Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 14 of 175
Found at i:4010353 original size:3 final size:3
Alignment explanation
Indices: 4010345--4010394 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
4010335 GTTCAAAATG
4010345 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4010393 TA
1 TA
4010395 TGGTTAGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4013429 original size:4 final size:4
Alignment explanation
Indices: 4013420--4013455 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
4013410 CTAGGTAAAT
*
4013420 TTTC TTTC TTGC TTTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTT
4013456 GAAGTCGGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.90
5 3 0.10
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:4013437 original size:13 final size:13
Alignment explanation
Indices: 4013419--4013454 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
4013409 TCTAGGTAAA
4013419 TTTTCTTTCTTGC
1 TTTTCTTTCTTGC
*
4013432 TTTTCTTTCTTTC
1 TTTTCTTTCTTGC
4013445 -TTTCTTTCTT
1 TTTTCTTTCTT
4013455 TGAAGTCGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTTCTTTCTTGC
Found at i:4028571 original size:16 final size:16
Alignment explanation
Indices: 4028550--4028582 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4028540 TCTTCAAAAC
4028550 ACCACTCATGCATGTG
1 ACCACTCATGCATGTG
4028566 ACCACTCATGCATGTG
1 ACCACTCATGCATGTG
4028582 A
1 A
4028583 TTCTTTTTTA
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:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (16 bp):
ACCACTCATGCATGTG
Found at i:4029494 original size:54 final size:55
Alignment explanation
Indices: 4029436--4029545 Score: 127
Period size: 55 Copynumber: 2.0 Consensus size: 55
4029426 ACCTTCGAAC
* * *
4029436 TAGGGACACACGA-CTGTGTCCCA-GCTTGTGTCCTCA-CTCGTGTAACTCTCTGAG
1 TAGGGACACACGATC-ATGTCACATGCTCGTGTCC-CAGCTCGTGTAACTCTCTGAG
* * *
4029490 TAGGGTCACACGATCATGTCACATGCTCGTGTGCCAGGTCGTGTAACTCTCTGAG
1 TAGGGACACACGATCATGTCACATGCTCGTGTCCCAGCTCGTGTAACTCTCTGAG
4029545 T
1 T
4029546 TGCCCCACAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
54 20 0.43
55 27 0.57
ACGTcount: A:0.19, C:0.27, G:0.25, T:0.28
Consensus pattern (55 bp):
TAGGGACACACGATCATGTCACATGCTCGTGTCCCAGCTCGTGTAACTCTCTGAG
Found at i:4030352 original size:18 final size:17
Alignment explanation
Indices: 4030320--4030360 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
4030310 CATATCAATT
*
4030320 GCATAATATAAGCATAA
1 GCATAAAATAAGCATAA
4030337 GCATAAAATCAAGCATAA
1 GCATAAAAT-AAGCATAA
*
4030355 CCATAA
1 GCATAA
4030361 GCTTGATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.54, C:0.17, G:0.10, T:0.20
Consensus pattern (17 bp):
GCATAAAATAAGCATAA
Found at i:4038738 original size:41 final size:41
Alignment explanation
Indices: 4038681--4038830 Score: 228
Period size: 41 Copynumber: 3.7 Consensus size: 41
4038671 TTTAACATAT
*
4038681 TCACCAGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCAGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* * * *
4038722 TCACCGGCACTTAGCCTGCTAGGTTTATAACTTGATTTAGA
1 TCACCAGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
4038763 TCACCAGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCAGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* *
4038804 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCAGCACTTAGCCTGCTAGGCTTA
4038831 AAGTCCTAAT
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 98 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (41 bp):
TCACCAGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:4046555 original size:40 final size:41
Alignment explanation
Indices: 4046458--4046556 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 41
4046448 TTGATCTCGG
* * * *
4046458 TTTCGCACATTTAGTGCCCGTTATTTAACATAATTATTTAA
1 TTTCGCACACTTAGTGCTCGTTATTCAACATAATCATTTAA
* *
4046499 TTTCGCACACTTAGTGCTCGTTATTCAACCTCATCATTTAA
1 TTTCGCACACTTAGTGCTCGTTATTCAACATAATCATTTAA
4046540 -TTCGCACACTTAGTGCT
1 TTTCGCACACTTAGTGCT
4046557 AATCATATAG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 17 0.33
41 35 0.67
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.40
Consensus pattern (41 bp):
TTTCGCACACTTAGTGCTCGTTATTCAACATAATCATTTAA
Found at i:4053644 original size:36 final size:36
Alignment explanation
Indices: 4053518--4053788 Score: 137
Period size: 36 Copynumber: 7.2 Consensus size: 36
4053508 TATGTATTTT
*
4053518 TCGGTTTATCCGACTAGCGCTAGGCGCAAATCATTG
1 TCGGTTTATCCGACTAGCGCTGGGCGCAAATCATTG
* * * * * ** *
4053554 TTGATTTATCCGACTAGTGTTGGGCACATTTGATATCG
1 TCGGTTTATCCGACTAGCGCTGGGCGCAAATCAT-T-G
** * *
4053592 TCGGTTTATCTAACTAGCGCTGGGCGTAACTCATTG
1 TCGGTTTATCCGACTAGCGCTGGGCGCAAATCATTG
* * * ** * *
4053628 TCGGTTTATCCGACTAGTGTTGGGTACACATTTGATATCA
1 TCGGTTTATCCGACTAGCGCTGGG--CGCAAATCAT-T-G
* * * * *
4053668 TCGATTTATCTGACTAACGCTGGGAGCAAAACATTG
1 TCGGTTTATCCGACTAGCGCTGGGCGCAAATCATTG
* ** * * * *
4053704 TCGGTTTATCTGACTAATGTTGGGCACACATTTGATATCG
1 TCGGTTTATCCGACTAGCGCTGGGCGCA-A-ATCAT-T-G
* * *
4053744 TCAGTTTATCCGACTAGCGTTGGGCGCAAAACATTG
1 TCGGTTTATCCGACTAGCGCTGGGCGCAAATCATTG
4053780 TCGGTTTAT
1 TCGGTTTAT
4053789 TCAACTGGTG
Statistics
Matches: 166, Mismatches: 59, Indels: 20
0.68 0.24 0.08
Matches are distributed among these distances:
36 78 0.47
37 5 0.03
38 37 0.22
39 3 0.02
40 43 0.26
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (36 bp):
TCGGTTTATCCGACTAGCGCTGGGCGCAAATCATTG
Found at i:4053691 original size:76 final size:75
Alignment explanation
Indices: 4053522--4053861 Score: 341
Period size: 76 Copynumber: 4.5 Consensus size: 75
4053512 TATTTTTCGG
* * * *
4053522 TTTATCCGACTAGCGCTAGGCGCAAATCATTGTTGATTTATCCGACTAGTGTTGGG-CACATTTG
1 TTTATCCGACTAGCGCTGGGCGCAAAACATTGTCGGTTTATCCGACTAGTGTTGGGACACATTTG
*
4053586 ATATCGTCGG
66 ATATCGTCGA
** * **
4053596 TTTATCTAACTAGCGCTGGGCGTAACTCATTGTCGGTTTATCCGACTAGTGTTGGGTACACATTT
1 TTTATCCGACTAGCGCTGGGCGCAAAACATTGTCGGTTTATCCGACTAGTGTTGGG-ACACATTT
*
4053661 GATATCATCGA
65 GATATCGTCGA
* * * * *
4053672 TTTATCTGACTAACGCTGGGAGCAAAACATTGTCGGTTTATCTGACTAATGTTGGGCACACATTT
1 TTTATCCGACTAGCGCTGGGCGCAAAACATTGTCGGTTTATCCGACTAGTGTTGGG-ACACATTT
4053737 GATATCGTC-A
65 GATATCGTCGA
* * * * **
4053747 GTTTATCCGACTAGCGTTGGGCGCAAAACATTGTCGGTTTATTCAACTGGTGCAGGG-CACA--T
1 -TTTATCCGACTAGCGCTGGGCGCAAAACATTGTCGGTTTATCCGACTAGTGTTGGGACACATTT
* *
4053809 -CTATCGTCGG
65 GATATCGTCGA
* * * *
4053819 TTTATCCAACTAGTGTTGGGCGCAAAACTTTGTTACGGTTTAT
1 TTTATCCGACTAGCGCTGGGCGCAAAACATTG-T-CGGTTTAT
4053862 TTGTCGGGCA
Statistics
Matches: 225, Mismatches: 35, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
71 36 0.16
72 2 0.01
73 8 0.04
74 53 0.24
75 1 0.00
76 125 0.56
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (75 bp):
TTTATCCGACTAGCGCTGGGCGCAAAACATTGTCGGTTTATCCGACTAGTGTTGGGACACATTTG
ATATCGTCGA
Found at i:4053766 original size:40 final size:40
Alignment explanation
Indices: 4053558--4053768 Score: 138
Period size: 36 Copynumber: 5.5 Consensus size: 40
4053548 TCATTGTTGA
*
4053558 TTTATCCGACTAGTGTTGGG--CACATTTGATATCGTCGG
1 TTTATCCGACTAGCGTTGGGCACACATTTGATATCGTCGG
** * ** * *
4053596 TTTATCTAACTAGCGCTGGGCGTA-A-CTCAT-T-GTCGG
1 TTTATCCGACTAGCGTTGGGCACACATTTGATATCGTCGG
* * * *
4053632 TTTATCCGACTAGTGTTGGGTACACATTTGATATCATCGA
1 TTTATCCGACTAGCGTTGGGCACACATTTGATATCGTCGG
* * * * * *
4053672 TTTATCTGACTAACGCTGGG-AGCA-A---AACATTGTCGG
1 TTTATCCGACTAGCGTTGGGCA-CACATTTGATATCGTCGG
* ** *
4053708 TTTATCTGACTAATGTTGGGCACACATTTGATATCGTCAG
1 TTTATCCGACTAGCGTTGGGCACACATTTGATATCGTCGG
4053748 TTTATCCGACTAGCGTTGGGC
1 TTTATCCGACTAGCGTTGGGC
4053769 GCAAAACATT
Statistics
Matches: 125, Mismatches: 36, Indels: 22
0.68 0.20 0.12
Matches are distributed among these distances:
36 48 0.38
37 4 0.03
38 22 0.18
39 4 0.03
40 47 0.38
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (40 bp):
TTTATCCGACTAGCGTTGGGCACACATTTGATATCGTCGG
Found at i:4053956 original size:24 final size:24
Alignment explanation
Indices: 4053923--4053980 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
4053913 AGCAATCCAT
4053923 TGAAGAAGGTTGAAAAGGATATAAA
1 TGAA-AAGGTTGAAAAGGATATAAA
*
4053948 TGAAAAGGTTGAAAAGGATATCAA
1 TGAAAAGGTTGAAAAGGATATAAA
*
4053972 CGAAAAGGT
1 TGAAAAGGT
4053981 CAGTATCTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.50, C:0.03, G:0.28, T:0.19
Consensus pattern (24 bp):
TGAAAAGGTTGAAAAGGATATAAA
Found at i:4056435 original size:11 final size:11
Alignment explanation
Indices: 4056419--4056461 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
4056409 TAGAATATAT
4056419 CCCATACCTTG
1 CCCATACCTTG
*
4056430 CCCATACCTTT
1 CCCATACCTTG
*
4056441 CCCATACC-TA
1 CCCATACCTTG
4056451 CCCATACCTTG
1 CCCATACCTTG
4056462 GAAAGGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.21, C:0.47, G:0.05, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:4056446 original size:22 final size:21
Alignment explanation
Indices: 4056418--4056460 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4056408 TTAGAATATA
*
4056418 TCCCATACCTTGCCCATACCTT
1 TCCCATACC-TACCCATACCTT
4056440 TCCCATACCTACCCATACCTT
1 TCCCATACCTACCCATACCTT
4056461 GGAAAGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.21, C:0.47, G:0.02, T:0.30
Consensus pattern (21 bp):
TCCCATACCTACCCATACCTT
Found at i:4057040 original size:36 final size:36
Alignment explanation
Indices: 4056993--4057084 Score: 157
Period size: 36 Copynumber: 2.6 Consensus size: 36
4056983 TACGACCGTT
4056993 TACGGTACTATTCACGTATATGGCACTATTCACGTA
1 TACGGTACTATTCACGTATATGGCACTATTCACGTA
*
4057029 TACGGTACTATTCACGTATATGGTACTATTCACGTA
1 TACGGTACTATTCACGTATATGGCACTATTCACGTA
* *
4057065 TACAGTACTGTTCACGTATA
1 TACGGTACTATTCACGTATA
4057085 CAATAGTTGG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (36 bp):
TACGGTACTATTCACGTATATGGCACTATTCACGTA
Found at i:4057086 original size:18 final size:18
Alignment explanation
Indices: 4056993--4057085 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
4056983 TACGACCGTT
4056993 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
4057011 TATGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
4057029 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
4057047 TATGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
4057065 TACAGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
4057083 TAC
1 TAC
4057086 AATAGTTGGG
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:4061149 original size:11 final size:11
Alignment explanation
Indices: 4061133--4061175 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
4061123 TAGAATATAT
4061133 CCCATACCTTG
1 CCCATACCTTG
*
4061144 CCCATACCTTT
1 CCCATACCTTG
*
4061155 CCCATACC-TA
1 CCCATACCTTG
4061165 CCCATACCTTG
1 CCCATACCTTG
4061176 GAAAGGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.21, C:0.47, G:0.05, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:4061160 original size:22 final size:21
Alignment explanation
Indices: 4061132--4061174 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4061122 TTAGAATATA
*
4061132 TCCCATACCTTGCCCATACCTT
1 TCCCATACC-TACCCATACCTT
4061154 TCCCATACCTACCCATACCTT
1 TCCCATACCTACCCATACCTT
4061175 GGAAAGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.21, C:0.47, G:0.02, T:0.30
Consensus pattern (21 bp):
TCCCATACCTACCCATACCTT
Found at i:4066580 original size:14 final size:15
Alignment explanation
Indices: 4066548--4066581 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4066538 TAAATTTTAG
4066548 TTTTGGTTCCTCTAT
1 TTTTGGTTCCTCTAT
**
4066563 TTTTGGTTTTTCTAT
1 TTTTGGTTCCTCTAT
4066578 TTTT
1 TTTT
4066582 ATATTCTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.12, T:0.71
Consensus pattern (15 bp):
TTTTGGTTCCTCTAT
Found at i:4067762 original size:11 final size:11
Alignment explanation
Indices: 4067735--4067777 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
4067725 TGACCTTTCC
4067735 AAGGTATGGG-
1 AAGGTATGGGA
*
4067745 TAGGTATGGGA
1 AAGGTATGGGA
*
4067756 AAGGTATGGGC
1 AAGGTATGGGA
4067767 AAGGTATGGGA
1 AAGGTATGGGA
4067778 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:4067774 original size:22 final size:21
Alignment explanation
Indices: 4067735--4067777 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4067725 TGACCTTTCC
*
4067735 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
4067756 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
4067778 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:4071847 original size:18 final size:18
Alignment explanation
Indices: 4071824--4071916 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
4071814 CCCAACTACT
* *
4071824 GTATACGTGAACAATACC
1 GTATACGTGAATAGTACC
* *
4071842 GTATACATGAATAGTGCC
1 GTATACGTGAATAGTACC
* *
4071860 ATATACGTGAATAGTATC
1 GTATACGTGAATAGTACC
4071878 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
4071896 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
4071914 GTA
1 GTA
4071917 AACGGTCGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:4080905 original size:51 final size:51
Alignment explanation
Indices: 4080829--4080938 Score: 211
Period size: 51 Copynumber: 2.1 Consensus size: 51
4080819 AAAAACATAT
4080829 GCACCTCCCCTATCTCAATAATTACTTGAAACTCAAACTCAACAAGAATTG
1 GCACCTCCCCTATCTCAATAATTACTTGAAACTCAAACTCAACAAGAATTG
4080880 GCACCTCCCCTATCTCAATAATTACTTGAAACTCAAACTCAACAAGAATTG
1 GCACCTCCCCTATCTCAATAATTACTTGAAACTCAAACTCAACAAGAATTG
4080931 GCATCCTC
1 GCA-CCTC
4080939 ACTAAGGTTC
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 54 0.93
52 4 0.07
ACGTcount: A:0.35, C:0.31, G:0.08, T:0.25
Consensus pattern (51 bp):
GCACCTCCCCTATCTCAATAATTACTTGAAACTCAAACTCAACAAGAATTG
Found at i:4089901 original size:20 final size:19
Alignment explanation
Indices: 4089876--4089920 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
4089866 AATATTATAT
*
4089876 TTTTTCTTTATTTCTTTTTA
1 TTTTTCTTTATTT-TGTTTA
*
4089896 TTTTTC-TTATTTTGTTTC
1 TTTTTCTTTATTTTGTTTA
4089914 TTTTTCT
1 TTTTTCT
4089921 AGTATCTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
19 6 0.27
20 6 0.27
ACGTcount: A:0.07, C:0.11, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTATTTTGTTTA
Found at i:4090034 original size:26 final size:23
Alignment explanation
Indices: 4090005--4090056 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 23
4089995 TCATATACTT
4090005 ATTATTATTTTCTTCTTAATGTTCTC
1 ATTATTA-TTTCTT-TTAATGTT-TC
*
4090031 ATTATTATTTGTTTTAATGTTTC
1 ATTATTATTTCTTTTAATGTTTC
4090054 ATT
1 ATT
4090057 TCTTATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 5 0.20
24 8 0.32
25 5 0.20
26 7 0.28
ACGTcount: A:0.21, C:0.10, G:0.06, T:0.63
Consensus pattern (23 bp):
ATTATTATTTCTTTTAATGTTTC
Found at i:4091557 original size:6 final size:6
Alignment explanation
Indices: 4091546--4091646 Score: 152
Period size: 6 Copynumber: 17.0 Consensus size: 6
4091536 AGCTTATTTG
* *
4091546 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA- TTTTAT TTTCAT TTTCAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
4091593 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT GTTTT-T GTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT -TTTTAT TTTTAT TTTTAT
4091641 TTTTAT
1 TTTTAT
4091647 AGACTTATTT
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
5 8 0.09
6 76 0.86
7 4 0.05
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:4095901 original size:12 final size:12
Alignment explanation
Indices: 4095886--4095910 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4095876 AAAATAAAAC
4095886 TGATAATAATAA
1 TGATAATAATAA
4095898 TGATAATAATAA
1 TGATAATAATAA
4095910 T
1 T
4095911 AGTCAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TGATAATAATAA
Found at i:4100412 original size:121 final size:121
Alignment explanation
Indices: 4100253--4100495 Score: 414
Period size: 121 Copynumber: 2.0 Consensus size: 121
4100243 ATTAATAGAT
* * **
4100253 AATGAAAGGGTGAATGTTGGTGAGAATGTATCCGCAGTGTTATAGCGGAAAATGCCGGCAAAATG
1 AATGAAAGGGTGAATGTTGGTGAGAATGTATCCGCAGTGTTACAGCGAAAAATGCCAACAAAATG
* *
4100318 CAAGGATAGGGGCATGTTTGCAATACCATGCAAAATAGGCCATCTGGCAATTAAGA
66 CAAGGATAAGGGCATATTTGCAATACCATGCAAAATAGGCCATCTGGCAATTAAGA
*
4100374 AATGAAAGGGTGAATGTTGGTGAGAATGTATTCGCAGTGTTACAGCGAAAAATGCCAACAAAATG
1 AATGAAAGGGTGAATGTTGGTGAGAATGTATCCGCAGTGTTACAGCGAAAAATGCCAACAAAATG
*
4100439 CAAGGATAAGGGCATATTTGCAATACCATGCAAAATAGGCCATCTGGGAATTAAGA
66 CAAGGATAAGGGCATATTTGCAATACCATGCAAAATAGGCCATCTGGCAATTAAGA
4100495 A
1 A
4100496 GGCTATGTGT
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
121 114 1.00
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (121 bp):
AATGAAAGGGTGAATGTTGGTGAGAATGTATCCGCAGTGTTACAGCGAAAAATGCCAACAAAATG
CAAGGATAAGGGCATATTTGCAATACCATGCAAAATAGGCCATCTGGCAATTAAGA
Found at i:4101373 original size:4 final size:4
Alignment explanation
Indices: 4101360--4101427 Score: 70
Period size: 4 Copynumber: 16.5 Consensus size: 4
4101350 CAACCCAATT
4101360 TTTA -TTA TTTA TTTA TTTA TTTA TTTTA TTTA CTTTA TTTA -TTA CTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA TTTA TTTA -TTTA
4101409 TTTTA TTT- TATTA TTTA TT
1 -TTTA TTTA T-TTA TTTA TT
4101428 ACTTATTTGG
Statistics
Matches: 56, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
3 7 0.12
4 33 0.59
5 16 0.29
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:4101399 original size:26 final size:25
Alignment explanation
Indices: 4101359--4101435 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 25
4101349 GCAACCCAAT
4101359 TTTTA-TTATTTATTTATTTA-TTTA
1 TTTTATTTATTTATTTA-TTACTTTA
4101383 TTTTATTTACTTTATTTATTACTTTA
1 TTTTATTTA-TTTATTTATTACTTTA
4101409 TTTTATTT-TATTATTTATTAC-TTA
1 TTTTATTTAT-TTATTTATTACTTTA
4101433 TTT
1 TTT
4101436 GGATATTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
24 12 0.24
25 17 0.35
26 20 0.41
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTATTTATTTATTTATTACTTTA
Found at i:4104673 original size:6 final size:6
Alignment explanation
Indices: 4104662--4104688 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4104652 ATAAATAAAA
4104662 TTTCAT TTTCAT TTTCAT TTTCAT TTT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTT
4104689 TTACTCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTCAT
Found at i:4105306 original size:11 final size:11
Alignment explanation
Indices: 4105290--4105324 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
4105280 CATTTTAAAA
4105290 TTTTAGATATT
1 TTTTAGATATT
4105301 TTTTAGATATT
1 TTTTAGATATT
4105312 TTTTAGATATT
1 TTTTAGATATT
4105323 TT
1 TT
4105325 CTTTTAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (11 bp):
TTTTAGATATT
Found at i:4105984 original size:23 final size:23
Alignment explanation
Indices: 4105940--4105986 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
4105930 ATACTACCTA
* *
4105940 TTTTCTTTTCTTTCTTAGATTTC
1 TTTTCTTTCCTTTCTTACATTTC
4105963 TTTTCTTTCCTTTCTCT-CATTTC
1 TTTTCTTTCCTTTCT-TACATTTC
4105986 T
1 T
4105987 CATCATCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.06, C:0.23, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTTCTTTCCTTTCTTACATTTC
Found at i:4107257 original size:118 final size:118
Alignment explanation
Indices: 4107082--4107387 Score: 407
Period size: 118 Copynumber: 2.5 Consensus size: 118
4107072 GATAAAATCA
* * **
4107082 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGTTTTTGCTATAGT
1 AAGCAGGATGCTTTATCAGAAGAA--T-T----TCGCGCCCACGTGGACGCGCTTTTGCTACAAC
*
4107147 TGGTCCTGAAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTAT-AAAAACGCTTC
59 TGGTCCTG-AAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAATATAAAAAACGCTTC
*
4107207 AAGTAGGATGCTTTATCAGAAGAATTTCGCGCCCACGTGGACGCGCTTTTGCTACAACTGGTCCT
1 AAGCAGGATGCTTTATCAGAAGAATTTCGCGCCCACGTGGACGCGCTTTTGCTACAACTGGTCCT
4107272 GAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAATATAAAAAACGCTTC
66 GAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAATATAAAAAACGCTTC
*
4107325 AAGCAGGATGCTTTATCAGAAGAATTTATGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACA
1 AAGCAGGATGCTTTATCAGAAGAA--T-T----TCGCGCCCACGTGGACGCGCTTTTGCTACA
4107388 GTAGCATGTT
Statistics
Matches: 165, Mismatches: 8, Indels: 16
0.87 0.04 0.08
Matches are distributed among these distances:
117 39 0.24
118 70 0.42
120 1 0.01
121 1 0.01
122 1 0.01
123 1 0.01
125 52 0.32
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (118 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCGCGCCCACGTGGACGCGCTTTTGCTACAACTGGTCCT
GAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAATATAAAAAACGCTTC
Found at i:4108387 original size:21 final size:22
Alignment explanation
Indices: 4108358--4108419 Score: 99
Period size: 21 Copynumber: 2.9 Consensus size: 22
4108348 AATAAATTAT
*
4108358 TTTAGGGTTTTTAAGTTAAGGG
1 TTTAAGGTTTTTAAGTTAAGGG
4108380 -TTAAGGTTTTTAAGTTAAGGG
1 TTTAAGGTTTTTAAGTTAAGGG
*
4108401 TTTAGGGTTTTTAAGTTAA
1 TTTAAGGTTTTTAAGTTAA
4108420 AGTGTTAGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 20 0.54
22 17 0.46
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.47
Consensus pattern (22 bp):
TTTAAGGTTTTTAAGTTAAGGG
Found at i:4108427 original size:22 final size:21
Alignment explanation
Indices: 4108359--4108431 Score: 110
Period size: 22 Copynumber: 3.4 Consensus size: 21
4108349 ATAAATTATT
4108359 TTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
*
4108380 TTAAGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAAGGG
*
4108401 TTTAGGGTTTTTAAGTTAAAGTG
1 -TTAGGGTTTTTAAGTT-AAGGG
4108424 TTAGGGTT
1 TTAGGGTT
4108432 AGGGTTAGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
21 20 0.43
22 23 0.49
23 4 0.09
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (21 bp):
TTAGGGTTTTTAAGTTAAGGG
Found at i:4108568 original size:114 final size:108
Alignment explanation
Indices: 4108400--4108638 Score: 345
Period size: 107 Copynumber: 2.2 Consensus size: 108
4108390 TAAGTTAAGG
* * *
4108400 GTTTAGGGTTTTTAAGTTAAAGTGTTAGGGTTAGGGTTAGGGTTTTTGTTAGGGTTTGTCAATTA
1 GTTTAGGGTTTTTAAGTTAAAGGGTTAAGGTTAAGGTTAGGGTTTTTGTTAGGGTTTGTCAATTA
*
4108465 ATATCAAAATTTAATTATAATTTATAAATTTATAAATTTTTAATAAATTA
66 A-AT---AA-TAAATT-TAA-TTATAAATTTATAAATTTTTAATAAATTA
*
4108515 GTTTAGGGTTTTTAGGTT-AAGGGTTAAGGTTAAGGTTAGGGTTTTTGTTAGGGTTTGTCAATTA
1 GTTTAGGGTTTTTAAGTTAAAGGGTTAAGGTTAAGGTTAGGGTTTTTGTTAGGGTTTGTCAATTA
*
4108579 AATTATAAATTTAATTATAAATTTATAAATTTTTAATAAATTA
66 AATAATAAATTTAATTATAAATTTATAAATTTTTAATAAATTA
*
4108622 GTTTAAGGTTTTTAAGT
1 GTTTAGGGTTTTTAAGT
4108639 AATACCTCAA
Statistics
Matches: 116, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
107 44 0.38
108 3 0.03
109 5 0.04
110 1 0.01
113 2 0.02
114 44 0.38
115 17 0.15
ACGTcount: A:0.32, C:0.01, G:0.19, T:0.47
Consensus pattern (108 bp):
GTTTAGGGTTTTTAAGTTAAAGGGTTAAGGTTAAGGTTAGGGTTTTTGTTAGGGTTTGTCAATTA
AATAATAAATTTAATTATAAATTTATAAATTTTTAATAAATTA
Found at i:4108602 original size:12 final size:12
Alignment explanation
Indices: 4108574--4108603 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4108564 AGGGTTTGTC
*
4108574 AATTAAATTATA
1 AATTTAATTATA
4108586 AATTTAATTATA
1 AATTTAATTATA
4108598 AATTTA
1 AATTTA
4108604 TAAATTTTTA
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:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATTTAATTATA
Found at i:4108617 original size:19 final size:19
Alignment explanation
Indices: 4108577--4108620 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
4108567 GTTTGTCAAT
4108577 TAAA-TTATAAATTTAATTA
1 TAAATTTATAAATTT-ATTA
4108596 TAAATTTATAAATTT-TTAA
1 TAAATTTATAAATTTATT-A
4108615 TAAATT
1 TAAATT
4108621 AGTTTAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.09
19 11 0.48
20 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAATTTATAAATTTATTA
Found at i:4109124 original size:17 final size:19
Alignment explanation
Indices: 4109092--4109134 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
4109082 GACTCGAAAA
* *
4109092 AGGAAACATATAA-GGGTT
1 AGGATACATATAAGGGGCT
4109110 AGGATACAT-TAAGGGGCT
1 AGGATACATATAAGGGGCT
4109128 AGGATAC
1 AGGATAC
4109135 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.21
Consensus pattern (19 bp):
AGGATACATATAAGGGGCT
Found at i:4110995 original size:11 final size:11
Alignment explanation
Indices: 4110979--4111044 Score: 69
Period size: 11 Copynumber: 5.9 Consensus size: 11
4110969 TTAAATATGG
4110979 ATTTGAGAGAA
1 ATTTGAGAGAA
* *
4110990 ATTTGAAAGGA
1 ATTTGAGAGAA
*
4111001 ATTTGAGAGCA
1 ATTTGAGAGAA
4111012 ATTTGAGAGAA
1 ATTTGAGAGAA
* *
4111023 ACTTGAGAAAAA
1 ATTTGAG-AGAA
*
4111035 AATTGAGAGA
1 ATTTGAGAGA
4111045 GGATTAGTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
11 36 0.80
12 9 0.20
ACGTcount: A:0.47, C:0.03, G:0.26, T:0.24
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:4111402 original size:28 final size:29
Alignment explanation
Indices: 4111338--4111402 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 29
4111328 GTTTTCAGGG
*
4111338 AAAAGGGCCCATTCCGGTAAATAATAAAA
1 AAAAGGGCCCATTCCAGTAAATAATAAAA
* ** * *
4111367 TACCGGGCCCATTTCAGTAAAT-TTAAAA
1 AAAAGGGCCCATTCCAGTAAATAATAAAA
4111395 AAAAGGGC
1 AAAAGGGC
4111403 TTTTAATGGT
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (29 bp):
AAAAGGGCCCATTCCAGTAAATAATAAAA
Found at i:4111604 original size:18 final size:18
Alignment explanation
Indices: 4111581--4111623 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4111571 ATGATATCGG
*
4111581 TATTGATGATTGTGACGA
1 TATTGATGATAGTGACGA
* *
4111599 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
4111617 TATTGAT
1 TATTGAT
4111624 CGTGTCCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:4112319 original size:31 final size:29
Alignment explanation
Indices: 4112241--4112321 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 29
4112231 TAGTTGACGG
4112241 AGAAAAAGTTCAAGTACCAATCTGAGACA
1 AGAAAAAGTTCAAGTACCAATCTGAGACA
* * *
4112270 A-AAAAAATCTTAAATACCAATCTAGGAGA-A
1 AGAAAAAGT-TCAAGTACCAATCT--GAGACA
4112300 ATGAAAAAGTTCAAGTACCAAT
1 A-GAAAAAGTTCAAGTACCAAT
4112322 TTATATTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
28 6 0.15
29 13 0.32
30 2 0.05
31 14 0.34
32 6 0.15
ACGTcount: A:0.52, C:0.15, G:0.14, T:0.20
Consensus pattern (29 bp):
AGAAAAAGTTCAAGTACCAATCTGAGACA
Found at i:4113374 original size:16 final size:17
Alignment explanation
Indices: 4113355--4113395 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
4113345 TATTAGTTAT
4113355 ATAAATTTAATT-TAAA
1 ATAAATTTAATTATAAA
*
4113371 ATAACTTTAATTATAAA
1 ATAAATTTAATTATAAA
4113388 ATCAAATT
1 AT-AAATT
4113396 GTAAATCCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 11 0.52
17 6 0.29
18 4 0.19
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAAATTTAATTATAAA
Found at i:4118612 original size:18 final size:19
Alignment explanation
Indices: 4118586--4118621 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4118576 AAAGTATTCA
4118586 AATTCAACCCAA-AATAAT
1 AATTCAACCCAATAATAAT
*
4118604 AATTTAACCCAATAATAA
1 AATTCAACCCAATAATAA
4118622 CTATTGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (19 bp):
AATTCAACCCAATAATAAT
Found at i:4121420 original size:190 final size:190
Alignment explanation
Indices: 4121087--4121467 Score: 566
Period size: 190 Copynumber: 2.0 Consensus size: 190
4121077 TTATATTGTG
* * * ** * *
4121087 GTTACTAAGTGGAATTGTAACGCCCCATACCCGACCCAATCGTTGGGTCTACGTACCGAATGCTA
1 GTTACTAAGCGGAATTGTAACACCCCATACCCAACCCAATCCCTGAGTCTAAGTACCGAATGCTA
* *
4121152 CAAGAACCCGTTTAATTTTACTATACATTCATAATTAATTCAATTACATGTCAGAACAACTTGAA
66 CAAGAACCCATTTAATTTTACTATACATTCATAATTAATTCAATTACATGTAAGAACAACTTGAA
4121217 AACATAGGCCTAATTGCCACTAATCTCATACACTAAAGAAAGACCGTAATGATTTCTTAT
131 AACATAGGCCTAATTGCCACTAATCTCATACACTAAAGAAAGACCGTAATGATTTCTTAT
* * * *
4121277 GTTACTAAGCGGAATTGTAACACCCCATACCCAACTCGATCCCTGAGTC-AGAGTACTGGATGCT
1 GTTACTAAGCGGAATTGTAACACCCCATACCCAACCCAATCCCTGAGTCTA-AGTACCGAATGCT
* * *
4121341 ACAAGAACCTATTTAATTTTATTATGCATTCATAATTAATTCAATTACATGTAAGAACAACTTGA
65 ACAAGAACCCATTTAATTTTACTATACATTCATAATTAATTCAATTACATGTAAGAACAACTTGA
* * * *
4121406 AAACTTATGCCTAATTGCCACTAATCTCATACACTAAAGAAATATCGTAATGATTTCTTAT
130 AAACATAGGCCTAATTGCCACTAATCTCATACACTAAAGAAAGACCGTAATGATTTCTTAT
4121467 G
1 G
4121468 ACCTTAGTTT
Statistics
Matches: 170, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
189 1 0.01
190 169 0.99
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (190 bp):
GTTACTAAGCGGAATTGTAACACCCCATACCCAACCCAATCCCTGAGTCTAAGTACCGAATGCTA
CAAGAACCCATTTAATTTTACTATACATTCATAATTAATTCAATTACATGTAAGAACAACTTGAA
AACATAGGCCTAATTGCCACTAATCTCATACACTAAAGAAAGACCGTAATGATTTCTTAT
Found at i:4126880 original size:3 final size:3
Alignment explanation
Indices: 4126833--4126926 Score: 61
Period size: 3 Copynumber: 31.3 Consensus size: 3
4126823 TTTAGCATTT
* * * * *
4126833 TTA TTA TT- TTC TTCA TTA TTT TTA ATA -TA TTA TCA TCTT TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* *
4126878 TTA TTA TTA TTA TT- TATA TCA TTA TTA CTTA TCA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
4126923 TTA T
1 TTA T
4126927 ATAATAGCTT
Statistics
Matches: 71, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
2 6 0.08
3 58 0.82
4 7 0.10
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:4126887 original size:36 final size:38
Alignment explanation
Indices: 4126847--4126926 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 38
4126837 TATTTTCTTC
4126847 ATTATT-TTTAATAT-ATTATCATCTT-T-TATTATTATT
1 ATTATTATTT-ATATCATTATCA-CTTATATATTATTATT
*
4126883 ATTATTATTTATATCATTATTACTTATCATATTATTATT
1 ATTATTATTTATATCATTATCACTTAT-ATATTATTATT
4126922 ATTAT
1 ATTAT
4126927 ATAATAGCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
36 13 0.34
37 10 0.26
39 15 0.39
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (38 bp):
ATTATTATTTATATCATTATCACTTATATATTATTATT
Found at i:4127108 original size:5 final size:5
Alignment explanation
Indices: 4127100--4127152 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
4127090 ATATTATATA
* * * *
4127100 TATTT TATTT TATTT TATGT TATGT TATTTT TATCT TACTT TATTT T-TTT
1 TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT TATTT TATTT TATTT
4127150 TAT
1 TAT
4127153 AATTCACATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 4 0.10
5 32 0.80
6 4 0.10
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:4127390 original size:12 final size:12
Alignment explanation
Indices: 4127373--4127412 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
4127363 ATTTATCCTT
4127373 TATATTTTAAAA
1 TATATTTTAAAA
* *
4127385 TATATTTTTATA
1 TATATTTTAAAA
4127397 TATATTTTATAAA
1 TATATTTTA-AAA
4127410 TAT
1 TAT
4127413 TTTGTAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TATATTTTAAAA
Found at i:4127397 original size:10 final size:11
Alignment explanation
Indices: 4127373--4127415 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
4127363 ATTTATCCTT
*
4127373 TATATTTTAAAA
1 TATATTTT-ATA
4127385 TATATTTTTATA
1 TATA-TTTTATA
4127397 TATATTTTATA
1 TATATTTTATA
*
4127408 AATATTTT
1 TATATTTT
4127416 GTAATTCACG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 14 0.50
12 10 0.36
13 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATTTTATA
Found at i:4127466 original size:2 final size:2
Alignment explanation
Indices: 4127446--4127484 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
4127436 TATTTTAATT
*
4127446 TA TA TC TA TA T- TCA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
4127485 CTTTTATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4128011 original size:108 final size:108
Alignment explanation
Indices: 4127745--4128174 Score: 578
Period size: 108 Copynumber: 3.9 Consensus size: 108
4127735 AAGGAAAATA
* * * * * * *
4127745 TTTCAAATTGAGGCAATATTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
1 TTTCAAAATAAGGCAATATTTTGCGTTT-GAAAATTCGAG-GAACGTGCCCTAAGGTACTGGGTT
4127810 TCGATTTTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
64 TCGA--TTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
* * *
4127857 TTTCAAAAATAAGGTAATGTTTTGCGTTTGAAAATTCGAGGAACGTGTCCTAAGGTACTGGGTTT
1 TTTC-AAAATAAGGCAATATTTTGCGTTTGAAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
* *
4127922 CGATTTCTCGTTCCACCAAAT-GACTTAATATCCTTTTCAAAAA-T
65 CGATTTCTCGTTCGACCAAATAG-CTAAATATCCTTTT-AAAAACT
4127966 TTTCAAAATAAGGCAATATTTTGCGTTTGAAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTC
1 TTTCAAAATAAGGCAATATTTTGCGTTTGAAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTC
*
4128031 GATTCCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
66 GATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
* * * * *
4128074 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTTGAGGAACGTGCCCTAAGGTGCTGGGTTTC
1 TTTCAAAATAAGGCAATATTTTGCGTTTGAAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTC
* * *
4128139 GATTTCTCGTT-TATCCAAATTGCCAAATATCCTTTT
66 GATTTCTCGTTCGA-CCAAATAGCTAAATATCCTTTT
4128175 GAATTTTAAT
Statistics
Matches: 285, Mismatches: 27, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
107 6 0.02
108 181 0.64
109 36 0.13
110 5 0.02
111 23 0.08
112 14 0.05
113 20 0.07
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (108 bp):
TTTCAAAATAAGGCAATATTTTGCGTTTGAAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTC
GATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
Found at i:4128141 original size:216 final size:221
Alignment explanation
Indices: 4127739--4128149 Score: 652
Period size: 216 Copynumber: 1.9 Consensus size: 221
4127729 TCAAAAAAGG
* * * *
4127739 AAAATATTTCAAATTGAGGCAATATTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGC
1 AAAATATTTCAAAATAAGGCAATATTTTGCGTTTGGAAAATTCGAGAAAACATGCCCTAAGGTAC
*
4127804 TGGGTGTCGATTTTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAA
66 TGGGTGTCGA-TTTCCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAA
* *
4127869 GGTAATGTTTTGCGTTTGAAAATTCGAGGAACGTGTCCTAAGGTACTGGGTTTCGATTTCTCGTT
130 GGCAATGTTTTGCGTTTGAAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTT
4127934 CCACCAAATGACTTAATATCCTTTTCA
195 CCACCAAATGACTTAATATCCTTTTCA
* *
4127961 AAAAT-TTTCAAAATAAGGCAATATTTTGCGTTT-GAAAATTCGAG-GAACGTGCCCTAAGGTAC
1 AAAATATTTCAAAATAAGGCAATATTTTGCGTTTGGAAAATTCGAGAAAACATGCCCTAAGGTAC
* *
4128023 TGGGTTTCGA-TTCCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTC-AAAGTAAG
66 TGGGTGTCGATTTCCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAG
* * *
4128086 GCAATGTTTTGCGTTTGGAAATTTGAGGAACGTGCCCTAAGGTGCTGGGTTTCGATTTCTCGTT
131 GCAATGTTTTGCGTTTGAAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTT
4128150 TATCCAAATT
Statistics
Matches: 175, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
216 66 0.38
217 44 0.25
219 24 0.14
220 10 0.06
221 26 0.15
222 5 0.03
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (221 bp):
AAAATATTTCAAAATAAGGCAATATTTTGCGTTTGGAAAATTCGAGAAAACATGCCCTAAGGTAC
TGGGTGTCGATTTCCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAG
GCAATGTTTTGCGTTTGAAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTC
CACCAAATGACTTAATATCCTTTTCA
Found at i:4129618 original size:3 final size:3
Alignment explanation
Indices: 4129610--4129646 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
4129600 ATATGTAGGT
4129610 ATA ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA A
4129647 CAAAATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:4129656 original size:18 final size:21
Alignment explanation
Indices: 4129613--4129662 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
4129603 TGTAGGTATA
*
4129613 ATAATAATAATAATATATAAT
1 ATAATAATAATAACATATAAT
4129634 ATAATAATAATAACA-A-AAT
1 ATAATAATAATAACATATAAT
4129653 -TAATAA-AATA
1 ATAATAATAATA
4129663 GACTAAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 3 0.11
20 1 0.04
21 14 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAATAATAATAACATATAAT
Found at i:4129993 original size:52 final size:54
Alignment explanation
Indices: 4129918--4130022 Score: 178
Period size: 52 Copynumber: 2.0 Consensus size: 54
4129908 CACCTTTAAA
4129918 AAACTGCCAATCGTTCTCCC-TTTTTTATTCTTTT-TTTCTTTTCTTTTTTTTT
1 AAACTGCCAATCGTTCTCCCTTTTTTTATTCTTTTCTTTCTTTTCTTTTTTTTT
* *
4129970 AAACTGTCAATCGTTCTCCCTTTTTTTATTCTTTTCTTTTTTTTCTTTTTTTT
1 AAACTGCCAATCGTTCTCCCTTTTTTTATTCTTTTCTTTCTTTTCTTTTTTTT
4130023 CGACATTGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 19 0.39
53 14 0.29
54 16 0.33
ACGTcount: A:0.11, C:0.20, G:0.04, T:0.65
Consensus pattern (54 bp):
AAACTGCCAATCGTTCTCCCTTTTTTTATTCTTTTCTTTCTTTTCTTTTTTTTT
Found at i:4130015 original size:14 final size:14
Alignment explanation
Indices: 4129990--4130022 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4129980 TCGTTCTCCC
4129990 TTTTTTTATTCTTT
1 TTTTTTTATTCTTT
4130004 TCTTTTTT-TTCTTT
1 T-TTTTTTATTCTTT
4130018 TTTTT
1 TTTTT
4130023 CGACATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 8 0.44
15 6 0.33
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTATTCTTT
Found at i:4130188 original size:19 final size:20
Alignment explanation
Indices: 4130130--4130242 Score: 120
Period size: 21 Copynumber: 5.4 Consensus size: 20
4130120 AAATTAAATC
* *
4130130 TCTAAGATTACAAAATCATA
1 TCTAAGATTGCAATATCATA
*
4130150 TCTTCTAAGATTGTATATATCATA
1 ---TCTAAGATTGCA-ATATCATA
4130174 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCA-ATATCATA
*
4130195 TCTAGGATTGCATATATCATA
1 TCTAAGATTGCA-ATATCATA
4130216 TCTAAGATTGC-ATATCATA
1 TCTAAGATTGCAATATCATA
*
4130235 TTTAAGAT
1 TCTAAGAT
4130243 CTTATATCCT
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
19 15 0.18
21 50 0.61
23 10 0.12
24 7 0.09
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (20 bp):
TCTAAGATTGCAATATCATA
Found at i:4130250 original size:19 final size:21
Alignment explanation
Indices: 4130153--4130242 Score: 139
Period size: 21 Copynumber: 4.4 Consensus size: 21
4130143 AATCATATCT
*
4130153 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
4130174 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
*
4130195 TCTAGGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
4130216 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
*
4130235 TTTAAGAT
1 TCTAAGAT
4130243 CTTATATCCT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
19 15 0.23
21 50 0.77
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:4131110 original size:49 final size:48
Alignment explanation
Indices: 4131004--4131549 Score: 337
Period size: 48 Copynumber: 11.1 Consensus size: 48
4130994 AAAAAAAATT
* * **
4131004 ACACCAGCAGTACCAAAAAAAAAACTTTTAGGTGTTGGCCTGTCAATAACCTG
1 ACACCAGCAGTA-C-AAAAAAAAA-TTTTGGGTGCTGGCCTGTCAAT-GGC-G
* *
4131057 -CACCAGTAGTACAAAAAAAAATTTTGGGTGCTAGCCTGTCAATGGTCG
1 ACACCAGCAGTACAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGG-CG
* * * *
4131105 ACACCAGCAATACGAAAAAAAA-TTTGGGTGCTGGCTTGTTAATGGCCGG
1 ACACCAGCAGTACAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGG-C-G
* * **
4131154 TACCACCAGCA-T-GAAATAAATTTTTTGGGT-CTTGGCCTGTCAATGGCCG
1 -A-CACCAGCAGTACAAAAAAAAATTTTGGGTGC-TGGCCTGTCAATGG-CG
* * * * * * *
4131203 GCACCACCAGTATGAAATAAACAA-TTTGGGTACTGGCCTGTAAATGGTTG
1 ACACCAGCAGTA-CAAA-AAAAAATTTTGGGTGCTGGCCTGTCAATGG-CG
* * * * *
4131253 GCACCACCAATACGAAAAAAAAA-TTTGGGTGCTGGCTTGTTAATGGCTG
1 ACACCAGCAGTAC-AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGC-G
* * ** *
4131302 GCACCA-CTAATACGAAAAAAAAAAATTGGGTGCTGGCCTGTCAATGGTTG
1 ACACCAGC-AGTAC-AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGG-CG
* * * * * *
4131352 GCACCACCAGTAC-AAAAAAAACTTTGGGTGCCGGCCTATCAATGGCA
1 ACACCAGCAGTACAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCG
** * * **
4131399 ATCACCAATA-TACGAAAAAAAATTTTGGGTGTTGGCCTGTCAATAGTTG
1 A-CACCAGCAGTACAAAAAAAAATTTTGGGTGCTGGCCTGTCAAT-GGCG
* * *
4131448 GCACCAGGA-TACGAAAAAAAAA-TTTGGGTGC-GGACCTGTCAATGGCC
1 ACACCAGCAGTAC-AAAAAAAAATTTTGGGTGCTGG-CCTGTCAATGGCG
*
4131495 AGCACCAGCAGTACGAAAAAAAATTTT-GGTGCTGGCCTGTCAATGGCTG
1 A-CACCAGCAGTACAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGC-G
4131544 ACACCA
1 ACACCA
4131550 AATTTATCAA
Statistics
Matches: 396, Mismatches: 69, Indels: 61
0.75 0.13 0.12
Matches are distributed among these distances:
47 13 0.03
48 147 0.37
49 111 0.28
50 102 0.26
51 13 0.03
52 10 0.03
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.23
Consensus pattern (48 bp):
ACACCAGCAGTACAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCG
Found at i:4131124 original size:50 final size:48
Alignment explanation
Indices: 4131069--4131549 Score: 356
Period size: 48 Copynumber: 9.8 Consensus size: 48
4131059 CCAGTAGTAC
*
4131069 AAAAAAAAATTTTGGGTGCTAGCCTGTCAATGGTCGACACCAGCAATACG
1 AAAAAAAAA-TTTGGGTGCTGGCCTGTCAATGG-CGACACCAGCAATACG
* *
4131119 -AAAAAAAATTTGGGTGCTGGCTTGTTAATGGCCGGTACCACCAGC-AT--G
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGG-C-G-A-CACCAGCAATACG
*** * * * *
4131167 AAATAAATTTTTTGGGT-CTTGGCCTGTCAATGGCCGGCACCACCAGTATG
1 AAA-AAAAAATTTGGGTGC-TGGCCTGTCAATGG-CGACACCAGCAATACG
* * * * * *
4131217 AAATAAACAATTTGGGTACTGGCCTGTAAATGGTTGGCACCACCAATACG
1 AAA-AAAAAATTTGGGTGCTGGCCTGTCAATGG-CGACACCAGCAATACG
* * *
4131267 AAAAAAAAATTTGGGTGCTGGCTTGTTAATGGCTGGCACCA-CTAATACG
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGC-GACACCAGC-AATACG
* * * * *
4131316 AAAAAAAAAAATTGGGTGCTGGCCTGTCAATGGTTGGCACCACCAGTAC-
1 -AAAAAAAAATTTGGGTGCTGGCCTGTCAATGG-CGACACCAGCAATACG
* * * *
4131365 AAAAAAAACTTTGGGTGCCGGCCTATCAATGGCAATCACCA--ATATACG
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCGA-CACCAGCA-ATACG
* * ** * *
4131413 AAAAAAAATTTTGGGTGTTGGCCTGTCAATAGTTGGCACCAG-GATACG
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAAT-GGCGACACCAGCAATACG
* *
4131461 AAAAAAAAATTTGGGTGC-GGACCTGTCAATGGCCAGCACCAGCAGTACG
1 AAAAAAAAATTTGGGTGCTGG-CCTGTCAATGGCGA-CACCAGCAATACG
*
4131510 -AAAAAAAATTTTGGTGCTGGCCTGTCAATGGCTGACACCA
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGC-GACACCA
4131550 AATTTATCAA
Statistics
Matches: 349, Mismatches: 57, Indels: 52
0.76 0.12 0.11
Matches are distributed among these distances:
46 1 0.00
47 12 0.03
48 157 0.45
49 59 0.17
50 111 0.32
51 9 0.03
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (48 bp):
AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCGACACCAGCAATACG
Found at i:4131331 original size:99 final size:99
Alignment explanation
Indices: 4131069--4131549 Score: 430
Period size: 96 Copynumber: 4.9 Consensus size: 99
4131059 CCAGTAGTAC
* *
4131069 AAAAAAAAATTTTGGGTGCTAGCCTGTCAATGGTC-GACACCAGC-AATACG--AAAAAAAATTT
1 AAAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCAG-CACCA-CTAATACGAAAAAAAAAATTT
* * ** * ** *
4131130 GGGTGCTGGCTTGTTAATGGCCGGTACCACCAGCATG
63 GGGTGCTGGCCTGTCAATGGTTGGCACCACCAATACG
*** * * * * * *
4131167 AAATAAATTTTTTGGGT-CTTGGCCTGTCAATGGCCGGCACCACCAGTATGAAATAAACAATTTG
1 AAA-AAAAAATTTGGGTGC-TGGCCTGTCAATGGCCAGCACCACTAATACGAAAAAAAAAATTTG
* *
4131231 GGTACTGGCCTGTAAATGGTTGGCACCACCAATACG
64 GGTGCTGGCCTGTCAATGGTTGGCACCACCAATACG
* * ** *
4131267 AAAAAAAAATTTGGGTGCTGGCTTGTTAATGGCTGGCACCACTAATACGAAAAAAAAAAATTGGG
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCAGCACCACTAATACGAAAAAAAAAATTTGGG
*
4131332 TGCTGGCCTGTCAATGGTTGGCACCACCAGTAC-
66 TGCTGGCCTGTCAATGGTTGGCACCACCAATACG
* * * * * * *
4131365 AAAAAAAACTTTGGGTGCCGGCCTATCAATGGCAATCACCAAT-ATACG-AAAAAAAATTTTGGG
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCAGCACCACTAATACGAAAAAAAAAATTTGGG
* * **
4131428 TGTTGGCCTGTCAATAGTTGGCACCA-GGATACG
66 TGCTGGCCTGTCAATGGTTGGCACCACCAATACG
* *
4131461 AAAAAAAAATTTGGGTGC-GGACCTGTCAATGGCCAGCACCAGC-AGTACG--AAAAAAAATTTT
1 AAAAAAAAATTTGGGTGCTGG-CCTGTCAATGGCCAGCACCA-CTAATACGAAAAAAAAAATTTG
* *
4131522 GGTGCTGGCCTGTCAATGGCTGACACCA
64 GGTGCTGGCCTGTCAATGGTTGGCACCA
4131550 AATTTATCAA
Statistics
Matches: 311, Mismatches: 61, Indels: 24
0.79 0.15 0.06
Matches are distributed among these distances:
95 5 0.02
96 105 0.34
97 11 0.04
98 67 0.22
99 82 0.26
100 41 0.13
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (99 bp):
AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCAGCACCACTAATACGAAAAAAAAAATTTGGG
TGCTGGCCTGTCAATGGTTGGCACCACCAATACG
Found at i:4131491 original size:144 final size:146
Alignment explanation
Indices: 4131034--4131541 Score: 395
Period size: 149 Copynumber: 3.5 Consensus size: 146
4131024 AAAACTTTTA
* ** * ** * ** *
4131034 GGTGTTGGCCTGTCAATAACCTGCACCAGTAGTACAAAAAAAAATTTTGGGTGCTAGCCTGTCAA
1 GGTGCTGGCCTGTCAATGGCCAGCACCACCAGTACGAAAAAAAA-TTTGGGTGCCGGCCTATCAA
* * * * * * *
4131099 TGGTCGA-CACCAGCA-ATACG-AAAAAAAATTTGGGTGCTGGCTTGTTAATGGCCGGTACCACC
65 TGG-CAATCACCA--ATATACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATAGCTGGCACCACG
** * * ****
4131161 AGCATGAAATAAATTTTTTG
127 AATACGAAAAAAAAAAATTG
* * * * * *
4131181 GGT-CTTGGCCTGTCAATGGCCGGCACCACCAGTATGAAATAAACAATTTGGGTACTGGCCTGTA
1 GGTGC-TGGCCTGTCAATGGCCAGCACCACCAGTACGAAA-AAA-AATTTGGGTGCCGGCCTATC
**** * * *
4131245 AATGGTTGGCACCACCA-ATACGAAAAAAAAATTTGGGTGCTGGCTTGTTAATGGCTGGCACCAC
63 AATGGCAATCACCA--ATATACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATAGCTGGCACCAC
*
4131309 TAATACGAAAAAAAAAAATTG
126 GAATACGAAAAAAAAAAATTG
***
4131330 GGTGCTGGCCTGTCAATGGTTGGCACCACCAGTAC-AAAAAAAACTTTGGGTGCCGGCCTATCAA
1 GGTGCTGGCCTGTCAATGGCCAGCACCACCAGTACGAAAAAAAA-TTTGGGTGCCGGCCTATCAA
* * * *
4131394 TGGCAATCACCAATATACGAAAAAAAATTTTGGGTGTTGGCCTGTCAATAGTTGGCACCA-GGAT
65 TGGCAATCACCAATATACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATAGCTGGCACCACGAAT
*
4131458 ACG-AAAAAAAAATTTG
130 ACGAAAAAAAAAAATTG
* * * *
4131474 GGTGC-GGACCTGTCAATGGCCAGCACCAGCAGTACGAAAAAAAATTTTGGTGCTGGCCTGTCAA
1 GGTGCTGG-CCTGTCAATGGCCAGCACCACCAGTACGAAAAAAAATTTGGGTGCCGGCCTATCAA
4131538 TGGC
65 TGGC
4131542 TGACACCAAA
Statistics
Matches: 298, Mismatches: 53, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
143 2 0.01
144 61 0.20
145 14 0.05
146 42 0.14
147 57 0.19
148 38 0.13
149 83 0.28
150 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (146 bp):
GGTGCTGGCCTGTCAATGGCCAGCACCACCAGTACGAAAAAAAATTTGGGTGCCGGCCTATCAAT
GGCAATCACCAATATACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATAGCTGGCACCACGAATA
CGAAAAAAAAAAATTG
Found at i:4135829 original size:31 final size:31
Alignment explanation
Indices: 4135792--4135859 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
4135782 TTTTGAATTT
* *
4135792 TTTTCTGTTAATTTTTAC-TTTA-TTTTAAAA
1 TTTTCTGTAAATATTT-CTTTTATTTTTAAAA
4135822 TTATTCTGTAAATATTTCTTTTATTTTTAAAA
1 TT-TTCTGTAAATATTTCTTTTATTTTTAAAA
4135854 TTTTCT
1 TTTTCT
4135860 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 3 0.09
31 20 0.61
32 10 0.30
ACGTcount: A:0.26, C:0.07, G:0.03, T:0.63
Consensus pattern (31 bp):
TTTTCTGTAAATATTTCTTTTATTTTTAAAA
Found at i:4136903 original size:50 final size:51
Alignment explanation
Indices: 4136810--4136924 Score: 135
Period size: 50 Copynumber: 2.2 Consensus size: 51
4136800 ATTAGAAGGT
* * *
4136810 CAACACCTAAAATTATTTTTTTTCTATACACTGGTGCCAGCCATTGACAGGC
1 CAACACC-AAAAATATTTTTTTTCTACACACTGGTGCCAGCCATTGACAAGC
* *
4136862 CAACACCAAAAAT-TTTTTTTTCGTACA-AGTGGTGCCGGCCATTGACAAGC
1 CAACACCAAAAATATTTTTTTTC-TACACACTGGTGCCAGCCATTGACAAGC
*
4136912 CAGCACCCAAAAA
1 CAACA-CCAAAAA
4136925 AAAACTTTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
50 33 0.60
51 15 0.27
52 7 0.13
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (51 bp):
CAACACCAAAAATATTTTTTTTCTACACACTGGTGCCAGCCATTGACAAGC
Found at i:4136944 original size:50 final size:50
Alignment explanation
Indices: 4136880--4137539 Score: 507
Period size: 50 Copynumber: 12.9 Consensus size: 50
4136870 AAAATTTTTT
** * *
4136880 TTTCGTACAAGTGGTGCCGGCCATTGACAAGCCAGCACCCAAAAAAAAAC
1 TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAAAAA
* * * * * * * *
4136930 TTTCATACCGGTGGTACCAGTCATTGACAAGCCAACA-CCTAAAAAAAAA
1 TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAAAAA
* * * * **
4136979 TTTCGTACTGGTGGTGTCAGCCATTGACAAGCCAGCACCTAAAAAATAATTTTTT
1 TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAA-AA----AA
** * *
4137034 TTTCGTACTGGTGGTGCTAGCCATTAACAGGCCAGCTCCCAAAAAAAAAA
1 TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAAAAA
* * * * ***
4137084 TTTTTTGTACTGGAGTTACCGGCCATTGACAGGCCAGCACCCTAAAAAATTATTTTT
1 --TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCC-AAAAAA--A--AAA
* * * * * *
4137141 TTTCGTACTGCTCGTGTCGGCCATTCACAGGCCAGAACCCAAAAAAAAAT
1 TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAAAAA
** * * * *
4137191 TTTCGTA-TACTGGTGCTGACCATTGACAAGCAAGCACCCAAAAAAAAAAA
1 TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCC-AAAAAAAAAA
* * * * **
4137241 TTCCGTACTGCTGGTGCAGGCCATTAACAGGCCAGCACCCAAAAAAAACTTTTT
1 TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAAA----AA
** * *
4137295 TTTCGTA-TACTGGTACCGGCCATTGACAGGCCAGAACCCAAAAAAAAAA
1 TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAAAAA
* * * * * * *
4137344 TTTTGTATTGGTGATGCCGACCATTAATAGGCCATCACCCAAAAAAAAAA
1 TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAAAAA
* *
4137394 TTTCGTACTGGTGGTGCCGACCATTGACAAGCCAGCACCCAAAAAAAAAA
1 TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAAAAA
** * * *
4137444 TTTCGTACTACTGGTGCTGGCCATTGACAGGTCAACACCCAAAAAAAAAAA
1 TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCC-AAAAAAAAAA
* * * * *
4137495 TTTTGTATTGCTGGTGCCGGCCATTGACAGGCTAGCACCTAAAAA
1 TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAA
4137540 TTTTTTTTGT
Statistics
Matches: 481, Mismatches: 108, Indels: 42
0.76 0.17 0.07
Matches are distributed among these distances:
49 70 0.15
50 181 0.38
51 70 0.15
52 33 0.07
53 41 0.09
54 14 0.03
55 72 0.15
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (50 bp):
TTTCGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAAAAA
Found at i:4136993 original size:49 final size:49
Alignment explanation
Indices: 4136890--4137030 Score: 183
Period size: 49 Copynumber: 2.9 Consensus size: 49
4136880 TTTCGTACAA
* * *
4136890 GTGGTGCCGGCCATTGACAAGCCAGCACCCAAAAAAAAACTTTCATACCG
1 GTGGTACCAGCCATTGACAAGCCAGCACCTAAAAAAAAA-TTTCATACCG
* * * *
4136940 GTGGTACCAGTCATTGACAAGCCAACACCTAAAAAAAAATTTCGTACTG
1 GTGGTACCAGCCATTGACAAGCCAGCACCTAAAAAAAAATTTCATACCG
** *
4136989 GTGGTGTCAGCCATTGACAAGCCAGCACCTAAAAAATAATTT
1 GTGGTACCAGCCATTGACAAGCCAGCACCTAAAAAAAAATTT
4137031 TTTTTTCGTA
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 45 0.57
50 34 0.43
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (49 bp):
GTGGTACCAGCCATTGACAAGCCAGCACCTAAAAAAAAATTTCATACCG
Found at i:4137134 original size:154 final size:147
Alignment explanation
Indices: 4136841--4137132 Score: 314
Period size: 154 Copynumber: 1.9 Consensus size: 147
4136831 TTCTATACAC
* * *
4136841 TGGTGCCAGCCATTGACAGGCCAACACCAAAAATTTTTTTTTCGTACAAGTGGTGCCGGCCATTG
1 TGGTGCCAGCCATTGACAAGCCAACACCAAAAATTTTTTTTTCGTACAAGTGGTGCCAGCCATTA
* *
4136906 ACAAGCCAGCACCCAAAAAAAAACTTTCATACCGGTGGTACCAGTCATTGACAAGCCAACACCTA
66 ACAAGCCAGCACCCAAAAAAAAACTTTCATACCGGAGGTACCAGCCATTGACAAGCCAACACCT-
4136971 AAAAAAAATTTCGTACTGG
130 -AAAAAAATTTCGTACTGG
* * ** *
4136990 TGGTGTCAGCCATTGACAAGCCAGCACCTAAAAAATAATTTTTTTTTCGTACTGGTGGTGCTAGC
1 TGGTGCCAGCCATTGACAAGCCAACACC----AAA-AATTTTTTTTTCGTACAAGTGGTGCCAGC
* * * ** * * * *
4137055 CATTAACAGGCCAGCTCCCAAAAAAAAAATTTTTTGTACTGGAGTTACCGGCCATTGACAGGCCA
61 CATTAACAAGCCAGCACCC-AAAAAAAAA-CTTTCATACCGGAGGTACCAGCCATTGACAAGCCA
*
4137120 GCACCCTAAAAAA
124 ACA-CCTAAAAAA
4137133 TTATTTTTTT
Statistics
Matches: 115, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
149 25 0.22
153 3 0.03
154 41 0.36
155 15 0.13
156 28 0.24
157 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (147 bp):
TGGTGCCAGCCATTGACAAGCCAACACCAAAAATTTTTTTTTCGTACAAGTGGTGCCAGCCATTA
ACAAGCCAGCACCCAAAAAAAAACTTTCATACCGGAGGTACCAGCCATTGACAAGCCAACACCTA
AAAAAATTTCGTACTGG
Found at i:4137401 original size:153 final size:153
Alignment explanation
Indices: 4136891--4137539 Score: 548
Period size: 153 Copynumber: 4.2 Consensus size: 153
4136881 TTCGTACAAG
* * * * * * * * *
4136891 TGGTGCCGGCCATTGACAAGCCAGCACCCAAAAAAAAACTTTCATACCGGTGGTACCAGTCATTG
1 TGGTGCCGACCATTAACAGGCCAGCACCCAAAAAAAAAATTTCGTACTGGTGGTGCCGGCCATTG
* * * * ** * * * *
4136956 ACAAGCCAACACCTAAAAAAAA----ATTTCGTACTGGTGGTGTCAGCCATTGACAAGCCAGCA-
66 ACAGGCCAGCACCCAAAAAAAATTTTTTTTCGTACTACTGGTGCCGGCCATTGACAGGCCAGAAC
* * * *
4137016 CCTAAAAAATAATTTTTTTTTCGTAC
131 CCAAAAAAAAAATTTTGTATT-G--C
* * * * * * *
4137042 TGGTGGTGCTAGCCATTAACAGGCCAGCTCCCAAAAAAAAAATTTTTTGTACTGGAGTTACCGGC
1 TGGT-G-CCGA-CCATTAACAGGCCAGCACCCAAAAAAAAAA--TTTCGTACTGGTGGTGCCGGC
* * * * *
4137107 CATTGACAGGCCAGCACCCTAAAAAATTATTTTTTTTCGTACTGCTCGTGTCGGCCATTCACAGG
61 CATTGACAGGCCAGCACCC-AAAAAA-AATTTTTTTTCGTACTACTGGTGCCGGCCATTGACAGG
*
4137172 CCAGAACCC-AAAAAAAAATTTTCGTA-TAC
124 CCAGAACCCAAAAAAAAAATTTT-GTATTGC
* * * * * * *
4137201 TGGTGCTGACCATTGACAAGCAAGCACCCAAAAAAAAAAATTCCGTACTGCTGGTGCAGGCCATT
1 TGGTGCCGACCATTAACAGGCCAGCACCC-AAAAAAAAAATTTCGTACTGGTGGTGCCGGCCATT
* *
4137266 AACAGGCCAGCACCCAAAAAAAACTTTTTTTTCGTA-TACTGGTACCGGCCATTGACAGGCCAGA
65 GACAGGCCAGCACCCAAAAAAAA-TTTTTTTTCGTACTACTGGTGCCGGCCATTGACAGGCCAGA
*
4137330 ACCCAAAAAAAAAATTTTGTATTGG
129 ACCCAAAAAAAAAATTTTGTATTGC
* * * *
4137355 TGATGCCGACCATTAATAGGCCATCACCCAAAAAAAAAATTTCGTACTGGTGGTGCCGACCATTG
1 TGGTGCCGACCATTAACAGGCCAGCACCCAAAAAAAAAATTTCGTACTGGTGGTGCCGGCCATTG
* ** * *
4137420 ACAAGCCAGCACCCAAAAAAAA---AATTTCGTACTACTGGTGCTGGCCATTGACAGGTCA-ACA
66 ACAGGCCAGCACCCAAAAAAAATTTTTTTTCGTACTACTGGTGCCGGCCATTGACAGGCCAGA-A
4137481 CCCAAAAAAAAAAATTTTGTATTGC
130 CCC-AAAAAAAAAATTTTGTATTGC
* * * *
4137506 TGGTGCCGGCCATTGACAGGCTAGCACCTAAAAA
1 TGGTGCCGACCATTAACAGGCCAGCACCCAAAAA
4137540 TTTTTTTTGT
Statistics
Matches: 400, Mismatches: 78, Indels: 40
0.77 0.15 0.08
Matches are distributed among these distances:
149 8 0.02
150 27 0.07
151 51 0.13
152 1 0.00
153 84 0.21
154 80 0.20
155 32 0.08
156 46 0.12
157 17 0.04
158 2 0.00
159 5 0.01
162 44 0.11
163 3 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (153 bp):
TGGTGCCGACCATTAACAGGCCAGCACCCAAAAAAAAAATTTCGTACTGGTGGTGCCGGCCATTG
ACAGGCCAGCACCCAAAAAAAATTTTTTTTCGTACTACTGGTGCCGGCCATTGACAGGCCAGAAC
CCAAAAAAAAAATTTTGTATTGC
Found at i:4140260 original size:20 final size:20
Alignment explanation
Indices: 4140235--4140285 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
4140225 AAAAAACCCT
*
4140235 TTGACCGTTAACTTTAACAG
1 TTGACCATTAACTTTAACAG
*
4140255 TTGACCATTAACTTTAACGG
1 TTGACCATTAACTTTAACAG
*
4140275 TTGACTATTAA
1 TTGACCATTAA
4140286 AGTTAGTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
TTGACCATTAACTTTAACAG
Found at i:4140353 original size:12 final size:12
Alignment explanation
Indices: 4140336--4140363 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4140326 GTCACAATCA
4140336 TGACGTGACATG
1 TGACGTGACATG
4140348 TGACGTGACATG
1 TGACGTGACATG
4140360 TGAC
1 TGAC
4140364 AAAAAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (12 bp):
TGACGTGACATG
Found at i:4140424 original size:27 final size:29
Alignment explanation
Indices: 4140385--4140453 Score: 88
Period size: 27 Copynumber: 2.4 Consensus size: 29
4140375 AAAAATAAAT
*
4140385 AAAAATTATTAAATTTTAATAAAA-A-TGC
1 AAAAATTA-TAAATTTTAATAAAATAGTAC
* *
4140413 AAAAAATATAAATTTTATTAAAATAGTAC
1 AAAAATTATAAATTTTAATAAAATAGTAC
4140442 AAAAATTATAAA
1 AAAAATTATAAA
4140454 AAATTGTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.40
28 8 0.23
29 13 0.37
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAAATTATAAATTTTAATAAAATAGTAC
Found at i:4140463 original size:29 final size:29
Alignment explanation
Indices: 4140431--4140486 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
4140421 TAAATTTTAT
*
4140431 TAAAATAGTACAAAAATTATAAAAAATTG
1 TAAAATAGTACAAAAATCATAAAAAATTG
** *
4140460 TAAAATTTTATAAAAATCATAAAAAAT
1 TAAAATAGTACAAAAATCATAAAAAAT
4140487 ATAAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (29 bp):
TAAAATAGTACAAAAATCATAAAAAATTG
Found at i:4140464 original size:9 final size:10
Alignment explanation
Indices: 4140442--4140522 Score: 62
Period size: 10 Copynumber: 8.3 Consensus size: 10
4140432 AAAATAGTAC
4140442 AAAAATTATA
1 AAAAATTATA
*
4140452 AAAAATTGTA
1 AAAAATTATA
**
4140462 AAATTTTAT-
1 AAAAATTATA
*
4140471 AAAAATCATA
1 AAAAATTATA
4140481 AAAAA-TAT-
1 AAAAATTATA
*
4140489 AAAATTTAT-
1 AAAAATTATA
*
4140498 AGAAATGTATAA
1 AAAAAT-TAT-A
4140510 AAAAATTATA
1 AAAAATTATA
4140520 AAA
1 AAA
4140523 TTTTATAAAG
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
8 4 0.07
9 15 0.28
10 27 0.50
11 3 0.06
12 5 0.09
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (10 bp):
AAAAATTATA
Found at i:4140484 original size:67 final size:67
Alignment explanation
Indices: 4140367--4140531 Score: 171
Period size: 67 Copynumber: 2.5 Consensus size: 67
4140357 ATGTGACAAA
* * *
4140367 AAATGAT-AAAAAA-TAAATAAAAATTATTAAATTTTAATAAAAATGCAAAAAATATAAATTTTA
1 AAATGATAAAAAAATTATA-AAAAATTATAAAATTTTAATAAAAATGCAAAAAATATAAAATTTA
4140430 TTA-
65 -TAG
* *
4140433 AAAT-AGTACAAAAATTATAAAAAATTGTAAAATTTT-ATAAAAAT-CATAAAAAATATAAAATT
1 AAATGA-TAAAAAAATTATAAAAAATTATAAAATTTTAATAAAAATGC--AAAAAATATAAAATT
4140495 TATAG
63 TATAG
**
4140500 AAATGTATAAAAAAATTATAAAATTTTATAAA
1 AAATG-ATAAAAAAATTATAAAAAATTATAAA
4140532 GTCATAAGAA
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
65 2 0.02
66 15 0.18
67 40 0.49
68 24 0.29
69 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (67 bp):
AAATGATAAAAAAATTATAAAAAATTATAAAATTTTAATAAAAATGCAAAAAATATAAAATTTAT
AG
Found at i:4140538 original size:29 final size:29
Alignment explanation
Indices: 4140451--4140552 Score: 111
Period size: 29 Copynumber: 3.5 Consensus size: 29
4140441 CAAAAATTAT
* *
4140451 AAAAAATTGTAAAATTTTATAAAAATCAT-
1 AAAAAATTATAAAATTTTAT-AAAGTCATA
*
4140480 AAAAAA-TATAAAATTTATAGAAATGT-ATA
1 AAAAAATTATAAAATTT-TATAAA-GTCATA
4140509 AAAAAATTATAAAATTTTATAAAGTCATA
1 AAAAAATTATAAAATTTTATAAAGTCATA
* *
4140538 AGAAAATTAAAAAAT
1 AAAAAATTATAAAAT
4140553 GTAAAGAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
28 16 0.26
29 36 0.58
30 10 0.16
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAAAATTATAAAATTTTATAAAGTCATA
Found at i:4147961 original size:11 final size:11
Alignment explanation
Indices: 4147936--4147977 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
4147926 ATCAAATTTC
4147936 TAATTTTTTT-
1 TAATTTTTTTA
4147946 T-ATTTTTTTA
1 TAATTTTTTTA
*
4147956 TAATTTTTTAA
1 TAATTTTTTTA
*
4147967 TAATTTATTTA
1 TAATTTTTTTA
4147978 ATGGAATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 8 0.30
10 2 0.07
11 17 0.63
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:4148433 original size:20 final size:19
Alignment explanation
Indices: 4148379--4148433 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
4148369 TTCATAACAC
* *
4148379 TTTTTATAAATAATATATTT
1 TTTTTATAAATAA-AAATTA
*
4148399 TTTTTATAATTTAAAAAGTTA
1 TTTTTATAA-ATAAAAA-TTA
4148420 TTTTTATAAATAAA
1 TTTTTATAAATAAA
4148434 TTATGATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTTTATAAATAAAAATTA
Found at i:4148574 original size:25 final size:24
Alignment explanation
Indices: 4148533--4148598 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 24
4148523 TTCTTAACCC
*
4148533 ATAA-ATTTTTATAAATAAATATATT
1 ATAATATTTTTAT-AATAAATA-AAT
**
4148558 ATAATATTTTTATAATATGTAAAT
1 ATAATATTTTTATAATAAATAAAT
4148582 -TAAT-TTTTTATAATAAA
1 ATAATATTTTTATAATAAA
4148599 CTTTTTAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 11 0.31
23 4 0.11
24 2 0.06
25 10 0.29
26 8 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATAATATTTTTATAATAAATAAAT
Found at i:4157401 original size:16 final size:16
Alignment explanation
Indices: 4157380--4157415 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
4157370 TTTGGTTCGT
4157380 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
4157396 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
4157412 TGTA
1 TGTA
4157416 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:4157684 original size:17 final size:17
Alignment explanation
Indices: 4157643--4157707 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 17
4157633 AACATAATTA
4157643 TTATT-AAATATAT--T
1 TTATTAAAATATATAAT
* *
4157657 TTTTTATAATATATAAT
1 TTATTAAAATATATAAT
4157674 TTGA-TAAAATATATGAAT
1 TT-ATTAAAATATAT-AAT
4157692 TTATTAAAAT-TATAAT
1 TTATTAAAATATATAAT
4157708 ATATAATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 4 0.10
15 7 0.17
16 3 0.07
17 16 0.39
18 11 0.27
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTATTAAAATATATAAT
Found at i:4157711 original size:24 final size:22
Alignment explanation
Indices: 4157681--4157729 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 22
4157671 AATTTGATAA
4157681 AATATATGAAT-TTATTAAAATTAT
1 AATATAT-AATATTA-TAAAA-TAT
4157705 AATATATAATATTATAAAATAT
1 AATATATAATATTATAAAATAT
4157727 AAT
1 AAT
4157730 TTAAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.25
23 8 0.33
24 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATATATAATATTATAAAATAT
Found at i:4157720 original size:15 final size:15
Alignment explanation
Indices: 4157700--4157765 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
4157690 ATTTATTAAA
*
4157700 ATTATAATATATAAT
1 ATTATAAAATATAAT
4157715 ATTATAAAATAT-A-
1 ATTATAAAATATAAT
*
4157728 ATT-TAAAATA-ATT
1 ATTATAAAATATAAT
*
4157741 ATTATTAAATATAAT
1 ATTATAAAATATAAT
4157756 -TTAATAAAAT
1 ATT-ATAAAAT
4157766 TCTTAGTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
12 7 0.17
13 6 0.15
14 9 0.22
15 19 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTATAAAATATAAT
Found at i:4157766 original size:26 final size:26
Alignment explanation
Indices: 4157710--4157759 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
4157700 ATTATAATAT
4157710 ATAA-TATTATAAAATATAATTTAAA
1 ATAATTATTATAAAATATAATTTAAA
*
4157735 ATAATTATTATTAAATATAATTTAA
1 ATAATTATTATAAAATATAATTTAA
4157760 TAAAATTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATTATTATAAAATATAATTTAAA
Found at i:4173030 original size:4 final size:4
Alignment explanation
Indices: 4173021--4173045 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4173011 TTGCATTTTT
4173021 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
4173046 GCCAAAGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:4173907 original size:28 final size:26
Alignment explanation
Indices: 4173846--4173910 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 26
4173836 CAAAATATTA
4173846 TATTTAAT-TAATTTTAATATATTTT
1 TATTTAATATAATTTTAATATATTTT
* *
4173871 TA-AT-ATATAATGTTTTATATTATTTT
1 TATTTAATATAAT-TTTAATA-TATTTT
4173897 TATTTAATATAATT
1 TATTTAATATAATT
4173911 ATTCTTCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
23 2 0.06
24 5 0.16
25 8 0.25
26 8 0.25
27 2 0.06
28 7 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TATTTAATATAATTTTAATATATTTT
Found at i:4174012 original size:2 final size:2
Alignment explanation
Indices: 4174005--4174033 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4173995 AACCAACCTT
4174005 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4174034 TCATTCATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4175736 original size:38 final size:37
Alignment explanation
Indices: 4175670--4175754 Score: 98
Period size: 38 Copynumber: 2.3 Consensus size: 37
4175660 TTAAAATTAT
* * * *
4175670 TTATATTAAAAACACTACCAAAAAAATAAATGTTTTA
1 TTATATTAAAAACACAAACAAAAAAATAAATATGTTA
* *
4175707 TTATATTAAAAACACAAATAAATATAATAAATATGTTA
1 TTATATTAAAAACACAAACAAA-AAAATAAATATGTTA
*
4175745 TTGTATTAAA
1 TTATATTAAA
4175755 TATATTTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 19 0.47
38 21 0.52
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (37 bp):
TTATATTAAAAACACAAACAAAAAAATAAATATGTTA
Found at i:4177263 original size:9 final size:9
Alignment explanation
Indices: 4177242--4177327 Score: 63
Period size: 9 Copynumber: 9.4 Consensus size: 9
4177232 AAAATATTTT
4177242 TTTTTATAA
1 TTTTTATAA
4177251 -TTTTATAA
1 TTTTTATAA
4177259 TTTTTAATAA
1 TTTTT-ATAA
*
4177269 TTTTAATAA
1 TTTTTATAA
4177278 -TTTT-TAA
1 TTTTTATAA
4177285 TTTTTAAAAATAA
1 TTTTT----ATAA
*
4177298 ATTTTAT-A
1 TTTTTATAA
*
4177306 TTTTTAAAA
1 TTTTTATAA
*
4177315 TTTTTAAAA
1 TTTTTATAA
4177324 TTTT
1 TTTT
4177328 AAAAACGTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
7 3 0.05
8 21 0.33
9 24 0.38
10 8 0.13
13 7 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:4177296 original size:20 final size:21
Alignment explanation
Indices: 4177273--4177314 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
4177263 TAATAATTTT
*
4177273 AATAATTTTTA-ATTTTTAAA
1 AATAAATTTTATATTTTTAAA
4177293 AATAAATTTTATATTTTTAAA
1 AATAAATTTTATATTTTTAAA
4177314 A
1 A
4177315 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATAAATTTTATATTTTTAAA
Found at i:4177311 original size:38 final size:39
Alignment explanation
Indices: 4177255--4177332 Score: 106
Period size: 38 Copynumber: 2.0 Consensus size: 39
4177245 TTATAATTTT
* *
4177255 ATAATTTTTAATAATTTTAATAATTTTT-AATTTTTAAAA
1 ATAAATTTTAATAATTTTAA-AATTTTTAAAATTTTAAAA
*
4177294 ATAAATTTT-ATATTTTTAAAATTTTTAAAATTTTAAAA
1 ATAAATTTTAATAATTTTAAAATTTTTAAAATTTTAAAA
4177332 A
1 A
4177333 CGTAAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
37 7 0.20
38 20 0.57
39 8 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (39 bp):
ATAAATTTTAATAATTTTAAAATTTTTAAAATTTTAAAA
Found at i:4182037 original size:31 final size:31
Alignment explanation
Indices: 4182002--4182064 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
4181992 TGCATACCTA
4182002 CAATAACCCAAATTAAGAAAAAACCAAACTT
1 CAATAACCCAAATTAAGAAAAAACCAAACTT
4182033 CAATAACCCAAATTAAGAAAAAACCAAACTT
1 CAATAACCCAAATTAAGAAAAAACCAAACTT
4182064 C
1 C
4182065 CCAACCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.57, C:0.24, G:0.03, T:0.16
Consensus pattern (31 bp):
CAATAACCCAAATTAAGAAAAAACCAAACTT
Found at i:4185048 original size:22 final size:22
Alignment explanation
Indices: 4185020--4185063 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4185010 AACAGTCTAG
4185020 TGACTTAGATACAATTTTTTGA
1 TGACTTAGATACAATTTTTTGA
4185042 TGACTTAGATACAATTTTTTGA
1 TGACTTAGATACAATTTTTTGA
4185064 ATAGTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
TGACTTAGATACAATTTTTTGA
Found at i:4185310 original size:23 final size:24
Alignment explanation
Indices: 4185284--4185331 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
4185274 ATAAGAAAAT
*
4185284 AAATATAC-AAAAAAAATGCCCTA
1 AAATATACAAAAAAAAATGCACTA
4185307 AAATATACAAAAAAAAATGCACTA
1 AAATATACAAAAAAAAATGCACTA
4185331 A
1 A
4185332 GTACAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.65, C:0.15, G:0.04, T:0.17
Consensus pattern (24 bp):
AAATATACAAAAAAAAATGCACTA
Found at i:4186542 original size:18 final size:17
Alignment explanation
Indices: 4186509--4186547 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
4186499 TTTTATAAAT
4186509 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
4186527 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
4186544 TGTG
1 TGTG
4186548 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:4186825 original size:22 final size:23
Alignment explanation
Indices: 4186774--4186840 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 23
4186764 GTGTTATTGA
4186774 TCAGTGGTAGCTTCGGCTACATC
1 TCAGTGGTAGCTTCGGCTACATC
4186797 TCAGTGGTAGCTTCGGCTACAT-
1 TCAGTGGTAGCTTCGGCTACATC
4186819 TCAGTGGTAGCTTCGGCTACAT
1 TCAGTGGTAGCTTCGGCTACAT
4186841 ATCAATGTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 22 0.50
23 22 0.50
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATC
Found at i:4189353 original size:30 final size:30
Alignment explanation
Indices: 4189319--4189382 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
4189309 TGTAACAATT
*
4189319 AAGATAAGTTCTCAATTAAATTAATGTGGG
1 AAGATAAGTTCTCAATTAAATTAATGTGGA
4189349 AAGATAAGTTCTCAATTAAATTAATGTGGA
1 AAGATAAGTTCTCAATTAAATTAATGTGGA
4189379 AAGA
1 AAGA
4189383 ATATTACTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (30 bp):
AAGATAAGTTCTCAATTAAATTAATGTGGA
Found at i:4191578 original size:43 final size:43
Alignment explanation
Indices: 4191512--4191802 Score: 340
Period size: 43 Copynumber: 6.8 Consensus size: 43
4191502 ACGCCGCTAA
* * * *
4191512 CTTTAGCGGCGCTTTTACC-ACAAATGCCGCTAAAGACCAAGAT
1 CTTTAGCGGCGCTTCT-CCTACAAACGCCGCTAAAGACCATGAC
* * * * *
4191555 CTTTAGCAGCGTTTTTCCTACAAACGCCGCTAAAGACCAAGAT
1 CTTTAGCGGCGCTTCTCCTACAAACGCCGCTAAAGACCATGAC
*
4191598 CTTTAGCGGCGCTTCTCCTACGAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTCTCCTACAAACGCCGCTAAAGACCATGAC
* *
4191641 CTTTAGCTGCGCTTCTCCTACAATCGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTCTCCTACAAACGCCGCTAAAGACCATGAC
*
4191684 CTTTAGTGGCGCTTCTCCTACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTCTCCTACAAACGCCGCTAAAGACCATGAC
* * *
4191727 CTTTAGCGGCACTTTTCCCT-CAAACGCCGCTATAGA--ATAGAC
1 CTTTAGCGGCGCTTCT-CCTACAAACGCCGCTAAAGACCAT-GAC
* * *
4191769 CTTTAGCGACGCTTTTGAC-ACAAACGCCGCTAAA
1 CTTTAGCGGCGCTTCT-CCTACAAACGCCGCTAAA
4191803 AATATATCTT
Statistics
Matches: 220, Mismatches: 24, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
41 2 0.01
42 33 0.15
43 182 0.83
44 3 0.01
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (43 bp):
CTTTAGCGGCGCTTCTCCTACAAACGCCGCTAAAGACCATGAC
Found at i:4196249 original size:13 final size:13
Alignment explanation
Indices: 4196233--4196257 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4196223 AATCGATTTT
4196233 GGGAAAAAGAAGG
1 GGGAAAAAGAAGG
4196246 GGGAAAAAGAAG
1 GGGAAAAAGAAG
4196258 AATATTTCAT
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:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (13 bp):
GGGAAAAAGAAGG
Found at i:4196905 original size:21 final size:22
Alignment explanation
Indices: 4196876--4196938 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
4196866 GGCCTCGAAT
* *
4196876 CTCTAAACCCTA-AATCACTAA
1 CTCTTAACCCTATAACCACTAA
*
4196897 CTCTTAA-CCTATAACCTCTAA
1 CTCTTAACCCTATAACCACTAA
* *
4196918 CCCTTAACCC-CTAACCACTAA
1 CTCTTAACCCTATAACCACTAA
4196939 ATAATCTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.12
21 28 0.82
22 2 0.06
ACGTcount: A:0.37, C:0.38, G:0.00, T:0.25
Consensus pattern (22 bp):
CTCTTAACCCTATAACCACTAA
Found at i:4196974 original size:20 final size:21
Alignment explanation
Indices: 4196949--4196998 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
4196939 ATAATCTAAA
* *
4196949 CCCTAAACTCTAACC-CGAGC
1 CCCTAAACCCTAACCACGAAC
* *
4196969 CCCTAACCCCTAACCACTAAC
1 CCCTAAACCCTAACCACGAAC
4196990 CCCTAAACC
1 CCCTAAACC
4196999 TTATTTAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.32, C:0.50, G:0.04, T:0.14
Consensus pattern (21 bp):
CCCTAAACCCTAACCACGAAC
Found at i:4197640 original size:41 final size:41
Alignment explanation
Indices: 4197582--4197695 Score: 183
Period size: 41 Copynumber: 2.8 Consensus size: 41
4197572 AAATGTTTTT
*
4197582 GCGGCGCTTATCCAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
4197623 GCGGCGCTTTTCTAAAAACGCCGCTAAATCCTTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTA
*
4197664 GCAGCGCTTTTCCAAAAACGCCGCTAAAGCCC
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCC
4197696 CGAAAGGTCA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:4199526 original size:9 final size:9
Alignment explanation
Indices: 4199512--4199578 Score: 107
Period size: 9 Copynumber: 7.4 Consensus size: 9
4199502 TTTGGTTAAA
4199512 AATTAACCG
1 AATTAACCG
*
4199521 AATTAACCA
1 AATTAACCG
4199530 AATTAACCG
1 AATTAACCG
4199539 AATTAACCG
1 AATTAACCG
*
4199548 AATTACCCG
1 AATTAACCG
4199557 AATTAACCG
1 AATTAACCG
*
4199566 AATTAACCT
1 AATTAACCG
4199575 AATT
1 AATT
4199579 GAATCATACA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:4199697 original size:18 final size:18
Alignment explanation
Indices: 4199674--4199725 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
4199664 AATTTTTATG
**
4199674 ATTGGGTTGGATTGGGTA
1 ATTGGGTTGGATTGAATA
*
4199692 ATTGGGTTGAATTGAATA
1 ATTGGGTTGGATTGAATA
*
4199710 CTTGGGTTTGGATTGA
1 ATTGGG-TTGGATTGA
4199726 GTTTAGGTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.21, C:0.02, G:0.37, T:0.40
Consensus pattern (18 bp):
ATTGGGTTGGATTGAATA
Found at i:4200178 original size:20 final size:21
Alignment explanation
Indices: 4200132--4200171 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4200122 GAAATGAAAG
4200132 AAATTACAAATACTTTAAAAA
1 AAATTACAAATACTTTAAAAA
4200153 AAATTACAAATAC-TTAAAA
1 AAATTACAAATACTTTAAAA
4200172 TGTATTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATTACAAATACTTTAAAAA
Found at i:4203970 original size:18 final size:18
Alignment explanation
Indices: 4203949--4203983 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4203939 TATAAGTGTC
4203949 ATAAAAAATAAA-ATTTTG
1 ATAAAAAA-AAAGATTTTG
4203967 ATAAAAAAAAAGATTTT
1 ATAAAAAAAAAGATTTT
4203984 AAAAATGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
ATAAAAAAAAAGATTTTG
Found at i:4205706 original size:13 final size:13
Alignment explanation
Indices: 4205690--4205720 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
4205680 CAGAGCACTG
4205690 TTTCTCTTCCCGA
1 TTTCTCTTCCCGA
4205703 TTTCTCTTCCCGA
1 TTTCTCTTCCCGA
4205716 TTTCT
1 TTTCT
4205721 TGCACCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.35, G:0.06, T:0.52
Consensus pattern (13 bp):
TTTCTCTTCCCGA
Found at i:4207857 original size:20 final size:20
Alignment explanation
Indices: 4207821--4207859 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4207811 AATTTTTTAA
*
4207821 AAATATATTTATAATATAAT
1 AAATATATTAATAATATAAT
4207841 AAATATA-TAATACATATAA
1 AAATATATTAATA-ATATAA
4207860 ATTTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATATTAATAATATAAT
Found at i:4209344 original size:120 final size:120
Alignment explanation
Indices: 4209147--4210248 Score: 2080
Period size: 120 Copynumber: 9.2 Consensus size: 120
4209137 TTTTCAAGTT
4209147 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
4209212 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
4209267 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
4209332 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
4209387 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
**
4209452 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
4209507 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
4209572 TAATATAAAAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
4209627 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
4209692 TAATATAAGAATATTAATTATTAAGAA-TTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
4209746 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
4209811 TAATATAAGAATATTAATTATTAAGAAGTTTTTAAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
4209866 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
4209931 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
*
4209986 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
** *
4210051 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
4210106 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
4210171 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
4210226 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
4210249 TAAATATGAT
Statistics
Matches: 966, Mismatches: 15, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
119 119 0.12
120 847 0.88
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
Found at i:4209985 original size:18 final size:17
Alignment explanation
Indices: 4209957--4209991 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4209947 ATTATTAAGA
*
4209957 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
4209974 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
4209992 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:4210225 original size:18 final size:17
Alignment explanation
Indices: 4210197--4210231 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4210187 ATTATTAAGA
*
4210197 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
4210214 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
4210232 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:4210445 original size:44 final size:45
Alignment explanation
Indices: 4210396--4210481 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 45
4210386 ACCTCTATTC
* *
4210396 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCATTA
***
4210440 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCA
4210482 ATATACCTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 19 0.53
45 17 0.47
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.28
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCATTA
Found at i:4210491 original size:16 final size:16
Alignment explanation
Indices: 4210467--4210535 Score: 111
Period size: 16 Copynumber: 4.2 Consensus size: 16
4210457 GATTAGCTAT
4210467 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
4210483 TATACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
4210500 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
4210516 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
4210532 TACA
1 TACA
4210536 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
16 33 0.69
17 15 0.31
ACGTcount: A:0.36, C:0.36, G:0.01, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:4210509 original size:33 final size:32
Alignment explanation
Indices: 4210467--4210535 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
4210457 GATTAGCTAT
*
4210467 TACACCTCTAATCCAATATACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
4210500 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
4210532 TACA
1 TACA
4210536 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 8 0.24
33 26 0.76
ACGTcount: A:0.36, C:0.36, G:0.01, T:0.26
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:4215476 original size:26 final size:27
Alignment explanation
Indices: 4215447--4215513 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
4215437 AAGTTATTAT
4215447 AATTTTTA-AAA-ATATAAAAATTTTGA
1 AATTTTTATAAATATATAAAAATTTT-A
* *
4215473 AATTTTTATAAATATTTTAAAATTTTA
1 AATTTTTATAAATATATAAAAATTTTA
*
4215500 AATTTATTTTAAAT
1 AATTT-TTATAAAT
4215514 TTTTTGTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.23
27 9 0.26
28 18 0.51
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
AATTTTTATAAATATATAAAAATTTTA
Found at i:4215517 original size:19 final size:19
Alignment explanation
Indices: 4215466--4215576 Score: 66
Period size: 19 Copynumber: 5.7 Consensus size: 19
4215456 AAATATAAAA
*
4215466 ATTTTGAAATTTTTATAA-AT
1 ATTTT-AAATTTTTA-AATTT
*
4215486 ATTTTAAAATTTTAAATTT
1 ATTTTAAATTTTTAAATTT
** *
4215505 ATTTTAAATTTTT-TGTTGAG
1 ATTTTAAATTTTTAAATT--T
* * *
4215525 AGATTGAAATTTTTATAA-AT
1 A-TTTTAAATTTTTA-AATTT
*
4215545 ATTTTAAAATTTTAAATTT
1 ATTTTAAATTTTTAAATTT
4215564 ATTTTAAATTTTT
1 ATTTTAAATTTTT
4215577 TGTTGAGAGA
Statistics
Matches: 67, Mismatches: 17, Indels: 15
0.68 0.17 0.15
Matches are distributed among these distances:
18 6 0.09
19 44 0.66
20 7 0.10
21 10 0.15
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTTTAAATTTTTAAATTT
Found at i:4215537 original size:59 final size:59
Alignment explanation
Indices: 4215469--4215586 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
4215459 TATAAAAATT
4215469 TTGAAATTTTTATAAATATTTTAAAATTTTAAATTTATTTTAAATTTTTTGTTGAGAGA
1 TTGAAATTTTTATAAATATTTTAAAATTTTAAATTTATTTTAAATTTTTTGTTGAGAGA
4215528 TTGAAATTTTTATAAATATTTTAAAATTTTAAATTTATTTTAAATTTTTTGTTGAGAGA
1 TTGAAATTTTTATAAATATTTTAAAATTTTAAATTTATTTTAAATTTTTTGTTGAGAGA
4215587 GATCAATTTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.54
Consensus pattern (59 bp):
TTGAAATTTTTATAAATATTTTAAAATTTTAAATTTATTTTAAATTTTTTGTTGAGAGA
Found at i:4215554 original size:20 final size:20
Alignment explanation
Indices: 4215459--4215557 Score: 76
Period size: 20 Copynumber: 5.0 Consensus size: 20
4215449 TTTTTAAAAA
* *
4215459 TATAAAAATTTTGAAATTTT
1 TATAAATATTTTAAAATTTT
4215479 TATAAATATTTTAAAA-TTT
1 TATAAATATTTTAAAATTTT
* *
4215498 TA-AATTTATTTTAAATTTTT
1 TATAA-ATATTTTAAAATTTT
* ** * ** *
4215518 TGTTGAGAGATTGAAATTTT
1 TATAAATATTTTAAAATTTT
4215538 TATAAATATTTTAAAATTTT
1 TATAAATATTTTAAAATTTT
4215558 AAATTTATTT
Statistics
Matches: 56, Mismatches: 20, Indels: 6
0.68 0.24 0.07
Matches are distributed among these distances:
18 2 0.04
19 14 0.25
20 40 0.71
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (20 bp):
TATAAATATTTTAAAATTTT
Done.