Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 129 of 182
Found at i:40908214 original size:28 final size:28
Alignment explanation
Indices: 40908183--40908268 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 28
40908173 ACCATAAAGG
40908183 ATAATAAATTAAAATAAGTTTATATATA
1 ATAATAAATTAAAATAAGTTTATATATA
* * * *
40908211 ATAAAAAATAAAACCATATGTATAT-TA-A
1 ATAATAAATTAAA--ATAAGTTTATATATA
* *
40908239 ATAATAAATATAAATTAAATTTATAT-TA
1 ATAATAAAT-TAAAATAAGTTTATATATA
40908267 AT
1 AT
40908269 GTTAAATGAT
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
27 6 0.14
28 24 0.56
29 5 0.12
30 8 0.19
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
ATAATAAATTAAAATAAGTTTATATATA
Found at i:40908844 original size:37 final size:37
Alignment explanation
Indices: 40908803--40908913 Score: 183
Period size: 37 Copynumber: 3.1 Consensus size: 37
40908793 CTCCAAAATT
* *
40908803 GTTAGGAGTTCTAAACTCTAGTGGGTATCCATCTAAG
1 GTTAGGAGTTCTAAACTCTAGTAGGTATTCATCTAAG
40908840 GTTAGGAGTTCTAAACTCTAGTAGGTATTCATCT-A-
1 GTTAGGAGTTCTAAACTCTAGTAGGTATTCATCTAAG
40908875 -TTAGGAGTTCTAAACTCTAGTAGGTATTCATCTAAG
1 GTTAGGAGTTCTAAACTCTAGTAGGTATTCATCTAAG
40908911 GTT
1 GTT
40908914 GTAAAAGAGC
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
34 33 0.48
35 1 0.01
36 1 0.01
37 34 0.49
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (37 bp):
GTTAGGAGTTCTAAACTCTAGTAGGTATTCATCTAAG
Found at i:40908884 original size:34 final size:35
Alignment explanation
Indices: 40908803--40908908 Score: 169
Period size: 34 Copynumber: 3.0 Consensus size: 35
40908793 CTCCAAAATT
* *
40908803 GTTAGGAGTTCTAAACTCTAGTGGGTATCCATCTAA
1 GTTAGGAGTTCTAAACTCTAGTAGGTATTCATCT-A
40908839 GGTTAGGAGTTCTAAACTCTAGTAGGTATTCATCTA
1 -GTTAGGAGTTCTAAACTCTAGTAGGTATTCATCTA
40908875 -TTAGGAGTTCTAAACTCTAGTAGGTATTCATCTA
1 GTTAGGAGTTCTAAACTCTAGTAGGTATTCATCTA
40908909 AGGTTGTAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
34 34 0.51
36 1 0.01
37 32 0.48
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (35 bp):
GTTAGGAGTTCTAAACTCTAGTAGGTATTCATCTA
Found at i:40908898 original size:19 final size:19
Alignment explanation
Indices: 40908842--40908898 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
40908832 CATCTAAGGT
40908842 TAGGAGTTCTAAACTCTAG
1 TAGGAGTTCTAAACTCTAG
*
40908861 TAGGTA-TTC---A-TCTAT
1 TAGG-AGTTCTAAACTCTAG
40908876 TAGGAGTTCTAAACTCTAG
1 TAGGAGTTCTAAACTCTAG
40908895 TAGG
1 TAGG
40908899 TATTCATCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
14 1 0.03
15 11 0.37
16 1 0.03
18 1 0.03
19 15 0.50
20 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (19 bp):
TAGGAGTTCTAAACTCTAG
Found at i:40910708 original size:6 final size:6
Alignment explanation
Indices: 40910683--40910721 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
40910673 ACAATTTATA
* * *
40910683 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
40910722 ATTCTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:40914267 original size:22 final size:23
Alignment explanation
Indices: 40914242--40914284 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
40914232 TAAACGAAAT
*
40914242 TTAAACAT-GTAAACGCATTAGA
1 TTAAAAATAGTAAACGCATTAGA
*
40914264 TTAAAAATATTAAACGCATTA
1 TTAAAAATAGTAAACGCATTA
40914285 CAATTGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (23 bp):
TTAAAAATAGTAAACGCATTAGA
Found at i:40916109 original size:3 final size:3
Alignment explanation
Indices: 40916094--40916125 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
40916084 ATCATTAAGA
*
40916094 AAG AAG TAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
40916126 TGGTTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:40921734 original size:31 final size:31
Alignment explanation
Indices: 40921697--40921762 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
40921687 TACATAATAA
*
40921697 AAAATAATTTATACATA-A-AATACAATAAAAT
1 AAAATAA--TATACATATAGAATAAAATAAAAT
40921728 AAAATAATATACATATAGAATAAAATAAAAT
1 AAAATAATATACATATAGAATAAAATAAAAT
40921759 AAAA
1 AAAA
40921763 ATTACATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 8 0.25
30 1 0.03
31 23 0.72
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.26
Consensus pattern (31 bp):
AAAATAATATACATATAGAATAAAATAAAAT
Found at i:40921763 original size:6 final size:5
Alignment explanation
Indices: 40921711--40921762 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
40921701 TAATTTATAC
* * * *
40921711 ATAAA ATACA ATAAA ATAAA ATAAT ATACAT ATAGA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATA-AA ATAAA ATAAA ATAAA ATAAA
40921762 A
1 A
40921763 ATTACATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
5 35 0.88
6 5 0.12
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:40921852 original size:60 final size:59
Alignment explanation
Indices: 40921788--40921962 Score: 208
Period size: 60 Copynumber: 2.9 Consensus size: 59
40921778 GTCAGACTTG
* *
40921788 AATTTTTGGAAATTTTAGGGGTCAAATAATAATTTTTGAAAAGTTTAAGGGTCAAATTTA
1 AATTTTTGGAAAATTTAGGGGTCAAAT-ATAATTTTTGAAAAGTTTAAGGGTCAAATTGA
* * * * * * *
40921848 AATTTTTGGAAAATTTAAGGGTTAAATTTGAATTTTTGTAAAGTTTAGGGGTTAAATTGG
1 AATTTTTGGAAAATTTAGGGGTCAAATAT-AATTTTTGAAAAGTTTAAGGGTCAAATTGA
* * *
40921908 AATTTTTAGAAAATTTAGGGGTCAAATCA-AATTTTTAAAAAGGTTAAGGGTCAAA
1 AATTTTTGGAAAATTTAGGGGTCAAAT-ATAATTTTTGAAAAGTTTAAGGGTCAAA
40921963 AAATAATTTT
Statistics
Matches: 95, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
59 22 0.23
60 73 0.77
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (59 bp):
AATTTTTGGAAAATTTAGGGGTCAAATATAATTTTTGAAAAGTTTAAGGGTCAAATTGA
Found at i:40921941 original size:29 final size:29
Alignment explanation
Indices: 40921788--40921962 Score: 147
Period size: 30 Copynumber: 5.9 Consensus size: 29
40921778 GTCAGACTTG
* * *
40921788 AATTTTTGGAAATTTTAGGGGTCAAA-TAA
1 AATTTTT-GAAAATTTAAGGGTCAAATTTA
40921817 TAATTTTTGAAAAGTTTAAGGGTCAAATTTA
1 -AATTTTTGAAAA-TTTAAGGGTCAAATTTA
* *
40921848 AATTTTTGGAAAATTTAAGGGTTAAATTTG
1 AATTTTT-GAAAATTTAAGGGTCAAATTTA
* * * **
40921878 AATTTTTGTAAAGTTTAGGGGTTAAATTGG
1 AATTTTTG-AAAATTTAAGGGTCAAATTTA
* *
40921908 AATTTTTAGAAAATTTAGGGGTCAAA-TCA
1 AATTTTT-GAAAATTTAAGGGTCAAATTTA
* *
40921937 AATTTTTAAAAAGGTTAAGGGTCAAA
1 AATTTTTGAAAA-TTTAAGGGTCAAA
40921963 AAATAATTTT
Statistics
Matches: 124, Mismatches: 15, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
28 4 0.03
29 24 0.19
30 88 0.71
31 8 0.06
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (29 bp):
AATTTTTGAAAATTTAAGGGTCAAATTTA
Found at i:40922501 original size:22 final size:23
Alignment explanation
Indices: 40922476--40922520 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40922466 ACCTTAATTT
40922476 TTTG-TGATTTGTTTTTTAAAAA
1 TTTGTTGATTTGTTTTTTAAAAA
** *
40922498 TTTGTTTTTTTTTTTTTTAAAAA
1 TTTGTTGATTTGTTTTTTAAAAA
40922521 AGAACCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (23 bp):
TTTGTTGATTTGTTTTTTAAAAA
Found at i:40923741 original size:20 final size:19
Alignment explanation
Indices: 40923701--40923742 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
40923691 TTTTTCTCTC
40923701 TCTTTCTTTCCTTCTTCCT
1 TCTTTCTTTCCTTCTTCCT
* *
40923720 TCTTTCTTTACTTTCTTTCT
1 TCTTTCTTT-CCTTCTTCCT
40923740 TCT
1 TCT
40923743 CTCCCCCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (19 bp):
TCTTTCTTTCCTTCTTCCT
Found at i:40924366 original size:28 final size:28
Alignment explanation
Indices: 40924317--40924384 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
40924307 GTATTTTACA
* * *
40924317 AATTT-TATAATATTTTATATTTGTAAT
1 AATTTATATAATTTTTTAAATTTATAAT
*
40924344 AGTTTATATAATTTTTTAAATTTATAAT
1 AATTTATATAATTTTTTAAATTTATAAT
40924372 AATTTA-ATAATTT
1 AATTTATATAATTT
40924385 CTAATAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 11 0.31
28 24 0.69
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
AATTTATATAATTTTTTAAATTTATAAT
Found at i:40924383 original size:18 final size:18
Alignment explanation
Indices: 40924340--40924394 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
40924330 TTTATATTTG
*
40924340 TAATAGTTTAT-ATAATT
1 TAATAATTTATAATAATT
**
40924357 TTTTAAATTTATAATAATT
1 TAAT-AATTTATAATAATT
*
40924376 TAATAATTTCTAATAATT
1 TAATAATTTATAATAATT
40924394 T
1 T
40924395 TTCAAAATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 2 0.07
18 20 0.67
19 8 0.27
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TAATAATTTATAATAATT
Found at i:40924393 original size:28 final size:28
Alignment explanation
Indices: 40924335--40924394 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
40924325 AATATTTTAT
* * * *
40924335 ATTTGTAATAGTTTATATAATTTTTTAA
1 ATTTATAATAATTTATATAATTTCTAAA
40924363 ATTTATAATAATTTA-ATAATTTCTAATA
1 ATTTATAATAATTTATATAATTTCTAA-A
40924391 ATTT
1 ATTT
40924395 TTCAAAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (28 bp):
ATTTATAATAATTTATATAATTTCTAAA
Found at i:40924887 original size:19 final size:18
Alignment explanation
Indices: 40924847--40924928 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 18
40924837 TAATAAAAAA
* *
40924847 TTTATAATTTTTCTATAAT
1 TTTATAATTTTT-AATATT
40924866 TTTATAATATTTTAATATTT
1 TTTATAAT-TTTTAATA-TT
*
40924886 TTTATAACTTTGTCAAT-TT
1 TTTATAA-TTT-TTAATATT
*
40924905 TTTATGATATTTTAATAATT
1 TTTATAAT-TTTTAAT-ATT
40924925 TTTA
1 TTTA
40924929 GACTTGAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
18 5 0.10
19 21 0.41
20 20 0.39
21 5 0.10
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTATAATTTTTAATATT
Found at i:40924888 original size:20 final size:20
Alignment explanation
Indices: 40924865--40924928 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
40924855 TTTTCTATAA
40924865 TTTTATAATATTTTAATATT
1 TTTTATAATATTTTAATATT
* *
40924885 TTTTATAACT-TTGTCA-ATT
1 TTTTATAA-TATTTTAATATT
* *
40924904 TTTTATGATATTTTAATAAT
1 TTTTATAATATTTTAATATT
40924924 TTTTA
1 TTTTA
40924929 GACTTGAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.40
20 19 0.54
21 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTATAATATTTTAATATT
Found at i:40924907 original size:29 final size:30
Alignment explanation
Indices: 40924853--40924917 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
40924843 AAAATTTATA
*
40924853 ATTTTTCTATAATTTTATAATATTTTA-AT
1 ATTTTTCTATAACTTTATAATATTTTAGAT
* *
40924882 ATTTTT-TATAACTTTGTCAATTTTTTATGAT
1 ATTTTTCTATAACTTTAT-AATATTTTA-GAT
40924913 ATTTT
1 ATTTT
40924918 AATAATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 9 0.30
29 14 0.47
31 7 0.23
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (30 bp):
ATTTTTCTATAACTTTATAATATTTTAGAT
Found at i:40926082 original size:13 final size:13
Alignment explanation
Indices: 40926064--40926099 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
40926054 TTCTACAAAT
40926064 ACTTCATATAAAC
1 ACTTCATATAAAC
*
40926077 ACTTCATATAATC
1 ACTTCATATAAAC
*
40926090 ATTTCATATA
1 ACTTCATATA
40926100 TCTATTTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (13 bp):
ACTTCATATAAAC
Found at i:40926526 original size:45 final size:46
Alignment explanation
Indices: 40926462--40926590 Score: 161
Period size: 46 Copynumber: 2.8 Consensus size: 46
40926452 ATGGTTGAAG
* *
40926462 GATGCCATGGTGTCTTTCAACCATGGTCTTATTTA-TTCTCGACTT
1 GATGCCATGGTGTCTTTCAACCATGGTCTTATTCATTTCTCGACGT
* * * *
40926507 GATGCCATGGTATCTTTCAATCATGGTCTTATTCATTTTTCGTCGT
1 GATGCCATGGTGTCTTTCAACCATGGTCTTATTCATTTCTCGACGT
* * * *
40926553 GTTGCCATAGTGTCTTTCAACTATGGTCTTACTCATTT
1 GATGCCATGGTGTCTTTCAACCATGGTCTTATTCATTT
40926591 GATTGGTGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
45 32 0.45
46 39 0.55
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (46 bp):
GATGCCATGGTGTCTTTCAACCATGGTCTTATTCATTTCTCGACGT
Found at i:40926624 original size:45 final size:45
Alignment explanation
Indices: 40926555--40927070 Score: 434
Period size: 45 Copynumber: 11.5 Consensus size: 45
40926545 TTCGTCGTGT
** *
40926555 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTGATTGGTGA
1 TGCCATAACGTCTTTCAACTATGGTCTTACTCATTTGATTTGTGA
* * * * * * *
40926600 TTCCATAACATCTTTCCACCATGGTCTTACTCGA-TAGAATAGTGA
1 TGCCATAACGTCTTTCAACTATGGTCTTACTC-ATTTGATTTGTGA
* * *
40926645 TGCCATAACATCTTTCAGCTATGGTCTTACTCGTTTGATTTGTGA
1 TGCCATAACGTCTTTCAACTATGGTCTTACTCATTTGATTTGTGA
* * * *
40926690 TGTCATAATGTCTTTCAACTGTGGTCTTACTCGTTTGATTTGTGA
1 TGCCATAACGTCTTTCAACTATGGTCTTACTCATTTGATTTGTGA
* ** * *
40926735 CGCCATAGTGTCTTTCAACTATGGTCTTACTCGTTTAATTTGTGA
1 TGCCATAACGTCTTTCAACTATGGTCTTACTCATTTGATTTGTGA
* ** * ** * *
40926780 TGTCATAGTGTCTTTCAACAATGGTCTTACTCGA-TAAAATAGTGA
1 TGCCATAACGTCTTTCAACTATGGTCTTACTC-ATTTGATTTGTGA
* * * * * *
40926825 TGCCATAACATCTTT-TAGTATAGTCTTGCTCGTTTGATTTGTGA
1 TGCCATAACGTCTTTCAACTATGGTCTTACTCATTTGATTTGTGA
** * * *
40926869 TGCCATAGTGTCTTTCAACTATGGTCTTACTCGA-TAGAATAGTGA
1 TGCCATAACGTCTTTCAACTATGGTCTTACTC-ATTTGATTTGTGA
* * * *
40926914 TTCCATAACATCTTTC-AGTATGGTCTTACTCGTTTGATTTGTGA
1 TGCCATAACGTCTTTCAACTATGGTCTTACTCATTTGATTTGTGA
** * * *
40926958 TGCCATAGTGTCTTTCAACTATGGTCTTACTCGA-TAGAATAGTGA
1 TGCCATAACGTCTTTCAACTATGGTCTTACTC-ATTTGATTTGTGA
* * * * *
40927003 TGCCATAACGTCTTTCAGCTATAGTCTTACTCATTT-CTATGGTGG
1 TGCCATAACGTCTTTCAACTATGGTCTTACTCATTTGAT-TTGTGA
*
40927048 TGCCATAATGTCTTTCAACTATG
1 TGCCATAACGTCTTTCAACTATG
40927071 CTCTGATGCC
Statistics
Matches: 371, Mismatches: 89, Indels: 22
0.77 0.18 0.05
Matches are distributed among these distances:
44 65 0.18
45 305 0.82
46 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (45 bp):
TGCCATAACGTCTTTCAACTATGGTCTTACTCATTTGATTTGTGA
Found at i:40926883 original size:89 final size:89
Alignment explanation
Indices: 40926565--40927070 Score: 636
Period size: 90 Copynumber: 5.6 Consensus size: 89
40926555 TGCCATAGTG
* * * * ** * *
40926565 TCTTTCAACTATGGTCTTACTCATTTGATTGGTGATTCCATAACATCTTTCCACCATGGTCTTAC
1 TCTTTC-AGTATGGTCTTACTCGTTTGATTTGTGATGCCATAATGTCTTTCAACTATGGTCTTAC
40926630 TCGATAGAATAGTGATGCCATAACA
65 TCGATAGAATAGTGATGCCATAACA
* *
40926655 TCTTTCAGCTATGGTCTTACTCGTTTGATTTGTGATGTCATAATGTCTTTCAACTGTGGTCTTAC
1 TCTTTCAG-TATGGTCTTACTCGTTTGATTTGTGATGCCATAATGTCTTTCAACTATGGTCTTAC
* * * * * ***
40926720 TCGTTTGATTTGTGACGCCATAGTG
65 TCGATAGAATAGTGATGCCATAACA
* * * * *
40926745 TCTTTCAACTATGGTCTTACTCGTTTAATTTGTGATGTCATAGTGTCTTTCAACAATGGTCTTAC
1 TCTTTC-AGTATGGTCTTACTCGTTTGATTTGTGATGCCATAATGTCTTTCAACTATGGTCTTAC
*
40926810 TCGATAAAATAGTGATGCCATAACA
65 TCGATAGAATAGTGATGCCATAACA
* * * *
40926835 TCTTTTAGTATAGTCTTGCTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTACT
1 TCTTTCAGTATGGTCTTACTCGTTTGATTTGTGATGCCATAATGTCTTTCAACTATGGTCTTACT
*
40926900 CGATAGAATAGTGATTCCATAACA
66 CGATAGAATAGTGATGCCATAACA
*
40926924 TCTTTCAGTATGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTACT
1 TCTTTCAGTATGGTCTTACTCGTTTGATTTGTGATGCCATAATGTCTTTCAACTATGGTCTTACT
*
40926989 CGATAGAATAGTGATGCCATAACG
66 CGATAGAATAGTGATGCCATAACA
* * * * *
40927013 TCTTTCAGCTATAGTCTTACTCATTT-CTATGGTGGTGCCATAATGTCTTTCAACTATG
1 TCTTTCAG-TATGGTCTTACTCGTTTGAT-TTGTGATGCCATAATGTCTTTCAACTATG
40927071 CTCTGATGCC
Statistics
Matches: 360, Mismatches: 52, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
89 169 0.47
90 190 0.53
91 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.41
Consensus pattern (89 bp):
TCTTTCAGTATGGTCTTACTCGTTTGATTTGTGATGCCATAATGTCTTTCAACTATGGTCTTACT
CGATAGAATAGTGATGCCATAACA
Found at i:40927146 original size:44 final size:45
Alignment explanation
Indices: 40927074--40927284 Score: 199
Period size: 45 Copynumber: 4.7 Consensus size: 45
40927064 AACTATGCTC
**
40927074 TGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGAATAG
1 TGATGCCATAACGTCTTTCAACTATGGTCTTACTCGATAGAATAG
** * * * * * * *
40927119 TGATTTCATAACATCTTTC-AGTATGGTCTTACTTGTTTGATTTG
1 TGATGCCATAACGTCTTTCAACTATGGTCTTACTCGATAGAATAG
**
40927163 TGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGAATAG
1 TGATGCCATAACGTCTTTCAACTATGGTCTTACTCGATAGAATAG
* * * *** **
40927208 TGATGCCATAACGTCTTTCAGCTATGGTCCTACTCGTTTCTAGGG
1 TGATGCCATAACGTCTTTCAACTATGGTCTTACTCGATAGAATAG
* **
40927253 TGGTGCCATAGTGTCTTTCAACTATGGTCTTA
1 TGATGCCATAACGTCTTTCAACTATGGTCTTA
40927285 ATCATTTCTT
Statistics
Matches: 128, Mismatches: 37, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
44 33 0.26
45 95 0.74
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (45 bp):
TGATGCCATAACGTCTTTCAACTATGGTCTTACTCGATAGAATAG
Found at i:40927175 original size:89 final size:90
Alignment explanation
Indices: 40927074--40927284 Score: 318
Period size: 89 Copynumber: 2.4 Consensus size: 90
40927064 AACTATGCTC
**
40927074 TGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGAATAGTGATTTCATAACATCTTTCA
1 TGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGAATAGTGATGCCATAACATCTTTCA
* * **
40927139 G-TATGGTCTTACTTGTTTGAT-TTG
66 GCTATGGTCCTACTCGTTT-ATAGGG
*
40927163 TGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGAATAGTGATGCCATAACGTCTTTCA
1 TGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGAATAGTGATGCCATAACATCTTTCA
*
40927228 GCTATGGTCCTACTCGTTTCTAGGG
66 GCTATGGTCCTACTCGTTTATAGGG
*
40927253 TGGTGCCATAGTGTCTTTCAACTATGGTCTTA
1 TGATGCCATAGTGTCTTTCAACTATGGTCTTA
40927285 ATCATTTCTT
Statistics
Matches: 111, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
89 64 0.58
90 47 0.42
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (90 bp):
TGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGAATAGTGATGCCATAACATCTTTCA
GCTATGGTCCTACTCGTTTATAGGG
Found at i:40927224 original size:208 final size:208
Alignment explanation
Indices: 40926866--40927278 Score: 763
Period size: 208 Copynumber: 2.0 Consensus size: 208
40926856 GTTTGATTTG
40926866 TGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGAATAGTGATTCCATAACATCTTTCA
1 TGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGAATAGTGATTCCATAACATCTTTCA
40926931 GTATGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGA
66 GTATGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGA
* *
40926996 ATAGTGATGCCATAACGTCTTTCAGCTATAGTCTTACTCATTTCTATGGTGGTGCCATAATGTCT
131 ATAGTGATGCCATAACGTCTTTCAGCTATAGTCCTACTCATTTCTAGGGTGGTGCCATAATGTCT
40927061 TTCAACTATGCTC
196 TTCAACTATGCTC
*
40927074 TGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGAATAGTGATTTCATAACATCTTTCA
1 TGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGAATAGTGATTCCATAACATCTTTCA
*
40927139 GTATGGTCTTACTTGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGA
66 GTATGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGA
* * *
40927204 ATAGTGATGCCATAACGTCTTTCAGCTATGGTCCTACTCGTTTCTAGGGTGGTGCCATAGTGTCT
131 ATAGTGATGCCATAACGTCTTTCAGCTATAGTCCTACTCATTTCTAGGGTGGTGCCATAATGTCT
40927269 TTCAACTATG
196 TTCAACTATG
40927279 GTCTTAATCA
Statistics
Matches: 198, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
208 198 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (208 bp):
TGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGAATAGTGATTCCATAACATCTTTCA
GTATGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGATAGA
ATAGTGATGCCATAACGTCTTTCAGCTATAGTCCTACTCATTTCTAGGGTGGTGCCATAATGTCT
TTCAACTATGCTC
Found at i:40934202 original size:59 final size:58
Alignment explanation
Indices: 40934141--40934690 Score: 712
Period size: 59 Copynumber: 9.4 Consensus size: 58
40934131 TGGATACCCG
* * * * * * *
40934141 GGGGGCAAAATGGTAATTTTAGTGTAATCGGGGTTGAAGATGGAATCTTAAAAGATTC
1 GGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
** ** *
40934199 GGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAACAGAA-TTTAGAAGCTTC
1 GGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * * * *
40934257 GAGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAATAGAATTTTAAAAGATTT
1 GGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * *
40934316 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTTT
1 GGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
40934375 GGGGATAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTT-GAAAGTTTC
1 GGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAGATTC
* *
40934434 GGGGATAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
40934492 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
*
40934551 GGGGGTAAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
*
40934610 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
40934669 GAGGGTTAAAAT-ATAATTTTGG
1 G-GGGGTAAAATGGTAATTTTGG
40934691 AAAAGTTTTG
Statistics
Matches: 442, Mismatches: 39, Indels: 22
0.88 0.08 0.04
Matches are distributed among these distances:
57 4 0.01
58 124 0.28
59 297 0.67
60 17 0.04
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (58 bp):
GGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
Found at i:40934402 original size:176 final size:175
Alignment explanation
Indices: 40934141--40934688 Score: 760
Period size: 176 Copynumber: 3.1 Consensus size: 175
40934131 TGGATACCCG
* * * * * * *
40934141 GGGGGCAAAATGGTAA-TTTTAGTGTAATCGGGGTTGAAGATGGAATCTTAAAAGATTCGGGGGT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGT
* * ** *
40934205 AAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAACAGAATTTAGAAGCTTCGAGGGTAAAATGG
66 AAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTAGAAGATTCG-GGGTAAAATGG
* * *
40934270 TAATTTTCGGTGAAATCGGGGTCAAAAATAGAATTTTAAAAGATTT
130 TAATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTC
* * * *
40934316 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTTTGGGGAT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGT
* * *
40934381 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAGTTTCGGGGATAAAATG
66 AAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTAG-AAGATTCGGGG-TAAAATG
* * *
40934446 GTAATTTTTGGTGAAATCGAGGT-TAAAATGGAATTTTAGAAGATTC
129 GTAATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTC
* *
40934492 GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTAGAAGATTCGGGGGT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGT
40934557 AAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATG
66 AAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAA-TTTAGAAGATTC-GGGGTAAAATG
40934622 GTAATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTC
129 GTAATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTC
* *
40934669 GAGGGTTAAAAT-ATAATTTT
1 G-GGGGTAAAATGGTAATTTT
40934689 GGAAAAGTTT
Statistics
Matches: 328, Mismatches: 38, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
175 15 0.05
176 231 0.70
177 73 0.22
178 9 0.03
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.32
Consensus pattern (175 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGT
AAAATGGTAATTTTCGGTGAAATCAGGGTTAAAAATGGAATTTAGAAGATTCGGGGTAAAATGGT
AATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTC
Found at i:40934519 original size:235 final size:235
Alignment explanation
Indices: 40934147--40934688 Score: 777
Period size: 235 Copynumber: 2.3 Consensus size: 235
40934137 CCCGGGGGGC
* * * * * *
40934147 AAAATGGTAATTTT-AGTGTAATCGGGGTTGAAGATGGAATCTTAAAAGATTCGGGGGTAAAATG
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGATAAAATG
* *
40934211 GTAATTTTTGGTGAAATTAGGGTTAAAAACAGAATTTAGAAGCTTCGAGGGTAAAATGGTAATTT
66 GTAATTTTTGGTGAAATGAGGGTTAAAAACAGAATTTAGAAGATTCGAGGGTAAAATGGTAATTT
* * *
40934276 TCGGTGAAATCGGGGTCAAAAATAGAATTTTAAAAGATTTGGGGGTAAAATGGTAATTTTTGGTG
131 TCGGTGAAATCGAGGTCAAAAATAGAATTTTAAAAGATTCGGGGGTAAAATGGTAATTTTCGGTG
* * * *
40934341 AAATCGGGGTTAAAAATGGAATTTTGGAAGTTTTGGGGAT
196 AAATCAGGGTTAAAAATGGAATTTTAGAAGATTCGGGGAT
* *
40934381 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAGTTTCGGGGATAAAATG
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGATAAAATG
** *
40934446 GTAATTTTTGGTGAAATCGA-GGTT-AAAATGGAATTTTAGAAGATTCGGGGGTAAAATGGTAAT
66 GTAATTTTTGGTGAAAT-GAGGGTTAAAAACAGAA-TTTAGAAGATTCGAGGGTAAAATGGTAAT
* * *
40934509 TTTTGGTGAAATCGAGGTCAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATGGTAATTTTCGG
129 TTTCGGTGAAATCGAGGTCAAAAATAGAATTTTAAAAGATTCGGGGGTAAAATGGTAATTTTCGG
*
40934574 TGAAATCAGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGT
194 TGAAATCAGGGTTAAAAATGGAATTTTAGAAGATTCGGGGAT
* * *
40934616 AAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTCGAGGGTTAAAAT
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCG-GGGATAAAAT
*
40934681 -ATAATTTT
65 GGTAATTTT
40934689 GGAAAAGTTT
Statistics
Matches: 274, Mismatches: 30, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
234 21 0.08
235 243 0.89
236 10 0.04
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (235 bp):
AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGATAAAATG
GTAATTTTTGGTGAAATGAGGGTTAAAAACAGAATTTAGAAGATTCGAGGGTAAAATGGTAATTT
TCGGTGAAATCGAGGTCAAAAATAGAATTTTAAAAGATTCGGGGGTAAAATGGTAATTTTCGGTG
AAATCAGGGTTAAAAATGGAATTTTAGAAGATTCGGGGAT
Found at i:40936244 original size:20 final size:20
Alignment explanation
Indices: 40936219--40936257 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40936209 AGCTGGTGGG
* *
40936219 TGGAGCTGGTGGTCAGCAGA
1 TGGAGCGGGTGGCCAGCAGA
40936239 TGGAGCGGGTGGCCAGCAG
1 TGGAGCGGGTGGCCAGCAG
40936258 CAGTAGGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.49, T:0.15
Consensus pattern (20 bp):
TGGAGCGGGTGGCCAGCAGA
Found at i:40936338 original size:14 final size:14
Alignment explanation
Indices: 40936300--40936352 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
40936290 ATTTGGACTA
*
40936300 TTGTGATTGGGCCC
1 TTGTAATTGGGCCC
40936314 -T-TAATTGGGCCC
1 TTGTAATTGGGCCC
* *
40936326 TTGTAAATGGGCCA
1 TTGTAATTGGGCCC
40936340 TTGTAATTGGGCC
1 TTGTAATTGGGCC
40936353 GTGGGCCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.30
13 2 0.06
14 21 0.64
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.34
Consensus pattern (14 bp):
TTGTAATTGGGCCC
Found at i:40936409 original size:6 final size:6
Alignment explanation
Indices: 40936375--40936470 Score: 74
Period size: 6 Copynumber: 16.0 Consensus size: 6
40936365 CATTTGGACT
* ** *
40936375 TTTAAA TTTAATA TTTTAAT TTTTTA TTTAAA TTTAAA TTCAAA -TTAAA
1 TTTAAA TTTAA-A -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
40936424 TTTAGATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA --TAAA TTTAAA
1 TTTA-A-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40936471 ATCAATTTAA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
4 4 0.06
5 8 0.11
6 46 0.65
7 3 0.04
8 10 0.14
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:40936434 original size:25 final size:23
Alignment explanation
Indices: 40936403--40936461 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 23
40936393 ATTTTTTATT
* *
40936403 TAAATTTAAATTCAAATTAAATT
1 TAAATTTAAATTCAAAATAAATC
*
40936426 TAGATATTTAAATTTAAAATAAATC
1 TA-A-ATTTAAATTCAAAATAAATC
40936451 TAAATTTAAAT
1 TAAATTTAAAT
40936462 AAATTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 10 0.32
24 2 0.06
25 19 0.61
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATTTAAATTCAAAATAAATC
Found at i:40936437 original size:31 final size:31
Alignment explanation
Indices: 40936399--40936472 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
40936389 TTTAATTTTT
*
40936399 TATTTAAATTTAAATTCAAAT-TAAATTTAGA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAGA
40936430 TATTTAAATTTAAAATAAATCTAAATTTA-A
1 TATTTAAATTTAAAATAAATCTAAATTTAGA
40936460 -A--TAAATTTAAAAT
1 TATTTAAATTTAAAAT
40936473 CAATTTAACT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
27 12 0.29
29 1 0.02
30 5 0.12
31 23 0.56
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAGA
Found at i:40936472 original size:17 final size:17
Alignment explanation
Indices: 40936400--40936470 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
40936390 TTAATTTTTT
*
40936400 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAAAT-AA
*
40936418 A-TTAAATTT-AGAT--
1 ATTTAAATTTAAAATAA
40936431 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
40936448 ATCTAAATTT-AAATAA
1 ATTTAAATTTAAAATAA
40936464 ATTTAAA
1 ATTTAAA
40936471 ATCAATTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.18
15 3 0.07
16 14 0.32
17 17 0.39
18 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:40936876 original size:22 final size:22
Alignment explanation
Indices: 40936838--40936909 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
40936828 AACACAACAC
40936838 CAGCAACCTCTCTTGAAAAACCAG
1 CAGC-ACCT-TCTTGAAAAACCAG
* * *
40936862 CAGCATCTTCTTGAAATACCAA
1 CAGCACCTTCTTGAAAAACCAG
* *
40936884 CAGCACCTTCTTGGAAAGCCAG
1 CAGCACCTTCTTGAAAAACCAG
40936906 CAGC
1 CAGC
40936910 CAAGAACCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 33 0.82
23 3 0.08
24 4 0.10
ACGTcount: A:0.33, C:0.32, G:0.15, T:0.19
Consensus pattern (22 bp):
CAGCACCTTCTTGAAAAACCAG
Found at i:40938550 original size:24 final size:26
Alignment explanation
Indices: 40938523--40938571 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
40938513 TATTTTTTAA
40938523 AAAAATTATAAA-AATA-ATAAAAAT
1 AAAAATTATAAAGAATACATAAAAAT
*
40938547 AAAAATTCTAAAGAATACATAAAAA
1 AAAAATTATAAAGAATACATAAAAA
40938572 AAATTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
25 4 0.18
26 7 0.32
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (26 bp):
AAAAATTATAAAGAATACATAAAAAT
Found at i:40939095 original size:20 final size:20
Alignment explanation
Indices: 40939070--40939108 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40939060 AGCTGGTGGG
* *
40939070 TGGAGCTGGTGGTCAGCAGA
1 TGGAGCGGGTGGCCAGCAGA
40939090 TGGAGCGGGTGGCCAGCAG
1 TGGAGCGGGTGGCCAGCAG
40939109 CAGTAGGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.49, T:0.15
Consensus pattern (20 bp):
TGGAGCGGGTGGCCAGCAGA
Found at i:40939189 original size:14 final size:14
Alignment explanation
Indices: 40939151--40939203 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
40939141 ATTTGGACTA
*
40939151 TTGTGATTGGGCCC
1 TTGTAATTGGGCCC
40939165 -T-TAATTGGGCCC
1 TTGTAATTGGGCCC
* *
40939177 TTGTAAATGGGCCA
1 TTGTAATTGGGCCC
40939191 TTGTAATTGGGCC
1 TTGTAATTGGGCC
40939204 GTGGGCCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.30
13 2 0.06
14 21 0.64
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.34
Consensus pattern (14 bp):
TTGTAATTGGGCCC
Found at i:40939260 original size:6 final size:6
Alignment explanation
Indices: 40939226--40939321 Score: 74
Period size: 6 Copynumber: 16.0 Consensus size: 6
40939216 CATTTGGACT
* ** *
40939226 TTTAAA TTTAATA TTTTAAT TTTTTA TTTAAA TTTAAA TTCAAA -TTAAA
1 TTTAAA TTTAA-A -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
40939275 TTTAGATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA --TAAA TTTAAA
1 TTTA-A-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40939322 ATCAATTTAA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
4 4 0.06
5 8 0.11
6 46 0.65
7 3 0.04
8 10 0.14
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:40939285 original size:25 final size:23
Alignment explanation
Indices: 40939254--40939312 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 23
40939244 ATTTTTTATT
* *
40939254 TAAATTTAAATTCAAATTAAATT
1 TAAATTTAAATTCAAAATAAATC
*
40939277 TAGATATTTAAATTTAAAATAAATC
1 TA-A-ATTTAAATTCAAAATAAATC
40939302 TAAATTTAAAT
1 TAAATTTAAAT
40939313 AAATTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 10 0.32
24 2 0.06
25 19 0.61
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATTTAAATTCAAAATAAATC
Found at i:40939288 original size:31 final size:31
Alignment explanation
Indices: 40939250--40939323 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
40939240 TTTAATTTTT
*
40939250 TATTTAAATTTAAATTCAAAT-TAAATTTAGA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAGA
40939281 TATTTAAATTTAAAATAAATCTAAATTTA-A
1 TATTTAAATTTAAAATAAATCTAAATTTAGA
40939311 -A--TAAATTTAAAAT
1 TATTTAAATTTAAAAT
40939324 CAATTTAACT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
27 12 0.29
29 1 0.02
30 5 0.12
31 23 0.56
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAGA
Found at i:40939323 original size:17 final size:17
Alignment explanation
Indices: 40939251--40939321 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
40939241 TTAATTTTTT
*
40939251 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAAAT-AA
*
40939269 A-TTAAATTT-AGAT--
1 ATTTAAATTTAAAATAA
40939282 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
40939299 ATCTAAATTT-AAATAA
1 ATTTAAATTTAAAATAA
40939315 ATTTAAA
1 ATTTAAA
40939322 ATCAATTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.18
15 3 0.07
16 14 0.32
17 17 0.39
18 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:40939764 original size:68 final size:68
Alignment explanation
Indices: 40939654--40940364 Score: 1219
Period size: 68 Copynumber: 10.5 Consensus size: 68
40939644 TGATCTTGCT
* * * *
40939654 CGTGTTATCCACTCTACTTCAATTTCAAAGGGATGACCTTGCTCTTATTTCAATTTCGGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
40939719 CGA
66 AGA
*
40939722 TGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
**
40939787 ATT
66 AGA
*
40939790 CATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
40939855 AGA
66 AGA
40939858 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
40939923 AGA
66 AGA
*
40939926 CGTGGT-TCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
40939990 AGA
66 AGA
*
40939993 CGTGTCATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
40940058 ATA
66 AGA
*
40940061 CGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
40940126 AAA
66 AGA
* *
40940129 CGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
40940194 AAA
66 AGA
*
40940197 CGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
40940262 AGA
66 AGA
* *
40940265 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAAAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
40940330 AGA
66 AGA
*
40940333 CGTGGT-TCCACTCTACTTCAATTTCAAGGGGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGA
40940365 CGATGTTGAG
Statistics
Matches: 615, Mismatches: 27, Indels: 3
0.95 0.04 0.00
Matches are distributed among these distances:
67 91 0.15
68 524 0.85
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (68 bp):
CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
AGA
Found at i:40952390 original size:59 final size:58
Alignment explanation
Indices: 40952329--40952759 Score: 573
Period size: 59 Copynumber: 7.4 Consensus size: 58
40952319 TGGATACCCG
* * * * * *
40952329 GGGGGCAAAATGGTAATTTTGGTGTAATCGGGGTTGAAGATGGAATCTTAAAAGATTC
1 GGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
40952387 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAACGGAA-TTTAGAAGCTTC
1 GGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * * * *
40952444 GAGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAATAGAATTTTAAAAGATTT
1 GGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * *
40952503 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTTT
1 GGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
40952562 GGGGATAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTT-GAAAGTTTC
1 GGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAGATTC
*
40952621 GGGGATAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
*
40952680 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
40952739 GGGGTTAAAAT-ATAATTTTGG
1 GGGGGTAAAATGGTAATTTTGG
40952760 AAAAGTTTTG
Statistics
Matches: 336, Mismatches: 27, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
56 4 0.01
57 40 0.12
58 45 0.13
59 238 0.71
60 9 0.03
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.32
Consensus pattern (58 bp):
GGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
Found at i:40952778 original size:118 final size:118
Alignment explanation
Indices: 40952329--40952757 Score: 632
Period size: 118 Copynumber: 3.7 Consensus size: 118
40952319 TGGATACCCG
* * ** * *
40952329 GGGGGCAAAATGGTAATTTT-GGTGTAATCGGGGTTGAAGATGGAATCTTAAAAGATTCGGGGGT
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAAAAGATTCGGGGGT
* *
40952393 AAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAACGGAA-TTTAGAAGCTTC
66 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * *
40952444 GAGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAATAGAATTTTAAAAGATTTGGGGGT
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAAAAGATTCGGGGGT
* * *
40952509 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTTT
66 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * * * *
40952562 GGGGATAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAGTTTCGGGGAT
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAAAAGATTCGGGGGT
40952627 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
66 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
40952680 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTCGGGGTT
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAAAAGATTCGGGGGT
*
40952745 AAAAT-ATAATTTT
66 AAAATGGTAATTTT
40952758 GGAAAAGTTT
Statistics
Matches: 280, Mismatches: 31, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
115 18 0.06
116 67 0.24
117 15 0.05
118 180 0.64
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.32
Consensus pattern (118 bp):
GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAATGGAATTTTAAAAGATTCGGGGGT
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
Found at i:40954310 original size:20 final size:20
Alignment explanation
Indices: 40954285--40954323 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40954275 AGCTGGTGGG
* *
40954285 TGGAGCTGGTGGTCAGCAGA
1 TGGAGCGGGTGGCCAGCAGA
40954305 TGGAGCGGGTGGCCAGCAG
1 TGGAGCGGGTGGCCAGCAG
40954324 CAGTAGGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.49, T:0.15
Consensus pattern (20 bp):
TGGAGCGGGTGGCCAGCAGA
Found at i:40954404 original size:14 final size:14
Alignment explanation
Indices: 40954366--40954418 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
40954356 ATTTGGACTA
*
40954366 TTGTGATTGGGCCC
1 TTGTAATTGGGCCC
40954380 -T-TAATTGGGCCC
1 TTGTAATTGGGCCC
* *
40954392 TTGTAAATGGGCCA
1 TTGTAATTGGGCCC
40954406 TTGTAATTGGGCC
1 TTGTAATTGGGCC
40954419 GTGGGCCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.30
13 2 0.06
14 21 0.64
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.34
Consensus pattern (14 bp):
TTGTAATTGGGCCC
Found at i:40954475 original size:6 final size:6
Alignment explanation
Indices: 40954441--40954566 Score: 93
Period size: 6 Copynumber: 21.0 Consensus size: 6
40954431 CATTTGGACT
* ** *
40954441 TTTAAA TTTAATA TTTTAAT TTTTTA TTTAAA TTTAAA TTCAAA -TTAAA
1 TTTAAA TTTAA-A -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
40954490 TTTAGATA TTTAAA TTTAAA TTCAAA -TTAAA TTTAGATA TTTAAA -TTAAA
1 TTTA-A-A TTTAAA TTTAAA TTTAAA TTTAAA TTTA-A-A TTTAAA TTTAAA
* *
40954540 -ATAAA TCTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40954567 ATCAATTTAA
Statistics
Matches: 96, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
4 4 0.04
5 17 0.18
6 55 0.57
7 5 0.05
8 15 0.16
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:40954503 original size:31 final size:31
Alignment explanation
Indices: 40954465--40954554 Score: 148
Period size: 31 Copynumber: 2.9 Consensus size: 31
40954455 TTTAATTTTT
40954465 TATTTAAATTTAAATTCAAATTAAATTTAGA
1 TATTTAAATTTAAATTCAAATTAAATTTAGA
40954496 TATTTAAATTTAAATTCAAATTAAATTTAGA
1 TATTTAAATTTAAATTCAAATTAAATTTAGA
*
40954527 TATTTAAA-TTAAAAT-AAATCTAAATTTA
1 TATTTAAATTTAAATTCAAAT-TAAATTTA
40954555 AATAAATTTA
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
29 4 0.07
30 14 0.25
31 39 0.68
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAATTCAAATTAAATTTAGA
Found at i:40954517 original size:43 final size:42
Alignment explanation
Indices: 40954442--40954522 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 42
40954432 ATTTGGACTT
* ** *
40954442 TTAAATTTAATATTTTAATTTTTTATTTAAATTTAAATTCAAA
1 TTAAATTTAATATTTTAAATTTAAATTCAAA-TTAAATTCAAA
40954485 TTAAATTTAGATA-TTTAAATTTAAATTCAAATTAAATT
1 TTAAATTTA-ATATTTTAAATTTAAATTCAAATTAAATT
40954523 TAGATATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
42 7 0.21
43 23 0.70
44 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (42 bp):
TTAAATTTAATATTTTAAATTTAAATTCAAATTAAATTCAAA
Found at i:40954552 original size:16 final size:16
Alignment explanation
Indices: 40954531--40954566 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
40954521 TTTAGATATT
40954531 TAAATTAAAATAAATC
1 TAAATTAAAATAAATC
* *
40954547 TAAATTTAAATAAATT
1 TAAATTAAAATAAATC
40954563 TAAA
1 TAAA
40954567 ATCAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAATTAAAATAAATC
Found at i:40954971 original size:22 final size:22
Alignment explanation
Indices: 40954933--40955004 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
40954923 AACACAACAC
40954933 CAGCAACCTCTCTTGAAAAACCAG
1 CAGC-ACCT-TCTTGAAAAACCAG
* * *
40954957 CAGCATCTTCTTGAAATACCAA
1 CAGCACCTTCTTGAAAAACCAG
* *
40954979 CAGCACCTTCTTGGAAAGCCAG
1 CAGCACCTTCTTGAAAAACCAG
40955001 CAGC
1 CAGC
40955005 CAAGAACCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 33 0.82
23 3 0.08
24 4 0.10
ACGTcount: A:0.33, C:0.32, G:0.15, T:0.19
Consensus pattern (22 bp):
CAGCACCTTCTTGAAAAACCAG
Found at i:40956653 original size:25 final size:27
Alignment explanation
Indices: 40956617--40956667 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
40956607 ATATTTTTTA
40956617 AAAAATTATAAA-AATA-ATAAAAAAT
1 AAAAATTATAAAGAATACATAAAAAAT
*
40956642 AAAAATTCTAAAGAATACATAAAAAA
1 AAAAATTATAAAGAATACATAAAAAA
40956668 ATTAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.48
26 4 0.17
27 8 0.35
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.22
Consensus pattern (27 bp):
AAAAATTATAAAGAATACATAAAAAAT
Found at i:40968195 original size:35 final size:35
Alignment explanation
Indices: 40968155--40968226 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
40968145 TCATTTCGTT
40968155 ATCTATACTCATTATTCATGATCACATCCCATTTC
1 ATCTATACTCATTATTCATGATCACATCCCATTTC
40968190 ATCTATACTCATTATTCATGATCACATCCCATTTC
1 ATCTATACTCATTATTCATGATCACATCCCATTTC
40968225 AT
1 AT
40968227 TAACATACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.29, C:0.28, G:0.03, T:0.40
Consensus pattern (35 bp):
ATCTATACTCATTATTCATGATCACATCCCATTTC
Found at i:40968558 original size:18 final size:17
Alignment explanation
Indices: 40968524--40968571 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
40968514 GGAAGGTTTT
*
40968524 TTTCTCTTCTTTTTTTCC
1 TTTCT-TTCTTTCTTTCC
40968542 TTTCTTTCTTCTCTTTCC
1 TTTCTTTCTT-TCTTTCC
*
40968560 CTTCTTTCTTTC
1 TTTCTTTCTTTC
40968572 CTTTGTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTCTTTCTTTCTTTCC
Found at i:40969242 original size:30 final size:29
Alignment explanation
Indices: 40969186--40969242 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
40969176 CAATAAATCA
**
40969186 TTAATTAAAAATTACAATCATTTGAGCCC
1 TTAATTAAAAATTACAATCAACTGAGCCC
*
40969215 TTAATTAAAAGTTAGCAATCAACTGAGC
1 TTAATTAAAAATTA-CAATCAACTGAGC
40969243 TTTTCAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (29 bp):
TTAATTAAAAATTACAATCAACTGAGCCC
Found at i:40969555 original size:10 final size:9
Alignment explanation
Indices: 40969540--40969616 Score: 54
Period size: 10 Copynumber: 8.3 Consensus size: 9
40969530 ATTTTTCAAA
40969540 TTTATAATAT
1 TTTATAAT-T
40969550 TTTAT-ATT
1 TTTATAATT
40969558 TTTAATAATT
1 TTT-ATAATT
*
40969568 TATATAATT
1 TTTATAATT
40969577 TTCTAT-A--
1 TT-TATAATT
40969584 TTTATAATT
1 TTTATAATT
40969593 GTTTAATAATT
1 -TTT-ATAATT
*
40969604 TCTAATAATT
1 T-TTATAATT
40969614 TTT
1 TTT
40969617 CAAAATTCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 19
0.70 0.05 0.25
Matches are distributed among these distances:
6 3 0.06
7 3 0.06
8 4 0.07
9 13 0.24
10 24 0.44
11 7 0.13
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (9 bp):
TTTATAATT
Found at i:40969583 original size:28 final size:27
Alignment explanation
Indices: 40969542--40969604 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
40969532 TTTTCAAATT
*
40969542 TATAATATTTTATATTTTTAATAATTTA
1 TATAAT-TTTTATATTTATAATAATTTA
**
40969570 TATAATTTTCTATATTTATAATTGTTTA
1 TATAATTTT-TATATTTATAATAATTTA
40969598 -ATAATTT
1 TATAATTT
40969605 CTAATAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.32
28 21 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
TATAATTTTTATATTTATAATAATTTA
Found at i:40969604 original size:18 final size:17
Alignment explanation
Indices: 40969538--40969609 Score: 60
Period size: 16 Copynumber: 4.2 Consensus size: 17
40969528 GTATTTTTCA
* *
40969538 AATTTATAATATTTTAT
1 AATTTTTAATAATTTAT
40969555 -ATTTTTAATAATTTATAT
1 AATTTTTAATAA-TT-TAT
40969573 AATTTTCT-AT-ATTTAT
1 AATTTT-TAATAATTTAT
*
40969589 AATTGTTTAATAATTTCT
1 AATT-TTTAATAATTTAT
40969607 AAT
1 AAT
40969610 AATTTTTCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
16 17 0.38
17 8 0.18
18 12 0.27
19 7 0.16
20 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (17 bp):
AATTTTTAATAATTTAT
Found at i:40974246 original size:150 final size:146
Alignment explanation
Indices: 40973975--40974250 Score: 383
Period size: 150 Copynumber: 1.9 Consensus size: 146
40973965 AATTTCGTAT
* *
40973975 CTATAGTTTAATTTCGAAACAATGAGTCCTTATGTTTTTTTTTTATCAATATGTCCACATATTAG
1 CTATAATTTAATTTCGAAACAATAAGTCCTTATGTTTTTTTTTTATCAATATGTCCACATATTAG
*
40974040 TTGGTGTTAATATAGAATTTATAAGATTTAAATATGCTAAAGGTCTTTGTGCTTTTTTTTAAAAA
66 TTGGTGTTAATATAGAATTTATAAGATTTAAATATGCTAAAGGTCTGTGTGCTTTTTTTTAAAAA
40974105 AAAAATTAAATTTAGC
131 AAAAATTAAATTTAGC
* * * *
40974121 CTATAATTTAATTTTGAGACAATAAGTCGTTGTGCTTTTTTTTTTTATCAATATGTGTCCACATA
1 CTATAATTTAATTTCGAAACAATAAGTCCTTATG--TTTTTTTTTTATCAATA--TGTCCACATA
* * * **
40974186 TTTGTTGGTGTTAATGTAGAATTTATAAGGTTTAAATA-GCTAAAGGTACTAGTGTTTTTTTTTT
62 TTAGTTGGTGTTAATATAGAATTTATAAGATTTAAATATGCTAAAGGT-CT-GTGTGCTTTTTTT
40974250 T
125 T
40974251 TACAATAAAA
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
146 28 0.25
148 17 0.15
149 9 0.08
150 47 0.42
151 11 0.10
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (146 bp):
CTATAATTTAATTTCGAAACAATAAGTCCTTATGTTTTTTTTTTATCAATATGTCCACATATTAG
TTGGTGTTAATATAGAATTTATAAGATTTAAATATGCTAAAGGTCTGTGTGCTTTTTTTTAAAAA
AAAAATTAAATTTAGC
Found at i:40983721 original size:27 final size:27
Alignment explanation
Indices: 40983691--40983742 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
40983681 AATTAGACCC
*
40983691 TAAATTTCTA-AAACCTTCCAATTTACT
1 TAAATTTC-ACAAACATTCCAATTTACT
*
40983718 TAAATTTCACTAACATTCCAATTTA
1 TAAATTTCACAAACATTCCAATTTA
40983743 GTCCTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (27 bp):
TAAATTTCACAAACATTCCAATTTACT
Found at i:40990991 original size:43 final size:43
Alignment explanation
Indices: 40990922--40991100 Score: 175
Period size: 43 Copynumber: 4.2 Consensus size: 43
40990912 TCTTTAGCGG
* * * *
40990922 TAGCGACGCTTTTATC-CAAACGCCGCTATAGAACATGGTCCT
1 TAGCGGCGCTTTTACCACAAACACCGCTAAAGAACATGGTCCT
* * * * * *
40990964 TGGTGGCACTTTTACCGCAAACACCGCTAAAG-ACTATGATCTT
1 TAGCGGCGCTTTTACCACAAACACCGCTAAAGAAC-ATGGTCCT
* * *
40991007 TAGCAGCGCTTTTACCACAAACGCCACTAAAGAACATGG-CCTT
1 TAGCGGCGCTTTTACCACAAACACCGCTAAAGAACATGGTCC-T
* *
40991050 TAGCGGCGTTTTTACCACAAACACCGCTAAAGAACATGGTCTT
1 TAGCGGCGCTTTTACCACAAACACCGCTAAAGAACATGGTCCT
*
40991093 TAACGGCG
1 TAGCGGCG
40991101 GTAAAGACCA
Statistics
Matches: 108, Mismatches: 24, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
42 14 0.13
43 91 0.84
44 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
TAGCGGCGCTTTTACCACAAACACCGCTAAAGAACATGGTCCT
Found at i:40991112 original size:25 final size:25
Alignment explanation
Indices: 40991077--40991124 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40991067 CAAACACCGC
40991077 TAAAGAACATGGTCTTTAACGGCGG
1 TAAAGAACATGGTCTTTAACGGCGG
* * *
40991102 TAAAGACCATGGTTTTTAGCGGC
1 TAAAGAACATGGTCTTTAACGGC
40991125 ACTTTTACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (25 bp):
TAAAGAACATGGTCTTTAACGGCGG
Found at i:40991145 original size:68 final size:68
Alignment explanation
Indices: 40991034--40991162 Score: 186
Period size: 68 Copynumber: 1.9 Consensus size: 68
40991024 CAAACGCCAC
**
40991034 TAAAGAACATGGCCTTTAGCGGCGTTTTTACCACAAACACCGCTAAAGAACATGGTCTTTAACGG
1 TAAAGAACATGGCCTTTAGCGGCACTTTTACCACAAACACCGCTAAAGAACATGGTCTTTAACGG
40991099 CGG
66 CGG
* ** * * *
40991102 TAAAGACCATGGTTTTTAGCGGCACTTTTACCACAAACGCCGCTAAAGATCATGTTCTTTA
1 TAAAGAACATGGCCTTTAGCGGCACTTTTACCACAAACACCGCTAAAGAACATGGTCTTTA
40991163 GCAAACGCCG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 53 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (68 bp):
TAAAGAACATGGCCTTTAGCGGCACTTTTACCACAAACACCGCTAAAGAACATGGTCTTTAACGG
CGG
Found at i:40993715 original size:16 final size:15
Alignment explanation
Indices: 40993689--40993718 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40993679 AACCTGAATC
40993689 CATTAATCAAGAAGG
1 CATTAATCAAGAAGG
40993704 CATTATATCAAGAAG
1 CATTA-ATCAAGAAG
40993719 TTCACCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.23
Consensus pattern (15 bp):
CATTAATCAAGAAGG
Found at i:40998209 original size:82 final size:82
Alignment explanation
Indices: 40998061--40998228 Score: 194
Period size: 82 Copynumber: 2.0 Consensus size: 82
40998051 GAATTCCCTG
* * * * * **
40998061 ACCTTTAGCGGCGCTTATGGAAAAGCGTTGCTAATGCCCTCACATTTAACGACGCTTATTGAAAA
1 ACCTTTAGCGGCGCTTAGGGAAAAGAGCTGCTAATGACCTCACATTTAACGACACTTAGGGAAAA
40998126 GCACCGCTAATGACCTA
66 GCACCGCTAATGACCTA
* * * * *
40998143 ACCTTTAGCGGCGCTTAGGGGAAAGAGCTGCTAATGACCTGACCTTTAGC-AGCACTTAGGGGAA
1 ACCTTTAGCGGCGCTTAGGGAAAAGAGCTGCTAATGACCTCACATTTAACGA-CACTTAGGGAAA
* *
40998207 AGCGCCGCTAATGACCTG
65 AGCACCGCTAATGACCTA
40998225 ACCT
1 ACCT
40998229 AAAGCGGCAC
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
81 1 0.01
82 70 0.99
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (82 bp):
ACCTTTAGCGGCGCTTAGGGAAAAGAGCTGCTAATGACCTCACATTTAACGACACTTAGGGAAAA
GCACCGCTAATGACCTA
Found at i:40998239 original size:41 final size:41
Alignment explanation
Indices: 40998057--40998240 Score: 170
Period size: 41 Copynumber: 4.5 Consensus size: 41
40998047 ATTAGAATTC
* * * ** *
40998057 CCTGACCTTTAGCGGCGCTTATGGAAAAGCGTTGCTAATGC
1 CCTGACCTTTAGCGGCACTTAGGGGAAAGCGCCGCTAATGA
* * * * * ** * *
40998098 CCTCACATTTAACGACGCTTATTGAAAAGCACCGCTAATGA
1 CCTGACCTTTAGCGGCACTTAGGGGAAAGCGCCGCTAATGA
* * * *
40998139 CCTAACCTTTAGCGGCGCTTAGGGGAAAGAGCTGCTAATGA
1 CCTGACCTTTAGCGGCACTTAGGGGAAAGCGCCGCTAATGA
*
40998180 CCTGACCTTTAGCAGCACTTAGGGGAAAGCGCCGCTAATGA
1 CCTGACCTTTAGCGGCACTTAGGGGAAAGCGCCGCTAATGA
**
40998221 CCTGACCTAAAGCGGCACTT
1 CCTGACCTTTAGCGGCACTT
40998241 TTACTTAAAC
Statistics
Matches: 116, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 116 1.00
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (41 bp):
CCTGACCTTTAGCGGCACTTAGGGGAAAGCGCCGCTAATGA
Found at i:41001849 original size:17 final size:17
Alignment explanation
Indices: 41001827--41001875 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 17
41001817 TAGAATGATA
41001827 AATATTAAATTATATTT
1 AATATTAAATTATATTT
* *
41001844 AATATTAAAATAATTTCTTT
1 AATATT-AAAT--TATATTT
41001864 AATATTAAATTA
1 AATATTAAATTA
41001876 ACAAAATACT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 7 0.27
18 4 0.15
19 4 0.15
20 11 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTAAATTATATTT
Found at i:41007225 original size:2 final size:2
Alignment explanation
Indices: 41007218--41007273 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
41007208 AGTCTCAAGT
41007218 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41007260 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
41007274 AAGTGTTAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41019147 original size:14 final size:13
Alignment explanation
Indices: 41019124--41019153 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
41019114 CAGTTGTGTG
41019124 AAATTTAAAATTA
1 AAATTTAAAATTA
41019137 AAATCTTAAAATTA
1 AAAT-TTAAAATTA
41019151 AAA
1 AAA
41019154 AAATCAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATTTAAAATTA
Found at i:41019219 original size:4 final size:4
Alignment explanation
Indices: 41019210--41019236 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
41019200 TTACAATATT
41019210 ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT
41019237 TGAATTGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:41020023 original size:32 final size:33
Alignment explanation
Indices: 41019977--41020045 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
41019967 TCAGACCCTT
41019977 AAAAGTTAG-AAAAA-AATTTTAAATCCCTTAAA
1 AAAAGTTAGAAAAAATAATTTTAAA-CCCTTAAA
**
41020009 AAAAGTT-GACAAAAATAATTTTGGACCCTTAAA
1 AAAAGTTAGA-AAAAATAATTTTAAACCCTTAAA
41020042 AAAA
1 AAAA
41020046 AAAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 1 0.03
32 7 0.22
33 17 0.53
34 7 0.22
ACGTcount: A:0.55, C:0.10, G:0.09, T:0.26
Consensus pattern (33 bp):
AAAAGTTAGAAAAAATAATTTTAAACCCTTAAA
Found at i:41034499 original size:358 final size:358
Alignment explanation
Indices: 41033842--41034559 Score: 1427
Period size: 358 Copynumber: 2.0 Consensus size: 358
41033832 TCCAAGGAGC
41033842 ATGTAATTGCACCGACACACACTCTTGTAATGATAGTTTGTTTAACACTTGCAGTGAAGTGTTCC
1 ATGTAATTGCACCGACACACACTCTTGTAATGATAGTTTGTTTAACACTTGCAGTGAAGTGTTCC
41033907 CCCTTGTTAAGTCACAATGCACCCACATTGAAGTGTCTTTTATTAGTAGAAATAATTATAAACAA
66 CCCTTGTTAAGTCACAATGCACCCACATTGAAGTGTCTTTTATTAGTAGAAATAATTATAAACAA
41033972 AGCTGCAAAATGGCAAGTTAATTCAAGATTCAAAGAATGATACTATTCATTTATTATTAATGCAA
131 AGCTGCAAAATGGCAAGTTAATTCAAGATTCAAAGAATGATACTATTCATTTATTATTAATGCAA
41034037 TTTCAACCATTTATCCAAAAATAGAAGGATTCAACATTTAATCACATTCATCCAATTCATGCATT
196 TTTCAACCATTTATCCAAAAATAGAAGGATTCAACATTTAATCACATTCATCCAATTCATGCATT
41034102 AACATTCCAAATAATTCAAGATTTAAGCATCAAATGAAAAAATTGTGGTCACATTTTTCTTAACT
261 AACATTCCAAATAATTCAAGATTTAAGCATCAAATGAAAAAATTGTGGTCACATTTTTCTTAACT
41034167 ATGCATACTTTCATTCACTAAAAAAATAAATAT
326 ATGCATACTTTCATTCACTAAAAAAATAAATAT
41034200 ATGTAATTGCACCGACACACACTCTTGTAATGATAGTTTGTTTAACACTTGCAGTGAAGTGTTCC
1 ATGTAATTGCACCGACACACACTCTTGTAATGATAGTTTGTTTAACACTTGCAGTGAAGTGTTCC
41034265 CCCTTGTTAAGTCACAATGCACCCACATTGAAGTGTCTTTTATTAGTAGAAATAATTATAAACAA
66 CCCTTGTTAAGTCACAATGCACCCACATTGAAGTGTCTTTTATTAGTAGAAATAATTATAAACAA
*
41034330 AGCTGCAAAATGGCAAGTTAATTCAAGATTCAAAGAATGATACTATTCATTTATTATTGATGCAA
131 AGCTGCAAAATGGCAAGTTAATTCAAGATTCAAAGAATGATACTATTCATTTATTATTAATGCAA
41034395 TTTCAACCATTTATCCAAAAATAGAAGGATTCAACATTTAATCACATTCATCCAATTCATGCATT
196 TTTCAACCATTTATCCAAAAATAGAAGGATTCAACATTTAATCACATTCATCCAATTCATGCATT
41034460 AACATTCCAAATAATTCAAGATTTAAGCATCAAATGAAAAAATTGTGGTCACATTTTTCTTAACT
261 AACATTCCAAATAATTCAAGATTTAAGCATCAAATGAAAAAATTGTGGTCACATTTTTCTTAACT
41034525 ATGCATACTTTCATTCACTAAAAAAATAAATAT
326 ATGCATACTTTCATTCACTAAAAAAATAAATAT
41034558 AT
1 AT
41034560 TCTTAAACTT
Statistics
Matches: 359, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
358 359 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.33
Consensus pattern (358 bp):
ATGTAATTGCACCGACACACACTCTTGTAATGATAGTTTGTTTAACACTTGCAGTGAAGTGTTCC
CCCTTGTTAAGTCACAATGCACCCACATTGAAGTGTCTTTTATTAGTAGAAATAATTATAAACAA
AGCTGCAAAATGGCAAGTTAATTCAAGATTCAAAGAATGATACTATTCATTTATTATTAATGCAA
TTTCAACCATTTATCCAAAAATAGAAGGATTCAACATTTAATCACATTCATCCAATTCATGCATT
AACATTCCAAATAATTCAAGATTTAAGCATCAAATGAAAAAATTGTGGTCACATTTTTCTTAACT
ATGCATACTTTCATTCACTAAAAAAATAAATAT
Found at i:41034711 original size:17 final size:17
Alignment explanation
Indices: 41034691--41034728 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
41034681 AAATGTGAGA
41034691 ACAATGAAAATGCAATG
1 ACAATGAAAATGCAATG
* *
41034708 ACAATTAAAATGTAATG
1 ACAATGAAAATGCAATG
41034725 ACAA
1 ACAA
41034729 CTAGAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (17 bp):
ACAATGAAAATGCAATG
Found at i:41039844 original size:24 final size:22
Alignment explanation
Indices: 41039787--41039847 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 22
41039777 ATTCTTATTT
41039787 AATTAATAAATATATATTTTTAAA
1 AATTAA-AAAT-TATATTTTTAAA
41039811 AATTATAAAATTATATTATTTATAA
1 AATTA-AAAATTATATT-TTTA-AA
*
41039836 ATTTAAAAATTA
1 AATTAAAAATTA
41039848 AACATATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 6 0.18
24 20 0.61
25 7 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTAAAAATTATATTTTTAAA
Found at i:41041517 original size:22 final size:22
Alignment explanation
Indices: 41041492--41041535 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41041482 GAATTCATAA
* *
41041492 TTTAAATCTAAAATTTTAAAAG
1 TTTAAATATAAAATTTGAAAAG
*
41041514 TTTAAATATATAATTTGAAAAG
1 TTTAAATATAAAATTTGAAAAG
41041536 CTTATCACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (22 bp):
TTTAAATATAAAATTTGAAAAG
Found at i:41042741 original size:15 final size:14
Alignment explanation
Indices: 41042721--41042774 Score: 67
Period size: 15 Copynumber: 3.8 Consensus size: 14
41042711 AACTTAATAA
41042721 ATAATATTATAGTAT
1 ATAATATTATA-TAT
41042736 ATAATATTATA-AT
1 ATAATATTATATAT
41042749 AT-ATATATATATAT
1 ATAATAT-TATATAT
41042763 ATAAGTATTATA
1 ATAA-TATTATA
41042775 CTTAATATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.11
13 8 0.23
14 4 0.11
15 16 0.46
16 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (14 bp):
ATAATATTATATAT
Found at i:41042748 original size:8 final size:8
Alignment explanation
Indices: 41042721--41042774 Score: 56
Period size: 8 Copynumber: 6.4 Consensus size: 8
41042711 AACTTAATAA
41042721 ATAATATT
1 ATAATATT
*
41042729 ATAGTA-T
1 ATAATATT
41042736 ATAATATT
1 ATAATATT
41042744 ATAATATAT
1 ATAATAT-T
41042753 ATATATATAT
1 ATA-ATAT-T
41042763 ATAAGTATT
1 ATAA-TATT
41042772 ATA
1 ATA
41042775 CTTAATATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
7 6 0.15
8 13 0.32
9 9 0.22
10 12 0.30
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (8 bp):
ATAATATT
Found at i:41043130 original size:13 final size:13
Alignment explanation
Indices: 41043100--41043149 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
41043090 TTTAACATTG
* *
41043100 CTTTTAATAATTA
1 CTTTTAAAAAGTA
*
41043113 CTTTTAAAAAGTG
1 CTTTTAAAAAGTA
*
41043126 TTTTTAAAAAGTA
1 CTTTTAAAAAGTA
41043139 CTTTTAAAAAG
1 CTTTTAAAAAG
41043150 CTTGGTTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (13 bp):
CTTTTAAAAAGTA
Found at i:41043855 original size:28 final size:28
Alignment explanation
Indices: 41043815--41043883 Score: 138
Period size: 28 Copynumber: 2.5 Consensus size: 28
41043805 TACATGGACC
41043815 GATTATTTAACTAGTAAATAAAGTACAA
1 GATTATTTAACTAGTAAATAAAGTACAA
41043843 GATTATTTAACTAGTAAATAAAGTACAA
1 GATTATTTAACTAGTAAATAAAGTACAA
41043871 GATTATTTAACTA
1 GATTATTTAACTA
41043884 CACAAATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35
Consensus pattern (28 bp):
GATTATTTAACTAGTAAATAAAGTACAA
Found at i:41045262 original size:20 final size:20
Alignment explanation
Indices: 41045237--41045285 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
41045227 AATCGAATCG
* * *
41045237 AGTCAATTCAAAAAATTTTA
1 AGTCAAGTCAAAAAAATTCA
41045257 AGTCAAGTCAAAAAAATTCA
1 AGTCAAGTCAAAAAAATTCA
41045277 AGTCAAGTC
1 AGTCAAGTC
41045286 GAGTTGAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (20 bp):
AGTCAAGTCAAAAAAATTCA
Found at i:41047140 original size:3 final size:3
Alignment explanation
Indices: 41047132--41047163 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41047122 CTTATTCGAT
41047132 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41047164 TTAAAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41047739 original size:10 final size:10
Alignment explanation
Indices: 41047726--41047764 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
41047716 ATAAATAGAT
41047726 ATAAAAATAA
1 ATAAAAATAA
*
41047736 ATAAAGATGAA
1 ATAAAAAT-AA
*
41047747 ATAAGAATAA
1 ATAAAAATAA
41047757 ATAAAAAT
1 ATAAAAAT
41047765 TATACAAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (10 bp):
ATAAAAATAA
Found at i:41048622 original size:20 final size:20
Alignment explanation
Indices: 41048597--41048661 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
41048587 AAACCGCATA
*
41048597 AAAAATAACATCCAAACAAC
1 AAAAATAACAACCAAACAAC
41048617 AAAAATAACAACCAAAACAGCAAC
1 AAAAATAACAACC--AA-A-CAAC
* *
41048641 AAAAATAACAGCAAAACAAC
1 AAAAATAACAACCAAACAAC
41048661 A
1 A
41048662 TTAAAAACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 17 0.45
21 1 0.03
22 4 0.11
23 1 0.03
24 15 0.39
ACGTcount: A:0.68, C:0.23, G:0.03, T:0.06
Consensus pattern (20 bp):
AAAAATAACAACCAAACAAC
Found at i:41048628 original size:12 final size:12
Alignment explanation
Indices: 41048611--41048656 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
41048601 ATAACATCCA
41048611 AACAACAAAAAT
1 AACAACAAAAAT
* *
41048623 AACAACCAAAAC
1 AACAACAAAAAT
*
41048635 AGCAACAAAAAT
1 AACAACAAAAAT
*
41048647 AACAGCAAAA
1 AACAACAAAA
41048657 CAACATTAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.70, C:0.22, G:0.04, T:0.04
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:41048645 original size:24 final size:23
Alignment explanation
Indices: 41048613--41048658 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
41048603 AACATCCAAA
41048613 CAACAAAAATAACAACCAAAACAG
1 CAACAAAAATAAC-ACCAAAACAG
*
41048637 CAACAAAAATAACAGCAAAACA
1 CAACAAAAATAACACCAAAACA
41048659 ACATTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.67, C:0.24, G:0.04, T:0.04
Consensus pattern (23 bp):
CAACAAAAATAACACCAAAACAG
Found at i:41048646 original size:44 final size:43
Alignment explanation
Indices: 41048585--41048693 Score: 121
Period size: 44 Copynumber: 2.5 Consensus size: 43
41048575 AAACAATAGT
* * *
41048585 AAAAACCGCATAAAAAATAACATCCAAACAACA-AAAATAACAAC
1 AAAAACAGCA-AAAAAATAACAGCAAAACAACATAAAA-AACAAC
* * *
41048629 CAAAACAGCAACAAAAATAACAGCAAAACAACATTAAAAACAAT
1 AAAAACAGCAA-AAAAATAACAGCAAAACAACATAAAAAACAAC
*
41048673 AAAAATAGCAAAAAAATAACA
1 AAAAACAGCAAAAAAATAACA
41048694 AAGATAACAG
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
43 11 0.20
44 41 0.75
45 3 0.05
ACGTcount: A:0.68, C:0.19, G:0.04, T:0.09
Consensus pattern (43 bp):
AAAAACAGCAAAAAAATAACAGCAAAACAACATAAAAAACAAC
Found at i:41048759 original size:21 final size:22
Alignment explanation
Indices: 41048716--41048786 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 22
41048706 AAACAGTATG
* *
41048716 AAAACAACAACCAAACAACAGTAA
1 AAAACAATAACC--ACAAAAGTAA
* *
41048740 AAAATAA-CACCACAAAAGTAA
1 AAAACAATAACCACAAAAGTAA
41048761 AAAACAATAACCA-AAACAGTAA
1 AAAACAATAACCACAAA-AGTAA
41048783 AAAA
1 AAAA
41048787 AGCACCAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 18 0.45
22 13 0.32
23 3 0.08
24 6 0.15
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (22 bp):
AAAACAATAACCACAAAAGTAA
Found at i:41048793 original size:20 final size:20
Alignment explanation
Indices: 41048699--41048798 Score: 76
Period size: 22 Copynumber: 4.6 Consensus size: 20
41048689 TAACAAAGAT
* *
41048699 AACAGCAAAACAGTATGAAAAC
1 AACACCAAAACAGTA--AAAAA
41048721 AACAACCAAACAACAGTAAAAAA
1 AAC-ACC-AA-AACAGTAAAAAA
41048744 TAACACCACAAA-AGTAAAAAA
1 -AACACCA-AAACAGTAAAAAA
*
41048765 CAATAACCAAAACAGTAAAAAA
1 -AA-CACCAAAACAGTAAAAAA
*
41048787 AGCACCAAAACA
1 AACACCAAAACA
41048799 TCAAATATAA
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
20 9 0.14
21 15 0.23
22 19 0.29
23 10 0.15
24 5 0.08
25 7 0.11
ACGTcount: A:0.65, C:0.21, G:0.07, T:0.07
Consensus pattern (20 bp):
AACACCAAAACAGTAAAAAA
Found at i:41049101 original size:24 final size:23
Alignment explanation
Indices: 41049038--41049102 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
41049028 AATTTTGGTG
*
41049038 AAATCAAAAGTTTTCT-TTTTCTTT
1 AAATCAAAA-TTTT-TATTTTCTTA
**
41049062 AAA-CAAAATTACTATTTTCTTAA
1 AAATCAAAATTTTTATTTTCTT-A
41049085 AAATCAAAATTTTTATTT
1 AAATCAAAATTTTTATTT
41049103 CGAAATGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
21 1 0.03
22 9 0.27
23 8 0.24
24 15 0.45
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATCAAAATTTTTATTTTCTTA
Found at i:41049240 original size:142 final size:139
Alignment explanation
Indices: 41049053--41049519 Score: 509
Period size: 142 Copynumber: 3.3 Consensus size: 139
41049043 AAAAGTTTTC
* * *
41049053 TTTTTCTTTAAACAAAATTACTATTTTCTTAAAAATCAAAATTTTTATTTCGAAATGGTT-AAAA
1 TTTTTTTTTAAA-AAAATTATTATTTTCTTAAAAATCAAAATTTTTATTTCAAAATGGTTAAAAA
41049117 A-AAAACTTTATTTAAAAATTTTAATTTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTT
65 ATAAAACTTTATTTAAAAA-TTTAATTTTTTTCTTTAAAATGACTAAAAAACATATTTTTA-TTT
41049181 TTAAAACCTTAAA
128 TTAAAA-CTTAAA
* * *
41049194 GTTTATTTTTTAAAAAAATTATTATTTTTTTAAAAATTAAAGTTTTTATTTCTAAAA-GAGTTAA
1 -TTT-TTTTTTAAAAAAATTATTATTTTCTTAAAAATCAAAATTTTTATTTC-AAAATG-GTT-A
* * * *
41049258 AAAAATAAAACTTTATTTAAAAAAATTAAAATTTTTCCTTTAAAATGATTAAAAAAACATATTTT
61 AAAAATAAAACTTTATTT--AAAAATTTAATTTTTTTCTTTAAAATGACT-AAAAAACATATTTT
* *
41049323 TATTTTTAAAATTTGAA
123 TATTTTTAAAACTTAAA
* * * * * * *
41049340 CTTTTTTTAAAAAAAATAATCA-CTACTTAAAAATCAAAATTTTTATTTCAAAATAGTTAAAAAA
1 TTTTTTTTTAAAAAAATTATTATTTTCTTAAAAATCAAAATTTTTATTTCAAAATGGTT-AAAAA
*
41049404 ATCAAAACTTTATTTAAAAATTTAATTTTTTTCCTTTAAAATGACTAAAAAACATATTCTTATTT
65 AT-AAAACTTTATTTAAAAATTTAATTTTTTT-CTTTAAAATGACTAAAAAACATATTTTTATTT
41049469 TTAGAAA-TCTAAA
128 TTA-AAACT-TAAA
*
41049482 CTTTTTTTTTTAAAAAACACTATT-TTTTC-T-AAAATCAA
1 --TTTTTTTTTAAAAAA-ATTATTATTTTCTTAAAAATCAA
41049520 GTTATTTTTC
Statistics
Matches: 272, Mismatches: 35, Indels: 35
0.80 0.10 0.10
Matches are distributed among these distances:
141 36 0.13
142 71 0.26
143 56 0.21
144 30 0.11
145 12 0.04
146 16 0.06
147 30 0.11
148 21 0.08
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (139 bp):
TTTTTTTTTAAAAAAATTATTATTTTCTTAAAAATCAAAATTTTTATTTCAAAATGGTTAAAAAA
TAAAACTTTATTTAAAAATTTAATTTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTTTA
AAACTTAAA
Found at i:41049497 original size:143 final size:142
Alignment explanation
Indices: 41049080--41049498 Score: 526
Period size: 142 Copynumber: 2.9 Consensus size: 142
41049070 TTACTATTTT
* *
41049080 CTTAAAAATCAAAATTTTTATTTCGAAATGGTT--AAAAA-AAAACTTTATTTAAAAATTTTAAT
1 CTTAAAAATCAAAATTTTTATTTCAAAATAGTTAAAAAAATAAAACTTTATTTAAAAA-TTTAAT
* *
41049142 TTTTTT-CTTTAAAATGACTAAAAAACATATTTTTATTTTTTAAAACCTTAAAGTTTATTTTTTA
65 TTTTTTCCTTTAAAATGACTAAAAAACATATTTTTA-TTTTTAAAATC-TAAACTTT-TTTTTTA
* * * *
41049206 AAAAAATTATTATTTT
127 AAAAAATAATCATCTA
* * * * *
41049222 TTTAAAAATTAAAGTTTTTATTTCTAAAAGAGTTAAAAAAATAAAACTTTATTTAAAAAAATTAA
1 CTTAAAAATCAAAATTTTTATTTC-AAAATAGTTAAAAAAATAAAACTTTATTT-AAAAATTTAA
** * * * *
41049287 AATTTTTCCTTTAAAATGATTAAAAAAACATATTTTTATTTTTAAAATTTGAAC-TTTTTTTAAA
64 TTTTTTTCCTTTAAAATGACT-AAAAAACATATTTTTATTTTTAAAATCTAAACTTTTTTTTTAA
41049351 AAAAATAATCA-CTA
128 AAAAATAATCATCTA
41049365 CTTAAAAATCAAAATTTTTATTTCAAAATAGTTAAAAAAATCAAAACTTTATTTAAAAATTTAAT
1 CTTAAAAATCAAAATTTTTATTTCAAAATAGTTAAAAAAAT-AAAACTTTATTTAAAAATTTAAT
* *
41049430 TTTTTTCCTTTAAAATGACTAAAAAACATATTCTTATTTTTAGAAATCTAAACTTTTTTTTTTAA
65 TTTTTTCCTTTAAAATGACTAAAAAACATATTTTTATTTTTA-AAATCTAAACTTTTTTTTTAAA
41049495 AAAA
129 AAAA
41049499 CACTATTTTT
Statistics
Matches: 235, Mismatches: 32, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
141 21 0.09
142 72 0.31
143 53 0.23
144 16 0.07
145 7 0.03
146 24 0.10
147 26 0.11
148 16 0.07
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (142 bp):
CTTAAAAATCAAAATTTTTATTTCAAAATAGTTAAAAAAATAAAACTTTATTTAAAAATTTAATT
TTTTTCCTTTAAAATGACTAAAAAACATATTTTTATTTTTAAAATCTAAACTTTTTTTTTAAAAA
AATAATCATCTA
Found at i:41050296 original size:27 final size:27
Alignment explanation
Indices: 41050186--41050296 Score: 89
Period size: 27 Copynumber: 3.9 Consensus size: 27
41050176 ATTTAATAAA
41050186 TTTAGGTACCAAATT-GAATCTAAAAAAAG
1 TTTAGGTACCAAATTAGAA---AAAAAAAG
* *
41050215 CTTAGGTACCAGAATAAGAAAAAAATGTCAAG
1 TTTAGGTACCA-AATTAGAAAAAAA----AAG
* * **
41050247 TTCAGGTACCAAATTGGGTAAAAAAAG
1 TTTAGGTACCAAATTAGAAAAAAAAAG
41050274 TTTAGGTACCAAATTAGAAAAAA
1 TTTAGGTACCAAATTAGAAAAAA
41050297 GTGTTAAATT
Statistics
Matches: 64, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
27 22 0.34
28 5 0.08
29 10 0.16
30 3 0.05
31 12 0.19
32 12 0.19
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (27 bp):
TTTAGGTACCAAATTAGAAAAAAAAAG
Found at i:41050309 original size:58 final size:58
Alignment explanation
Indices: 41050183--41050377 Score: 230
Period size: 58 Copynumber: 3.3 Consensus size: 58
41050173 AATATTTAAT
* ** * *
41050183 AAATTTAGGTACCAAATTGAATCTAAAAAAAGCTTAGGTACCAGAATAAGAAAAAAATGTC
1 AAATTCAGGTACCAAATTG--GGTAAAAAAAGTTTAGGTACCA-AATTAGAAAAAAATGTC
* * *
41050244 AAGTTCAGGTACCAAATTGGGTAAAAAAAGTTTAGGTACCAAATTAGAAAAAAGTGTT
1 AAATTCAGGTACCAAATTGGGTAAAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTC
* ** *
41050302 AAATTCAGGTATCAAATTGGGTCAAAAAAAGTTTAAATATCAAATTA-AAAAAAATGTC
1 AAATTCAGGTACCAAATTGGGT-AAAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTC
*
41050360 AAATTCAGATACCAAATT
1 AAATTCAGGTACCAAATT
41050378 CTATATTAAA
Statistics
Matches: 116, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
58 59 0.51
59 40 0.34
61 17 0.15
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (58 bp):
AAATTCAGGTACCAAATTGGGTAAAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTC
Found at i:41057235 original size:24 final size:23
Alignment explanation
Indices: 41057208--41057271 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
41057198 TCATCAACAT
41057208 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* * ***
41057232 TGTTCATAAACATGTTTGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
41057255 TGTTCGTGAACATGTTC
1 TGTTCGTGAACATGTTC
41057272 GATGAAGTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:41057305 original size:23 final size:23
Alignment explanation
Indices: 41057261--41057306 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
41057251 TTAATGTTCG
*
41057261 TGAACATGTTCGATGAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
41057284 TGAACATGTTC-ATGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
41057307 CAAACGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:41060109 original size:16 final size:16
Alignment explanation
Indices: 41060074--41060115 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
41060064 TAAAATTTTA
41060074 AAAAT-AAAATTAACC
1 AAAATAAAAATTAACC
*
41060089 AAAATAAAAATTTACC
1 AAAATAAAAATTAACC
41060105 AAAATAGAAAA
1 AAAATA-AAAA
41060116 GAAAGACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 5 0.21
16 15 0.62
17 4 0.17
ACGTcount: A:0.69, C:0.10, G:0.02, T:0.19
Consensus pattern (16 bp):
AAAATAAAAATTAACC
Found at i:41065913 original size:31 final size:32
Alignment explanation
Indices: 41065845--41065915 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
41065835 GTTTTGGATT
*
41065845 CCTTAAAAGCTGGAGAAAATTTTTTTTAAGCT
1 CCTTAAAAGCTGGAGAAAATTTTTTTTAAGCC
* * * *
41065877 TCTTAAAAGTTGG-TAAAATTTTTTTTGAGCC
1 CCTTAAAAGCTGGAGAAAATTTTTTTTAAGCC
41065908 CCTTAAAA
1 CCTTAAAA
41065916 ATTGAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 22 0.67
32 11 0.33
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (32 bp):
CCTTAAAAGCTGGAGAAAATTTTTTTTAAGCC
Found at i:41068602 original size:14 final size:15
Alignment explanation
Indices: 41068575--41068603 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41068565 TACTTCTTAC
41068575 AAATAATCATATAAA
1 AAATAATCATATAAA
41068590 AAATAAT-ATATAAA
1 AAATAATCATATAAA
41068604 TCGATTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATAATCATATAAA
Found at i:41073644 original size:10 final size:10
Alignment explanation
Indices: 41073621--41073668 Score: 55
Period size: 10 Copynumber: 4.7 Consensus size: 10
41073611 AGATTTGATG
41073621 ATTTTT-GTA
1 ATTTTTAGTA
41073630 A-TTTTAGTA
1 ATTTTTAGTA
41073639 ATTTTTTAAAGTA
1 A-TTTTT--AGTA
41073652 ATTTTTAGTA
1 ATTTTTAGTA
41073662 ATTTTTA
1 ATTTTTA
41073669 TGTTAAAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 4 0.12
9 5 0.15
10 11 0.32
11 4 0.12
12 5 0.15
13 5 0.15
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.60
Consensus pattern (10 bp):
ATTTTTAGTA
Found at i:41080603 original size:15 final size:15
Alignment explanation
Indices: 41080583--41080616 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
41080573 TTGCTTTTAA
41080583 TGTTGGAGTCAATTC
1 TGTTGGAGTCAATTC
41080598 TGTTGGAGTCAATTC
1 TGTTGGAGTCAATTC
41080613 TGTT
1 TGTT
41080617 TTGATTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.44
Consensus pattern (15 bp):
TGTTGGAGTCAATTC
Found at i:41094422 original size:25 final size:24
Alignment explanation
Indices: 41094377--41094423 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
41094367 TTTTTATTTT
* **
41094377 TTTAAAAATTTTTATTTTAAATTA
1 TTTAAAAATTTGTATGCTAAATTA
41094401 TTTAAAAATTATGTATGCTAAAT
1 TTTAAAAATT-TGTATGCTAAAT
41094424 CAGTAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (24 bp):
TTTAAAAATTTGTATGCTAAATTA
Found at i:41094704 original size:2 final size:2
Alignment explanation
Indices: 41094697--41094728 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41094687 CACCTTCTTC
41094697 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41094729 TTCTTCTGTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:41095939 original size:12 final size:12
Alignment explanation
Indices: 41095917--41095948 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
41095907 TTTCTCACCC
41095917 AAAGTAAAAAAAG
1 AAAG-AAAAAAAG
41095930 AAAGAAAAAAAG
1 AAAGAAAAAAAG
41095942 AAAGAAA
1 AAAGAAA
41095949 GGACACTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:41100096 original size:14 final size:14
Alignment explanation
Indices: 41100077--41100103 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41100067 GATGAACATT
41100077 ATTAGTTATGATTA
1 ATTAGTTATGATTA
41100091 ATTAGTTATGATT
1 ATTAGTTATGATT
41100104 GGGATTTAGT
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:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (14 bp):
ATTAGTTATGATTA
Found at i:41107262 original size:102 final size:104
Alignment explanation
Indices: 41107143--41107329 Score: 270
Period size: 102 Copynumber: 1.8 Consensus size: 104
41107133 TGGTATAACC
* * *
41107143 AAATTTTGGTCTCTCATGGCAATAACAAAATTGATGAG-GAATACCAAAA-TTTTAAAAATGTAT
1 AAATTTTGGTCTCTCATGGCAATAACAAAATTGATAAGTGAATACCAAAATTTTTAAAAACGAAT
41107206 CCTTAGATATATAACAAAATATCTAAGAAAAATCATTGG
66 CCTTAGATATATAACAAAATATCTAAGAAAAATCATTGG
* * ** * *
41107245 AAATTTTGGTTTCTCATGTCAATAACAAAATTTCTAAGTGAATATCAAAATTTTTAACAACGAAT
1 AAATTTTGGTCTCTCATGGCAATAACAAAATTGATAAGTGAATACCAAAATTTTTAAAAACGAAT
*
41107310 CTTTAGATATATAACAAAAT
66 CCTTAGATATATAACAAAAT
41107330 TGTTAGTAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
102 33 0.45
103 10 0.14
104 30 0.41
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (104 bp):
AAATTTTGGTCTCTCATGGCAATAACAAAATTGATAAGTGAATACCAAAATTTTTAAAAACGAAT
CCTTAGATATATAACAAAATATCTAAGAAAAATCATTGG
Found at i:41110618 original size:27 final size:27
Alignment explanation
Indices: 41110460--41110614 Score: 172
Period size: 27 Copynumber: 5.8 Consensus size: 27
41110450 CAAGCCCTTC
*
41110460 CAGAAT-ATAGCTCATTCGAGCCCAGA-A
1 CAGAATAAT-GCTCGTTCGAG-CCAGATA
* * * *
41110487 CA-AATTATGCTCATTCGACCCAAATA
1 CAGAATAATGCTCGTTCGAGCCAGATA
* *
41110513 CAGAATAATGCTCTTTCAAGCCAGATA
1 CAGAATAATGCTCGTTCGAGCCAGATA
*
41110540 CAGAATAATGCTCGTTTGAGCCAGATA
1 CAGAATAATGCTCGTTCGAGCCAGATA
* * *
41110567 TAGAATAATGATCGTTCGAGCTAGATA
1 CAGAATAATGCTCGTTCGAGCCAGATA
41110594 CAGAATAATGCTCGTTCGAGC
1 CAGAATAATGCTCGTTCGAGC
41110615 TAGAGTTTAG
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
25 4 0.04
26 16 0.15
27 89 0.82
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (27 bp):
CAGAATAATGCTCGTTCGAGCCAGATA
Found at i:41111289 original size:31 final size:31
Alignment explanation
Indices: 41111254--41111341 Score: 131
Period size: 31 Copynumber: 2.8 Consensus size: 31
41111244 TGTTGTTAAG
* ** *
41111254 GTCTAAAAAGCAGCAGGTACTTTGTACCGGT
1 GTCTAAAAAGTATTAGGTACTTTGTACCGAT
41111285 GTCTAAAAAGTATTAGGTACTTTGTACCGAT
1 GTCTAAAAAGTATTAGGTACTTTGTACCGAT
*
41111316 GTCTACAAAGTATTAGGTACTTTGTA
1 GTCTAAAAAGTATTAGGTACTTTGTA
41111342 TCCGTGTTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.33
Consensus pattern (31 bp):
GTCTAAAAAGTATTAGGTACTTTGTACCGAT
Found at i:41118640 original size:29 final size:29
Alignment explanation
Indices: 41118601--41118680 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
41118591 TTCATATTTT
41118601 AATAATAATTATATTAAAAATAT-TATTA
1 AATAATAATTATATTAAAAATATGTATTA
* * ** *
41118629 AATTATATATTATTTTATTAAT-TGTATTT
1 AATAATA-ATTATATTAAAAATATGTATTA
*
41118658 AATAATAATTATGTTAAAAATAT
1 AATAATAATTATATTAAAAATAT
41118681 AATAAAATAA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
28 18 0.45
29 22 0.55
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
AATAATAATTATATTAAAAATATGTATTA
Found at i:41118664 original size:57 final size:58
Alignment explanation
Indices: 41118598--41118724 Score: 161
Period size: 57 Copynumber: 2.2 Consensus size: 58
41118588 TAATTCATAT
* * * * *
41118598 TTTAATAATAATTATATTAAAAATATTATTAAAT-TA-TATATTATTTTATTA-ATTGTA
1 TTTAATAATAATTATATTAAAAATATAATAAAATAAATTAAATT-TTTT-TTACATTATA
*
41118655 TTTAATAATAATTATGTTAAAAATATAATAAAATAAATTAAATTTTTTTTACATTATA
1 TTTAATAATAATTATATTAAAAATATAATAAAATAAATTAAATTTTTTTTACATTATA
41118713 TTTAATAATAAT
1 TTTAATAATAAT
41118725 CATTAAAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
57 34 0.56
58 22 0.36
59 5 0.08
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (58 bp):
TTTAATAATAATTATATTAAAAATATAATAAAATAAATTAAATTTTTTTTACATTATA
Found at i:41122529 original size:39 final size:44
Alignment explanation
Indices: 41122474--41122578 Score: 114
Period size: 46 Copynumber: 2.5 Consensus size: 44
41122464 TTTCTTATGC
*
41122474 TATTACAGCATC-ATTCCATT-CAACCAA-ACACAA-GAA-TA-T
1 TATTACAGC-TCTATTCCATTCCAACCAACAAACAATGAATTACT
*
41122513 TATTACAGCTCTATTCCATTCCAATCAACCAAACAATTGAATTACT
1 TATTACAGCTCTATTCCATTCCAACCAA-CAAACAA-TGAATTACT
*
41122559 GATTACAGCTCTATTCCATT
1 TATTACAGCTCTATTCCATT
41122579 ACAGCTATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
38 2 0.04
39 17 0.31
40 6 0.11
42 5 0.09
44 3 0.05
45 2 0.04
46 20 0.36
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (44 bp):
TATTACAGCTCTATTCCATTCCAACCAACAAACAATGAATTACT
Found at i:41122577 original size:46 final size:44
Alignment explanation
Indices: 41122485--41122578 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
41122475 ATTACAGCAT
* *
41122485 CATTCCATTCAACCAAACACAAGAATATTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
*
41122529 CATTCCAATCAACCAAACA-ATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACA-AGAA-TA-TGATTACAGCTCTATTC
41122575 CATT
1 CATT
41122579 ACAGCTATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 2 0.05
46 20 0.45
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
Found at i:41122581 original size:16 final size:16
Alignment explanation
Indices: 41122560--41122631 Score: 117
Period size: 16 Copynumber: 4.5 Consensus size: 16
41122550 TGAATTACTG
41122560 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
41122576 ATTACAGCTATATTCC
1 ATTACAGCTCTATTCC
*
41122592 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
*
41122608 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
41122624 ATTACAGC
1 ATTACAGC
41122632 GAACCAAACG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.28, C:0.32, G:0.04, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:41129405 original size:25 final size:23
Alignment explanation
Indices: 41129377--41129422 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
41129367 GTTGGATCCA
41129377 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
41129402 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
41129423 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:41129509 original size:13 final size:13
Alignment explanation
Indices: 41129488--41129521 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
41129478 GCAATATAAT
41129488 AATAATAATCCTA
1 AATAATAATCCTA
*
41129501 AATATTAATCCTA
1 AATAATAATCCTA
*
41129514 AAAAATAA
1 AATAATAA
41129522 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:41130472 original size:11 final size:11
Alignment explanation
Indices: 41130450--41130485 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
41130440 CTCAAACATA
41130450 CTTTTGTCTTTT
1 CTTTT-TCTTTT
41130462 CTTTTTCTTTT
1 CTTTTTCTTTT
*
41130473 CTTTTTTTTTT
1 CTTTTTCTTTT
41130484 CT
1 CT
41130486 CAATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.81
Consensus pattern (11 bp):
CTTTTTCTTTT
Found at i:41130512 original size:24 final size:24
Alignment explanation
Indices: 41130475--41130529 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
41130465 TTTCTTTTCT
41130475 TTTTTTTTTCTCAATTTTTTTCAA
1 TTTTTTTTTCTCAATTTTTTTCAA
*
41130499 TTCTTTTTTT-TCAATTTTTTTCGA
1 TT-TTTTTTTCTCAATTTTTTTCAA
41130523 TTTTTTT
1 TTTTTTT
41130530 CTTTTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 5 0.17
24 17 0.59
25 7 0.24
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTTTTTTCTCAATTTTTTTCAA
Found at i:41130518 original size:9 final size:10
Alignment explanation
Indices: 41130478--41130530 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 10
41130468 CTTTTCTTTT
41130478 TTTTTTCTCAA
1 TTTTTT-TCAA
41130489 TTTTTTTCAA
1 TTTTTTTCAA
41130499 TTCTTTTTTTTCAA
1 ----TTTTTTTCAA
*
41130513 TTTTTTTCGA
1 TTTTTTTCAA
41130523 TTTTTTTC
1 TTTTTTTC
41130531 TTTTTTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
10 21 0.57
11 6 0.16
14 10 0.27
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:41130529 original size:13 final size:14
Alignment explanation
Indices: 41130489--41130519 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
41130479 TTTTTCTCAA
41130489 TTTTTTTCAATTCT
1 TTTTTTTCAATTCT
41130503 TTTTTTTCAATT-T
1 TTTTTTTCAATTCT
41130516 TTTT
1 TTTT
41130520 CGATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTTCAATTCT
Done.