Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold52
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: 1774672
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 127110 characters in sequence are not A, C, G, or T
File 6 of 9
Found at i:1103762 original size:14 final size:14
Alignment explanation
Indices: 1103739--1103768 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1103729 ATTTAAAATT
*
1103739 TATTTTTATATTAA
1 TATTTATATATTAA
1103753 TATTTATATATTAA
1 TATTTATATATTAA
1103767 TA
1 TA
1103769 ATTAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTTATATATTAA
Found at i:1104393 original size:3 final size:3
Alignment explanation
Indices: 1104385--1104413 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1104375 ATGCGGAGGT
1104385 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1104414 TTGGTAGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1106505 original size:16 final size:15
Alignment explanation
Indices: 1106480--1106515 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1106470 GTAATGATGG
*
1106480 TATATTTATA-AAAA
1 TATATATATATAAAA
1106494 TATATATATATAAAA
1 TATATATATATAAAA
1106509 TATATAT
1 TATATAT
1106516 TTTATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATATATATATAAAA
Found at i:1106525 original size:33 final size:30
Alignment explanation
Indices: 1106480--1106561 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 30
1106470 GTAATGATGG
1106480 TATA-TTTATAAAAA-TATATATATATAAAATA
1 TATATTTTATAAAAATTATA-ATA-AT-AAATA
*
1106511 TATATTTTATTAAAAATTTTAATAATAAATA
1 TATATTTTA-TAAAAATTATAATAATAAATA
* *
1106542 TATATTATATGCAAAATTAT
1 TATATTTTAT-AAAAATTAT
1106562 TTGAAAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
30 1 0.02
31 24 0.56
32 6 0.14
33 9 0.21
34 3 0.07
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (30 bp):
TATATTTTATAAAAATTATAATAATAAATA
Found at i:1108845 original size:19 final size:17
Alignment explanation
Indices: 1108827--1108864 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1108817 CTCATATTTA
1108827 TAATATAAATATGTATT
1 TAATATAAATATGTATT
1108844 TAATATAAATA--TATT
1 TAATATAAATATGTATT
1108859 TAATAT
1 TAATAT
1108865 TTTAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.48
17 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TAATATAAATATGTATT
Found at i:1111948 original size:18 final size:19
Alignment explanation
Indices: 1111910--1111953 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1111900 TTGTAAAAAA
*
1111910 ATATATCATATTAAAAATT
1 ATATATTATATTAAAAATT
* *
1111929 AT-TATTATATTAATATTT
1 ATATATTATATTAAAAATT
1111947 ATATATT
1 ATATATT
1111954 TTTATAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATATTATATTAAAAATT
Found at i:1111958 original size:22 final size:22
Alignment explanation
Indices: 1111928--1111969 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1111918 TATTAAAAAT
* *
1111928 TATTATTATATTAATATTTATA
1 TATTATTATAATAAAATTTATA
*
1111950 TATTTTTATAATAAAATTTA
1 TATTATTATAATAAAATTTA
1111970 AATAAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTATTATAATAAAATTTATA
Found at i:1117526 original size:7 final size:7
Alignment explanation
Indices: 1117514--1117552 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
1117504 AAATAATATT
1117514 TTTAAAA
1 TTTAAAA
1117521 TTTAAAA
1 TTTAAAA
1117528 TTTAAAA
1 TTTAAAA
*
1117535 -TTAATA
1 TTTAAAA
1117541 TTTATAAA
1 TTTA-AAA
1117549 TTTA
1 TTTA
1117553 TTTTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 5 0.18
7 17 0.61
8 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
TTTAAAA
Found at i:1117749 original size:17 final size:16
Alignment explanation
Indices: 1117719--1117754 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1117709 TAAATACGAT
*
1117719 TAATTAAAATATAATA
1 TAATTAAAAGATAATA
1117735 TAATATAAAAGATAATA
1 TAAT-TAAAAGATAATA
1117752 TAA
1 TAA
1117755 ATATGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
TAATTAAAAGATAATA
Found at i:1117783 original size:28 final size:28
Alignment explanation
Indices: 1117725--1117799 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
1117715 CGATTAATTA
1117725 AAATATAATATAATATAAAAGATAATAT
1 AAATATAATATAATATAAAAGATAATAT
* * * *
1117753 AAATATGATATAAATATATAA-ATATTTT
1 AAATATAATAT-AATATAAAAGATAATAT
1117781 AAAATATAA-ATAATATAAA
1 -AAATATAATATAATATAAA
1117800 TTATAAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 7 0.18
28 17 0.44
29 15 0.38
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (28 bp):
AAATATAATATAATATAAAAGATAATAT
Found at i:1117789 original size:16 final size:16
Alignment explanation
Indices: 1117748--1117836 Score: 81
Period size: 16 Copynumber: 5.3 Consensus size: 16
1117738 TATAAAAGAT
1117748 AATATAAATATGATATAA
1 AATATAAATAT--TATAA
*
1117766 ATATATAAATATTTTAA
1 A-ATATAAATATTATAA
*
1117783 AATATAAATAATATAA
1 AATATAAATATTATAA
*
1117799 ATTATAAATA-TATTAA
1 AATATAAATATTA-TAA
* *
1117815 AATTTAAATAAATATAA
1 AATATAAAT-ATTATAA
1117832 AATAT
1 AATAT
1117837 CTTATTCATA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.03
16 32 0.53
17 13 0.22
18 3 0.05
19 10 0.17
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (16 bp):
AATATAAATATTATAA
Found at i:1117797 original size:33 final size:33
Alignment explanation
Indices: 1117748--1117836 Score: 119
Period size: 32 Copynumber: 2.7 Consensus size: 33
1117738 TATAAAAGAT
*
1117748 AATATAAATATGATATAAATATATAAATATTTTAA
1 AATATAAATA--ATATAAATATATAAATATATTAA
1117783 AATATAAATAATATAAAT-TATAAATATATTAA
1 AATATAAATAATATAAATATATAAATATATTAA
*
1117815 AATTTAAATAAATATAAA-ATAT
1 AATATAAAT-AATATAAATATAT
1117837 CTTATTCATA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
32 21 0.42
33 19 0.38
35 10 0.20
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (33 bp):
AATATAAATAATATAAATATATAAATATATTAA
Found at i:1118012 original size:12 final size:12
Alignment explanation
Indices: 1117995--1118019 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1117985 ATAAAGATAA
1117995 TTTTTAATTTTT
1 TTTTTAATTTTT
1118007 TTTTTAATTTTT
1 TTTTTAATTTTT
1118019 T
1 T
1118020 ATAAGAATTC
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTAATTTTT
Found at i:1125183 original size:16 final size:16
Alignment explanation
Indices: 1125134--1125195 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
1125124 TAAATATATG
* *
1125134 AATATTTTAAAATATA
1 AATATATTAAAATTTA
1125150 AAT-TA-TACAAATTATA
1 AATATATTA-AAATT-TA
1125166 AATATATTAAAATTTA
1 AATATATTAAAATTTA
*
1125182 AATAAATATAAAAT
1 AATATAT-TAAAAT
1125196 ATCTTATCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 2 0.05
15 5 0.13
16 16 0.42
17 13 0.34
18 2 0.05
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATATTAAAATTTA
Found at i:1125193 original size:17 final size:18
Alignment explanation
Indices: 1125147--1125195 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
1125137 ATTTTAAAAT
1125147 ATAAATTATACAAATTATAA
1 ATAAA-TATA-AAATTATAA
*
1125167 ATATAT-TAAAATT-TAA
1 ATAAATATAAAATTATAA
1125183 ATAAATATAAAAT
1 ATAAATATAAAAT
1125196 ATCTTATCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.31
17 11 0.42
18 2 0.08
19 1 0.04
20 4 0.15
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAATATAAAATTATAA
Found at i:1126649 original size:23 final size:23
Alignment explanation
Indices: 1126605--1126649 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1126595 TAAAATTATT
*
1126605 TTAATTTAAATCAATCAGTTTAA
1 TTAATTTAAATCAATCAATTTAA
*
1126628 TTAATTT-AATCGATCGAATTTA
1 TTAATTTAAATCAATC-AATTTA
1126650 TCAAATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (23 bp):
TTAATTTAAATCAATCAATTTAA
Found at i:1127492 original size:181 final size:175
Alignment explanation
Indices: 1127125--1127519 Score: 475
Period size: 181 Copynumber: 2.2 Consensus size: 175
1127115 TATGTTGATT
*
1127125 TAAAATTTAATTTGATGATTTAAAATTTTTAATTT--AAAAAAAAAATATCATCTTAAAATTTGG
1 TAAAATTTGATTTGATGATTT-AAATTTTTAATTTAAAAAAAAAAAATATCATCTTAAAATTTGG
*
1127188 CATTTATTTTTGTAAGTCAAGTCTAATTAATTGATGGTTGAGAAGTTGTAACTTTATATCAATAG
65 CATTTATTTTTGTAAGTCAAGTCTAATTAATTGAGGGTTGAGAAGTTGTAACTTTATATCAATAG
*
1127253 TCTAACCAAAGTGAAATATACTGTACATAAACTTATTCATATATTAAC
130 TCTAACCAAAGTGAAATACACTGTACATAAACTTATTCA-ATATT-AC
* * *
1127301 TTAAAATTTGATTCGATGATTTGAATTTTTAATTTAAAAATAAAAATATATATCATCTTGAAATT
1 -TAAAATTTGATTTGATGATTTAAATTTTTAATTTAAAAA-AAAAA-A-ATATCATCTTAAAATT
*
1127366 TGGCATTTA-TTTTGTAAGTCAATTCTAATTAATTGAGGGTTGAGAAGTAGCTCTTTGTAACTTT
62 TGGCATTTATTTTTGTAAGTCAAGTCTAATTAATTGAGGGTTGAG-A--AG----TTGTAACTTT
* * *
1127430 ATATCAATAGTCTAACTAAAGTGAAATACA-TGGTGCATAGACTTATATC-A-ATT-C
120 ATATCAATAGTCTAACCAAAGTGAAATACACT-GTACATAAACTTAT-TCAATATTAC
*
1127484 -AAAATTTGATTTAATGATTTAAATTTATT-ATTTAAA
1 TAAAATTTGATTTGATGATTTAAATTT-TTAATTTAAA
1127520 TATTTTAAGA
Statistics
Matches: 190, Mismatches: 13, Indels: 26
0.83 0.06 0.11
Matches are distributed among these distances:
176 12 0.06
177 19 0.10
178 3 0.02
179 5 0.03
180 34 0.18
181 55 0.29
182 2 0.01
183 3 0.02
185 3 0.02
186 2 0.01
187 50 0.26
188 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.41
Consensus pattern (175 bp):
TAAAATTTGATTTGATGATTTAAATTTTTAATTTAAAAAAAAAAAATATCATCTTAAAATTTGGC
ATTTATTTTTGTAAGTCAAGTCTAATTAATTGAGGGTTGAGAAGTTGTAACTTTATATCAATAGT
CTAACCAAAGTGAAATACACTGTACATAAACTTATTCAATATTAC
Found at i:1129140 original size:2 final size:2
Alignment explanation
Indices: 1129135--1129162 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1129125 TTTAATTTAA
1129135 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
1129163 CATCTTAAAA
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:1135640 original size:42 final size:40
Alignment explanation
Indices: 1135532--1135641 Score: 107
Period size: 42 Copynumber: 2.7 Consensus size: 40
1135522 TAAAATTTTA
* * *
1135532 ATTTATTATTTCAAATAATA-TTAAAAATTATTAAAAAATT
1 ATTTATTATTT-AAATAATATTTTAAATTTAATAAAAAATT
* * *
1135572 ATTT-TTATATAAATATTTATAATTAAATTTAAATAAAAAATT
1 ATTTATTATTTAAATA-ATAT-TTTAAATTT-AATAAAAAATT
1135614 ATTTTATTATTTAAATAATATTTTAAAT
1 A-TTTATTATTTAAATAATATTTTAAAT
1135642 CGAATTAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
38 5 0.09
39 7 0.13
40 4 0.07
41 6 0.11
42 17 0.31
43 6 0.11
44 10 0.18
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (40 bp):
ATTTATTATTTAAATAATATTTTAAATTTAATAAAAAATT
Found at i:1136518 original size:22 final size:22
Alignment explanation
Indices: 1136493--1136537 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1136483 AATTAGTAAT
*
1136493 CCGACTCATAGACAAATATGTG
1 CCGACTCATAAACAAATATGTG
*
1136515 CCGACTCATAAATAAATATGTG
1 CCGACTCATAAACAAATATGTG
1136537 C
1 C
1136538 ACTAGATGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (22 bp):
CCGACTCATAAACAAATATGTG
Found at i:1138649 original size:16 final size:17
Alignment explanation
Indices: 1138628--1138659 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1138618 TTTTACTATT
1138628 TAAAAATATTA-AAATA
1 TAAAAATATTATAAATA
1138644 TAAAAATATTATAAAT
1 TAAAAATATTATAAAT
1138660 TAATATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAATATTATAAATA
Found at i:1139327 original size:18 final size:17
Alignment explanation
Indices: 1139294--1139336 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
1139284 ACTTATTCAT
*
1139294 ATTAATTTAAAATTTAA
1 ATTAATTAAAAATTTAA
*
1139311 TTTAATTAAATAATTTAA
1 ATTAATTAAA-AATTTAA
1139329 ATTAATTA
1 ATTAATTA
1139337 TTTAAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAATTAAAAATTTAA
Found at i:1139344 original size:22 final size:24
Alignment explanation
Indices: 1139296--1139351 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
1139286 TTATTCATAT
1139296 TAATTTAAAATTTAATTTAATTAAA
1 TAATTT-AAATTTAATTTAATTAAA
*
1139321 TAATTTAAA-TTAA-TTATTTAAA
1 TAATTTAAATTTAATTTAATTAAA
*
1139343 TATTTTAAA
1 TAATTTAAA
1139352 ATATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 16 0.55
23 4 0.14
24 3 0.10
25 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATTTAAATTTAATTTAATTAAA
Found at i:1139373 original size:17 final size:18
Alignment explanation
Indices: 1139353--1139390 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1139343 TATTTTAAAA
1139353 TATTAAAAATAAT-TTTT
1 TATTAAAAATAATATTTT
* *
1139370 TATTAATAATTATATTTT
1 TATTAAAAATAATATTTT
1139388 TAT
1 TAT
1139391 AATTAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTAAAAATAATATTTT
Found at i:1142734 original size:5 final size:5
Alignment explanation
Indices: 1142724--1142748 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1142714 TTTAACTTGA
1142724 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
1142749 GTCACCTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1145154 original size:16 final size:17
Alignment explanation
Indices: 1145135--1145169 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1145125 AATATTAAAA
*
1145135 TATATTATATTTA-ATT
1 TATATCATATTTATATT
1145151 TATATCATATTTATATT
1 TATATCATATTTATATT
1145168 TA
1 TA
1145170 AAATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATCATATTTATATT
Found at i:1145188 original size:9 final size:9
Alignment explanation
Indices: 1145162--1145205 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
1145152 ATATCATATT
1145162 TATATTTAA
1 TATATTTAA
*
1145171 AAT-TTTAA
1 TATATTTAA
1145179 TATATTTAA
1 TATATTTAA
*
1145188 TAATATTTAT
1 T-ATATTTAA
1145198 TATATTTA
1 TATATTTA
1145206 TATTTATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 7 0.23
9 15 0.50
10 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TATATTTAA
Found at i:1145759 original size:22 final size:22
Alignment explanation
Indices: 1145732--1145799 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
1145722 TTAAAAATAA
*
1145732 ATATATTAATTTTTATATTTTT
1 ATATATTAATTTTTATATTTAT
*
1145754 ATATATAAATATTTT-TATTTAT
1 ATATATTAAT-TTTTATATTTAT
* *
1145776 A-AAAATATATTTTTATATTTAT
1 ATATATTA-ATTTTTATATTTAT
1145798 AT
1 AT
1145800 TTAAATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 7 0.19
22 26 0.70
23 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATATTAATTTTTATATTTAT
Found at i:1145767 original size:16 final size:16
Alignment explanation
Indices: 1145746--1145778 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1145736 ATTAATTTTT
1145746 ATATTTTTATATATAA
1 ATATTTTTATATATAA
*
1145762 ATATTTTTATTTATAA
1 ATATTTTTATATATAA
1145778 A
1 A
1145779 AATATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTTTATATATAA
Found at i:1145781 original size:18 final size:16
Alignment explanation
Indices: 1145746--1145792 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
1145736 ATTAATTTTT
*
1145746 ATATTTTTATATATAA
1 ATATTTTTATATAAAA
1145762 ATATTTTTATTTATAAAA
1 ATATTTTTA--TATAAAA
1145780 ATATATTTT-TATA
1 ATAT-TTTTATATA
1145793 TTTATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 13 0.48
18 10 0.37
19 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATTTTTATATAAAA
Found at i:1145790 original size:16 final size:18
Alignment explanation
Indices: 1145745--1145793 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
1145735 TATTAATTTT
1145745 TATATTTTTATATATAAA
1 TATATTTTTATATATAAA
* *
1145763 TAT-TTTTATTTATAAAAA
1 TATATTTT-TATATATAAA
1145781 TATATTTTTATAT
1 TATATTTTTATAT
1145794 TTATATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.15
18 18 0.69
19 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTTTTATATATAAA
Found at i:1148926 original size:17 final size:15
Alignment explanation
Indices: 1148892--1148921 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1148882 AACAAAACCA
1148892 AAAAAAAAAAAAGGC
1 AAAAAAAAAAAAGGC
*
1148907 AAAAAACAAAAAGGC
1 AAAAAAAAAAAAGGC
1148922 CCAAAGCTGC
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:0.77, C:0.10, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGGC
Found at i:1150741 original size:25 final size:26
Alignment explanation
Indices: 1150687--1150735 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
1150677 TTAATATTAT
*
1150687 ATATTTTATAATAAAATTAAATAAAA
1 ATATTTTATAATAAAAGTAAATAAAA
1150713 ATATTATT-TAAT-AAAGTAAATAA
1 ATATT-TTATAATAAAAGTAAATAA
1150736 TGATATAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 10 0.48
26 9 0.43
27 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
ATATTTTATAATAAAAGTAAATAAAA
Found at i:1151581 original size:18 final size:19
Alignment explanation
Indices: 1151538--1151581 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1151528 AAAATCAAGA
* *
1151538 AATAATTATTTTTAATGAT
1 AATAATTATATTAAATGAT
1151557 AAT-ATTATATTAAAT-AT
1 AATAATTATATTAAATGAT
1151574 AATAATTA
1 AATAATTA
1151582 ATAATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 14 0.64
19 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AATAATTATATTAAATGAT
Found at i:1151604 original size:34 final size:34
Alignment explanation
Indices: 1151559--1151626 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
1151549 TTAATGATAA
* *
1151559 TATTATATTAAATATAATAATTAATAATTTTATT
1 TATTATATTAAATATAATAATTAAAAATATTATT
* * *
1151593 TATTATTTTAAATATATTTATTAAAAATATTATT
1 TATTATATTAAATATAATAATTAAAAATATTATT
1151627 AGATATGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
TATTATATTAAATATAATAATTAAAAATATTATT
Found at i:1151823 original size:14 final size:14
Alignment explanation
Indices: 1151804--1151833 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1151794 AAAAAAATTA
*
1151804 ATTTAAAGATTTTT
1 ATTTAAAAATTTTT
1151818 ATTTAAAAATTTTT
1 ATTTAAAAATTTTT
1151832 AT
1 AT
1151834 CTTATCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
ATTTAAAAATTTTT
Found at i:1152351 original size:21 final size:21
Alignment explanation
Indices: 1152327--1152368 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1152317 TTTTTTATTT
*
1152327 AAAT-TTAATTATAAAATATAA
1 AAATATTAA-TATAAAAAATAA
1152348 AAATATTAATATAAAAAATAA
1 AAATATTAATATAAAAAATAA
1152369 TTTTTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATATTAATATAAAAAATAA
Found at i:1152824 original size:13 final size:13
Alignment explanation
Indices: 1152807--1152837 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1152797 AAACCCTTCA
1152807 CAAAAAAAGAAAG
1 CAAAAAAAGAAAG
*
1152820 GAAAAAAAGAAAG
1 CAAAAAAAGAAAG
1152833 CAAAA
1 CAAAA
1152838 GAAATGACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.00
Consensus pattern (13 bp):
CAAAAAAAGAAAG
Found at i:1157133 original size:24 final size:24
Alignment explanation
Indices: 1157101--1157151 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
1157091 GGTGGCTTGT
1157101 ACTGAGTGCATTCAACTTCTGTTA
1 ACTGAGTGCATTCAACTTCTGTTA
1157125 ACTGAGTGCATTCAACTTCTGTTA
1 ACTGAGTGCATTCAACTTCTGTTA
1157149 ACT
1 ACT
1157152 TCCGTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (24 bp):
ACTGAGTGCATTCAACTTCTGTTA
Found at i:1158312 original size:16 final size:17
Alignment explanation
Indices: 1158281--1158313 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1158271 TTATTGTATC
*
1158281 AAAATTTATATAAATAT
1 AAAATATATATAAATAT
1158298 AAAATATAT-TAAATAT
1 AAAATATATATAAATAT
1158314 GATTATGATA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATATATATAAATAT
Found at i:1158564 original size:19 final size:19
Alignment explanation
Indices: 1158521--1158557 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1158511 AAAATTATTA
*
1158521 AAATATAATATAAATTTAT
1 AAATATATTATAAATTTAT
1158540 AAATATATTA-AAATTTAT
1 AAATATATTATAAATTTAT
1158558 TTAATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATATTATAAATTTAT
Found at i:1158582 original size:31 final size:33
Alignment explanation
Indices: 1158544--1158604 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 33
1158534 ATTTATAAAT
*
1158544 ATATTAAAATTTAT-TTAATAT-TATTATTAAC
1 ATATTAAAATTTATATAAATATATATTATTAAC
1158575 ATATTAAAATTTATATAAATATATATTATT
1 ATATTAAAATTTATATAAATATATATTATT
1158605 TTAAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 14 0.52
32 6 0.22
33 7 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (33 bp):
ATATTAAAATTTATATAAATATATATTATTAAC
Found at i:1158617 original size:15 final size:14
Alignment explanation
Indices: 1158579--1158638 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 14
1158569 ATTAACATAT
*
1158579 TAAAATTTATATAAA
1 TAAAA-TTATTTAAA
*
1158594 TATATATTATTTTAAA
1 TA-AAATTA-TTTAAA
*
1158610 TAAAATTA-TTATA
1 TAAAATTATTTAAA
*
1158623 TAAAATTATATAAA
1 TAAAATTATTTAAA
1158637 TA
1 TA
1158639 TAATATAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
13 12 0.33
14 5 0.14
15 10 0.28
16 9 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAAATTATTTAAA
Found at i:1158621 original size:18 final size:20
Alignment explanation
Indices: 1158584--1158621 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1158574 CATATTAAAA
*
1158584 TTTATATAAATATATATTAT
1 TTTAAATAAATATATATTAT
1158604 TTTAAATAAA-AT-TATTAT
1 TTTAAATAAATATATATTAT
1158622 ATAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAATAAATATATATTAT
Found at i:1159362 original size:21 final size:20
Alignment explanation
Indices: 1159337--1159376 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1159327 TAATAAAAAA
1159337 TTAT-TTTTAT-ATTAATATT
1 TTATATTTTATAATTAA-ATT
1159356 TTATATTTTATAATTAAATT
1 TTATATTTTATAATTAAATT
1159376 T
1 T
1159377 AAATATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATATTTTATAATTAAATT
Found at i:1159815 original size:3 final size:3
Alignment explanation
Indices: 1159807--1159837 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1159797 GTACTTGAGT
1159807 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1159838 AAGCATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1160691 original size:12 final size:12
Alignment explanation
Indices: 1160674--1160698 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1160664 ACAAGTCCTC
1160674 TCTTCTTTTTTT
1 TCTTCTTTTTTT
1160686 TCTTCTTTTTTT
1 TCTTCTTTTTTT
1160698 T
1 T
1160699 TTTCATAGAA
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TCTTCTTTTTTT
Found at i:1165122 original size:2 final size:2
Alignment explanation
Indices: 1165115--1165163 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
1165105 AAGAAAAGGA
* *
1165115 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AC 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
1165157 AT -T AT AT
1 AT AT AT AT
1165164 GCAATGTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1165635 original size:21 final size:21
Alignment explanation
Indices: 1165611--1165651 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1165601 TAATTTTATT
*
1165611 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TAAAAAATATA
1165632 TAAATATTAATAAAAAATAT
1 TAAATATTAATAAAAAATAT
1165652 TTTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATATTAATAAAAAATATA
Found at i:1166637 original size:5 final size:5
Alignment explanation
Indices: 1166619--1166699 Score: 66
Period size: 5 Copynumber: 16.6 Consensus size: 5
1166609 AAAAAAAATG
1166619 ATATA AT-T- ATATA ATATAA ATATA ATA-A A-A-A ATATA ATATA ATAT-
1 ATATA ATATA ATATA ATAT-A ATATA ATATA ATATA ATATA ATATA ATATA
* *
1166664 ATATA ATAAA ATATAAA ATATA ATTTAA ATATA ATA
1 ATATA ATATA ATAT--A ATATA ATAT-A ATATA ATA
1166700 AGATATATTA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
3 5 0.08
4 9 0.14
5 35 0.56
6 9 0.14
7 5 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:1166659 original size:36 final size:36
Alignment explanation
Indices: 1166608--1166679 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
1166598 TTATAAAAAT
*
1166608 TAAAAAAAATGATATAAT-TATATAATATAAATATAA
1 TAAAAAAAATAATATAATATATATAATA-AAATATAA
*
1166644 TAAAAAATATAATATAATATATATAATAAAATATAA
1 TAAAAAAAATAATATAATATATATAATAAAATATAA
1166680 AATATAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 24 0.73
37 9 0.27
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (36 bp):
TAAAAAAAATAATATAATATATATAATAAAATATAA
Found at i:1166674 original size:26 final size:26
Alignment explanation
Indices: 1166627--1166714 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 26
1166617 TGATATAATT
*
1166627 ATATAATATAAATATAATAAAAAATATA
1 ATATAATAT--ATATAATAAAATATATA
*
1166655 ATATAATATATATAATAAAATATAAA
1 ATATAATATATATAATAAAATATATA
* *
1166681 ATATAATTTAAATATAATAAGATATATTA
1 ATATAA--TATATATAATAAAATATA-TA
1166710 ATATA
1 ATATA
1166715 TCAAAATTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
26 21 0.40
28 25 0.48
29 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (26 bp):
ATATAATATATATAATAAAATATATA
Found at i:1166682 original size:31 final size:31
Alignment explanation
Indices: 1166619--1166696 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
1166609 AAAAAAAATG
*
1166619 ATATAATT-ATATAATATAAATATAATAAAAA
1 ATATAATTAATAT-ATATAAATAAAATAAAAA
*
1166650 ATATAATATAATATATAT-AATAAAATATAAA
1 ATATAAT-TAATATATATAAATAAAATAAAAA
1166681 ATATAATTTAA-ATATA
1 ATATAA-TTAATATATA
1166697 ATAAGATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 5 0.12
31 27 0.64
32 6 0.14
33 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (31 bp):
ATATAATTAATATATATAAATAAAATAAAAA
Found at i:1166683 original size:12 final size:12
Alignment explanation
Indices: 1166626--1166697 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 12
1166616 ATGATATAAT
*
1166626 TATATAATATAAA
1 TATAAAATA-AAA
1166639 TATAATAA-AAAA
1 TATAA-AATAAAA
* *
1166651 TATAATATAATA
1 TATAAAATAAAA
*
1166663 TATATAATAAAA
1 TATAAAATAAAA
*
1166675 TATAAAATATAA
1 TATAAAATAAAA
*
1166687 TTTAAATATAA
1 TATAAA-ATAA
1166698 TAAGATATAT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
11 1 0.02
12 35 0.76
13 8 0.17
14 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TATAAAATAAAA
Found at i:1166754 original size:18 final size:18
Alignment explanation
Indices: 1166705--1166757 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
1166695 TAATAAGATA
1166705 TATTAATATATCAAAATT
1 TATTAATATATCAAAATT
*
1166723 TA-T-ATA-A-CATAATT
1 TATTAATATATCAAAATT
*
1166737 TATTAATATATTAAAATT
1 TATTAATATATCAAAATT
1166755 TAT
1 TAT
1166758 ATTAGCATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
14 8 0.29
15 2 0.07
16 6 0.21
17 2 0.07
18 10 0.36
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAATATATCAAAATT
Found at i:1166794 original size:20 final size:18
Alignment explanation
Indices: 1166769--1166811 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
1166759 TTAGCATATA
* *
1166769 ATATAT-TAAATATGATT
1 ATATATATAAAAATAATT
1166786 ATGATATATAAAAATAATT
1 AT-ATATATAAAAATAATT
1166805 ATATATA
1 ATATATA
1166812 AACTAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 9 0.41
19 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
ATATATATAAAAATAATT
Found at i:1167512 original size:10 final size:10
Alignment explanation
Indices: 1167499--1167536 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1167489 TTTTTTATTA
1167499 ATTTAAATTG
1 ATTTAAATTG
*
1167509 ATTT-GATTG
1 ATTTAAATTG
1167518 ATTTAAATTG
1 ATTTAAATTG
1167528 ATATTAAAT
1 AT-TTAAAT
1167537 AATTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.33
10 10 0.42
11 6 0.25
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (10 bp):
ATTTAAATTG
Found at i:1167561 original size:12 final size:12
Alignment explanation
Indices: 1167544--1167568 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1167534 AATAATTAAA
1167544 ATATTTTTATTT
1 ATATTTTTATTT
1167556 ATATTTTTATTT
1 ATATTTTTATTT
1167568 A
1 A
1167569 ATTATAAAAT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATATTTTTATTT
Found at i:1167619 original size:42 final size:43
Alignment explanation
Indices: 1167550--1167632 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
1167540 TAAAATATTT
*
1167550 TTATTTATATTTTTATTTAATTATAAAATAAT-TAATATAAAAA
1 TTATTTATAATTTTATTTAATTATAAAATAATAT-ATATAAAAA
*
1167593 TTATTTTTAATTTTATATTAA-T-TAAAATAATATATATAAA
1 TTATTTATAATTTTAT-TTAATTATAAAATAATATATATAAA
1167633 TAATATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
42 16 0.44
43 16 0.44
44 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (43 bp):
TTATTTATAATTTTATTTAATTATAAAATAATATATATAAAAA
Found at i:1168946 original size:2 final size:2
Alignment explanation
Indices: 1168939--1168963 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1168929 TTGATAGCCT
1168939 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 T
1168964 GAATTGCACA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1169016 original size:80 final size:80
Alignment explanation
Indices: 1168883--1169038 Score: 276
Period size: 80 Copynumber: 1.9 Consensus size: 80
1168873 GAGCAGTGTC
* * *
1168883 TGAATTGTACACCTCTTATTGTTGGAATTATTGGACCAGCATAAATTTGATAGCCTTATATATAT
1 TGAATTGCACACCTCTTATTGTTGAAATTATTGGACAAGCATAAATTTGATAGCCTTATATATAT
1168948 ATATATATATATATA
66 ATATATATATATATA
*
1168963 TGAATTGCACACCTCTTATTTTTGAAATTATTGGACAAGCATAAATTTGATAGCCTTATATATAT
1 TGAATTGCACACCTCTTATTGTTGAAATTATTGGACAAGCATAAATTTGATAGCCTTATATATAT
1169028 ATATATATATA
66 ATATATATATA
1169039 AAAAGAAATT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (80 bp):
TGAATTGCACACCTCTTATTGTTGAAATTATTGGACAAGCATAAATTTGATAGCCTTATATATAT
ATATATATATATATA
Found at i:1170296 original size:13 final size:13
Alignment explanation
Indices: 1170270--1170309 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1170260 TGATATTAAA
1170270 ATAATTA-A-AAT
1 ATAATTATACAAT
1170281 ATAATTATACAAT
1 ATAATTATACAAT
1170294 ATAAATTAT-CAAT
1 AT-AATTATACAAT
1170307 ATA
1 ATA
1170310 TCAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 7 0.27
12 2 0.08
13 11 0.42
14 6 0.23
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATTATACAAT
Found at i:1171055 original size:2 final size:2
Alignment explanation
Indices: 1171048--1171084 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1171038 CACTTGGGAA
1171048 AT AT AT AT AT 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 AT AT AT AT AT A
1171085 AAGTTTAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1171218 original size:12 final size:12
Alignment explanation
Indices: 1171197--1171228 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1171187 ATGAAATGTT
1171197 TATATATATATG
1 TATATATATATG
*
1171209 TATATGTATATG
1 TATATATATATG
1171221 TATATATA
1 TATATATA
1171229 GTACAATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (12 bp):
TATATATATATG
Found at i:1171469 original size:2 final size:2
Alignment explanation
Indices: 1171462--1171501 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1171452 AACTTCATAA
1171462 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
1171502 GAAGTCCGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1173105 original size:2 final size:2
Alignment explanation
Indices: 1173098--1173161 Score: 57
Period size: 2 Copynumber: 34.5 Consensus size: 2
1173088 TTAATATAAA
* * * *
1173098 AT AT AT AT AT AT AT AC AT AA AT -T A- AA AT A- AT A- AA AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1173135 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
1173162 CATAAATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
1 5 0.10
2 46 0.90
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1176466 original size:2 final size:2
Alignment explanation
Indices: 1176461--1176499 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1176451 GATGTGTGTG
1176461 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1176500 GTAGTTTCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1178674 original size:15 final size:15
Alignment explanation
Indices: 1178637--1178675 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1178627 AAATTTTTAA
*
1178637 ATTATTAAATATAAT
1 ATTATTAAAAATAAT
*
1178652 ATTGTTAAAAATAAT
1 ATTATTAAAAATAAT
*
1178667 TTTATTAAA
1 ATTATTAAA
1178676 CTTTTCTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
ATTATTAAAAATAAT
Found at i:1184339 original size:22 final size:21
Alignment explanation
Indices: 1184314--1184355 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1184304 AATGTTTATT
* *
1184314 TAAATTTTAAGTATAAAATATC
1 TAAATATTAA-TAAAAAATATC
1184336 TAAATATTAATAAAAAATAT
1 TAAATATTAATAAAAAATAT
1184356 TTTTTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAATATTAATAAAAAATATC
Found at i:1185334 original size:10 final size:10
Alignment explanation
Indices: 1185319--1185386 Score: 72
Period size: 10 Copynumber: 6.9 Consensus size: 10
1185309 GAATATAATT
1185319 ATATAATAAA
1 ATATAATAAA
1185329 ATATAATAAA
1 ATATAATAAA
1185339 ATATAATATATA
1 ATATAATA-A-A
1185351 TATATAATAAA
1 -ATATAATAAA
1185362 A-AT-ATAAA
1 ATATAATAAA
*
1185370 ATA-AAT-TA
1 ATATAATAAA
1185378 ATATAATAA
1 ATATAATAA
1185387 GAAATTAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
8 10 0.20
9 8 0.16
10 19 0.39
11 2 0.04
12 2 0.04
13 8 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
ATATAATAAA
Found at i:1185336 original size:5 final size:5
Alignment explanation
Indices: 1185310--1185385 Score: 63
Period size: 5 Copynumber: 15.8 Consensus size: 5
1185300 TAAAAAAATG
* *
1185310 AATAT AAT-T -ATAT AATAA AATAT AATAA AATAT AATAT -ATAT -ATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* *
1185356 AATAAA AATAT AAAAT AA-ATT AATAT AATA
1 AAT-AT AATAT AATAT AATA-T AATAT AATA
1185386 AGAAATTAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
3 2 0.03
4 11 0.19
5 40 0.69
6 5 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:1185372 original size:26 final size:26
Alignment explanation
Indices: 1185328--1185399 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
1185318 TATATAATAA
*
1185328 AATATAAT-AAAATATAATATATA-T
1 AATATAATAAAAATATAAAATATATT
*
1185352 -ATATAATAAAAATATAAAATAAATT
1 AATATAATAAAAATATAAAATATATT
*
1185377 AATATAATAAGAAAT-TAATATAT
1 AATATAATAA-AAATATAAAATAT
1185400 CAAATTTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 7 0.17
24 13 0.32
25 1 0.03
26 15 0.38
27 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (26 bp):
AATATAATAAAAATATAAAATATATT
Found at i:1185385 original size:13 final size:12
Alignment explanation
Indices: 1185319--1185386 Score: 56
Period size: 13 Copynumber: 5.8 Consensus size: 12
1185309 GAATATAATT
1185319 ATATAAT-AA-A
1 ATATAATAAATA
1185329 ATATAAT-AA-A
1 ATATAATAAATA
*
1185339 ATATAATATATA
1 ATATAATAAATA
1185351 TATATAATAAA-A
1 -ATATAATAAATA
1185363 ATATAAAATAAATTA
1 ATAT--AATAAA-TA
1185378 ATATAATAA
1 ATATAATAA
1185387 GAAATTAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
10 17 0.35
11 5 0.10
12 2 0.04
13 20 0.41
15 5 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATATAATAAATA
Found at i:1185391 original size:16 final size:15
Alignment explanation
Indices: 1185362--1185398 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
1185352 ATATAATAAA
*
1185362 AATATAAAATAAATT
1 AATATAAAAGAAATT
1185377 AATATAATAAGAAATT
1 AATATAA-AAGAAATT
1185393 AATATA
1 AATATA
1185399 TCAAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
AATATAAAAGAAATT
Found at i:1185405 original size:29 final size:26
Alignment explanation
Indices: 1185328--1185391 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 26
1185318 TATATAATAA
* *
1185328 AATATAAT-AAAATATAATATATA-T
1 AATATAATAAAAATATAAAATAAATT
1185352 -ATATAATAAAAATATAAAATAAATT
1 AATATAATAAAAATATAAAATAAATT
1185377 AATATAATAAGAAAT
1 AATATAATAA-AAAT
1185392 TAATATATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 7 0.21
24 13 0.38
25 1 0.03
26 9 0.26
27 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
AATATAATAAAAATATAAAATAAATT
Found at i:1185410 original size:29 final size:26
Alignment explanation
Indices: 1185329--1185412 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 26
1185319 ATATAATAAA
* *
1185329 ATATAAT-AAAATAT--AATATATAT
1 ATATAATAAAAATATAAAATAAATTT
*
1185352 ATATAATAAAAATATAAAATAAATTA
1 ATATAATAAAAATATAAAATAAATTT
1185378 ATATAATAAGAAAT-TAATATATCAAATTT
1 ATATAATAA-AAATATAA-A-AT-AAATTT
1185407 ATATAA
1 ATATAA
1185413 CATAATTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
23 7 0.14
24 7 0.14
26 18 0.36
27 5 0.10
28 2 0.04
29 11 0.22
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (26 bp):
ATATAATAAAAATATAAAATAAATTT
Found at i:1186180 original size:10 final size:10
Alignment explanation
Indices: 1186167--1186209 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1186157 AGTTTTATTA
1186167 ATTTAAATTG
1 ATTTAAATTG
*
1186177 ATTT-GATTG
1 ATTTAAATTG
1186186 ATTTAAATTG
1 ATTTAAATTG
*
1186196 ATATTAAATAG
1 AT-TTAAATTG
1186207 ATT
1 ATT
1186210 AAAAGATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
9 8 0.29
10 11 0.39
11 9 0.32
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.49
Consensus pattern (10 bp):
ATTTAAATTG
Found at i:1187684 original size:85 final size:82
Alignment explanation
Indices: 1187543--1187698 Score: 233
Period size: 85 Copynumber: 1.9 Consensus size: 82
1187533 GGCAGTGTCC
* *
1187543 TGAATTGTACACCTCTTATTGTTGGAATTATGGGACCAGCATAAATTTGATAGCCTTATATATAT
1 TGAATTGCACACCTCTTATTGTTGGAATTATGGGACAAGCATAAATTTGATAGCCTTATATA-AT
1187608 ATATAATTATATAGTATA
65 ATATAATTATATAGTATA
* *
1187626 TGAATTGCACACCTCTTATT-TTAAATGAATTATTGGACAAGCATAAATTTGATAGCCTTATATA
1 TGAATTGCACACCTCTTATTGTT---GGAATTATGGGACAAGCATAAATTTGATAGCCTTATATA
1187690 ATATATAAT
63 ATATATAAT
1187699 ATAAAAAGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
82 2 0.03
83 19 0.29
84 9 0.14
85 36 0.55
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.39
Consensus pattern (82 bp):
TGAATTGCACACCTCTTATTGTTGGAATTATGGGACAAGCATAAATTTGATAGCCTTATATAATA
TATAATTATATAGTATA
Found at i:1187780 original size:31 final size:30
Alignment explanation
Indices: 1187745--1187810 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1187735 ATAGTATTAA
*
1187745 AATTTAAATATAAATTACGAATGATTTTTTT
1 AATTTAAACATAAATT-CGAATGATTTTTTT
* * * *
1187776 AATTTAAACATATATTTGATTGTTTTTTTT
1 AATTTAAACATAAATTCGAATGATTTTTTT
1187806 AATTT
1 AATTT
1187811 TTTTTCAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (30 bp):
AATTTAAACATAAATTCGAATGATTTTTTT
Found at i:1188958 original size:13 final size:12
Alignment explanation
Indices: 1188940--1188970 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
1188930 AAAATAATTA
1188940 AATATAATTATAC
1 AATATAATTAT-C
1188953 AATATAATTATC
1 AATATAATTATC
1188965 AATATA
1 AATATA
1188971 TCAATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (12 bp):
AATATAATTATC
Found at i:1189720 original size:2 final size:2
Alignment explanation
Indices: 1189713--1189745 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1189703 TGGGAAATAG
1189713 AT AT AT 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 AT AT AT A
1189746 AATTTAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1189846 original size:21 final size:21
Alignment explanation
Indices: 1189806--1189846 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1189796 ATATTATTTT
* *
1189806 TAAAAATTTCATAAATAAATA
1 TAAAAATTTCAAAAAGAAATA
*
1189827 TAAAAATTTTAAAAAGAAAT
1 TAAAAATTTCAAAAAGAAAT
1189847 GAACTTGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
TAAAAATTTCAAAAAGAAATA
Found at i:1190145 original size:16 final size:15
Alignment explanation
Indices: 1190124--1190167 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 15
1190114 AAAACTCATA
1190124 AATATATATATATGAT
1 AATATATATATAT-AT
1190140 AATATATATAATATAT
1 AATATATAT-ATATAT
1190156 AATATAGTATAT
1 AATATA-TATAT
1190168 GAAGTCCGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:1192069 original size:16 final size:17
Alignment explanation
Indices: 1192048--1192080 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1192038 ATTAAATTAA
1192048 TAAATTAAATTT-ATTT
1 TAAATTAAATTTGATTT
*
1192064 TAAATTTAATTTGATTT
1 TAAATTAAATTTGATTT
1192081 GATTTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TAAATTAAATTTGATTT
Found at i:1194276 original size:24 final size:24
Alignment explanation
Indices: 1194244--1194294 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
1194234 GGTGGCTTGT
1194244 ACTGAGTGCATTCAACTTCTGTTA
1 ACTGAGTGCATTCAACTTCTGTTA
1194268 ACTGAGTGCATTCAACTTCTGTTA
1 ACTGAGTGCATTCAACTTCTGTTA
1194292 ACT
1 ACT
1194295 TCCGTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (24 bp):
ACTGAGTGCATTCAACTTCTGTTA
Found at i:1195732 original size:31 final size:33
Alignment explanation
Indices: 1195694--1195754 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 33
1195684 ATGTATAAAT
*
1195694 ATATTAAAATTTAT-TTAATAT-TATTATTAAC
1 ATATTAAAATTTATATAAATATATATTATTAAC
1195725 ATATTAAAATTTATATAAATATATATTATT
1 ATATTAAAATTTATATAAATATATATTATT
1195755 TTAAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 14 0.52
32 6 0.22
33 7 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (33 bp):
ATATTAAAATTTATATAAATATATATTATTAAC
Found at i:1195776 original size:12 final size:12
Alignment explanation
Indices: 1195759--1195783 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1195749 ATTATTTTAA
1195759 ATAAAATTATAT
1 ATAAAATTATAT
1195771 ATAAAATTATAT
1 ATAAAATTATAT
1195783 A
1 A
1195784 AATATAATAT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAAAATTATAT
Found at i:1195801 original size:22 final size:22
Alignment explanation
Indices: 1195735--1195801 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
1195725 ATATTAAAAT
*
1195735 TTATATAAATAT-ATATTATT-
1 TTATATAAATATAATATAATTA
* *
1195755 TTAAATAAA-ATTATATATAA-AA
1 TTATATAAATA-TA-ATATAATTA
1195777 TTATATAAATATAATATAATTA
1 TTATATAAATATAATATAATTA
1195799 TTA
1 TTA
1195802 CGAATCATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
19 1 0.03
20 9 0.25
21 6 0.17
22 19 0.53
23 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTATATAAATATAATATAATTA
Found at i:1196533 original size:21 final size:20
Alignment explanation
Indices: 1196508--1196547 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1196498 TAATAAAAAA
1196508 TTAT-TTTTAT-ATTAATATT
1 TTATATTTTATAATTAA-ATT
1196527 TTATATTTTATAATTAAATT
1 TTATATTTTATAATTAAATT
1196547 T
1 T
1196548 AAATATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATATTTTATAATTAAATT
Found at i:1196987 original size:3 final size:3
Alignment explanation
Indices: 1196979--1197009 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1196969 GTACTTGAGT
1196979 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1197010 AAGCATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1197863 original size:12 final size:12
Alignment explanation
Indices: 1197846--1197870 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1197836 ACAAGTCCTC
1197846 TCTTCTTTTTTT
1 TCTTCTTTTTTT
1197858 TCTTCTTTTTTT
1 TCTTCTTTTTTT
1197870 T
1 T
1197871 TTTTCATAGA
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TCTTCTTTTTTT
Found at i:1202293 original size:2 final size:2
Alignment explanation
Indices: 1202286--1202336 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
1202276 AAGAAAAGGA
* *
1202286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1202328 AT AT -T AT AT
1 AT AT AT AT AT
1202337 GCAATGTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1202809 original size:21 final size:21
Alignment explanation
Indices: 1202785--1202825 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1202775 TAATTTTATT
*
1202785 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TAAAAAATATA
1202806 TAAATATTAATAAAAAATAT
1 TAAATATTAATAAAAAATAT
1202826 TTTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATATTAATAAAAAATATA
Found at i:1203807 original size:5 final size:5
Alignment explanation
Indices: 1203789--1203843 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
1203779 AAAAAAAATG
1203789 ATATA AT-T- ATATA ATATAA ATATA ATA-A A-A-A ATATA ATATA ATATAA
1 ATATA ATATA ATATA ATAT-A ATATA ATATA ATATA ATATA ATATA ATAT-A
1203836 ATATA ATA
1 ATATA ATA
1203844 AGATATATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
3 5 0.11
4 5 0.11
5 24 0.55
6 10 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
ATATA
Found at i:1203813 original size:11 final size:11
Alignment explanation
Indices: 1203797--1203843 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
1203787 TGATATAATT
1203797 ATATAATATAA
1 ATATAATATAA
1203808 ATAT-A-ATAA
1 ATATAATATAA
1203817 A-A-AATAT-A
1 ATATAATATAA
1203825 ATATAATATAA
1 ATATAATATAA
1203836 ATATAATA
1 ATATAATA
1203844 AGATATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 4 0.13
9 8 0.26
10 6 0.19
11 13 0.42
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1203831 original size:28 final size:29
Alignment explanation
Indices: 1203797--1203858 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 29
1203787 TGATATAATT
1203797 ATATAATATAAATATAATAAAAAATA-TA
1 ATATAATATAAATATAATAAAAAATATTA
* *
1203825 ATATAATATAAATATAATAAGATATATTA
1 ATATAATATAAATATAATAAAAAATATTA
1203854 ATATA
1 ATATA
1203859 TCAAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 24 0.77
29 7 0.23
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (29 bp):
ATATAATATAAATATAATAAAAAATATTA
Found at i:1203849 original size:16 final size:15
Alignment explanation
Indices: 1203789--1203850 Score: 62
Period size: 16 Copynumber: 4.3 Consensus size: 15
1203779 AAAAAAAATG
*
1203789 ATATAATTAT-AT-A
1 ATATAAATATAATAA
1203802 ATATAAATATAAT-A
1 ATATAAATATAATAA
1203816 A-A-AAATATAATATA
1 ATATAAATATAATA-A
1203830 ATATAAATATAATAA
1 ATATAAATATAATAA
1203845 GATATA
1 -ATATA
1203851 TTAATATATC
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
12 9 0.21
13 10 0.24
14 6 0.14
15 2 0.05
16 15 0.36
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
ATATAAATATAATAA
Found at i:1203898 original size:18 final size:18
Alignment explanation
Indices: 1203849--1203901 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
1203839 TAATAAGATA
1203849 TATTAATATATCAAAATT
1 TATTAATATATCAAAATT
*
1203867 TA-T-ATA-A-CATAATT
1 TATTAATATATCAAAATT
*
1203881 TATTAATATATTAAAATT
1 TATTAATATATCAAAATT
1203899 TAT
1 TAT
1203902 ATTAGCATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
14 8 0.29
15 2 0.07
16 6 0.21
17 2 0.07
18 10 0.36
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAATATATCAAAATT
Found at i:1203938 original size:20 final size:18
Alignment explanation
Indices: 1203913--1203955 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
1203903 TTAGCATATA
* *
1203913 ATATAT-TAAATATGATT
1 ATATATATAAAAATAATT
1203930 ATGATATATAAAAATAATT
1 AT-ATATATAAAAATAATT
1203949 ATATATA
1 ATATATA
1203956 GACTAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 9 0.41
19 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
ATATATATAAAAATAATT
Found at i:1206120 original size:2 final size:2
Alignment explanation
Indices: 1206113--1206149 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1206103 TTGATAGCCT
1206113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1206150 GAATTGCACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1207462 original size:13 final size:13
Alignment explanation
Indices: 1207436--1207475 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1207426 TGATATTAAA
1207436 ATAATTA-A-AAT
1 ATAATTATACAAT
1207447 ATAATTATACAAT
1 ATAATTATACAAT
1207460 ATAAATTAT-CAAT
1 AT-AATTATACAAT
1207473 ATA
1 ATA
1207476 TCAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 7 0.27
12 2 0.08
13 11 0.42
14 6 0.23
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATTATACAAT
Found at i:1208219 original size:2 final size:2
Alignment explanation
Indices: 1208212--1208248 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1208202 CACTTGGGAA
1208212 AT AT AT AT AT 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 AT AT AT AT AT A
1208249 AAGTTTAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1208382 original size:12 final size:12
Alignment explanation
Indices: 1208361--1208392 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1208351 ATGAAATGTT
1208361 TATATATATATG
1 TATATATATATG
*
1208373 TATATGTATATG
1 TATATATATATG
1208385 TATATATA
1 TATATATA
1208393 GTACAATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (12 bp):
TATATATATATG
Found at i:1210252 original size:2 final size:2
Alignment explanation
Indices: 1210239--1210314 Score: 63
Period size: 2 Copynumber: 40.5 Consensus size: 2
1210229 TTACATATTA
* * * *
1210239 AT AT AA AT AT AT AT AT AT AT AT -T AC AT AA AT -T A- AA AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1210277 AT AA AA AT A- AT 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 AT AT AT AT AT AT A
1210315 CATAAATTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
1 5 0.08
2 55 0.92
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1212176 original size:2 final size:2
Alignment explanation
Indices: 1212171--1212196 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1212161 GGTGTCAAAC
1212171 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
1212197 GAAGGCTTAA
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:1214627 original size:19 final size:21
Alignment explanation
Indices: 1214605--1214646 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1214595 TTCAATAATA
1214605 ATTTATA-TA-TTTATGTTAT
1 ATTTATATTATTTTATGTTAT
*
1214624 ATTTATATTATTTTATTTTAT
1 ATTTATATTATTTTATGTTAT
1214645 AT
1 AT
1214647 AATCATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 2 0.10
21 11 0.55
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTATATTATTTTATGTTAT
Found at i:1214667 original size:20 final size:21
Alignment explanation
Indices: 1214638--1214717 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 21
1214628 ATATTATTTT
1214638 ATTTTATATAATCATATTTA-AA
1 ATTTTATAT-AT-ATATTTATAA
*
1214660 ATTTTATATATATTTTTATAA
1 ATTTTATATATATATTTATAA
*
1214681 ATTTTAATATGTTCATATTATATAA
1 ATTTT-ATAT-AT-ATATT-TATAA
*
1214706 AATTTAT-TATAT
1 ATTTTATATATAT
1214718 TTATATATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
20 6 0.12
21 11 0.23
22 14 0.29
23 2 0.04
24 6 0.12
25 9 0.19
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (21 bp):
ATTTTATATATATATTTATAA
Found at i:1214718 original size:5 final size:5
Alignment explanation
Indices: 1214695--1214757 Score: 51
Period size: 5 Copynumber: 13.0 Consensus size: 5
1214685 TAATATGTTC
* * * *
1214695 ATATT ATATA AAATT -TATT ATATT -TA-T ATATT CATATT ATTTT ATATC
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT -ATATT ATATT ATATT
*
1214743 ATATT ATATT TTATT
1 ATATT ATATT ATATT
1214758 TTTTTTCTGA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
3 1 0.02
4 7 0.16
5 32 0.71
6 5 0.11
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:1214752 original size:17 final size:18
Alignment explanation
Indices: 1214710--1214756 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
1214700 ATATAAAATT
1214710 TATTATATTTATATATTCA
1 TATTATATTT-TATATTCA
1214729 TA-T-TATTTTATA-TCA
1 TATTATATTTTATATTCA
1214744 TATTATATTTTAT
1 TATTATATTTTAT
1214757 TTTTTTTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.19
16 5 0.19
17 13 0.50
18 1 0.04
19 2 0.08
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTATATTTTATATTCA
Found at i:1215117 original size:23 final size:21
Alignment explanation
Indices: 1215056--1215119 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
1215046 TTTTTTAAAA
1215056 ATTAATA-TTAT-TATTTTTAT
1 ATTAATATTTATAT-TTTTTAT
*
1215076 ATTAATATTTATATATTTTAT
1 ATTAATATTTATATTTTTTAT
1215097 GATTAA-ATTTAAATATTTTTTAT
1 -ATTAATATTT--ATATTTTTTAT
1215120 TAAATAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 7 0.19
21 14 0.38
22 6 0.16
23 10 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTAATATTTATATTTTTTAT
Found at i:1216073 original size:12 final size:12
Alignment explanation
Indices: 1216056--1216092 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1216046 CAAATTTAGG
*
1216056 ATATATATATAT
1 ATATATATGTAT
1216068 ATATATATGTAT
1 ATATATATGTAT
*
1216080 ATGTATATGTAT
1 ATATATATGTAT
1216092 A
1 A
1216093 GTTTGGGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:1216619 original size:22 final size:24
Alignment explanation
Indices: 1216594--1216655 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
1216584 TATACGTTCA
1216594 TATATTTAT-ATTA-TTTTTATAT
1 TATATTTATAATTATTTTTTATAT
1216616 TATA-TTATAATTATTTTTTTATAT
1 TATATTTATAATTA-TTTTTTATAT
* *
1216640 TATATATAAAATTATT
1 TATATTTATAATTATT
1216656 AAATATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.12
22 8 0.24
24 15 0.44
25 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TATATTTATAATTATTTTTTATAT
Found at i:1216629 original size:16 final size:17
Alignment explanation
Indices: 1216594--1216667 Score: 50
Period size: 16 Copynumber: 4.5 Consensus size: 17
1216584 TATACGTTCA
**
1216594 TATATTTATATTATTTT
1 TATATTTATATTATAAT
1216611 TATA-TTATATTATAAT
1 TATATTTATATTATAAT
1216627 TAT-TTT-T-TTAT-AT
1 TATATTTATATTATAAT
* * *
1216640 TATATATAAAATTATTAAA
1 TATAT-TTATATTA-TAAT
1216659 TATATTTAT
1 TATATTTAT
1216668 TTAATTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
13 5 0.12
14 5 0.12
15 2 0.05
16 15 0.35
17 7 0.16
18 3 0.07
19 6 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATTTATATTATAAT
Found at i:1216634 original size:24 final size:26
Alignment explanation
Indices: 1216602--1216656 Score: 87
Period size: 24 Copynumber: 2.2 Consensus size: 26
1216592 CATATATTTA
*
1216602 TATTATTTTTATATTATAT-TATAAT
1 TATTATTTTTATATTATATATAAAAT
1216627 TATT-TTTTTATATTATATATAAAAT
1 TATTATTTTTATATTATATATAAAAT
1216652 TATTA
1 TATTA
1216657 AATATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TATTATTTTTATATTATATATAAAAT
Found at i:1217324 original size:2 final size:2
Alignment explanation
Indices: 1217317--1217357 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1217307 CATTAAGTTT
1217317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1217358 TTCATTGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1220738 original size:3 final size:3
Alignment explanation
Indices: 1220730--1220778 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
1220720 CATGAAAGTG
*
1220730 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1220778 A
1 A
1220779 ATTTTACTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1220843 original size:26 final size:27
Alignment explanation
Indices: 1220807--1220860 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
1220797 TGTTAGATTT
*
1220807 TTAATATTTATA-AATATTTA-ATTAAA
1 TTAATAATTATATAA-ATTTATATTAAA
1220833 TTAATAATTATATAAATTTATATTAAA
1 TTAATAATTATATAAATTTATATTAAA
1220860 T
1 T
1220861 GATTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TTAATAATTATATAAATTTATATTAAA
Found at i:1221856 original size:9 final size:9
Alignment explanation
Indices: 1221844--1221877 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1221834 AAACATAAAA
1221844 AATATTTAT
1 AATATTTAT
1221853 AATATTATAT
1 AATATT-TAT
1221863 AA-ATTTAT
1 AATATTTAT
1221871 AATATTT
1 AATATTT
1221878 TAAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.22
9 13 0.57
10 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
AATATTTAT
Found at i:1222029 original size:3 final size:3
Alignment explanation
Indices: 1222021--1222050 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1222011 TATATGTAAG
1222021 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1222051 GTGCATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1222775 original size:3 final size:3
Alignment explanation
Indices: 1222767--1222801 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1222757 AAATTTTACC
1222767 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1222802 AATATAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.