Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 136 of 279
Found at i:43942719 original size:24 final size:24
Alignment explanation
Indices: 43942692--43942741 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
43942682 TGGTTTCAAC
*
43942692 AATTATAATAAAATATTTTTTTGA
1 AATTATAATAAAATAATTTTTTGA
* *
43942716 AATTATAATTATATAATTTTTTGA
1 AATTATAATAAAATAATTTTTTGA
43942740 AA
1 AA
43942742 AACTTCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
AATTATAATAAAATAATTTTTTGA
Found at i:43946587 original size:46 final size:46
Alignment explanation
Indices: 43946519--43946609 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 46
43946509 TATATATACA
* * * *
43946519 CATCTCATACATTTCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACAATTCTCACATTAACCATTCGGCTTCACCACATATC
* *
43946565 CATCTCATACACATT-TCGCATTAACCATTCGGCTTCCCCACATAT
1 CATCTCATACA-ATTCTCACATTAACCATTCGGCTTCACCACATAT
43946610 ATACACTTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 36 0.95
47 2 0.05
ACGTcount: A:0.26, C:0.33, G:0.07, T:0.34
Consensus pattern (46 bp):
CATCTCATACAATTCTCACATTAACCATTCGGCTTCACCACATATC
Found at i:43946652 original size:22 final size:22
Alignment explanation
Indices: 43946626--43946701 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
43946616 TTCCACGTTC
43946626 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
43946648 ATCACACATAT-G-CATGTTC-ACATT
1 AT--CACAT-TGGCCA--TTCGGCCTT
43946672 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
43946695 ATCACAT
1 ATCACAT
43946702 ATATACATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 13 0.32
23 11 0.27
24 11 0.27
25 6 0.15
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:43946674 original size:47 final size:47
Alignment explanation
Indices: 43946623--43946883 Score: 414
Period size: 47 Copynumber: 5.6 Consensus size: 47
43946613 CACTTCCACG
*
43946623 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACAAATGCATGTTCACA
* * *
43946670 TTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACAAATGCATGTTCACA
**
43946717 TTCATCACATTGGCCATTCGATCTTATCACACAAATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACAAATGCATGTTCACA
* *
43946764 CTCATCACATTGGCCATTCGGCCTTAGCACACAAATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACAAATGCATGTTCACA
* *
43946811 TTCATCACATTTGCCATTCGGCCTTAGCACACAAATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACAAATGCATGTTCACA
* *
43946858 TTCATCACATTTGCCACTCGGCCTTA
1 TTCATCACATTGGCCATTCGGCCTTA
43946884 GCTCATATAT
Statistics
Matches: 200, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 200 1.00
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACACAAATGCATGTTCACA
Found at i:43946690 original size:94 final size:94
Alignment explanation
Indices: 43946589--43946914 Score: 412
Period size: 94 Copynumber: 3.5 Consensus size: 94
43946579 TTCGCATTAA
* * *
43946589 CCATTCGG-CTTCCCCACATATATACACT-TCCACGTTCATCACATTGGCCATTCGGCCTTATCA
1 CCATTCGGCCTT-CACACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCA
*
43946652 CACATATGCATGTTCACATTCATCACATTGG
64 CACAAATGCATGTTCACATTCATCACATTGG
**
43946683 CCATTCGGCCTT-ATCACATATATACATGTTCACATTCATCACATTGGCCATTCGATCTTATCAC
1 CCATTCGGCCTTCA-CACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
*
43946747 ACAAATGCATGTTCACACTCATCACATTGG
65 ACAAATGCATGTTCACATTCATCACATTGG
* * *
43946777 CCATTCGGCCTTAGCACACA-A-ATGCATGTTCACATTCATCACATTTGCCATTCGGCCTTAGCA
1 CCATTCGGCCTT--CACACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCA
*
43946840 CACAAATGCATGTTCACATTCATCACATTTG
64 CACAAATGCATGTTCACATTCATCACATTGG
* * ** *
43946871 CCACTCGGCCTT-AGCTCATATATACACATTCACATCCATCACAT
1 CCATTCGGCCTTCA-CACATATATACATGTTCACATTCATCACAT
43946915 AAAATCCTAA
Statistics
Matches: 203, Mismatches: 20, Indels: 18
0.84 0.08 0.07
Matches are distributed among these distances:
91 1 0.00
92 3 0.01
93 2 0.01
94 188 0.93
95 4 0.02
96 4 0.02
97 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.30
Consensus pattern (94 bp):
CCATTCGGCCTTCACACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACA
CAAATGCATGTTCACATTCATCACATTGG
Found at i:43946819 original size:23 final size:23
Alignment explanation
Indices: 43946793--43946866 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
43946783 GGCCTTAGCA
43946793 CACAAATGCATGTTCACATTCAT
1 CACAAATGCATGTTCACATTCAT
** * *
43946816 CACATTTGCCA--TTCGGCCTTAGCA-
1 CACAAATG-CATGTTC-ACATT--CAT
43946840 CACAAATGCATGTTCACATTCAT
1 CACAAATGCATGTTCACATTCAT
43946863 CACA
1 CACA
43946867 TTTGCCACTC
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 5 0.14
23 15 0.42
24 11 0.31
25 5 0.14
ACGTcount: A:0.31, C:0.30, G:0.11, T:0.28
Consensus pattern (23 bp):
CACAAATGCATGTTCACATTCAT
Found at i:43946903 original size:47 final size:47
Alignment explanation
Indices: 43946623--43946914 Score: 404
Period size: 47 Copynumber: 6.2 Consensus size: 47
43946613 CACTTCCACG
*
43946623 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTAGCACACATATGCATGTTCACA
* * *
43946670 TTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTAGCACACATATGCATGTTCACA
** * *
43946717 TTCATCACATTGGCCATTCGATCTTATCACACAAATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTAGCACACATATGCATGTTCACA
* *
43946764 CTCATCACATTGGCCATTCGGCCTTAGCACACAAATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTAGCACACATATGCATGTTCACA
* *
43946811 TTCATCACATTTGCCATTCGGCCTTAGCACACAAATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTAGCACACATATGCATGTTCACA
* * * * * **
43946858 TTCATCACATTTGCCACTCGGCCTTAGCTCATATATACACATTCACA
1 TTCATCACATTGGCCATTCGGCCTTAGCACACATATGCATGTTCACA
*
43946905 TCCATCACAT
1 TTCATCACAT
43946915 AAAATCCTAA
Statistics
Matches: 224, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 224 1.00
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.31
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTAGCACACATATGCATGTTCACA
Found at i:43950220 original size:3 final size:3
Alignment explanation
Indices: 43950212--43950636 Score: 305
Period size: 3 Copynumber: 139.7 Consensus size: 3
43950202 TTTTATTTTA
* * * *
43950212 ATT ATT ATT A-T ATT ATT ATT GTT ATT ACT AGT ATT -TT -TT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * ** * * *
43950257 ATC ATT ATT ATT ATT ATT -TT CACT ATA ACC ATT ATT TTCT GTT ATC
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT AT-T ATT ATT
* * * *
43950303 ATT ATT ATT ACT ATT ACT ATT TTT A-C ATT ATT ATT -TAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
* * * *
43950347 ATT GTT ATT ATT ATT CCTG ATT -TT ATT ATT AATGT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT -AT-T ATT ATT ATT ATT
* * * * * *
43950394 CTT CATT -TT ATC CTT ATT ATT ATT TTT ACT ATT ATC ATT ATT ATT
1 ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
43950439 AACCT ATT ATT GTT CTT ATT AGT ACGTT ATT ATT ATT -TCCT ATT -TT
1 -A-TT ATT ATT ATT ATT ATT ATT A--TT ATT ATT ATT AT--T ATT ATT
* * * **
43950485 TTT A-T ATT ATT ATTT GTT GTT AAC ATAT ATT AGTGT ATT ATT ATT ATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT AT-T ATT A-T-T ATT ATT ATT ATT
43950533 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43950581 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43950629 ATT ATT AT
1 ATT ATT AT
43950637 ACTATTAAAC
Statistics
Matches: 332, Mismatches: 63, Indels: 54
0.74 0.14 0.12
Matches are distributed among these distances:
2 19 0.06
3 286 0.86
4 20 0.06
5 7 0.02
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:43950897 original size:3 final size:3
Alignment explanation
Indices: 43950889--43950915 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
43950879 CGATCTTTAC
43950889 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
43950916 TACTACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:43951001 original size:3 final size:3
Alignment explanation
Indices: 43950980--43951035 Score: 85
Period size: 3 Copynumber: 18.3 Consensus size: 3
43950970 TTTGTCCTTG
* *
43950980 TAT TAT TGT TAT TCTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43951026 TAT TAT TAT T
1 TAT TAT TAT T
43951036 TGTTTTATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 46 0.96
4 2 0.04
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:43954599 original size:17 final size:17
Alignment explanation
Indices: 43954577--43954610 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43954567 ATCCACTAAT
*
43954577 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
43954594 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
43954611 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:43959238 original size:17 final size:17
Alignment explanation
Indices: 43959216--43959249 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43959206 ATCCACTAAT
*
43959216 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
43959233 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
43959250 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:43963877 original size:17 final size:17
Alignment explanation
Indices: 43963855--43963888 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43963845 ATCCACTAAT
*
43963855 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
43963872 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
43963889 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:43972523 original size:3 final size:3
Alignment explanation
Indices: 43972515--43972544 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
43972505 ATTAATTAGG
43972515 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43972545 AAACTGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:43972848 original size:21 final size:22
Alignment explanation
Indices: 43972804--43972853 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
43972794 AATAACTTCA
* *
43972804 TAAAATATAATTTAGATAATTT
1 TAAAATATAATTAAAATAATTT
*
43972826 TAAAATGTAATTAAAAT-ATTT
1 TAAAATATAATTAAAATAATTT
43972847 TAAAATA
1 TAAAATA
43972854 GTTAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
TAAAATATAATTAAAATAATTT
Found at i:43972860 original size:19 final size:20
Alignment explanation
Indices: 43972822--43972860 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
43972812 AATTTAGATA
43972822 ATTTTAAAATGTAATTAAAAT
1 ATTTTAAAA-GTAATTAAAAT
*
43972843 ATTTTAAAA-TAGTTAAAA
1 ATTTTAAAAGTAATTAAAA
43972861 AAAAGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
ATTTTAAAAGTAATTAAAAT
Found at i:43978608 original size:16 final size:16
Alignment explanation
Indices: 43978540--43978609 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 16
43978530 AATCAAATAA
43978540 AATTTT-AATTTTTAAT
1 AATTTTAAATTTTT-AT
*
43978556 AA-TTTATATTTTTAT
1 AATTTTAAATTTTTAT
**
43978571 AATTTTTAAATAATTA-
1 AA-TTTTAAATTTTTAT
43978587 AA--TTAAATTTTTAT
1 AATTTTAAATTTTTAT
43978601 AATTTTAAA
1 AATTTTAAA
43978610 ATAGTGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
13 9 0.21
14 2 0.05
15 7 0.17
16 15 0.36
17 9 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTTAAATTTTTAT
Found at i:43978629 original size:30 final size:30
Alignment explanation
Indices: 43978560--43978629 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
43978550 TTTAATAATT
* * * *
43978560 TATATTTTTATAATTTTTAAATAATTAAAT
1 TATAATTTTATAATTTTAAAATAATGAAAA
*
43978590 TA-AATTTTTATAATTTTAAAATAGTGAAAA
1 TATAA-TTTTATAATTTTAAAATAATGAAAA
43978620 TATAATTTTA
1 TATAATTTTA
43978630 ATTTTACCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 1 0.03
30 30 0.91
31 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (30 bp):
TATAATTTTATAATTTTAAAATAATGAAAA
Found at i:43984536 original size:3 final size:3
Alignment explanation
Indices: 43984523--43984560 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
43984513 ATAAAGTAAG
43984523 AAT AA- AAT AAT AAT AAT AAT AAT AAT AACT AATT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AA-T AAT A
43984561 TTGAGCGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.06
3 24 0.75
4 6 0.19
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:43986381 original size:25 final size:23
Alignment explanation
Indices: 43986353--43986399 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
43986343 AAATTCATTA
43986353 AAATTATATATAAATATATCAAATT
1 AAATTATA-ATAAAT-TATCAAATT
*
43986378 AAATTATAATAAATTATTAAAT
1 AAATTATAATAAATTATCAAAT
43986400 GTTTGCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATTATAATAAATTATCAAATT
Found at i:43986502 original size:23 final size:24
Alignment explanation
Indices: 43986452--43986503 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
43986442 AATATAAATC
*
43986452 TTAAA-TGTTTTTAAAACATTAAT
1 TTAAATTGTTCTTAAAACATTAAT
* *
43986475 ATAAATTGTTCTTAAAA-TTTAAT
1 TTAAATTGTTCTTAAAACATTAAT
43986498 TTAAAT
1 TTAAAT
43986504 ATATAAATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (24 bp):
TTAAATTGTTCTTAAAACATTAAT
Found at i:43988067 original size:4 final size:4
Alignment explanation
Indices: 43988058--43988111 Score: 63
Period size: 4 Copynumber: 13.0 Consensus size: 4
43988048 AATCATTACT
* * *
43988058 TGTA TGTA TGTA TGGA TGTA TGTA TGGA TGTA TGTA TGTGAA TGTA CGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT--A TGTA TGTA
43988108 TGTA
1 TGTA
43988112 GTTTGAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
4 38 0.90
6 4 0.10
ACGTcount: A:0.26, C:0.02, G:0.30, T:0.43
Consensus pattern (4 bp):
TGTA
Found at i:43988078 original size:12 final size:12
Alignment explanation
Indices: 43988061--43988109 Score: 71
Period size: 12 Copynumber: 3.9 Consensus size: 12
43988051 CATTACTTGT
43988061 ATGTATGTATGG
1 ATGTATGTATGG
43988073 ATGTATGTATGG
1 ATGTATGTATGG
43988085 ATGTATGTATGTG
1 ATGTATGTATG-G
*
43988098 AATGTACGTATG
1 -ATGTATGTATG
43988110 TAGTTTGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
12 23 0.68
13 1 0.03
14 10 0.29
ACGTcount: A:0.27, C:0.02, G:0.31, T:0.41
Consensus pattern (12 bp):
ATGTATGTATGG
Found at i:43990937 original size:22 final size:23
Alignment explanation
Indices: 43990912--43990971 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
43990902 TGGACTGAAT
43990912 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
43990934 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
43990956 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
43990972 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:43990939 original size:4 final size:4
Alignment explanation
Indices: 43990921--43990954 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
43990911 TATAAAAATT
43990921 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
43990955 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:43995859 original size:21 final size:21
Alignment explanation
Indices: 43995835--43995876 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
43995825 TAGAAATTAC
43995835 TAAA-AAAATTAATACATAAAA
1 TAAATAAAA-TAATACATAAAA
* *
43995856 TAAATACAATAATAGATAAAA
1 TAAATAAAATAATACATAAAA
43995877 CGAGATGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAATAAAATAATACATAAAA
Found at i:43997606 original size:50 final size:50
Alignment explanation
Indices: 43997487--43997735 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
43997477 GATAATAACA
* * * ** * *
43997487 TGCCAAAGCCACGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
43997538 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
43997588 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
43997638 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
43997693 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
43997736 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 22, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:43997661 original size:100 final size:104
Alignment explanation
Indices: 43997486--43997735 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
43997476 TGATAATAAC
* **
43997486 ATGCCAAAGCCACGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
43997551 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
43997588 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
43997651 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
43997693 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
43997736 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 35 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:43997851 original size:13 final size:13
Alignment explanation
Indices: 43997830--43997861 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
43997820 GCTTGGATCA
*
43997830 TCATCAAATAAAT
1 TCATAAAATAAAT
43997843 TCATAAAATAAAT
1 TCATAAAATAAAT
43997856 TCATAA
1 TCATAA
43997862 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:43998107 original size:30 final size:30
Alignment explanation
Indices: 43998073--43998130 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
43998063 CCTCGACTCT
**
43998073 AACTTTTTTAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
43998103 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
43998131 AAGGCTCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:44000423 original size:23 final size:22
Alignment explanation
Indices: 44000371--44000423 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
44000361 TCCTCGTCTT
*
44000371 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
44000393 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
44000416 TTTCTTTT
1 TTTCTTTT
44000424 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:44008760 original size:41 final size:41
Alignment explanation
Indices: 44008714--44008814 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 41
44008704 TCGACCTCGA
*
44008714 GTCGATGAGACACTGGGTGTCACTAAATTT-CTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAG
* ** * *
44008754 ATTCGATGAGGTACT-GG-GT-ACCAACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAG
*
44008793 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
44008815 ACTATTACTT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
38 17 0.37
39 13 0.28
40 4 0.09
41 12 0.26
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.28
Consensus pattern (41 bp):
GTCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAG
Found at i:44008823 original size:39 final size:39
Alignment explanation
Indices: 44008716--44008850 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
44008706 GACCTCGAGT
* * *
44008716 CGATGAGACACTGGGTGTC-ACTAAATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAACT--ATTACTTCGGCTAG-TC
** ** *
44008757 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
44008795 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
44008834 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
44008851 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 3 0.04
41 15 0.20
42 3 0.04
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:44013869 original size:20 final size:20
Alignment explanation
Indices: 44013840--44013879 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
44013830 ATTTAAGTAT
*
44013840 TAAAATATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
44013860 TAAAAGATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
44013880 AATAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TAAAAGATATTTATTAATTA
Found at i:44016089 original size:6 final size:6
Alignment explanation
Indices: 44016078--44016102 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
44016068 CTTGTTTTTC
44016078 TATAAT TATAAT TATAAT TATAAT T
1 TATAAT TATAAT TATAAT TATAAT T
44016103 GTTATATTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATAAT
Found at i:44035612 original size:37 final size:37
Alignment explanation
Indices: 44035562--44035635 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
44035552 AAAAAATTGA
44035562 AAGTTTCTATACATATATGCTGGAAGTATATGATGAT
1 AAGTTTCTATACATATATGCTGGAAGTATATGATGAT
*
44035599 AAGTTTCTATACATATGTGCTGGAAGTATATGATGAT
1 AAGTTTCTATACATATATGCTGGAAGTATATGATGAT
44035636 TTGGCATGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (37 bp):
AAGTTTCTATACATATATGCTGGAAGTATATGATGAT
Found at i:44039723 original size:23 final size:23
Alignment explanation
Indices: 44039685--44039731 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
44039675 AGGATTTATA
44039685 ATATTCTGGGTGTGTTTGGGCTGG
1 ATATTCTGGGTGTGTTTGGG-TGG
44039709 ATATTCT-GGTGTGTTTGGGTGG
1 ATATTCTGGGTGTGTTTGGGTGG
44039731 A
1 A
44039732 ATCCGCGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.17
23 12 0.52
24 7 0.30
ACGTcount: A:0.11, C:0.06, G:0.40, T:0.43
Consensus pattern (23 bp):
ATATTCTGGGTGTGTTTGGGTGG
Found at i:44040727 original size:41 final size:40
Alignment explanation
Indices: 44040679--44040757 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
44040669 CGTGTGAGAA
* *
44040679 TGAGATAGCTCTCGACTATATATGGCACTTAGTGTGCGATT
1 TGAGATAGCTCT-GACTATATACGACACTTAGTGTGCGATT
* * *
44040720 TGAGATAGCTGTGGCTATGTACGACACTTAGTGTGCGA
1 TGAGATAGCTCTGACTATATACGACACTTAGTGTGCGA
44040758 GATATAGAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
40 22 0.67
41 11 0.33
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (40 bp):
TGAGATAGCTCTGACTATATACGACACTTAGTGTGCGATT
Found at i:44040782 original size:28 final size:28
Alignment explanation
Indices: 44040742--44040818 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 28
44040732 GGCTATGTAC
44040742 GACACTTAGTGTGCGAGATATAGAGTAT
1 GACACTTAGTGTGCGAGATATAGAGTAT
* *
44040770 GACACTTAGTGTGCAAGATATCGAGTAT
1 GACACTTAGTGTGCGAGATATAGAGTAT
* *
44040798 GGCACTTAGTGTGCGAAATAT
1 GACACTTAGTGTGCGAGATAT
44040819 TTAGTATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (28 bp):
GACACTTAGTGTGCGAGATATAGAGTAT
Found at i:44046017 original size:27 final size:27
Alignment explanation
Indices: 44045727--44046009 Score: 415
Period size: 27 Copynumber: 10.5 Consensus size: 27
44045717 ATTACCAAAG
* *
44045727 TACCCTCAATTTATAGAATTACCGTTC
1 TACCCTCGATTTATAGAATTACCGTTT
*
44045754 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
44045781 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
44045808 TACCCTCGATTTACAGAATTACAGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
44045835 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
44045862 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
44045889 TACCCTCGATTTATCA-AATTACTGTTT
1 TACCCTCGATTTAT-AGAATTACCGTTT
*
44045916 TACCCTTGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
44045943 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * *
44045970 TACCCTTGACTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
44045997 TACCCTCAATTTA
1 TACCCTCGATTTA
44046010 CAAAATTATT
Statistics
Matches: 228, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.00
27 226 0.99
28 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCGTTT
Found at i:44046028 original size:81 final size:81
Alignment explanation
Indices: 44045700--44046061 Score: 413
Period size: 81 Copynumber: 4.5 Consensus size: 81
44045690 ATTACTGAAA
* * * *** * * *
44045700 TACCCTCAAATTATAAAATTACCAAAGTACCCTCAATTTATAGAATTACCGTTCTACCCTCGATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATT
44045765 TATAGAATTACC-ATTT
66 TATAGAATTACCGA-TT
* *
44045781 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACAGTTTTACCCTCGATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATT
* *
44045846 TATAGAATTATCGTTT
66 TATAGAATTACCGATT
* * *
44045862 TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATCA-AATTACTGTTTTACCCTTGAT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTA-CAGAATTACCGTTTTACCCTCGAT
*
44045926 TTATAGAATTACCGTTT
65 TTATAGAATTACCGATT
* * *
44045943 TACCCTCGATTTATAGAATTACCATTTTACCCTTGACTTACAGAATTACCGTTTTACCCTCAATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATT
* * ** **
44046008 TACAAAATTATTGAAA
66 TATAGAATTACCGATT
* * ***
44046024 TACCCTTGATTTATAAAATTACCAAAATACCCTCGATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATT
44046062 AGTAAAATTT
Statistics
Matches: 240, Mismatches: 38, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
80 2 0.01
81 236 0.98
82 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.38
Consensus pattern (81 bp):
TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATT
TATAGAATTACCGATT
Found at i:44046051 original size:27 final size:27
Alignment explanation
Indices: 44045916--44046299 Score: 275
Period size: 27 Copynumber: 14.2 Consensus size: 27
44045906 ATTACTGTTT
* ****
44045916 TACCCTTGATTTATAGAATTACCGTTT
1 TACCCTTGATTTATAAAATTACCAAAA
* * ***
44045943 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTTGATTTATAAAATTACCAAAA
* * * ****
44045970 TACCCTTGACTTACAGAATTACCGTTT
1 TACCCTTGATTTATAAAATTACCAAAA
** * ***
44045997 TACCCTCAATTTACAAAATTATTGAAA
1 TACCCTTGATTTATAAAATTACCAAAA
44046024 TACCCTTGATTTATAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * *
44046051 TACCCTCGA-TTAGTAAAATTTCTAAAA
1 TACCCTTGATTTA-TAAAATTACCAAAA
* * * * *
44046078 TGCCCCTGGTTTGTAAAATTACTAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * *
44046105 TACCCTTGGTTTATAAAATTGCCAGAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * *
44046132 TACCCCTGTTTTGTAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * * **
44046159 TACCCCTGATTTGTGAAATTACTTAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * *
44046186 TACCCTCGACTTGTAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* *
44046213 TACCATTGGTTTATAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* *
44046240 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * * *
44046267 TACCATTGATTTGTGAAATTACCGAAA
1 TACCCTTGATTTATAAAATTACCAAAA
44046294 TACCCT
1 TACCCT
44046300 CAGTTTGCAA
Statistics
Matches: 292, Mismatches: 63, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
26 3 0.01
27 287 0.98
28 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (27 bp):
TACCCTTGATTTATAAAATTACCAAAA
Found at i:44046055 original size:54 final size:54
Alignment explanation
Indices: 44045997--44046410 Score: 261
Period size: 54 Copynumber: 7.6 Consensus size: 54
44045987 ATTACCGTTT
* * * * *
44045997 TACCCTCAATTTACAAAATTATTGAAATACCCTTGATTTATAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAA
* * * *
44046051 TACCCTCGA-TTAGTAAAATT-TCTAAAATGCCCCTGGTTTGTAAAATTACTAAAA
1 TACCCTCGATTTA-TAAAATTATC-GAAATACCCCTGATTTGTAAAATTACCAAAA
* * * * *
44046105 TACCCTTGGTTTATAAAATT-GCCAGAATACCCCTGTTTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTATCGA-AATACCCCTGATTTGTAAAATTACCAAAA
* * * *
44046159 TACCC-CTGATTTGTGAAATTA-CTTAAATA-CCCTCGACTTGTAAAATTACCAAAA
1 TACCCTC-GATTTATAAAATTATC-GAAATACCCCT-GATTTGTAAAATTACCAAAA
* * * * * * *
44046213 TACCATTGGTTTATAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAA
* * * * * * * **
44046267 TACCATTGATTTGTGAAATTACCGAAATA-CCCTCAGTTTGCAAAATTACTGAAA
1 TACCCTCGATTTATAAAATTATCGAAATACCCCTGA-TTTGTAAAATTACCAAAA
* * * ** * ****
44046321 TACCCTCAACTTGTA-AAAATTA-CCAAAGTACCCCCGATTTACAGAATTACCGTTT
1 TACCCTCGA-TT-TATAAAATTATCGAAA-TACCCCTGATTTGTAAAATTACCAAAA
* *
44046376 TACCCTCGATTTACAAAATTATTGAAATACCCCTG
1 TACCCTCGATTTATAAAATTATCGAAATACCCCTG
44046411 TAGGGTAGAA
Statistics
Matches: 282, Mismatches: 60, Indels: 36
0.75 0.16 0.10
Matches are distributed among these distances:
53 14 0.05
54 222 0.79
55 41 0.15
56 5 0.02
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (54 bp):
TACCCTCGATTTATAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAA
Found at i:44046096 original size:81 final size:81
Alignment explanation
Indices: 44046011--44046325 Score: 339
Period size: 81 Copynumber: 3.9 Consensus size: 81
44046001 CTCAATTTAC
* * * * *
44046011 AAAATTATTGAAATACCCTTGATTTATAAAATTACCAAAATACCCTCGATTAGTAAAATTTCTAA
1 AAAATTACTAAAATACCCTTGATTTATAAAATTACCAAAATACCCTCGTTTAGTAAAATTACCAA
*
44046076 AATGCCCCTGGTTTGT
66 AATACCCCTGGTTTGT
* * * *
44046092 AAAATTACTAAAATACCCTTGGTTTATAAAATTGCCAGAATACCC-CTGTTTTGTAAAATTACCA
1 AAAATTACTAAAATACCCTTGATTTATAAAATTACCAAAATACCCTC-GTTTAGTAAAATTACCA
*
44046156 AAATACCCCTGATTTGT
65 AAATACCCCTGGTTTGT
* * * * * * *
44046173 GAAATTACTTAAATACCCTCGACTTGTAAAATTACCAAAATACCATTGGTTTA-TAAAATTACCA
1 AAAATTACTAAAATACCCTTGATTTATAAAATTACCAAAATACC-CTCGTTTAGTAAAATTACCA
*
44046237 AAATACCCTTGGTTTGT
65 AAATACCCCTGGTTTGT
* * * * * * **
44046254 AAAATTACCAAAATACCATTGATTTGTGAAATTACCGAAATACCCTCAGTTT-GCAAAATTACTG
1 AAAATTACTAAAATACCCTTGATTTATAAAATTACCAAAATACCCTC-GTTTAGTAAAATTACCA
44046318 AAATACCC
65 AAATACCC
44046326 TCAACTTGTA
Statistics
Matches: 192, Mismatches: 37, Indels: 10
0.80 0.15 0.04
Matches are distributed among these distances:
80 2 0.01
81 186 0.97
82 4 0.02
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (81 bp):
AAAATTACTAAAATACCCTTGATTTATAAAATTACCAAAATACCCTCGTTTAGTAAAATTACCAA
AATACCCCTGGTTTGT
Found at i:44046306 original size:27 final size:28
Alignment explanation
Indices: 44046021--44046353 Score: 249
Period size: 27 Copynumber: 12.3 Consensus size: 28
44046011 AAAATTATTG
* *
44046021 AAATACCCT-TGATTTATAAAATTACCA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * *
44046048 AAATACCCTC-GATTAGTAAAATTTCTA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * * *
44046075 AAATGCCC-CTGGTTTGTAAAATTACTA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * * *
44046102 AAATACCCT-TGGTTTATAAAATTGCCA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * *
44046129 GAATACCC-CTGTTTTGTAAAATTACCA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * **
44046156 AAATACCC-CTGATTTGTGAAATTACTT
1 AAATACCCTCAGATTTGTAAAATTACCA
*
44046183 AAATACCCTC-GACTTGTAAAATTACCA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * * *
44046210 AAATACCAT-TGGTTTATAAAATTACCA
1 AAATACCCTCAGATTTGTAAAATTACCA
* *
44046237 AAATACCCT-TGGTTTGTAAAATTACCA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * * *
44046264 AAATACCAT-TGATTTGTGAAATTACCG
1 AAATACCCTCAGATTTGTAAAATTACCA
* **
44046291 AAATACCCTCAG-TTTGCAAAATTACTG
1 AAATACCCTCAGATTTGTAAAATTACCA
*
44046318 AAATACCCTCA-ACTTGTAAAAATTACCA
1 AAATACCCTCAGATTTGT-AAAATTACCA
*
44046346 AAGTACCC
1 AAATACCC
44046354 CCGATTTACA
Statistics
Matches: 252, Mismatches: 45, Indels: 17
0.80 0.14 0.05
Matches are distributed among these distances:
26 1 0.00
27 234 0.93
28 17 0.07
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (28 bp):
AAATACCCTCAGATTTGTAAAATTACCA
Found at i:44046406 original size:27 final size:28
Alignment explanation
Indices: 44046174--44046407 Score: 110
Period size: 27 Copynumber: 8.6 Consensus size: 28
44046164 CTGATTTGTG
**
44046174 AAATTACTTAAATACCCTCGACTTGT--A
1 AAATTACCGAAATACCCTCGACTT-TACA
* * * * *
44046201 AAATTACCAAAATACCATTG-GTTTATA
1 AAATTACCGAAATACCCTCGACTTTACA
* * * **
44046228 AAATTACCAAAATACCCTTG-GTTTGTA
1 AAATTACCGAAATACCCTCGACTTTACA
* * * ***
44046255 AAATTACCAAAATACCATTGA-TTTGTG
1 AAATTACCGAAATACCCTCGACTTTACA
* *
44046282 AAATTACCGAAATACCCTC-AGTTTGCA
1 AAATTACCGAAATACCCTCGACTTTACA
* *
44046309 AAATTACTGAAATACCCTCAACTTGTA-A
1 AAATTACCGAAATACCCTCGACTT-TACA
*
44046337 AAATTACC-AAAGTACCCCCGA-TTTACA
1 AAATTACCGAAA-TACCCTCGACTTTACA
* ***
44046364 GAATTACCGTTTTACCCTCGA-TTTACA
1 AAATTACCGAAATACCCTCGACTTTACA
**
44046391 AAATTATTGAAATACCC
1 AAATTACCGAAATACCC
44046408 CTGTAGGGTA
Statistics
Matches: 167, Mismatches: 31, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
25 1 0.01
26 5 0.03
27 142 0.85
28 18 0.11
29 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (28 bp):
AAATTACCGAAATACCCTCGACTTTACA
Found at i:44046422 original size:27 final size:27
Alignment explanation
Indices: 44046392--44046558 Score: 219
Period size: 27 Copynumber: 6.2 Consensus size: 27
44046382 CGATTTACAA
*
44046392 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* *
44046419 AATTACCGAAATACCCCTATAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
*
44046446 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
*
44046473 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* *
44046500 AATTCTCGAAATACCCTTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* * * *
44046527 AATTA-CTGAGATACCCTTGTGGGGTAA
1 AATTATC-GAAATACCCCTGTAGGGTAG
44046554 AATTA
1 AATTA
44046559 CCATTTTGCC
Statistics
Matches: 126, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
26 1 0.01
27 125 0.99
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.29
Consensus pattern (27 bp):
AATTATCGAAATACCCCTGTAGGGTAG
Found at i:44046552 original size:81 final size:81
Alignment explanation
Indices: 44046390--44046558 Score: 241
Period size: 81 Copynumber: 2.1 Consensus size: 81
44046380 CTCGATTTAC
* *
44046390 AAAATTATTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTATTGA
1 AAAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTACTGA
44046455 AATACCCCTGTAGGGT
66 AATACCCCTGTAGGGT
* * * *
44046471 AGAATTATCGAAATACCCTTGTAGGGTAGAATT-CTCGAAATACCCTTGTAGGGTAGAATTACTG
1 AAAATTATCGAAATACCCCTGTAGGGTAGAATTAC-CGAAATACCCCTATAGGGTAGAATTACTG
* * *
44046535 AGATACCCTTGTGGGGT
65 AAATACCCCTGTAGGGT
44046552 AAAATTA
1 AAAATTA
44046559 CCATTTTGCC
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 1 0.01
81 76 0.99
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (81 bp):
AAAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTACTGA
AATACCCCTGTAGGGT
Found at i:44046835 original size:24 final size:25
Alignment explanation
Indices: 44046765--44046858 Score: 145
Period size: 25 Copynumber: 3.8 Consensus size: 25
44046755 AGGAAGTGCT
* *
44046765 AAAAGGGCTTTGCCCCAGTTTACTG
1 AAAAGAGCTTTGCCCCAGTTTACCG
44046790 AAAAGAGCTTTGCCCCAGTTTACCG
1 AAAAGAGCTTTGCCCCAGTTTACCG
*
44046815 AAAAGAGCTTTG-CCCAGTTTACCA
1 AAAAGAGCTTTGCCCCAGTTTACCG
*
44046839 AAAAGGGCTTTGCCCCAGTT
1 AAAAGAGCTTTGCCCCAGTT
44046859 ATTAAAAGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
24 22 0.34
25 42 0.66
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAGAGCTTTGCCCCAGTTTACCG
Found at i:44047114 original size:31 final size:30
Alignment explanation
Indices: 44047079--44047160 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 30
44047069 CGTTTACAGT
*
44047079 AAAGGCTTCAGCCCAGTGATATGATT-TACG
1 AAAGGCTTCAGCCCAGT-ATATGATTAAACG
* * **
44047109 AAAAGGCTTCGGCCTAGTA-ACCATTAAACG
1 -AAAGGCTTCAGCCCAGTATATGATTAAACG
44047139 AAAGGCTTCAGCCCAGTATATG
1 AAAGGCTTCAGCCCAGTATATG
44047161 TCGAGACCGA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
29 20 0.50
30 5 0.12
31 15 0.38
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (30 bp):
AAAGGCTTCAGCCCAGTATATGATTAAACG
Found at i:44050255 original size:42 final size:42
Alignment explanation
Indices: 44050196--44050282 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
44050186 AGAAAACATC
* *
44050196 ACCAAAATCTTGATGCTGGAGTCAGGATTGTTCGGATGCTGA
1 ACCAAAATCTTGATGCTGGAGTCAAGATTGTTCAGATGCTGA
44050238 ACCAAAATCTTGATGCTGGAGTCAAGATTGTTCAGATGCTGA
1 ACCAAAATCTTGATGCTGGAGTCAAGATTGTTCAGATGCTGA
44050280 ACC
1 ACC
44050283 GGGACACTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (42 bp):
ACCAAAATCTTGATGCTGGAGTCAAGATTGTTCAGATGCTGA
Found at i:44050816 original size:23 final size:23
Alignment explanation
Indices: 44050756--44050820 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
44050746 CTTGATTAGT
44050756 ATACGACACAT-AAGTGCCTGAA
1 ATACGACACATGAAGTGCCTGAA
* *
44050778 AT--GACACACGAGGTGCCTGAA
1 ATACGACACATGAAGTGCCTGAA
*
44050799 ATACGACACATGATGTGCCTGA
1 ATACGACACATGAAGTGCCTGA
44050821 TCGACAAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 6 0.17
21 12 0.33
22 2 0.06
23 16 0.44
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (23 bp):
ATACGACACATGAAGTGCCTGAA
Found at i:44051034 original size:16 final size:17
Alignment explanation
Indices: 44051008--44051041 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
44050998 TTCAATACAT
44051008 ATTCATCATTCAACTCA
1 ATTCATCATTCAACTCA
*
44051025 ATTC-TCATTCAATTCA
1 ATTCATCATTCAACTCA
44051041 A
1 A
44051042 CAGTAACACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTCATCATTCAACTCA
Found at i:44053670 original size:17 final size:16
Alignment explanation
Indices: 44053641--44053674 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
44053631 GTCCTCCCTC
44053641 ATTTATCACTTGAGCA
1 ATTTATCACTTGAGCA
*
44053657 ATTTAATCATTTGAGCA
1 ATTT-ATCACTTGAGCA
44053674 A
1 A
44053675 ATTTTGCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (16 bp):
ATTTATCACTTGAGCA
Found at i:44058617 original size:18 final size:18
Alignment explanation
Indices: 44058594--44058634 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
44058584 AGGAAAAAAA
44058594 AGAAATT-GAATTATGAAT
1 AGAAATTGGAATTATG-AT
*
44058612 AGAAATTGGAATTGTGAT
1 AGAAATTGGAATTATGAT
44058630 AGAAA
1 AGAAA
44058635 GAGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (18 bp):
AGAAATTGGAATTATGAT
Found at i:44059143 original size:20 final size:20
Alignment explanation
Indices: 44059120--44059157 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44059110 GTTATTAAGT
44059120 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
44059140 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
44059158 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:44059380 original size:16 final size:19
Alignment explanation
Indices: 44059341--44059380 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 19
44059331 GGACTTAATT
44059341 ATTATATTATACTATGTAA
1 ATTATATTATACTATGTAA
*
44059360 GTTATATTA-A-T-TGTAA
1 ATTATATTATACTATGTAA
44059376 ATTAT
1 ATTAT
44059381 TTGTAAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
16 9 0.47
17 1 0.05
18 1 0.05
19 8 0.42
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (19 bp):
ATTATATTATACTATGTAA
Found at i:44060219 original size:29 final size:29
Alignment explanation
Indices: 44060182--44060238 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
44060172 CACCTTGACA
* *
44060182 CGAATTCTCAATGAACAAGTTCTTCACCG
1 CGAACTCTCAACGAACAAGTTCTTCACCG
44060211 CGAACTCTCAACGAACAAGTTCTTCACC
1 CGAACTCTCAACGAACAAGTTCTTCACC
44060239 TCTTCTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.25
Consensus pattern (29 bp):
CGAACTCTCAACGAACAAGTTCTTCACCG
Found at i:44061309 original size:13 final size:14
Alignment explanation
Indices: 44061262--44061312 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
44061252 ACTGTTTCCG
44061262 TGAA-ATTTATTCA
1 TGAATATTTATTCA
44061275 TGAATATTTATTCA
1 TGAATATTTATTCA
44061289 TGAATATTTATT-A
1 TGAATATTTATTCA
44061302 -GAAATATTTAT
1 TG-AATATTTAT
44061313 GAATTATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 1 0.03
13 14 0.39
14 21 0.58
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (14 bp):
TGAATATTTATTCA
Found at i:44061479 original size:86 final size:86
Alignment explanation
Indices: 44061375--44061546 Score: 317
Period size: 86 Copynumber: 2.0 Consensus size: 86
44061365 TTAGTTTAAA
44061375 GGGCTAAATTGCATAAGGAATAAAAGTTTAATTATAAATTAAAGAAGTAAAAGGGACTAATCTAG
1 GGGCTAAATTGCATAAGGAATAAAAGTTTAATTATAAATTAAAGAAGTAAAAGGGACTAATCTAG
* *
44061440 TAATTAGACCCTATGTGCCAT
66 TAATCAGACCCTAAGTGCCAT
*
44061461 GGGCTAAATTGCATAAGGAATAAAAGTTTAATTATAGATTAAAGAAGTAAAAGGGACTAATCTAG
1 GGGCTAAATTGCATAAGGAATAAAAGTTTAATTATAAATTAAAGAAGTAAAAGGGACTAATCTAG
44061526 TAATCAGACCCTAAGTGCCAT
66 TAATCAGACCCTAAGTGCCAT
44061547 ATGTGTGTTA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (86 bp):
GGGCTAAATTGCATAAGGAATAAAAGTTTAATTATAAATTAAAGAAGTAAAAGGGACTAATCTAG
TAATCAGACCCTAAGTGCCAT
Found at i:44061740 original size:4 final size:4
Alignment explanation
Indices: 44061731--44061765 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
44061721 GAGCAAATGT
44061731 GAAA GAAA G-AA GAAA GAAA GAAA GAAA GAAA -AAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
44061766 GGAAATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:44068586 original size:13 final size:14
Alignment explanation
Indices: 44068539--44068589 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
44068529 ACTGTTTCCG
44068539 TGAA-ATTTATTCA
1 TGAATATTTATTCA
44068552 TGAATATTTATTCA
1 TGAATATTTATTCA
44068566 TGAATATTTATT-A
1 TGAATATTTATTCA
44068579 -GAAATATTTAT
1 TG-AATATTTAT
44068590 GAATTATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 1 0.03
13 14 0.39
14 21 0.58
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (14 bp):
TGAATATTTATTCA
Found at i:44078295 original size:17 final size:18
Alignment explanation
Indices: 44078264--44078298 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
44078254 AATTTAATTA
*
44078264 TTTTATCTAATAAATATC
1 TTTTATCTAAAAAATATC
44078282 TTTTA-CTAAAAAATATC
1 TTTTATCTAAAAAATATC
44078299 ACAAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTATCTAAAAAATATC
Found at i:44078796 original size:41 final size:41
Alignment explanation
Indices: 44078746--44078828 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
44078736 ACTTAATAAT
*
44078746 GATTACACTTTTACAATTTAGTCCCCATATTATAGTTAACC
1 GATTACACTTTTACAATTTAGTCCCCATACTATAGTTAACC
*
44078787 GATTGCACTTTTACAATTTAGTCCCCATACTATAGTTAACC
1 GATTACACTTTTACAATTTAGTCCCCATACTATAGTTAACC
44078828 G
1 G
44078829 CTTTCTCGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (41 bp):
GATTACACTTTTACAATTTAGTCCCCATACTATAGTTAACC
Found at i:44107315 original size:2 final size:2
Alignment explanation
Indices: 44107308--44107340 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44107298 CAGATGAGGC
44107308 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 A
44107341 ATAGAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:44108162 original size:13 final size:13
Alignment explanation
Indices: 44108144--44108170 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44108134 AAGAAAGTAT
44108144 TGAAACATGTTTC
1 TGAAACATGTTTC
44108157 TGAAACATGTTTC
1 TGAAACATGTTTC
44108170 T
1 T
44108171 ATTACTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGAAACATGTTTC
Found at i:44114238 original size:13 final size:14
Alignment explanation
Indices: 44114220--44114248 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
44114210 TCTTCTAATA
44114220 ATTTAATTAT-TAT
1 ATTTAATTATATAT
44114233 ATTTAATTATATAT
1 ATTTAATTATATAT
44114247 AT
1 AT
44114249 AAATCATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTAATTATATAT
Found at i:44118523 original size:19 final size:19
Alignment explanation
Indices: 44118499--44118536 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
44118489 CTTTGAACTG
44118499 AAAGAAAACTTGAAACTTT
1 AAAGAAAACTTGAAACTTT
*
44118518 AAAGAAAACTTGAACCTTT
1 AAAGAAAACTTGAAACTTT
44118537 CCTCGAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (19 bp):
AAAGAAAACTTGAAACTTT
Found at i:44120690 original size:31 final size:31
Alignment explanation
Indices: 44120655--44120731 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
44120645 ATGTATAATT
* * * *
44120655 TTTTGGACAAGTTTAAGTATCAATTAGATAC
1 TTTTGGACAAGTTCAAGTACCAACTAAATAC
44120686 TTTTGGACAAGTTCAAGTACCAACTAAATAC
1 TTTTGGACAAGTTCAAGTACCAACTAAATAC
44120717 TTTTGGACAAGTTCA
1 TTTTGGACAAGTTCA
44120732 TAGGGCAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (31 bp):
TTTTGGACAAGTTCAAGTACCAACTAAATAC
Found at i:44122306 original size:3 final size:3
Alignment explanation
Indices: 44122298--44122346 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
44122288 GGTTTAGAAT
44122298 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44122346 T
1 T
44122347 CAAAACTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:44129684 original size:112 final size:112
Alignment explanation
Indices: 44129487--44129767 Score: 562
Period size: 112 Copynumber: 2.5 Consensus size: 112
44129477 AATGCCATTG
44129487 GCTAGCGAAGATAATATAGTTTTAAGATCTACATTAGTGCTAACTCTGTTTACGCATAAACAAAT
1 GCTAGCGAAGATAATATAGTTTTAAGATCTACATTAGTGCTAACTCTGTTTACGCATAAACAAAT
44129552 ACGCCTTGCACACCAAGTCAATGAAAATTAAGATTAAGAAGCTATTA
66 ACGCCTTGCACACCAAGTCAATGAAAATTAAGATTAAGAAGCTATTA
44129599 GCTAGCGAAGATAATATAGTTTTAAGATCTACATTAGTGCTAACTCTGTTTACGCATAAACAAAT
1 GCTAGCGAAGATAATATAGTTTTAAGATCTACATTAGTGCTAACTCTGTTTACGCATAAACAAAT
44129664 ACGCCTTGCACACCAAGTCAATGAAAATTAAGATTAAGAAGCTATTA
66 ACGCCTTGCACACCAAGTCAATGAAAATTAAGATTAAGAAGCTATTA
44129711 GCTAGCGAAGATAATATAGTTTTAAGATCTACATTAGTGCTAACTCTGTTTACGCAT
1 GCTAGCGAAGATAATATAGTTTTAAGATCTACATTAGTGCTAACTCTGTTTACGCAT
44129768 GTAGCTGATG
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 169 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (112 bp):
GCTAGCGAAGATAATATAGTTTTAAGATCTACATTAGTGCTAACTCTGTTTACGCATAAACAAAT
ACGCCTTGCACACCAAGTCAATGAAAATTAAGATTAAGAAGCTATTA
Found at i:44132158 original size:45 final size:45
Alignment explanation
Indices: 44132109--44132197 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
44132099 TATAATTTAG
44132109 TTTTTCATGTATAAACGTTATTGTAGAAAAGTTTATTAGTCAAAT
1 TTTTTCATGTATAAACGTTATTGTAGAAAAGTTTATTAGTCAAAT
44132154 TTTTTCATGTATAAACGTTATTGTAGAAAAGTTTATTAGTCAAA
1 TTTTTCATGTATAAACGTTATTGTAGAAAAGTTTATTAGTCAAA
44132198 CTTGCTCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (45 bp):
TTTTTCATGTATAAACGTTATTGTAGAAAAGTTTATTAGTCAAAT
Found at i:44135229 original size:25 final size:25
Alignment explanation
Indices: 44135195--44135246 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
44135185 CATATATGCC
44135195 ATTGCTAATTCCCTAATGGTCTCAG
1 ATTGCTAATTCCCTAATGGTCTCAG
44135220 ATTGCTAATTCCCTAATGGTCTCAG
1 ATTGCTAATTCCCTAATGGTCTCAG
44135245 AT
1 AT
44135247 ACTTTAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (25 bp):
ATTGCTAATTCCCTAATGGTCTCAG
Found at i:44141485 original size:5 final size:5
Alignment explanation
Indices: 44141470--44141499 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
44141460 ATCAAAATGT
44141470 AAAAGG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAA-G AAAAG AAAAG AAAAG AAAAG AAAA
44141500 ACAAACTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:44143388 original size:26 final size:27
Alignment explanation
Indices: 44143321--44143388 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
44143311 AACAACGATA
* *
44143321 AAAACTAAATCTAACTTTTTAAATCCG
1 AAAACTAAATCTAACTTTTCAAATACG
* *
44143348 AAAA-TAAAAAACTAA-TTTTCAAATATG
1 AAAACT--AAATCTAACTTTTCAAATACG
44143375 AAAACTAAATCTAA
1 AAAACTAAATCTAA
44143389 AACTCTTACT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
26 8 0.24
27 17 0.52
28 8 0.24
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.29
Consensus pattern (27 bp):
AAAACTAAATCTAACTTTTCAAATACG
Found at i:44150128 original size:61 final size:64
Alignment explanation
Indices: 44149999--44150128 Score: 164
Period size: 61 Copynumber: 2.1 Consensus size: 64
44149989 GAAAACAAAA
* *
44149999 TAAATTATTTAAGTTTATTTTTTACCTAATTAATATTTAGAAACTATTTATACTTAGATATTAC
1 TAAATTATTAAAGTTTATTTTTTACCAAATTAATATTTAGAAACTATTTATACTTAGATATTAC
* * *
44150063 --AATTATTAAATTTTA-TTTTTACCAAATTAATATTTAGATACTATTTCGTA-TTAG-T-TTAC
1 TAAATTATTAAAGTTTATTTTTTACCAAATTAATATTTAGAAACTATTT-ATACTTAGATATTAC
44150122 TAAATTA
1 TAAATTA
44150129 AACTAAATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
59 4 0.07
60 1 0.02
61 38 0.66
62 15 0.26
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.50
Consensus pattern (64 bp):
TAAATTATTAAAGTTTATTTTTTACCAAATTAATATTTAGAAACTATTTATACTTAGATATTAC
Found at i:44150162 original size:14 final size:12
Alignment explanation
Indices: 44150130--44150159 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
44150120 ACTAAATTAA
44150130 ACTAAATATATC
1 ACTAAATATATC
44150142 ACTAAATATATC
1 ACTAAATATATC
*
44150154 ATTAAA
1 ACTAAA
44150160 AATTATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (12 bp):
ACTAAATATATC
Found at i:44153056 original size:20 final size:20
Alignment explanation
Indices: 44153033--44153098 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 20
44153023 AAAGAATAAC
44153033 ATTAATAATAAAAAAATCAA
1 ATTAATAATAAAAAAATCAA
*
44153053 ATTAAAATACAAAAAATAAAATCAA
1 ATT--AAT--AATAAA-AAAATCAA
44153078 ATTAA-AATAAAAAAAT-AA
1 ATTAATAATAAAAAAATCAA
44153096 ATT
1 ATT
44153099 CCACCATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
18 5 0.13
19 5 0.13
20 8 0.21
22 3 0.08
23 2 0.05
24 5 0.13
25 11 0.28
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (20 bp):
ATTAATAATAAAAAAATCAA
Found at i:44153079 original size:19 final size:19
Alignment explanation
Indices: 44153039--44153096 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
44153029 TAACATTAAT
*
44153039 AATAAAAAAATCAAATTAA
1 AATAAAAAAATCAAAATAA
44153058 AATACAAAAAAT-AAAATCAA
1 AATA-AAAAAATCAAAAT-AA
*
44153078 ATTAAAATAAA--AAAATAA
1 AATAAAA-AAATCAAAATAA
44153096 A
1 A
44153097 TTCCACCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 3 0.09
19 16 0.47
20 15 0.44
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (19 bp):
AATAAAAAAATCAAAATAA
Found at i:44153084 original size:18 final size:18
Alignment explanation
Indices: 44153021--44153072 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 18
44153011 TCTACTAGAC
44153021 AAAAAGAATAACATTAATAAT
1 AAAAA-AATAA-ATTAA-AAT
44153042 AAAAAAATCAAATTAAAAT
1 AAAAAAAT-AAATTAAAAT
44153061 ACAAAAAATAAA
1 A-AAAAAATAAA
44153073 ATCAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.24
20 15 0.52
21 7 0.24
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAAAATAAATTAAAAT
Found at i:44153108 original size:25 final size:25
Alignment explanation
Indices: 44153045--44153096 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
44153035 TAATAATAAA
44153045 AAAATCAAATTAAAATACAAAAAAT
1 AAAATCAAATTAAAATACAAAAAAT
44153070 AAAATCAAATTAAAATA-AAAAAAT
1 AAAATCAAATTAAAATACAAAAAAT
44153094 AAA
1 AAA
44153097 TTCCACCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (25 bp):
AAAATCAAATTAAAATACAAAAAAT
Found at i:44154769 original size:17 final size:17
Alignment explanation
Indices: 44154747--44154780 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
44154737 ATCCACTAAT
*
44154747 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
44154764 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
44154781 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:44158416 original size:17 final size:17
Alignment explanation
Indices: 44158394--44158427 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
44158384 ATCCACTAAT
*
44158394 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
44158411 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
44158428 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:44166018 original size:22 final size:20
Alignment explanation
Indices: 44165992--44166033 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
44165982 GTTATAAGTT
44165992 TAAAAATTAAAATTAATTTAAA
1 TAAAAATT-AAATT-ATTTAAA
44166014 TAAAAATTAAATTATTTAAA
1 TAAAAATTAAATTATTTAAA
44166034 AATTAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATTAAATTATTTAAA
Found at i:44166019 original size:16 final size:16
Alignment explanation
Indices: 44165995--44166040 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
44165985 ATAAGTTTAA
*
44165995 AAATTAAAATTAATTT
1 AAATAAAAATTAATTT
*
44166011 AAATAAAAATTAAATT
1 AAATAAAAATTAATTT
**
44166027 ATTTAAAAATTAAT
1 AAATAAAAATTAAT
44166041 AAAATTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATAAAAATTAATTT
Found at i:44166036 original size:22 final size:22
Alignment explanation
Indices: 44165991--44166051 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 22
44165981 TGTTATAAGT
44165991 TTAAAAATTAAAATTAATTTAAA
1 TTAAAAATT-AAATTAATTTAAA
44166014 -TAAAAATTAAATT-ATTTAAAAA
1 TTAAAAATTAAATTAATTT--AAA
44166036 TTAATAAAATTAAATT
1 TT-A-AAAATTAAATT
44166052 TCTTCAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 4 0.12
21 5 0.15
22 11 0.33
23 1 0.03
24 1 0.03
25 11 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAAAAATTAAATTAATTTAAA
Found at i:44166045 original size:20 final size:20
Alignment explanation
Indices: 44165992--44166047 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
44165982 GTTATAAGTT
44165992 TAAAAATTAAAATTAATTTAAA
1 TAAAAA-TAAAATT-ATTTAAA
*
44166014 TAAAAATTAAATTATTTAAA
1 TAAAAATAAAATTATTTAAA
*
44166034 -AATTAATAAAATTA
1 TAA-AAATAAAATTA
44166048 AATTTCTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 16 0.53
21 6 0.20
22 6 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATAAAATTATTTAAA
Found at i:44171201 original size:17 final size:18
Alignment explanation
Indices: 44171174--44171212 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
44171164 CATGCTAGTT
44171174 TTTTGAATTTTTATGAAA
1 TTTTGAATTTTTATGAAA
* *
44171192 TTTT-AATTTTTTTTAAA
1 TTTTGAATTTTTATGAAA
44171209 TTTT
1 TTTT
44171213 TAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTGAATTTTTATGAAA
Found at i:44171825 original size:31 final size:32
Alignment explanation
Indices: 44171766--44171830 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
44171756 TTATCAAAAA
44171766 AAATTATTTAAAAATAATTTATTATTAT-ATT
1 AAATTATTTAAAAATAATTTATTATTATAATT
*
44171797 AAATTATTTAATTAA-AATTTA-TAGTTATAATT
1 AAATTATTTAA-AAATAATTTATTA-TTATAATT
44171829 AA
1 AA
44171831 TATTTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 2 0.07
31 21 0.70
32 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (32 bp):
AAATTATTTAAAAATAATTTATTATTATAATT
Found at i:44182871 original size:19 final size:19
Alignment explanation
Indices: 44182837--44182898 Score: 90
Period size: 19 Copynumber: 3.2 Consensus size: 19
44182827 ATTACAAAAA
44182837 AAATAATTTTTAAAAATTCT
1 AAATAATTTTT-AAAATTCT
44182857 AAATAATTTTTAAAATTCT
1 AAATAATTTTTAAAATTCT
*
44182876 AAAT-ATTTATAAAAATTCT
1 AAATAATTT-TTAAAATTCT
44182895 AAAT
1 AAAT
44182899 TTTATATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
18 4 0.10
19 25 0.62
20 11 0.28
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATAATTTTTAAAATTCT
Found at i:44182898 original size:26 final size:25
Alignment explanation
Indices: 44182869--44182922 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
44182859 ATAATTTTTA
44182869 AAATTCTAAATATTTATAAAAATTCT
1 AAATTCTAAATATTTA-AAAAATTCT
* * *
44182895 AAATTTTATATTTTTAAAAAATTCT
1 AAATTCTAAATATTTAAAAAATTCT
44182920 AAA
1 AAA
44182923 AAATATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATTCTAAATATTTAAAAAATTCT
Found at i:44182929 original size:25 final size:26
Alignment explanation
Indices: 44182881--44182930 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
44182871 ATTCTAAATA
***
44182881 TTTATAAAAATTCTAAATTTTATATT
1 TTTATAAAAATTCTAAAAAATATATT
44182907 TTTA-AAAAATTCTAAAAAATATAT
1 TTTATAAAAATTCTAAAAAATATAT
44182931 AAAGAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTATAAAAATTCTAAAAAATATATT
Found at i:44196781 original size:11 final size:11
Alignment explanation
Indices: 44196765--44196789 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44196755 ATATCTAGAA
44196765 TTCTCTTCATT
1 TTCTCTTCATT
44196776 TTCTCTTCATT
1 TTCTCTTCATT
44196787 TTC
1 TTC
44196790 ATCATCTGAA
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:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:44199103 original size:6 final size:6
Alignment explanation
Indices: 44199092--44199125 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
44199082 TGTAAGATAT
* *
44199092 TGTTAC TGTTAC TGTTAC CGTTAC TATTAC TGTT
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TGTT
44199126 TTTTTATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.50
Consensus pattern (6 bp):
TGTTAC
Found at i:44199389 original size:18 final size:18
Alignment explanation
Indices: 44199336--44199496 Score: 74
Period size: 18 Copynumber: 8.5 Consensus size: 18
44199326 AAAGATCGAC
*
44199336 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAA-TTGAT
* *
44199355 TGTTACTGTATATTTGAT
1 TGTTACTGAATAATTGAT
*
44199373 T-TCTACTGAATAATTGAC
1 TGT-TACTGAATAATTGAT
44199391 TGTTACTGGGTAACCGATCAATTGAT
1 TGTTACT--G--A---AT-AATTGAT
* *
44199417 TGATACTGAATAACTGAT
1 TGTTACTGAATAATTGAT
** *
44199435 TAATATTGAATAATTGAT
1 TGTTACTGAATAATTGAT
* * *
44199453 TGTTACCGAATAACTGAC
1 TGTTACTGAATAATTGAT
* * * *
44199471 TATTACTAAATAAATAAT
1 TGTTACTGAATAATTGAT
44199489 TGTT-CTGA
1 TGTTACTGA
44199497 TACGTTAATG
Statistics
Matches: 106, Mismatches: 26, Indels: 22
0.69 0.17 0.14
Matches are distributed among these distances:
17 4 0.04
18 70 0.66
19 14 0.13
20 1 0.01
22 2 0.02
24 1 0.01
25 2 0.02
26 12 0.11
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (18 bp):
TGTTACTGAATAATTGAT
Found at i:44199483 original size:36 final size:36
Alignment explanation
Indices: 44199410--44199492 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
44199400 GTAACCGATC
* * * * *
44199410 AATTGATTGATACTGAATAACTGATTAATATTGAAT
1 AATTGATTGTTACCGAATAACTGACTAATACTAAAT
*
44199446 AATTGATTGTTACCGAATAACTGACTATTACTAAAT
1 AATTGATTGTTACCGAATAACTGACTAATACTAAAT
* *
44199482 AAATAATTGTT
1 AATTGATTGTT
44199493 CTGATACGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (36 bp):
AATTGATTGTTACCGAATAACTGACTAATACTAAAT
Found at i:44203365 original size:29 final size:30
Alignment explanation
Indices: 44203316--44203375 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
44203306 AGAATTGGAT
* *
44203316 AAAATTAAAATTTTATGTATAAAATTACAC
1 AAAATTAAAAGTTTATATATAAAATTACAC
*
44203346 AAAATT-AAAGTTTATATATACAATTACAC
1 AAAATTAAAAGTTTATATATAAAATTACAC
44203375 A
1 A
44203376 TTAAATCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTAAAAGTTTATATATAAAATTACAC
Found at i:44217163 original size:16 final size:16
Alignment explanation
Indices: 44217142--44217174 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
44217132 CTCTAAGGAG
44217142 CATACTTATATTTTGC
1 CATACTTATATTTTGC
44217158 CATACTTATATTTTGC
1 CATACTTATATTTTGC
44217174 C
1 C
44217175 TTTGCAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.48
Consensus pattern (16 bp):
CATACTTATATTTTGC
Found at i:44218861 original size:6 final size:6
Alignment explanation
Indices: 44218850--44218885 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
44218840 TCTTCACTCA
44218850 CCATAT CCATAT CCATAT CCATAT CCATAT CCATAT
1 CCATAT CCATAT CCATAT CCATAT CCATAT CCATAT
44218886 GCTGCTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
CCATAT
Found at i:44229870 original size:26 final size:26
Alignment explanation
Indices: 44229824--44229883 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
44229814 TGACTTAAAT
*
44229824 CTCAAACCTTAAACCTTAAAC-CTAA
1 CTCAAACCTCAAACCTTAAACTCTAA
*
44229849 GCTCAAACCTCAAA-TTTCAAACTCTAA
1 -CTCAAACCTCAAACCTT-AAACTCTAA
44229876 -TCAAACCT
1 CTCAAACCT
44229884 TGAACCCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 10 0.33
26 16 0.53
27 4 0.13
ACGTcount: A:0.42, C:0.32, G:0.02, T:0.25
Consensus pattern (26 bp):
CTCAAACCTCAAACCTTAAACTCTAA
Found at i:44230648 original size:23 final size:22
Alignment explanation
Indices: 44230617--44230659 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
44230607 AAATTTAAAT
*
44230617 TTATCTATTTTTATTTTAAAAAA
1 TTATCTATTTAT-TTTTAAAAAA
*
44230640 TTATTTATTTATTTTTAAAA
1 TTATCTATTTATTTTTAAAA
44230660 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATCTATTTATTTTTAAAAAA
Found at i:44244658 original size:7 final size:8
Alignment explanation
Indices: 44244642--44244669 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
44244632 TAAATTTGGG
44244642 TTTTCTTT
1 TTTTCTTT
44244650 TTTTCTTT
1 TTTTCTTT
44244658 TTTTCTTT
1 TTTTCTTT
44244666 TTTT
1 TTTT
44244670 TTAGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTCTTT
Found at i:44246528 original size:20 final size:21
Alignment explanation
Indices: 44246503--44246542 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
44246493 ATTAAATTGT
* *
44246503 TAAATT-TATTTATATTTTTC
1 TAAATTCTATATAAATTTTTC
44246523 TAAATTCTATATAAATTTTT
1 TAAATTCTATATAAATTTTT
44246543 AAATAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TAAATTCTATATAAATTTTTC
Found at i:44246545 original size:19 final size:18
Alignment explanation
Indices: 44246495--44246546 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
44246485 TAAAAAAAAT
* *
44246495 TAAATTGTTAAATTTATT
1 TAAATTTTTAAATTTATA
*
44246513 TATATTTTTCTAAATTCTATA
1 TA-AATTTT-TAAATT-TATA
44246534 TAAATTTTTAAAT
1 TAAATTTTTAAAT
44246547 AATAATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 2 0.07
19 9 0.33
20 11 0.41
21 5 0.19
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (18 bp):
TAAATTTTTAAATTTATA
Found at i:44246570 original size:20 final size:21
Alignment explanation
Indices: 44246531--44246581 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
44246521 TCTAAATTCT
*
44246531 ATATAAAT-TTTTAAATAATA
1 ATATAAATAATTTAAATAATA
44246551 ATATAAATAATTTAAA-AATA
1 ATATAAATAATTTAAATAATA
*
44246571 TTA-AAATAATT
1 ATATAAATAATT
44246582 AGACATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 8 0.29
20 14 0.50
21 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATAAATAATTTAAATAATA
Found at i:44248036 original size:18 final size:18
Alignment explanation
Indices: 44248004--44248041 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
44247994 CGTAAATATG
*
44248004 AAAAAAATTAGGTAC-AA
1 AAAAAAATTAAGTACGAA
44248021 AAAAAAATGTAAGTACGAA
1 AAAAAAAT-TAAGTACGAA
44248040 AA
1 AA
44248042 TGAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 6 0.33
19 4 0.22
ACGTcount: A:0.66, C:0.05, G:0.13, T:0.16
Consensus pattern (18 bp):
AAAAAAATTAAGTACGAA
Found at i:44250753 original size:24 final size:25
Alignment explanation
Indices: 44250726--44250774 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
44250716 GTCCCATTAA
44250726 TTTCTTAGAT-TCTTCCCTTTTTTT
1 TTTCTTAGATCTCTTCCCTTTTTTT
** *
44250750 TTTCTTTTATCTTTTCCCTTTTTTT
1 TTTCTTAGATCTCTTCCCTTTTTTT
44250775 CTGGTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTCTTAGATCTCTTCCCTTTTTTT
Found at i:44252341 original size:18 final size:18
Alignment explanation
Indices: 44252318--44252359 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
44252308 ATAATGCTAC
*
44252318 AATAACCA-TAAACATAGT
1 AATAACCATTAAA-ATAAT
*
44252336 AATAACGATTAAAATAAT
1 AATAACCATTAAAATAAT
44252354 AATAAC
1 AATAAC
44252360 AACAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.24
Consensus pattern (18 bp):
AATAACCATTAAAATAAT
Found at i:44252384 original size:3 final size:3
Alignment explanation
Indices: 44252378--44252560 Score: 92
Period size: 3 Copynumber: 60.7 Consensus size: 3
44252368 AATAGAAGAC
* * * *
44252378 AAT AAT AAT AAT -AT ATT AAT AAA AAT AAT AAT -AT AAA AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** ** *
44252424 AAT AAA AAT -AT GTT TCT AAT AAT AAT AAAT CAAT AAT GAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT -AAT
* * * *
44252471 ATAT ACAA AAT AAT AGT AAC AGT AAT AA- AAT AAGT -AT AAT -AT AAT
1 A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
* * *
44252516 AA- ATAT AAT AAT AAT AAT ATAT AAT AAT AAC AAT ATT AAA AAT AA
1 AAT A-AT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA
44252561 CACTCTCCCT
Statistics
Matches: 134, Mismatches: 33, Indels: 26
0.69 0.17 0.13
Matches are distributed among these distances:
2 12 0.09
3 103 0.77
4 19 0.14
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:44252405 original size:23 final size:24
Alignment explanation
Indices: 44252378--44252560 Score: 77
Period size: 23 Copynumber: 7.2 Consensus size: 24
44252368 AATAGAAGAC
* *
44252378 AATAATAATAAT-ATATTAATAAA
1 AATAATAATAATAAAAATAATAAA
44252401 AATAATAAT-ATAAAAATAATAAA
1 AATAATAATAATAAAAATAATAAA
* * ***
44252424 AATAAAAATATGTTTCTAATAATAATA
1 AATAATAATA--ATAAAAATAATAA-A
*
44252451 AATCAATAATGATAATAAATATATACAA
1 AAT-AATAATAATAA-AAATA-ATA-AA
* * *
44252479 AATAATAGTAACAGTAATAA-AATAAG
1 AATAATAAT-A-A-TAAAAATAATAAA
* *
44252505 TATAAT-ATAATAAATATAATAATAAT
1 AATAATAATAAT-AA-A-AATAATAAA
* *
44252531 AATATATAATAATAACAATATTAAA
1 AATA-ATAATAATAAAAATAATAAA
44252556 AATAA
1 AATAA
44252561 CACTCTCCCT
Statistics
Matches: 117, Mismatches: 25, Indels: 35
0.66 0.14 0.20
Matches are distributed among these distances:
22 3 0.03
23 29 0.25
24 2 0.02
25 14 0.12
26 24 0.21
27 20 0.17
28 18 0.15
29 4 0.03
30 3 0.03
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (24 bp):
AATAATAATAATAAAAATAATAAA
Found at i:44252413 original size:14 final size:15
Alignment explanation
Indices: 44252395--44252433 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
44252385 ATAATATATT
44252395 AATAAAAATAAT-AA
1 AATAAAAATAATAAA
*
44252409 TATAAAAATAATAAA
1 AATAAAAATAATAAA
44252424 AATAAAAATA
1 AATAAAAATA
44252434 TGTTTCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAAAAATAATAAA
Found at i:44252418 original size:20 final size:21
Alignment explanation
Indices: 44252381--44252428 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
44252371 AGAAGACAAT
**
44252381 AATAATAATATATTAATAA-A
1 AATAATAATATAAAAATAATA
44252401 AATAATAATATAAAAATAATA
1 AATAATAATATAAAAATAATA
44252422 AA-AATAA
1 AATAATAA
44252429 AAATATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAATAATATAAAAATAATA
Found at i:44252458 original size:14 final size:13
Alignment explanation
Indices: 44252440--44252560 Score: 64
Period size: 14 Copynumber: 9.5 Consensus size: 13
44252430 AATATGTTTC
44252440 TAATAATAATAAA
1 TAATAATAATAAA
*
44252453 TCAATAATGAT-AA
1 T-AATAATAATAAA
44252466 T-A-AATATATACAA
1 TAATAATA-ATA-AA
*
44252479 -AATAATAGTAACA
1 TAATAATAATAA-A
44252492 GTAATAA-AATAAGTA
1 -TAATAATAATAA--A
44252507 TAAT-ATAATAAA
1 TAATAATAATAAA
44252519 T-ATAATAAT-AA
1 TAATAATAATAAA
44252530 TAATATATAAT-AA
1 TAATA-ATAATAAA
* *
44252543 TAACAATATTAAA
1 TAATAATAATAAA
44252556 -AATAA
1 TAATAA
44252561 CACTCTCCCT
Statistics
Matches: 85, Mismatches: 8, Indels: 31
0.69 0.06 0.25
Matches are distributed among these distances:
10 3 0.04
11 8 0.09
12 19 0.22
13 24 0.28
14 25 0.29
15 6 0.07
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:44252502 original size:20 final size:18
Alignment explanation
Indices: 44252477--44252525 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
44252467 AAATATATAC
44252477 AAAATAATAGTAACAGTAAT
1 AAAATAATA-TAACA-TAAT
*
44252497 AAAATAAGTATAATATAAT
1 AAAATAA-TATAACATAAT
44252516 AAATATAATA
1 AAA-ATAATA
44252526 ATAATAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 9 0.35
20 15 0.58
21 2 0.08
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (18 bp):
AAAATAATATAACATAAT
Found at i:44252815 original size:17 final size:17
Alignment explanation
Indices: 44252793--44252850 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
44252783 TTTGTAGGCA
44252793 AGTGGGGTGATGGAGTT
1 AGTGGGGTGATGGAGTT
*
44252810 AGT--GG-GATGG-TTT
1 AGTGGGGTGATGGAGTT
* *
44252823 AATTGGGTGATGGAGTT
1 AGTGGGGTGATGGAGTT
44252840 AGTGGGGTGAT
1 AGTGGGGTGAT
44252851 TTAGTAGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
13 4 0.12
14 5 0.16
15 4 0.12
16 5 0.16
17 14 0.44
ACGTcount: A:0.19, C:0.00, G:0.48, T:0.33
Consensus pattern (17 bp):
AGTGGGGTGATGGAGTT
Found at i:44252861 original size:30 final size:30
Alignment explanation
Indices: 44252797--44252861 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
44252787 TAGGCAAGTG
* *
44252797 GGGTGATGGAGTTAGTGGGATGGTTTAATT
1 GGGTGATGGAGTTAGTGGGATGATTTAATA
* *
44252827 GGGTGATGGAGTTAGTGGGGTGATTTAGTA
1 GGGTGATGGAGTTAGTGGGATGATTTAATA
44252857 GGGTG
1 GGGTG
44252862 TGGGGGTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.18, C:0.00, G:0.48, T:0.34
Consensus pattern (30 bp):
GGGTGATGGAGTTAGTGGGATGATTTAATA
Found at i:44254255 original size:21 final size:21
Alignment explanation
Indices: 44254229--44254269 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
44254219 TAACAGGAGT
44254229 GCTGACGTGGCAAGTTAACTA
1 GCTGACGTGGCAAGTTAACTA
*
44254250 GCTGACGTGGCCAGTTAACT
1 GCTGACGTGGCAAGTTAACT
44254270 TGTCACGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (21 bp):
GCTGACGTGGCAAGTTAACTA
Found at i:44254547 original size:15 final size:15
Alignment explanation
Indices: 44254511--44254557 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
44254501 ACAAAAAACC
*
44254511 AGAGGAA-AAGAAGT
1 AGAGGAAGAAGAAGA
44254525 AGAGGAAGAAGAAGA
1 AGAGGAAGAAGAAGA
* * *
44254540 AGATGAAGCAGTAGA
1 AGAGGAAGAAGAAGA
44254555 AGA
1 AGA
44254558 AGGAGCAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 7 0.25
15 21 0.75
ACGTcount: A:0.55, C:0.02, G:0.36, T:0.06
Consensus pattern (15 bp):
AGAGGAAGAAGAAGA
Found at i:44255562 original size:20 final size:20
Alignment explanation
Indices: 44255525--44255562 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44255515 TGATGGGGAG
*
44255525 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
44255545 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
44255563 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:44257515 original size:46 final size:46
Alignment explanation
Indices: 44257462--44257643 Score: 240
Period size: 46 Copynumber: 4.0 Consensus size: 46
44257452 AGTGTGCTCT
* *
44257462 CTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGAGTAAGACCATAGTTGAAAGATACCATGGCAAC
* *
44257508 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATAGTTGAAAGATACCATGGCAAC
* ** *
44257554 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATAGTTGAAAGATACCATGGCAAC
* * * *
44257600 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGAGTAAGACCATAGTTGAAAGATACCATGGCA
44257644 TCATGTCAAA
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 121 0.99
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATAGTTGAAAGATACCATGGCAAC
Done.