Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 20 of 173
Found at i:5613058 original size:21 final size:22
Alignment explanation
Indices: 5613032--5613080 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
5613022 AATACCTTCT
*
5613032 GAAAAAAAACA-TATTTTAAAA
1 GAAAAAAAACATTATTCTAAAA
* *
5613053 GAAAAAAAATATTATTCTAATA
1 GAAAAAAAACATTATTCTAAAA
5613075 GAAAAA
1 GAAAAA
5613081 CTGAAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.24
Consensus pattern (22 bp):
GAAAAAAAACATTATTCTAAAA
Found at i:5615862 original size:24 final size:24
Alignment explanation
Indices: 5615833--5615914 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
5615823 GTCTTCATCT
**
5615833 TCTTCATCTTCCCCTCGACCCCCG
1 TCTTCATCTTCATCTCGACCCCCG
* *
5615857 TATTCATCTTCATCTCGACCCTCG
1 TCTTCATCTTCATCTCGACCCCCG
* * *
5615881 CCTTCATTTTCATCTCCACCCCCG
1 TCTTCATCTTCATCTCGACCCCCG
5615905 TCTTCATCTT
1 TCTTCATCTT
5615915 TGTCTCCATC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.12, C:0.45, G:0.06, T:0.37
Consensus pattern (24 bp):
TCTTCATCTTCATCTCGACCCCCG
Found at i:5615920 original size:24 final size:24
Alignment explanation
Indices: 5615850--5615922 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
5615840 CTTCCCCTCG
* * *
5615850 ACCCCCGTATTCATCTTCATCTCG
1 ACCCCCGTCTTCATCTTTATCTCC
* *
5615874 ACCCTCGCCTTCAT-TTTCATCTCC
1 ACCCCCGTCTTCATCTTT-ATCTCC
*
5615898 ACCCCCGTCTTCATCTTTGTCTCC
1 ACCCCCGTCTTCATCTTTATCTCC
5615922 A
1 A
5615923 TCTCCTTCTT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
23 2 0.05
24 34 0.87
25 3 0.08
ACGTcount: A:0.14, C:0.44, G:0.07, T:0.36
Consensus pattern (24 bp):
ACCCCCGTCTTCATCTTTATCTCC
Found at i:5617869 original size:16 final size:18
Alignment explanation
Indices: 5617838--5617872 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
5617828 AAAATAGTTT
5617838 AAAATATTTTAGAAATTA
1 AAAATATTTTAGAAATTA
5617856 AAAAT-TTTTA-AAATTA
1 AAAATATTTTAGAAATTA
5617872 A
1 A
5617873 CTTAGTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 5 0.29
18 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AAAATATTTTAGAAATTA
Found at i:5619620 original size:18 final size:16
Alignment explanation
Indices: 5619588--5619621 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
5619578 CAAAATATCT
5619588 AAAAATTTTAAATTTA
1 AAAAATTTTAAATTTA
5619604 AAAAATTATTAAAATTTA
1 AAAAATT-TT-AAATTTA
5619622 CTTTAGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAAATTTTAAATTTA
Found at i:5620343 original size:17 final size:17
Alignment explanation
Indices: 5620321--5620354 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5620311 TTAGATCTAT
5620321 TCTATCAAGTTATTTGA
1 TCTATCAAGTTATTTGA
*
5620338 TCTATCGAGTTATTTGA
1 TCTATCAAGTTATTTGA
5620355 AGATGCACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (17 bp):
TCTATCAAGTTATTTGA
Found at i:5620486 original size:19 final size:19
Alignment explanation
Indices: 5620462--5620501 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5620452 TTTATTTTTT
* *
5620462 ATTAGAACCGAAAAGTTTA
1 ATTAGAACAGAAAAGTATA
*
5620481 ATTAGAATAGAAAAGTATA
1 ATTAGAACAGAAAAGTATA
5620500 AT
1 AT
5620502 AAAAGTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.28
Consensus pattern (19 bp):
ATTAGAACAGAAAAGTATA
Found at i:5628019 original size:27 final size:28
Alignment explanation
Indices: 5627980--5628033 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
5627970 GTTCGGTTCG
*
5627980 GTTTTCGATTTTTCTATACTAATTTTTT
1 GTTTTCGATTTTTCTAGACTAATTTTTT
* *
5628008 GTTTT-GATTTTTTTAGACTTATTTTT
1 GTTTTCGATTTTTCTAGACTAATTTTT
5628034 ATATGTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.17, C:0.07, G:0.09, T:0.67
Consensus pattern (28 bp):
GTTTTCGATTTTTCTAGACTAATTTTTT
Found at i:5633262 original size:18 final size:18
Alignment explanation
Indices: 5633235--5633270 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5633225 ATTATTCTAT
*
5633235 AATTTTTAAAAAGTATTA
1 AATTTATAAAAAGTATTA
*
5633253 AATTTATAAAATGTATTA
1 AATTTATAAAAAGTATTA
5633271 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
AATTTATAAAAAGTATTA
Found at i:5633294 original size:22 final size:23
Alignment explanation
Indices: 5633252--5633308 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
5633242 AAAAAGTATT
*
5633252 AAATTTATAAAATGTATTATAAA
1 AAATATATAAAATGTATTATAAA
*
5633275 AAATATATATAAT-TATTATAAA
1 AAATATATAAAATGTATTATAAA
* *
5633297 AATTAAATAAAA
1 AAATATATAAAA
5633309 ATATTGATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
AAATATATAAAATGTATTATAAA
Found at i:5633313 original size:22 final size:21
Alignment explanation
Indices: 5633288--5633349 Score: 76
Period size: 19 Copynumber: 3.0 Consensus size: 21
5633278 TATATATAAT
5633288 TATTATAAAAATTAAATAAAAA
1 TATTAT-AAAATTAAATAAAAA
5633310 TATTGAT---ATTAAATAAAAA
1 TATT-ATAAAATTAAATAAAAA
*
5633329 TATTATAAAATAAAATAAAAA
1 TATTATAAAATTAAATAAAAA
5633350 ACCGTCCCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
18 2 0.06
19 16 0.46
21 11 0.31
22 4 0.11
23 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TATTATAAAATTAAATAAAAA
Found at i:5633894 original size:21 final size:21
Alignment explanation
Indices: 5633844--5633899 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 21
5633834 GTGAGGCAAG
*
5633844 GAGG-GGGGAC-GGTGGGGGA
1 GAGGAGGGGACGGGTTGGGGA
*
5633863 GAGGAGTGGGACGGGTTGGGGT
1 GAGGAG-GGGACGGGTTGGGGA
*
5633885 GGGGAGGGGA-GGGTT
1 GAGGAGGGGACGGGTT
5633900 TTTTATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 4 0.13
20 6 0.19
21 9 0.29
22 12 0.39
ACGTcount: A:0.14, C:0.04, G:0.70, T:0.12
Consensus pattern (21 bp):
GAGGAGGGGACGGGTTGGGGA
Found at i:5633965 original size:21 final size:21
Alignment explanation
Indices: 5633926--5633978 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
5633916 ATTAATTAAT
5633926 TTTTTATAATAATTATTTATAA
1 TTTTTATAATAATTATTTAT-A
5633948 TTTTTATAATACA-T-TTTATA
1 TTTTTATAATA-ATTATTTATA
5633968 TTTTTAGTAAT
1 TTTTTA-TAAT
5633979 TTTAATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.24
21 9 0.31
22 12 0.41
23 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTTTATAATAATTATTTATA
Found at i:5646653 original size:21 final size:21
Alignment explanation
Indices: 5646618--5646659 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5646608 AATCTCATTA
*
5646618 CTACAGTATCCAATCTCACCG
1 CTACAGTAACCAATCTCACCG
* *
5646639 CTACAGTAACTAATCTTACCG
1 CTACAGTAACCAATCTCACCG
5646660 TCACTGCTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.33, G:0.10, T:0.26
Consensus pattern (21 bp):
CTACAGTAACCAATCTCACCG
Found at i:5668683 original size:15 final size:15
Alignment explanation
Indices: 5668665--5668710 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
5668655 GTAGGAGGCT
5668665 GAGCAATTGGTGGAG
1 GAGCAATTGGTGGAG
* * *
5668680 GAGCCATAGGTGGCG
1 GAGCAATTGGTGGAG
*
5668695 GAGCAAGTGGTGGAG
1 GAGCAATTGGTGGAG
5668710 G
1 G
5668711 GGGTGAGGGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.24, C:0.11, G:0.50, T:0.15
Consensus pattern (15 bp):
GAGCAATTGGTGGAG
Found at i:5676861 original size:24 final size:24
Alignment explanation
Indices: 5676834--5676885 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5676824 AATCAAAGTC
* *
5676834 AAATATATTAT-GTTAATAAATGCT
1 AAATATATTATACTT-ATAAATACT
5676858 AAATATATTATACTTATAAATACT
1 AAATATATTATACTTATAAATACT
5676882 AAAT
1 AAAT
5676886 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTTATAAATACT
Found at i:5683865 original size:25 final size:23
Alignment explanation
Indices: 5683830--5683876 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
5683820 GATAGAAATT
*
5683830 TTAAAATATAAAATATAAAATAA
1 TTAAAATATAAAAAATAAAATAA
*
5683853 TTAAAACTGATAAAAAATAGAATA
1 TTAAAA-T-ATAAAAAATAAAATA
5683877 TATAGACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 1 0.05
25 13 0.65
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (23 bp):
TTAAAATATAAAAAATAAAATAA
Found at i:5687895 original size:3 final size:3
Alignment explanation
Indices: 5687889--5687925 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5687879 ATCCATCGAT
5687889 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5687926 TAAATTAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:5690783 original size:23 final size:22
Alignment explanation
Indices: 5690757--5690809 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
5690747 ATATTTTTAT
*
5690757 TAAATATATATAAAAATTAAAAA
1 TAAATATATA-AAAAATCAAAAA
*
5690780 TAAATATATAAAAAATCAGAAA
1 TAAATATATAAAAAATCAAAAA
*
5690802 TATATATA
1 TAAATATA
5690810 AATTAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
TAAATATATAAAAAATCAAAAA
Found at i:5690818 original size:18 final size:18
Alignment explanation
Indices: 5690781--5690831 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
5690771 AATTAAAAAT
* * *
5690781 AAATATATAAAAAATCAG
1 AAATATATATAAATTAAG
5690799 AAATATATATAAATTAAG
1 AAATATATATAAATTAAG
*
5690817 AAA-AAATATAAATTA
1 AAATATATATAAATTA
5690832 TAAAAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 11 0.38
18 18 0.62
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AAATATATATAAATTAAG
Found at i:5690825 original size:17 final size:17
Alignment explanation
Indices: 5690805--5690840 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
5690795 TCAGAAATAT
5690805 ATATAAATTA-AGAAAAA
1 ATATAAATTATA-AAAAA
5690822 ATATAAATTATAAAAAA
1 ATATAAATTATAAAAAA
5690839 AT
1 AT
5690841 TTACAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
ATATAAATTATAAAAAA
Found at i:5690825 original size:21 final size:19
Alignment explanation
Indices: 5690762--5690840 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 19
5690752 TTTATTAAAT
5690762 ATATATAAAAATTAAAAATAA
1 ATATAT-AAAATTAAAAA-AA
* *
5690783 ATATATAAAA--AATCAGAA
1 ATATATAAAATTAA-AAAAA
*
5690801 ATATATATAAATTAAGAAAA
1 ATATATA-AAATTAAAAAAA
5690821 A-ATAT-AAATTATAAAAAA
1 ATATATAAAATTA-AAAAAA
5690839 AT
1 AT
5690841 TTACAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
17 6 0.13
18 17 0.36
19 8 0.17
20 8 0.17
21 8 0.17
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (19 bp):
ATATATAAAATTAAAAAAA
Found at i:5690833 original size:28 final size:28
Alignment explanation
Indices: 5690789--5690856 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
5690779 ATAAATATAT
* * * *
5690789 AAAAAATCAGAAATATATATAAATTAAG
1 AAAAAATCATAAATATAAAAAAATTAAC
*
5690817 AAAAAAT-ATAAATTATAAAAAAATTTAC
1 AAAAAATCATAAA-TATAAAAAAATTAAC
*
5690845 AAAAAATGATAA
1 AAAAAATCATAA
5690857 TTGAAAAGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 4 0.12
28 25 0.76
29 4 0.12
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.25
Consensus pattern (28 bp):
AAAAAATCATAAATATAAAAAAATTAAC
Found at i:5691571 original size:20 final size:19
Alignment explanation
Indices: 5691543--5691584 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5691533 TTGAAAATTC
5691543 AATAATATATAAAAATTAAA
1 AATAATATA-AAAAATTAAA
* *
5691563 AATATTATAAAAATTTAAA
1 AATAATATAAAAAATTAAA
5691582 AAT
1 AAT
5691585 GTTTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAATATAAAAAATTAAA
Found at i:5691591 original size:18 final size:18
Alignment explanation
Indices: 5691536--5691584 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
5691526 ATAATTTTTG
*
5691536 AAAATTCAATAATA-TATA
1 AAAATT-AAAAATATTATA
5691554 AAAATTAAAAATATTATA
1 AAAATTAAAAATATTATA
5691572 AAAATTTAAAAAT
1 AAAA-TTAAAAAT
5691585 GTTTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 14 0.50
19 8 0.29
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTAAAAATATTATA
Found at i:5696534 original size:24 final size:24
Alignment explanation
Indices: 5696506--5696557 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5696496 TTCGTAGATA
* *
5696506 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
5696530 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
5696554 AAAT
1 AAAT
5696558 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:5698474 original size:24 final size:24
Alignment explanation
Indices: 5698447--5698498 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
5698437 TTCGTAGGTC
5698447 AAATAAATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
*
5698471 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
5698495 AAAT
1 AAAT
5698499 CTTCTAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:5699074 original size:19 final size:19
Alignment explanation
Indices: 5699044--5699098 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 19
5699034 CCCGGCCCGC
5699044 ATATAT-TAATTTTTATAT
1 ATATATATAATTTTTATAT
* *
5699062 TTTTATATAA-TTTTA-AT
1 ATATATATAATTTTTATAT
*
5699079 ATATATATAATTTTAATAT
1 ATATATATAATTTTTATAT
5699098 A
1 A
5699099 GATGCAACTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 10 0.34
18 13 0.45
19 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATATATAATTTTTATAT
Found at i:5699087 original size:17 final size:17
Alignment explanation
Indices: 5699065--5699098 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5699055 TTTATATTTT
5699065 TATATAATTTTAATATA
1 TATATAATTTTAATATA
5699082 TATATAATTTTAATATA
1 TATATAATTTTAATATA
5699099 GATGCAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATAATTTTAATATA
Found at i:5707537 original size:16 final size:16
Alignment explanation
Indices: 5707517--5707569 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
5707507 AAAAATTATG
*
5707517 TTTTCCATCCTTCTAG
1 TTTTCCATCCTTCTAA
* *
5707533 TTTTCTACCCCTTC-AA
1 TTTTCCA-TCCTTCTAA
*
5707549 TTTTCCATCCTCCTAA
1 TTTTCCATCCTTCTAA
5707565 TTTTC
1 TTTTC
5707570 TTTCCACTCT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 4 0.14
16 20 0.69
17 5 0.17
ACGTcount: A:0.15, C:0.34, G:0.02, T:0.49
Consensus pattern (16 bp):
TTTTCCATCCTTCTAA
Found at i:5728655 original size:22 final size:22
Alignment explanation
Indices: 5728618--5728672 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
5728608 ATGTTAAATT
*
5728618 GAGAGA-AGAGAGGGAGAGG-GG
1 GAGAGAGAGGGAGGGAG-GGAGG
5728639 GAG-GAGGAGGGAGGGAGGGAGG
1 GAGAGA-GAGGGAGGGAGGGAGG
5728661 GAGAGAGAGGGA
1 GAGAGAGAGGGA
5728673 ATGCAAGCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 2 0.07
21 5 0.17
22 20 0.69
23 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (22 bp):
GAGAGAGAGGGAGGGAGGGAGG
Found at i:5728670 original size:18 final size:16
Alignment explanation
Indices: 5728627--5728672 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 16
5728617 TGAGAGAAGA
5728627 GAGGGAGAGG-GGGAG
1 GAGGGAGAGGAGGGAG
5728642 GA-GGAG-GGAGGGAGG
1 GAGGGAGAGGAGGGA-G
5728657 GAGGGAGAGAGAGGGA
1 GAGGGAGAG-GAGGGA
5728673 ATGCAAGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.08
14 8 0.31
15 5 0.19
16 4 0.15
17 1 0.04
18 6 0.23
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (16 bp):
GAGGGAGAGGAGGGAG
Found at i:5738020 original size:20 final size:20
Alignment explanation
Indices: 5737994--5738043 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
5737984 AGAGCCATTA
5737994 ATATCGATACC-AATAGAAAT
1 ATATCGATACCAAATAG-AAT
*
5738014 TTATCGATACCAAATAGAAT
1 ATATCGATACCAAATAGAAT
5738034 ATATCGATAC
1 ATATCGATAC
5738044 TTGATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (20 bp):
ATATCGATACCAAATAGAAT
Found at i:5748404 original size:18 final size:18
Alignment explanation
Indices: 5748373--5748407 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5748363 TGCCTCGACC
*
5748373 CCTCTTCCACGATAACCA
1 CCTCTGCCACGATAACCA
*
5748391 CCTCTGCCATGATAACC
1 CCTCTGCCACGATAACC
5748408 TCTTCTGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.43, G:0.09, T:0.23
Consensus pattern (18 bp):
CCTCTGCCACGATAACCA
Found at i:5752710 original size:17 final size:18
Alignment explanation
Indices: 5752679--5752714 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5752669 AATTTAACTT
5752679 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
5752697 TAATT-AATTTTTTAAAA
1 TAATTAAATTATTTAAAA
5752714 T
1 T
5752715 TATAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:5758225 original size:10 final size:10
Alignment explanation
Indices: 5758195--5758236 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
5758185 ATCACAAGTC
5758195 TTGTGATATA
1 TTGTGATATA
*
5758205 GTGTGATATA
1 TTGTGATATA
5758215 TTGTGATATA
1 TTGTGATATA
*
5758225 TATATGATATA
1 T-TGTGATATA
5758236 T
1 T
5758237 GTAGAAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (10 bp):
TTGTGATATA
Found at i:5765931 original size:17 final size:17
Alignment explanation
Indices: 5765891--5765939 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
5765881 TTTAGATAGT
*
5765891 AAAAGAAAAAGAAGAGG
1 AAAAGAAAAAGAAGAAG
** *
5765908 AGGAGAAGAAGAAGAAG
1 AAAAGAAAAAGAAGAAG
*
5765925 AAAAGAAAAATAAGA
1 AAAAGAAAAAGAAGA
5765940 GAAGAAATAG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAAGAAGAAG
Found at i:5767026 original size:21 final size:21
Alignment explanation
Indices: 5767002--5767072 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
5766992 TGTTGATGAG
*
5767002 TTGGGGCAGCTTTTTGCTGAA
1 TTGGGGCAGCTTATTGCTGAA
* * *
5767023 TTGGAGTAGCTTATTGCTGAG
1 TTGGGGCAGCTTATTGCTGAA
*
5767044 TTGGGGCAGCTTCTTGCTGAA
1 TTGGGGCAGCTTATTGCTGAA
5767065 TTGGGGCA
1 TTGGGGCA
5767073 ACCTTGATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.15, C:0.14, G:0.35, T:0.35
Consensus pattern (21 bp):
TTGGGGCAGCTTATTGCTGAA
Found at i:5769572 original size:26 final size:27
Alignment explanation
Indices: 5769537--5769651 Score: 90
Period size: 27 Copynumber: 4.3 Consensus size: 27
5769527 CAAAAGGGCA
* **
5769537 TTCTCTTCATAAATCGCC-CAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
* * * *
5769563 TTCTTTTCATAGATAGCTATAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
* *
5769590 GTCTTTTCA-AAGATAACCATAAAGGCT
1 TTCTTTTCATAA-ATAACCACAAAGGCT
* * *
5769617 TCCTTTTCATAGATCACCACAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
*
5769644 TCCTTTTC
1 TTCTTTTC
5769652 TAGTGTGTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
26 15 0.21
27 56 0.78
28 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (27 bp):
TTCTTTTCATAAATAACCACAAAGGCT
Found at i:5769586 original size:27 final size:27
Alignment explanation
Indices: 5769556--5769651 Score: 120
Period size: 27 Copynumber: 3.6 Consensus size: 27
5769546 TAAATCGCCC
* *
5769556 AAAGGCTTTCTTTTCATAGATAGCTAT
1 AAAGGCTTTCTTTTCATAGATAACCAT
* *
5769583 AAAGGCTGTCTTTTCAAAGATAACCAT
1 AAAGGCTTTCTTTTCATAGATAACCAT
* * *
5769610 AAAGGCTTCCTTTTCATAGATCACCAC
1 AAAGGCTTTCTTTTCATAGATAACCAT
*
5769637 AAAGGCTTCCTTTTC
1 AAAGGCTTTCTTTTC
5769652 TAGTGTGTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (27 bp):
AAAGGCTTTCTTTTCATAGATAACCAT
Found at i:5773280 original size:45 final size:45
Alignment explanation
Indices: 5773212--5773341 Score: 151
Period size: 45 Copynumber: 2.9 Consensus size: 45
5773202 GGAAGGAAGA
* *
5773212 ATTAGTGGCTTCGTCCACGACCTACATGATAGCTTGTCTATGAAT
1 ATTAGTGGCTTCATCCACAACCTACATGATAGCTTGTCTATGAAT
* *
5773257 ATTAGTGGCTTCATCCACAACCTACATAGCA-A-CTTGTTTGTGAAT
1 ATTAGTGGCTTCATCCACAACCTACAT-G-ATAGCTTGTCTATGAAT
* *
5773302 ATTAGTGG-TTTATCCACAACCTACAT-AGTAGCTTATCTAT
1 ATTAGTGGCTTCATCCACAACCTACATGA-TAGCTTGTCTAT
5773342 AAATTTGGAG
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.01
43 1 0.01
44 23 0.32
45 44 0.61
46 2 0.03
47 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (45 bp):
ATTAGTGGCTTCATCCACAACCTACATGATAGCTTGTCTATGAAT
Found at i:5774272 original size:92 final size:92
Alignment explanation
Indices: 5774115--5774302 Score: 331
Period size: 92 Copynumber: 2.0 Consensus size: 92
5774105 CAAAATTACT
* * *
5774115 AATATTTGCAAATGAGATTTCTTAATACATTTAATTTTGAAGTTAATGTGTTTTTCCTGAATAAC
1 AATATTTACAAATGAAATTTCTTAATACATTTAATTCTGAAGTTAATGTGTTTTTCCTGAATAAC
*
5774180 GACGAATAACCAAGGTATTTAGTTTTG
66 GACGAATAACCAAGGTATTTAATTTTG
5774207 AATATTTACAAATGAAATTTCTTAATACATTTAATTCTGAAGTTAATGTGTTTTTCCTGAATAAC
1 AATATTTACAAATGAAATTTCTTAATACATTTAATTCTGAAGTTAATGTGTTTTTCCTGAATAAC
*
5774272 GATGAATAACCAAGGTATTTAATTTTG
66 GACGAATAACCAAGGTATTTAATTTTG
5774299 AATA
1 AATA
5774303 AATAAACGAA
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (92 bp):
AATATTTACAAATGAAATTTCTTAATACATTTAATTCTGAAGTTAATGTGTTTTTCCTGAATAAC
GACGAATAACCAAGGTATTTAATTTTG
Found at i:5777586 original size:14 final size:15
Alignment explanation
Indices: 5777569--5777598 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5777559 ATTTATATAA
5777569 TAACAATA-AAATAT
1 TAACAATATAAATAT
5777583 TAACAATATAAATAT
1 TAACAATATAAATAT
5777598 T
1 T
5777599 TTTACCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
TAACAATATAAATAT
Found at i:5779962 original size:2 final size:2
Alignment explanation
Indices: 5779955--5779989 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5779945 ATTTAATTAA
5779955 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5779990 ACAGATGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5784804 original size:41 final size:42
Alignment explanation
Indices: 5784742--5784831 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 42
5784732 ATAGGAGCGA
*
5784742 AAATGGG-GAGAAAGAATGAGGAAAGAGAAAAAAAAAAAAAG
1 AAATGGGAGAGAAAGAAGGAGGAAAGAGAAAAAAAAAAAAAG
* * * ***
5784783 AAATGGGAGAGAAA-AGGGAGGAAAGATAGAGGGAAAAAAAG
1 AAATGGGAGAGAAAGAAGGAGGAAAGAGAAAAAAAAAAAAAG
5784824 AAATGGGA
1 AAATGGGA
5784832 AGGAAAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 35 0.85
42 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.34, T:0.06
Consensus pattern (42 bp):
AAATGGGAGAGAAAGAAGGAGGAAAGAGAAAAAAAAAAAAAG
Found at i:5788446 original size:139 final size:139
Alignment explanation
Indices: 5788174--5788446 Score: 361
Period size: 139 Copynumber: 2.0 Consensus size: 139
5788164 AAACTTAGGC
* * *
5788174 TTAATATATAGATTGGCTCCTAAACTTGGCAACTTTTCTCAAATTAGCTCCTAAACTTTTTTTTG
1 TTAATATACAGATTGGCCCCTAAACTTGGCAACTTTTCTCAAATTAGCCCCTAAACTTTTTTTTG
* * * * * *
5788239 GATCACATTGGTCCCTAAGGTTGGCATCCGTTACACAAATTGGTCCCTATAGTTAAAACCGTTAG
66 GATCACAGTGGTCCCTAAGGTTGGCATCCATTACACAAATTAGTCCCTACAGCTAAAACAGTTAG
5788304 TTTTAAGGT
131 TTTTAAGGT
* *
5788313 TTAATATACAGATTGGCCCCTAAACTTGGCAGCTTTTCTCACATT-GTCCCCTAAACTCTTTTTT
1 TTAATATACAGATTGGCCCCTAAACTTGGCAACTTTTCTCAAATTAG-CCCCTAAACT-TTTTTT
* * * * *
5788377 TGGGTCATAGTGGTCCCTAAGGTTGGCATCCATTGCATAAATTAGTCCCTACA-CTAACACAGTT
64 TGGATCACAGTGGTCCCTAAGGTTGGCATCCATTACACAAATTAGTCCCTACAGCTAAAACAGTT
*
5788441 TGTTTT
129 AGTTTT
5788447 TGAAGATTTT
Statistics
Matches: 115, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
138 1 0.01
139 63 0.55
140 51 0.44
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.37
Consensus pattern (139 bp):
TTAATATACAGATTGGCCCCTAAACTTGGCAACTTTTCTCAAATTAGCCCCTAAACTTTTTTTTG
GATCACAGTGGTCCCTAAGGTTGGCATCCATTACACAAATTAGTCCCTACAGCTAAAACAGTTAG
TTTTAAGGT
Found at i:5788629 original size:16 final size:16
Alignment explanation
Indices: 5788602--5788655 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
5788592 TTATAAATTA
*
5788602 TAAAAATTCAAAAAAG
1 TAAAAATACAAAAAAG
* *
5788618 TAAATATACAAAAAAA
1 TAAAAATACAAAAAAG
5788634 TAAAAATA-AAAAAAG
1 TAAAAATACAAAAAAG
*
5788649 TTAAAAT
1 TAAAAAT
5788656 TTAACATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 12 0.38
16 20 0.62
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (16 bp):
TAAAAATACAAAAAAG
Found at i:5788728 original size:23 final size:19
Alignment explanation
Indices: 5788715--5788753 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
5788705 ATCTAAAACT
5788715 ATATAACAAATAAAATTAAAA
1 ATAT-ACAAAT-AAATTAAAA
5788736 ATATACAAATAAA-TAAAA
1 ATATACAAATAAATTAAAA
5788754 GTCAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 6 0.33
21 4 0.22
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (19 bp):
ATATACAAATAAATTAAAA
Found at i:5789085 original size:36 final size:36
Alignment explanation
Indices: 5789012--5789085 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
5789002 AAATTTGATA
* * *
5789012 TTTTTATTTTCAATTTATACATATTCTTTTTTATTT
1 TTTTTATTTTCAATTTATACATATTATATTCTATTT
5789048 TTTTTATTTTCAATTTATATACATA-TATATTCT-TTT
1 TTTTTATTTTCAA-TT-TATACATATTATATTCTATTT
5789084 TT
1 TT
5789086 AAAAGTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 18 0.55
37 7 0.21
38 8 0.24
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (36 bp):
TTTTTATTTTCAATTTATACATATTATATTCTATTT
Found at i:5789526 original size:19 final size:19
Alignment explanation
Indices: 5789484--5789545 Score: 83
Period size: 19 Copynumber: 3.2 Consensus size: 19
5789474 ATTACAAAAT
5789484 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
5789504 AATTCAAAATAAGTTTT-AA
1 AATTCAAAATAA-TTTTAAA
5789523 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TAAA
5789542 AATT
1 AATT
5789546 ATAAAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.08
18 2 0.05
19 18 0.46
20 12 0.31
21 4 0.10
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:5790841 original size:15 final size:17
Alignment explanation
Indices: 5790815--5790852 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
5790805 AGCTCAAAGC
5790815 ATAAGTAGAAAAGAAAT
1 ATAAGTAGAAAAGAAAT
*
5790832 A-AAGTA-AAAATAAAT
1 ATAAGTAGAAAAGAAAT
5790847 ATAAGT
1 ATAAGT
5790853 TGTAGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 9 0.47
17 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (17 bp):
ATAAGTAGAAAAGAAAT
Found at i:5794301 original size:20 final size:21
Alignment explanation
Indices: 5794255--5794302 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
5794245 ATCTAATTAA
5794255 AAATATTTAATAATTATATTT
1 AAATATTTAATAATTATATTT
5794276 AAATATTTAA-AA-TATAGTTT
1 AAATATTTAATAATTATA-TTT
*
5794296 ATATATT
1 AAATATT
5794303 AGAAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 11 0.44
21 10 0.40
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
AAATATTTAATAATTATATTT
Found at i:5794311 original size:29 final size:30
Alignment explanation
Indices: 5794269--5794349 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 30
5794259 ATTTAATAAT
*
5794269 TATATTTAAATATTTAA-AAT-ATAGTTTA
1 TATATTAAAATATTTAATAATAATAGTTTA
* *
5794297 TATATTAGAAATATTTAATATTAATATTTTA
1 TATATTA-AAATATTTAATAATAATAGTTTA
*
5794328 TATATTAAAATA-TTAACAATAA
1 TATATTAAAATATTTAATAATAA
5794350 GTTATAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.13
29 18 0.40
30 7 0.16
31 14 0.31
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (30 bp):
TATATTAAAATATTTAATAATAATAGTTTA
Found at i:5794324 original size:13 final size:15
Alignment explanation
Indices: 5794293--5794335 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
5794283 TAAAATATAG
*
5794293 TTTATATATTAGAAAT
1 TTTATATATTA-ATAT
5794309 ATTTA-ATATTAATAT
1 -TTTATATATTAATAT
5794324 TTTATATATTAA
1 TTTATATATTAA
5794336 AATATTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.17
15 10 0.42
16 6 0.25
17 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TTTATATATTAATAT
Found at i:5797908 original size:13 final size:13
Alignment explanation
Indices: 5797890--5797925 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
5797880 TTTTTTACAC
5797890 AAATAATATATAA
1 AAATAATATATAA
5797903 AAATAAT-TATAA
1 AAATAATATATAA
5797915 AAATAAGTATA
1 AAATAA-TATA
5797926 CTGAACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.52
13 8 0.38
14 2 0.10
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
AAATAATATATAA
Found at i:5798651 original size:30 final size:30
Alignment explanation
Indices: 5798612--5798683 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
5798602 AAAAACCTTA
*
5798612 AATTAAATTT-TTTATTATTATTAATAAATT
1 AATTAAATTTATTT-TTATTAATAATAAATT
* *
5798642 AATTGAATTTATTTTTATTAATAATTAATT
1 AATTAAATTTATTTTTATTAATAATAAATT
*
5798672 AATAAAAATTTA
1 AAT-TAAATTTA
5798684 AGAATTCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 26 0.74
31 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
AATTAAATTTATTTTTATTAATAATAAATT
Found at i:5799288 original size:25 final size:25
Alignment explanation
Indices: 5799252--5799307 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 25
5799242 ATATATATAT
5799252 TTTTTTATTTTTAAATTTTAAAATA
1 TTTTTTATTTTTAAATTTTAAAATA
* *
5799277 CTTTTTTATTTTTTATTTTTAAAATA
1 -TTTTTTATTTTTAAATTTTAAAATA
5799303 TTTTT
1 TTTTT
5799308 GGTGTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTTTATTTTTAAATTTTAAAATA
Found at i:5801851 original size:20 final size:19
Alignment explanation
Indices: 5801813--5801855 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
5801803 AATAATAATT
5801813 TAATATTTTACTAAAAATAA
1 TAATATTTTACTAAAAAT-A
*
5801833 TAATATTTTA-TAAGTAATA
1 TAATATTTTACTAA-AAATA
5801852 TAAT
1 TAAT
5801856 GTGTGTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
TAATATTTTACTAAAAATA
Found at i:5802564 original size:38 final size:37
Alignment explanation
Indices: 5802498--5802572 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 37
5802488 TTTTTACTTT
*
5802498 TTTTTTATTTTTAAAATATTTTAAAAATACTTTTTTTA
1 TTTTTTATTTTTAAAATATTTTAAAAATA-TATTTTTA
**
5802536 TTTTTTATTTTTAAAATATTTTTCAAATATATTTTTA
1 TTTTTTATTTTTAAAATATTTTAAAAATATATTTTTA
5802573 AAATTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 7 0.21
38 27 0.79
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (37 bp):
TTTTTTATTTTTAAAATATTTTAAAAATATATTTTTA
Found at i:5802576 original size:13 final size:12
Alignment explanation
Indices: 5802541--5802574 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
5802531 TTTTATTTTT
5802541 TATTTTTAAA-A
1 TATTTTTAAATA
5802552 TATTTTTCAAATA
1 TATTTTT-AAATA
5802565 TATTTTTAAA
1 TATTTTTAAA
5802575 ATTTTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.33
12 6 0.29
13 8 0.38
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (12 bp):
TATTTTTAAATA
Found at i:5802851 original size:34 final size:34
Alignment explanation
Indices: 5802790--5802854 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
5802780 TGTATGTTTA
* * *
5802790 AATCGATTGTCATGTTGTAATACTGCTTCTTTTG
1 AATCAATTGTCATGGTGAAATACTGCTTCTTTTG
* *
5802824 AATCAATTGTTATGGTGAAATATTGCTTCTT
1 AATCAATTGTCATGGTGAAATACTGCTTCTT
5802855 CTTCTTTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (34 bp):
AATCAATTGTCATGGTGAAATACTGCTTCTTTTG
Found at i:5813001 original size:20 final size:20
Alignment explanation
Indices: 5812976--5813041 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
5812966 TAATGGAAAG
5812976 AAATCAAAGGATTGAGAATC
1 AAATCAAAGGATTGAGAATC
* * * **
5812996 AAATCAATGTAATG-GAAAG
1 AAATCAAAGGATTGAGAATC
*
5813015 AAATCAAAAGATTGAGAATC
1 AAATCAAAGGATTGAGAATC
5813035 AAATCAA
1 AAATCAA
5813042 TGTAAACAAG
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
19 13 0.38
20 21 0.62
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCAAAGGATTGAGAATC
Found at i:5813019 original size:39 final size:39
Alignment explanation
Indices: 5812965--5813046 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
5812955 AAGCAAAACA
*
5812965 GTAATGGAAAGAAATCAAAGGATTGAGAATCAAATCAAT
1 GTAATGGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
5813004 GTAATGGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
1 GTAATGGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
5813043 GTAA
1 GTAA
5813047 ACAAGATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (39 bp):
GTAATGGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
Found at i:5813020 original size:19 final size:19
Alignment explanation
Indices: 5812964--5813022 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
5812954 GAAGCAAAAC
5812964 AGTAATGGAAAGAAATCAA
1 AGTAATGGAAAGAAATCAA
* * **
5812983 AGGATTGAGAATCAAATCAA
1 AGTAATG-GAAAGAAATCAA
*
5813003 TGTAATGGAAAGAAATCAA
1 AGTAATGGAAAGAAATCAA
5813022 A
1 A
5813023 AGATTGAGAA
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.19
Consensus pattern (19 bp):
AGTAATGGAAAGAAATCAA
Found at i:5813909 original size:18 final size:20
Alignment explanation
Indices: 5813886--5813931 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
5813876 TTTTATGATT
*
5813886 TATATATTTAT-TACCT-TA
1 TATATATATATGTACCTATA
*
5813904 TATATATATATGTACGTATA
1 TATATATATATGTACCTATA
5813924 TATATATA
1 TATATATA
5813932 ATACTTTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.42
19 4 0.17
20 10 0.42
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (20 bp):
TATATATATATGTACCTATA
Found at i:5814068 original size:108 final size:110
Alignment explanation
Indices: 5813860--5814068 Score: 314
Period size: 108 Copynumber: 1.9 Consensus size: 110
5813850 TTTAAGTTTA
* * * * *
5813860 TATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATATATATATATGTACGTATAT
1 TATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATATGTACGTATAT
*
5813925 ATATATAATACTTTCTATACATATTTTATAATTTCTCTCTCTCTC
66 ATATATAATACTTTCTATACACATTTTATAATTTCTCTCTCTCTC
5813970 TATATATAATCATTATCTTTATGATCTATATATTTATTAAC-T-TATATATATATGTACGTATAT
1 TATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATATGTACGTATAT
* * * *
5814033 ATGTATTATATTTTCTATCCACATTTTATAATTTCT
66 ATATATAATACTTTCTATACACATTTTATAATTTCT
5814069 ATATGTATAT
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
108 52 0.58
109 1 0.01
110 36 0.40
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.53
Consensus pattern (110 bp):
TATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATATGTACGTATAT
ATATATAATACTTTCTATACACATTTTATAATTTCTCTCTCTCTC
Found at i:5815726 original size:9 final size:9
Alignment explanation
Indices: 5815712--5815805 Score: 118
Period size: 9 Copynumber: 10.4 Consensus size: 9
5815702 TTTGGTTAAA
5815712 AATTAACCG
1 AATTAACCG
*
5815721 AATTAACCA
1 AATTAACCG
5815730 AATTAACCG
1 AATTAACCG
*
5815739 AATTACCCG
1 AATTAACCG
5815748 AATTAACCG
1 AATTAACCG
5815757 AATT-ACTCG
1 AATTAAC-CG
*
5815766 AATTAACTG
1 AATTAACCG
5815775 AATTAACCG
1 AATTAACCG
* *
5815784 TATTACCCG
1 AATTAACCG
*
5815793 AATTAACCT
1 AATTAACCG
5815802 AATT
1 AATT
5815806 GAATCATACA
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
8 2 0.03
9 68 0.94
10 2 0.03
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:5831433 original size:55 final size:55
Alignment explanation
Indices: 5831349--5831461 Score: 226
Period size: 55 Copynumber: 2.1 Consensus size: 55
5831339 GACATATTTT
5831349 AGGCAAATATCACAATTATTGAGATATTCAATCAAACTATTTTAGCATGGAAATA
1 AGGCAAATATCACAATTATTGAGATATTCAATCAAACTATTTTAGCATGGAAATA
5831404 AGGCAAATATCACAATTATTGAGATATTCAATCAAACTATTTTAGCATGGAAATA
1 AGGCAAATATCACAATTATTGAGATATTCAATCAAACTATTTTAGCATGGAAATA
5831459 AGG
1 AGG
5831462 TCCCTACATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (55 bp):
AGGCAAATATCACAATTATTGAGATATTCAATCAAACTATTTTAGCATGGAAATA
Found at i:5851787 original size:23 final size:23
Alignment explanation
Indices: 5851757--5851805 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
5851747 AACACAGTTT
5851757 GGATTCCTCAATCCTATATCTAC
1 GGATTCCTCAATCCTATATCTAC
5851780 GGATTCCTCAATCCTATATCTAC
1 GGATTCCTCAATCCTATATCTAC
5851803 GGA
1 GGA
5851806 GCCTTGCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.33
Consensus pattern (23 bp):
GGATTCCTCAATCCTATATCTAC
Found at i:5854892 original size:25 final size:25
Alignment explanation
Indices: 5854864--5854911 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
5854854 ATTATAATGT
5854864 AAGACAAAAAATAAGCTAAACGCAC
1 AAGACAAAAAATAAGCTAAACGCAC
*
5854889 AAGATAAAAAATAAGCTAAACGC
1 AAGACAAAAAATAAGCTAAACGC
5854912 GCCGTACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.60, C:0.17, G:0.12, T:0.10
Consensus pattern (25 bp):
AAGACAAAAAATAAGCTAAACGCAC
Found at i:5855412 original size:9 final size:9
Alignment explanation
Indices: 5855387--5855416 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5855377 ATTATCAATC
5855387 AAATTTTAA
1 AAATTTTAA
5855396 ATAATTTTAA
1 A-AATTTTAA
5855406 AAATTTTAA
1 AAATTTTAA
5855415 AA
1 AA
5855417 TGATATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAATTTTAA
Found at i:5866914 original size:11 final size:11
Alignment explanation
Indices: 5866898--5866922 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5866888 CTAAATTTGC
5866898 AAAAAAAAAAG
1 AAAAAAAAAAG
5866909 AAAAAAAAAAG
1 AAAAAAAAAAG
5866920 AAA
1 AAA
5866923 CAATTGTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:5867093 original size:31 final size:29
Alignment explanation
Indices: 5867058--5867116 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
5867048 ATCTTAAAAT
*
5867058 TATACATGAATATTGATTTAATGTGCAATTG
1 TATACATGAATATTAATTT-A-GTGCAATTG
* *
5867089 TATACATTAATTTTAATTTAGTGCAATT
1 TATACATGAATATTAATTTAGTGCAATT
5867117 ATACATATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.32
30 1 0.04
31 16 0.64
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.46
Consensus pattern (29 bp):
TATACATGAATATTAATTTAGTGCAATTG
Found at i:5873694 original size:26 final size:26
Alignment explanation
Indices: 5873657--5873707 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
5873647 CGGAGAGTCT
5873657 TTAATCAGGAAGCTCACAAAGAACCC
1 TTAATCAGGAAGCTCACAAAGAACCC
* *
5873683 TTAATCATGAAGCTCACGAAGAACC
1 TTAATCAGGAAGCTCACAAAGAACC
5873708 ATATAACGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (26 bp):
TTAATCAGGAAGCTCACAAAGAACCC
Found at i:5874395 original size:20 final size:20
Alignment explanation
Indices: 5874357--5874396 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5874347 CCATGTATTT
* *
5874357 CATAAAATTTAGAATTTTTC
1 CATAAAATTTACAACTTTTC
*
5874377 CATAAATTTTACAACTTTTC
1 CATAAAATTTACAACTTTTC
5874397 AATTTAGTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (20 bp):
CATAAAATTTACAACTTTTC
Found at i:5875516 original size:25 final size:25
Alignment explanation
Indices: 5875469--5875516 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5875459 ATTTTTATTT
* **
5875469 AAATAATTCTTTAAATTTGTATAAA
1 AAATAATTATTTAAATTAATATAAA
*
5875494 AAATAATTATTTACATTAATATA
1 AAATAATTATTTAAATTAATATA
5875517 TAAATTTCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
AAATAATTATTTAAATTAATATAAA
Found at i:5885621 original size:6 final size:6
Alignment explanation
Indices: 5885590--5885614 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5885580 GACATAATGC
5885590 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
5885615 AATAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:5898087 original size:36 final size:36
Alignment explanation
Indices: 5898039--5898132 Score: 109
Period size: 37 Copynumber: 2.6 Consensus size: 36
5898029 GGGTCTCCAA
* *
5898039 AATCACATTTCAATTCAATTTCACTTTTTCACTTTC
1 AATCACAATTCAATTCAATTTCACTTTTCCACTTTC
* *
5898075 AATCACAATTCAATTCAAAATTCACTTTTCCATTTTC
1 AATCACAATTCAATTC-AATTTCACTTTTCCACTTTC
*
5898112 AAGTCA-ATATTCATTTCAATT
1 AA-TCACA-ATTCAATTCAATT
5898133 CCACACATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
36 15 0.31
37 23 0.47
38 11 0.22
ACGTcount: A:0.33, C:0.22, G:0.01, T:0.44
Consensus pattern (36 bp):
AATCACAATTCAATTCAATTTCACTTTTCCACTTTC
Found at i:5898133 original size:36 final size:35
Alignment explanation
Indices: 5898039--5898133 Score: 102
Period size: 36 Copynumber: 2.6 Consensus size: 35
5898029 GGGTCTCCAA
* *
5898039 AATCACATTTCAATTCAATTTCACTTTTTCACTTTC
1 AATCACAATTCAATTCAA-TTCACTTTTCCACTTTC
*
5898075 AATCACAATTCAATTCAAAATTCACTTTTCCATTTTC
1 AATCACAATTCAATTC--AATTCACTTTTCCACTTTC
*
5898112 AAGTCA-ATATTCATTTCAATTC
1 AA-TCACA-ATTCAATTCAATTC
5898134 CACACATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
36 20 0.39
37 18 0.35
38 13 0.25
ACGTcount: A:0.33, C:0.23, G:0.01, T:0.43
Consensus pattern (35 bp):
AATCACAATTCAATTCAATTCACTTTTCCACTTTC
Found at i:5898444 original size:17 final size:18
Alignment explanation
Indices: 5898412--5898445 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5898402 ATTTTCTTTT
5898412 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
5898430 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
5898446 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:5898836 original size:9 final size:9
Alignment explanation
Indices: 5898819--5898858 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
5898809 TTAGTTTTTC
*
5898819 CTTTTCTTT
1 CTTTCCTTT
5898828 CTTTCCTTT
1 CTTTCCTTT
* *
5898837 CTTTTCTCT
1 CTTTCCTTT
5898846 CTTTCCTTT
1 CTTTCCTTT
5898855 CTTT
1 CTTT
5898859 TCTCCCTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (9 bp):
CTTTCCTTT
Found at i:5898842 original size:18 final size:18
Alignment explanation
Indices: 5898819--5898862 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
5898809 TTAGTTTTTC
*
5898819 CTTTTCTTTCTTTCCTTT
1 CTTTTCTCTCTTTCCTTT
5898837 CTTTTCTCTCTTTCCTTT
1 CTTTTCTCTCTTTCCTTT
5898855 CTTTTCTC
1 CTTTTCTC
5898863 CCTGTTTCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTTCTCTCTTTCCTTT
Found at i:5899207 original size:14 final size:17
Alignment explanation
Indices: 5899170--5899225 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
5899160 TACAATTTTC
*
5899170 ATAATTCAATTTATTAAT
1 ATAATT-AATTTAATAAT
*
5899188 -TAATATAATATTTATAAT
1 ATAAT-TAAT-TTAATAAT
5899206 ATAATTAATTTAATAAT
1 ATAATTAATTTAATAAT
5899223 ATA
1 ATA
5899226 CTTTACAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 17 0.53
18 11 0.34
19 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAATTAATTTAATAAT
Found at i:5900115 original size:21 final size:21
Alignment explanation
Indices: 5900089--5900156 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
5900079 AGTATTTTTT
5900089 AAAAAGTATTTTAAAAATTAA
1 AAAAAGTATTTTAAAAATTAA
**
5900110 AAAAAGTATTTTTAAAATATTTT
1 AAAAAGTA-TTTTAAAA-ATTAA
*
5900133 TAAAA-TATTTT-AAAATTAA
1 AAAAAGTATTTTAAAAATTAA
5900152 AAAAA
1 AAAAA
5900157 AATTAAAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 7 0.18
20 3 0.08
21 12 0.31
22 10 0.26
23 7 0.18
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAAAGTATTTTAAAAATTAA
Found at i:5900122 original size:34 final size:33
Alignment explanation
Indices: 5900060--5900138 Score: 124
Period size: 35 Copynumber: 2.4 Consensus size: 33
5900050 ACCAAAAATT
5900060 TATTTTAAAAATTAAAAAAAGTATTTTTTAAAAA
1 TATTTTAAAAATTAAAAAAAGTATTTTTT-AAAA
5900094 GTATTTTAAAAATTAAAAAAAGTA-TTTTTAAAA
1 -TATTTTAAAAATTAAAAAAAGTATTTTTTAAAA
*
5900127 TATTTTTAAAAT
1 TATTTTAAAAAT
5900139 ATTTTAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
32 11 0.26
33 4 0.09
34 5 0.12
35 23 0.53
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (33 bp):
TATTTTAAAAATTAAAAAAAGTATTTTTTAAAA
Found at i:5900132 original size:10 final size:10
Alignment explanation
Indices: 5900119--5900188 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
5900109 AAAAAAGTAT
5900119 TTTTAAAATA
1 TTTTAAAATA
5900129 TTTTTAAAATA
1 -TTTTAAAATA
5900140 TTTT-AAA-A
1 TTTTAAAATA
** *
5900148 TTAAAAAAAA
1 TTTTAAAATA
* *
5900158 ATTAAAAAGTA
1 TTTTAAAA-TA
5900169 TTTTTAAAATA
1 -TTTTAAAATA
5900180 TTTTAAAAT
1 TTTTAAAAT
5900189 TAAAAAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
8 3 0.06
9 6 0.12
10 20 0.42
11 13 0.27
12 6 0.12
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (10 bp):
TTTTAAAATA
Found at i:5900132 original size:11 final size:11
Alignment explanation
Indices: 5900111--5900148 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
5900101 AAAAATTAAA
5900111 AAAAGTATTTTT
1 AAAA-TATTTTT
5900123 AAAATATTTTT
1 AAAATATTTTT
5900134 AAAATA-TTTT
1 AAAATATTTTT
5900144 AAAAT
1 AAAAT
5900149 TAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 9 0.35
11 13 0.50
12 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:5900169 original size:51 final size:48
Alignment explanation
Indices: 5900101--5900243 Score: 163
Period size: 44 Copynumber: 3.0 Consensus size: 48
5900091 AAAGTATTTT
* *
5900101 AAAAATTAAAAAAAGTATTTTTAAAATATTTTTAAAATATTTTAAAATTAAAA
1 AAAAATT--AAAAAGTATTTTTAAAATA-TTTTAAAATA-TTAAAAAAT-AAA
*
5900154 AAAAATTAAAAAGTATTTTTAAAATATTTT-AAA-ATTAAAAAATAAT
1 AAAAATTAAAAAGTATTTTTAAAATATTTTAAAATATTAAAAAATAAA
*
5900200 AAAAA--AAAAAGTATTTTAAAAATATTTT-AAA-ATTAAAAAATAAA
1 AAAAATTAAAAAGTATTTTTAAAATATTTTAAAATATTAAAAAATAAA
5900244 TATATTTATT
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
44 37 0.44
46 7 0.08
47 7 0.08
48 1 0.01
49 3 0.04
50 4 0.05
51 19 0.22
53 7 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (48 bp):
AAAAATTAAAAAGTATTTTTAAAATATTTTAAAATATTAAAAAATAAA
Found at i:5904347 original size:17 final size:17
Alignment explanation
Indices: 5904317--5904349 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5904307 ATTCGAATAC
5904317 TATCAGACCCATTCCTG
1 TATCAGACCCATTCCTG
5904334 TATCA-ACCCTATTCCT
1 TATCAGACCC-ATTCCT
5904350 TATATTACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.36, G:0.06, T:0.33
Consensus pattern (17 bp):
TATCAGACCCATTCCTG
Found at i:5904748 original size:11 final size:11
Alignment explanation
Indices: 5904732--5904757 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5904722 AGAAAATTAA
5904732 TTTTTTCATAT
1 TTTTTTCATAT
5904743 TTTTTTCATAT
1 TTTTTTCATAT
5904754 TTTT
1 TTTT
5904758 CCCTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTCATAT
Found at i:5905620 original size:19 final size:20
Alignment explanation
Indices: 5905548--5905600 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
5905538 GCCCGTTTTA
5905548 TTTTTTTAATTTTAAAATAT
1 TTTTTTTAATTTTAAAATAT
5905568 TTTTTTTAATTTTAAAATAT
1 TTTTTTTAATTTTAAAATAT
5905588 TTTTTTTAATTTT
1 TTTTTTTAATTTT
5905601 TTTAATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTTTAATTTTAAAATAT
Found at i:5905631 original size:29 final size:29
Alignment explanation
Indices: 5905570--5905632 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
5905560 TAAAATATTT
** *
5905570 TTTTTAATTTTAAAATATTTTTTTTAATT
1 TTTTTAATTTTAAAATATTTTTTAAAATA
5905599 TTTTTAATTTTAAAATA-TTTTTAAAATAA
1 TTTTTAATTTTAAAATATTTTTTAAAAT-A
5905628 TTTTT
1 TTTTT
5905633 TGGTATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTTTAATTTTAAAATATTTTTTAAAATA
Found at i:5908214 original size:6 final size:6
Alignment explanation
Indices: 5908181--5908213 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
5908171 TTAAATTAAT
*
5908181 TTTTTA TTTTTA TTTTTA TTTTTA TTTCTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
5908214 CGTAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:5913059 original size:93 final size:92
Alignment explanation
Indices: 5912896--5913072 Score: 221
Period size: 93 Copynumber: 1.9 Consensus size: 92
5912886 CTCAGTTGAT
* * * * * **
5912896 GTTTAAAGGTTAGTTGCATTAAGTTCGCAACCTCCAGATTATTCGAGTTAACTTAGTTAAGCTTG
1 GTTTAAAGGTTAGTTGCATTAAGCTCGCAACCTCCAAATTATTCAAGTTAACTGAATTAAGCTCA
*
5912961 TAACTCTAAAACAACTCGCAAACTTAC
66 CAACTCTAAAACAACTCGCAAACTTAC
* *
5912988 GTTTCAAAGGTTAGTTG-AGTTAAGCTCGCAGCCTCCAAATTATTCAAGTTAGCTGAATTAAGCT
1 GTTT-AAAGGTTAGTTGCA-TTAAGCTCGCAACCTCCAAATTATTCAAGTTAACTGAATTAAGCT
* *
5913052 CACAACTCTGAAACAGCTCGC
64 CACAACTCTAAAACAACTCGC
5913073 GAACCTATGT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
92 5 0.07
93 66 0.93
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (92 bp):
GTTTAAAGGTTAGTTGCATTAAGCTCGCAACCTCCAAATTATTCAAGTTAACTGAATTAAGCTCA
CAACTCTAAAACAACTCGCAAACTTAC
Found at i:5913602 original size:104 final size:103
Alignment explanation
Indices: 5913493--5913779 Score: 299
Period size: 104 Copynumber: 2.8 Consensus size: 103
5913483 CTAGCTCATT
* * * * *
5913493 CTACTAAGGTTAGCTAAATTAAGATCGCAATCTCCGATTATTTAAGTTCACTGATTTAAGATCGC
1 CTACTAAGGCTCGCTGATTTAAGATCGCAATCTCCGATTATTTGAGTTCACTGATTTAAGATCGC
* *
5913558 AACTCTTAACAGCTCACTAATCTACGTTCACAGCTAATA
66 AACTC-TAACAACTCACTAATCTACGTTCACAACTAATA
* * * * *
5913597 TTACTAAGGCTCGTTGATTTAAGATCGCAA-CATCCAATTATTTGAGTTCGCTGATTTAAGAACG
1 CTACTAAGGCTCGCTGATTTAAGATCGCAATC-TCCGATTATTTGAGTTCACTGATTTAAGATCG
* * * * * *
5913661 CAACTGCTAACAACTCGCTGATTTATGTTCACAACTGATG
65 CAACT-CTAACAACTCACTAATCTACGTTCACAACTAATA
* * * * *
5913701 CTACTAAGGCTCGCTGATTTAAGATTGCAGTTTCCGATTATTTGAGTT-AGTTGATTTAAGATTG
1 CTACTAAGGCTCGCTGATTTAAGATCGCAATCTCCGATTATTTGAGTTCA-CTGATTTAAGATCG
*
5913765 CAATTCCTAACAACT
65 CAACT-CTAACAACT
5913780 TGCTGACATA
Statistics
Matches: 149, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
103 1 0.01
104 147 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (103 bp):
CTACTAAGGCTCGCTGATTTAAGATCGCAATCTCCGATTATTTGAGTTCACTGATTTAAGATCGC
AACTCTAACAACTCACTAATCTACGTTCACAACTAATA
Found at i:5913841 original size:104 final size:104
Alignment explanation
Indices: 5913525--5913841 Score: 323
Period size: 104 Copynumber: 3.0 Consensus size: 104
5913515 GATCGCAATC
* * * * * *
5913525 TCCGATTATTTAAGTTCA-CTGATTTAAGATCGCAACTCTTAACAGCTCACTAATC-TACGTTCA
1 TCCGATTATTTGAGTT-AGCTGATTTAAGAACGCAACTCCTAACAACTCGCTGA-CATACGTTCA
* * * *
5913588 CAGCTAATATTACTAAGGCTCGTTGATTTAAGATCGCAACA
64 CAGCTGATATTACTAAGGCTCGCTGATTTAAGATTGCAGCA
* * * ** *
5913629 TCCAATTATTTGAGTTCGCTGATTTAAGAACGCAACTGCTAACAACTCGCTGATTTATGTTCACA
1 TCCGATTATTTGAGTTAGCTGATTTAAGAACGCAACTCCTAACAACTCGCTGACATACGTTCACA
* ** **
5913694 ACTGATGCTACTAAGGCTCGCTGATTTAAGATTGCAGTT
66 GCTGATATTACTAAGGCTCGCTGATTTAAGATTGCAGCA
* ** * * *
5913733 TCCGATTATTTGAGTTAGTTGATTTAAGATTGCAATTCCTAACAACTTGCTGACATACGTTCAGA
1 TCCGATTATTTGAGTTAGCTGATTTAAGAACGCAACTCCTAACAACTCGCTGACATACGTTCACA
* * * *
5913798 GTTGATATTACTAAAGCTCGCTGATTTGAGATTGCAGCC
66 GCTGATATTACTAAGGCTCGCTGATTTAAGATTGCAGCA
5913837 TCCGA
1 TCCGA
5913842 ATAGCTCGTT
Statistics
Matches: 171, Mismatches: 40, Indels: 4
0.80 0.19 0.02
Matches are distributed among these distances:
104 171 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (104 bp):
TCCGATTATTTGAGTTAGCTGATTTAAGAACGCAACTCCTAACAACTCGCTGACATACGTTCACA
GCTGATATTACTAAGGCTCGCTGATTTAAGATTGCAGCA
Found at i:5917398 original size:12 final size:12
Alignment explanation
Indices: 5917381--5917414 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
5917371 AAATTAATCC
5917381 TTTCTCAATTAT
1 TTTCTCAATTAT
5917393 TTTCTCAATTAT
1 TTTCTCAATTAT
5917405 TTTCTCAATT
1 TTTCTCAATT
5917415 TCCTCTCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTCTCAATTAT
Found at i:5917423 original size:11 final size:11
Alignment explanation
Indices: 5917407--5917515 Score: 66
Period size: 11 Copynumber: 10.3 Consensus size: 11
5917397 TCAATTATTT
5917407 TCTCAATTTCC
1 TCTCAATTTCC
5917418 TCTCAATTTCC
1 TCTCAATTTCC
* * * *
5917429 TTTTAAATTGC
1 TCTCAATTTCC
5917440 TCTCAATTTCC
1 TCTCAATTTCC
*
5917451 TTTCAAATTT-C
1 TCTC-AATTTCC
*
5917462 TCTCAA-ATCC
1 TCTCAATTTCC
* **
5917472 -AT--ATTTAA
1 TCTCAATTTCC
*
5917480 TCTCAATTTGC
1 TCTCAATTTCC
* *
5917491 TTTCAATTTGC
1 TCTCAATTTCC
5917502 TCTCAATTTCC
1 TCTCAATTTCC
5917513 TCT
1 TCT
5917516 TAAATCCTTA
Statistics
Matches: 71, Mismatches: 21, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 3 0.04
10 3 0.04
11 58 0.82
12 5 0.07
ACGTcount: A:0.23, C:0.27, G:0.03, T:0.48
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:5917445 original size:22 final size:22
Alignment explanation
Indices: 5917417--5917520 Score: 85
Period size: 22 Copynumber: 4.9 Consensus size: 22
5917407 TCTCAATTTC
5917417 CTCTCAATTTCCTTTTAAATTG
1 CTCTCAATTTCCTTTTAAATTG
* *
5917439 CTCTCAATTTCCTTTCAAATTT
1 CTCTCAATTTCCTTTTAAATTG
*
5917461 CTCTCAA-ATCCATATTT-AA---
1 CTCTCAATTTCC-T-TTTAAATTG
* * *
5917480 -TCTCAATTTGCTTTCAATTTG
1 CTCTCAATTTCCTTTTAAATTG
*
5917501 CTCTCAATTTCCTCTTAAAT
1 CTCTCAATTTCCTTTTAAAT
5917521 CCTTATTTTT
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
17 2 0.03
18 8 0.13
19 2 0.03
21 3 0.05
22 45 0.73
23 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.03, T:0.47
Consensus pattern (22 bp):
CTCTCAATTTCCTTTTAAATTG
Found at i:5917548 original size:14 final size:14
Alignment explanation
Indices: 5917531--5917570 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
5917521 CCTTATTTTT
5917531 AATTATTTTAAAAA
1 AATTATTTTAAAAA
*
5917545 AATTATTTTTTAAAA
1 AATTA-TTTTAAAAA
5917560 AATT-TTTTAAA
1 AATTATTTTAAA
5917571 TCGTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 6 0.26
14 5 0.22
15 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTATTTTAAAAA
Found at i:5922306 original size:125 final size:125
Alignment explanation
Indices: 5922084--5922369 Score: 455
Period size: 125 Copynumber: 2.3 Consensus size: 125
5922074 CCCAAACATG
*
5922084 CTACTGTAGCAAAAATGTGTCCACGTGGGAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGC
1 CTACTGTAGCAAAAACGTGTCCACGTGGGAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGC
* * *
5922149 TTGAAGCATTTTTTATACTATTTGCTTAGAAACGTCAACTTGAAATTACTTTTTCAGGAC
66 TTGAAGCATTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATTACTTTTTCAGGAC
* * * *
5922209 CTACTGTAGCAAAAGCGTGTCCACGTGGGAGCGGTTTCAAAAATTCTTCTGATAAAGCATTCTGC
1 CTACTGTAGCAAAAACGTGTCCACGTGGGAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGC
** * *
5922274 TTGAAGTGTTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTTTAGGAC
66 TTGAAGCATTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATTACTTTTTCAGGAC
*
5922334 CTACTGTATCAAAAACGTGTCCACGTGGGAGCGATT
1 CTACTGTAGCAAAAACGTGTCCACGTGGGAGCGATT
5922370 CCCTTAATAA
Statistics
Matches: 146, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
125 146 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (125 bp):
CTACTGTAGCAAAAACGTGTCCACGTGGGAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGC
TTGAAGCATTTTTTATACTATTTGCTCAGAAACATCAACTCGAAATTACTTTTTCAGGAC
Found at i:5930623 original size:38 final size:38
Alignment explanation
Indices: 5930572--5930648 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
5930562 AAGAATGGTA
5930572 AATTTGTATGTCATTATAGTGGTGTTATAGGACACACT
1 AATTTGTATGTCATTATAGTGGTGTTATAGGACACACT
5930610 AATTTGTATGTCATTATAGTGGTGTTATAGGACACACT
1 AATTTGTATGTCATTATAGTGGTGTTATAGGACACACT
5930648 A
1 A
5930649 GACCTATATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (38 bp):
AATTTGTATGTCATTATAGTGGTGTTATAGGACACACT
Found at i:5934156 original size:33 final size:33
Alignment explanation
Indices: 5934119--5934222 Score: 127
Period size: 33 Copynumber: 3.4 Consensus size: 33
5934109 CATTTTGTGT
5934119 CTTATTTAGGATATTATGATGACATTTGATGGG
1 CTTATTTAGGATATTATGATGACATTTGATGGG
* *
5934152 CTTATTTAGG--A-TAT-CT---ATTTG-T-GT
1 CTTATTTAGGATATTATGATGACATTTGATGGG
5934176 CTTATTTAGGATATTATGATGACATTTGATGGG
1 CTTATTTAGGATATTATGATGACATTTGATGGG
5934209 CTTATTTAGGATAT
1 CTTATTTAGGATAT
5934223 CTATTGTTGG
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
24 11 0.19
25 1 0.02
26 6 0.10
27 3 0.05
28 1 0.02
29 1 0.02
30 3 0.05
31 6 0.10
32 1 0.02
33 25 0.43
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.46
Consensus pattern (33 bp):
CTTATTTAGGATATTATGATGACATTTGATGGG
Found at i:5934200 original size:57 final size:57
Alignment explanation
Indices: 5934112--5934227 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
5934102 TCATCTTCAT
5934112 TTTGTGTCTTATTTAGGATATTATGATGACATTTGATGGGCTTATTTAGGATATCTA
1 TTTGTGTCTTATTTAGGATATTATGATGACATTTGATGGGCTTATTTAGGATATCTA
5934169 TTTGTGTCTTATTTAGGATATTATGATGACATTTGATGGGCTTATTTAGGATATCTA
1 TTTGTGTCTTATTTAGGATATTATGATGACATTTGATGGGCTTATTTAGGATATCTA
5934226 TT
1 TT
5934228 GTTGGATTCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (57 bp):
TTTGTGTCTTATTTAGGATATTATGATGACATTTGATGGGCTTATTTAGGATATCTA
Found at i:5959704 original size:22 final size:22
Alignment explanation
Indices: 5959663--5959705 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5959653 AAGAAAATTT
* * *
5959663 AAAATTTATTTTTTATATTATG
1 AAAATTAATTTTTCAAATTATG
5959685 AAAATTAATTTTTCAAATTAT
1 AAAATTAATTTTTCAAATTAT
5959706 AATCTTGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
AAAATTAATTTTTCAAATTATG
Found at i:5960280 original size:18 final size:16
Alignment explanation
Indices: 5960248--5960282 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5960238 CAAGAGAGGG
5960248 AGAAAAGAAGAAAGAA
1 AGAAAAGAAGAAAGAA
5960264 AGAAAAGAGACGAAAGAA
1 AGAAAAGA-A-GAAAGAA
5960282 A
1 A
5960283 ATGTATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAGAAAGAA
Found at i:5963509 original size:62 final size:61
Alignment explanation
Indices: 5963433--5963662 Score: 361
Period size: 62 Copynumber: 3.7 Consensus size: 61
5963423 CAATGTACCT
*
5963433 AATTTATATTACAAAGTTTGTTCTAATTTTTAATGTTGTAATGTATTTAATTTATATAGCAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATA-CAA
* * *
5963495 AATTTATATTACAAAGTTTGTTCTAATTTTTAATGTTGTGATGTATTTAATTTATATAAAAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATAT-ACAA
5963557 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATA-TACAA
* * * *
5963619 AATTTATATTATAAAGTTTGTTCCAAGTTTTAGTGTTTTAATGT
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGT
5963663 TGTAATGTTG
Statistics
Matches: 157, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
62 155 0.99
63 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (61 bp):
AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATACAA
Found at i:5963596 original size:124 final size:125
Alignment explanation
Indices: 5963433--5963725 Score: 387
Period size: 124 Copynumber: 2.3 Consensus size: 125
5963423 CAATGTACCT
*
5963433 AATTTATATTACAAAGTTTGTTCTAATTTTTAATGTTGTAATGTATTTAATTTATA-TAGCAAAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTA-CAAAA
* * * *
5963497 TTTATATTACAAAGTTTGTTCTAATTTTTAATGTTGTGATGTATTTAAT-TT--ATATAAAAA
65 TTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT-TGTAATGTTCAAT-TAAAAA
5963557 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTACAAAAT
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTACAAAAT
* * * ***
5963622 TTATATTATAAAGTTTGTTCCAAGTTTTAGTGTTTTAATGTTGTAATGTTGCAATTAATCT
66 TTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTGTAATGTT-CAATTAAAAA
** *
5963683 AATTTATTACCACAAAGTTTGTTCCAAGTTTTAATGTTGTAAT
1 AATTTA-TATTACAAAGTTTGTTCCAATTTTTAATGTTGTAAT
5963726 TAATCTAATT
Statistics
Matches: 149, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
123 5 0.03
124 98 0.66
125 2 0.01
126 9 0.06
127 35 0.23
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (125 bp):
AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTACAAAAT
TTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTGTAATGTTCAATTAAAAA
Found at i:5964081 original size:33 final size:33
Alignment explanation
Indices: 5963998--5964084 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
5963988 TTGAACTGGA
* * *
5963998 AGGAGTGCTGTACTACGATGGATACGACCCGGG
1 AGGAGTGCTGTACTGCGGTGGATACGACCCAGG
** * *
5964031 AGGAGTGGAGTAATGCGGTGGATAC-AGGCCAGG
1 AGGAGTGCTGTACTGCGGTGGATACGA-CCCAGG
5964064 AGGAGTGCTGTACTGCGGTGG
1 AGGAGTGCTGTACTGCGGTGG
5964085 TACTGGACTA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 1 0.02
33 42 0.98
ACGTcount: A:0.23, C:0.16, G:0.43, T:0.18
Consensus pattern (33 bp):
AGGAGTGCTGTACTGCGGTGGATACGACCCAGG
Found at i:5964904 original size:14 final size:14
Alignment explanation
Indices: 5964885--5964919 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5964875 TAAATTACAT
5964885 GTTAGAATAGTATC
1 GTTAGAATAGTATC
5964899 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
5964913 ATTAGAA
1 GTTAGAA
5964920 AAAAAATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:5966804 original size:26 final size:25
Alignment explanation
Indices: 5966775--5966823 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
5966765 TTCTATTTAT
5966775 TTTTTTACCTTCTTTTTCTCCTTCTC
1 TTTTTTACCTTCTTTTTC-CCTTCTC
* *
5966801 TTTTTTTCTTTCTTTTTCCCTTC
1 TTTTTTACCTTCTTTTTCCCTTC
5966824 CCTTCCCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTTTACCTTCTTTTTCCCTTCTC
Found at i:5968226 original size:56 final size:56
Alignment explanation
Indices: 5968140--5968264 Score: 223
Period size: 56 Copynumber: 2.2 Consensus size: 56
5968130 TCTGCACAAA
*
5968140 ACCCTCATTTGGCACACCTCTTTTGTTGTAGGATAGTTTCAAAAAATATGGTTCCT
1 ACCCTCATTTGGCACACCTCTTTTGTTGTAGGACAGTTTCAAAAAATATGGTTCCT
5968196 ACCCTCATTTGGCACACCTCTTTTGTTGTAGGACAGTTTCAAAAAATATGGTTCCT
1 ACCCTCATTTGGCACACCTCTTTTGTTGTAGGACAGTTTCAAAAAATATGGTTCCT
* *
5968252 ATCCTCCTTTGGC
1 ACCCTCATTTGGC
5968265 CCGCGACATT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 66 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (56 bp):
ACCCTCATTTGGCACACCTCTTTTGTTGTAGGACAGTTTCAAAAAATATGGTTCCT
Found at i:5972182 original size:23 final size:23
Alignment explanation
Indices: 5972156--5972211 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
5972146 CACTTATGGG
5972156 CCTAAAATTGGGCTTACGTGGCC
1 CCTAAAATTGGGCTTACGTGGCC
5972179 CCTAAAATTGGGCTTACGTGGCC
1 CCTAAAATTGGGCTTACGTGGCC
*
5972202 CTTAACAATT
1 CCTAA-AATT
5972212 CAGGGTCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 27 0.87
24 4 0.13
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (23 bp):
CCTAAAATTGGGCTTACGTGGCC
Found at i:5976609 original size:21 final size:22
Alignment explanation
Indices: 5976580--5976626 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
5976570 CAGAAGGAGT
*
5976580 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
5976602 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
5976623 GAGT
1 GAGT
5976627 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:5978047 original size:18 final size:18
Alignment explanation
Indices: 5978024--5978064 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
5978014 TCCAAGAAGT
5978024 ACTAGGGGTTATACGAGG
1 ACTAGGGGTTATACGAGG
5978042 ACTAGGGGTTATACGAGG
1 ACTAGGGGTTATACGAGG
5978060 ACTAG
1 ACTAG
5978065 TCTCAGATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.37, T:0.22
Consensus pattern (18 bp):
ACTAGGGGTTATACGAGG
Found at i:5979747 original size:13 final size:13
Alignment explanation
Indices: 5979729--5979753 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5979719 AATTGCTTAT
5979729 CAAATGCATATAC
1 CAAATGCATATAC
5979742 CAAATGCATATA
1 CAAATGCATATA
5979754 TATTTAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
CAAATGCATATAC
Found at i:5980000 original size:41 final size:41
Alignment explanation
Indices: 5979939--5980041 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 41
5979929 ATTCGGTACG
* * *
5979939 CCGGCTTTTAGCCTGCTAGACTTATAGTCCGAA-ATATATCA
1 CCGGCATTAAGCCTGCTAGACGTATAGTCCGAATA-ATATCA
* * *
5979980 CCGGCATTAAGCCTGTTAGACGTATAGTCTGAATAATTTCA
1 CCGGCATTAAGCCTGCTAGACGTATAGTCCGAATAATATCA
* *
5980021 CCGGCATAAAGCCTACTAGAC
1 CCGGCATTAAGCCTGCTAGAC
5980042 ATAAAGTCTG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 51 0.98
42 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (41 bp):
CCGGCATTAAGCCTGCTAGACGTATAGTCCGAATAATATCA
Found at i:5980050 original size:41 final size:41
Alignment explanation
Indices: 5979977--5980072 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
5979967 CCGAAATATA
* ** * *
5979977 TCACCGGCATTAAGCCTGTTAGACGTATAGTCTGAATAATT
1 TCACCGGCATAAAGCCTACTAGACATAAAGTCTGAATAATT
*
5980018 TCACCGGCATAAAGCCTACTAGACATAAAGTCTGAATTATT
1 TCACCGGCATAAAGCCTACTAGACATAAAGTCTGAATAATT
*
5980059 TCACTGGCAATAAA
1 TCACCGGC-ATAAA
5980073 TCAGATTAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 42 0.89
42 5 0.11
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (41 bp):
TCACCGGCATAAAGCCTACTAGACATAAAGTCTGAATAATT
Found at i:5981281 original size:27 final size:27
Alignment explanation
Indices: 5981216--5981282 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
5981206 TTTGTTTAAT
* * *
5981216 TATAATATTATAATATAATATATATAT
1 TATAATATTATAATATAATATAAAAAC
*
5981243 TATAACATTTATAAT-TAATATAAAAAC
1 TATAATA-TTATAATATAATATAAAAAC
5981270 TATATATATTATA
1 TATA-ATATTATA
5981283 CACAAGCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
27 24 0.73
28 9 0.27
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
TATAATATTATAATATAATATAAAAAC
Found at i:5982653 original size:46 final size:44
Alignment explanation
Indices: 5982564--5982657 Score: 138
Period size: 46 Copynumber: 2.1 Consensus size: 44
5982554 ATTACAACAT
5982564 CATTCCATTCAACCAAATACAAGAATATTATTACAGCTCTATTC
1 CATTCCATTCAACCAAATACAAGAATATTATTACAGCTCTATTC
5982608 CATTCCATTCAACC-AA-ACAATTGAATTACTTATTACAGCTCTATTC
1 CATTCCATTCAACCAAATACAA--GAA-TA-TTATTACAGCTCTATTC
5982654 CATT
1 CATT
5982658 ACAGCTCAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
42 4 0.09
43 2 0.04
44 17 0.37
45 2 0.04
46 21 0.46
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAATACAAGAATATTATTACAGCTCTATTC
Done.