
1158922 TTATGGT
64 TTATGGT
* * *** ** *
1158929 GTGTAAGACAATATCTTGGCTATGGCAACATGAAGAGTCTGCCAAGACATTAAACATGAGGAATT
1 GTGTAAGACCATAGCTCAACTATGGCAACATGAAGAGTCTGCCAAGATGTTAAACATGGGGAATT
1158994 ATGGT
66 ATGGT
* * * *
1158999 CTGTAAGACCATAGCTCAACTATGGCAACATGAAGAGTCTACCACGATGTTAAAGATGGGGAATT
1 GTGTAAGACCATAGCTCAACTATGGCAACATGAAGAGTCTGCCAAGATGTTAAACATGGGGAATT
1159064 ATGGT
66 ATGGT
1159069 GTGTAAGACCATAGCTCAACTATGGCAACATG
1 GTGTAAGACCATAGCTCAACTATGGCAACATG
1159101 TAGATGTTCG
Statistics
Matches: 149, Mismatches: 22, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
70 108 0.72
71 41 0.28
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (70 bp):
GTGTAAGACCATAGCTCAACTATGGCAACATGAAGAGTCTGCCAAGATGTTAAACATGGGGAATT
ATGGT
Found at i:1161232 original size:13 final size:13
Alignment explanation
Indices: 1161214--1161239 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1161204 GAATCTGATG
1161214 TGAGAGAGGTCCA
1 TGAGAGAGGTCCA
1161227 TGAGAGAGGTCCA
1 TGAGAGAGGTCCA
1161240 AAACCCCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.38, T:0.15
Consensus pattern (13 bp):
TGAGAGAGGTCCA
Found at i:1165920 original size:6 final size:6
Alignment explanation
Indices: 1165911--1165939 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1165901 GATTTTCTCC
1165911 AAAATG AAAATG AAAATG AAAATG AAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAAT
1165940 AGAGAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:1165965 original size:69 final size:71
Alignment explanation
Indices: 1165866--1166002 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 71
1165856 TGAAATGGAT
* *
1165866 AAATGGAGAAATAGGAAACATTTGAAAATGATTATGATTTTCTCCAAAATGAAAATG-AAAATGA
1 AAATAGAGAAATAGGAAACATTTGAAAATGAATATGATTTTCTCCAAAATGAAAATGAAAAATGA
1165930 AAATGA
66 AAATGA
* * *
1165936 AAATAGAGAAAT-GGAATCATTTGGAAATGAATATGGTTTTCTCCAAAATGAAAATGAAAAATGA
1 AAATAGAGAAATAGGAAACATTTGAAAATGAATATGATTTTCTCCAAAATGAAAATGAAAAATGA
1166000 AAA
66 AAA
1166003 AGACCTAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 40 0.66
70 21 0.34
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.26
Consensus pattern (71 bp):
AAATAGAGAAATAGGAAACATTTGAAAATGAATATGATTTTCTCCAAAATGAAAATGAAAAATGA
AAATGA
Found at i:1173354 original size:21 final size:22
Alignment explanation
Indices: 1173330--1173374 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1173320 TATGAATTAA
1173330 ATTGAATGTGAATT-TTA-ATAG
1 ATTGAAT-TGAATTATTATATAG
*
1173351 ATTGAATTTAATTATTATATAG
1 ATTGAATTGAATTATTATATAG
1173373 AT
1 AT
1173375 CAAGAGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (22 bp):
ATTGAATTGAATTATTATATAG
Found at i:1178019 original size:23 final size:23
Alignment explanation
Indices: 1177993--1178036 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1177983 AAACATGATA
1177993 TGTCTTATACCCTTTCCTTACTT
1 TGTCTTATACCCTTTCCTTACTT
1178016 TGTCTTATACCCTTTCCTTAC
1 TGTCTTATACCCTTTCCTTAC
1178037 AATCAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.14, C:0.32, G:0.05, T:0.50
Consensus pattern (23 bp):
TGTCTTATACCCTTTCCTTACTT
Found at i:1178130 original size:22 final size:22
Alignment explanation
Indices: 1178105--1178148 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1178095 TGTGCTGCTG
*
1178105 TTTGCAATTTTTGGATT-ATTTA
1 TTTGCAAATTTT-GATTAATTTA
*
1178127 TTTGTAAATTTTGATTAATTTA
1 TTTGCAAATTTTGATTAATTTA
1178149 ATTATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.59
Consensus pattern (22 bp):
TTTGCAAATTTTGATTAATTTA
Found at i:1179667 original size:12 final size:12
Alignment explanation
Indices: 1179650--1179675 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1179640 TAGGCTATTT
1179650 AGTTGAGAATGG
1 AGTTGAGAATGG
1179662 AGTTGAGAATGG
1 AGTTGAGAATGG
1179674 AG
1 AG
1179676 CATGCTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.42, T:0.23
Consensus pattern (12 bp):
AGTTGAGAATGG
Found at i:1179955 original size:13 final size:13
Alignment explanation
Indices: 1179937--1179961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1179927 TATTTTAATA
1179937 TTATTTTGTGTGT
1 TTATTTTGTGTGT
1179950 TTATTTTGTGTG
1 TTATTTTGTGTG
1179962 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:1191564 original size:19 final size:17
Alignment explanation
Indices: 1191532--1191571 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
1191522 ATTTTAGTAT
1191532 TGAAAAAATAAACAAAA
1 TGAAAAAATAAACAAAA
1191549 TGAAAATAAGTAAACAAAA
1 TGAAAA-AA-TAAACAAAA
1191568 -GAAA
1 TGAAA
1191572 TAACAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 6 0.29
19 9 0.43
ACGTcount: A:0.72, C:0.05, G:0.10, T:0.12
Consensus pattern (17 bp):
TGAAAAAATAAACAAAA
Found at i:1192282 original size:9 final size:9
Alignment explanation
Indices: 1192265--1192354 Score: 58
Period size: 9 Copynumber: 10.0 Consensus size: 9
1192255 NNNNNNNNNN
*
1192265 CTTATATAA
1 CTTACATAA
1192274 CTTACATAA
1 CTTACATAA
1192283 CTTACATAA
1 CTTACATAA
* * *
1192292 -ATATATAT
1 CTTACATAA
*
1192300 CATATCATAA
1 CTTA-CATAA
1192310 CTTACATAA
1 CTTACATAA
*
1192319 CTTATATAA
1 CTTACATAA
* * *
1192328 -ATATATAT
1 CTTACATAA
*
1192336 CATATCATAA
1 CTTA-CATAA
1192346 CTTACATAA
1 CTTACATAA
1192355 AACTTTGGAT
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
8 11 0.17
9 41 0.64
10 12 0.19
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (9 bp):
CTTACATAA
Found at i:1192331 original size:27 final size:27
Alignment explanation
Indices: 1192265--1192355 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
1192255 NNNNNNNNNN
*
1192265 CTTATATAACT-TACATAACTTACATAA
1 CTTATATAAATAT-CATAACTTACATAA
* *
1192292 -ATATATATCATATCATAACTTACATAA
1 CTTATATA-AATATCATAACTTACATAA
* *
1192319 CTTATATAAATAT-ATATCATATCATAA
1 CTTATATAAATATCATAACTTA-CATAA
*
1192346 CTTACATAAA
1 CTTATATAAA
1192356 ACTTTGGATC
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
26 12 0.23
27 33 0.63
28 7 0.13
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.37
Consensus pattern (27 bp):
CTTATATAAATATCATAACTTACATAA
Found at i:1192375 original size:41 final size:36
Alignment explanation
Indices: 1192270--1192354 Score: 161
Period size: 36 Copynumber: 2.4 Consensus size: 36
1192260 NNNNNCTTAT
*
1192270 ATAACTTACATAACTTACATAAATATATATCATATC
1 ATAACTTACATAACTTATATAAATATATATCATATC
1192306 ATAACTTACATAACTTATATAAATATATATCATATC
1 ATAACTTACATAACTTATATAAATATATATCATATC
1192342 ATAACTTACATAA
1 ATAACTTACATAA
1192355 AACTTTGGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (36 bp):
ATAACTTACATAACTTATATAAATATATATCATATC
Found at i:1197410 original size:13 final size:14
Alignment explanation
Indices: 1197394--1197422 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1197384 TTTTAAATAT
1197394 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
1197407 TTATAATGGTTTAA
1 TTATAATGGTTTAA
1197421 TT
1 TT
1197423 TTTCATTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:1198282 original size:43 final size:42
Alignment explanation
Indices: 1198237--1198368 Score: 133
Period size: 43 Copynumber: 3.1 Consensus size: 42
1198227 ACATGACTTT
*
1198237 TAGCAGCGCTTTTACTAAAAACGCCGCTAAAGGTCATGTTCTT
1 TAGCAGCG-TTTTACTAAAAACGCCGCTAAAGGTCATGTTCTA
* **
1198280 TAGCAGCGTTCGTA-GGAAAA-GCACGCTAAAGGTCATGTTCTA
1 TAGCAGCGTT-TTACTAAAAACGC-CGCTAAAGGTCATGTTCTA
** * * *
1198322 TAGTGGCGTTTTTCTGAGAAACACCGCTAAAGGTCATGTTCTA
1 TAGCAGCGTTTTACT-AAAAACGCCGCTAAAGGTCATGTTCTA
1198365 TAGC
1 TAGC
1198369 GGCTTTTTTC
Statistics
Matches: 71, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
41 3 0.04
42 32 0.45
43 35 0.49
44 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (42 bp):
TAGCAGCGTTTTACTAAAAACGCCGCTAAAGGTCATGTTCTA
Found at i:1198377 original size:43 final size:42
Alignment explanation
Indices: 1198254--1198378 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 42
1198244 GCTTTTACTA
* * * ** *
1198254 AAAACGCCGCTAAAGGTCATGTTCTTTAGCAGCGTTCGTAGG
1 AAAACACCGCTAAAGGTCATGTTCTATAGCGGCGTTTTTCGG
* *
1198296 AAAAGCA-CGCTAAAGGTCATGTTCTATAGTGGCGTTTTTCTG
1 AAAA-CACCGCTAAAGGTCATGTTCTATAGCGGCGTTTTTCGG
*
1198338 AGAAACACCGCTAAAGGTCATGTTCTATAGCGGCTTTTTTC
1 A-AAACACCGCTAAAGGTCATGTTCTATAGCGGCGTTTTTC
1198379 CACATAAACG
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 35 0.50
43 35 0.50
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.30
Consensus pattern (42 bp):
AAAACACCGCTAAAGGTCATGTTCTATAGCGGCGTTTTTCGG
Found at i:1203740 original size:31 final size:29
Alignment explanation
Indices: 1203671--1203744 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
1203661 ACAACAAGAT
**
1203671 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATACCA
*
1203700 AACATAAGTGACTAAAATGTAACATGAACCA
1 AACATAAGTGACTAAAACGTAACAT--ACCA
*
1203731 AACAAAAGTGACTA
1 AACATAAGTGACTA
1203745 TTTTAGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATACCA
Found at i:1210107 original size:3 final size:3
Alignment explanation
Indices: 1210099--1210132 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1210089 AAATTGTAGG
1210099 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1210133 CTTCTTGAAG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.