Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008506.1 Hibiscus syriacus cultivar Beakdansim tig00111358_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1253200
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 6 of 6
Found at i:1114106 original size:17 final size:15
Alignment explanation
Indices: 1114084--1114124 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
1114074 CTAAAAATAA
1114084 TTAAAATATATATAATT
1 TTAAAATATAT-T-ATT
1114101 TTAAAATAT-TTATT
1 TTAAAATATATTATT
1114115 TTAAAA-ATAT
1 TTAAAATATAT
1114125 CAGAAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 2 0.09
14 10 0.43
15 1 0.04
16 1 0.04
17 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAAAATATATTATT
Found at i:1115668 original size:3 final size:3
Alignment explanation
Indices: 1115653--1115749 Score: 164
Period size: 3 Copynumber: 33.0 Consensus size: 3
1115643 ATTTATTTAT
1115653 TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1115698 TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1115744 TAA TAA
1 TAA TAA
1115750 AAGTAAACTG
Statistics
Matches: 90, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
2 6 0.07
3 81 0.90
4 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1126488 original size:64 final size:64
Alignment explanation
Indices: 1126435--1126598 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 64
1126425 CGGTGCACCA
*
1126435 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * **
1126499 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
1126564 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
1126599 CAATTAATTC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 32 0.37
65 54 0.63
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:1126587 original size:17 final size:19
Alignment explanation
Indices: 1126549--1126595 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1126539 ATATTCAGAG
1126549 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
1126568 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
1126585 TGCATTCGATG
1 TGCA-TCGATG
1126596 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:1126618 original size:65 final size:62
Alignment explanation
Indices: 1126439--1126645 Score: 204
Period size: 65 Copynumber: 3.2 Consensus size: 62
1126429 GCACCAAGTG
* *
1126439 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGC-CTGAGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-TCACT-AGTGCATCGATGCATGG--AG
1126503 -
62 A
* *
1126503 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTCACTAGTGCATCGATGCATGGAG-
1126567 A
62 A
* * * * *
1126568 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCACTAGTGCATCGATGCATGG-AGA
*
1126633 TGCATCGGTGCAT
1 TGCATCGATGCAT
1126646 CACCTCAAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
63 3 0.02
64 35 0.29
65 77 0.63
66 5 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCACTAGTGCATCGATGCATGGAGA
Found at i:1126838 original size:20 final size:21
Alignment explanation
Indices: 1126815--1126854 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1126805 GAATCGAATA
1126815 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1126835 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1126855 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1127250 original size:2 final size:2
Alignment explanation
Indices: 1127243--1127319 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
1127233 GTCAAACCAA
1127243 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1127285 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1127320 GTTCAATCAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1132720 original size:22 final size:21
Alignment explanation
Indices: 1132694--1132740 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
1132684 AAGGTCAAAA
*
1132694 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
1132716 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
1132736 ATCAA
1 ATCAA
1132741 TTACGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:1134960 original size:64 final size:63
Alignment explanation
Indices: 1134824--1134961 Score: 161
Period size: 64 Copynumber: 2.2 Consensus size: 63
1134814 GCACCAAGTG
* * * * **
1134824 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATCAAATGCATTCGATGTTTAAAAATAGCCAGAATGCATCGATGCATGGC-AA
** *
1134888 TGCATCGATGCATCAAATGCATTCGATGTTTTAAAAATATTCAGAATGCATCGGTGCATGG-AA
1 TGCATCGATGCATCAAATGCATTCGATG-TTTAAAAATAGCCAGAATGCATCGATGCATGGCAA
1134951 TGCATTCGATG
1 TGCA-TCGATG
1134962 TTTCAATTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
63 4 0.06
64 33 0.52
65 26 0.41
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTAAAAATAGCCAGAATGCATCGATGCATGGCAA
Found at i:1134993 original size:46 final size:46
Alignment explanation
Indices: 1134888--1134994 Score: 135
Period size: 46 Copynumber: 2.3 Consensus size: 46
1134878 GCATGGCTTG
** *
1134888 TGCATCGATGCATCAAATGCATTCGATGTTTTAAAAATATTCAGAA
1 TGCATCGATGCATGGAATGCATTCGATGTTTCAAAAATATTCAGAA
* ** *
1134934 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTA-ATTCACTAA
1 TGCATCGATGCATGGAATGCATTCGATGTTTCAAAAATATTCA-GAA
1134980 TGCATCGATGCATGG
1 TGCATCGATGCATGG
1134995 TTGATGCATC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 5 0.10
46 47 0.90
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (46 bp):
TGCATCGATGCATGGAATGCATTCGATGTTTCAAAAATATTCAGAA
Found at i:1135182 original size:20 final size:21
Alignment explanation
Indices: 1135159--1135198 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1135149 GAATCGAATA
1135159 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1135179 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1135199 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1135626 original size:15 final size:17
Alignment explanation
Indices: 1135601--1135637 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1135591 TTTTGTTCTA
*
1135601 TTTTTATTTTCCTATT-
1 TTTTTATTTTCATATTG
1135617 TTTTTA-TTTCATATTG
1 TTTTTATTTTCATATTG
1135633 TTTTT
1 TTTTT
1135638 TTATTTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTATTTTCATATTG
Found at i:1135682 original size:24 final size:24
Alignment explanation
Indices: 1135655--1135709 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
1135645 CTCTTTTACA
* * *
1135655 TTTTTTATATTTTTATATTTTATT
1 TTTTTTAAAATTTAATATTTTATT
* *
1135679 TTTTCTAAAATTTAATATTTTCTT
1 TTTTTTAAAATTTAATATTTTATT
1135703 TTGTTTT
1 TT-TTTT
1135710 GTTTTTCTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTTTTAAAATTTAATATTTTATT
Found at i:1135779 original size:16 final size:15
Alignment explanation
Indices: 1135724--1135779 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
1135714 TTCTTTTAAC
*
1135724 ATTTATCTATTTATTT
1 ATTTATTTA-TTATTT
1135740 ATTTATTTATTATTT
1 ATTTATTTATTATTT
*
1135755 TTTTCATTTGA-TATTT
1 ATTT-ATTT-ATTATTT
1135771 CATTTATTT
1 -ATTTATTT
1135780 TACCATCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.26
16 21 0.62
17 4 0.12
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (15 bp):
ATTTATTTATTATTT
Found at i:1146663 original size:117 final size:116
Alignment explanation
Indices: 1146445--1146664 Score: 275
Period size: 117 Copynumber: 1.9 Consensus size: 116
1146435 ACTTTCAAAT
* * * *
1146445 AAAATTCTTTTTCAAAGATTTCAAATTTCATTTTTGAGAGATCTAAATCCTTCTTCAATATTTCA
1 AAAATTCTTTTTCAAAGATTTCAAATTTAATTTTTGAAAGATCTAAATCATTCTTCAACATTTCA
*
1146510 TTTTGATTTTCAAAATCCATTTTAGCTTCTAGAAGAAGTTTGTTTAATTTG
66 TTTTGATTTTCAAAATCCATTTTAGCTTCTAAAAGAAGTTTGTTTAATTTG
* * * * *
1146561 AAAATTTCTTTTTCAAA-ATTTTTAGATTTAATTTTTGAAAGCTCTAACTCATTTTTCAACATTT
1 AAAA-TTCTTTTTCAAAGA-TTTCAAATTTAATTTTTGAAAGATCTAAATCATTCTTCAACATTT
* *
1146625 CATTTTGATTTT-ATAAGTCTATTTTAGCTT-TCAAAAGAAG
64 CATTTTGATTTTCA-AAATCCATTTTAGCTTCT-AAAAGAAG
1146665 ATCATTTTTA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
116 7 0.08
117 81 0.92
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (116 bp):
AAAATTCTTTTTCAAAGATTTCAAATTTAATTTTTGAAAGATCTAAATCATTCTTCAACATTTCA
TTTTGATTTTCAAAATCCATTTTAGCTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:1153888 original size:2 final size:2
Alignment explanation
Indices: 1153881--1153912 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1153871 TTGTTGATGC
1153881 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1153913 TTATTTGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1157261 original size:18 final size:18
Alignment explanation
Indices: 1157238--1157272 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1157228 CATATTTATT
*
1157238 TATATAAAATATAATATA
1 TATATAAAAAATAATATA
1157256 TATATAAAAAATAATAT
1 TATATAAAAAATAATAT
1157273 TATGATCTCA
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATATAAAAAATAATATA
Found at i:1158289 original size:30 final size:29
Alignment explanation
Indices: 1158250--1158310 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
1158240 AGTCATACAA
* *
1158250 TTTCTAAATTTGATA-TCTCAAAATAATTT
1 TTTCTAAATTTGACACTC-CAAAATAAATT
1158279 TTTCTCAAATTTGACACTCCAAAATAAATT
1 TTTCT-AAATTTGACACTCCAAAATAAATT
1158309 TT
1 TT
1158311 CGGGCTTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.18
30 21 0.75
31 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (29 bp):
TTTCTAAATTTGACACTCCAAAATAAATT
Found at i:1159077 original size:117 final size:117
Alignment explanation
Indices: 1158767--1159113 Score: 599
Period size: 117 Copynumber: 3.0 Consensus size: 117
1158757 TGTGTTGCTT
1158767 GGTATCTCCTA-TTTTTCTAAGTTAGTCG-AAAGGTACTCAAATGATCGCTTGAGTGTGTTTGAT
1 GGTATCTCCTATTTTTTCTAAGTTAGTCGAAAAGGTACTCAAATGATCGCTTGAGTGTGTTTGAT
*
1158830 ATTGTACCTTGACTAACTTTCAAATTAAATTTTTTATCAATCCACTATTGTC
66 ATTGTACCTTGACTAACTTTCAAATGAAATTTTTTATCAATCCACTATTGTC
* *
1158882 GGTATCTCCTATTTTTTTATAAGTTAGTCGAAAAGGTACTCAAATGATCGCTTGAGTGGGTTTGA
1 GGTATCTCCTA-TTTTTTCTAAGTTAGTCGAAAAGGTACTCAAATGATCGCTTGAGTGTGTTTGA
* * *
1158947 TATTGTACATTGACTAACTTTCAAATGAAAATTTTTATCAATCCACTATTTTC
65 TATTGTACCTTGACTAACTTTCAAATGAAATTTTTTATCAATCCACTATTGTC
*
1159000 GGTATCTCCTATTTTTTCTAAGTTAGTCGAAAAGGTACTCAAATGATAGCTTGAGTGTGTTTGAT
1 GGTATCTCCTATTTTTTCTAAGTTAGTCGAAAAGGTACTCAAATGATCGCTTGAGTGTGTTTGAT
*
1159065 ATTGTACCTTGACTAACTTTCAAATGAATTTTTTTATCAATCCACTATT
66 ATTGTACCTTGACTAACTTTCAAATGAAATTTTTTATCAATCCACTATT
1159114 ACAAATCTTT
Statistics
Matches: 217, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
115 11 0.05
117 113 0.52
118 93 0.43
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (117 bp):
GGTATCTCCTATTTTTTCTAAGTTAGTCGAAAAGGTACTCAAATGATCGCTTGAGTGTGTTTGAT
ATTGTACCTTGACTAACTTTCAAATGAAATTTTTTATCAATCCACTATTGTC
Found at i:1159684 original size:43 final size:44
Alignment explanation
Indices: 1159359--1159694 Score: 278
Period size: 44 Copynumber: 7.7 Consensus size: 44
1159349 TAATTTTAGT
* * ** * *
1159359 TTTTTATCTTTATAATTGAGGTACCTAATTTTTAT-AATC-CTAT
1 TTTTTACCTTTATAATTGATGCCCCTAATTTTTTTCAATCTC-AC
* * * * *
1159402 TTTTTATCTTTATAATTGAGGCCCTTAATTTTTTTAAATCTCATT
1 TTTTTACCTTTATAATTGATGCCCCTAATTTTTTTCAATCTCA-C
* * ** *
1159447 TTTTTACATTTATAATTGTTGATCCTAA-GTTTTTCAATCTCAC
1 TTTTTACCTTTATAATTGATGCCCCTAATTTTTTTCAATCTCAC
* * * * *
1159490 TTTGTACATTTATAATT-AAGCTCCTGATTTTTTTTCAATCTCAC
1 TTTTTACCTTTATAATTGATGCCCCT-AATTTTTTTCAATCTCAC
* * *
1159534 TTTTTACCTTTATAATT-ATGACTCCTAATTTTTTTCAAAC-CCC
1 TTTTTACCTTTATAATTGATG-CCCCTAATTTTTTTCAATCTCAC
*
1159577 TTTTTTA-CTTATATAATTTA-GTCCCCTAATTTTTTTCAATCTCA-
1 -TTTTTACCTT-TATAATTGATG-CCCCTAATTTTTTTCAATCTCAC
* *
1159621 TATTTTACCTTTAAAATTGATGCCCCTAATTTTTTT-AGTCTCAC
1 T-TTTTACCTTTATAATTGATGCCCCTAATTTTTTTCAATCTCAC
*
1159665 TTTTTACCTTTATAATTGATGTCCCTAATT
1 TTTTTACCTTTATAATTGATGCCCCTAATT
1159695 AAACAACACA
Statistics
Matches: 244, Mismatches: 35, Indels: 28
0.79 0.11 0.09
Matches are distributed among these distances:
42 5 0.02
43 87 0.36
44 118 0.48
45 34 0.14
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.52
Consensus pattern (44 bp):
TTTTTACCTTTATAATTGATGCCCCTAATTTTTTTCAATCTCAC
Found at i:1160057 original size:25 final size:25
Alignment explanation
Indices: 1160023--1160070 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1160013 AACAACTATA
*
1160023 ATATACTAATATATATATATAAAGT
1 ATATAATAATATATATATATAAAGT
*
1160048 ATATAATAATATATCTATATAAA
1 ATATAATAATATATATATATAAA
1160071 CAATATAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
ATATAATAATATATATATATAAAGT
Found at i:1160076 original size:25 final size:25
Alignment explanation
Indices: 1160022--1160077 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
1160012 AAACAACTAT
* *
1160022 AATATACTAATATATATATATAAAG
1 AATATAATAATATATATATATAAAC
* *
1160047 TATATAATAATATATCTATATAAAC
1 AATATAATAATATATATATATAAAC
1160072 AATATA
1 AATATA
1160078 GTTTATTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (25 bp):
AATATAATAATATATATATATAAAC
Found at i:1160105 original size:11 final size:11
Alignment explanation
Indices: 1160089--1160249 Score: 109
Period size: 11 Copynumber: 15.0 Consensus size: 11
1160079 TTTATTATTT
*
1160089 TAAACTATGTA
1 TAAACTATATA
1160100 TAAACTATATA
1 TAAACTATATA
*
1160111 T--ACTATAAA
1 TAAACTATATA
1160120 TAAACTATATA
1 TAAACTATATA
** *
1160131 GTTTATTA-ATA
1 -TAAACTATATA
*
1160142 TAAAATATATA
1 TAAACTATATA
*
1160153 TGAACTATATA
1 TAAACTATATA
* *
1160164 TAGAC--TATG
1 TAAACTATATA
1160173 TAAACTATATA
1 TAAACTATATA
1160184 TAAACTATATA
1 TAAACTATATA
** *
1160195 GTTTA-TATTTA
1 -TAAACTATATA
* *
1160206 TATACTATGTA
1 TAAACTATATA
*
1160217 TAAACTATTTA
1 TAAACTATATA
*
1160228 TATACTATATA
1 TAAACTATATA
*
1160239 TGAACTATATA
1 TAAACTATATA
1160250 GTTTATTAAT
Statistics
Matches: 115, Mismatches: 27, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
9 15 0.13
10 7 0.06
11 87 0.76
12 6 0.05
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (11 bp):
TAAACTATATA
Found at i:1160131 original size:53 final size:54
Alignment explanation
Indices: 1160063--1160267 Score: 200
Period size: 64 Copynumber: 3.6 Consensus size: 54
1160053 ATAATATATC
*
1160063 TATATAAACAATATAGTTTATTATTT-TAAACTATGTATAAACTATATATACTA
1 TATATAAACTATATAGTTTATTATTTATAAACTATGTATAAACTATATATACTA
* * * * *
1160116 TAAATAAACTATATAGTTTATTAATATAAAATATATATGAACTATATATAGACTATGTAAACTA
1 TATATAAACTATATAGTTTA-T--TAT----T-TATA--AACTATGTATAAACTATATATACTA
*
1160180 TATATAAACTATATAGTTTA-TATTTATATACTATGTATAAACTATTTATATACTA
1 TATATAAACTATATAGTTTATTATTTATAAACTATGTATAAACTA--TATATACTA
* *
1160235 TATATGAACTATATAGTTTATTA-ATATAAACTA
1 TATATAAACTATATAGTTTATTATTTATAAACTA
1160268 GATAAAATAT
Statistics
Matches: 123, Mismatches: 15, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
53 31 0.25
54 1 0.01
55 38 0.31
56 6 0.05
60 4 0.03
61 1 0.01
62 2 0.02
64 40 0.33
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (54 bp):
TATATAAACTATATAGTTTATTATTTATAAACTATGTATAAACTATATATACTA
Found at i:1160201 original size:20 final size:20
Alignment explanation
Indices: 1160093--1160267 Score: 80
Period size: 20 Copynumber: 8.7 Consensus size: 20
1160083 TTATTTTAAA
*
1160093 CTATGTATAAACTATATA-T
1 CTATATATAAACTATATAGT
*
1160112 ACTATAAATAAACTATATAGT
1 -CTATATATAAACTATATAGT
* * *
1160133 TTATTAATATAAAATATATATGAA
1 CTA-T-ATATAAACTATATA-G-T
* * **
1160157 CTATATATAGACTATGTAAA
1 CTATATATAAACTATATAGT
1160177 CTATATATAAACTATATAGT
1 CTATATATAAACTATATAGT
*
1160197 -T-TATAT---TTATATA--
1 CTATATATAAACTATATAGT
*
1160210 CTATGTATAAACTATTTATA-T
1 CTATATATAAACTA--TATAGT
*
1160231 ACTATATATGAACTATATAGT
1 -CTATATATAAACTATATAGT
*
1160252 TTATTAATATAAACTA
1 CTA-T-ATATAAACTA
1160268 GATAAAATAT
Statistics
Matches: 116, Mismatches: 22, Indels: 32
0.68 0.13 0.19
Matches are distributed among these distances:
14 1 0.01
15 10 0.09
18 7 0.06
19 1 0.01
20 45 0.39
21 4 0.03
22 44 0.38
23 2 0.02
24 2 0.02
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (20 bp):
CTATATATAAACTATATAGT
Found at i:1160518 original size:32 final size:32
Alignment explanation
Indices: 1160476--1160581 Score: 124
Period size: 32 Copynumber: 3.3 Consensus size: 32
1160466 ATATTGATTT
*
1160476 TTTTTCGGTTCAGATCAATATCGGATCGATTGT
1 TTTTT-GGTTCAGATCAATATCGGATCGATTGA
* * *
1160509 TTTTTGGTTCGGATCAATATCGGATCGGTTAA
1 TTTTTGGTTCAGATCAATATCGGATCGATTGA
* * *
1160541 TTTTTGGGTCA-AGTCAATATCGAATCGGTTGA
1 TTTTTGGTTCAGA-TCAATATCGGATCGATTGA
1160573 TTTTTGGTT
1 TTTTTGGTT
1160582 TCGGTCAACC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
31 1 0.02
32 57 0.90
33 5 0.08
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.43
Consensus pattern (32 bp):
TTTTTGGTTCAGATCAATATCGGATCGATTGA
Found at i:1161202 original size:21 final size:20
Alignment explanation
Indices: 1161177--1161240 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
1161167 AAGTAAAATT
1161177 TTAATTATTTTTATTATAAA
1 TTAATTATTTTTATTATAAA
1161197 TCTAA-TATTTTT-TTAATAAA
1 T-TAATTATTTTTATT-ATAAA
* *
1161217 TT-ATCAATTTTATT-TAAA
1 TTAATTATTTTTATTATAAA
1161235 TTAATT
1 TTAATT
1161241 TATTATTCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
18 7 0.19
19 10 0.28
20 16 0.44
21 3 0.08
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAATTATTTTTATTATAAA
Found at i:1161488 original size:10 final size:11
Alignment explanation
Indices: 1161468--1161565 Score: 50
Period size: 10 Copynumber: 9.3 Consensus size: 11
1161458 GTCAGATCTA
1161468 TATATATAAAC
1 TATATATAAAC
1161479 TATA-ATAAAC
1 TATATATAAAC
*
1161489 TATATAGT---T
1 TATATA-TAAAC
* * *
1161498 TACATATGAAG
1 TATATATAAAC
1161509 TAT--ATAAAC
1 TATATATAAAC
1161518 TATATATAAACC
1 TATATATAAA-C
*
1161530 ATTATATATATA-
1 --TATATATAAAC
*
1161542 TATATATATA-
1 TATATATAAAC
1161552 TATATATAAAC
1 TATATATAAAC
1161563 TAT
1 TAT
1161566 GTAGTTTATT
Statistics
Matches: 68, Mismatches: 8, Indels: 22
0.69 0.08 0.22
Matches are distributed among these distances:
8 1 0.01
9 12 0.18
10 29 0.43
11 15 0.22
12 2 0.03
14 9 0.13
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (11 bp):
TATATATAAAC
Found at i:1161537 original size:2 final size:2
Alignment explanation
Indices: 1161532--1161559 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1161522 TATAAACCAT
1161532 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1161560 AACTATGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1161552 original size:39 final size:38
Alignment explanation
Indices: 1161466--1161553 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 38
1161456 TTGTCAGATC
* *
1161466 TATATATATAAACTATAATAAACTATATAGTTTACATA
1 TATATATATAAACTATAATAAACCATATAGTATACATA
*
1161504 TGA-AGTATATAAACTATATATAAACCATTATA-TATATATA
1 T-ATA-TATATAAACTATA-ATAAACCA-TATAGTATACATA
1161544 TATATATATA
1 TATATATATA
1161554 TATATAAACT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
38 2 0.05
39 21 0.50
40 15 0.36
41 4 0.10
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (38 bp):
TATATATATAAACTATAATAAACCATATAGTATACATA
Found at i:1162084 original size:96 final size:95
Alignment explanation
Indices: 1161951--1162135 Score: 230
Period size: 95 Copynumber: 1.9 Consensus size: 95
1161941 AAATCCTTTG
* * *
1161951 ATTTTTTTGGATCAAACACCCCAAATTCAACTCTTGTTTATTTGTGTTCATCCTCAAAACCCTCA
1 ATTTTTTTGGATCAAACACCCCAAACTCAACTATTGTTCATTTGTGTTCATCC-CAAAACCCTCA
* * *
1162016 TTTGTTCTTTACAAACGCCAAAACCAAACCT
65 TTTGATCCTTACAAACACCAAAACCAAACCT
* * * *
1162047 ATTTTTTT-TATCAAACA-CCCAAACCCTCAACTATTGTTCATTTGTGTTCATCCCCAAATCCTT
1 ATTTTTTTGGATCAAACACCCCAAA--CTCAACTATTGTTCATTTGTGTTCATCCCAAAACCCTC
*
1162110 ATTTGATCCTTACAAACACCTAAACC
64 ATTTGATCCTTACAAACACCAAAACC
1162136 CAAAATCCAA
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
94 6 0.08
95 37 0.49
96 33 0.43
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (95 bp):
ATTTTTTTGGATCAAACACCCCAAACTCAACTATTGTTCATTTGTGTTCATCCCAAAACCCTCAT
TTGATCCTTACAAACACCAAAACCAAACCT
Found at i:1162139 original size:96 final size:94
Alignment explanation
Indices: 1161951--1162290 Score: 263
Period size: 103 Copynumber: 3.4 Consensus size: 94
1161941 AAATCCTTTG
* * * *
1161951 ATTTTTTTGGATCAAACACCCCAAA--TTCAACTCTTGTTTATTTGTGTTCATCCTCAAAACCCT
1 ATTTTTTT-TATCAAACA-CCCAAACCCTCAACTCTTGTTCATTTGTGTTCATCC-CCAAA-CCT
* * * * *
1162014 CATTTGTTCTTTACAAACGCCAAAACCAAACCT
62 TATTTGATCCTTACAAACACCAAACCCAAACCT
*
1162047 ATTTTTTTTATCAAACACCCAAACCCTCAACTATTGTTCATTTGTGTTCATCCCCAAATCCTTAT
1 ATTTTTTTTATCAAACACCCAAACCCTCAACTCTTGTTCATTTGTGTTCATCCCCAAA-CCTTAT
1162112 TTGATCCTTACAAACACCTAAACCCAAAATCCAACCT
65 TTGATCCTTACAAACACC-AAACCC---A---AACCT
** * * * * * * *
1162149 ATTTTTTCCATTTAAACACTCAAACCCTTAACCCTTATTCATCTATGTTCATCCCCAAACCTTTA
1 ATTTTTTTTA-TCAAACACCCAAACCCTCAACTCTTGTTCATTTGTGTTCATCCCCAAACC-TTA
* * *
1162214 TTTAATCCTTACAAACACCAAACCGAAAACCCA
64 TTTGATCCTTACAAACACCAAACC-CAAA-CCT
* *
1162247 ACTTGTTTTTTAATCAAACACCTAAACCCTAAAC-CTTTGTTCAT
1 A-TT-TTTTTT-ATCAAACACCCAAACCCTCAACTC-TTGTTCAT
1162291 CCCCAAACCC
Statistics
Matches: 196, Mismatches: 31, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
94 6 0.03
95 32 0.16
96 38 0.19
97 2 0.01
98 3 0.02
99 4 0.02
100 29 0.15
101 1 0.01
102 20 0.10
103 61 0.31
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.34
Consensus pattern (94 bp):
ATTTTTTTTATCAAACACCCAAACCCTCAACTCTTGTTCATTTGTGTTCATCCCCAAACCTTATT
TGATCCTTACAAACACCAAACCCAAACCT
Found at i:1162190 original size:103 final size:98
Alignment explanation
Indices: 1162027--1162349 Score: 290
Period size: 103 Copynumber: 3.3 Consensus size: 98
1162017 TTGTTCTTTA
* * * ** *
1162027 CAAACGCCAAAACCAAACCTATTTTTT-TTATCAAACACCCAAACCCTCAACTATTGTTCATTTG
1 CAAAC-CCAAAACCCAACCTATTTTTTATT-T-AAACACTCAAACCCTAAACCCTTATTCATTT-
1162091 TGTTCATCCCCAAATCCTTATTTGATCCTTACAAACAC
62 TGTTCATCCCCAAA-CCTTATTTGATCCTTACAAACAC
* * *
1162129 CTAAACCCAAAATCCAACCTATTTTTTCCATTTAAACACTCAAACCCTTAACCCTTATTCATCTA
1 C-AAACCCAAAACCCAACCTATTTTTT--ATTTAAACACTCAAACCCTAAACCCTTATTCAT-TT
*
1162194 TGTTCATCCCCAAACCTTTATTTAATCCTTACAAACAC
62 TGTTCATCCCCAAACC-TTATTTGATCCTTACAAACAC
* * ** *
1162232 CAAACCGAAAACCCAA-C--TTGTTT-TTT--A-A-TCAAACACCTAAACCC-TAAAC-CTTTGT
1 CAAACCCAAAACCCAACCTATTTTTTATTTAAACACTCAAAC-CCTAAACCCTTATTCATTTTGT
* *
1162287 TCATCCCCAAACCCTTGTTTGATCCTTATAAACACC
65 TCATCCCCAAA-CCTTATTTGATCCTTACAAACA-C
*
1162323 CAAAACCAAAACCCAACCTATTTTTTA
1 CAAACCCAAAACCCAACCTATTTTTTA
1162350 GATCTAACTG
Statistics
Matches: 185, Mismatches: 23, Indels: 33
0.77 0.10 0.14
Matches are distributed among these distances:
90 32 0.17
91 17 0.09
92 10 0.05
93 9 0.05
94 6 0.03
96 3 0.02
99 5 0.03
101 1 0.01
102 35 0.19
103 63 0.34
104 2 0.01
105 2 0.01
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (98 bp):
CAAACCCAAAACCCAACCTATTTTTTATTTAAACACTCAAACCCTAAACCCTTATTCATTTTGTT
CATCCCCAAACCTTATTTGATCCTTACAAACAC
Found at i:1162510 original size:47 final size:47
Alignment explanation
Indices: 1162459--1162603 Score: 157
Period size: 47 Copynumber: 3.1 Consensus size: 47
1162449 GAGAGTGCTC
* * *
1162459 TTCATCTTTTGTTTATATTCTTTAACCCTAAACCCTAACTGAGACTA
1 TTCATATTTTGTTCATATTCTTTAACCCTAAACCCTAACCGAGACTA
* ** * * * * *
1162506 TTCATATATTACTCATATTCTCTAACCTTAAACCTTAACCAATACTA
1 TTCATATTTTGTTCATATTCTTTAACCCTAAACCCTAACCGAGACTA
* * *
1162553 TTCATATTTTGTTCATCTTCTTTAACCCTAAA-TCTAACCGAGACTC
1 TTCATATTTTGTTCATATTCTTTAACCCTAAACCCTAACCGAGACTA
1162599 TTCAT
1 TTCAT
1162604 CTACTTCAGT
Statistics
Matches: 76, Mismatches: 22, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
46 14 0.18
47 62 0.82
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.41
Consensus pattern (47 bp):
TTCATATTTTGTTCATATTCTTTAACCCTAAACCCTAACCGAGACTA
Found at i:1165288 original size:64 final size:64
Alignment explanation
Indices: 1165210--1165346 Score: 256
Period size: 64 Copynumber: 2.1 Consensus size: 64
1165200 ACAAGCATCA
*
1165210 TGTTAAATGCTTCTTGAATGATTATGCGCTGATTCTACTTGATATTGCTTGATTTAGAAATGTT
1 TGTTAAATGCTTCTTGAATGATTATGCCCTGATTCTACTTGATATTGCTTGATTTAGAAATGTT
*
1165274 TGTTAAATGCTTCTTGAATGATTATGCCCTGATTCTTCTTGATATTGCTTGATTTAGAAATGTT
1 TGTTAAATGCTTCTTGAATGATTATGCCCTGATTCTACTTGATATTGCTTGATTTAGAAATGTT
1165338 TGTTAAATG
1 TGTTAAATG
1165347 TTTGATTCTA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 71 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (64 bp):
TGTTAAATGCTTCTTGAATGATTATGCCCTGATTCTACTTGATATTGCTTGATTTAGAAATGTT
Found at i:1165700 original size:97 final size:97
Alignment explanation
Indices: 1165582--1165772 Score: 301
Period size: 97 Copynumber: 2.0 Consensus size: 97
1165572 TTCTAAATAG
* * *
1165582 TTACTCATATTAAATTATGTTGGTAACATTTCGGCTTTTAAAGCTGAAAAGTTGCCCGTCATTTA
1 TTACTCATATTAAATTATGTTGGTAACATTTCAGCTTTTAAAGCTGAAAAGTTGCACGTAATTTA
1165647 ATAATGTTGGCAGCATTTAGATCTTTTGAAAT
66 ATAATGTTGGCAGCATTTAGATCTTTTGAAAT
* ** * * *
1165679 TTACTCATGTTAAATTATGTTGGTGGCATTTTAGTTTTTAAAGTTGAAAAGTTGCACGTAATTTA
1 TTACTCATATTAAATTATGTTGGTAACATTTCAGCTTTTAAAGCTGAAAAGTTGCACGTAATTTA
1165744 ATAATGTTGGCAGCATTTAGATCTTTTGA
66 ATAATGTTGGCAGCATTTAGATCTTTTGA
1165773 GATAAAAGTT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 85 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (97 bp):
TTACTCATATTAAATTATGTTGGTAACATTTCAGCTTTTAAAGCTGAAAAGTTGCACGTAATTTA
ATAATGTTGGCAGCATTTAGATCTTTTGAAAT
Found at i:1166325 original size:19 final size:19
Alignment explanation
Indices: 1166301--1166342 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1166291 TATTATAAAC
1166301 TCAAAATCTCACAACTTCA
1 TCAAAATCTCACAACTTCA
* * *
1166320 TCAAAATCTTATAATTTCA
1 TCAAAATCTCACAACTTCA
1166339 TCAA
1 TCAA
1166343 TGGTAATTTA
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:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (19 bp):
TCAAAATCTCACAACTTCA
Found at i:1170596 original size:69 final size:70
Alignment explanation
Indices: 1170508--1170642 Score: 227
Period size: 69 Copynumber: 1.9 Consensus size: 70
1170498 AGGCAAGATC
* *
1170508 ACTTTAGACTGAAATAGATAAATTATTAGTACCGTGTAATGCTCACTGTG-TTTATTATTTTCCT
1 ACTTTAGACTGAAATAGATAAATTAATAGTACCGTATAATGCTCACTGTGCTTTATTATTTTCCT
1170572 AGAAA
66 AGAAA
* *
1170577 ACTTTGGACTGATATAGATAAATTAATAGTACCGTATAATGCTCACTGTGCTTTATTATTTTCCT
1 ACTTTAGACTGAAATAGATAAATTAATAGTACCGTATAATGCTCACTGTGCTTTATTATTTTCCT
1170642 A
66 A
1170643 AGTATGTCCC
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
69 46 0.75
70 15 0.25
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (70 bp):
ACTTTAGACTGAAATAGATAAATTAATAGTACCGTATAATGCTCACTGTGCTTTATTATTTTCCT
AGAAA
Found at i:1173125 original size:35 final size:35
Alignment explanation
Indices: 1173086--1173156 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
1173076 ATTTAATTAA
1173086 ACGAAAAAAGAAACCTTATT-AGCAATCATTCATTT
1 ACGAAAAAAGAAACCTTATTCA-CAATCATTCATTT
* * *
1173121 ACGAACAAAGAAACGTTATTCACAATCATTCGTTT
1 ACGAAAAAAGAAACCTTATTCACAATCATTCATTT
1173156 A
1 A
1173157 ATAAATATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 31 0.97
36 1 0.03
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (35 bp):
ACGAAAAAAGAAACCTTATTCACAATCATTCATTT
Found at i:1173504 original size:28 final size:28
Alignment explanation
Indices: 1173471--1173527 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
1173461 CAAAAAACAT
1173471 AAGATATTG-TCACTTTTGTTTTTATTTA
1 AAGATA-TGATCACTTTTGTTTTTATTTA
1173499 AAGATATGATCACTTTTGTTTTTATTTA
1 AAGATATGATCACTTTTGTTTTTATTTA
1173527 A
1 A
1173528 TTAAGATGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.54
Consensus pattern (28 bp):
AAGATATGATCACTTTTGTTTTTATTTA
Found at i:1174037 original size:39 final size:38
Alignment explanation
Indices: 1173930--1174038 Score: 130
Period size: 39 Copynumber: 2.8 Consensus size: 38
1173920 ATTCATAATC
* *
1173930 CTTAAAGTATTTCACACTAAAATTCTAAAATTCTAATTT
1 CTTAAA-TATTTCACACTAACATTCTAAATTTCTAATTT
* * *
1173969 CTTAAAT-TTTGACACCATAACGTTCTAAATTTTTAATTT
1 CTTAAATATTTCACA-C-TAACATTCTAAATTTCTAATTT
1174008 CTTAAATTATTTCACACTAACATTCTAAATT
1 CTTAAA-TATTTCACACTAACATTCTAAATT
1174039 ATTTTTTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
37 6 0.10
38 2 0.03
39 43 0.73
40 2 0.03
41 6 0.10
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.43
Consensus pattern (38 bp):
CTTAAATATTTCACACTAACATTCTAAATTTCTAATTT
Found at i:1174110 original size:16 final size:15
Alignment explanation
Indices: 1174089--1174135 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
1174079 TTTAATTATA
1174089 TTTAATTATTTTAAAT
1 TTTAATTATTTT-AAT
* *
1174105 TTTAATAATTTTTAT
1 TTTAATTATTTTAAT
*
1174120 TTCAATTA-TTTAAT
1 TTTAATTATTTTAAT
1174134 TT
1 TT
1174136 GATTTTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 7 0.27
15 8 0.31
16 11 0.42
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAATTATTTTAAT
Found at i:1174118 original size:26 final size:25
Alignment explanation
Indices: 1174070--1174118 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1174060 AACTTCAAAA
*
1174070 TATTTGAAATTTAATTATATTTAAT
1 TATTTGAAATTTAATAATATTTAAT
* *
1174095 TATTTTAAATTTTAATAATTTTTA
1 TATTTGAAA-TTTAATAATATTTA
1174119 TTTCAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
TATTTGAAATTTAATAATATTTAAT
Found at i:1174206 original size:9 final size:8
Alignment explanation
Indices: 1174174--1174202 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1174164 TATATTATAG
1174174 AATTTTA-
1 AATTTTAT
1174181 AATTTTAT
1 AATTTTAT
1174189 AATTTTAT
1 AATTTTAT
1174197 AATTTT
1 AATTTT
1174203 TATATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
AATTTTAT
Found at i:1174337 original size:25 final size:24
Alignment explanation
Indices: 1174287--1174369 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 24
1174277 ATATAATATA
1174287 ATTTTATA-TATA-TTAACTTAAAAT
1 ATTTTATATTA-ACTTAA-TTAAAAT
1174311 ATCTTTATATTAACTT-ATTAAATAT
1 AT-TTTATATTAACTTAATTAAA-AT
*
1174336 ATTTTACAATTAACTTAATATAAAAAT
1 ATTTTA-TATTAACTTAAT-T-AAAAT
1174363 ATTTTAT
1 ATTTTAT
1174370 TTTTATTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
24 11 0.22
25 20 0.41
26 6 0.12
27 9 0.18
28 3 0.06
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTTATATTAACTTAATTAAAAT
Found at i:1174424 original size:26 final size:26
Alignment explanation
Indices: 1174356--1174445 Score: 94
Period size: 26 Copynumber: 3.3 Consensus size: 26
1174346 TAACTTAATA
*
1174356 TAAAAATATTTTATTTT-TATTTTCATT
1 TAAAAATA-TTTATTTTAT-TTTTTATT
*
1174383 TAAAAATATTTTTTTTATTTTTTATT
1 TAAAAATATTTATTTTATTTTTTATT
*
1174409 TAAAAATATATATTTTACTTTAATTTA-T
1 TAAAAATATTTATTTTA-TTT--TTTATT
1174437 TAAAAATAT
1 TAAAAATAT
1174446 GACTAAATTG
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
26 29 0.53
27 12 0.22
28 10 0.18
29 4 0.07
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TAAAAATATTTATTTTATTTTTTATT
Found at i:1175860 original size:18 final size:19
Alignment explanation
Indices: 1175825--1175861 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1175815 CACGGAATGT
1175825 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1175845 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1175862 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1176303 original size:27 final size:27
Alignment explanation
Indices: 1176245--1176310 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
1176235 CTAAGATATA
1176245 ATATTTATTATATTTTCTATATATAATT
1 ATATTTATT-TATTTTCTATATATAATT
* *
1176273 -TATTTATTTATTTATCT-TTTATATTT
1 ATATTTATTTATTT-TCTATATATAATT
*
1176299 ATATTTAATTAT
1 ATATTTATTTAT
1176311 GCATACTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (27 bp):
ATATTTATTTATTTTCTATATATAATT
Found at i:1179588 original size:16 final size:16
Alignment explanation
Indices: 1179567--1179601 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1179557 TGCGATCAAC
*
1179567 GAAAGGGAGAGGAGAA
1 GAAAGGGAGAAGAGAA
1179583 GAAAGGGAGAAGAGAA
1 GAAAGGGAGAAGAGAA
1179599 GAA
1 GAA
1179602 CTCTTACCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (16 bp):
GAAAGGGAGAAGAGAA
Found at i:1179680 original size:32 final size:33
Alignment explanation
Indices: 1179629--1179702 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 33
1179619 ATGAATTTTT
*
1179629 CGCAAAGGCAAGCTAAA-GGGGAGAAGAAGATA
1 CGCAGAGGCAAGCTAAAGGGGGAGAAGAAGATA
* *
1179661 CGCAGAGGCAAGCTCAAGGGGGGAGAAGAATATA
1 CGCAGAGGCAAGCT-AAAGGGGGAGAAGAAGATA
*
1179695 CACAGAGG
1 CGCAGAGG
1179703 AAAAGGGGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 13 0.36
33 2 0.06
34 21 0.58
ACGTcount: A:0.42, C:0.15, G:0.36, T:0.07
Consensus pattern (33 bp):
CGCAGAGGCAAGCTAAAGGGGGAGAAGAAGATA
Found at i:1194508 original size:59 final size:59
Alignment explanation
Indices: 1194437--1194836 Score: 590
Period size: 59 Copynumber: 6.8 Consensus size: 59
1194427 ATGACATTAA
* *
1194437 GTGTGCTAACATGATAATAAATTCATACTAAGTGTATGGATTTCCGTATAGGGCACTTT
1 GTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
* *
1194496 GTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATATGGCACTTT
1 GTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
*
1194555 GTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTTTAGGGCACTTT
1 GTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
* * * * *
1194614 GTGTGCTAACATGATAAGAAATTCATATTGAGAGTATGAATTTCCTTATATGGCACTTT
1 GTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
*
1194673 GTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTT
1 GTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
* * * * * *
1194732 GTGTGCTAACAAGATAAGAAATTCATATTGAGAGTATGGATTTCCTTATAGGGCACTTT
1 GTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
* * * *
1194791 GTGTGCTAACAAGAT---AAATTCAAACTAAATGTATGAATTTTCGTAT
1 GTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1194837 TGGCATTTGG
Statistics
Matches: 307, Mismatches: 34, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
56 23 0.07
59 284 0.93
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.36
Consensus pattern (59 bp):
GTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
Found at i:1195932 original size:36 final size:36
Alignment explanation
Indices: 1195880--1196017 Score: 197
Period size: 36 Copynumber: 3.9 Consensus size: 36
1195870 ACGATGCTGG
*
1195880 ACATTGATATACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* * * *
1195916 ACATTGATATATGAATGTATCAAAGTTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
1195952 ACATTGATACACGAATGTACCAAAACTGATATGA-A
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
1195987 ACATTGATACACGAATGTATCAAAGTTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1196018 ATGGATAAAT
Statistics
Matches: 91, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 29 0.32
36 62 0.68
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:1200707 original size:36 final size:36
Alignment explanation
Indices: 1200667--1200805 Score: 215
Period size: 36 Copynumber: 3.9 Consensus size: 36
1200657 ACGGTGCTGG
1200667 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
1200703 ACATTGATACACAAATGTATCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
1200739 ACATTGATACATGAATGTACCAAAACTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* * *
1200775 ACATTGATACACGAATATATCAAAGTTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1200806 ATGGATAAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 92 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.27
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:1209786 original size:65 final size:64
Alignment explanation
Indices: 1209670--1209795 Score: 175
Period size: 65 Copynumber: 2.0 Consensus size: 64
1209660 TATGCATAAG
* * *
1209670 CCATGCATCGATGCACCTTAGCTATTTTCAAACATTGAATGCATTTTATGCATCGATGCACATA
1 CCATGCATCGATGCACCTCAGCTATTTTCAAACATCGAATGCAATTTATGCATCGATGCACATA
*
1209734 CCATGCATCGATGCA-CTCCAGGCT-TGTTTGAAACATCGAATGCAATTTATGCATCGATGCAC
1 CCATGCATCGATGCACCT-CA-GCTAT-TTTCAAACATCGAATGCAATTTATGCATCGATGCAC
1209796 CCTTAGTGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
63 2 0.04
64 17 0.31
65 36 0.65
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (64 bp):
CCATGCATCGATGCACCTCAGCTATTTTCAAACATCGAATGCAATTTATGCATCGATGCACATA
Found at i:1215607 original size:21 final size:21
Alignment explanation
Indices: 1215581--1215645 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 21
1215571 TTGTGCATAA
1215581 TGCATCGATACACTATGAAGG
1 TGCATCGATACACTATGAAGG
* * *
1215602 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGAT--A-CACTATGAAGG
*
1215626 TGCATCGATACATTATGAAG
1 TGCATCGATACACTATGAAG
1215646 ATTCACCGAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
21 15 0.44
22 1 0.03
23 1 0.03
24 17 0.50
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (21 bp):
TGCATCGATACACTATGAAGG
Found at i:1215645 original size:45 final size:44
Alignment explanation
Indices: 1215581--1215678 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 44
1215571 TTGTGCATAA
* *
1215581 TGCATCGATACACTATGAAGGTGCATCGATGCA-TCCCTTTGAATG
1 TGCATCGATACACTATGAAGATGCACCGATGCACT-CC-TTGAATG
* *
1215626 TGCATCGATACATTATGAAGATTCACCGATGCACTCCTTGAATG
1 TGCATCGATACACTATGAAGATGCACCGATGCACTCCTTGAATG
*
1215670 TACATCGAT
1 TGCATCGAT
1215679 GCACAATGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
44 15 0.32
45 31 0.66
46 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
TGCATCGATACACTATGAAGATGCACCGATGCACTCCTTGAATG
Found at i:1218391 original size:45 final size:47
Alignment explanation
Indices: 1218340--1218441 Score: 131
Period size: 46 Copynumber: 2.2 Consensus size: 47
1218330 TAAGCCATGC
*
1218340 ATCGATGCACCT-CA-GCTAT-TTTCAAACATCGAATGCATTTTATGA
1 ATCGATGCACCTCCAGGCT-TGTTTCAAACATCGAATGCAATTTATGA
* *
1218385 ATCGATGCA-CTCCAGGCTTGTTTGAAACATCGAATGCAATTTATGC
1 ATCGATGCACCTCCAGGCTTGTTTCAAACATCGAATGCAATTTATGA
*
1218431 ATCGAAGCACC
1 ATCGATGCACC
1218442 CTTAGTGCAC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
44 2 0.04
45 12 0.24
46 34 0.69
47 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (47 bp):
ATCGATGCACCTCCAGGCTTGTTTCAAACATCGAATGCAATTTATGA
Found at i:1220503 original size:22 final size:23
Alignment explanation
Indices: 1220475--1220520 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1220465 AGTCATCAGT
1220475 CCTTCTAGAAA-TGCTGACTAGA
1 CCTTCTAGAAACTGCTGACTAGA
1220497 CCTTCTAGAAACTGCTGACTAGA
1 CCTTCTAGAAACTGCTGACTAGA
1220520 C
1 C
1220521 GTCACGCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (23 bp):
CCTTCTAGAAACTGCTGACTAGA
Found at i:1221102 original size:23 final size:23
Alignment explanation
Indices: 1221076--1221121 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1221066 ATTTGATCCG
*
1221076 GATTAGTAGATTAAATAACAATA
1 GATTAATAGATTAAATAACAATA
1221099 GATTAATAGATTAAATAACAATA
1 GATTAATAGATTAAATAACAATA
1221122 AACACAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.30
Consensus pattern (23 bp):
GATTAATAGATTAAATAACAATA
Found at i:1225574 original size:8 final size:8
Alignment explanation
Indices: 1225561--1225585 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1225551 GTTTCATATC
1225561 AATTCTCA
1 AATTCTCA
1225569 AATTCTCA
1 AATTCTCA
1225577 AATTCTCA
1 AATTCTCA
1225585 A
1 A
1225586 TATTATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (8 bp):
AATTCTCA
Found at i:1226758 original size:14 final size:16
Alignment explanation
Indices: 1226739--1226770 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1226729 CGGATCTTTC
1226739 TTCA-TTTCTAT-ATT
1 TTCATTTTCTATGATT
1226753 TTCATTTTCTATGATT
1 TTCATTTTCTATGATT
1226769 TT
1 TT
1226771 ATCGGTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 7 0.44
16 5 0.31
ACGTcount: A:0.19, C:0.12, G:0.03, T:0.66
Consensus pattern (16 bp):
TTCATTTTCTATGATT
Found at i:1227905 original size:135 final size:138
Alignment explanation
Indices: 1227753--1228025 Score: 327
Period size: 135 Copynumber: 2.0 Consensus size: 138
1227743 TGTTGCACGG
* * *
1227753 ATATTTAAAATTAATTAGGTTAATACCATTTTCTATTTGTAGCCATGTAAATGATTGTTACCAGA
1 ATATTTAAAATTAATTAGGCTAATACCATTATCTATTTGTAACCATGTAAATGATTGTTACCAGA
* * *
1227818 TGCAATATCATGTTGTT-GATGT-TTTTTTC-TTCTTTTGTCTGAATATTTTCCTTCAGGTCTGA
66 TGCAATATCATGTTGTTGGATGTGTTTTTTCGTTCTTTTGTCGGAATATGTTCCTTCAAGTCTGA
1227880 ATCCTTTT
131 ATCCTTTT
** * * ** * ***
1227888 ATATTTAAAATTAATTAGGCTAATGTCGTTATCTGTTTGTAACTGTGTAAATGGTTGTTAGTGGA
1 ATATTTAAAATTAATTAGGCTAATACCATTATCTATTTGTAACCATGTAAATGATTGTTACCAGA
* * * * *
1227953 TGCAATATCCTGTTGTTGGTTTTGTTTTTTCGTTCTTTTTTCGGAGTATGTTCCTTCAAGTCTGA
66 TGCAATATCATGTTGTTGGATGTGTTTTTTCGTTCTTTTGTCGGAATATGTTCCTTCAAGTCTGA
*
1228018 ATTCTTTT
131 ATCCTTTT
1228026 TGGAGTCTTT
Statistics
Matches: 113, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
135 68 0.60
136 3 0.03
137 7 0.06
138 35 0.31
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.49
Consensus pattern (138 bp):
ATATTTAAAATTAATTAGGCTAATACCATTATCTATTTGTAACCATGTAAATGATTGTTACCAGA
TGCAATATCATGTTGTTGGATGTGTTTTTTCGTTCTTTTGTCGGAATATGTTCCTTCAAGTCTGA
ATCCTTTT
Found at i:1229138 original size:38 final size:38
Alignment explanation
Indices: 1229061--1229138 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 38
1229051 ATTGAATATG
* * * *
1229061 ATATATTTTTATATAAATTATGTTGAAGTAAAATTTTA
1 ATATATTTTTAAATAAATTATGTTAAAATAAAATATTA
**
1229099 ATATATATTTTAAATAAATTATG-TAAAATTTAATATTA
1 ATATAT-TTTTAAATAAATTATGTTAAAATAAAATATTA
1229137 AT
1 AT
1229139 TAAAATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
38 18 0.55
39 15 0.45
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (38 bp):
ATATATTTTTAAATAAATTATGTTAAAATAAAATATTA
Found at i:1229240 original size:42 final size:42
Alignment explanation
Indices: 1229177--1229264 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
1229167 ATAATAAAAT
* * *
1229177 AATATATTATAGATGATTTTTTGTATAACTAATTTTTATTTA
1 AATATATTATAGATGAATTTTTATATAAATAATTTTTATTTA
*
1229219 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATAGATGAATTTTTATATAAATAATTTTTATTTA
1229261 AATA
1 AATA
1229265 GTTATAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (42 bp):
AATATATTATAGATGAATTTTTATATAAATAATTTTTATTTA
Found at i:1229254 original size:15 final size:15
Alignment explanation
Indices: 1229234--1229264 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1229224 ATTATCGATG
1229234 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1229249 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1229264 A
1 A
1229265 GTTATAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1230496 original size:14 final size:14
Alignment explanation
Indices: 1230477--1230503 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1230467 GCACTGACTG
1230477 AATAAATAAATAAA
1 AATAAATAAATAAA
1230491 AATAAATAAATAA
1 AATAAATAAATAA
1230504 TTTGATCGTT
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAATAAATAAA
Found at i:1236914 original size:41 final size:41
Alignment explanation
Indices: 1236869--1237009 Score: 109
Period size: 41 Copynumber: 3.4 Consensus size: 41
1236859 AAAACTATCA
1236869 CGGCGTTTGTATAAAAACACTACTAAATTACCACTCTATTG
1 CGGCGTTTGTATAAAAACACTACTAAATTACCACTCTATTG
1236910 CGGCGTTTGT-TGAAAAA-A-TGGCACTATAA--A-CATCTCTATTG
1 CGGCGTTTGTAT-AAAAACACT---ACTA-AATTACCA-CTCTATTG
* * *
1236951 CGGCATTTTAGCTATAAATAC-C-GCTAAATTACCACTCTATTG
1 CGGC-GTTT-G-TATAAAAACACTACTAAATTACCACTCTATTG
*
1236993 CGGCGTTTGTTTAAAAA
1 CGGCGTTTGTATAAAAA
1237010 ACGCCGCTAA
Statistics
Matches: 79, Mismatches: 6, Indels: 32
0.68 0.05 0.27
Matches are distributed among these distances:
39 7 0.09
40 7 0.09
41 34 0.43
42 20 0.25
43 5 0.06
44 5 0.06
45 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Consensus pattern (41 bp):
CGGCGTTTGTATAAAAACACTACTAAATTACCACTCTATTG
Found at i:1237017 original size:42 final size:42
Alignment explanation
Indices: 1236869--1237020 Score: 111
Period size: 42 Copynumber: 3.7 Consensus size: 42
1236859 AAAACTATCA
* * *
1236869 CGGCGTTTGTAT-AAAAACACTACTAAATTACCACTCTATTG
1 CGGCGTTTGTTTAAAAAACGCCACTAAATTACCACTCTATTG
* * *
1236910 CGGCGTTTGTTGAAAAAATGGCACTATAA--A-CATCTCTATTG
1 CGGCGTTTGTTTAAAAAACGCCACTA-AATTACCA-CTCTATTG
* * * *
1236951 CGGCATTT-TAGCTATAAATA--CCGCTAAATTACCACTCTATTG
1 CGGCGTTTGT--TTA-AAAAACGCCACTAAATTACCACTCTATTG
*
1236993 CGGCGTTTGTTTAAAAAACGCCGCTAAA
1 CGGCGTTTGTTTAAAAAACGCCACTAAA
1237021 GTATTATTTT
Statistics
Matches: 84, Mismatches: 15, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
40 9 0.11
41 32 0.38
42 34 0.40
43 9 0.11
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (42 bp):
CGGCGTTTGTTTAAAAAACGCCACTAAATTACCACTCTATTG
Found at i:1245512 original size:229 final size:228
Alignment explanation
Indices: 1245107--1245555 Score: 808
Period size: 229 Copynumber: 2.0 Consensus size: 228
1245097 TGTAATTATC
* * *
1245107 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
1245172 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
1245237 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
1245302 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTTCAAAAAAGTATA
*
1245335 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
1245400 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
1245465 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
1245530 GAAACATAAATTACATAACTTTCAAA
195 GAAACATAAATTACATAACTTTCAAA
1245556 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
228 36 0.17
229 175 0.83
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTCAAAAAAGTATA
Found at i:1245641 original size:21 final size:20
Alignment explanation
Indices: 1245617--1245666 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1245607 AAAACGATAT
1245617 ACCAGGTAAAAATATGATAAA
1 ACCAGGTAAAAA-ATGATAAA
1245638 ACCA-GTAACAAAATGATAAA
1 ACCAGGTAA-AAAATGATAAA
1245658 ACC-GGTAAA
1 ACCAGGTAAA
1245667 TTTAAAAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.04
20 19 0.70
21 7 0.26
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.16
Consensus pattern (20 bp):
ACCAGGTAAAAAATGATAAA
Found at i:1245811 original size:20 final size:19
Alignment explanation
Indices: 1245788--1245834 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1245778 CGATATAACA
1245788 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
* *
1245808 GGTATCAAAATGATAAAACT
1 GGTA-AAAAATGATAAAACC
1245828 GGTAAAA
1 GGTAAAA
1245835 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1248180 original size:33 final size:33
Alignment explanation
Indices: 1248138--1248203 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1248128 AAATAGATGG
*
1248138 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
1248171 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1248204 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1248435 original size:14 final size:14
Alignment explanation
Indices: 1248399--1248436 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1248389 AAGAAAGAGG
1248399 GAGGAGGAAGAAAA
1 GAGGAGGAAGAAAA
*
1248413 GA-GATGGAAGAAAT
1 GAGGA-GGAAGAAAA
1248427 GAGGAGGAAG
1 GAGGAGGAAG
1248437 GAAGTCGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.05
Consensus pattern (14 bp):
GAGGAGGAAGAAAA
Found at i:1250003 original size:19 final size:19
Alignment explanation
Indices: 1249979--1250027 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1249969 AATGTCGAGT
1249979 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1249998 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
1250017 TATTTTTGTAT
1 TAATTTTGTAT
1250028 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1250553 original size:199 final size:199
Alignment explanation
Indices: 1250176--1251661 Score: 2816
Period size: 199 Copynumber: 7.5 Consensus size: 199
1250166 TGTCGATCCA
1250176 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
* *
1250241 TCTAAAT-ATGTGTCGACAATAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATTAATGGAAAA
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
*
1250304 CAGGGTGCACCCATAAAGTCTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
131 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
1250369 AAAG
196 AAAG
*
1250373 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1250438 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
*
1250503 CAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
131 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
1250568 AAAG
196 AAAG
1250572 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1250637 TCTAAATAATGTGTCGACACTAA-ATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
1250701 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
131 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
1250766 AAAG
196 AAAG
*
1250770 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1250835 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
1250900 CA-GGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCA
131 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
1250963 AAAG
196 AAAG
1250967 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1251032 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
1251097 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
131 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
1251162 AAAG
196 AAAG
1251166 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
*
1251231 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATTAATGGAAAA
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
1251295 CAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCC-
131 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
1251358 AAAG
196 AAAG
1251362 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1251427 TCTAAATAAT-TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAA
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
*
1251490 CAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCA
131 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
1251554 AAAG
196 AAAG
1251558 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATA-G
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1251622 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
1251662 CTAATTTAAA
Statistics
Matches: 1269, Mismatches: 12, Indels: 17
0.98 0.01 0.01
Matches are distributed among these distances:
195 109 0.09
196 190 0.15
197 267 0.21
198 343 0.27
199 360 0.28
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (199 bp):
TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
AAAG
Found at i:1250932 original size:396 final size:395
Alignment explanation
Indices: 1250176--1251661 Score: 2815
Period size: 396 Copynumber: 3.8 Consensus size: 395
1250166 TGTCGATCCA
1250176 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
* *
1250241 TCTAAAT-ATGTGTCGACAATAATATAGTTTGTGTCGATATTTTTTTCCAGAATTAATGGAAAAC
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAAC
*
1250305 AGGGTGCACCCATAAAGTCTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
131 AGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
1250370 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAAT
196 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAAT
1250435 ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGA
261 ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGA
1250500 AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAC
326 AAAC-AGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAAC
1250565 CCAAAAG
389 CCAAAAG
1250572 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1250637 TCTAAATAATGTGTCGACACTAA-ATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAA
1250701 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
130 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
1250766 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
195 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
1250831 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGG
260 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGG
1250896 AAAACAGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACC
325 AAAACAGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACC
1250961 CAAAAG
390 CAAAAG
1250967 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1251032 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAA
1251097 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
130 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
*
1251162 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGA
195 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
*
1251227 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATTAATGG
260 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGG
1251291 AAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAAC
325 AAAACA-GGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAAC
1251356 CC-AAAG
389 CCAAAAG
1251362 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1251427 TCTAAATAAT-TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAAC
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAAC
*
1251491 AAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAA
131 AGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
*
1251555 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGAT
196 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAAT
1251620 A-GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
261 ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
1251662 CTAATTTAAA
Statistics
Matches: 1080, Mismatches: 6, Indels: 13
0.98 0.01 0.01
Matches are distributed among these distances:
391 41 0.04
392 82 0.08
393 72 0.07
394 29 0.03
395 227 0.21
396 393 0.36
397 236 0.22
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (395 bp):
TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAAC
AGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAAT
ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGA
AAACAGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCC
AAAAG
Found at i:1251304 original size:594 final size:592
Alignment explanation
Indices: 1250176--1251661 Score: 2813
Period size: 594 Copynumber: 2.5 Consensus size: 592
1250166 TGTCGATCCA
1250176 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
* *
1250241 TCTAAAT-ATGTGTCGACAATAATATAGTTTGTGTCGATATTTTTTTCCAGAATTAATGGAAAAC
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAAC
*
1250305 AGGGTGCACCCATAAAGTCTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
131 A-GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
*
1250370 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAAT
195 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGAT
1250435 ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGA
260 ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGA
1250500 AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAC
325 AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAC
1250565 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
390 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
1250630 GGATATGTCTAAATAATGTGTCGACACTAAATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
455 GGATATGTCTAAATAATGTGTCGACACTAAATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1250695 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
520 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCG
1250760 AACCCAAAAG
584 AACCC-AAAG
*
1250770 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1250835 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAA
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAA
1250900 CAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAA
130 CAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
1250964 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGAT
195 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGAT
1251029 ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGA
260 ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGA
*
1251094 AAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAC
325 AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAC
1251159 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
390 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
1251224 GGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATTAA
455 GGATATGTCTAAATAATGTGTCGACACTAA-ATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
1251288 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCG
519 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCG
1251353 AACCCAAAG
584 AACCCAAAG
1251362 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
1251427 TCTAAATAAT-TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAAC
66 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAAC
1251491 AAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAA
131 -AGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
1251555 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGAT
195 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGAT
1251620 A-GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
260 ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
1251662 CTAATTTAAA
Statistics
Matches: 879, Mismatches: 8, Indels: 14
0.98 0.01 0.02
Matches are distributed among these distances:
590 66 0.08
591 142 0.16
592 93 0.11
593 30 0.03
594 447 0.51
595 76 0.09
596 25 0.03
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (592 bp):
TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATATG
TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAAC
AGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAA
AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGATA
TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAA
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
GATATGTCTAAATAATGTGTCGACACTAAATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATG
GAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAA
CCCAAAG
Found at i:1253120 original size:6 final size:6
Alignment explanation
Indices: 1253096--1253192 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
1253086 AGCGGTCGCA
* * * * * *
1253096 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGA- GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * *
1253143 GAAGCT GGCGAT GAAGAT GACGAT GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
1253191 GA
1 GA
1253193 TGATCCAA
Statistics
Matches: 73, Mismatches: 17, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
5 4 0.05
6 69 0.95
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:1253131 original size:3 final size:3
Alignment explanation
Indices: 1253111--1253196 Score: 75
Period size: 3 Copynumber: 29.0 Consensus size: 3
1253101 TGAAGCTGAC
* * * * * ** *
1253111 GAT GAA GAT GAC GAT GAT GAT GAT GA- GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
1253158 GAT GAC GAT GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1253197 CCAA
Statistics
Matches: 64, Mismatches: 18, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:1253144 original size:41 final size:42
Alignment explanation
Indices: 1253099--1253188 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 42
1253089 GGTCGCAGAA
1253099 GATGAAGCTGACGATGAAGATGACGATGATGATGATGA-GAC
1 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
* *
1253140 GATGAAGCTGGCGATGAAGATGACGATGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1253182 GATGAAG
1 GATGAAG
1253189 ATGATGATCC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 37 0.80
42 9 0.20
ACGTcount: A:0.36, C:0.08, G:0.36, T:0.21
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
Found at i:1253193 original size:12 final size:12
Alignment explanation
Indices: 1253099--1253196 Score: 81
Period size: 12 Copynumber: 8.2 Consensus size: 12
1253089 GGTCGCAGAA
* *
1253099 GATGAAGCTGAC
1 GATGAAGATGAT
*
1253111 GATGAAGATGAC
1 GATGAAGATGAT
*
1253123 GATGATGATGAT
1 GATGAAGATGAT
* *
1253135 GA-GACGATGAA
1 GATGAAGATGAT
* ** *
1253146 GCTGGCGATGAA
1 GATGAAGATGAT
*
1253158 GATGACGATGAT
1 GATGAAGATGAT
*
1253170 GATGATGATGAT
1 GATGAAGATGAT
1253182 GATGAAGATGAT
1 GATGAAGATGAT
1253194 GAT
1 GAT
1253197 CCAA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
11 8 0.11
12 65 0.89
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.22
Consensus pattern (12 bp):
GATGAAGATGAT
Done.