Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chrUn_random
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: 10571689
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 1662808 characters in sequence are not A, C, G, or T
File 10 of 30
Found at i:3273916 original size:27 final size:27
Alignment explanation
Indices: 3273886--3273943 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
3273876 TTGGAGTAAA
*
3273886 AGGGTAAAATGGTAATTTTGCCACC-CT
1 AGGGCAAAATGGTAATTTT-CCACCACT
*
3273913 AGGGGCAAAATTGTAATTTTCCACCACT
1 A-GGGCAAAATGGTAATTTTCCACCACT
3273941 AGG
1 AGG
3273944 ACATTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (27 bp):
AGGGCAAAATGGTAATTTTCCACCACT
Found at i:3285910 original size:28 final size:30
Alignment explanation
Indices: 3285869--3285933 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
3285859 GTCTATGGGC
*
3285869 AATTTTTCAGTTTT-T-GGGGCAAAAATGT
1 AATTTTTCACTTTTATAGGGGCAAAAATGT
* *
3285897 AATTTTTGACTTTTATAGGGGCAAAAGTGT
1 AATTTTTCACTTTTATAGGGGCAAAAATGT
*
3285927 AAATTTT
1 AATTTTT
3285934 AAAAAATTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 12 0.39
29 1 0.03
30 18 0.58
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (30 bp):
AATTTTTCACTTTTATAGGGGCAAAAATGT
Found at i:3287100 original size:13 final size:13
Alignment explanation
Indices: 3287082--3287107 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3287072 AGGAGAAATT
3287082 ATGATTTTATAAA
1 ATGATTTTATAAA
3287095 ATGATTTTATAAA
1 ATGATTTTATAAA
3287108 TTTTTTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
ATGATTTTATAAA
Found at i:3312722 original size:2 final size:2
Alignment explanation
Indices: 3312715--3312748 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3312705 NNNNNNNNNN
3312715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3312749 AAGAAAAACG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3313043 original size:18 final size:17
Alignment explanation
Indices: 3313020--3313079 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
3313010 CCAGCCGGTG
*
3313020 CTTTTCTTTCTCTTCTTC
1 CTTTTCTTTCTCTT-TTT
*
3313038 CTTTTCTCTTATCTTTTGT
1 CTTTTCT-TTCTCTTTT-T
*
3313057 CTTTTCCTTCTCTTTTT
1 CTTTTCTTTCTCTTTTT
3313074 CTTTTC
1 CTTTTC
3313080 ACATGCCAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 7 0.19
18 17 0.47
19 12 0.33
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (17 bp):
CTTTTCTTTCTCTTTTT
Found at i:3313945 original size:2 final size:2
Alignment explanation
Indices: 3313938--3313992 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
3313928 AAGCATGTTG
3313938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3313979 AT AN AT AT A- AT AT A
1 AT AT AT AT AT AT AT A
3313993 AAGAAAACGA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3317979 original size:76 final size:76
Alignment explanation
Indices: 3317850--3317995 Score: 220
Period size: 76 Copynumber: 1.9 Consensus size: 76
3317840 TAGTACTAAT
* * * *
3317850 CCACATTTTGTATAAGCATAAACTTATTCAGATTGCTTGCAGTTCTTTATAAAAAGATAACACAC
1 CCACATTTTGCATAAGCATAAACTTATCCAGATTGCTTACAGTCCTTTATAAAAAGATAACACAC
3317915 ACACACACACA
66 ACACACACACA
* * * *
3317926 CCACATTTTGCATAAGCATATACTTATCCGGATTGTTTACAGTCCTTTGTAAAAAGATAACACAC
1 CCACATTTTGCATAAGCATAAACTTATCCAGATTGCTTACAGTCCTTTATAAAAAGATAACACAC
3317991 ACACA
66 ACACA
3317996 TTGGAAATCC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (76 bp):
CCACATTTTGCATAAGCATAAACTTATCCAGATTGCTTACAGTCCTTTATAAAAAGATAACACAC
ACACACACACA
Found at i:3319845 original size:20 final size:21
Alignment explanation
Indices: 3319820--3319862 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3319810 TAAGTTAAAA
3319820 AAAAG-AAAGAATA-AATGATT
1 AAAAGAAAAGAATATAA-GATT
3319840 AAAAGAAAAGAATATAAGATT
1 AAAAGAAAAGAATATAAGATT
3319861 AA
1 AA
3319863 TGTAATTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 14 0.67
22 2 0.10
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (21 bp):
AAAAGAAAAGAATATAAGATT
Found at i:3322209 original size:6 final size:6
Alignment explanation
Indices: 3322200--3322225 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3322190 ACTACATCTT
3322200 CATCAG CATCAG CATCAG CATCAG CA
1 CATCAG CATCAG CATCAG CATCAG CA
3322226 CCATCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.15, T:0.15
Consensus pattern (6 bp):
CATCAG
Found at i:3328799 original size:26 final size:26
Alignment explanation
Indices: 3328770--3328828 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
3328760 ATTTTCTAGT
*
3328770 TTTCCTTTGT-TTTTCTCTATTCTTCC
1 TTTCCTTTCTATTTTCTCTATTCTT-C
* * *
3328796 TTTCCTCTCTATTTTCTCTCTTGTTC
1 TTTCCTTTCTATTTTCTCTATTCTTC
3328822 TTTCCTT
1 TTTCCTT
3328829 ATGGCCGGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.03, C:0.29, G:0.03, T:0.64
Consensus pattern (26 bp):
TTTCCTTTCTATTTTCTCTATTCTTC
Found at i:3331586 original size:11 final size:11
Alignment explanation
Indices: 3331566--3331595 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3331556 CAATATACCC
3331566 AACAAAAAACA
1 AACAAAAAACA
*
3331577 AACAACAAACA
1 AACAAAAAACA
3331588 AACAAAAA
1 AACAAAAA
3331596 TAAAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (11 bp):
AACAAAAAACA
Found at i:3334616 original size:45 final size:43
Alignment explanation
Indices: 3334567--3334693 Score: 155
Period size: 45 Copynumber: 2.8 Consensus size: 43
3334557 ATGTTTGGCT
* *
3334567 TGTTACATGCCATGTACAAAAACCTATGACAAGTCATGGTTAGCG
1 TGTTACATGCCATGTACAAAAA--TGTGACAAGTCATGGTAAGCG
* * *
3334612 TGTTACATGCTATGTACAAAAATATGTGACAAGCCATGGTAAGCT
1 TGTTACATGCCATGTAC-AAAA-ATGTGACAAGTCATGGTAAGCG
*
3334657 TGTTGCATGCCATGTACAAAATATGTGACAAGTCATG
1 TGTTACATGCCATGTACAAAA-ATGTGACAAGTCATG
3334694 TACAAAAACT
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
44 19 0.26
45 48 0.67
46 4 0.06
47 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (43 bp):
TGTTACATGCCATGTACAAAAATGTGACAAGTCATGGTAAGCG
Found at i:3334707 original size:24 final size:23
Alignment explanation
Indices: 3334667--3334713 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
3334657 TGTTGCATGC
3334667 CATGTACAAAATATGTGACAAGT
1 CATGTACAAAATATGTGACAAGT
3334690 CATGTACAAAA-ACTTGTGACAAGT
1 CATGTACAAAATA--TGTGACAAGT
3334714 TACCGTTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 1 0.05
23 11 0.50
24 10 0.45
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (23 bp):
CATGTACAAAATATGTGACAAGT
Found at i:3334745 original size:45 final size:45
Alignment explanation
Indices: 3334690--3334919 Score: 255
Period size: 45 Copynumber: 5.1 Consensus size: 45
3334680 TGTGACAAGT
* ** ** *
3334690 CATGTACAAAAACTTGTGACAAGTTACCGTTAGCTTGCTACACGC
1 CATGTACAAAAACCTGTGACAAGCCATAGTTAGCTTGTTACACGC
* *
3334735 CATTTACAAAAACCTGTGACAAGCCATAGTTAGCGTGTTACACGC
1 CATGTACAAAAACCTGTGACAAGCCATAGTTAGCTTGTTACACGC
* * ** * *
3334780 TATATACAAAAATATGTGACAAGCCAT-GATTAGCTTGTTACAAGT
1 CATGTACAAAAACCTGTGACAAGCCATAG-TTAGCTTGTTACACGC
* *
3334825 CATGTACAAAAACCTGTGACAAGCTATGGTTAGCTTGTTACACGC
1 CATGTACAAAAACCTGTGACAAGCCATAGTTAGCTTGTTACACGC
* * * * *
3334870 CATGTACAAAAACCTATGACAAGCCATGGTTAGGTTTTTACATGC
1 CATGTACAAAAACCTGTGACAAGCCATAGTTAGCTTGTTACACGC
3334915 CATGT
1 CATGT
3334920 TGAAAAAAAA
Statistics
Matches: 156, Mismatches: 27, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
44 1 0.01
45 154 0.99
46 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (45 bp):
CATGTACAAAAACCTGTGACAAGCCATAGTTAGCTTGTTACACGC
Found at i:3334788 original size:113 final size:114
Alignment explanation
Indices: 3334575--3334807 Score: 279
Period size: 113 Copynumber: 2.1 Consensus size: 114
3334565 CTTGTTACAT
** * * * *
3334575 GCCATGTACAAAAACCTATGACAAGTCATGGTTAGCGTGTTACATGCTATGTACAAAAATATGTG
1 GCCATGTACAAAAACCTATGACAAGTCACCGTTAGCGTGCTACACGCCATGTACAAAAACATGTG
* * * * *
3334640 ACAAGCCATGGTAAGCTTGTTGCATGCCATGTAC-AAAATATGTGACAA
66 ACAAGCCATAGTAAGCGTGTTACACGCCATATACAAAAATATGTGACAA
* * * * * * *
3334688 GTCATGTACAAAAACTTGTGACAAGTTACCGTTAGCTTGCTACACGCCATTTACAAAAACCTGTG
1 GCCATGTACAAAAACCTATGACAAGTCACCGTTAGCGTGCTACACGCCATGTACAAAAACATGTG
* *
3334753 ACAAGCCATAGTTAGCGTGTTACACGCTATATACAAAAATATGTGACAA
66 ACAAGCCATAGTAAGCGTGTTACACGCCATATACAAAAATATGTGACAA
3334802 GCCATG
1 GCCATG
3334808 ATTAGCTTGT
Statistics
Matches: 98, Mismatches: 21, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
113 79 0.81
114 19 0.19
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (114 bp):
GCCATGTACAAAAACCTATGACAAGTCACCGTTAGCGTGCTACACGCCATGTACAAAAACATGTG
ACAAGCCATAGTAAGCGTGTTACACGCCATATACAAAAATATGTGACAA
Found at i:3334945 original size:31 final size:30
Alignment explanation
Indices: 3334907--3335039 Score: 108
Period size: 31 Copynumber: 4.7 Consensus size: 30
3334897 GGTTAGGTTT
*
3334907 TTACATGCCATGTTGAAAAAAAATACTACTG
1 TTACACGCCATGTTGAAAAAAAATACTA-TG
*
3334938 TTACATGCCATG-T---AAAAAA-AC-ATG
1 TTACACGCCATGTTGAAAAAAAATACTATG
*
3334962 TTACACGCCATGGTT--AAAAAAGT--T-TG
1 TTACACGCCAT-GTTGAAAAAAAATACTATG
* *
3334988 TTACACGCCATGTTGAAAAAAACTATTATTG
1 TTACACGCCATGTTGAAAAAAAATACTA-TG
*
3335019 TTACACACCATGTTGAAAAAA
1 TTACACGCCATGTTGAAAAAA
3335040 TATTGTTGTT
Statistics
Matches: 87, Mismatches: 4, Indels: 22
0.77 0.04 0.19
Matches are distributed among these distances:
24 12 0.14
25 5 0.06
26 16 0.18
27 18 0.21
29 1 0.01
30 1 0.01
31 34 0.39
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.29
Consensus pattern (30 bp):
TTACACGCCATGTTGAAAAAAAATACTATG
Found at i:3334979 original size:26 final size:25
Alignment explanation
Indices: 3334936--3335010 Score: 89
Period size: 26 Copynumber: 3.0 Consensus size: 25
3334926 AAAATACTAC
*
3334936 TGTTACATGCCATG-TAAAAAAACA
1 TGTTACACGCCATGTTAAAAAAACA
***
3334960 TGTTACACGCCATGGTTAAAAAAGTT
1 TGTTACACGCCAT-GTTAAAAAAACA
3334986 TGTTACACGCCATGTTGAAAAAAAC
1 TGTTACACGCCATGTT-AAAAAAAC
3335011 TATTATTGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
24 12 0.29
25 4 0.10
26 26 0.62
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (25 bp):
TGTTACACGCCATGTTAAAAAAACA
Found at i:3335048 original size:29 final size:31
Alignment explanation
Indices: 3334985--3335052 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
3334975 TTAAAAAAGT
*
3334985 TTGTTACACGCCATGTTGAAAAAAACTATTA
1 TTGTTACACACCATGTTGAAAAAAACTATTA
*
3335016 TTGTTACACACCATGTTG-AAAAAA-TATTG
1 TTGTTACACACCATGTTGAAAAAAACTATTA
3335045 TTGTTACA
1 TTGTTACA
3335053 TGACATATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 12 0.34
30 6 0.17
31 17 0.49
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (31 bp):
TTGTTACACACCATGTTGAAAAAAACTATTA
Found at i:3335479 original size:23 final size:23
Alignment explanation
Indices: 3335448--3335496 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3335438 TTGGTGTTTT
3335448 AAAAGTGTAAGAAAGAGAAATCTG
1 AAAAGTGTAAGAAAGAGAAATC-G
* *
3335472 AAAA-TGTAGGAGAGAGAAATCG
1 AAAAGTGTAAGAAAGAGAAATCG
3335494 AAA
1 AAA
3335497 GCATAGCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 15 0.65
24 4 0.17
ACGTcount: A:0.55, C:0.04, G:0.27, T:0.14
Consensus pattern (23 bp):
AAAAGTGTAAGAAAGAGAAATCG
Found at i:3340071 original size:64 final size:66
Alignment explanation
Indices: 3339963--3340096 Score: 166
Period size: 64 Copynumber: 2.1 Consensus size: 66
3339953 ATGGGCTCTT
* * ** * *
3339963 TTTTTTTTCTTTTTTTTCTCTCCTTCCTTATTGCTCTTTAGTGATGGGTTCTTCTTCTTTT-TTT
1 TTTTCTTTCTTTTTTTTCTCTCCTTCCTCATTGCTCTCCAGTGATGGGCTCTTCTTCTTTTCTTC
3340027 C
66 C
* *
3340028 TTTTCTTTC-TTTTTTTCTCTCCTTCCTCCTTG-TACTCCGGTGATGGGCTCTTCTTCTTTTCTT
1 TTTTCTTTCTTTTTTTTCTCTCCTTCCTCATTGCT-CTCCAGTGATGGGCTCTTCTTCTTTTCTT
3340091 CC
65 CC
3340093 TTTT
1 TTTT
3340097 TCTCTCTCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
63 1 0.02
64 43 0.73
65 15 0.25
ACGTcount: A:0.04, C:0.25, G:0.10, T:0.62
Consensus pattern (66 bp):
TTTTCTTTCTTTTTTTTCTCTCCTTCCTCATTGCTCTCCAGTGATGGGCTCTTCTTCTTTTCTTC
C
Found at i:3341111 original size:2 final size:2
Alignment explanation
Indices: 3341106--3341145 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
3341096 AAAGGANTAT
* *
3341106 TA TA TA TG TA TA TA TA TA TA -A TA TT TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3341146 GTAATAGTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3341134 original size:17 final size:17
Alignment explanation
Indices: 3341109--3341148 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
3341099 GGANTATTAT
3341109 ATATGTATATATATATA
1 ATATGTATATATATATA
*
3341126 ATATTTATATATATAT-
1 ATATGTATATATATATA
3341142 ATATGTA
1 ATATGTA
3341149 ATAGTGCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
ATATGTATATATATATA
Found at i:3343335 original size:72 final size:71
Alignment explanation
Indices: 3343238--3343407 Score: 184
Period size: 72 Copynumber: 2.4 Consensus size: 71
3343228 TCTGGAAATC
* *
3343238 AAGTTTAGAGATGATGTCTCGATACTTGGCA-AGT-AGGTCTCGATAC-GTACTCACTTGCTCTT
1 AAGTTTAAAGATGAAGTCTCGATACTTGG-ATAGTGA-GTCTCGATACTGTACT-ACTTGCTCTT
*
3343300 TAAAATTTG
63 TAAAAATTG
* * * * * *
3343309 AAGTTTTAAAGATGAGGTCTCAATACTTTGATAGTGAGTCTTGATACTTTAGTACTTGCTCTTTA
1 AAG-TTTAAAGATGAAGTCTCGATACTTGGATAGTGAGTCTCGATACTGTACTACTTGCTCTTTA
3343374 AAAATTG
65 AAAATTG
* *
3343381 AAGTCTAAAGATTAAGTCTCGATACTT
1 AAGTTTAAAGATGAAGTCTCGATACTT
3343408 TAAAGCTACG
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
71 24 0.29
72 55 0.66
73 4 0.05
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (71 bp):
AAGTTTAAAGATGAAGTCTCGATACTTGGATAGTGAGTCTCGATACTGTACTACTTGCTCTTTAA
AAATTG
Found at i:3349274 original size:12 final size:12
Alignment explanation
Indices: 3349257--3349281 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3349247 ATCTTTTGAA
3349257 AATGTATGTATG
1 AATGTATGTATG
3349269 AATGTATGTATG
1 AATGTATGTATG
3349281 A
1 A
3349282 TATGACATGT
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:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AATGTATGTATG
Found at i:3353446 original size:24 final size:26
Alignment explanation
Indices: 3353414--3353464 Score: 88
Period size: 24 Copynumber: 2.0 Consensus size: 26
3353404 AAGAACTTCA
3353414 TTTTATTTATCCAAT-AA-GTAGTTC
1 TTTTATTTATCCAATAAATGTAGTTC
3353438 TTTTATTTATCCAATAAATGTAGTTC
1 TTTTATTTATCCAATAAATGTAGTTC
3353464 T
1 T
3353465 CACCATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 15 0.60
25 2 0.08
26 8 0.32
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (26 bp):
TTTTATTTATCCAATAAATGTAGTTC
Found at i:3356009 original size:72 final size:73
Alignment explanation
Indices: 3355922--3356072 Score: 166
Period size: 72 Copynumber: 2.1 Consensus size: 73
3355912 TAGACAATTA
* * *
3355922 CTCTTT-AAAATTTGAAGTTCTGAAGA-CAAGGTCTCAATACTTTGAAAATGAG-TCTCAATACT
1 CTCTTTGAAAATTTGAA-ATCTAAAGATCAA-GTCTCAATACTTGGAAAATGAGTTCTCAATACT
* *
3355984 TTGGCACTTG
64 TTCGAACTTG
* * ** *
3355994 CTCTTTGAAAA-TTGAAATCTAAAGATGAAGTCTCAATACTTGGTAGCTTAGTTCTCAATACTTT
1 CTCTTTGAAAATTTGAAATCTAAAGATCAAGTCTCAATACTTGGAAAATGAGTTCTCAATACTTT
3356058 CGAACTTG
66 CGAACTTG
3356066 CTCTTTG
1 CTCTTTG
3356073 GAATTTGCAA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
71 24 0.36
72 38 0.58
73 4 0.06
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (73 bp):
CTCTTTGAAAATTTGAAATCTAAAGATCAAGTCTCAATACTTGGAAAATGAGTTCTCAATACTTT
CGAACTTG
Found at i:3360884 original size:31 final size:31
Alignment explanation
Indices: 3360846--3360908 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
3360836 CATCTTTCTT
3360846 TGGTGTTGTTATACATAGAGACTTGAATATA
1 TGGTGTTGTTATACATAGAGACTTGAATATA
3360877 TGGTGTTGTTATACATAGAGACTTGAATATA
1 TGGTGTTGTTATACATAGAGACTTGAATATA
3360908 T
1 T
3360909 TCTTTCTCTC
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:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (31 bp):
TGGTGTTGTTATACATAGAGACTTGAATATA
Found at i:3381096 original size:12 final size:12
Alignment explanation
Indices: 3381079--3381103 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3381069 GCCTTTTGAA
3381079 AATGTATGTATG
1 AATGTATGTATG
3381091 AATGTATGTATG
1 AATGTATGTATG
3381103 A
1 A
3381104 TATGACATGT
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:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AATGTATGTATG
Found at i:3392921 original size:12 final size:12
Alignment explanation
Indices: 3392904--3392928 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3392894 CTAATCAAAC
3392904 TAAATAAAATAT
1 TAAATAAAATAT
3392916 TAAATAAAATAT
1 TAAATAAAATAT
3392928 T
1 T
3392929 TTATTTCTTA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAATAAAATAT
Found at i:3409785 original size:36 final size:36
Alignment explanation
Indices: 3409728--3409796 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
3409718 TGAAACTACT
3409728 TTTTCAAGACTCAAGAATAACC-TTTACAACCAAATC
1 TTTTCAAGACTCAAGAATAACCTTTTAC-ACCAAATC
* *
3409764 TTTTCAAGACT-TAGACTTAACCTTTTACACCAA
1 TTTTCAAGACTCAAGA-ATAACCTTTTACACCAA
3409797 TCGTTTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 3 0.10
36 21 0.72
37 5 0.17
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.32
Consensus pattern (36 bp):
TTTTCAAGACTCAAGAATAACCTTTTACACCAAATC
Found at i:3411136 original size:29 final size:29
Alignment explanation
Indices: 3411080--3411136 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
3411070 TGTATAAGAG
* * *
3411080 AAGCTGTACATGAACAGGTATAATAGAAA
1 AAGCTATACATGAACAGGTACAAAAGAAA
* *
3411109 AAGCTATACGTGAATAGGTACAAAAGAA
1 AAGCTATACATGAACAGGTACAAAAGAA
3411137 CAAGGTAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.19
Consensus pattern (29 bp):
AAGCTATACATGAACAGGTACAAAAGAAA
Found at i:3413905 original size:15 final size:17
Alignment explanation
Indices: 3413885--3413919 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3413875 TTGTAATTTT
3413885 TTTTA-TTTA-AAAATA
1 TTTTATTTTATAAAATA
3413900 TTTTATTTTATAAAATA
1 TTTTATTTTATAAAATA
3413917 TTT
1 TTT
3413920 ATATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 4 0.22
17 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTATTTTATAAAATA
Found at i:3423253 original size:41 final size:42
Alignment explanation
Indices: 3423196--3423277 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
3423186 AAATAATCTT
3423196 TGAAGTTCAAGACCAAGTAG-CAAGACCCTTGAAGCAAAGTA
1 TGAAGTTCAAGACCAAGTAGACAAGACCCTTGAAGCAAAGTA
* * *
3423237 TGAAGTTCAAGGCCAAGTTGACAAGACCCTTGAAGTAAAGT
1 TGAAGTTCAAGACCAAGTAGACAAGACCCTTGAAGCAAAGT
3423278 GCCCAAATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 18 0.49
42 19 0.51
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (42 bp):
TGAAGTTCAAGACCAAGTAGACAAGACCCTTGAAGCAAAGTA
Found at i:3423297 original size:50 final size:48
Alignment explanation
Indices: 3423241--3423366 Score: 139
Period size: 50 Copynumber: 2.5 Consensus size: 48
3423231 AAAGTATGAA
*
3423241 GTTCAAGGCCAAGTTGACAAGACCCTTGAAGTAAAGTGC-CCAAATC-ATT
1 GTTCAAGG-CAAGTT-ACAAGACCCTTGAAGCAAAGT-CTCCAAATCAATT
*
3423290 CGTTCAAGAGCAAGTCATCAAGACCCTTGAAGCAAAGTCTCCAAATCAATT
1 -GTTCAAG-GCAAGTTA-CAAGACCCTTGAAGCAAAGTCTCCAAATCAATT
* *
3423341 GTTCAAGATCAAGTTATAAGACCCTT
1 GTTCAAG-GCAAGTTACAAGACCCTT
3423367 AAAATGAAGT
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
49 11 0.16
50 52 0.78
51 4 0.06
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (48 bp):
GTTCAAGGCAAGTTACAAGACCCTTGAAGCAAAGTCTCCAAATCAATT
Found at i:3423547 original size:50 final size:50
Alignment explanation
Indices: 3423493--3423598 Score: 115
Period size: 50 Copynumber: 2.1 Consensus size: 50
3423483 TCAAAATCTC
* * * *
3423493 CAAATTGTTCATTGAAGAACAAGTCGT-GAAGACCCTTGAAACGAAGTCTA
1 CAAATTATTCATTAAAGAACAAGTCGTCAAAG-CCCTTGAAACGAAGTATA
* ** * *
3423543 CAAATCATTCATTAAAGATTAAGTCGTCAAAGCCCTTGAAATGAAGTATC
1 CAAATTATTCATTAAAGAACAAGTCGTCAAAGCCCTTGAAACGAAGTATA
3423593 CAAATT
1 CAAATT
3423599 CAAGTCATTA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
50 42 0.93
51 3 0.07
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (50 bp):
CAAATTATTCATTAAAGAACAAGTCGTCAAAGCCCTTGAAACGAAGTATA
Found at i:3423745 original size:49 final size:49
Alignment explanation
Indices: 3423691--3423820 Score: 156
Period size: 49 Copynumber: 2.7 Consensus size: 49
3423681 AATCATTCGT
* * *
3423691 TCAAGATTAAGTCATCAAAACCCTTGAAGTGAAAGCTC-CAAGAGTTTG-
1 TCAAGATTAAGTCA-CAAAACCCTTGAAGTGAAAGATCTAAAAAGTTTGC
* * * *
3423739 TCCAAGATCAAGTAAAAAAACCCTTGAAGTGAAATATCTAAAAAGTTTGC
1 T-CAAGATTAAGTCACAAAACCCTTGAAGTGAAAGATCTAAAAAGTTTGC
*
3423789 TCAAGATTAAGTCACAAAACCCTTGAGGTGAA
1 TCAAGATTAAGTCACAAAACCCTTGAAGTGAA
3423821 TATTGAAGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
48 21 0.31
49 46 0.68
50 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.24
Consensus pattern (49 bp):
TCAAGATTAAGTCACAAAACCCTTGAAGTGAAAGATCTAAAAAGTTTGC
Found at i:3427233 original size:39 final size:39
Alignment explanation
Indices: 3427180--3427255 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
3427170 GAGGTGCACC
3427180 AGTCTTGTTCGTGAAGAAGAAGGATGAGTCGATGAGATT
1 AGTCTTGTTCGTGAAGAAGAAGGATGAGTCGATGAGATT
* *
3427219 AGTCTTGTTTGTGAAGAAGAAGGATGAGTGGATGAGA
1 AGTCTTGTTCGTGAAGAAGAAGGATGAGTCGATGAGA
3427256 CTATGTATCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.32, C:0.05, G:0.36, T:0.28
Consensus pattern (39 bp):
AGTCTTGTTCGTGAAGAAGAAGGATGAGTCGATGAGATT
Found at i:3431781 original size:40 final size:38
Alignment explanation
Indices: 3431689--3431791 Score: 102
Period size: 43 Copynumber: 2.6 Consensus size: 38
3431679 GAATAATCTA
3431689 TTTTTGGAATAATATGTTGATTCATGGTATTTTGTTTG
1 TTTTTGGAATAATATGTTGATTCATGGTATTTTGTTTG
* * *
3431727 TTGACTCATAGGAATAATGTGTTTATTCAGTGGTATTTTGTTTG
1 TT---T--TTGGAATAATATGTTGATTCA-TGGTATTTTGTTTG
*
3431771 TTTTTGG--GAATATGTTGATTC
1 TTTTTGGAATAATATGTTGATTC
3431792 GTGATATTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
37 11 0.21
38 2 0.04
39 3 0.06
41 2 0.04
43 18 0.35
44 16 0.31
ACGTcount: A:0.21, C:0.05, G:0.22, T:0.51
Consensus pattern (38 bp):
TTTTTGGAATAATATGTTGATTCATGGTATTTTGTTTG
Found at i:3435312 original size:2 final size:2
Alignment explanation
Indices: 3435300--3435375 Score: 116
Period size: 2 Copynumber: 38.0 Consensus size: 2
3435290 TCCATGATAC
* * * *
3435300 AT AT AT CT AT AT AT GT AT GT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3435342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3435376 CCATCATCAT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3435485 original size:42 final size:42
Alignment explanation
Indices: 3435430--3435569 Score: 138
Period size: 42 Copynumber: 3.3 Consensus size: 42
3435420 TCCCCACTAA
* * * * *
3435430 CACATGGCTGGGTCAGCATTGGCTTATAAGCACTCCTACTCG
1 CACATAGCCGGGTCATCATCGGCTTATAAGCACTTCTACTCG
* *
3435472 CACATAGCCGGGTCATCATCGGCTTATGCA-CACTTCTACACG
1 CACATAGCCGGGTCATCATCGGCTTAT-AAGCACTTCTACTCG
** * * ** *
3435514 CACATAGTTGGGTCATCATCAGCATATGTGCATTTCTACTCG
1 CACATAGCCGGGTCATCATCGGCTTATAAGCACTTCTACTCG
3435556 CACATAGCCGGGTC
1 CACATAGCCGGGTC
3435570 CACATTAGCA
Statistics
Matches: 79, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
42 78 0.99
43 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.26
Consensus pattern (42 bp):
CACATAGCCGGGTCATCATCGGCTTATAAGCACTTCTACTCG
Found at i:3435581 original size:42 final size:42
Alignment explanation
Indices: 3435460--3435569 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
3435450 GGCTTATAAG
* * *
3435460 CACTCCTACTCGCACATAGCCGGGTCATCATCGGCTTATGCA
1 CACTTCTACTCGCACATAGCCGGGTCATCATCAGCATATGCA
* ** **
3435502 CACTTCTACACGCACATAGTTGGGTCATCATCAGCATATGTG
1 CACTTCTACTCGCACATAGCCGGGTCATCATCAGCATATGCA
*
3435544 CATTTCTACTCGCACATAGCCGGGTC
1 CACTTCTACTCGCACATAGCCGGGTC
3435570 CACATTAGCA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (42 bp):
CACTTCTACTCGCACATAGCCGGGTCATCATCAGCATATGCA
Found at i:3440034 original size:23 final size:21
Alignment explanation
Indices: 3440007--3440051 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
3439997 CACCTTAATC
*
3440007 TTATTCAAACAACCAAACTTAAA
1 TTATT-AAA-AACCAAAATTAAA
*
3440030 TTATTAAAAAGCAAAATTAAA
1 TTATTAAAAACCAAAATTAAA
3440051 T
1 T
3440052 CTAACAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 3 0.15
23 5 0.25
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.29
Consensus pattern (21 bp):
TTATTAAAAACCAAAATTAAA
Found at i:3441959 original size:19 final size:17
Alignment explanation
Indices: 3441926--3441960 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
3441916 AAATGAGGAT
3441926 TGCTCCCCTTATGTGTA
1 TGCTCCCCTTATGTGTA
3441943 TGCTCTCCCTTAGTGTGT
1 TGCTC-CCCTTA-TGTGT
3441961 GCATATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 6 0.38
19 5 0.31
ACGTcount: A:0.09, C:0.29, G:0.20, T:0.43
Consensus pattern (17 bp):
TGCTCCCCTTATGTGTA
Found at i:3451739 original size:9 final size:9
Alignment explanation
Indices: 3451715--3451765 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
3451705 ATTAAGCAAA
3451715 AATTATAATT
1 AATTA-AATT
*
3451725 ATTTAAATT
1 AATTAAATT
3451734 AATTAAGATT
1 AATTAA-ATT
3451744 ATATTAAATT
1 A-ATTAAATT
*
3451754 AATGAAA-T
1 AATTAAATT
3451762 AATT
1 AATT
3451766 TAACCAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 4 0.11
9 14 0.40
10 12 0.34
11 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (9 bp):
AATTAAATT
Found at i:3451936 original size:115 final size:113
Alignment explanation
Indices: 3451724--3452338 Score: 505
Period size: 115 Copynumber: 5.4 Consensus size: 113
3451714 AAATTATAAT
* * * * * * * **
3451724 TATTTAAATTAATTAAGATTATATTAAATTAATGAAATAATTTAACCAATCAA-AAACAT-AT-T
1 TATTTAAATTAATTAAGGTT-TAATGAATTAATTAAATAATTTAACTAATTAAGTAATGTAATGT
*
3451786 TTAGTAATTAAGCAATTAATTAAATTAGTTATATTATATAATTTAAAGA
65 TTAGTAATTAAGCAATTAATTAAATTAGTAATATTATATAATTTAAAGA
* * * ** *
3451835 TATTTAAATTAGTTAAGGCATTAATGAGTTAATTAAATAATTTAGTTGATTAAGTAATGTAATGT
1 TATTTAAATTAATTAAGG-TTTAATGAATTAATTAAATAATTTAACTAATTAAGTAATGTAATGT
* * *
3451900 GTTAGTAATTAAGCAATTAATTAAATAAGTAATATTATATAATATT--TGTT
65 -TTAGTAATTAAGCAATTAATTAAATTAGTAATATTATATAAT-TTAAAG-A
* * *
3451950 TATTTAAATTAATTAAGGTTTAA-GAAAATTAATTACATAATTTAACTAATTAA--AAAGAATCA
1 TATTTAAATTAATTAAGGTTTAATG--AATTAATTAAATAATTTAACTAATTAAGTAATG--TAA
* * * *
3452012 TGTATTAGTAATCAAGTAATTAATTAAATTAGTAA-ATTAAGTAAAATTTATAA-T
62 TGT-TTAGTAATTAAGCAATTAATTAAATTAGTAATATT-A-TATAATTTA-AAGA
* * * * * **
3452066 TATTTAAATTAATTAAGGTTTTATCAAATTAATGAAATAATTTAACTAATCAAATGAA-AAAATG
1 TATTTAAATTAATTAAGGTTTAAT-GAATTAATTAAATAATTTAACTAATTAAGT-AATGTAATG
* * *
3452130 TTTTAGTTAATTAAGCAATTAATTAAAATTAGTAATATTTTTTAATTTAAAAA
64 -TTTAG-TAATTAAGCAATTAATT-AAATTAGTAATATTATATAATTTAAAGA
* * **
3452183 TATTTAAATTAATTAAGGTGTTAATGAGTTAATTAGATAATTTAGTTAATTAAGTAATGTAATGT
1 TATTTAAATTAATTAAGGT-TTAATGAATTAATTAAATAATTTAACTAATTAAGTAATGTAATGT
* * * * ** **
3452248 TTAGTAATTAAGCAATTAACTAAATAAGTAATAATATGTAATATTTTATT
65 TTAGTAATTAAGCAATTAATTAAATTAGTAATATTATATAAT-TTAAAGA
* * *
3452298 TATTTAAATTAATTAAGGTTTTATTAAATTAATAAAATAAT
1 TATTTAAATTAATTAAGG-TTTAATGAATTAATTAAATAAT
3452339 ATTTTATATT
Statistics
Matches: 401, Mismatches: 73, Indels: 56
0.76 0.14 0.11
Matches are distributed among these distances:
111 39 0.10
112 4 0.01
113 6 0.01
114 26 0.06
115 168 0.42
116 71 0.18
117 68 0.17
118 14 0.03
119 5 0.01
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.42
Consensus pattern (113 bp):
TATTTAAATTAATTAAGGTTTAATGAATTAATTAAATAATTTAACTAATTAAGTAATGTAATGTT
TAGTAATTAAGCAATTAATTAAATTAGTAATATTATATAATTTAAAGA
Found at i:3452318 original size:232 final size:229
Alignment explanation
Indices: 3451895--3452338 Score: 547
Period size: 232 Copynumber: 1.9 Consensus size: 229
3451885 TAAGTAATGT
****
3451895 AATGTGTTAGTAATTAAGCAATTAATTAAATAAGTAATATTATATAATATTTGTTTATTTAAATT
1 AATGTGTTAGTAATTAAGCAATTAATTAAATAAGTAATATTATATAATATTAAAATATTTAAATT
*
3451960 AATTAAGGTTTAAGAAAATTAATTACATAATTTAACTAATTAAAAAGAATCATGTATTAGTAATC
66 AATTAAGGTTTAAG-AAATTAATTACATAATTTAACTAATTAAAAAG-ATAATGTATTAGTAATC
* * * *
3452025 AAGTAATTAATTAAATTAGTAAATTAAGTAAAATTTATAATTATTTAAATTAATTAAGGTTTTAT
129 AAGCAATTAACTAAATAAGTAAAATAAGTAAAATTTATAATTATTTAAATTAATTAAGGTTTTAT
*
3452090 CAAATTAATGAAATAATTTAACTAATCAAATGAAAA
194 CAAATTAATAAAATAATTTAACTAATCAAATGAAAA
* * * *
3452126 AATGTTTTAGTTAATTAAGCAATTAATTAAAATTAGTAATATTTTTTAAT-TTAAAAATATTTAA
1 AATGTGTTAG-TAATTAAGCAATTAATT-AAATAAGTAATATTATATAATATT-AAAATATTTAA
* * ** *
3452190 ATTAATTAAGGTGTTAATG-AGTTAATTAGATAATTTAGTTAATTAAGTAATG-TAATGT-TTAG
63 ATTAATTAAGGT-TTAA-GAAATTAATTACATAATTTAACTAATTAA--AAAGATAATGTATTAG
* * * *
3452252 TAATTAAGCAATTAACTAAATAAGTAATAATATGTAATATTT-TATTTATTTAAATTAATTAAGG
124 TAATCAAGCAATTAACTAAATAAGTAA-AATAAGTAAAATTTATAATTATTTAAATTAATTAAGG
*
3452316 TTTTATTAAATTAATAAAATAAT
188 TTTTATCAAATTAATAAAATAAT
3452339 ATTTTATATT
Statistics
Matches: 181, Mismatches: 24, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
231 9 0.05
232 88 0.49
233 76 0.42
234 4 0.02
235 4 0.02
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (229 bp):
AATGTGTTAGTAATTAAGCAATTAATTAAATAAGTAATATTATATAATATTAAAATATTTAAATT
AATTAAGGTTTAAGAAATTAATTACATAATTTAACTAATTAAAAAGATAATGTATTAGTAATCAA
GCAATTAACTAAATAAGTAAAATAAGTAAAATTTATAATTATTTAAATTAATTAAGGTTTTATCA
AATTAATAAAATAATTTAACTAATCAAATGAAAA
Found at i:3456994 original size:2 final size:2
Alignment explanation
Indices: 3456987--3457018 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3456977 TTTCGTACTA
*
3456987 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3457019 TGGATGTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3463355 original size:12 final size:12
Alignment explanation
Indices: 3463340--3463381 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
3463330 CGAGAGCAAG
3463340 AAAAAGAGAGAA
1 AAAAAGAGAGAA
*
3463352 AAAAAAAGAGAA
1 AAAAAGAGAGAA
*
3463364 AAAAA-AGAAAA
1 AAAAAGAGAGAA
3463375 AAAAAGA
1 AAAAAGA
3463382 AATGAGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAGAA
Found at i:3463357 original size:14 final size:13
Alignment explanation
Indices: 3463340--3463390 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
3463330 CGAGAGCAAG
3463340 AAAAAGAGAGAAAA
1 AAAAAGAGA-AAAA
3463354 AAAAAGAGAAAAA
1 AAAAAGAGAAAAA
3463367 AAAGAA-A-AAAAA
1 AAA-AAGAGAAAAA
*
3463379 AGAAATGAGAAA
1 A-AAAAGAGAAA
3463391 GGGAAACGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
12 7 0.22
13 11 0.34
14 14 0.44
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAAAGAGAAAAA
Found at i:3463391 original size:21 final size:21
Alignment explanation
Indices: 3463338--3463381 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
3463328 CCCGAGAGCA
*
3463338 AGAAAAAGAGAGAAAAAAAAAG
1 AGAAAAA-AAAGAAAAAAAAAG
3463360 AGAAAAAAAAGAAAAAAAAAG
1 AGAAAAAAAAGAAAAAAAAAG
3463381 A
1 A
3463382 AATGAGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AGAAAAAAAAGAAAAAAAAAG
Found at i:3467136 original size:2 final size:2
Alignment explanation
Indices: 3467129--3467156 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3467119 TTTATGCTGA
3467129 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3467157 CGTTAGTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3471998 original size:22 final size:21
Alignment explanation
Indices: 3471970--3472031 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 21
3471960 TTCTAGTAGG
3471970 TTAAAAGTATTCGTCCACTTC
1 TTAAAAGTATTCGTCCACTTC
3471991 ATTAAAAGTATTCGTCCA---C
1 -TTAAAAGTATTCGTCCACTTC
*
3472010 TTAAAAGTATGCGTCCACTTC
1 TTAAAAGTATTCGTCCACTTC
3472031 T
1 T
3472032 GGTGGGATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 16 0.44
19 1 0.03
21 2 0.06
22 17 0.47
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (21 bp):
TTAAAAGTATTCGTCCACTTC
Found at i:3472015 original size:18 final size:18
Alignment explanation
Indices: 3471970--3472029 Score: 75
Period size: 18 Copynumber: 3.1 Consensus size: 18
3471960 TTCTAGTAGG
3471970 TTAAAAGTATTCGTCCACTTC
1 TTAAAAGTATTCGTCCA---C
3471991 ATTAAAAGTATTCGTCCAC
1 -TTAAAAGTATTCGTCCAC
*
3472010 TTAAAAGTATGCGTCCAC
1 TTAAAAGTATTCGTCCAC
3472028 TT
1 TT
3472030 CTGGTGGGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 19 0.51
19 1 0.03
22 17 0.46
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (18 bp):
TTAAAAGTATTCGTCCAC
Found at i:3472058 original size:29 final size:27
Alignment explanation
Indices: 3472023--3472185 Score: 121
Period size: 28 Copynumber: 5.9 Consensus size: 27
3472013 AAAGTATGCG
3472023 TCCACTTCTGGTGGGATAAAAGTTATCCA
1 TCCACTTCTGGTGGG-T-AAAGTTATCCA
* *
3472052 TCCACTTTTGATGGGGTAAAGTTATCCA
1 TCCACTTCTGGT-GGGTAAAGTTATCCA
* * * *
3472080 TCCTCTTTTGGTAGGGTAAAGTTTTACA
1 TCCACTTCTGGT-GGGTAAAGTTATCCA
* * **
3472108 TCCACTTCTGGTGGCTAAAATTATGTA
1 TCCACTTCTGGTGGGTAAAGTTATCCA
* * ** **
3472135 TCCATTTCTAGTAAGTAAAGTTATATA
1 TCCACTTCTGGTGGGTAAAGTTATCCA
*
3472162 TCCACTTTTGGTGGGTTAAA-TTAT
1 TCCACTTCTGGTGGG-TAAAGTTAT
3472186 TCTTAGAATT
Statistics
Matches: 106, Mismatches: 26, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
27 44 0.42
28 48 0.45
29 11 0.10
30 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (27 bp):
TCCACTTCTGGTGGGTAAAGTTATCCA
Found at i:3472137 original size:27 final size:26
Alignment explanation
Indices: 3472107--3472185 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 26
3472097 AAAGTTTTAC
*
3472107 ATCCACTTCTGGTGGCTAAAATTATGT
1 ATCCACTTCTGGTGG-TAAAATTATAT
* * * *
3472134 ATCCATTTCTAGTAAGTAAAGTTATAT
1 ATCCACTTCTGGT-GGTAAAATTATAT
* *
3472161 ATCCACTTTTGGTGGGTTAAATTAT
1 ATCCACTTCTGGT-GGTAAAATTAT
3472186 TCTTAGAATT
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (26 bp):
ATCCACTTCTGGTGGTAAAATTATAT
Found at i:3475527 original size:2 final size:2
Alignment explanation
Indices: 3475520--3475546 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3475510 CATGTTAATC
3475520 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3475547 AATTGTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3476720 original size:8 final size:8
Alignment explanation
Indices: 3476707--3476752 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
3476697 TTGGTGTTAT
3476707 TATACATA
1 TATACATA
3476715 TATACATA
1 TATACATA
*
3476723 TATATATA
1 TATACATA
3476731 TATACATA
1 TATACATA
*
3476739 TATATATA
1 TATACATA
*
3476747 CATACA
1 TATACA
3476753 CGGATATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
TATACATA
Found at i:3476725 original size:2 final size:2
Alignment explanation
Indices: 3476707--3476746 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
3476697 TTGGTGTTAT
* * *
3476707 TA TA CA TA TA TA CA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3476747 CATACACGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:3476729 original size:12 final size:12
Alignment explanation
Indices: 3476707--3476750 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
3476697 TTGGTGTTAT
3476707 TATACATATATA
1 TATACATATATA
* *
3476719 CATATATATATA
1 TATACATATATA
3476731 TATACATATATA
1 TATACATATATA
3476743 TATACATA
1 TATACATA
3476751 CACGGATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (12 bp):
TATACATATATA
Found at i:3476731 original size:16 final size:16
Alignment explanation
Indices: 3476707--3476752 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
3476697 TTGGTGTTAT
*
3476707 TATACATATATACATA
1 TATATATATATACATA
3476723 TATATATATATACATA
1 TATATATATATACATA
*
3476739 TATATATACATACA
1 TATATATATATACA
3476753 CGGATATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (16 bp):
TATATATATATACATA
Found at i:3516222 original size:62 final size:61
Alignment explanation
Indices: 3516045--3516980 Score: 803
Period size: 62 Copynumber: 15.3 Consensus size: 61
3516035 AAACATAAAA
* ** * *
3516045 AGATTTAAGCCCAATTTAACCGGCATCCAAGATGTTTAAGTCCAGTTATATTGGCACAAAG
1 AGATTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCACAAAG
* * * * * *
3516106 ACATTTAAGCCCAATTTGGCTCGCATTCAAGATGTTTAAGTCTAGTTATGTTGGCACAAAG
1 AGATTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCACAAAG
* * *
3516167 AGATTTAAGCCCAAATTTAGCTAGCATCCAAGATGTGTAAGTCCAATTATATTGGCACAAAG
1 AGATTTAAGCCC-AATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCACAAAG
* * * * * *
3516229 ACG-TTTAAGCTCAATTTAGCTAGCATCCAAGATGTTTAAGTCTAGCTATGTCGGCACAAAA
1 A-GATTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCACAAAG
* * * *
3516290 AGATTTAAGCCCAAATCTAGCTAGCATCTAAGATGT-TGAAGTCCAATTATATTGGCACAAAG
1 AGATTTAAGCCC-AATTTAGCTAGCATCCAAGATGTAT-AAGTCCAGTTATGTTGGCACAAAG
* * *
3516352 ATG-TTTAAGCCTAATTTAGCTAGCATCCAAGATGTTTAAGTCTAGTGCTATGTTGGCACAAAG
1 A-GATTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGT--TATGTTGGCACAAAG
* * * * * * *
3516415 AGATTTAAGCCCAAATTTAGCTGGCATTCAAGATGTTTAAG-CATAGCTATATTGGCATAAAG
1 AGATTTAAGCCC-AATTTAGCTAGCATCCAAGATGTATAAGTC-CAGTTATGTTGGCACAAAG
* * * * *
3516477 ACATTTAAG-CCAATTTACCTAGCATCCAAGATGTATAAATCCAGTTACGTTGGCATGAAA-
1 AGATTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCA-CAAAG
* * * * *
3516537 AGACATTAAG-CCAATTTACCTAGCATCCAAGATGTATAAATCCAGTTATGTTGGTATGAAA-
1 AGA-TTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCA-CAAAG
* * * ** * * * * *
3516598 ATATATTAAGACTAATCAAACTGGCATCCAAGATGTACAAGTCCAGTTACGTTGGCATGAAA-
1 AGAT-TTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCA-CAAAG
* ** * * * **
3516660 AGATATTAAGCCTAATCAAACTGGCATCCAAGATGTGTAAGTCCAGTTACATTGGCACAAA-
1 AGAT-TTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCACAAAG
* * *
3516721 AGGAGTTTAAGCCCAATTTA-CTTAGCATCCAAGATGTATAAGTCCATTTTTGTTGGCATGAAAG
1 A-GA-TTTAAGCCCAATTTAGC-TAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCA-CAAAG
* * *
3516785 A-ATTTAAGCCCAA--TA--TTGCATCAAAGATGTATAAGTCTAGTTATGTTGGCACAAA-
1 AGATTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCACAAAG
* * *
3516840 AGGAGTTTAAGCCCAATTTACCTAGCATCCAAGATGTATAAATCCAGTTACGTTGGCACAAA-
1 A-GA-TTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCACAAAG
* ** * * * **
3516902 AGGAGTTTAAACCCAATCAAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCACGAAAG
1 A-GA-TTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCAC-AAAG
*
3516966 -GATTTAAGCCTAATT
1 AGATTTAAGCCCAATT
3516981 AAGTTGGCAC
Statistics
Matches: 735, Mismatches: 109, Indels: 62
0.81 0.12 0.07
Matches are distributed among these distances:
55 1 0.00
56 3 0.00
57 32 0.04
58 11 0.01
59 2 0.00
60 38 0.05
61 237 0.32
62 348 0.47
63 33 0.04
64 30 0.04
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (61 bp):
AGATTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCACAAAG
Found at i:3516279 original size:123 final size:121
Alignment explanation
Indices: 3516042--3516965 Score: 855
Period size: 123 Copynumber: 7.5 Consensus size: 121
3516032 ACCAAACATA
* *
3516042 AAAAGATTTAAGCCCAATTTAACCGGCATCCAAGATGTTTAAGTCCAGTTATATTGGCACAAAGA
1 AAAAGATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCCAGTTATATTGGCACAAAGA
* * * * * *
3516107 CATTTAAGCCCAATTTGGCTCGCATTCAAGATGTTTAAGTCTAGTTATGTTGGCAC
66 CGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCAC
* * * *
3516163 AAAGAGATTTAAGCCCAAATTTAGCTAGCATCCAAGATGTGTAAGTCCAATTATATTGGCACAAA
1 AAA-AGATTTAAGCCC-AATTTAACTGGCATCCAAGATGTATAAGTCCAGTTATATTGGCACAAA
* * * * *
3516228 GACGTTTAAGCTCAATTTAGCTAGCATCCAAGATGTTTAAGTCTAGCTATGTCGGCAC
64 GACGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCAC
* * * * *
3516286 AAAAAGATTTAAGCCCAAATCTAGCTAGCATCTAAGATGT-TGAAGTCCAATTATATTGGCACAA
1 -AAAAGATTTAAGCCC-AATTTAACTGGCATCCAAGATGTAT-AAGTCCAGTTATATTGGCACAA
* * * *
3516350 AGATGTTTAAGCCTAATTTAGCTAGCATCCAAGATGTTTAAGTCTAGTGCTATGTTGGCAC
63 AGACGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGT--TATGTTGGCAC
* * * * * *
3516411 AAAGAGATTTAAGCCCAAATTTAGCTGGCATTCAAGATGTTTAAG-CATAGCTATATTGGCATAA
1 AAA-AGATTTAAGCCC-AATTTAACTGGCATCCAAGATGTATAAGTC-CAGTTATATTGGCACAA
* * * * *
3516475 AGACATTTAAG-CCAATTTACCTAGCATCCAAGATGTATAAATCCAGTTACGTTGGCATG
63 AGACGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCA-C
* * * * * * *
3516534 AAAAGACATTAAG-CCAATTTACCTAGCATCCAAGATGTATAAATCCAGTTATGTTGGTATGAAA
1 AAAAGA-TTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCCAGTTATATTGGCA-CAAA
** * * ** * * * * *
3516598 -ATATATTAAGACTAATCAAACTGGCATCCAAGATGTACAAGTCCAGTTACGTTGGCATG
64 GACGT-TTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCA-C
* ** * *
3516657 AAAAGATATTAAGCCTAATCAAACTGGCATCCAAGATGTGTAAGTCCAGTTACATTGGCACAAAA
1 AAAAGAT-TTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCCAGTTATATTGGCAC-AAA
* * *
3516722 GGA-GTTTAAGCCCAATTTA-CTTAGCATCCAAGATGTATAAGTCCATTTTTGTTGGCAT
64 -GACGTTTAAGCCCAATTTAGC-TAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCAC
* * * * *
3516780 GAAAGAATTTAAGCCCAA--T-A-TTGCATCAAAGATGTATAAGTCTAGTTATGTTGGCACAAAA
1 AAAAG-ATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCCAGTTATATTGGCAC-AAA
* * *
3516841 GGA-GTTTAAGCCCAATTTACCTAGCATCCAAGATGTATAAATCCAGTTACGTTGGCAC
64 -GACGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCAC
* ** * *
3516899 AAAAGGAGTTTAAACCCAATCAAACTGGCATCCAAGATGTATAAGTCTAGTTACATTGGCACGAA
1 AAAA-GA-TTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCCAGTTATATTGGCAC-AA
3516964 AG
63 AG
3516966 GATTTAAGCC
Statistics
Matches: 674, Mismatches: 100, Indels: 56
0.81 0.12 0.07
Matches are distributed among these distances:
119 90 0.13
120 13 0.02
121 39 0.06
122 36 0.05
123 270 0.40
124 156 0.23
125 68 0.10
126 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (121 bp):
AAAAGATTTAAGCCCAATTTAACTGGCATCCAAGATGTATAAGTCCAGTTATATTGGCACAAAGA
CGTTTAAGCCCAATTTAGCTAGCATCCAAGATGTATAAGTCCAGTTATGTTGGCAC
Found at i:3516716 original size:31 final size:30
Alignment explanation
Indices: 3516619--3516716 Score: 72
Period size: 31 Copynumber: 3.2 Consensus size: 30
3516609 CTAATCAAAC
* *
3516619 TGGCATCCAAGATGTACAAGTCCAGTTACGT
1 TGGCATCCAAGATGT-TAAGTCCAGTTACAT
** * * * * *
3516650 TGGCATGAAAAGATATTAAG-CCTAATCAAAC
1 TGGCAT-CCAAGATGTTAAGTCC-AGTTACAT
3516681 TGGCATCCAAGATGTGTAAGTCCAGTTACAT
1 TGGCATCCAAGATGT-TAAGTCCAGTTACAT
3516712 TGGCA
1 TGGCA
3516717 CAAAAGGAGT
Statistics
Matches: 47, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
30 8 0.17
31 31 0.66
32 8 0.17
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (30 bp):
TGGCATCCAAGATGTTAAGTCCAGTTACAT
Found at i:3529948 original size:18 final size:18
Alignment explanation
Indices: 3529913--3529947 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3529903 AGTTTGAAGG
3529913 GTGTCTCTAGTTTATTTT
1 GTGTCTCTAGTTTATTTT
*
3529931 GTGTCTTTA-TTTATTTT
1 GTGTCTCTAGTTTATTTT
3529948 TAAATTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.09, G:0.14, T:0.66
Consensus pattern (18 bp):
GTGTCTCTAGTTTATTTT
Found at i:3547877 original size:16 final size:16
Alignment explanation
Indices: 3547856--3547886 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3547846 TTAGCTGTAG
*
3547856 TTAATTAGTTTTTAAT
1 TTAATTAGTTATTAAT
3547872 TTAATTAGTTATTAA
1 TTAATTAGTTATTAA
3547887 AAGTTTGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TTAATTAGTTATTAAT
Found at i:3555164 original size:20 final size:20
Alignment explanation
Indices: 3555147--3555184 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3555137 CCTCAAATCT
3555147 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
3555167 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
3555185 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:3558060 original size:21 final size:21
Alignment explanation
Indices: 3558036--3558075 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3558026 TGTGGCTGAA
3558036 TTTGATGATATTTCATGATAT
1 TTTGATGATATTTCATGATAT
* *
3558057 TTTGGTGATATTTGATGAT
1 TTTGATGATATTTCATGAT
3558076 TGGTGAGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.03, G:0.20, T:0.53
Consensus pattern (21 bp):
TTTGATGATATTTCATGATAT
Found at i:3558070 original size:10 final size:10
Alignment explanation
Indices: 3558035--3558075 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
3558025 TTGTGGCTGA
3558035 ATTTGATGAT
1 ATTTGATGAT
*
3558045 ATTTCATGAT
1 ATTTGATGAT
*
3558055 ATTTTGGTGAT
1 A-TTTGATGAT
3558066 ATTTGATGAT
1 ATTTGATGAT
3558076 TGGTGAGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (10 bp):
ATTTGATGAT
Found at i:3561119 original size:13 final size:13
Alignment explanation
Indices: 3561101--3561130 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3561091 AAATCACGAG
3561101 ATAAGTAAATTGT
1 ATAAGTAAATTGT
3561114 ATAAGTAAATTGT
1 ATAAGTAAATTGT
3561127 ATAA
1 ATAA
3561131 ATACATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (13 bp):
ATAAGTAAATTGT
Found at i:3567835 original size:28 final size:28
Alignment explanation
Indices: 3567804--3567860 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
3567794 TGGAGAATAG
**
3567804 GGGCAAAATGGTAATTTTACCACC-CCAA
1 GGGCAAAACAGTAATTTT-CCACCACCAA
3567832 GGGCAAAACAGTAATTTTCCACCACCAA
1 GGGCAAAACAGTAATTTTCCACCACCAA
3567860 G
1 G
3567861 ACACTTGTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (28 bp):
GGGCAAAACAGTAATTTTCCACCACCAA
Found at i:3587116 original size:5 final size:5
Alignment explanation
Indices: 3587106--3587185 Score: 56
Period size: 5 Copynumber: 15.4 Consensus size: 5
3587096 GTAAGTCAAT
* * *
3587106 TTTTA TTTTA TTTTA -TTTA -CTTA TTTTA CTTCA TTTCTCA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT-T-A -TTTTA
* *
3587152 TTTAGA TTTTA TTTTA TTATTA TTTCA TTTTA TT
1 TTT-TA TTTTA TTTTA TT-TTA TTTTA TTTTA TT
3587186 ATTTCATTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
4 7 0.12
5 37 0.63
6 10 0.17
7 2 0.03
8 3 0.05
ACGTcount: A:0.21, C:0.07, G:0.01, T:0.70
Consensus pattern (5 bp):
TTTTA
Found at i:3587176 original size:16 final size:16
Alignment explanation
Indices: 3587157--3587188 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3587147 TTTTATTTAG
*
3587157 ATTTTATTTTATTATT
1 ATTTCATTTTATTATT
3587173 ATTTCATTTTATTATT
1 ATTTCATTTTATTATT
3587189 TCATTTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTCATTTTATTATT
Found at i:3587186 original size:13 final size:13
Alignment explanation
Indices: 3587168--3587201 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
3587158 TTTTATTTTA
3587168 TTATTATTTCATT
1 TTATTATTTCATT
3587181 TTATTATTTCATT
1 TTATTATTTCATT
3587194 TTGATTAT
1 TT-ATTAT
3587202 CAATCCAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTATTTCATT
Found at i:3590567 original size:4 final size:4
Alignment explanation
Indices: 3590560--3590585 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3590550 TATATATATA
3590560 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
3590586 AAAAATGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:3593668 original size:12 final size:12
Alignment explanation
Indices: 3593651--3593675 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3593641 TGGAACCTAT
3593651 CATCACAATTAA
1 CATCACAATTAA
3593663 CATCACAATTAA
1 CATCACAATTAA
3593675 C
1 C
3593676 TTAATTCTCA
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:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (12 bp):
CATCACAATTAA
Found at i:3596441 original size:37 final size:37
Alignment explanation
Indices: 3596355--3596451 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
3596345 AAGGCAGTGT
* * *
3596355 GGTTGTGCTTGACCCATAAAAGGCAATGACTTGTGAA
1 GGTTGTGCTTGATCCATAAAAGACAATGACTTCTGAA
* * * *
3596392 GGTTGGGATTGATCTATAAAAGACAATGGCTTCTGAA
1 GGTTGTGCTTGATCCATAAAAGACAATGACTTCTGAA
*
3596429 GGTTGTCCTTGATCCATAAAAGA
1 GGTTGTGCTTGATCCATAAAAGA
3596452 TAGTAACATG
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (37 bp):
GGTTGTGCTTGATCCATAAAAGACAATGACTTCTGAA
Found at i:3601430 original size:2 final size:2
Alignment explanation
Indices: 3601423--3601481 Score: 66
Period size: 2 Copynumber: 30.0 Consensus size: 2
3601413 CTAGGCAAAC
* * * *
3601423 AT AT AT AT AT AT AC AT AC AT AT AC AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3601465 AT AT AT AT -T AT AC AT AT
1 AT AT AT AT AT AT AT AT AT
3601482 CAATTCTTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:3605498 original size:28 final size:27
Alignment explanation
Indices: 3605462--3605514 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
3605452 ATATCCTGGT
*
3605462 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
3605489 GGTGGTAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
3605515 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:3605941 original size:19 final size:19
Alignment explanation
Indices: 3605917--3605963 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
3605907 GCACTACCCC
3605917 CCTTAAAATAAAATTTTGA
1 CCTTAAAATAAAATTTTGA
3605936 CCTTAAAATAAAATTTTGA
1 CCTTAAAATAAAATTTTGA
*
3605955 CCTCAAAAT
1 CCTTAAAAT
3605964 TTCACTTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.34
Consensus pattern (19 bp):
CCTTAAAATAAAATTTTGA
Found at i:3615078 original size:42 final size:42
Alignment explanation
Indices: 3615013--3615179 Score: 223
Period size: 42 Copynumber: 4.0 Consensus size: 42
3615003 TGTGAAAAGG
**
3615013 AAAAGGTGTACATGAAAAGGTACAAGAGAAC-AAGATAAGA-A
1 AAAAGGTGTATGTGAAAAGGTACAAGAGAACAAAG-TAAGAGA
* * *
3615054 CACAAGGTGTATGTGAAAAAGTACAAGAAAACAAAGTAAGAGA
1 -AAAAGGTGTATGTGAAAAGGTACAAGAGAACAAAGTAAGAGA
*
3615097 AAAAAGTGTATGTGAAAAGGTACAAGAGAACAAAGTAAGAGA
1 AAAAGGTGTATGTGAAAAGGTACAAGAGAACAAAGTAAGAGA
*
3615139 AAAAGGTGTATGTGAAAAGGTACCAGAGAAC-AAGCTAAGAG
1 AAAAGGTGTATGTGAAAAGGTACAAGAGAACAAAG-TAAGAG
3615180 TGAGAGGAAG
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
41 3 0.03
42 104 0.94
43 4 0.04
ACGTcount: A:0.53, C:0.08, G:0.26, T:0.14
Consensus pattern (42 bp):
AAAAGGTGTATGTGAAAAGGTACAAGAGAACAAAGTAAGAGA
Found at i:3620263 original size:109 final size:109
Alignment explanation
Indices: 3620069--3620279 Score: 359
Period size: 109 Copynumber: 1.9 Consensus size: 109
3620059 ACCTATTTCA
* *
3620069 ACCAAAAGAAAGGACGGTGGTCTGTTAGGGGTTGGAGGGAGGTAGGCGTGGTGTGAACTTCACCA
1 ACCAAAAGAAAGGACGGTGGACTGTTAGGGGTTGGAGGGAGGTAGGCGTGGTGTGAACTTAACCA
*
3620134 ACTACTAGTATCAATAGGGTCATGGTTGCAAATTTTTCAAGTTT
66 ACTACTAGTATCAATAGGGTCATGGTTACAAATTTTTCAAGTTT
**
3620178 ACCAAAAGAAAGGGGGGTGGACTGTTAGGGGTTGGAGGGAGGTAGGCGTGGTGTGAACTTAACCA
1 ACCAAAAGAAAGGACGGTGGACTGTTAGGGGTTGGAGGGAGGTAGGCGTGGTGTGAACTTAACCA
* *
3620243 ACTACTAGTATCAATTGGGTCATGGTTACAATTTTTT
66 ACTACTAGTATCAATAGGGTCATGGTTACAAATTTTT
3620280 TTTTATTTGG
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
109 95 1.00
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.27
Consensus pattern (109 bp):
ACCAAAAGAAAGGACGGTGGACTGTTAGGGGTTGGAGGGAGGTAGGCGTGGTGTGAACTTAACCA
ACTACTAGTATCAATAGGGTCATGGTTACAAATTTTTCAAGTTT
Found at i:3630033 original size:5 final size:5
Alignment explanation
Indices: 3630023--3630053 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
3630013 CAGCACCTGC
3630023 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
3630054 ACCCTAGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:3661606 original size:54 final size:54
Alignment explanation
Indices: 3661546--3661650 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
3661536 ATGGTGATAT
* **
3661546 TGTCCGGCTATGTGCACGATGTGATGGGATGCACATGAGTTGGGTGAGATGAGA
1 TGTCCGGCTATGTGCACGATATGATGGGATGCACATGAGCAGGGTGAGATGAGA
* *
3661600 TGTCCGGCTATGTGCACGATATGGTGGGATGCACATTAGCAGGGTGAGATG
1 TGTCCGGCTATGTGCACGATATGATGGGATGCACATGAGCAGGGTGAGATG
3661651 CACATGATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.22, C:0.14, G:0.38, T:0.26
Consensus pattern (54 bp):
TGTCCGGCTATGTGCACGATATGATGGGATGCACATGAGCAGGGTGAGATGAGA
Found at i:3662643 original size:135 final size:135
Alignment explanation
Indices: 3662400--3662663 Score: 368
Period size: 135 Copynumber: 2.0 Consensus size: 135
3662390 AAACTATTAC
* **
3662400 CGCAGCACTAGGAGAATCATGGTCGTGGCACTAAGTTGAAAAGGTGCACCATACTAGAGGCTGAG
1 CGCAGCACTAGGAGAATCATGGTCATGGCACTAAGTTGAAAAGGTGCACCATACTAGAGGCCAAG
* * * *
3662465 AGCATATAATCGTGGTGCCAAAAAAAAGCAGTGCGATGCGGTGCGGTGTTGCAAAGGCTTGTCAC
66 AGCACATAATCGCGGTGCCAAAAAAAAGCAGTGCGATGCGGTGCGATGCTGCAAAGGCTTGTCAC
3662530 GCTGT
131 GCTGT
* * *
3662535 CGCAGCACTGGGAGAATCATGG-CTATGGCACTAAGTTGGAAGGGTGCACCATACTAGAGGCCAA
1 CGCAGCACTAGGAGAATCATGGTC-ATGGCACTAAGTTGAAAAGGTGCACCATACTAGAGGCCAA
* *** * *
3662599 GAGCACATAATCGCGGTGCCAAAAAAGATTGGTGCGGTGTGGTGCGATGCTGCAAAGGCTTGTCA
65 GAGCACATAATCGCGGTGCCAAAAAAAAGCAGTGCGATGCGGTGCGATGCTGCAAAGGCTTGTCA
3662664 TGGCTTCGCG
Statistics
Matches: 112, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
134 1 0.01
135 111 0.99
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (135 bp):
CGCAGCACTAGGAGAATCATGGTCATGGCACTAAGTTGAAAAGGTGCACCATACTAGAGGCCAAG
AGCACATAATCGCGGTGCCAAAAAAAAGCAGTGCGATGCGGTGCGATGCTGCAAAGGCTTGTCAC
GCTGT
Found at i:3663528 original size:16 final size:15
Alignment explanation
Indices: 3663500--3663538 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3663490 TTAGGTTTTG
*
3663500 TTAATTAATTTAGTGT
1 TTAATTAAGTTAGT-T
*
3663516 TTGATTAAGTTAGTT
1 TTAATTAAGTTAGTT
3663531 TTAATTAA
1 TTAATTAA
3663539 TTTTCTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (15 bp):
TTAATTAAGTTAGTT
Found at i:3677506 original size:16 final size:16
Alignment explanation
Indices: 3677485--3677521 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
3677475 GTGGTGTTAG
*
3677485 TTTAATTTTACTTTAC
1 TTTAATTTTAATTTAC
3677501 TTTAATTTTAATTTAC
1 TTTAATTTTAATTTAC
3677517 TTTAA
1 TTTAA
3677522 GAAGAGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAATTTTAATTTAC
Found at i:3679354 original size:48 final size:48
Alignment explanation
Indices: 3679278--3679369 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
3679268 TGGGCTATAA
*
3679278 TTTTCGGAGTAATAGTTTGGTTCTTATGGAAATGGAAAAATGCATATG
1 TTTTCGGAGTAACAGTTTGGTTCTTATGGAAATGGAAAAATGCATATG
* * * *
3679326 TTTTTGGAGTAACAGTTTGGTTTTTATGGAAGTGGAGAAATGCA
1 TTTTCGGAGTAACAGTTTGGTTCTTATGGAAATGGAAAAATGCA
3679370 CATACTTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.29, C:0.05, G:0.27, T:0.38
Consensus pattern (48 bp):
TTTTCGGAGTAACAGTTTGGTTCTTATGGAAATGGAAAAATGCATATG
Found at i:3697942 original size:23 final size:23
Alignment explanation
Indices: 3697912--3697955 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3697902 GGTTTAATAT
*
3697912 GTACTAGTTTTTGAGCATTGTTA
1 GTACTAGTCTTTGAGCATTGTTA
3697935 GTACTAGTCTTTGAGCATTGT
1 GTACTAGTCTTTGAGCATTGT
3697956 CAATGTCCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.45
Consensus pattern (23 bp):
GTACTAGTCTTTGAGCATTGTTA
Found at i:3709109 original size:50 final size:50
Alignment explanation
Indices: 3709054--3709166 Score: 118
Period size: 50 Copynumber: 2.3 Consensus size: 50
3709044 AAGATCAAGT
* * * * *
3709054 GATAACCTTTACCCAATCCATAAAGGGATTTTTGCTTTTTAATGAGAAGC
1 GATAACCCTTACACAATCCACAAAGAGATTTTTGCTTTCTAATGAGAAGC
* * * * * * *
3709104 GATAACCGTCACAGAATCCACAAAGAGATTTTTTCTTTCTGATGGGAAGT
1 GATAACCCTTACACAATCCACAAAGAGATTTTTGCTTTCTAATGAGAAGC
3709154 GATAACCCTTACA
1 GATAACCCTTACA
3709167 AAATAACTTT
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (50 bp):
GATAACCCTTACACAATCCACAAAGAGATTTTTGCTTTCTAATGAGAAGC
Found at i:3711332 original size:4 final size:4
Alignment explanation
Indices: 3711323--3711385 Score: 81
Period size: 4 Copynumber: 15.8 Consensus size: 4
3711313 AGCTAACATA
* *
3711323 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
3711371 CATG CATG CATG TAT
1 TATG TATG TATG TAT
3711386 AGCCCAACAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.43
Consensus pattern (4 bp):
TATG
Found at i:3712668 original size:21 final size:21
Alignment explanation
Indices: 3712643--3712684 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3712633 AACGAGAGTT
3712643 TCTCGTTGCAGCGAGAATCAA
1 TCTCGTTGCAGCGAGAATCAA
*
3712664 TCTCGTTGCAGTGAGAATCAA
1 TCTCGTTGCAGCGAGAATCAA
3712685 AACATCAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (21 bp):
TCTCGTTGCAGCGAGAATCAA
Found at i:3718718 original size:15 final size:15
Alignment explanation
Indices: 3718700--3718748 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
3718690 CTAACAAGTA
3718700 ATTTTAATATTTAAT
1 ATTTTAATATTTAAT
**
3718715 ATTTTTTTATTTAAT
1 ATTTTAATATTTAAT
* *
3718730 A-TTTAGTATTTAAG
1 ATTTTAATATTTAAT
3718744 ATTTT
1 ATTTT
3718749 TTTTAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (15 bp):
ATTTTAATATTTAAT
Found at i:3727288 original size:47 final size:47
Alignment explanation
Indices: 3727219--3727326 Score: 189
Period size: 47 Copynumber: 2.3 Consensus size: 47
3727209 TAAAATAGAA
* *
3727219 TTTCGAGCGAACAGTTGGGAATCCAAAACTGTCGGAAGACTATAGCC
1 TTTCGAGGGAACAGCTGGGAATCCAAAACTGTCGGAAGACTATAGCC
*
3727266 TTTCGAGGGAACAGCTGGGAATCCAAAACTGTTGGAAGACTATAGCC
1 TTTCGAGGGAACAGCTGGGAATCCAAAACTGTCGGAAGACTATAGCC
3727313 TTTCGAGGGAACAG
1 TTTCGAGGGAACAG
3727327 AGTTTCCCCA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.21
Consensus pattern (47 bp):
TTTCGAGGGAACAGCTGGGAATCCAAAACTGTCGGAAGACTATAGCC
Found at i:3740434 original size:72 final size:72
Alignment explanation
Indices: 3740345--3740486 Score: 214
Period size: 72 Copynumber: 2.0 Consensus size: 72
3740335 TGGAAATAGA
*
3740345 GAGTTTGTTGTAGTAAAGGTAAAAAACAG-ATAAGTTTGTCAAATTTTCTATTGAAGTTAAGATT
1 GAGTTTGTTGTAGTAAAGGTAAAAAA-AGAATAAGTTTGTCAAATTTCCTATTGAAGTTAAGATT
3740409 GGACCTGT
65 GGACCTGT
* * * **
3740417 GAGTTTGTTGTCGTAAAGGTAAAGAATGAATAAGTTTGTCAAATTTCCTATTGAAGTTGGGATTG
1 GAGTTTGTTGTAGTAAAGGTAAAAAAAGAATAAGTTTGTCAAATTTCCTATTGAAGTTAAGATTG
3740482 GACCT
66 GACCT
3740487 ATGAAATTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 1 0.02
72 62 0.98
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (72 bp):
GAGTTTGTTGTAGTAAAGGTAAAAAAAGAATAAGTTTGTCAAATTTCCTATTGAAGTTAAGATTG
GACCTGT
Found at i:3740679 original size:144 final size:144
Alignment explanation
Indices: 3740417--3741911 Score: 1646
Period size: 144 Copynumber: 10.4 Consensus size: 144
3740407 TTGGACCTGT
* *
3740417 GAGTTTGTTGTCGTAAAGGTAAAGAA-TGAATAAGTTTGTCAAATTTCCTATTGAAGTTGGGATT
1 GAGTTTGTTGTTGTAAAGGTAAAGAACTG-ATAAGTTTGTCAAATTTCCTATTGAAGCTGGGATT
* * * *
3740481 GGACCTATGAAATTTTTATCA-AGCAATTCAAGATCAGAAAGAGATCTTAACAACCCAATTTCTT
65 GGACCTGTGAAATTGTTGTCAGA-CAATTCAAGCTCAGAAAGAGATCTTAACAACCCAATTTCTT
* **
3740545 GAAGAATAAAACCAGA
129 GAGGAATGGAACCAGA
* * * * * *
3740561 GAGTTTGTTATTATAAAGGTAAAGAACTGATAAATCTGTCAAATTTTCTATTAAAGCTGGGATTG
1 GAGTTTGTTGTTGTAAAGGTAAAGAACTGATAAGTTTGTCAAATTTCCTATTGAAGCTGGGATTG
* * ** * * *
3740626 GACCTATAAAATTGTTGTCAGACAATTCAAGCTTGGAAAGAGATCTTAGCAACCCAGTTTCTTAA
66 GACCTGTGAAATTGTTGTCAGACAATTCAAGCTCAGAAAGAGATCTTAACAACCCAATTTCTTGA
* * *
3740691 GAAATGGAATCAAA
131 GGAATGGAACCAGA
* ** *
3740705 GAGTTTGTTGTTGTAAAGGTAAAGAA-TGGATAAGTTTG-CTAACTTTCCTATTGAAATTGGAAT
1 GAGTTTGTTGTTGTAAAGGTAAAGAACT-GATAAGTTTGTC-AAATTTCCTATTGAAGCTGGGAT
* * * * * * *
3740768 TGAACCTGTGAAATTGTTATCAGACAATGCAAGCTTAGAAGGAGATTTTACCAACCCAATTTCTT
64 TGGACCTGTGAAATTGTTGTCAGACAATTCAAGCTCAGAAAGAGATCTTAACAACCCAATTTCTT
* *
3740833 G-GGAAATGAAACTAGA
129 GAGG-AATGGAACCAGA
* * **
3740849 GAGTTTGTTGTTGTAAAGGTGAAGAACGGATAAGTTTGTCAAATTTCCTATTGAAGCTAAGATTG
1 GAGTTTGTTGTTGTAAAGGTAAAGAACTGATAAGTTTGTCAAATTTCCTATTGAAGCTGGGATTG
* * * * * * *
3740914 GACTTGTGAAATTGTTGTTAGACAAGTCAAGCTTAGAAGGAGATCTTAGCAACCTAATTTCTTGA
66 GACCTGTGAAATTGTTGTCAGACAATTCAAGCTCAGAAAGAGATCTTAACAACCCAATTTCTTGA
3740979 GGAATGGAACCAGA
131 GGAATGGAACCAGA
* * * *
3740993 GAGTTTGTTGTTGTAAAGGTATAGAACGGATAAGTTTATCAAATTTCCTATTGAAACTGGGATTG
1 GAGTTTGTTGTTGTAAAGGTAAAGAACTGATAAGTTTGTCAAATTTCCTATTGAAGCTGGGATTG
* * * * *
3741058 AACTTGTGAAATTGTTGTCAGACAGTGT-AAGCTTAGAAAGAGATCTTAGCAACCCAATTTCTTG
66 GACCTGTGAAATTGTTGTCAGACAAT-TCAAGCTCAGAAAGAGATCTTAACAACCCAATTTCTTG
* *
3741122 GGGAATGGAACTAGA
130 AGGAATGGAACCAGA
* * * * * * * *
3741137 GAGTTTGTTGTTGTAAAGGTAAACAAATCATAAATTTGTTAAATTTCCTATTGCAGCTAGAATTG
1 GAGTTTGTTGTTGTAAAGGTAAAGAACTGATAAGTTTGTCAAATTTCCTATTGAAGCTGGGATTG
* ** * * * *
3741202 AACCCATTAAATTGTTGTCAGACAATTCAAGGTCAGAAAGAGATCTTAACAATCCAATTTCTTGG
66 GACCTGTGAAATTGTTGTCAGACAATTCAAGCTCAGAAAGAGATCTTAACAACCCAATTTCTTGA
*
3741267 GGAATGGAACTAGA
131 GGAATGGAACCAGA
* * **
3741281 GAGTTTGTTGTTGTAAAGATAAAAAAAAGATAAGTTTGTCAAATTTCCTATTGAAGCTGGGATTG
1 GAGTTTGTTGTTGTAAAGGTAAAGAACTGATAAGTTTGTCAAATTTCCTATTGAAGCTGGGATTG
* * * * *
3741346 GACTTGTAAAATTGTTATCAGACAATGCAAGCTTAGAAAGAGATCTTAACAACCCAATTTCTTG-
66 GACCTGTGAAATTGTTGTCAGACAATTCAAGCTCAGAAAGAGATCTTAACAACCCAATTTCTTGA
* *
3741410 GGAAATGGAACTAAA
131 GG-AATGGAACCAGA
* * * **
3741425 GAGTTTGTTGTTGTAAAGGTAAACAAAC-CATAAATTTGTCAAATTTCCTATTGAAGCTATGATT
1 GAGTTTGTTGTTGTAAAGGTAAA-GAACTGATAAGTTTGTCAAATTTCCTATTGAAGCTGGGATT
* * * *
3741489 GAACCTATTAAATTGTTGTCAGACAATTCAAGGTCAGAAAGAGATCTTAACAACCCAATTTCTT-
65 GGACCTGTGAAATTGTTGTCAGACAATTCAAGCTCAGAAAGAGATCTTAACAACCCAATTTCTTG
*
3741553 AGGGAATGGAACTAGA
130 A-GGAATGGAACCAGA
* **
3741569 AAGTTTGTTGTTGTAAAGGTAAAGAAAAGATACA-TTTGTCAAATTTCCTATTGAAGCTGGGATT
1 GAGTTTGTTGTTGTAAAGGTAAAGAACTGATA-AGTTTGTCAAATTTCCTATTGAAGCTGGGATT
* * * * * *
3741633 TGACTTTTGAAATTGTTATCAGACAATTCAAGGTCAGAAAGAGATCTTAATAACCCAATTTCTTG
65 GGACCTGTGAAATTGTTGTCAGACAATTCAAGCTCAGAAAGAGATCTTAACAACCCAATTTCTTG
* *
3741698 GGGAATGGAATCAGA
130 AGGAATGGAACCAGA
* * * ** * *
3741713 GAGTTTGTTGTTATTAAGATAAAGAA-TGGATAAGTTTACCAAATTTCCTGTTGAAGTTGGGATT
1 GAGTTTGTTGTTGTAAAGGTAAAGAACT-GATAAGTTTGTCAAATTTCCTATTGAAGCTGGGATT
* * * * * * *
3741777 GGACTTGTGAAATTGTTGTAAGATAATTCAAGATCAGAAAGTGATCTTAACAATCCAATTTTTTG
65 GGACCTGTGAAATTGTTGTCAGACAATTCAAGCTCAGAAAGAGATCTTAACAACCCAATTTCTTG
*
3741842 -GAAAATGGAACCAGA
130 AG-GAATGGAACCAGA
* * * * *
3741857 GAGTTTGTTGCTATAAAGGTAAAGAACAGATAAGTTTATTAAATTTCCTATTGAA
1 GAGTTTGTTGTTGTAAAGGTAAAGAACTGATAAGTTTGTCAAATTTCCTATTGAA
3741912 TGAATACTTC
Statistics
Matches: 1148, Mismatches: 182, Indels: 42
0.84 0.13 0.03
Matches are distributed among these distances:
143 10 0.01
144 1125 0.98
145 13 0.01
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.32
Consensus pattern (144 bp):
GAGTTTGTTGTTGTAAAGGTAAAGAACTGATAAGTTTGTCAAATTTCCTATTGAAGCTGGGATTG
GACCTGTGAAATTGTTGTCAGACAATTCAAGCTCAGAAAGAGATCTTAACAACCCAATTTCTTGA
GGAATGGAACCAGA
Found at i:3752796 original size:13 final size:13
Alignment explanation
Indices: 3752778--3752802 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3752768 AGAGAAATTG
3752778 TGATTTTATAAAA
1 TGATTTTATAAAA
3752791 TGATTTTATAAA
1 TGATTTTATAAA
3752803 TTTTTTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:3754239 original size:39 final size:39
Alignment explanation
Indices: 3754196--3754362 Score: 212
Period size: 39 Copynumber: 4.3 Consensus size: 39
3754186 AAGCTCCTGA
**
3754196 CAGAGAACAATACATCAAAAAACCATGATATTGATCCAG
1 CAGAGAACAATACATCAAAAAACCATGATAGGGATCCAG
* *
3754235 CAGAGAACAATATATCAGAAAACCATGATAGGGATCC-G
1 CAGAGAACAATACATCAAAAAACCATGATAGGGATCCAG
* *
3754273 ACAGAGAACAATACATCAGAAAACCATGATAGGGATCCAA
1 -CAGAGAACAATACATCAAAAAACCATGATAGGGATCCAG
* * * *
3754313 CAGAGAACAACACATCCGAGAAA-CATGGTAGGGATCCAG
1 CAGAGAACAATACAT-CAAAAAACCATGATAGGGATCCAG
3754352 CAGAGAACAAT
1 CAGAGAACAAT
3754363 TCCAATGATA
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 107 0.96
40 4 0.04
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (39 bp):
CAGAGAACAATACATCAAAAAACCATGATAGGGATCCAG
Found at i:3754296 original size:78 final size:78
Alignment explanation
Indices: 3754194--3754362 Score: 234
Period size: 78 Copynumber: 2.2 Consensus size: 78
3754184 GGAAGCTCCT
** * * *
3754194 GACAGAGAACAATACATCAAAAAACCATGATATTGATCCAGCAGAGAACAATATATCAGA-AAAC
1 GACAGAGAACAATACATCAAAAAACCATGATAGGGATCCAACAGAGAACAACACATCAGAGAAA-
3754258 CATGATAGGGATCC
65 CATGATAGGGATCC
* *
3754272 GACAGAGAACAATACATCAGAAAACCATGATAGGGATCCAACAGAGAACAACACATCCGAGAAAC
1 GACAGAGAACAATACATCAAAAAACCATGATAGGGATCCAACAGAGAACAACACATCAGAGAAAC
*
3754337 ATGGTAGGGATCC
66 ATGATAGGGATCC
3754350 -AGCAGAGAACAAT
1 GA-CAGAGAACAAT
3754363 TCCAATGATA
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
77 1 0.01
78 77 0.95
79 3 0.04
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.14
Consensus pattern (78 bp):
GACAGAGAACAATACATCAAAAAACCATGATAGGGATCCAACAGAGAACAACACATCAGAGAAAC
ATGATAGGGATCC
Found at i:3756416 original size:14 final size:14
Alignment explanation
Indices: 3756374--3756418 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
3756364 AGCAAACTAA
3756374 GGTATTCTCTACAG
1 GGTATTCTCTACAG
3756388 GGTATATCATCTACAG
1 GGTAT-TC-TCTACAG
3756404 GGTATTCTCTACAG
1 GGTATTCTCTACAG
3756418 G
1 G
3756419 ATATAAACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.45
15 4 0.14
16 12 0.41
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (14 bp):
GGTATTCTCTACAG
Found at i:3758500 original size:17 final size:16
Alignment explanation
Indices: 3758478--3758512 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 16
3758468 AGTTTTCTTT
3758478 TTATTTATATTATTTAA
1 TTATTTATA-TATTTAA
3758495 TTATTTATATATTTAA
1 TTATTTATATATTTAA
3758511 TT
1 TT
3758513 GTTGTGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTATATATTTAA
Found at i:3762425 original size:21 final size:22
Alignment explanation
Indices: 3762375--3762431 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
3762365 TTTATCTAGC
* *
3762375 TATAT-TTTATATTTCATTTTAT
1 TATATATTTAT-TTTCATTTAAG
3762397 TATATATTT-TTTTCATTTAAG
1 TATATATTTATTTTCATTTAAG
*
3762418 TATTTATTTATTTT
1 TATATATTTATTTT
3762432 TGCTATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 17 0.57
22 10 0.33
23 3 0.10
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (22 bp):
TATATATTTATTTTCATTTAAG
Found at i:3765537 original size:19 final size:19
Alignment explanation
Indices: 3765515--3765551 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3765505 TTTTTCCCCT
3765515 TTTTTTCCTTTTTCCTTTC
1 TTTTTTCCTTTTTCCTTTC
*
3765534 TTTTTTCTTTTTTCCTTT
1 TTTTTTCCTTTTTCCTTT
3765552 TCATTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTTCCTTTTTCCTTTC
Found at i:3776636 original size:34 final size:34
Alignment explanation
Indices: 3776594--3776700 Score: 187
Period size: 34 Copynumber: 3.1 Consensus size: 34
3776584 CATTTCCTCC
* *
3776594 CTCTCTCAACATATCATGTAGAGTGCTTAATCTT
1 CTCTCTCAACATATCATGCAGAGTGCTAAATCTT
3776628 CTCTCTCAACATATCATGCAGAGTGCTAAATCTT
1 CTCTCTCAACATATCATGCAGAGTGCTAAATCTT
*
3776662 TTCTCTCAACATATCATGCAGAGTGCTAAATCTT
1 CTCTCTCAACATATCATGCAGAGTGCTAAATCTT
3776696 CTCTC
1 CTCTC
3776701 CATAACACTC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.36
Consensus pattern (34 bp):
CTCTCTCAACATATCATGCAGAGTGCTAAATCTT
Found at i:3782845 original size:144 final size:144
Alignment explanation
Indices: 3782669--3783798 Score: 1295
Period size: 144 Copynumber: 7.8 Consensus size: 144
3782659 CAGTTGAAGG
* * * * * *
3782669 AAAGAGAAAGAGAAGACAAATTACTTAGATTTCCTAAAGAATGTGGAATAACACC-GTTTATGAT
1 AAAGACAAAGATAAGACAAATTACTCAAATTTCCTAAAGAATGAGGAATAACACCAG-TTAAGAT
* * *
3782733 ATTATTTGACAAGTCGAGAAGTTGTAGAGATCTCAGAAGTCCAATTTCCTGAGGTATGAAACCCG
65 ATTATTTGACAAGTCAAGAAGTTGTAGAGATCTCAGAAGTCCAATTTCTTGGGGTATGAAACCCG
3782798 AGATCTTGTTGCCCC
130 AGATCTTGTTGCCCC
* *
3782813 AAAGATAAAGATAAGACAAATTACTCAAATTTCCTAAAGAATGTGGAATAACACCAGTTAAGATA
1 AAAGACAAAGATAAGACAAATTACTCAAATTTCCTAAAGAATGAGGAATAACACCAGTTAAGATA
* * *
3782878 TTATGTGACAAGTCAAGAAGTTGTAGAGATCTCATAAATCCAATTTCTTGGGGTATGAAACCCGA
66 TTATTTGACAAGTCAAGAAGTTGTAGAGATCTCAGAAGTCCAATTTCTTGGGGTATGAAACCCGA
3782943 GATCTTGTTGCCCC
131 GATCTTGTTGCCCC
* * * * * * *
3782957 AAAAATAAAGATAAGACAAATTGCTCAAATTT-TTGAGAGAATGAGGAATAACACCGGTTAACAT
1 AAAGACAAAGATAAGACAAATTACTCAAATTTCCT-AAAGAATGAGGAATAACACCAGTTAAGAT
* ** * * * * * **
3783021 ATTATCTCCCAAGCCAAG-CGTTCGTAGAGATCTTAGAAGTCCAATTTCATGGGGGATGCTACCC
65 ATTATTTGACAAGTCAAGAAGTT-GTAGAGATCTCAGAAGTCCAATTTCTTGGGGTATGAAACCC
* *
3783085 GAGATTTTGTTACCCC
129 GAGATCTTGTTGCCCC
* * * * *
3783101 GAAGACCAAGAAAAGACAAATTACTCAAATTTCCTAAAGAATGTGGAATAACACCAGTTAAGGTA
1 AAAGACAAAGATAAGACAAATTACTCAAATTTCCTAAAGAATGAGGAATAACACCAGTTAAGATA
* *
3783166 TTATTTGACAAGTCAAGAAGTTGTAGAGATCTCATAAATCCAATTTCTTGGGGTATGAAACCCGA
66 TTATTTGACAAGTCAAGAAGTTGTAGAGATCTCAGAAGTCCAATTTCTTGGGGTATGAAACCCGA
3783231 GATCTTGTTGCCCC
131 GATCTTGTTGCCCC
* * * *
3783245 AAA-AAAGGAAGATAAGACAAATTACTCAAATTT-CTGAGAGAATGAGGAATAACACCGGTTAAC
1 AAAGACA--AAGATAAGACAAATTACTCAAATTTCCT-AAAGAATGAGGAATAACACCAGTTAAG
* ** * * * * * **
3783308 ATATTATCTCCCAAGCCAAG-CGTTCGTAGAGATCTTAGAAGTCCAATTTCATGGGGGATGCTAC
63 ATATTATTTGACAAGTCAAGAAGTT-GTAGAGATCTCAGAAGTCCAATTTCTTGGGGTATGAAAC
* *
3783372 CCGAGATTTTGTTACCCC
127 CCGAGATCTTGTTGCCCC
* * * * * *
3783390 GAAGACCAAGAAAAGACAAATTACTTAAATTTCCTAAAGAATGTGGAATAACACCAGTTAAGGTA
1 AAAGACAAAGATAAGACAAATTACTCAAATTTCCTAAAGAATGAGGAATAACACCAGTTAAGATA
* **
3783455 TTATTTGACAAGTCAAGAAGTTGTAGAGATCTCATAAACCCAATTTCTTGGGGTATGAAACCCGA
66 TTATTTGACAAGTCAAGAAGTTGTAGAGATCTCAGAAGTCCAATTTCTTGGGGTATGAAACCCGA
3783520 GATCTTGTTGCCCC
131 GATCTTGTTGCCCC
* * * * *
3783534 AAAAATAAAGATAAGACAAATTACTCAAATTT-CTGAGAGAATGAGGAATAACACCGGTTAACAT
1 AAAGACAAAGATAAGACAAATTACTCAAATTTCCT-AAAGAATGAGGAATAACACCAGTTAAGAT
* ** * * * * **
3783598 ATTATCTCCCAAGCCAAG-CGTTCGTAGAGATCTTAGAAGTCCAATTTCTTGGGGGATGCTACCC
65 ATTATTTGACAAGTCAAGAAGTT-GTAGAGATCTCAGAAGTCCAATTTCTTGGGGTATGAAACCC
* *
3783662 GAGATTTTGTTACCCC
129 GAGATCTTGTTGCCCC
* * * * * * * *
3783678 GAAGACCAAGAAAAGACAAATTACTTAAATTTCCCAAAGAACGAGGAAGAACACCAGTTAAGGTA
1 AAAGACAAAGATAAGACAAATTACTCAAATTTCCTAAAGAATGAGGAATAACACCAGTTAAGATA
* * *
3783743 TTATTTGACAAGTCAAGAAGTTTTAGAGATGTTAGAAGTCCAATTTCTTGGGGTAT
66 TTATTTGACAAGTCAAGAAGTTGTAGAGATCTCAGAAGTCCAATTTCTTGGGGTAT
3783799 TTTACCATAG
Statistics
Matches: 818, Mismatches: 152, Indels: 32
0.82 0.15 0.03
Matches are distributed among these distances:
143 10 0.01
144 681 0.83
145 126 0.15
146 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.26
Consensus pattern (144 bp):
AAAGACAAAGATAAGACAAATTACTCAAATTTCCTAAAGAATGAGGAATAACACCAGTTAAGATA
TTATTTGACAAGTCAAGAAGTTGTAGAGATCTCAGAAGTCCAATTTCTTGGGGTATGAAACCCGA
GATCTTGTTGCCCC
Found at i:3783787 original size:577 final size:577
Alignment explanation
Indices: 3782676--3783798 Score: 1827
Period size: 577 Copynumber: 1.9 Consensus size: 577
3782666 AGGAAAGAGA
* * * * ** * *
3782676 AAGAGAAGACAAATTACTTAGATTTCCTAAAGAATGTGGAATAACACCGTTTATGATATTATTTG
1 AAGAGAAGACAAATTACTCAAATTTCCTAAAGAATGAGGAATAACACCGGTTAACATATTATCTC
* * * *
3782741 ACAAGTCGAGAAGTTGTAGAGATCTCAGAAGTCCAATTTCCTGAGGTATGAAACCCGAGATCTTG
66 ACAAGCCAAGAAGTTGTAGAGATCTCAGAAGTCCAATTTCATGAGGGATGAAACCCGAGATCTTG
* * *
3782806 TTGCCCCAAAGATAAAGATAAGACAAATTACTCAAATTTCCTAAAGAATGTGGAATAACACCAGT
131 TTACCCCAAAGACAAAGAAAAGACAAATTACTCAAATTTCCTAAAGAATGTGGAATAACACCAGT
*
3782871 TAAGATATTATGTGACAAGTCAAGAAGTTGTAGAGATCTCATAAATCCAATTTCTTGGGGTATGA
196 TAAGATATTATGTGACAAGTCAAGAAGTTGTAGAGATCTCATAAACCCAATTTCTTGGGGTATGA
* *
3782936 AACCCGAGATCTTGTTGCCCCAAAAATAAAGATAAGACAAATTGCTCAAATTTTTGAGAGAATGA
261 AACCCGAGATCTTGTTGCCCCAAAAATAAAGATAAGACAAATTACTCAAATTTCTGAGAGAATGA
3783001 GGAATAACACCGGTTAACATATTATCTCCCAAGCCAAGCGTTCGTAGAGATCTTAGAAGTCCAAT
326 GGAATAACACCGGTTAACATATTATCTCCCAAGCCAAGCGTTCGTAGAGATCTTAGAAGTCCAAT
3783066 TTCATGGGGGATGCTACCCGAGATTTTGTTACCCCGAAGACCAAGAAAAGACAAATTACTCAAAT
391 TTCATGGGGGATGCTACCCGAGATTTTGTTACCCCGAAGACCAAGAAAAGACAAATTACTCAAAT
* * * *
3783131 TTCCTAAAGAATGTGGAATAACACCAGTTAAGGTATTATTTGACAAGTCAAGAAGTTGTAGAGAT
456 TTCCCAAAGAACGAGGAAGAACACCAGTTAAGGTATTATTTGACAAGTCAAGAAGTTGTAGAGAT
*
3783196 CTCATAAATCCAATTTCTTGGGGTATGAAACCCGAGATCTTGTTGCCCCAAAAAAGG
521 CTCAGAAATCCAATTTCTTGGGGTATGAAACCCGAGATCTTGTTGCCCCAAAAAAGG
* *
3783253 AAGATAAGACAAATTACTCAAATTT-CTGAGAGAATGAGGAATAACACCGGTTAACATATTATCT
1 AAGAGAAGACAAATTACTCAAATTTCCT-AAAGAATGAGGAATAACACCGGTTAACATATTATCT
* * * * ** *
3783317 CCCAAGCCAAG-CGTTCGTAGAGATCTTAGAAGTCCAATTTCATGGGGGATGCTACCCGAGATTT
65 CACAAGCCAAGAAGTT-GTAGAGATCTCAGAAGTCCAATTTCATGAGGGATGAAACCCGAGATCT
* * *
3783381 TGTTACCCCGAAGACCAAGAAAAGACAAATTACTTAAATTTCCTAAAGAATGTGGAATAACACCA
129 TGTTACCCCAAAGACAAAGAAAAGACAAATTACTCAAATTTCCTAAAGAATGTGGAATAACACCA
* *
3783446 GTTAAGGTATTATTTGACAAGTCAAGAAGTTGTAGAGATCTCATAAACCCAATTTCTTGGGGTAT
194 GTTAAGATATTATGTGACAAGTCAAGAAGTTGTAGAGATCTCATAAACCCAATTTCTTGGGGTAT
3783511 GAAACCCGAGATCTTGTTGCCCCAAAAATAAAGATAAGACAAATTACTCAAATTTCTGAGAGAAT
259 GAAACCCGAGATCTTGTTGCCCCAAAAATAAAGATAAGACAAATTACTCAAATTTCTGAGAGAAT
3783576 GAGGAATAACACCGGTTAACATATTATCTCCCAAGCCAAGCGTTCGTAGAGATCTTAGAAGTCCA
324 GAGGAATAACACCGGTTAACATATTATCTCCCAAGCCAAGCGTTCGTAGAGATCTTAGAAGTCCA
* *
3783641 ATTTCTTGGGGGATGCTACCCGAGATTTTGTTACCCCGAAGACCAAGAAAAGACAAATTACTTAA
389 ATTTCATGGGGGATGCTACCCGAGATTTTGTTACCCCGAAGACCAAGAAAAGACAAATTACTCAA
*
3783706 ATTTCCCAAAGAACGAGGAAGAACACCAGTTAAGGTATTATTTGACAAGTCAAGAAGTTTTAGAG
454 ATTTCCCAAAGAACGAGGAAGAACACCAGTTAAGGTATTATTTGACAAGTCAAGAAGTTGTAGAG
* * *
3783771 ATGTTAGAAGTCCAATTTCTTGGGGTAT
519 ATCTCAGAAATCCAATTTCTTGGGGTAT
3783799 TTTACCATAG
Statistics
Matches: 501, Mismatches: 43, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
576 5 0.01
577 496 0.99
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.26
Consensus pattern (577 bp):
AAGAGAAGACAAATTACTCAAATTTCCTAAAGAATGAGGAATAACACCGGTTAACATATTATCTC
ACAAGCCAAGAAGTTGTAGAGATCTCAGAAGTCCAATTTCATGAGGGATGAAACCCGAGATCTTG
TTACCCCAAAGACAAAGAAAAGACAAATTACTCAAATTTCCTAAAGAATGTGGAATAACACCAGT
TAAGATATTATGTGACAAGTCAAGAAGTTGTAGAGATCTCATAAACCCAATTTCTTGGGGTATGA
AACCCGAGATCTTGTTGCCCCAAAAATAAAGATAAGACAAATTACTCAAATTTCTGAGAGAATGA
GGAATAACACCGGTTAACATATTATCTCCCAAGCCAAGCGTTCGTAGAGATCTTAGAAGTCCAAT
TTCATGGGGGATGCTACCCGAGATTTTGTTACCCCGAAGACCAAGAAAAGACAAATTACTCAAAT
TTCCCAAAGAACGAGGAAGAACACCAGTTAAGGTATTATTTGACAAGTCAAGAAGTTGTAGAGAT
CTCAGAAATCCAATTTCTTGGGGTATGAAACCCGAGATCTTGTTGCCCCAAAAAAGG
Found at i:3783843 original size:288 final size:288
Alignment explanation
Indices: 3782675--3783798 Score: 1804
Period size: 288 Copynumber: 3.9 Consensus size: 288
3782665 AAGGAAAGAG
* * * * * * ** *
3782675 AAAGAGAAGACAAATTACTTAGATTTCCT-AAAGAATGTGGAATAACACCGTTTATGATATTATT
1 AAAGATAAGACAAATTACTCAAATTT-CTGAGAGAATGAGGAATAACACCGGTTAACATATTATC
** * * * * * * * ** *
3782739 TGACAAGTCGAGAAGTT-GTAGAGATCTCAGAAGTCCAATTTCCTGAGGTATGAAACCCGAGATC
65 TCCCAAGCCAAG-CGTTCGTAGAGATCTTAGAAGTCCAATTTCATGGGGGATGCTACCCGAGATT
* * ** *
3782803 TTGTTGCCCCAAAGATAAAGATAAGACAAATTACTCAAATTTCCTAAAGAATGTGGAATAACACC
129 TTGTTACCCCGAAGACCAAGAAAAGACAAATTACTCAAATTTCCTAAAGAATGTGGAATAACACC
* *
3782868 AGTTAAGATATTATGTGACAAGTCAAGAAGTTGTAGAGATCTCATAAATCCAATTTCTTGGGGTA
194 AGTTAAGGTATTATTTGACAAGTCAAGAAGTTGTAGAGATCTCATAAATCCAATTTCTTGGGGTA
3782933 TGAAACCCGAGATCTTGTTGCCCCAAAAAT
259 TGAAACCCGAGATCTTGTTGCCCCAAAAAT
* *
3782963 AAAGATAAGACAAATTGCTCAAATTTTTGAGAGAATGAGGAATAACACCGGTTAACATATTATCT
1 AAAGATAAGACAAATTACTCAAATTTCTGAGAGAATGAGGAATAACACCGGTTAACATATTATCT
3783028 CCCAAGCCAAGCGTTCGTAGAGATCTTAGAAGTCCAATTTCATGGGGGATGCTACCCGAGATTTT
66 CCCAAGCCAAGCGTTCGTAGAGATCTTAGAAGTCCAATTTCATGGGGGATGCTACCCGAGATTTT
3783093 GTTACCCCGAAGACCAAGAAAAGACAAATTACTCAAATTTCCTAAAGAATGTGGAATAACACCAG
131 GTTACCCCGAAGACCAAGAAAAGACAAATTACTCAAATTTCCTAAAGAATGTGGAATAACACCAG
3783158 TTAAGGTATTATTTGACAAGTCAAGAAGTTGTAGAGATCTCATAAATCCAATTTCTTGGGGTATG
196 TTAAGGTATTATTTGACAAGTCAAGAAGTTGTAGAGATCTCATAAATCCAATTTCTTGGGGTATG
3783223 AAACCCGAGATCTTGTTGCCCCAAAAA-
261 AAACCCGAGATCTTGTTGCCCCAAAAAT
3783250 AGGAAGATAAGACAAATTACTCAAATTTCTGAGAGAATGAGGAATAACACCGGTTAACATATTAT
1 A--AAGATAAGACAAATTACTCAAATTTCTGAGAGAATGAGGAATAACACCGGTTAACATATTAT
3783315 CTCCCAAGCCAAGCGTTCGTAGAGATCTTAGAAGTCCAATTTCATGGGGGATGCTACCCGAGATT
64 CTCCCAAGCCAAGCGTTCGTAGAGATCTTAGAAGTCCAATTTCATGGGGGATGCTACCCGAGATT
*
3783380 TTGTTACCCCGAAGACCAAGAAAAGACAAATTACTTAAATTTCCTAAAGAATGTGGAATAACACC
129 TTGTTACCCCGAAGACCAAGAAAAGACAAATTACTCAAATTTCCTAAAGAATGTGGAATAACACC
*
3783445 AGTTAAGGTATTATTTGACAAGTCAAGAAGTTGTAGAGATCTCATAAACCCAATTTCTTGGGGTA
194 AGTTAAGGTATTATTTGACAAGTCAAGAAGTTGTAGAGATCTCATAAATCCAATTTCTTGGGGTA
3783510 TGAAACCCGAGATCTTGTTGCCCCAAAAAT
259 TGAAACCCGAGATCTTGTTGCCCCAAAAAT
3783540 AAAGATAAGACAAATTACTCAAATTTCTGAGAGAATGAGGAATAACACCGGTTAACATATTATCT
1 AAAGATAAGACAAATTACTCAAATTTCTGAGAGAATGAGGAATAACACCGGTTAACATATTATCT
*
3783605 CCCAAGCCAAGCGTTCGTAGAGATCTTAGAAGTCCAATTTCTTGGGGGATGCTACCCGAGATTTT
66 CCCAAGCCAAGCGTTCGTAGAGATCTTAGAAGTCCAATTTCATGGGGGATGCTACCCGAGATTTT
* * * * *
3783670 GTTACCCCGAAGACCAAGAAAAGACAAATTACTTAAATTTCCCAAAGAACGAGGAAGAACACCAG
131 GTTACCCCGAAGACCAAGAAAAGACAAATTACTCAAATTTCCTAAAGAATGTGGAATAACACCAG
* * * * *
3783735 TTAAGGTATTATTTGACAAGTCAAGAAGTTTTAGAGATGTTAGAAGTCCAATTTCTTGGGGTAT
196 TTAAGGTATTATTTGACAAGTCAAGAAGTTGTAGAGATCTCATAAATCCAATTTCTTGGGGTAT
3783799 TTTACCATAG
Statistics
Matches: 786, Mismatches: 45, Indels: 10
0.93 0.05 0.01
Matches are distributed among these distances:
287 5 0.01
288 498 0.63
289 282 0.36
290 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.26
Consensus pattern (288 bp):
AAAGATAAGACAAATTACTCAAATTTCTGAGAGAATGAGGAATAACACCGGTTAACATATTATCT
CCCAAGCCAAGCGTTCGTAGAGATCTTAGAAGTCCAATTTCATGGGGGATGCTACCCGAGATTTT
GTTACCCCGAAGACCAAGAAAAGACAAATTACTCAAATTTCCTAAAGAATGTGGAATAACACCAG
TTAAGGTATTATTTGACAAGTCAAGAAGTTGTAGAGATCTCATAAATCCAATTTCTTGGGGTATG
AAACCCGAGATCTTGTTGCCCCAAAAAT
Found at i:3786389 original size:2 final size:2
Alignment explanation
Indices: 3786355--3786381 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3786345 AAATATCGAG
3786355 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 T
3786382 GCATATATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3786617 original size:105 final size:104
Alignment explanation
Indices: 3786503--3786705 Score: 397
Period size: 105 Copynumber: 1.9 Consensus size: 104
3786493 TAAATTAAAT
3786503 TATTGACTAATTTTTATTTGGGTACTTTTCATATATGGGCTCCATGCATAAGGCGTTTATAAGAA
1 TATTGACTAATTTTTATTTGGGTACTTTTCATATATGGGCTCCATGCATAAGGCGTTTATAAGAA
3786568 TAGGTCTCCCCATAATTTTAACTGTTTTTTATTNTTCAAG
66 TAGGTCTCCCCATAATTTTAACTGTTTTTTATT-TTCAAG
3786608 TATTGACTAATTTTTATTTGGGTACTTTTCATATATGGGCTCCATGCATAAGGCGTTTATAAGAA
1 TATTGACTAATTTTTATTTGGGTACTTTTCATATATGGGCTCCATGCATAAGGCGTTTATAAGAA
3786673 TAGGTCTCCCCATAATTTTAACTGTTTTTTATT
66 TAGGTCTCCCCATAATTTTAACTGTTTTTTATT
3786706 CAAGAGAAAT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.44
Consensus pattern (104 bp):
TATTGACTAATTTTTATTTGGGTACTTTTCATATATGGGCTCCATGCATAAGGCGTTTATAAGAA
TAGGTCTCCCCATAATTTTAACTGTTTTTTATTTTCAAG
Found at i:3787327 original size:23 final size:23
Alignment explanation
Indices: 3787273--3787328 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
3787263 TTGTTCTTAG
*
3787273 CATTACATGACATGTTTAAAGAT
1 CATTACGTGACATGTTTAAAGAT
* * *
3787296 CATTGCGTGACTTGTTTATAGAT
1 CATTACGTGACATGTTTAAAGAT
3787319 CATTACGTGA
1 CATTACGTGA
3787329 TTTAATGTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (23 bp):
CATTACGTGACATGTTTAAAGAT
Found at i:3791221 original size:23 final size:23
Alignment explanation
Indices: 3791190--3791261 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
3791180 AGTTGATATT
3791190 GAATTGCGTGAATGGTGGAGATG
1 GAATTGCGTGAATGGTGGAGATG
* * *** * * *
3791213 GAATGGCGTCACCAGTTGATATT
1 GAATTGCGTGAATGGTGGAGATG
3791236 GAATTGCGTGAATGGTGGAGATG
1 GAATTGCGTGAATGGTGGAGATG
3791259 GAA
1 GAA
3791262 AGTAATTAAT
Statistics
Matches: 33, Mismatches: 16, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.08, G:0.38, T:0.26
Consensus pattern (23 bp):
GAATTGCGTGAATGGTGGAGATG
Found at i:3791290 original size:23 final size:23
Alignment explanation
Indices: 3791264--3791331 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
3791254 AGATGGAAAG
3791264 TAATTAATATGGAATCGAGTGAC
1 TAATTAATATGGAATCGAGTGAC
** * * *
3791287 TAATCGATTTGGAATGGCGTGAC
1 TAATTAATATGGAATCGAGTGAC
*
3791310 T-ATTAAATATGGAATCGTGTGA
1 TAATT-AATATGGAATCGAGTGA
3791332 ACCGTTAAGA
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
22 2 0.06
23 32 0.94
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.32
Consensus pattern (23 bp):
TAATTAATATGGAATCGAGTGAC
Found at i:3791430 original size:23 final size:23
Alignment explanation
Indices: 3791404--3791454 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
3791394 GTGCCGTTAG
*
3791404 TAGTTATTATGGAATTGCG-TGAC
1 TAGTTATTATGGAATCGCGCT-AC
3791427 TAGTTATTATGGAATCGCGCTAC
1 TAGTTATTATGGAATCGCGCTAC
3791450 TAGTT
1 TAGTT
3791455 GATATATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (23 bp):
TAGTTATTATGGAATCGCGCTAC
Found at i:3791634 original size:61 final size:60
Alignment explanation
Indices: 3791455--3791641 Score: 275
Period size: 61 Copynumber: 3.1 Consensus size: 60
3791445 GCTACTAGTT
* * *
3791455 GATATATTTAAAATCTATCGATAGATATTTCGAATGCTTGGAAGATGTAACGGTAACTAC
1 GATATATTTAAAATCTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTAGCTTC
* *
3791515 TGATATATTTAAAATCCATCGATAGATATTTTGAATGCTTGGAAGATGAAACGGTAGCTGTC
1 -GATATATTTAAAATCTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTAGCT-TC
* * *
3791577 GATATATTTAAAATCTATCAATAGATATTTCGAATGCTTGGAAAATGAAACGATAGCTATC
1 GATATATTTAAAATCTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTAGCT-TC
3791638 GATA
1 GATA
3791642 GATATTTCGA
Statistics
Matches: 114, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
61 113 0.99
62 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.33
Consensus pattern (60 bp):
GATATATTTAAAATCTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTAGCTTC
Found at i:3791658 original size:103 final size:103
Alignment explanation
Indices: 3791532--3791744 Score: 320
Period size: 103 Copynumber: 2.1 Consensus size: 103
3791522 TTTAAAATCC
* * *
3791532 ATCGATAGATATTTTGAATGCTTGGAAGATGAAACGGTAGCTGTCGATA-TATTTAAAATCTATC
1 ATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGCAGCTATCGATACT-TTTAAAATCTATC
*
3791596 AATAGATATTTCGAATGCTTGGAAAATGAAACGATAGCT
65 AATAGATATTTCGAATGCTTAGAAAATGAAACGATAGCT
* * * *
3791635 ATCGATAGATATTTCGAATGCTTGTAAGATGAAAGGGCATCTATCGATACTTTTAAAATCTATCG
1 ATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGCAGCTATCGATACTTTTAAAATCTATCA
* *
3791700 ATAGATATTTCGAATGCTTAGAAGATGAAACGGTAGCT
66 ATAGATATTTCGAATGCTTAGAAAATGAAACGATAGCT
3791738 ATCGATA
1 ATCGATA
3791745 TATTTAAAAT
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
103 98 0.99
104 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (103 bp):
ATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGCAGCTATCGATACTTTTAAAATCTATCA
ATAGATATTTCGAATGCTTAGAAAATGAAACGATAGCT
Found at i:3791679 original size:42 final size:42
Alignment explanation
Indices: 3791589--3791683 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
3791579 TATATTTAAA
* *
3791589 ATCTATCAATAGATATTTCGAATGCTTGGAAAATGAAACGAT
1 ATCTATCGATAGATATTTCGAATGCTTGGAAAATGAAACGAC
* * * * *
3791631 AGCTATCGATAGATATTTCGAATGCTTGTAAGATGAAAGGGC
1 ATCTATCGATAGATATTTCGAATGCTTGGAAAATGAAACGAC
3791673 ATCTATCGATA
1 ATCTATCGATA
3791684 CTTTTAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (42 bp):
ATCTATCGATAGATATTTCGAATGCTTGGAAAATGAAACGAC
Found at i:3791698 original size:61 final size:61
Alignment explanation
Indices: 3791633--3792075 Score: 672
Period size: 61 Copynumber: 7.3 Consensus size: 61
3791623 GAAACGATAG
* * * *
3791633 CTATCGATAGATATTTCGAATGCTTGTAAGATGAAAGGGCATCTATCGATACT-TTTAAAAT
1 CTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTAACTATCGATA-TATTTAAAAT
* *
3791694 CTATCGATAGATATTTCGAATGCTTAGAAGATGAAACGGTAGCTATCGATATATTTAAAAT
1 CTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTAACTATCGATATATTTAAAAT
* * **
3791755 TTATTGATAGATATTTCGAATGCTTGGAAGATGAAACGACAACTATCGATATATTTAAAAT
1 CTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTAACTATCGATATATTTAAAAT
* * * *
3791816 TTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTATCTATCAATATATTTAAAAG
1 CTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTAACTATCGATATATTTAAAAT
* * * *
3791877 CTATCAATAGATATTTCGAATTCTTGGAAGATGAAACGGCAACTATCGATATATTTAAAAG
1 CTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTAACTATCGATATATTTAAAAT
*
3791938 CTATCGATAGATATTTCGAATGCTTGGAAGATGAAACAGTAACTATCGATATATTTAAAAT
1 CTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTAACTATCGATATATTTAAAAT
** *
3791999 CTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTATTTATCGATATATTTAGAAT
1 CTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTAACTATCGATATATTTAAAAT
3792060 CTATCGATAGATATTT
1 CTATCGATAGATATTT
3792076 TGCTCATAGA
Statistics
Matches: 349, Mismatches: 32, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
60 1 0.00
61 348 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (61 bp):
CTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGTAACTATCGATATATTTAAAAT
Found at i:3791745 original size:164 final size:164
Alignment explanation
Indices: 3791469--3791805 Score: 507
Period size: 164 Copynumber: 2.1 Consensus size: 164
3791459 TATTTAAAAT
* *
3791469 CTATCGATAGATATTTCGAATGCTTGGAAGATGTAACGGTAACTACTGATATATTTAAAATCCAT
1 CTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGCAACTACTGATATATTTAAAATCCAT
* * *
3791534 CGATAGATATTTTGAATGCTTGGAAGATGAAACGGTAGCTGTCGATATATTTAAAATCTATCAAT
66 CGATAGATATTTCGAATGCTTAGAAGATGAAACGGTAGCTATCGATATATTTAAAATCTATCAAT
* *
3791599 AGATATTTCGAATGCTTGGAAAATGAAACGATAG
131 AGATATTTCGAATGCTTGGAAAATGAAACGACAA
* * * *
3791633 CTATCGATAGATATTTCGAATGCTTGTAAGATGAAAGGGCATCTA-TCGATACT-TTTAAAATCT
1 CTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGCAACTACT-GATA-TATTTAAAATCC
* **
3791696 ATCGATAGATATTTCGAATGCTTAGAAGATGAAACGGTAGCTATCGATATATTTAAAATTTATTG
64 ATCGATAGATATTTCGAATGCTTAGAAGATGAAACGGTAGCTATCGATATATTTAAAATCTATCA
*
3791761 ATAGATATTTCGAATGCTTGGAAGATGAAACGACAA
129 ATAGATATTTCGAATGCTTGGAAAATGAAACGACAA
3791797 CTATCGATA
1 CTATCGATA
3791806 TATTTAAAAT
Statistics
Matches: 156, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
163 1 0.01
164 154 0.99
165 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (164 bp):
CTATCGATAGATATTTCGAATGCTTGGAAGATGAAACGGCAACTACTGATATATTTAAAATCCAT
CGATAGATATTTCGAATGCTTAGAAGATGAAACGGTAGCTATCGATATATTTAAAATCTATCAAT
AGATATTTCGAATGCTTGGAAAATGAAACGACAA
Found at i:3798106 original size:21 final size:24
Alignment explanation
Indices: 3798081--3798127 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
3798071 TAAACATCAT
3798081 TTTTTATTT-TATTATAT-TTTTG
1 TTTTTATTTATATTATATGTTTTG
*
3798103 TTTTTATTTATTTTATATGTTTTG
1 TTTTTATTTATATTATATGTTTTG
3798127 T
1 T
3798128 GGGATCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.41
23 7 0.32
24 6 0.27
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (24 bp):
TTTTTATTTATATTATATGTTTTG
Found at i:3799474 original size:2 final size:2
Alignment explanation
Indices: 3799467--3799491 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3799457 AAAGCTTAAT
3799467 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
3799492 TATATAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3800341 original size:11 final size:11
Alignment explanation
Indices: 3800321--3800359 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3800311 GATTCATAAA
*
3800321 AAAAAAATTTT
1 AAAAAAATTTC
*
3800332 AAAAACATTTC
1 AAAAAAATTTC
*
3800343 AAAAAAAATTC
1 AAAAAAATTTC
3800354 AAAAAA
1 AAAAAA
3800360 GAAGTGGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAAAATTTC
Done.