Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold133
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: 2564099
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17052 characters in sequence are not A, C, G, or T
File 12 of 17
Found at i:1573213 original size:2 final size:2
Alignment explanation
Indices: 1573206--1573251 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1573196 AACGTGGCCA
1573206 AT AT AT AT 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 AT AT AT AT
1573248 AT AT
1 AT AT
1573252 TAATTAATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1575763 original size:19 final size:20
Alignment explanation
Indices: 1575715--1575763 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
1575705 AAATTTTCCA
*
1575715 ATTT-AAGAAAATAAATATT
1 ATTTAAAGAAAATAAATAAT
*
1575734 ATTTATA-AAAAT-AATAAT
1 ATTTAAAGAAAATAAATAAT
1575752 ATTTAAAGAAAA
1 ATTTAAAGAAAA
1575764 AATTAAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 11 0.44
19 13 0.52
20 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
ATTTAAAGAAAATAAATAAT
Found at i:1579942 original size:16 final size:17
Alignment explanation
Indices: 1579921--1579958 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
1579911 ATTATCAATT
1579921 TTTGAC-AAAAGTATTA
1 TTTGACAAAAAGTATTA
1579937 TTTGACATAAAAAGTATTA
1 TTTGAC--AAAAAGTATTA
1579956 TTT
1 TTT
1579959 TTATTCACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
19 13 0.68
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (17 bp):
TTTGACAAAAAGTATTA
Found at i:1582847 original size:21 final size:21
Alignment explanation
Indices: 1582823--1582864 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1582813 AATTTTATTT
1582823 AATATTAAAATTATTT-TTTAA
1 AATATTAAAATT-TTTGTTTAA
*
1582844 AATATTTAAATTTTTGTTTAA
1 AATATTAAAATTTTTGTTTAA
1582865 TTAAATAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
AATATTAAAATTTTTGTTTAA
Found at i:1584207 original size:20 final size:20
Alignment explanation
Indices: 1584184--1584255 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
1584174 ATTTAATATT
1584184 TATTAATTATTAAAATTATA
1 TATTAATTATTAAAATTATA
* * *
1584204 TATTTACTATTACAATTATA
1 TATTAATTATTAAAATTATA
*
1584224 TATTTAATGT-TTAAATATTTTA
1 TA-TTAAT-TATTAAA-ATTATA
1584246 TAATTAATTA
1 T-ATTAATTA
1584256 ATCAATTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
20 19 0.47
21 8 0.20
22 12 0.30
23 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (20 bp):
TATTAATTATTAAAATTATA
Found at i:1584434 original size:3 final size:3
Alignment explanation
Indices: 1584428--1584471 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
1584418 AAATTAGGGT
* * * *
1584428 TTA TTA TTA TTA GTA TTA TTA TTA TCA TTA TCA TTA TCA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1584472 TTTCTGGTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1584457 original size:12 final size:12
Alignment explanation
Indices: 1584430--1584471 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
1584420 ATTAGGGTTT
1584430 ATTATTATTAGT-
1 ATTATTATTA-TC
1584442 ATTATTATTATC
1 ATTATTATTATC
*
1584454 ATTATCATTATC
1 ATTATTATTATC
1584466 ATTATT
1 ATTATT
1584472 TTTCTGGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 1 0.04
12 26 0.96
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:1590155 original size:15 final size:15
Alignment explanation
Indices: 1590132--1590161 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1590122 ACTCACTTTC
1590132 TTTTCCCTTTTTTTT
1 TTTTCCCTTTTTTTT
*
1590147 TTTTTCCTTTTTTTT
1 TTTTCCCTTTTTTTT
1590162 GAACGTCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCCCTTTTTTTT
Found at i:1590419 original size:17 final size:18
Alignment explanation
Indices: 1590394--1590427 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1590384 ATTTAATTAA
1590394 TAATAATTTA-TTATTTT
1 TAATAATTTATTTATTTT
*
1590411 TAATTATTTATTTATTT
1 TAATAATTTATTTATTT
1590428 ATGTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TAATAATTTATTTATTTT
Found at i:1590440 original size:21 final size:21
Alignment explanation
Indices: 1590390--1590440 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
1590380 TTAAATTTAA
* *
1590390 TTAATAA-TAATTTATTATTT
1 TTAATAATTTATTTATTATGT
*
1590410 TTAATTATTTATTTATTTATGT
1 TTAATAATTTATTTA-TTATGT
1590432 TTAA-AATTT
1 TTAATAATTT
1590441 TTAAATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 6 0.24
21 10 0.40
22 9 0.36
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTAATAATTTATTTATTATGT
Found at i:1590689 original size:2 final size:2
Alignment explanation
Indices: 1590677--1590723 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
1590667 TACTTTAATC
* *
1590677 AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1590718 AA AT AT
1 AT AT AT
1590724 TTTTAAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1591268 original size:7 final size:7
Alignment explanation
Indices: 1591258--1591286 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1591248 TTTTTTGCTT
1591258 TTTGTTC
1 TTTGTTC
1591265 TTTGTTC
1 TTTGTTC
1591272 TTTGTTC
1 TTTGTTC
1591279 TTT-TTC
1 TTTGTTC
1591285 TT
1 TT
1591287 CATATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (7 bp):
TTTGTTC
Found at i:1591962 original size:16 final size:18
Alignment explanation
Indices: 1591928--1591971 Score: 67
Period size: 16 Copynumber: 2.6 Consensus size: 18
1591918 TTTAAATTAT
1591928 TATTTTTAATAATAAAAA
1 TATTTTTAATAATAAAAA
1591946 TATTTTT-ATAA-AAAAA
1 TATTTTTAATAATAAAAA
1591962 TA-TTTTAATA
1 TATTTTTAATA
1591972 TTATTATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.16
16 10 0.40
17 4 0.16
18 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTTTTAATAATAAAAA
Found at i:1593809 original size:2 final size:2
Alignment explanation
Indices: 1593802--1593828 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1593792 TACACGCCAT
1593802 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1593829 TTAACTTCCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1594095 original size:25 final size:25
Alignment explanation
Indices: 1594067--1594123 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
1594057 TATTTTAATT
1594067 AAATATTTAATTTTT-TTAATATAAA
1 AAATATTTAATTTTTATTAATA-AAA
*
1594092 AAATATTTTATTTTTAAATTAATAAAA
1 AAATATTTAATTTTT--ATTAATAAAA
1594119 AAATA
1 AAATA
1594124 CTATAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 14 0.50
27 8 0.29
28 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATATTTAATTTTTATTAATAAAA
Found at i:1597938 original size:13 final size:13
Alignment explanation
Indices: 1597920--1597944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1597910 AGCATTGATC
1597920 AATTTTTTTTATT
1 AATTTTTTTTATT
1597933 AATTTTTTTTAT
1 AATTTTTTTTAT
1597945 CTAGTGGTAG
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
AATTTTTTTTATT
Found at i:1599879 original size:3 final size:3
Alignment explanation
Indices: 1599871--1599902 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1599861 TTTTGATGTG
*
1599871 GAA GAA GAA GAA GAA GAA GAA GAA GGA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1599903 GAGTTTGTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1600252 original size:28 final size:26
Alignment explanation
Indices: 1600221--1600283 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
1600211 CTTATATTTT
1600221 ATAATATTTTTATATAAATAAAATATGA
1 ATAATATTTTTA-ATAAA-AAAATATGA
*
1600249 ATAAT-TTTTTAATATAAAAATATGA
1 ATAATATTTTTAATAAAAAAATATGA
* *
1600274 AAAAAATTTT
1 ATAATATTTT
1600284 AAAGTAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 12 0.39
26 8 0.26
27 6 0.19
28 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (26 bp):
ATAATATTTTTAATAAAAAAATATGA
Found at i:1603038 original size:5 final size:5
Alignment explanation
Indices: 1603010--1603208 Score: 66
Period size: 5 Copynumber: 40.4 Consensus size: 5
1603000 TTTGAGTATG
* * *
1603010 ATATA ATTATA AGAT- ATA-A ATATA ATATA AAATA ATTAAA ATATA ATATAAA
1 ATATA A-TATA ATATA ATATA ATATA ATATA ATATA A-TATA ATATA ATAT--A
* * * * * *
1603062 ATATA ATATG ATATAA AAATA ATATA A-AT- ATTTAA ATATA TTA-A ATTTT
1 ATATA ATATA ATAT-A ATATA ATATA ATATA ATAT-A ATATA ATATA ATATA
* * * *
1603111 AT-TAA ATATA A-ATA AT-TA ATATA ATAAA AT-TT ATTTA A-ATT ATATA
1 ATAT-A ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* *
1603157 ATA-A AT-TAA ATATA ATTATA ATATA A-AAA TATATA ACTATG ATATA
1 ATATA ATAT-A ATATA A-TATA ATATA ATATA -ATATA A-TATA ATATA
1603203 A-ATA AT
1 ATATA AT
1603209 TATTTTTTAA
Statistics
Matches: 141, Mismatches: 28, Indels: 50
0.64 0.13 0.23
Matches are distributed among these distances:
3 1 0.01
4 32 0.23
5 76 0.54
6 27 0.19
7 5 0.04
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:1603086 original size:33 final size:35
Alignment explanation
Indices: 1603012--1603101 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 35
1603002 TGAGTATGAT
*
1603012 ATAATTATAAGATATAAATATAATATAAAATAATTA
1 ATAA-TATAAGATATAAATATAATATAAAATAATAA
* * *
1603048 A-AATATAATATA-AAATATAATATGATATAA-AA
1 ATAATATAAGATATAAATATAATATAAAATAATAA
1603080 ATAATATAA-ATATTTAAATATA
1 ATAATATAAGATA--TAAATATA
1603102 TTAAATTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
32 5 0.11
33 23 0.50
34 8 0.17
35 9 0.20
36 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (35 bp):
ATAATATAAGATATAAATATAATATAAAATAATAA
Found at i:1603144 original size:32 final size:34
Alignment explanation
Indices: 1603082--1603172 Score: 114
Period size: 33 Copynumber: 2.6 Consensus size: 34
1603072 ATATAAAAAT
* * *
1603082 AATATAAATATTTAAATATATTAAATTTTA-TTA
1 AATATAAATAATTAAATATAATAAAATTTATTTA
1603115 AATATAAATAATT-AATATAATAAAATTTATTTA
1 AATATAAATAATTAAATATAATAAAATTTATTTA
1603148 AATTATATAATAAATTAAATATAAT
1 AA-TATA-AAT-AATTAAATATAAT
1603173 TATAATATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
32 14 0.28
33 17 0.34
34 4 0.08
35 3 0.06
36 4 0.08
37 8 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
AATATAAATAATTAAATATAATAAAATTTATTTA
Found at i:1604856 original size:17 final size:18
Alignment explanation
Indices: 1604817--1604858 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1604807 TTTATTTATT
1604817 TATTTATTTGATATTTAA
1 TATTTATTTGATATTTAA
*
1604835 AATTT-TTTGATA-TTAA
1 TATTTATTTGATATTTAA
1604851 GTATTTAT
1 -TATTTAT
1604859 AGTTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 4 0.20
17 11 0.55
18 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
TATTTATTTGATATTTAA
Found at i:1605563 original size:2 final size:2
Alignment explanation
Indices: 1605556--1605581 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1605546 AATGATTTTA
1605556 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
1605582 GTTATGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1606077 original size:19 final size:17
Alignment explanation
Indices: 1606049--1606084 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
1606039 AATTTTGTCA
1606049 TTGTTTTTATATTATTTT
1 TTGTTTTTATATT-TTTT
1606067 TTGTATTTTATATTTTTT
1 TTGT-TTTTATATTTTTT
1606085 ATATGGACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (17 bp):
TTGTTTTTATATTTTTT
Found at i:1609799 original size:3 final size:3
Alignment explanation
Indices: 1609791--1609815 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1609781 TAAAAAGGGG
1609791 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1609816 AATATTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1610404 original size:12 final size:13
Alignment explanation
Indices: 1610389--1610425 Score: 53
Period size: 11 Copynumber: 3.1 Consensus size: 13
1610379 ATTTGTAAAA
1610389 ATTAATT-TTTTT
1 ATTAATTATTTTT
1610401 ATTAATTATTTTT
1 ATTAATTATTTTT
1610414 ATT--TTATTTTT
1 ATTAATTATTTTT
1610425 A
1 A
1610426 AATGATGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.38
12 7 0.29
13 8 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
ATTAATTATTTTT
Found at i:1610534 original size:10 final size:10
Alignment explanation
Indices: 1610521--1610553 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
1610511 TAAATAAATA
1610521 AATATAATTT
1 AATATAATTT
1610531 AATATAATTT
1 AATATAATTT
1610541 AATATAATTT
1 AATATAATTT
1610551 AAT
1 AAT
1610554 TTAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AATATAATTT
Found at i:1610537 original size:20 final size:20
Alignment explanation
Indices: 1610514--1610563 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1610504 ATTTAAATAA
1610514 ATAAATAAATATAATTTAAT
1 ATAAATAAATATAATTTAAT
* *
1610534 ATAATTTAATATAATTTAAT
1 ATAAATAAATATAATTTAAT
*
1610554 TTAAAATAAA
1 AT-AAATAAA
1610564 ATTTTTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAATAAATATAATTTAAT
Found at i:1613935 original size:9 final size:8
Alignment explanation
Indices: 1613906--1613967 Score: 63
Period size: 8 Copynumber: 7.4 Consensus size: 8
1613896 ACAATGAGGG
1613906 AAGAAGAAA
1 AAGAA-AAA
1613915 GAAGAAATAA
1 -AAGAAA-AA
*
1613925 AGGAAAAA
1 AAGAAAAA
1613933 AAG-AAAA
1 AAGAAAAA
1613940 AAGAAAATA
1 AAGAAAA-A
1613949 AAGAAAAA
1 AAGAAAAA
*
1613957 AAGAAAGA
1 AAGAAAAA
1613965 AAG
1 AAG
1613968 GAAACGGGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
7 7 0.15
8 18 0.39
9 14 0.30
10 7 0.15
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (8 bp):
AAGAAAAA
Found at i:1613943 original size:24 final size:24
Alignment explanation
Indices: 1613909--1613967 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 24
1613899 ATGAGGGAAG
*
1613909 AAGAAAGAAG-AAATAAAGGAAAAA
1 AAGAAAAAAGAAAATAAA-GAAAAA
1613933 AAGAAAAAAGAAAATAAAGAAAAA
1 AAGAAAAAAGAAAATAAAGAAAAA
1613957 AAGAAAGAAAG
1 AAGAAA-AAAG
1613968 GAAACGGGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 21 0.66
25 11 0.34
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (24 bp):
AAGAAAAAAGAAAATAAAGAAAAA
Found at i:1613960 original size:17 final size:16
Alignment explanation
Indices: 1613906--1613967 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 16
1613896 ACAATGAGGG
1613906 AAGAAGAAAGAAGAAATAA
1 AAGAA-AAA-AAGAAA-AA
*
1613925 AGGAAAAAAAG-AAAA
1 AAGAAAAAAAGAAAAA
1613940 AAGAAAATAAAGAAAAA
1 AAGAAAA-AAAGAAAAA
*
1613957 AAGAAAGAAAG
1 AAGAAAAAAAG
1613968 GAAACGGGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 8 0.21
16 10 0.26
17 13 0.34
18 3 0.08
19 4 0.11
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (16 bp):
AAGAAAAAAAGAAAAA
Found at i:1613965 original size:4 final size:4
Alignment explanation
Indices: 1613909--1613967 Score: 50
Period size: 4 Copynumber: 14.8 Consensus size: 4
1613899 ATGAGGGAAG
* * * *
1613909 AAGA AAG- AAGA AATA AAGGA AAAA AAGA AA-A AAGAA AATA AAGA AAAA
1 AAGA AAGA AAGA AAGA AA-GA AAGA AAGA AAGA AAG-A AAGA AAGA AAGA
1613957 AAGA AAGA AAG
1 AAGA AAGA AAG
1613968 GAAACGGGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
3 6 0.14
4 31 0.72
5 6 0.14
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (4 bp):
AAGA
Found at i:1617833 original size:15 final size:15
Alignment explanation
Indices: 1617813--1617842 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1617803 TCATTCAAGA
1617813 ACTTTCAAATTTCAG
1 ACTTTCAAATTTCAG
1617828 ACTTTCAAATTTCAG
1 ACTTTCAAATTTCAG
1617843 TTTGAAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
ACTTTCAAATTTCAG
Found at i:1623972 original size:27 final size:28
Alignment explanation
Indices: 1623929--1623982 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
1623919 ATGAGAGAAA
1623929 TTTATTTTATCATTTATAATTT-TTATT
1 TTTATTTTATCATTTATAATTTCTTATT
*
1623956 TTTATTTTAATCA-TTATTATTTCTTAT
1 TTTATTTT-ATCATTTATAATTTCTTAT
1623983 ACATATATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTATTTTATCATTTATAATTTCTTATT
Found at i:1624220 original size:20 final size:19
Alignment explanation
Indices: 1624172--1624230 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
1624162 TTTCTCTCCT
1624172 ATTTTTTTTATT--TTTTTC
1 ATTTTTTTT-TTCCTTTTTC
*
1624190 AATTTTTTTTTCCTTTTTC
1 ATTTTTTTTTTCCTTTTTC
* *
1624209 ATTTCTTTTTTTTCTCTTTC
1 ATTT-TTTTTTTCCTTTTTC
1624229 AT
1 AT
1624231 CCTTAAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 2 0.06
18 8 0.24
19 9 0.26
20 15 0.44
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (19 bp):
ATTTTTTTTTTCCTTTTTC
Found at i:1624545 original size:23 final size:24
Alignment explanation
Indices: 1624514--1624559 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1624504 CTTTTTCTTA
*
1624514 ATTAGTTA-TATTTTTAAAAAAAT
1 ATTAATTATTATTTTTAAAAAAAT
*
1624537 ATTAATTATTTTTTTTAAAAAAA
1 ATTAATTATTATTTTTAAAAAAA
1624560 GTAACCTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTAATTATTATTTTTAAAAAAAT
Found at i:1626933 original size:33 final size:33
Alignment explanation
Indices: 1626896--1626962 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1626886 TTCAACGATT
1626896 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1626929 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1626962 T
1 T
1626963 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1626934 original size:13 final size:13
Alignment explanation
Indices: 1626916--1626940 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1626906 CATAAAATGT
1626916 TGTATCGATACAA
1 TGTATCGATACAA
1626929 TGTATCGATACA
1 TGTATCGATACA
1626941 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1627022 original size:13 final size:13
Alignment explanation
Indices: 1627004--1627028 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1626994 ATTACTCAAA
1627004 TGTATCGATACAT
1 TGTATCGATACAT
1627017 TGTATCGATACA
1 TGTATCGATACA
1627029 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1627081 original size:52 final size:51
Alignment explanation
Indices: 1627017--1627165 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
1627007 ATCGATACAT
**
1627017 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
1627069 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
1627121 TGTATCGATACACTATTCAATATATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT
1627166 TCATATTTCG
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.97
53 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1628176 original size:43 final size:43
Alignment explanation
Indices: 1628115--1628201 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
1628105 TCGATTTTCA
1628115 AACACCCCCCAAGTTAAGTTCAAGCTAGCCTCAATCAATGAGG
1 AACACCCCCCAAGTTAAGTTCAAGCTAGCCTCAATCAATGAGG
1628158 AACACCCCCCAAGTTAAGTTCAAGCTAGCCTCAATCAATGAGG
1 AACACCCCCCAAGTTAAGTTCAAGCTAGCCTCAATCAATGAGG
1628201 A
1 A
1628202 TTAGCTTGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.36, C:0.30, G:0.16, T:0.18
Consensus pattern (43 bp):
AACACCCCCCAAGTTAAGTTCAAGCTAGCCTCAATCAATGAGG
Found at i:1631321 original size:32 final size:32
Alignment explanation
Indices: 1631248--1631326 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
1631238 ACGTATTTAA
*
1631248 AATATTATATATTTATATAAATTTTGACACGTT
1 AATATT-TATATTTATATAAATTTTAACACGTT
* **
1631281 AATAATTTAT-TTTATATAAATTTTAATATTTT
1 AAT-ATTTATATTTATATAAATTTTAACACGTT
1631313 ATATATTTATATTT
1 A-ATATTTATATTT
1631327 TATTCATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
32 25 0.64
33 11 0.28
34 3 0.08
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (32 bp):
AATATTTATATTTATATAAATTTTAACACGTT
Found at i:1634128 original size:2 final size:2
Alignment explanation
Indices: 1634123--1634165 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1634113 TGTGTATTGC
1634123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1634164 AT
1 AT
1634166 CGATATGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1636816 original size:8 final size:8
Alignment explanation
Indices: 1636805--1636844 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1636795 CTTGTTTCTG
*
1636805 CATGCATG
1 CATGCATA
1636813 CATGCATA
1 CATGCATA
*
1636821 CATACATA
1 CATGCATA
1636829 CATGCATA
1 CATGCATA
*
1636837 CATTCATA
1 CATGCATA
1636845 TATATATAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (8 bp):
CATGCATA
Found at i:1638494 original size:44 final size:44
Alignment explanation
Indices: 1638443--1638575 Score: 200
Period size: 44 Copynumber: 3.1 Consensus size: 44
1638433 GTTTTTTTTA
* *
1638443 ATTTTATTATATGTTAAATATATCTATTAATAGTTTTCCTACTT
1 ATTTTATTATATGTTAAATATATCTATTGATAGTTTTCCTGCTT
*
1638487 ATTTTATTATATGTTAAATATATCTTTTGATAG--TT-CTGCTT
1 ATTTTATTATATGTTAAATATATCTATTGATAGTTTTCCTGCTT
* *
1638528 ATTTTATTATGTGTTAAATATATCTATTGATAGTTTTCTTGCTT
1 ATTTTATTATATGTTAAATATATCTATTGATAGTTTTCCTGCTT
1638572 ATTT
1 ATTT
1638576 CTAGCATGCG
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
41 36 0.45
42 2 0.03
43 2 0.03
44 40 0.50
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (44 bp):
ATTTTATTATATGTTAAATATATCTATTGATAGTTTTCCTGCTT
Found at i:1638543 original size:41 final size:42
Alignment explanation
Indices: 1638443--1638562 Score: 179
Period size: 41 Copynumber: 2.8 Consensus size: 42
1638433 GTTTTTTTTA
*
1638443 ATTTTATTATATGTTAAATATATCTATTAATAGTTTTCCTACTT
1 ATTTTATTATATGTTAAATATATCTATTGATAG--TTCCTACTT
* *
1638487 ATTTTATTATATGTTAAATATATCTTTTGATAGTT-CTGCTT
1 ATTTTATTATATGTTAAATATATCTATTGATAGTTCCTACTT
*
1638528 ATTTTATTATGTGTTAAATATATCTATTGATAGTT
1 ATTTTATTATATGTTAAATATATCTATTGATAGTT
1638563 TTCTTGCTTA
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 38 0.54
42 2 0.03
44 31 0.44
ACGTcount: A:0.30, C:0.07, G:0.08, T:0.55
Consensus pattern (42 bp):
ATTTTATTATATGTTAAATATATCTATTGATAGTTCCTACTT
Found at i:1639781 original size:56 final size:58
Alignment explanation
Indices: 1639715--1639831 Score: 202
Period size: 57 Copynumber: 2.1 Consensus size: 58
1639705 GATATTTGAC
*
1639715 AGGACAATGCTGTCTT-TATGGTAAGCCTTGTATTTTAA-TTTTGTTATTTTTGGTCA
1 AGGACAATGCTGTCTTATATAGTAAGCCTTGTATTTTAATTTTTGTTATTTTTGGTCA
*
1639771 AGGACAATGCTGTCTTATATAGTAAGCCTTGTATTTTAATTTTTTTTATTTTTGGTCA
1 AGGACAATGCTGTCTTATATAGTAAGCCTTGTATTTTAATTTTTGTTATTTTTGGTCA
1639829 AGG
1 AGG
1639832 GGAAGAGGGA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
56 16 0.28
57 21 0.37
58 20 0.35
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (58 bp):
AGGACAATGCTGTCTTATATAGTAAGCCTTGTATTTTAATTTTTGTTATTTTTGGTCA
Found at i:1641202 original size:17 final size:18
Alignment explanation
Indices: 1641180--1641213 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1641170 TTTAAATTTT
*
1641180 ATCAAAT-AATTTTTATA
1 ATCAAATCAAATTTTATA
1641197 ATCAAATCAAATTTTAT
1 ATCAAATCAAATTTTAT
1641214 TGGTTTAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (18 bp):
ATCAAATCAAATTTTATA
Found at i:1641418 original size:16 final size:17
Alignment explanation
Indices: 1641399--1641438 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1641389 ATTACTATTT
1641399 AAATTAAAATAAAAT-A
1 AAATTAAAATAAAATAA
*
1641415 AAATT-AAATTAAATAA
1 AAATTAAAATAAAATAA
1641431 AAATTAAA
1 AAATTAAA
1641439 CAAAATCAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 8 0.38
16 11 0.52
17 2 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATTAAAATAAAATAA
Found at i:1641444 original size:16 final size:15
Alignment explanation
Indices: 1641399--1641444 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
1641389 ATTACTATTT
1641399 AAATTAAAATAAAATA
1 AAATT-AAATAAAATA
*
1641415 AAATTAAATTAAATAA
1 AAATTAAATAAAAT-A
*
1641431 AAATTAAACAAAAT
1 AAATTAAATAAAAT
1641445 CAGCAAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATTAAATAAAATA
Found at i:1645606 original size:16 final size:15
Alignment explanation
Indices: 1645587--1645631 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1645577 GACTTAAAAT
*
1645587 TCGAAATAATCCGAA
1 TCGAAATGATCCGAA
*
1645602 CTCGAAATGACCCGAA
1 -TCGAAATGATCCGAA
1645618 TCTGAAATGATCCG
1 TC-GAAATGATCCG
1645632 GACAATTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (15 bp):
TCGAAATGATCCGAA
Found at i:1646472 original size:16 final size:16
Alignment explanation
Indices: 1646451--1646515 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 16
1646441 TGATCTGAAT
1646451 CCGAAATGACCCGAAC
1 CCGAAATGACCCGAAC
1646467 CCGAAATGACCCGAAC
1 CCGAAATGACCCGAAC
* * *
1646483 TCGAAATGATCCGAAT
1 CCGAAATGACCCGAAC
* *
1646499 CCGAAATAACCCAAAC
1 CCGAAATGACCCGAAC
1646515 C
1 C
1646516 TAAAAAGACT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.40, C:0.34, G:0.15, T:0.11
Consensus pattern (16 bp):
CCGAAATGACCCGAAC
Found at i:1646688 original size:16 final size:17
Alignment explanation
Indices: 1646659--1646691 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1646649 CTTTTTTTAT
*
1646659 TAAATTATATTTTAATA
1 TAAATAATATTTTAATA
1646676 TAAATAATA-TTTAATA
1 TAAATAATATTTTAATA
1646692 ATTTATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATAATATTTTAATA
Found at i:1646698 original size:29 final size:31
Alignment explanation
Indices: 1646661--1646784 Score: 80
Period size: 32 Copynumber: 3.8 Consensus size: 31
1646651 TTTTTTATTA
1646661 AATTATATTTTAATAT-AA-ATAATATTTAAT
1 AATT-TATTTTAATATAAATATAATATTTAAT
*
1646691 AATTTA--TTAATATAAATATAATTTTTAATAAT
1 AATTTATTTTAATATAAATATAA-TATT--TAAT
* *
1646723 ATATTGTATTATTTAAAATAATTATAAT-TTTAAT
1 A-ATT-TA-T-TTTAATATAAATATAATATTTAAT
1646757 AATTTATTTTGTTAATAT-AATATAATAT
1 AATTTA--TT-TTAATATAAATATAATAT
1646785 ATTATTTTTA
Statistics
Matches: 75, Mismatches: 5, Indels: 25
0.71 0.05 0.24
Matches are distributed among these distances:
27 7 0.09
28 2 0.03
29 6 0.08
30 7 0.09
32 15 0.20
33 15 0.20
34 7 0.09
36 2 0.03
37 1 0.01
38 13 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (31 bp):
AATTTATTTTAATATAAATATAATATTTAAT
Found at i:1646700 original size:27 final size:29
Alignment explanation
Indices: 1646656--1646727 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
1646646 TTACTTTTTT
* * *
1646656 TATTAAATTATATTTTAATAT-AA-ATAA
1 TATTTAATAATATATTAATATAAATATAA
*
1646683 TATTTAATAATTTATTAATATAAATATAA
1 TATTTAATAATATATTAATATAAATATAA
*
1646712 TTTTTAATAATATATT
1 TATTTAATAATATATT
1646728 GTATTATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 17 0.46
28 2 0.05
29 18 0.49
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TATTTAATAATATATTAATATAAATATAA
Found at i:1646754 original size:37 final size:37
Alignment explanation
Indices: 1646697--1646863 Score: 127
Period size: 38 Copynumber: 4.7 Consensus size: 37
1646687 TAATAATTTA
* *
1646697 TTAATATAAATATAATTTTTAATAATATATTGTATTAT
1 TTAAAATAAATATAA-TTTTAATAATATATTTTATTAT
* * *
1646735 TTAAAATAATTATAATTTTAATAATTTATTTTGTTAAT
1 TTAAAATAAATATAATTTTAATAATATATTTTATT-AT
* * *
1646773 ATAATATAATATATTATTTT--TAATA-A-TTT-TTAT
1 TTAAAATAA-ATATAATTTTAATAATATATTTTATTAT
* ** *
1646806 TCAGCATAAATATAATTTT-AT-TTATATTTTATTA-
1 TTAAAATAAATATAATTTTAATAATATATTTTATTAT
*
1646840 TTAAAAT-AATATATTTTTAATAAT
1 TTAAAATAAATATAATTTTAATAAT
1646864 TCATATATAC
Statistics
Matches: 100, Mismatches: 21, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
32 11 0.11
33 19 0.19
34 11 0.11
35 7 0.07
36 1 0.01
37 21 0.21
38 22 0.22
39 8 0.08
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (37 bp):
TTAAAATAAATATAATTTTAATAATATATTTTATTAT
Found at i:1646796 original size:40 final size:39
Alignment explanation
Indices: 1646694--1646801 Score: 116
Period size: 37 Copynumber: 2.8 Consensus size: 39
1646684 ATTTAATAAT
* *
1646694 TTAT-TAATATAA-ATATAATTTTTAATAATATATTGTA
1 TTATATAATATAATATATTATTTTTAATAATTTATTGTA
* * * * *
1646731 TTATTTAAAATAAT-TA-TAATTTTAATAATTTATTTTG
1 TTATATAATATAATATATTATTTTTAATAATTTATTGTA
1646768 TTAATATAATATAATATATTATTTTTAATAATTT
1 TT-ATATAATATAATATATTATTTTTAATAATTT
1646802 TTATTCAGCA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
37 22 0.39
38 19 0.33
39 2 0.04
40 14 0.25
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (39 bp):
TTATATAATATAATATATTATTTTTAATAATTTATTGTA
Found at i:1646856 original size:32 final size:33
Alignment explanation
Indices: 1646694--1646858 Score: 86
Period size: 37 Copynumber: 4.7 Consensus size: 33
1646684 ATTTAATAAT
* * *
1646694 TTATTAATATAAATATAATTTTTAATAATATATTGTA
1 TTATTAAAAT-AATATAA-TTTT-AT-TTATATTTTA
*
1646731 TTATTTAAAATAATTATAATTTTAATAATT-TATTTTG
1 TTA-TTAAAATAA-TATAATTTT-AT--TTATATTTTA
* *
1646768 TTAATATAATATAATAT-ATTATT-TTTAATAATTT-
1 TT-AT-TAAAATAATATAATT-TTATTT-ATATTTTA
**
1646802 TTATTCAGCATAAATATAATTTTATTTATATTTTA
1 TTATT-AAAAT-AATATAATTTTATTTATATTTTA
*
1646837 TTATTAAAATAATATATTTTTA
1 TTATTAAAATAATATAATTTTA
1646859 ATAATTCATA
Statistics
Matches: 103, Mismatches: 12, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
32 1 0.01
33 18 0.17
34 18 0.17
35 17 0.17
36 3 0.03
37 25 0.24
38 21 0.20
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (33 bp):
TTATTAAAATAATATAATTTTATTTATATTTTA
Found at i:1648560 original size:21 final size:19
Alignment explanation
Indices: 1648493--1648568 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 19
1648483 ATAATCTCTT
1648493 AATTTTTTTAAAATAAATAA
1 AATTTTTTT-AAATAAATAA
* * **
1648513 AA-TTCTTGATAAT-TTTAA
1 AATTTTTTTA-AATAAATAA
1648531 AATTTTTTTAAATAAATAA
1 AATTTTTTTAAATAAATAA
*
1648550 AATTATCTTTTAATTAAAT
1 AATT-T-TTTTAAATAAAT
1648569 CTCTACTTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
18 9 0.21
19 19 0.45
20 3 0.07
21 11 0.26
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (19 bp):
AATTTTTTTAAATAAATAA
Found at i:1648741 original size:9 final size:9
Alignment explanation
Indices: 1648727--1648755 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1648717 TCACGTGTCC
1648727 TTTTTCTTT
1 TTTTTCTTT
1648736 TTTTTCTTT
1 TTTTTCTTT
1648745 TTTTT-TTT
1 TTTTTCTTT
1648753 TTT
1 TTT
1648756 CTGATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1648746 original size:15 final size:15
Alignment explanation
Indices: 1648726--1648757 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1648716 ATCACGTGTC
1648726 CTTTTTCTTTTTTTT
1 CTTTTTCTTTTTTTT
*
1648741 CTTTTTTTTTTTTTT
1 CTTTTTCTTTTTTTT
1648756 CT
1 CT
1648758 GATTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
CTTTTTCTTTTTTTT
Found at i:1649356 original size:21 final size:22
Alignment explanation
Indices: 1649317--1649357 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
1649307 TATTTTTTAA
1649317 TAAAATAATATTTAATTAATTT
1 TAAAATAATATTTAATTAATTT
1649339 TAAAA-AA-ATTTACATTAAT
1 TAAAATAATATTTA-ATTAAT
1649358 AAATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAAATAATATTTAATTAATTT
Found at i:1649474 original size:104 final size:110
Alignment explanation
Indices: 1649317--1649583 Score: 350
Period size: 111 Copynumber: 2.5 Consensus size: 110
1649307 TATTTTTTAA
* * *
1649317 TAAAATAATATTTAATTAATTTTAAAAAAATTTACATTAATAAATTAAAATATT-A-AT-TATTT
1 TAAAATAATATTTAATTAAATTTAAAAAAATTTATATTAACAAATTAAAATATTAATATATATTT
* *
1649379 TT-T-AAATTAAAAAGGGTTTATTATTATTA-TTTTTAATAAAAT
66 TTATAAAAATAAAAAGGATTTATTATTATTATTTTTTAATAAAAT
*
1649421 TAAAATTAATATTCAATTAAATTTAAAAAAA-TTATATTAACAAATTAAAATATTAATTATATAT
1 TAAAA-TAATATTTAATTAAATTTAAAAAAATTTATATTAACAAATTAAAATATTAA-TATATAT
* *
1649485 TTTTATAAAAATAAAAAGTATTTTTTATTATTATTTTTTAATAAAAT
64 TTTTATAAAAATAAAAAGGATTTATTATTATTATTTTTTAATAAAAT
* * *
1649532 AAAAAATGATATTTAATTAAATTAAAAAAAAATTTATATTAACAAATTAAAA
1 -TAAAATAATATTTAATTAAATT-TAAAAAAATTTATATTAACAAATTAAAA
1649584 AAAACTTTTA
Statistics
Matches: 140, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
104 26 0.19
105 24 0.17
107 2 0.01
108 7 0.05
109 1 0.01
110 22 0.16
111 28 0.20
112 11 0.08
113 19 0.14
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (110 bp):
TAAAATAATATTTAATTAAATTTAAAAAAATTTATATTAACAAATTAAAATATTAATATATATTT
TTATAAAAATAAAAAGGATTTATTATTATTATTTTTTAATAAAAT
Found at i:1649561 original size:26 final size:25
Alignment explanation
Indices: 1649532--1649587 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1649522 TTAATAAAAT
*
1649532 AAAAAATGATAT-TTAATTAAATTAAA
1 AAAAAAT-ATATATTAA-CAAATTAAA
*
1649558 AAAAAATTTATATTAACAAATTAAA
1 AAAAAATATATATTAACAAATTAAA
1649583 AAAAA
1 AAAAA
1649588 CTTTTAAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (25 bp):
AAAAAATATATATTAACAAATTAAA
Found at i:1649609 original size:113 final size:110
Alignment explanation
Indices: 1649318--1649583 Score: 274
Period size: 104 Copynumber: 2.4 Consensus size: 110
1649308 ATTTTTTAAT
* * * * * *
1649318 AAAATAATATTTAATTAATTTTAAAAAAATTTACATTAATAAATTAAAATATTAATTAT-T---T
1 AAAATAATATTCAATTAA-ATTAAAAAAAATTATATTAACAAATTAAAATATAAATTATATAAAT
* * ** * *
1649379 TT--TAAATTAAAAAGGGTTTATTATTATTATTTTTAATAAAATTA
65 TTAAAAAAATAAAAAGTATTTTTTATTATTATTTTTAATAAAATAA
* * * **
1649423 AAATTAATATTCAATTAAATTTAAAAAAATTATATTAACAAATTAAAATATTAATTATATATTTT
1 AAAATAATATTCAATTAAATTAAAAAAAATTATATTAACAAATTAAAATATAAATTATATAAATT
*
1649488 TATAAAAATAAAAAGTATTTTTTATTATTATTTTTTAATAAAATAA
66 TAAAAAAATAAAAAGTATTTTTTATTATTA-TTTTTAATAAAATAA
* *
1649534 AAAATGATATTTAATTAAATTAAAAAAAAATTTATATTAACAAATTAAAA
1 AAAATAATATTCAATTAAATT-AAAAAAAA-TTATATTAACAAATTAAAA
1649584 AAAACTTTTA
Statistics
Matches: 135, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
104 35 0.26
105 17 0.13
108 3 0.02
110 22 0.16
111 32 0.24
112 7 0.05
113 19 0.14
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (110 bp):
AAAATAATATTCAATTAAATTAAAAAAAATTATATTAACAAATTAAAATATAAATTATATAAATT
TAAAAAAATAAAAAGTATTTTTTATTATTATTTTTAATAAAATAA
Found at i:1650095 original size:124 final size:123
Alignment explanation
Indices: 1649898--1650257 Score: 448
Period size: 124 Copynumber: 2.9 Consensus size: 123
1649888 AAATATTATT
* *
1649898 ATAAT-AAAAA-CTTTTTTAATTTAAAATTTTTTA-TTTTTAAAAACATAATAATTAATATTTTA
1 ATAATAAAAAACCTTTTTTATTTTAAAATTTTTTATTTTTTAAAAATATAATAATTAA-ATTTTA
* *
1649960 ATTTGTTAATGTAGAATTTTAAACTTAATTAAATGTTATTTTTTATTTTATT-AAAAATA
65 ATTTGTTAATGTA-ATTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAAATA
1650019 ATAATAAAAAACCTTTTTTATTTTAAAATTTTTTATTTTTATAAAAATATAATAATTAAATTTTA
1 ATAATAAAAAACCTTTTTTATTTTAAAATTTTTTATTTTT-TAAAAATATAATAATTAAATTTTA
* *
1650084 ATTTGTTAATGTAATTTCTTAAACTAAATTAAATATTATTTTTAATTTTATTAAAAAATA
65 ATTTGTTAATGTAATTT-TTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAAATA
* * *
1650144 ATAATAATAAACCTTTTTTTATTTTTATTTAAATTTTTTATTATTTAAAAATA-ATTAA-T--AT
1 ATAATAAAAAACC-TTTTTTA-TTTTA---AAATTTTTTATTTTTTAAAAATATAATAATTAAAT
* * *
1650205 TTTAATTTATTAATATAATTTTTTTTAAAATTAATTAAATATTATTTTTTATT
61 TTTAATTTGTTAATGTAA---TTTTTAAACTTAATTAAATATTATTTTTTATT
1650258 AAAAATAATA
Statistics
Matches: 211, Mismatches: 14, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
121 5 0.02
122 5 0.02
123 25 0.12
124 54 0.26
125 54 0.26
126 7 0.03
127 32 0.15
128 7 0.03
129 8 0.04
130 14 0.07
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (123 bp):
ATAATAAAAAACCTTTTTTATTTTAAAATTTTTTATTTTTTAAAAATATAATAATTAAATTTTAA
TTTGTTAATGTAATTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAAATA
Found at i:1650236 original size:25 final size:27
Alignment explanation
Indices: 1650208--1650266 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
1650198 TTAATATTTT
*
1650208 AATTTATT-AATATAATTTTTT-TTAA
1 AATTAATTAAATATAATTTTTTATTAA
*
1650233 AATTAATTAAATATTATTTTTTATTAA
1 AATTAATTAAATATAATTTTTTATTAA
*
1650260 AAATAAT
1 AATTAAT
1650267 AATTAATCCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 7 0.24
26 12 0.41
27 10 0.34
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
AATTAATTAAATATAATTTTTTATTAA
Found at i:1650261 original size:27 final size:25
Alignment explanation
Indices: 1650208--1650273 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
1650198 TTAATATTTT
*
1650208 AATTTATTAATATAATTTTTTTTAA
1 AATTAATTAATATAATTTTTTTTAA
*
1650233 AATTAATTAAATATTATTTTTTATTAA
1 AATTAATT-AATATAATTTTTT-TTAA
*
1650260 AAATAA-TAAT-TAAT
1 AATTAATTAATATAAT
1650274 CCGTTATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 3 0.09
25 10 0.29
26 13 0.37
27 9 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
AATTAATTAATATAATTTTTTTTAA
Found at i:1650909 original size:22 final size:24
Alignment explanation
Indices: 1650884--1650933 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
1650874 AATACAATAC
*
1650884 AAATACAATATAAAAAT-A-ATTA
1 AAATACAACATAAAAATAACATTA
*
1650906 AAATATAACATAAAAATAACATTA
1 AAATACAACATAAAAATAACATTA
1650930 AAAT
1 AAAT
1650934 GATATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.62
23 1 0.04
24 8 0.33
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (24 bp):
AAATACAACATAAAAATAACATTA
Found at i:1651039 original size:11 final size:11
Alignment explanation
Indices: 1651025--1651090 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 11
1651015 TATATAAAAG
1651025 ATATAAATATA
1 ATATAAATATA
1651036 ATATAAAAAATATA
1 ATAT---AAATATA
1651050 AT-TAAA-ATA
1 ATATAAATATA
1651059 CA-ATAAA-ATA
1 -ATATAAATATA
*
1651069 ATATAAATATG
1 ATATAAATATA
1651080 ATATAAATATA
1 ATATAAATATA
1651091 TGAATGTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
9 4 0.09
10 16 0.35
11 16 0.35
13 1 0.02
14 9 0.20
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (11 bp):
ATATAAATATA
Found at i:1651058 original size:20 final size:20
Alignment explanation
Indices: 1651010--1651068 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1651000 TTTATAATCT
*
1651010 TTAAATATATAAAAGATATAA
1 TTAAA-ATATAAAAAATATAA
* *
1651031 ATATAATATAAAAAATATAA
1 TTAAAATATAAAAAATATAA
*
1651051 TTAAAATACAATAAAATA
1 TTAAAATATAA-AAAATA
1651069 ATATAAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 22 0.71
21 9 0.29
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
TTAAAATATAAAAAATATAA
Found at i:1651091 original size:19 final size:19
Alignment explanation
Indices: 1651011--1651160 Score: 62
Period size: 19 Copynumber: 7.8 Consensus size: 19
1651001 TTATAATCTT
*
1651011 TAAATAT-ATA-AAAGATA
1 TAAATATAATATAAATATA
1651028 TAAATATAATATAAAAAATATAA
1 TAAATATAATAT---AAATAT-A
*
1651051 TTAAAATACAATA-AAATAATA
1 -T-AAATATAATATAAAT-ATA
*
1651072 TAAATATGATATAAATATA
1 TAAATATAATATAAATATA
* * * *
1651091 TGAATGTATAAAATATATATG
1 T-AA-ATATAATATAAATATA
* * * *
1651112 TAAAAATATTATATATTTA
1 TAAATATAATATAAATATA
1651131 T-AATAT-AT-TAAATA-A
1 TAAATATAATATAAATATA
*
1651146 TAAAAATAATATAAA
1 TAAATATAATATAAA
1651161 CAAAAATATA
Statistics
Matches: 98, Mismatches: 20, Indels: 29
0.67 0.14 0.20
Matches are distributed among these distances:
15 2 0.02
16 8 0.08
17 10 0.10
18 11 0.11
19 23 0.23
20 9 0.09
21 17 0.17
22 7 0.07
23 1 0.01
24 1 0.01
25 9 0.09
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (19 bp):
TAAATATAATATAAATATA
Found at i:1651112 original size:15 final size:15
Alignment explanation
Indices: 1651075--1651125 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
1651065 AATAATATAA
1651075 ATATG-ATATAAATAT
1 ATATGTATA-AAATAT
1651090 ATGAATGTATAAAATAT
1 AT--ATGTATAAAATAT
1651107 ATATGTA-AAAATATT
1 ATATGTATAAAATA-T
1651122 ATAT
1 ATAT
1651126 ATTTATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 6 0.19
15 12 0.38
17 11 0.34
18 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (15 bp):
ATATGTATAAAATAT
Found at i:1651210 original size:9 final size:9
Alignment explanation
Indices: 1651196--1651240 Score: 63
Period size: 9 Copynumber: 4.8 Consensus size: 9
1651186 TCTCTCTTTC
1651196 TTCTTTTTT
1 TTCTTTTTT
1651205 TTCTTTTTT
1 TTCTTTTTT
1651214 TTCTTTCTCTT
1 TTCTTT-T-TT
1651225 TTCTTTTTT
1 TTCTTTTTT
*
1651234 TTATTTT
1 TTCTTTT
1651241 CCTCTTTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
9 23 0.70
10 2 0.06
11 8 0.24
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:1651228 original size:20 final size:20
Alignment explanation
Indices: 1651203--1651263 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
1651193 TTCTTCTTTT
1651203 TTTTCTTTTTTTTCTTTCTC
1 TTTTCTTTTTTTTCTTTCTC
*
1651223 TTTTCTTTTTTTTATTT-TCC
1 TTTTCTTTTTTTTCTTTCT-C
*
1651243 TCTTTC-TTTCTTTCTTTCTC
1 T-TTTCTTTTTTTTCTTTCTC
1651263 T
1 T
1651264 CATTCCTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 1 0.03
20 29 0.83
21 5 0.14
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTTTTTCTTTCTC
Found at i:1651231 original size:25 final size:25
Alignment explanation
Indices: 1651190--1651241 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1651180 TTTTTCTCTC
1651190 TCTTTCTTCTTTTTTTTCTTTT-TTT
1 TCTTTCTTCTTTTTTTT-TTTTATTT
1651215 TCTTTC-TCTTTTCTTTTTTTTATTT
1 TCTTTCTTCTTTT-TTTTTTTTATTT
1651240 TC
1 TC
1651242 CTCTTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (25 bp):
TCTTTCTTCTTTTTTTTTTTTATTT
Found at i:1651256 original size:29 final size:30
Alignment explanation
Indices: 1651179--1651259 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 30
1651169 TAAATCCATA
*
1651179 ATTTTTCTCTCTCTTTC-TTCTTTTTTTTC
1 ATTTTTCTCTTTCTTTCTTTCTTTTTTTTC
* * *
1651208 TTTTTTTTCTTTCTCT-TTTCTTTTTTTT-
1 ATTTTTCTCTTTCTTTCTTTCTTTTTTTTC
*
1651236 ATTTTCCTCTTTCTTTCTTTCTTT
1 ATTTTTCTCTTTCTTTCTTTCTTT
1651260 CTCTCATTCC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 12 0.29
29 30 0.71
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (30 bp):
ATTTTTCTCTTTCTTTCTTTCTTTTTTTTC
Found at i:1652664 original size:14 final size:14
Alignment explanation
Indices: 1652626--1652665 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1652616 TATGTTATTT
1652626 AAAAATAAAAATCA
1 AAAAATAAAAATCA
* *
1652640 AAAACTTAAAATCA
1 AAAAATAAAAATCA
1652654 AAAAATAAAAAT
1 AAAAATAAAAAT
1652666 AAATTTCTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAATAAAAATCA
Found at i:1654634 original size:16 final size:16
Alignment explanation
Indices: 1654598--1654635 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1654588 TAGTAAGGTA
*
1654598 AAAAAAATTGAAGATG
1 AAAAAAATTGAAGAAG
*
1654614 TAAAAAATTGAAGAAG
1 AAAAAAATTGAAGAAG
1654630 AAAAAA
1 AAAAAA
1654636 GTAAAAAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (16 bp):
AAAAAAATTGAAGAAG
Found at i:1659694 original size:19 final size:20
Alignment explanation
Indices: 1659655--1659696 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1659645 TATAATTAAA
1659655 TTTAAATAAAAATAAATTAT
1 TTTAAATAAAAATAAATTAT
*
1659675 TTTAAATAAAAATTAA-TAT
1 TTTAAATAAAAATAAATTAT
1659694 TTT
1 TTT
1659697 GAGTTAGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAATAAAAATAAATTAT
Found at i:1660161 original size:16 final size:16
Alignment explanation
Indices: 1660131--1660180 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
1660121 GAGATTATGA
*
1660131 TTAAATTAATCTTAAAT
1 TTAAA-TAATTTTAAAT
1660148 TTAAATAATTTTAAAT
1 TTAAATAATTTTAAAT
* *
1660164 TTAAGTTATTTTAAAT
1 TTAAATAATTTTAAAT
1660180 T
1 T
1660181 CAAAACATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 25 0.83
17 5 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
TTAAATAATTTTAAAT
Found at i:1664851 original size:21 final size:21
Alignment explanation
Indices: 1664834--1664886 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
1664824 TGTTATAATT
1664834 TCGATAATGTTT-CATATAAC
1 TCGATAATGTTTGCATATAAC
*
1664854 TCTATAATGTTTGCATA-AAC
1 TCGATAATGTTTGCATATAAC
1664874 TCGATAATGTTTG
1 TCGATAATGTTTG
1664887 TATCTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (21 bp):
TCGATAATGTTTGCATATAAC
Found at i:1665022 original size:28 final size:30
Alignment explanation
Indices: 1664965--1665020 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
1664955 ATGATTCATG
* *
1664965 TAATATAAAATGTATATATATATATAAATA
1 TAATATAAAATATATATACATATATAAATA
1664995 TAATA-AAAATATAT-TACATATGATAA
1 TAATATAAAATATATATACATAT-ATAA
1665021 TAAACTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.26
29 12 0.52
30 5 0.22
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (30 bp):
TAATATAAAATATATATACATATATAAATA
Found at i:1665039 original size:20 final size:21
Alignment explanation
Indices: 1665016--1665054 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1665006 TATTACATAT
1665016 GATAATA-AACTTATGTAATA
1 GATAATATAACTTATGTAATA
*
1665036 GATAATATAATTTATGTAA
1 GATAATATAACTTATGTAA
1665055 CTATTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (21 bp):
GATAATATAACTTATGTAATA
Found at i:1665129 original size:17 final size:17
Alignment explanation
Indices: 1665107--1665160 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1665097 TTTGCATAAA
1665107 ATATGAAATACGTATAT
1 ATATGAAATACGTATAT
* *
1665124 ATATGAAGT--GTATAAA
1 ATATGAAATACGTAT-AT
*
1665140 ATATGAAATACATATAT
1 ATATGAAATACGTATAT
1665157 ATAT
1 ATAT
1665161 ATATGAAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 4 0.14
16 9 0.31
17 13 0.45
18 3 0.10
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (17 bp):
ATATGAAATACGTATAT
Found at i:1665145 original size:16 final size:17
Alignment explanation
Indices: 1665102--1665149 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
1665092 TTTAGTTTGC
1665102 ATAAAATATGAAATACGT
1 ATAAAATATGAAATA-GT
* *
1665120 AT-ATATATGAAGT-GT
1 ATAAAATATGAAATAGT
1665135 ATAAAATATGAAATA
1 ATAAAATATGAAATA
1665150 CATATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 4 0.17
16 9 0.38
17 9 0.38
18 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.31
Consensus pattern (17 bp):
ATAAAATATGAAATAGT
Found at i:1672360 original size:16 final size:16
Alignment explanation
Indices: 1672339--1672370 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1672329 TTAACCAAAA
1672339 GGTAAAATGTAGTCGC
1 GGTAAAATGTAGTCGC
1672355 GGTAAAATGTAGTCGC
1 GGTAAAATGTAGTCGC
1672371 TTTCTCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.25
Consensus pattern (16 bp):
GGTAAAATGTAGTCGC
Found at i:1673687 original size:13 final size:13
Alignment explanation
Indices: 1673669--1673693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1673659 CATCATGCTT
1673669 TGTATCGATACAA
1 TGTATCGATACAA
1673682 TGTATCGATACA
1 TGTATCGATACA
1673694 TACATAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1673690 original size:33 final size:33
Alignment explanation
Indices: 1673648--1673713 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1673638 ACATATCCAG
**
1673648 ATGTATCGATACAT-CATGCTTTGTATCGATACA
1 ATGTATCGATACATACAT-AATTGTATCGATACA
1673681 ATGTATCGATACATACATAATTGTATCGATACA
1 ATGTATCGATACATACATAATTGTATCGATACA
1673714 TGAAACTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (33 bp):
ATGTATCGATACATACATAATTGTATCGATACA
Found at i:1675445 original size:13 final size:13
Alignment explanation
Indices: 1675427--1675451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1675417 ATTTTACTTA
1675427 GTATCGATACATT
1 GTATCGATACATT
1675440 GTATCGATACAT
1 GTATCGATACAT
1675452 ATTTTTGGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1675448 original size:33 final size:32
Alignment explanation
Indices: 1675406--1675467 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
1675396 CATACCCAAA
1675406 TGTATCGATACAT-TTTACTTAGTATCGATACAT
1 TGTATCGATACATATTT--TTAGTATCGATACAT
*
1675439 TGTATCGATACATATTTTTGGTATCGATA
1 TGTATCGATACATATTTTTAGTATCGATA
1675468 TATCATGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 11 0.41
33 13 0.48
34 3 0.11
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.44
Consensus pattern (32 bp):
TGTATCGATACATATTTTTAGTATCGATACAT
Found at i:1676089 original size:32 final size:34
Alignment explanation
Indices: 1676048--1676140 Score: 113
Period size: 32 Copynumber: 2.7 Consensus size: 34
1676038 CAAGTGATTG
1676048 AGAGGTTCTATCTTAGCCTTGAAAGATA-G-TGT
1 AGAGGTTCTATCTTAGCCTTGAAAGATAGGTTGT
1676080 AGAGGTTCTATCTTAGCCTTTGTAAAAGATAGGGTTGT
1 AGAGGTTCTATCTTAGCC-TTG--AAAGATA-GGTTGT
*
1676118 A-AGGTTATATCTTAGCCTT-AAAG
1 AGAGGTTCTATCTTAGCCTTGAAAG
1676141 GTAAACAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
32 18 0.33
33 7 0.13
35 7 0.13
36 2 0.04
37 16 0.30
38 4 0.07
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (34 bp):
AGAGGTTCTATCTTAGCCTTGAAAGATAGGTTGT
Found at i:1676834 original size:36 final size:36
Alignment explanation
Indices: 1676787--1676862 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
1676777 CTCAAGACAA
1676787 TCATATAGCTCTCATTGTCTTTTATGGAGAATATAT
1 TCATATAGCTCTCATTGTCTTTTATGGAGAATATAT
1676823 TCATATAGCTCTCATTGTCTTTTATGGAGAATATAT
1 TCATATAGCTCTCATTGTCTTTTATGGAGAATATAT
1676859 TCAT
1 TCAT
1676863 TTATATGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (36 bp):
TCATATAGCTCTCATTGTCTTTTATGGAGAATATAT
Found at i:1680957 original size:140 final size:140
Alignment explanation
Indices: 1680705--1680984 Score: 542
Period size: 140 Copynumber: 2.0 Consensus size: 140
1680695 CCTATAGGCT
*
1680705 CTGATACTACTATTGGGAACCTTGAGATAGTGTAGCCTCATGCCATAATTGACTAATAACAGGAT
1 CTGATACTACTATTGGGAACCTTGAGATAGTGCAGCCTCATGCCATAATTGACTAATAACAGGAT
1680770 AATAGTAACTAACAAAGTGAAAAGTAAATGAGAAAAACAATCGAACTTTCTTTGGATCTTTAGAG
66 AATAGTAACTAACAAAGTGAAAAGTAAATGAGAAAAACAATCGAACTTTCTTTGGATCTTTAGAG
1680835 AAGGATTTGC
131 AAGGATTTGC
*
1680845 CTGATACTACTATTGGGAACCTTGAGATAGTGCAGCCTCATGCTATAATTGACTAATAACAGGAT
1 CTGATACTACTATTGGGAACCTTGAGATAGTGCAGCCTCATGCCATAATTGACTAATAACAGGAT
1680910 AATAGTAACTAACAAAGTGAAAAGTAAATGAGAAAAACAATCGAACTTTCTTTGGATCTTTAGAG
66 AATAGTAACTAACAAAGTGAAAAGTAAATGAGAAAAACAATCGAACTTTCTTTGGATCTTTAGAG
1680975 AAGGATTTGC
131 AAGGATTTGC
1680985 ATGTTGTAAT
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (140 bp):
CTGATACTACTATTGGGAACCTTGAGATAGTGCAGCCTCATGCCATAATTGACTAATAACAGGAT
AATAGTAACTAACAAAGTGAAAAGTAAATGAGAAAAACAATCGAACTTTCTTTGGATCTTTAGAG
AAGGATTTGC
Found at i:1686797 original size:13 final size:13
Alignment explanation
Indices: 1686779--1686805 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1686769 ATAGTAACCC
1686779 ATGTATCGATACA
1 ATGTATCGATACA
1686792 ATGTATCGATACA
1 ATGTATCGATACA
1686805 A
1 A
1686806 AGAAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1686823 original size:33 final size:33
Alignment explanation
Indices: 1686780--1686855 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
1686770 TAGTAACCCA
*
1686780 TGTATCGATACAATGTATCGATACAAAGAAAAT
1 TGTATCGATACAATGTATCAATACAAAGAAAAT
* *
1686813 TGTATTGATACAATGTATCAATACAAAGAACAT
1 TGTATCGATACAATGTATCAATACAAAGAAAAT
*
1686846 CGTATCGATA
1 TGTATCGATA
1686856 AATCTGGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.29
Consensus pattern (33 bp):
TGTATCGATACAATGTATCAATACAAAGAAAAT
Found at i:1691891 original size:13 final size:13
Alignment explanation
Indices: 1691873--1691910 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
1691863 CAATTCTTCA
1691873 TGTATCGATACAT
1 TGTATCGATACAT
1691886 TGTATCGATACAT
1 TGTATCGATACAT
1691899 TGTATCGATACA
1 TGTATCGATACA
1691911 ATATGCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1693835 original size:13 final size:13
Alignment explanation
Indices: 1693817--1693842 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1693807 CTATTTATGA
1693817 TGTATCGATACAC
1 TGTATCGATACAC
1693830 TGTATCGATACAC
1 TGTATCGATACAC
1693843 ATAAATATGT
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:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1693939 original size:16 final size:15
Alignment explanation
Indices: 1693912--1693942 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1693902 GTGATACGTG
1693912 AACAGTATGAACAGT
1 AACAGTATGAACAGT
1693927 AACAGTGATGAACAGT
1 AACAGT-ATGAACAGT
1693943 GATGTATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (15 bp):
AACAGTATGAACAGT
Found at i:1694799 original size:21 final size:21
Alignment explanation
Indices: 1694774--1694825 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1694764 GCTCTCCCCC
1694774 TTAATACAAACGTTCTTCCCT
1 TTAATACAAACGTTCTTCCCT
*
1694795 TTAATACAAATGTTCTTCCCT
1 TTAATACAAACGTTCTTCCCT
1694816 TTAATACAAA
1 TTAATACAAA
1694826 ATTTATACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (21 bp):
TTAATACAAACGTTCTTCCCT
Found at i:1695677 original size:13 final size:13
Alignment explanation
Indices: 1695659--1695683 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1695649 ACTGAAGCAA
1695659 TGTATCGATACAT
1 TGTATCGATACAT
1695672 TGTATCGATACA
1 TGTATCGATACA
1695684 ATCTGGAAAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1697371 original size:84 final size:83
Alignment explanation
Indices: 1697217--1697384 Score: 198
Period size: 84 Copynumber: 2.0 Consensus size: 83
1697207 ATTTTCCACT
* * * *
1697217 TGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAACT
1 TGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAACT
1697282 AATTGATTTACTTTCATTC
66 AATTGATTTACTTTC-TTC
* * *
1697301 TGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTAC
1 TGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTAA
* *
1697363 ACTTATTGATTTATTTTCTTC
63 ACTAATTGATTTACTTTCTTC
1697384 T
1 T
1697385 TTGAGTTTAG
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
82 6 0.08
83 13 0.18
84 53 0.74
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.52
Consensus pattern (83 bp):
TGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAACT
AATTGATTTACTTTCTTC
Found at i:1699469 original size:13 final size:13
Alignment explanation
Indices: 1699451--1699476 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1699441 CTATTTATGA
1699451 TGTATCGATACAC
1 TGTATCGATACAC
1699464 TGTATCGATACAC
1 TGTATCGATACAC
1699477 ATAAATATGT
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:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1700244 original size:17 final size:17
Alignment explanation
Indices: 1700224--1700297 Score: 53
Period size: 17 Copynumber: 4.3 Consensus size: 17
1700214 AAATTATTTT
1700224 AATAATAAATTTATATA
1 AATAATAAATTTATATA
* *
1700241 AATAA-ACTAATCGTA-ATC
1 AATAATA--AAT-TTATATA
* * * *
1700259 AATAAAAAAATTATTTT
1 AATAATAAATTTATATA
1700276 AATAATAAATTTATATA
1 AATAATAAATTTATATA
1700293 AATAA
1 AATAA
1700298 CCTAATCGTA
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
16 3 0.07
17 26 0.62
18 10 0.24
19 3 0.07
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (17 bp):
AATAATAAATTTATATA
Found at i:1700271 original size:52 final size:52
Alignment explanation
Indices: 1700213--1700323 Score: 213
Period size: 52 Copynumber: 2.1 Consensus size: 52
1700203 AGGGGAGCTT
1700213 AAAATTATTTTAATAATAAATTTATATAAATAAACTAATCGTAATCAATAAA
1 AAAATTATTTTAATAATAAATTTATATAAATAAACTAATCGTAATCAATAAA
*
1700265 AAAATTATTTTAATAATAAATTTATATAAATAACCTAATCGTAATCAATAAA
1 AAAATTATTTTAATAATAAATTTATATAAATAAACTAATCGTAATCAATAAA
1700317 AAAATTA
1 AAAATTA
1700324 ATAATAATTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (52 bp):
AAAATTATTTTAATAATAAATTTATATAAATAAACTAATCGTAATCAATAAA
Found at i:1704389 original size:15 final size:16
Alignment explanation
Indices: 1704369--1704408 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1704359 CTCATATTAT
1704369 ATTTTTTA-AATTTAA
1 ATTTTTTATAATTTAA
*
1704384 ATTTTTGATAATTTAA
1 ATTTTTTATAATTTAA
*
1704400 TTTTTTTAT
1 ATTTTTTAT
1704409 TAAGTTTCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
ATTTTTTATAATTTAA
Found at i:1705906 original size:12 final size:12
Alignment explanation
Indices: 1705889--1705920 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1705879 GAAAACAAAG
1705889 GCTGCCAACTGT
1 GCTGCCAACTGT
1705901 GCTGCCAACTGT
1 GCTGCCAACTGT
*
1705913 GCCGCCAA
1 GCTGCCAA
1705921 TTTTGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.38, G:0.25, T:0.19
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:1705957 original size:27 final size:27
Alignment explanation
Indices: 1705919--1705971 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1705909 CTGTGCCGCC
*
1705919 AATTTTGAAATTCAATTTGAAACAGTA
1 AATTATGAAATTCAATTTGAAACAGTA
*
1705946 AATTATGAAATTCAGTTTGAAACAGT
1 AATTATGAAATTCAATTTGAAACAGT
1705972 GAAGGTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (27 bp):
AATTATGAAATTCAATTTGAAACAGTA
Found at i:1706875 original size:13 final size:13
Alignment explanation
Indices: 1706857--1706882 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1706847 CAATTTTTTG
1706857 TGTATCGATACAT
1 TGTATCGATACAT
1706870 TGTATCGATACAT
1 TGTATCGATACAT
1706883 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1707630 original size:21 final size:21
Alignment explanation
Indices: 1707589--1707632 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1707579 CTCCCCTTTA
* *
1707589 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1707610 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1707631 TC
1 TC
1707633 ATAGCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1709454 original size:13 final size:13
Alignment explanation
Indices: 1709436--1709461 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1709426 AATAATCACC
1709436 TGTATCGATACAA
1 TGTATCGATACAA
1709449 TGTATCGATACAA
1 TGTATCGATACAA
1709462 AGAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1713398 original size:21 final size:21
Alignment explanation
Indices: 1713369--1713413 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1713359 AAGTTTTCAT
*
1713369 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1713389 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1713411 TTT
1 TTT
1713414 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1715650 original size:13 final size:13
Alignment explanation
Indices: 1715632--1715657 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1715622 CAATTTTTTG
1715632 TGTATCGATACAT
1 TGTATCGATACAT
1715645 TGTATCGATACAT
1 TGTATCGATACAT
1715658 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1720503 original size:12 final size:12
Alignment explanation
Indices: 1720486--1720517 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1720476 GAAAACAAAG
1720486 GCTGCCAACTGT
1 GCTGCCAACTGT
1720498 GCTGCCAACTGT
1 GCTGCCAACTGT
*
1720510 GCCGCCAA
1 GCTGCCAA
1720518 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.38, G:0.25, T:0.19
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:1726885 original size:18 final size:18
Alignment explanation
Indices: 1726860--1726898 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1726850 TGAAAATATC
*
1726860 AAATGCATGG-GAAATGA
1 AAATGCATGGAAAAATGA
1726877 AAATGGCATGGAAAAATGA
1 AAAT-GCATGGAAAAATGA
1726896 AAA
1 AAA
1726899 AAAAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 6 0.32
19 9 0.47
ACGTcount: A:0.54, C:0.05, G:0.26, T:0.15
Consensus pattern (18 bp):
AAATGCATGGAAAAATGA
Found at i:1727139 original size:24 final size:24
Alignment explanation
Indices: 1727112--1727188 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
1727102 CATCAAGGGG
1727112 AAAGAAACTTAAGTCTATAAATTA
1 AAAGAAACTTAAGTCTATAAATTA
** * * ****
1727136 AAAGTTACATAATGGC-ATCAAGGGG
1 AAAGAAACTTAA-GTCTAT-AAATTA
1727161 AAAGAAACTTAAGTCTATAAATTA
1 AAAGAAACTTAAGTCTATAAATTA
1727185 AAAG
1 AAAG
1727189 TTACATAATG
Statistics
Matches: 34, Mismatches: 16, Indels: 6
0.61 0.29 0.11
Matches are distributed among these distances:
24 19 0.56
25 15 0.44
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.25
Consensus pattern (24 bp):
AAAGAAACTTAAGTCTATAAATTA
Found at i:1727155 original size:49 final size:49
Alignment explanation
Indices: 1727102--1727201 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
1727092 GCTTATAAAT
1727102 CATCAAGGGGAAAGAAACTTAAGTCTATAAATTAAAAGTTACATAATGG
1 CATCAAGGGGAAAGAAACTTAAGTCTATAAATTAAAAGTTACATAATGG
1727151 CATCAAGGGGAAAGAAACTTAAGTCTATAAATTAAAAGTTACATAATGG
1 CATCAAGGGGAAAGAAACTTAAGTCTATAAATTAAAAGTTACATAATGG
1727200 CA
1 CA
1727202 ATCTAGCCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (49 bp):
CATCAAGGGGAAAGAAACTTAAGTCTATAAATTAAAAGTTACATAATGG
Found at i:1729521 original size:20 final size:21
Alignment explanation
Indices: 1729487--1729529 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1729477 TAATTAAAAT
1729487 TTTTAGCTTCAGTAAA-ATAA
1 TTTTAGCTTCAGTAAATATAA
1729507 TTTTA-CTTCATGTAAATATAA
1 TTTTAGCTTCA-GTAAATATAA
1729528 TT
1 TT
1729530 AAATAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 10 0.48
21 6 0.29
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTTAGCTTCAGTAAATATAA
Found at i:1737447 original size:10 final size:10
Alignment explanation
Indices: 1737432--1737474 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
1737422 TTTCACTTCG
1737432 TTTGTTTCTT
1 TTTGTTTCTT
*
1737442 TTTGTTTTATGT
1 TTTG-TTTCT-T
1737454 TTTGTTTCTT
1 TTTGTTTCTT
1737464 TTTGTTT-TT
1 TTTGTTTCTT
1737473 TT
1 TT
1737475 ATTTATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 4 0.14
10 12 0.41
11 8 0.28
12 5 0.17
ACGTcount: A:0.02, C:0.05, G:0.12, T:0.81
Consensus pattern (10 bp):
TTTGTTTCTT
Found at i:1738591 original size:108 final size:108
Alignment explanation
Indices: 1738402--1738618 Score: 389
Period size: 108 Copynumber: 2.0 Consensus size: 108
1738392 AGTGAAAAAG
*
1738402 AAAGAAAATGAAGAGTAGCATATCATGTCATAGGAATACAAATTTATCTAAAGCAAACAAGCTCA
1 AAAGAAAATGAAGAGTAGCATATCATGTCATAGGAATACAAATTTATCTAAAGCAAACAAGCCCA
1738467 CAATAGCTGTTATTCATACATAAAGAACCAATGCAGCAGATCA
66 CAATAGCTGTTATTCATACATAAAGAACCAATGCAGCAGATCA
* *
1738510 AAAGAAAATGAAGAGTAGCATATCATGTCATAGGAATACAAATTTATTTAGAGCAAACAAGCCCA
1 AAAGAAAATGAAGAGTAGCATATCATGTCATAGGAATACAAATTTATCTAAAGCAAACAAGCCCA
* *
1738575 CAATAGCTGTTATTCATACATAACGACCCAATGCAGCAGATCA
66 CAATAGCTGTTATTCATACATAAAGAACCAATGCAGCAGATCA
1738618 A
1 A
1738619 GCAGATCAAG
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 104 1.00
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.22
Consensus pattern (108 bp):
AAAGAAAATGAAGAGTAGCATATCATGTCATAGGAATACAAATTTATCTAAAGCAAACAAGCCCA
CAATAGCTGTTATTCATACATAAAGAACCAATGCAGCAGATCA
Done.