Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_pilon, whole genome shotgun sequence
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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 51
Found at i:1066314 original size:16 final size:17
Alignment explanation
Indices: 1066293--1066334 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1066283 TGTTGATGTA
1066293 CTTTCAA-CTTCTTTTC
1 CTTTCAATCTTCTTTTC
*
1066309 CTTTCAATTTTCTTTTTC
1 CTTTCAATCTTC-TTTTC
*
1066327 TTTTCAAT
1 CTTTCAAT
1066335 TTTCAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 7 0.32
17 3 0.14
18 12 0.55
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (17 bp):
CTTTCAATCTTCTTTTC
Found at i:1066331 original size:18 final size:19
Alignment explanation
Indices: 1066304--1066349 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
1066294 TTTCAACTTC
* *
1066304 TTTTCCTTTCAATTTTC-T
1 TTTTCTTTTCAATTTTCAA
1066322 TTTTCTTTTCAATTTTCAA
1 TTTTCTTTTCAATTTTCAA
1066341 TTTTCTTTT
1 TTTTCTTTT
1066350 TCCTTTCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTCTTTTCAATTTTCAA
Found at i:1075485 original size:15 final size:15
Alignment explanation
Indices: 1075465--1075500 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1075455 ATTATTAGCT
*
1075465 TTATAATATATGTTA
1 TTATAATATATATTA
1075480 TTATAATATATATTA
1 TTATAATATATATTA
*
1075495 TGATAA
1 TTATAA
1075501 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:1079752 original size:15 final size:15
Alignment explanation
Indices: 1079732--1079767 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1079722 ATTATTAGCT
*
1079732 TTATAATATATGTTA
1 TTATAATATATATTA
1079747 TTATAATATATATTA
1 TTATAATATATATTA
*
1079762 TGATAA
1 TTATAA
1079768 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:1082192 original size:81 final size:81
Alignment explanation
Indices: 1082055--1082207 Score: 207
Period size: 81 Copynumber: 1.9 Consensus size: 81
1082045 CCCTTTGTTC
* * * * *
1082055 TTCATCGGGTATAGAGCTTTCTAGATTTGATTTTTGAACAAGAGCAACGTGCATTAATCCACCAC
1 TTCATCGAGTATAGAGCTTTCTAGATTTGATTCTTCAACAAGAGCAACATGAATTAATCCACCAC
*
1082120 CATTTCCCAATCAATG
66 CACTTCCCAATCAATG
* * * * *
1082136 TTCATCGAGTCTAGAGCTTTCTAGGTTTGATTCTTCAATAAGAGCAACATTAATTAATCCCCCAC
1 TTCATCGAGTATAGAGCTTTCTAGATTTGATTCTTCAACAAGAGCAACATGAATTAATCCACCAC
1082201 CACTTCC
66 CACTTCC
1082208 TTATCACCTC
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (81 bp):
TTCATCGAGTATAGAGCTTTCTAGATTTGATTCTTCAACAAGAGCAACATGAATTAATCCACCAC
CACTTCCCAATCAATG
Found at i:1087436 original size:17 final size:17
Alignment explanation
Indices: 1087392--1087438 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
1087382 AGTTGGTTAT
1087392 TTAATTAAACTAGTTCA
1 TTAATTAAACTAGTTCA
* * *
1087409 TTCATTTAACTTGTTCA
1 TTAATTAAACTAGTTCA
1087426 TTAATTAAACTAG
1 TTAATTAAACTAG
1087439 CTCTTTTATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (17 bp):
TTAATTAAACTAGTTCA
Found at i:1091817 original size:18 final size:18
Alignment explanation
Indices: 1091796--1091831 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1091786 ACAAAAAGGG
*
1091796 AAAAAGAAAAAAAGAAAA
1 AAAAACAAAAAAAGAAAA
*
1091814 AAAAACATAAAAAGAAAA
1 AAAAACAAAAAAAGAAAA
1091832 CAAGGGAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (18 bp):
AAAAACAAAAAAAGAAAA
Found at i:1091831 original size:32 final size:31
Alignment explanation
Indices: 1091761--1091831 Score: 72
Period size: 34 Copynumber: 2.2 Consensus size: 31
1091751 CAAAAAGAAT
* *
1091761 AGAAAAAAAACAAAAATAAAAAAGCACAAAA
1 AGAAAAAAAACAAAAAAAAAAAAACACAAAA
*
1091792 AGGGAAAAAGAAA-AAAAGAAAAAAAAACATAAAA
1 A--GAAAAA-AAACAAAA-AAAAAAAAACACAAAA
1091826 AGAAAA
1 AGAAAA
1091832 CAAGGGAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
31 1 0.03
32 5 0.15
33 10 0.30
34 17 0.52
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.03
Consensus pattern (31 bp):
AGAAAAAAAACAAAAAAAAAAAAACACAAAA
Found at i:1093432 original size:187 final size:187
Alignment explanation
Indices: 1093117--1093490 Score: 748
Period size: 187 Copynumber: 2.0 Consensus size: 187
1093107 TCCTCCAAGT
1093117 TTTGTTATGGTGTATCCTCATCCACATGACTTGCACATGATGCATCTGGTTGTTTATGAGATGAC
1 TTTGTTATGGTGTATCCTCATCCACATGACTTGCACATGATGCATCTGGTTGTTTATGAGATGAC
1093182 ATATGTGGCTAGTGATGGAAGCTAGCACCATAGTAACCTAACTAGGTGAGTGGGTAGCTTAGCTA
66 ATATGTGGCTAGTGATGGAAGCTAGCACCATAGTAACCTAACTAGGTGAGTGGGTAGCTTAGCTA
1093247 GACACCTAGTATCACTATAGATACCTTCAACAACCTTGAGTCCTCAGCTACCATCTA
131 GACACCTAGTATCACTATAGATACCTTCAACAACCTTGAGTCCTCAGCTACCATCTA
1093304 TTTGTTATGGTGTATCCTCATCCACATGACTTGCACATGATGCATCTGGTTGTTTATGAGATGAC
1 TTTGTTATGGTGTATCCTCATCCACATGACTTGCACATGATGCATCTGGTTGTTTATGAGATGAC
1093369 ATATGTGGCTAGTGATGGAAGCTAGCACCATAGTAACCTAACTAGGTGAGTGGGTAGCTTAGCTA
66 ATATGTGGCTAGTGATGGAAGCTAGCACCATAGTAACCTAACTAGGTGAGTGGGTAGCTTAGCTA
1093434 GACACCTAGTATCACTATAGATACCTTCAACAACCTTGAGTCCTCAGCTACCATCTA
131 GACACCTAGTATCACTATAGATACCTTCAACAACCTTGAGTCCTCAGCTACCATCTA
1093491 ACTATTGTTC
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
187 187 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (187 bp):
TTTGTTATGGTGTATCCTCATCCACATGACTTGCACATGATGCATCTGGTTGTTTATGAGATGAC
ATATGTGGCTAGTGATGGAAGCTAGCACCATAGTAACCTAACTAGGTGAGTGGGTAGCTTAGCTA
GACACCTAGTATCACTATAGATACCTTCAACAACCTTGAGTCCTCAGCTACCATCTA
Found at i:1093818 original size:30 final size:30
Alignment explanation
Indices: 1093754--1093818 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
1093744 GCTAATAATG
* *
1093754 AGCTAAGATAATGATAAAATGTATAAGATG
1 AGCTAAGATAATGATAAAATGAATAAGATA
* * * *
1093784 AGCTATGATAATGATTATATGAATGAGATA
1 AGCTAAGATAATGATAAAATGAATAAGATA
1093814 AGCTA
1 AGCTA
1093819 GAGTAAGATG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (30 bp):
AGCTAAGATAATGATAAAATGAATAAGATA
Found at i:1103984 original size:59 final size:59
Alignment explanation
Indices: 1103912--1104032 Score: 161
Period size: 59 Copynumber: 2.1 Consensus size: 59
1103902 GAAGGGTTGG
* * * ** *
1103912 TTAGAGCCATATTATCGGGTTTGCCTTTTCATTGCGACGAAGAGGGTTTGATTGGACAC
1 TTAGAGCCATATTAACGAGTTTGCCTTTTCATTACGACGAAGAGGGTTCAATAGGACAC
* * *
1103971 TTAGAGCCATATTAACGAGTTTTCCTTTTCATTACGACTATGAGGGTTCAATAGGACAC
1 TTAGAGCCATATTAACGAGTTTGCCTTTTCATTACGACGAAGAGGGTTCAATAGGACAC
1104030 TTA
1 TTA
1104033 TCCATCTATT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (59 bp):
TTAGAGCCATATTAACGAGTTTGCCTTTTCATTACGACGAAGAGGGTTCAATAGGACAC
Found at i:1109601 original size:17 final size:17
Alignment explanation
Indices: 1109567--1109619 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1109557 TATATAAAGT
*
1109567 TAGTTCTTTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
1109584 TAGTTCATTCATTTAAC
1 TAGTTCATTAATTAAAC
*
1109601 T-TTATCATTAATTAAAC
1 TAGT-TCATTAATTAAAC
1109618 TA
1 TA
1109620 ACTCTTTGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 1 0.04
17 27 0.96
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:1115868 original size:29 final size:29
Alignment explanation
Indices: 1115826--1115895 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
1115816 ATATCCAAAT
1115826 GAACTTGATAAATTGGTAAAAGTTCAACA
1 GAACTTGATAAATTGGTAAAAGTTCAACA
* *
1115855 GAACTTGATAAATTGGTAGAAGTTTAACA
1 GAACTTGATAAATTGGTAAAAGTTCAACA
*
1115884 GAACTTCATAAA
1 GAACTTGATAAA
1115896 AGAGGAAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (29 bp):
GAACTTGATAAATTGGTAAAAGTTCAACA
Found at i:1125170 original size:11 final size:11
Alignment explanation
Indices: 1125154--1125178 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1125144 ATTAAAGAAG
1125154 AAAAGAAAAAT
1 AAAAGAAAAAT
1125165 AAAAGAAAAAT
1 AAAAGAAAAAT
1125176 AAA
1 AAA
1125179 TTACAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAGAAAAAT
Found at i:1126237 original size:22 final size:23
Alignment explanation
Indices: 1126209--1126253 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1126199 GGGAGCGTAT
*
1126209 GGGTATTGGTACAACTT-CATAG
1 GGGTATTGATACAACTTGCATAG
*
1126231 GGGTATTGATACCACTTGCATAG
1 GGGTATTGATACAACTTGCATAG
1126254 ATTTAAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (23 bp):
GGGTATTGATACAACTTGCATAG
Found at i:1128607 original size:12 final size:13
Alignment explanation
Indices: 1128590--1128622 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1128580 TGTGCAAAAA
*
1128590 TTTGAAAACT-AT
1 TTTGAAAACTAAG
1128602 TTTGAAAACTAAG
1 TTTGAAAACTAAG
1128615 TTTGAAAA
1 TTTGAAAA
1128623 ATTATTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACTAAG
Found at i:1128689 original size:20 final size:20
Alignment explanation
Indices: 1128647--1128690 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1128637 AGTTTTCATG
*
1128647 AAAAACAACAGAATTAAATC
1 AAAAACAACAGAATTAAAAC
*
1128667 AAAAACAACA-ATTTAAAAAC
1 AAAAACAACAGAATT-AAAAC
1128687 AAAA
1 AAAA
1128691 GCACATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.70, C:0.14, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAACAACAGAATTAAAAC
Found at i:1134394 original size:12 final size:12
Alignment explanation
Indices: 1134377--1134402 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1134367 CACGTCCTAT
1134377 AATTGAAGAAGA
1 AATTGAAGAAGA
1134389 AATTGAAGAAGA
1 AATTGAAGAAGA
1134401 AA
1 AA
1134403 AATAGGTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (12 bp):
AATTGAAGAAGA
Found at i:1147917 original size:97 final size:97
Alignment explanation
Indices: 1147793--1148352 Score: 588
Period size: 96 Copynumber: 5.8 Consensus size: 97
1147783 ATGGCATCCC
* * *
1147793 TTCTGCC-AAAATGCACCATTTCGTCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAAATGTAT
1 TTCTGCCAAAAATGCACCATTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAAATGCAC
* * * *
1147857 CGTTAGACATTTAGCTTGCATTAGTTGCACCT
66 CGTTAGGCATTTAACTTGCATTAGTGGCACAT
* * ** *
1147889 TTCTGCCAAAAATGGACCATTTTATCTAACTTGCATTAGTGGCATATTTCTGCC-AAAAATACAC
1 TTCTGCCAAAAATGCACCATTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAAATGCAC
*
1147953 TGTTAGGCATTTAACTTGCATTAGTGGCAGC-T
66 CGTTAGGCATTTAACTTGCATTAGTGGCA-CAT
* * * * * *
1147985 TTCTGCCAAAAAAGCATCATTTCATCTTACTTGCATT-GAGGAACCTTTCT-ACAAAAAATGGCA
1 TTCTGCCAAAAATGCACCATTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAAAT-GCA
1148048 CCGTTAGGCATTTAACTTGCATTAGTGGCACAT
65 CCGTTAGGCATTTAACTTGCATTAGTGGCACAT
** * * * *
1148081 TTCTGTAAAAAAATACACCATTTCATCTAACTTTCATTAGTGACGCCTTTCTGCCAAAAAATGCA
1 TTCTG-CCAAAAATGCACCATTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAAATGCA
*
1148146 CCTTTAGGCATTTAACTTGCATTAGTGGCACAT
65 CCGTTAGGCATTTAACTTGCATTAGTGGCACAT
* * * * *
1148179 ATCTGCAAAAAATGCACCATTCCATATAACTTGCATTAGTGGCACCTTTCTGCC-AAAAATGAAC
1 TTCTGCCAAAAATGCACCATTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAAATGCAC
* * * * * *
1148243 CATT--TCATCTAACTTGTATTAGTGGTACCT
66 CGTTAGGCATTTAACTTGCATTAGTGGCACAT
* * *
1148273 TTTTGCCAAAAATGCACC-TTTAGGCATATAACTTGCA-T--TGGCACCTTTCTGCC-AAAAATA
1 TTCTGCCAAAAATGCACCATTT---CATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAAATG
* **
1148333 CAACGTTAAACATTTAACTT
63 CACCGTTAGGCATTTAACTT
1148353 TCAATTTAGA
Statistics
Matches: 389, Mismatches: 62, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
93 27 0.07
94 37 0.10
95 26 0.07
96 134 0.34
97 109 0.28
98 48 0.12
99 8 0.02
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (97 bp):
TTCTGCCAAAAATGCACCATTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAAATGCAC
CGTTAGGCATTTAACTTGCATTAGTGGCACAT
Found at i:1147940 original size:47 final size:47
Alignment explanation
Indices: 1147784--1148331 Score: 471
Period size: 47 Copynumber: 11.4 Consensus size: 47
1147774 TTTTCATTTA
* *
1147784 TGGCATCCCTTCTGCC-AAAATGCACCATTTCGTCTAACTTGCATTAG
1 TGGCA-CCTTTCTGCCAAAAATGCACCATTTCATCTAACTTGCATTAG
* * * * * *
1147831 TGGCACCTTTCTGCCAAAAAATGTATCGTTAGACATTTAGCTTGCATTAG
1 TGGCACCTTTCTGCC-AAAAATGCACCATT--TCATCTAACTTGCATTAG
* * *
1147881 TTGCACCTTTCTGCCAAAAATGGACCATTTTATCTAACTTGCATTAG
1 TGGCACCTTTCTGCCAAAAATGCACCATTTCATCTAACTTGCATTAG
** * ** * *
1147928 TGGCATATTTCTGCCAAAAATACACTGTTAGGCATTTAACTTGCATTAG
1 TGGCACCTTTCTGCCAAAAATGCACCATT--TCATCTAACTTGCATTAG
* * * *
1147977 TGGCAGCTTTCTGCCAAAAAAGCATCATTTCATCTTACTTGCATT-G
1 TGGCACCTTTCTGCCAAAAATGCACCATTTCATCTAACTTGCATTAG
* * * * * * *
1148023 AGGAACCTTTCTACAAAAAATGGCACCGTTAGGCATTTAACTTGCATTAG
1 TGGCACCTTTCTGCCAAAAAT-GCACCATT--TCATCTAACTTGCATTAG
* ** * *
1148073 TGGCACATTTCTGTAAAAAAATACACCATTTCATCTAACTTTCATTAG
1 TGGCACCTTTCTG-CCAAAAATGCACCATTTCATCTAACTTGCATTAG
* * *
1148121 TGACGCCTTTCTGCCAAAAAATGCACC-TTTAGGCATTTAACTTGCATTAG
1 TGGCACCTTTCTGCC-AAAAATGCACCATTT---CATCTAACTTGCATTAG
* * * * *
1148171 TGGCACATATCTGCAAAAAATGCACCATTCCATATAACTTGCATTAG
1 TGGCACCTTTCTGCCAAAAATGCACCATTTCATCTAACTTGCATTAG
* *
1148218 TGGCACCTTTCTGCCAAAAATGAACCATTTCATCTAACTTGTATTAG
1 TGGCACCTTTCTGCCAAAAATGCACCATTTCATCTAACTTGCATTAG
* * *
1148265 TGGTACCTTTTTGCCAAAAATGCACC-TTTAGGCATATAACTTGCA-T--
1 TGGCACCTTTCTGCCAAAAATGCACCATTT---CATCTAACTTGCATTAG
1148311 TGGCACCTTTCTGCCAAAAAT
1 TGGCACCTTTCTGCCAAAAAT
1148332 ACAACGTTAA
Statistics
Matches: 396, Mismatches: 86, Indels: 39
0.76 0.17 0.07
Matches are distributed among these distances:
46 47 0.12
47 142 0.36
48 46 0.12
49 83 0.21
50 71 0.18
51 7 0.02
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (47 bp):
TGGCACCTTTCTGCCAAAAATGCACCATTTCATCTAACTTGCATTAG
Found at i:1160612 original size:406 final size:408
Alignment explanation
Indices: 1159830--1160645 Score: 1577
Period size: 406 Copynumber: 2.0 Consensus size: 408
1159820 ATAAGGCACA
1159830 AAATTCAAGGCAAAGAACTAACAAATAATATAATTTCAACTCCATCAAAACAAATATTAAGCACA
1 AAATTCAAGGCAAAGAACTAACAAATAATATAATTTCAACTCCATCAAAACAAATATTAAGCACA
1159895 ACAAGATAAAAAGACTACATATATCAAACAACAAAATGCATTTTTTTTCTCTTTGTTATTGTTTC
66 ACAAGATAAAAAGACTACATATATCAAACAACAAAATGCATTTTTTTTCTCTTTGTTATTGTTTC
1159960 GTTTTTCATTTCACATCTTTGCTTTTTCTTTTTCTTTCGAATAACCTTTTTTCGTTCGAACTGCT
131 GTTTTTCATTTCACATCTTTGCTTTTTCTTTTTCTTTCGAATAACCTTTTTTCGTTCGAACTGCT
1160025 ATTTTTTTCGCATTCTACCTTTTTTTTCGATGGAGCATACAATGGTAAAATTATTCACTTGCCCT
196 ATTTTTTTCGCATTCTACCTTTTTTTTCGATGGAGCATACAATGGTAAAATTATTCACTTGCCCT
1160090 GAAGAAGGTAGAAAAGAGGGATAAAATAAAAGGCTCGGGTTTATAAATGTGGTGAAAACAAAGAA
261 GAAGAAGGTAGAAAAGAGGGATAAAATAAAAGGCTCGGGTTTATAAATGTGGTGAAAACAAAGAA
1160155 ACGAAAAGAAAGGCTCAAAAGTGTTTAACTAAAGGGAAAATGCATGGTAGGCTATTTAGTGGGGA
326 ACGAAAAGAAAGGCTCAAAAGTGTTTAACTAAAGGGAAAATGCATGGTAGGCTATTTAGTGGGGA
1160220 AACGAAATAGTTAATCCT
391 AACGAAATAGTTAATCCT
1160238 AAATTCAAGGCAAAGAACTAACAAAT-A-ATAATTTCAACTCCATCAAAACAAATATTAAGCACA
1 AAATTCAAGGCAAAGAACTAACAAATAATATAATTTCAACTCCATCAAAACAAATATTAAGCACA
1160301 ACAAGATAAAAAGACTACATATATCAAACAACAAAATGCATTTTTTTTCTCTTTGTTATTGTTTC
66 ACAAGATAAAAAGACTACATATATCAAACAACAAAATGCATTTTTTTTCTCTTTGTTATTGTTTC
1160366 GTTTTTCATTTCACATCTTTGCTTTTTCTTTTTCTTTCGAATAACCTTTTTTCGTTCGAACTGCT
131 GTTTTTCATTTCACATCTTTGCTTTTTCTTTTTCTTTCGAATAACCTTTTTTCGTTCGAACTGCT
1160431 ATTTTTTTCGCATTCTACCTTTTTTTTCGATGGAGCATACAATGGTAAAATTATTCACTTGCCCT
196 ATTTTTTTCGCATTCTACCTTTTTTTTCGATGGAGCATACAATGGTAAAATTATTCACTTGCCCT
1160496 GAAGAAGGTAGAAAAGAGGGATAAAATAAAAAGGCTCGGGTTTATAAATGTGGTGAAAACAAAGA
261 GAAGAAGGTAGAAAAGAGGGATAAAAT-AAAAGGCTCGGGTTTATAAATGTGGTGAAAACAAAGA
*
1160561 AACG-AGA-AAAGGCTCAAAAGTGTTTAACTAAAGGGAAAATGCATGGGTAGGCTATTTAGTGGG
325 AACGAAAAGAAAGGCTCAAAAGTGTTTAACTAAAGGGAAAATGCAT-GGTAGGCTATTTAGTGGG
1160624 GAAACGAAATAGTTAATCCT
389 GAAACGAAATAGTTAATCCT
1160644 AA
1 AA
1160646 GGTGCCCAAA
Statistics
Matches: 405, Mismatches: 1, Indels: 6
0.98 0.00 0.01
Matches are distributed among these distances:
405 37 0.09
406 300 0.74
407 42 0.10
408 26 0.06
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (408 bp):
AAATTCAAGGCAAAGAACTAACAAATAATATAATTTCAACTCCATCAAAACAAATATTAAGCACA
ACAAGATAAAAAGACTACATATATCAAACAACAAAATGCATTTTTTTTCTCTTTGTTATTGTTTC
GTTTTTCATTTCACATCTTTGCTTTTTCTTTTTCTTTCGAATAACCTTTTTTCGTTCGAACTGCT
ATTTTTTTCGCATTCTACCTTTTTTTTCGATGGAGCATACAATGGTAAAATTATTCACTTGCCCT
GAAGAAGGTAGAAAAGAGGGATAAAATAAAAGGCTCGGGTTTATAAATGTGGTGAAAACAAAGAA
ACGAAAAGAAAGGCTCAAAAGTGTTTAACTAAAGGGAAAATGCATGGTAGGCTATTTAGTGGGGA
AACGAAATAGTTAATCCT
Found at i:1170495 original size:31 final size:30
Alignment explanation
Indices: 1170455--1170573 Score: 80
Period size: 31 Copynumber: 3.9 Consensus size: 30
1170445 CTAAGGGTGA
*
1170455 ATCTTGGGCCTAAGAGCCTACCCAAGAAAG
1 ATCTCGGGCCTAAGAGCCTACCCAAGAAAG
* * * **
1170485 TTCTCAGGGCC-ATGAGGCCTACCAAAGTGAG
1 ATCTC-GGGCCTAAGA-GCCTACCCAAGAAAG
* *
1170516 ATCTCGGGGCTACAGGGCCTACCCAAGAAAG
1 ATCTCGGGCCTA-AGAGCCTACCCAAGAAAG
* * *
1170547 GTGTCGGGGTCGT-AGAGCCTACCCAAG
1 ATCTC-GGG-CCTAAGAGCCTACCCAAG
1170574 GGTCACCTTG
Statistics
Matches: 65, Mismatches: 18, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
30 10 0.15
31 50 0.77
32 4 0.06
33 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (30 bp):
ATCTCGGGCCTAAGAGCCTACCCAAGAAAG
Found at i:1171331 original size:22 final size:22
Alignment explanation
Indices: 1171306--1171357 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
1171296 AGATCTTTCG
* *
1171306 AAGTCGATGGTTTGACCGGTCA
1 AAGTCAATGGTCTGACCGGTCA
*
1171328 AAGTTAATGGTCTGACCGGTCA
1 AAGTCAATGGTCTGACCGGTCA
*
1171350 AGGTCAAT
1 AAGTCAAT
1171358 AGTTAGGCCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (22 bp):
AAGTCAATGGTCTGACCGGTCA
Found at i:1171403 original size:20 final size:19
Alignment explanation
Indices: 1171375--1171416 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
1171365 CCGATCAACA
*
1171375 GTTCGGGTCAGGTCAACCTG
1 GTTCCGGTCAGGTCAACC-G
1171395 GTTCCGGTCAGGTCAACCG
1 GTTCCGGTCAGGTCAACCG
1171414 GTT
1 GTT
1171417 TAGTTTTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.26, G:0.33, T:0.26
Consensus pattern (19 bp):
GTTCCGGTCAGGTCAACCG
Found at i:1173586 original size:19 final size:19
Alignment explanation
Indices: 1173556--1173607 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1173546 AAAAATGAAT
1173556 ATCAAT-TTAAAATTAAGC-
1 ATCAATATTAAAATTAA-CA
1173574 ATCAA-AGTTAAAATTAACA
1 ATCAATA-TTAAAATTAACA
1173593 ATCAATATTAAAATT
1 ATCAATATTAAAATT
1173608 TACGTATCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.20
19 23 0.77
20 1 0.03
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (19 bp):
ATCAATATTAAAATTAACA
Found at i:1174346 original size:35 final size:34
Alignment explanation
Indices: 1174307--1174407 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 34
1174297 AATTCTAAAC
1174307 AAATAAAATACTTAAATTAATTATTATTTTTAATA
1 AAATAAAATA-TTAAATTAATTATTATTTTTAATA
* * *
1174342 AAAT--AATA-TAAATTAATTA-TAATTCTATTA
1 AAATAAAATATTAAATTAATTATTATTTTTAATA
* *
1174372 AAATTAAAAT-TT-AATTAATGATTAATTTTAAATA
1 AAA-TAAAATATTAAATTAATTATT-ATTTTTAATA
1174406 AA
1 AA
1174408 TCCTTGTACT
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
30 11 0.21
31 12 0.23
32 8 0.15
33 9 0.17
34 8 0.15
35 4 0.08
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (34 bp):
AAATAAAATATTAAATTAATTATTATTTTTAATA
Found at i:1174374 original size:30 final size:30
Alignment explanation
Indices: 1174308--1174407 Score: 85
Period size: 30 Copynumber: 3.2 Consensus size: 30
1174298 ATTCTAAACA
* * *
1174308 AATAAAATACTTAAATTAATTATTATTTTT
1 AATAAAATAATTAAATTAATTATTAATTCT
1174338 AATAAAATAATATAAATTAATTA-TAATTCT
1 AATAAAATAAT-TAAATTAATTATTAATTCT
* * * *
1174368 ATTAAAATTAAAATTTAATTAATGATTAATTTT
1 AATAAAA-T--AATTAAATTAATTATTAATTCT
1174401 AAATAAA
1 -AATAAA
1174408 TCCTTGTACT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
30 21 0.38
31 12 0.21
32 9 0.16
33 9 0.16
34 5 0.09
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (30 bp):
AATAAAATAATTAAATTAATTATTAATTCT
Found at i:1175430 original size:31 final size:29
Alignment explanation
Indices: 1175377--1175434 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 29
1175367 TAGCATGTTT
1175377 AAAAATAAAACTTAAAATGAAAACGAAAAC
1 AAAAATAAAACTTAAAATGAAAA-GAAAAC
1175407 AAAAATGAAAACTTGAAAA-GAAAAGAAA
1 AAAAAT-AAAACTT-AAAATGAAAAGAAA
1175435 TAACTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 10 0.38
31 12 0.46
32 4 0.15
ACGTcount: A:0.71, C:0.07, G:0.10, T:0.12
Consensus pattern (29 bp):
AAAAATAAAACTTAAAATGAAAAGAAAAC
Found at i:1179332 original size:3 final size:3
Alignment explanation
Indices: 1179324--1179391 Score: 91
Period size: 3 Copynumber: 22.0 Consensus size: 3
1179314 AAATTTAAAT
* *
1179324 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1179372 TATA TTA TTTA TTA ATA TTA
1 T-TA TTA -TTA TTA TTA TTA
1179392 CAAAAATCAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
3 51 0.89
4 6 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1179687 original size:21 final size:21
Alignment explanation
Indices: 1179663--1179716 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1179653 TCGAGCTCTA
1179663 TGGTGAGTCACCGCCATAGCT
1 TGGTGAGTCACCGCCATAGCT
1179684 TGGTGAGTCACCGCCATAGCT
1 TGGTGAGTCACCGCCATAGCT
*
1179705 TGGTGACTCACC
1 TGGTGAGTCACC
1179717 AAAGACTGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.24
Consensus pattern (21 bp):
TGGTGAGTCACCGCCATAGCT
Found at i:1180738 original size:15 final size:14
Alignment explanation
Indices: 1180691--1180750 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
1180681 ATCCATTAGT
*
1180691 TTTTAATATTATTA
1 TTTTAATTTTATTA
*
1180705 CATTTAATTTCT-TTCA
1 -TTTTAATTT-TATT-A
1180721 TTTTAATTATTATTA
1 TTTTAATT-TTATTA
1180736 TTTT-ATTTTATTA
1 TTTTAATTTTATTA
1180749 TT
1 TT
1180751 ACGTTTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
13 8 0.21
14 3 0.08
15 22 0.58
16 5 0.13
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTAATTTTATTA
Found at i:1180821 original size:14 final size:14
Alignment explanation
Indices: 1180804--1180835 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1180794 TATTATTAAG
1180804 TTATATAATATATA
1 TTATATAATATATA
*
1180818 TTATATAATATTTA
1 TTATATAATATATA
1180832 TTAT
1 TTAT
1180836 TTATTTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATATAATATATA
Found at i:1181238 original size:17 final size:15
Alignment explanation
Indices: 1181208--1181243 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
1181198 AAATTATAGT
1181208 AATAAATTTAAATTA
1 AATAAATTTAAATTA
1181223 AATAGAATTATAAATTA
1 AATA-AATT-TAAATTA
1181240 AATA
1 AATA
1181244 TATCTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 4 0.21
17 11 0.58
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
AATAAATTTAAATTA
Found at i:1181722 original size:16 final size:15
Alignment explanation
Indices: 1181701--1181735 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1181691 TCTTTCAAAT
1181701 TTTTTATTACTTATTA
1 TTTTTA-TACTTATTA
*
1181717 TTTTTATACTTTTTA
1 TTTTTATACTTATTA
1181732 TTTT
1 TTTT
1181736 ATTTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATACTTATTA
Found at i:1183839 original size:21 final size:21
Alignment explanation
Indices: 1183815--1183873 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
1183805 TTCATATATA
1183815 CATTTTCATTTTGCATCTTTG
1 CATTTTCATTTTGCATCTTTG
1183836 CATTTTCATTTTGCATCTTTG
1 CATTTTCATTTTGCATCTTTG
*
1183857 AATTTTTCATTTTGCAT
1 CA-TTTTCATTTTGCAT
1183874 TCATACTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 22 0.61
22 14 0.39
ACGTcount: A:0.17, C:0.17, G:0.08, T:0.58
Consensus pattern (21 bp):
CATTTTCATTTTGCATCTTTG
Found at i:1183874 original size:7 final size:7
Alignment explanation
Indices: 1183815--1183874 Score: 70
Period size: 7 Copynumber: 8.6 Consensus size: 7
1183805 TTCATATATA
1183815 CATTTT-
1 CATTTTG
1183821 CATTTTG
1 CATTTTG
1183828 CATCTTTG
1 CAT-TTTG
1183836 CATTTT-
1 CATTTTG
1183842 CATTTTG
1 CATTTTG
1183849 CATCTTTG
1 CAT-TTTG
* *
1183857 AATTTTT
1 CATTTTG
1183864 CATTTTG
1 CATTTTG
1183871 CATT
1 CATT
1183875 CATACTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
6 12 0.26
7 21 0.46
8 13 0.28
ACGTcount: A:0.17, C:0.17, G:0.08, T:0.58
Consensus pattern (7 bp):
CATTTTG
Found at i:1186451 original size:26 final size:27
Alignment explanation
Indices: 1186421--1186471 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
1186411 TATACTCATC
*
1186421 CAGCAAAGAAAGAAGAAA-GAAAAATT
1 CAGCAAAGAAAGAAAAAAGGAAAAATT
1186447 CAGCAAAGAAAGAAAAAAGGAAAAA
1 CAGCAAAGAAAGAAAAAAGGAAAAA
1186472 GAAAAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.69, C:0.08, G:0.20, T:0.04
Consensus pattern (27 bp):
CAGCAAAGAAAGAAAAAAGGAAAAATT
Found at i:1186472 original size:18 final size:17
Alignment explanation
Indices: 1186451--1186521 Score: 92
Period size: 18 Copynumber: 4.1 Consensus size: 17
1186441 AAAATTCAGC
1186451 AAAGAAAGAAAAAAGGAA
1 AAAGAAA-AAAAAAGGAA
1186469 AAAG-AAAAAAAA-GAA
1 AAAGAAAAAAAAAGGAA
*
1186484 AAAAAAAAGAAAAAGGAAA
1 AAAGAAAA-AAAAAGG-AA
1186503 AAAGAAAAAAAAAGGAA
1 AAAGAAAAAAAAAGGAA
1186520 AA
1 AA
1186522 TTGAATCAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
15 6 0.13
16 9 0.19
17 11 0.23
18 12 0.26
19 9 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAAAGGAA
Found at i:1186512 original size:7 final size:7
Alignment explanation
Indices: 1186455--1186512 Score: 75
Period size: 7 Copynumber: 8.4 Consensus size: 7
1186445 TTCAGCAAAG
1186455 AAAGAAA
1 AAAGAAA
*
1186462 AAAGGAA
1 AAAGAAA
1186469 AAAGAAA
1 AAAGAAA
1186476 AAA-AAGA
1 AAAGAA-A
1186483 AAA-AAA
1 AAAGAAA
1186489 AAAGAAA
1 AAAGAAA
*
1186496 AAGGAAA
1 AAAGAAA
1186503 AAAGAAA
1 AAAGAAA
1186510 AAA
1 AAA
1186513 AAAGGAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
6 6 0.13
7 39 0.87
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:1186532 original size:25 final size:25
Alignment explanation
Indices: 1186451--1186521 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
1186441 AAAATTCAGC
* *
1186451 AAAGAAAGAAAAAAGGAAAAAGAAAAA
1 AAAGAAA-AAAAAAAGAAAAAG-GAAA
1186478 AAAGAAAAAAAAAAGAAAAAGGAAA
1 AAAGAAAAAAAAAAGAAAAAGGAAA
*
1186503 AAAGAAAAAAAAAGGAAAA
1 AAAGAAAAAAAAAAGAAAA
1186522 TTGAATCAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 21 0.51
26 13 0.32
27 7 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (25 bp):
AAAGAAAAAAAAAAGAAAAAGGAAA
Found at i:1188658 original size:114 final size:114
Alignment explanation
Indices: 1188458--1188791 Score: 551
Period size: 114 Copynumber: 2.9 Consensus size: 114
1188448 CACGTTCTCG
* * *
1188458 TAGTAGAAATAAGGAGCCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTACCTGATATGGTTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1188523 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGTTCA
66 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGTTCA
* *
1188572 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
*
1188637 GGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGTTCA
66 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGTTCA
* * *
1188686 TTGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCAGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
* * * *
1188751 GGTAGGAATCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAA
1188792 CTGAATGATC
Statistics
Matches: 204, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 204 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGTTCA
Found at i:1190949 original size:54 final size:53
Alignment explanation
Indices: 1190867--1191022 Score: 167
Period size: 54 Copynumber: 3.0 Consensus size: 53
1190857 TTGAGAAATA
* *
1190867 TGAGCAGAAGCCACAGAAAAGGATGAATGTATTGTCAAATGCTTTACGAACATC
1 TGAGCAGAAACCACAGAAAAGGATGAATGTATTGTCAAATGTTTTACGAAC-TC
* * * * *
1190921 TGAGCAAAAACCACAGAAAAGGATGAATGTGTTATCAAGTGTTTTAC-ATCTC
1 TGAGCAGAAACCACAGAAAAGGATGAATGTATTGTCAAATGTTTTACGAACTC
* * *
1190973 -GA-CAGAAACCACAGGGAAAA-TATGAATGCACTGTCAAATGTTTTACGAAC
1 TGAGCAGAAACCACA--GAAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
1191023 CTGCTATTCT
Statistics
Matches: 84, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
50 10 0.12
51 22 0.26
52 9 0.11
53 2 0.02
54 41 0.49
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (53 bp):
TGAGCAGAAACCACAGAAAAGGATGAATGTATTGTCAAATGTTTTACGAACTC
Found at i:1191287 original size:85 final size:87
Alignment explanation
Indices: 1191144--1191315 Score: 330
Period size: 85 Copynumber: 2.0 Consensus size: 87
1191134 TCTTTCCACA
1191144 GAAAGAGAGCTGAAATTTTAACAACAAGAAACTAGTGGTACCAACTAAGGTTGAACTACAGGTTG
1 GAAAGAGAGCTGAAATTTTAACAACAAGAAACTAGTGGTACCAACTAAGGTTGAACTACAGGTTG
1191209 -TGTT-AGCATCTCGACATGAT
66 TTGTTAAGCATCTCGACATGAT
1191229 GAAAGAGAGCTGAAATTTTAACAACAAGAAACTAGTGGTACCAACTAAGGTTGAACTACAGGTTG
1 GAAAGAGAGCTGAAATTTTAACAACAAGAAACTAGTGGTACCAACTAAGGTTGAACTACAGGTTG
1191294 TTGTTAAGCATCTCGACATGAT
66 TTGTTAAGCATCTCGACATGAT
1191316 ATGGTCCAAG
Statistics
Matches: 85, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
85 65 0.76
86 4 0.05
87 16 0.19
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (87 bp):
GAAAGAGAGCTGAAATTTTAACAACAAGAAACTAGTGGTACCAACTAAGGTTGAACTACAGGTTG
TTGTTAAGCATCTCGACATGAT
Found at i:1191502 original size:22 final size:22
Alignment explanation
Indices: 1191473--1191527 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1191463 ATCTACACTC
1191473 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1191495 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1191517 TTCAAAGATGA
1 TTCAAAGATGA
1191528 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1192416 original size:186 final size:186
Alignment explanation
Indices: 1192076--1192448 Score: 588
Period size: 186 Copynumber: 2.0 Consensus size: 186
1192066 CCAATCAACA
** * *
1192076 TGTTATTTCAAAAAACAAAATGAGAAAACAATTTTTATAGTTTCTCATTTTATTTTTTCTAAAAT
1 TGTTATTTCAAAAAACAAAATGAGAAAACAATTTCCATAGTTTCTCAATTTATCTTTTCTAAAAT
* *
1192141 GAAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACAT
66 GAAATTGTTGAAAAGTAAGAAAACGATTTCCATAGTTTTATTACTTAGTAAACTATTTCCCACAT
* * *
1192206 CTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGT
131 CTATAAGCCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTCTTGATGT
* **
1192262 TGTTATTTTGAAAAAA-AATAATGAGAAAATGATTTCCATAGTTTCTCAATTTATCTTTTCTAAA
1 TGTTA-TTTCAAAAAACAA-AATGAGAAAACAATTTCCATAGTTTCTCAATTTATCTTTTCTAAA
*
1192326 ATGAAATTGTTGAAAAGTAAGAAAACGATTTTCATAG-TTTATTACTTAGTAAACTATTTCCCAC
64 ATGAAATTGTTGAAAAGTAAGAAAACGATTTCCATAGTTTTATTACTTAGTAAACTATTTCCCAC
*
1192390 ATCTGTAAGCCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTCTTGATGT
129 ATCTATAAGCCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTCTTGATGT
1192448 T
1 T
1192449 TTCAAAACCT
Statistics
Matches: 171, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
186 88 0.51
187 83 0.49
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (186 bp):
TGTTATTTCAAAAAACAAAATGAGAAAACAATTTCCATAGTTTCTCAATTTATCTTTTCTAAAAT
GAAATTGTTGAAAAGTAAGAAAACGATTTCCATAGTTTTATTACTTAGTAAACTATTTCCCACAT
CTATAAGCCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTCTTGATGT
Found at i:1192515 original size:76 final size:77
Alignment explanation
Indices: 1192389--1192576 Score: 299
Period size: 76 Copynumber: 2.5 Consensus size: 77
1192379 CTATTTCCCA
1192389 CATCTGTAAGCCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTCTTGATGTTTTC-A
1 CATCTGTAAGCCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTCTTGATGTTTTCAA
1192453 AAACCTTAGGGT
66 AAACCTTAGGGT
* * *
1192465 CATCTGTAAGTCCC-GCAGTTCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAG-CCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTCTTGATGTTTTCA
*
1192529 AAAACCTTCGGGT
65 AAAACCTTAGGGT
* *
1192542 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGCCCTGCAGTGCATGATGTTTCCAAA
1192577 CATTTTCATC
Statistics
Matches: 102, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
76 59 0.58
77 43 0.42
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (77 bp):
CATCTGTAAGCCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTCTTGATGTTTTCAA
AAACCTTAGGGT
Found at i:1193958 original size:15 final size:15
Alignment explanation
Indices: 1193938--1194008 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
1193928 ATCCAGTAGT
1193938 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
1193953 TTTTAAT-TTCTTTC
1 TTTTAATATTATTAC
1193967 ATTTTAATTATTATTA-
1 -TTTTAA-TATTATTAC
*
1193983 TTTTATTTTATTATTAC
1 TTTTA--ATATTATTAC
*
1194000 GTTTAATAT
1 TTTTAATAT
1194009 ATGTTAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
14 5 0.12
15 21 0.49
16 9 0.21
17 8 0.19
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:1194072 original size:14 final size:15
Alignment explanation
Indices: 1194053--1194085 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1194043 TTATTATAAG
1194053 TTATATAA-ATATAT
1 TTATATAATATATAT
*
1194067 TTATATAATATTTAT
1 TTATATAATATATAT
1194082 TTAT
1 TTAT
1194086 TTATTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATAATATATAT
Found at i:1194397 original size:17 final size:15
Alignment explanation
Indices: 1194367--1194402 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
1194357 AAATTATAGT
1194367 AATAAATTTAAATTA
1 AATAAATTTAAATTA
1194382 AATAGAATTATAAATTA
1 AATA-AATT-TAAATTA
1194399 AATA
1 AATA
1194403 TATCTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 4 0.21
17 11 0.58
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
AATAAATTTAAATTA
Found at i:1203844 original size:23 final size:24
Alignment explanation
Indices: 1203816--1203869 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
1203806 AAAATTAACA
1203816 AAGAAAATCAAAGCACTC-AAAAG
1 AAGAAAATCAAAGCACTCAAAAAG
* *
1203839 AAGAAATTGAAAGCACTCAAAAAG
1 AAGAAAATCAAAGCACTCAAAAAG
1203863 AAGAAAA
1 AAGAAAA
1203870 AAGAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.13, G:0.15, T:0.09
Consensus pattern (24 bp):
AAGAAAATCAAAGCACTCAAAAAG
Found at i:1222254 original size:13 final size:13
Alignment explanation
Indices: 1222238--1222270 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1222228 TTAATTTTGA
1222238 AAATTAAAATTTT
1 AAATTAAAATTTT
1222251 AAA-TAAAATTTT
1 AAATTAAAATTTT
*
1222263 AAGTTAAA
1 AAATTAAA
1222271 GTTTGATCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
AAATTAAAATTTT
Found at i:1227700 original size:65 final size:63
Alignment explanation
Indices: 1227631--1227796 Score: 190
Period size: 65 Copynumber: 2.6 Consensus size: 63
1227621 AAATAGCCAG
**
1227631 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATTTG
1 AGTGCATCGATGCATGG-TGGTGCATCGATGCATCAAATGCATTCGATG--TTCAATAAAATTCA
1227695 T
63 T
* * * **
1227696 AGTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCAT
1 AGTGCATCGATGCATGGT-GGTGCATCGATGCATCAAATGCATTCGATGTTCAATAAAATTCAT
* *
1227760 GGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 AGTGCATCGATGCATGG--TGGTGCATCGATGCATCA
1227797 CTCTGAAAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
63 3 0.04
64 23 0.27
65 58 0.68
66 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (63 bp):
AGTGCATCGATGCATGGTGGTGCATCGATGCATCAAATGCATTCGATGTTCAATAAAATTCAT
Found at i:1232646 original size:117 final size:118
Alignment explanation
Indices: 1232426--1232647 Score: 259
Period size: 117 Copynumber: 1.9 Consensus size: 118
1232416 CTTTCAAATT
* * * *
1232426 AAAATTTTATTTTTCAATATTTTCAAATTTCATTTTTGAAAGTTCTAAATCCTTCTTCAAGAGTT
1 AAAATTTTATTTTTCAAAATTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACAGTT
* *
1232491 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTTG
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
* * * * * * *
1232544 AAAA-TTTCTTTTTCAAAATTTTTAGATTTTAGTTTTGAAAGCTCTAACTCCTTTTTCAACATTT
1 AAAATTTTATTTTTCAAAATTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACAGTT
* * * **
1232608 CATTTTGTTTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
66 CATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
1232648 ATCATTTTTA
Statistics
Matches: 85, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
117 77 0.91
118 8 0.09
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (118 bp):
AAAATTTTATTTTTCAAAATTTTCAAATTTCAGTTTTGAAAGCTCTAAATCCTTCTTCAACAGTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:1234008 original size:64 final size:63
Alignment explanation
Indices: 1233931--1234131 Score: 190
Period size: 65 Copynumber: 3.1 Consensus size: 63
1233921 TGGACCCTTA
* * * * *
1233931 GTGCACCGATGCATTAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCACAGTGCATCGATGCATGG-TG
* * * *
1233995 GTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAA-ATCCTCAGTGCGTCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCACAGTGCATCGATGCATGGT-
*
1234059 T
63 G
* ** * *
1234060 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATAGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCACAGTGCATCGATGCATGG--T
1234124 G
63 G
1234125 GTGCATC
1 GTGCATC
1234132 ACTCTGAAAA
Statistics
Matches: 110, Mismatches: 20, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 44 0.40
65 57 0.52
66 4 0.04
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCACAGTGCATCGATGCATGGTG
Found at i:1235198 original size:4 final size:4
Alignment explanation
Indices: 1235189--1235215 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1235179 ACTTAAAACA
1235189 TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TAT
1235216 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:1239793 original size:18 final size:17
Alignment explanation
Indices: 1239770--1239803 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1239760 AATTTACGTC
1239770 AGAAACTAAACTTGAATA
1 AGAAAC-AAACTTGAATA
*
1239788 AGAAACCAACTTGAAT
1 AGAAACAAACTTGAAT
1239804 CCGATGATAA
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:0.53, C:0.15, G:0.12, T:0.21
Consensus pattern (17 bp):
AGAAACAAACTTGAATA
Found at i:1247755 original size:201 final size:201
Alignment explanation
Indices: 1247373--1247854 Score: 450
Period size: 201 Copynumber: 2.4 Consensus size: 201
1247363 GAACTATTCG
* * ** *
1247373 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAATAAGAACTGTCGAGTTTGATTTCATTCAGC
1 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAATAAAAAATGTCGAGTTCAATTCCATTCAGC
* * * * *
1247438 TCGAGGGCTTATCAACCTCATAGTAGCAGCAAGGAACTACTTTCTGATTAAAGTTTAAACTAAGG
66 TCGAGGACATATCAACCGCATAGTAACAACAAGGAACTACTTTCTGATTAAAGTTTAAACTAAGG
* * *
1247503 TCTTTAAATCAAGAAGAAAACCTAGGTCACCTGGGATTTAACAACAATGAACTATCTCTTAGTCG
131 CCTTTAAATCAAGAAGAAAACCTAGCTCACCTGCGATTTAACAACAATGAACTATCTCTTAGTCG
1247568 AATTTA
196 AATTTA
* * * **
1247574 CAACATATCTCAAGGCGAGAAGGGTTATCTGTCAATAAAAAATTTCGAGTTCAATTCCATTCTTC
1 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAATAAAAAATGTCGAGTTCAATTCCATTCAGC
* * * * * * * *
1247639 TCGATGACATATTAACCGCATGGTAACAACGA-TATACTACTTTCTGGTTGAAA-TTTAAATTGA
66 TCGAGGACATATCAACCGCATAGTAACAACAAGGA-ACTACTTTCTGATT-AAAGTTTAAACTAA
* * **** * * * **
1247702 GGCCTTTAAGTCAAGAAGAAGACCTAGCTTGGGTGCGATTTAGCAATAATGAACTATATCCCAGT
129 GGCCTTTAAATCAAGAAGAAAACCTAGCTCACCTGCGATTTAACAACAATGAACTATCTCTTAGT
*
1247767 C-ATGTTTA
194 CGA-ATTTA
* * * ** * * * * *
1247775 TAGCATAGCTTAAGATGAGAAGGGCTATCTATCAACAAAAACCT-TTGAGTTCAATTCCATTAAG
1 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAATAAAAA-ATGTCGAGTTCAATTCCATTCAG
* *
1247839 CTCAAGGGCATATCAA
65 CTCGAGGACATATCAA
1247855 ACACATGGTA
Statistics
Matches: 221, Mismatches: 56, Indels: 8
0.78 0.20 0.03
Matches are distributed among these distances:
200 2 0.01
201 215 0.97
202 4 0.02
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (201 bp):
CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAATAAAAAATGTCGAGTTCAATTCCATTCAGC
TCGAGGACATATCAACCGCATAGTAACAACAAGGAACTACTTTCTGATTAAAGTTTAAACTAAGG
CCTTTAAATCAAGAAGAAAACCTAGCTCACCTGCGATTTAACAACAATGAACTATCTCTTAGTCG
AATTTA
Found at i:1248750 original size:21 final size:21
Alignment explanation
Indices: 1248721--1248785 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
1248711 GTAGAGGAAA
* *
1248721 ACCTATTATAATCGAATTCAT
1 ACCTGTTATAATCGAATTCAC
1248742 ACCTGTTATAATCGAATTCAC
1 ACCTGTTATAATCGAATTCAC
1248763 ACCTGTTATAATCGAATTCAC
1 ACCTGTTATAATCGAATTCAC
1248784 AC
1 AC
1248786 GAGCATTCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (21 bp):
ACCTGTTATAATCGAATTCAC
Found at i:1256417 original size:32 final size:32
Alignment explanation
Indices: 1256366--1256455 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
1256356 TCAAGTAGAG
* * * *
1256366 TTAGGTTCAGGTCATGGTCATGTTGATTTAAAA
1 TTAGATTCAGTTCA-GGTCAAGTTAATTTAAAA
*
1256399 TTAGATTCAGTTCAGGTCAAGTTAATTTCAAA
1 TTAGATTCAGTTCAGGTCAAGTTAATTTAAAA
*
1256431 TTAGA-TCAATATCAGGTCAAGTTAA
1 TTAGATTCAGT-TCAGGTCAAGTTAA
1256456 AACAGTTCGT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
31 4 0.08
32 34 0.68
33 12 0.24
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (32 bp):
TTAGATTCAGTTCAGGTCAAGTTAATTTAAAA
Found at i:1261647 original size:26 final size:26
Alignment explanation
Indices: 1261590--1261640 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
1261580 AATTCTATAG
1261590 TGACAAGGGGTACCTATTTTACGATA
1 TGACAAGGGGTACCTATTTTACGATA
1261616 TGACAAGGGGTACCTATTTTACGAT
1 TGACAAGGGGTACCTATTTTACGAT
1261641 TGGACAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (26 bp):
TGACAAGGGGTACCTATTTTACGATA
Found at i:1262746 original size:11 final size:10
Alignment explanation
Indices: 1262721--1262745 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1262711 TTTTTGTGCC
1262721 TTTTTCTTTT
1 TTTTTCTTTT
1262731 TTTTTCTTTT
1 TTTTTCTTTT
1262741 TTTTT
1 TTTTT
1262746 TTGATGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:1264529 original size:24 final size:24
Alignment explanation
Indices: 1264497--1264544 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1264487 GATGCATGTA
1264497 TCACGTTCTCATTCATACTTTTCT
1 TCACGTTCTCATTCATACTTTTCT
1264521 TCACGTTCTCATTCATACTTTTCT
1 TCACGTTCTCATTCATACTTTTCT
1264545 GCTTTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.29, G:0.04, T:0.50
Consensus pattern (24 bp):
TCACGTTCTCATTCATACTTTTCT
Found at i:1277967 original size:17 final size:17
Alignment explanation
Indices: 1277945--1277981 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1277935 CTACGTTGTT
1277945 GCCTTTCTATTTTGATC
1 GCCTTTCTATTTTGATC
1277962 GCCTTTCTATTTTGATC
1 GCCTTTCTATTTTGATC
1277979 GCC
1 GCC
1277982 ATATTAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.27, G:0.14, T:0.49
Consensus pattern (17 bp):
GCCTTTCTATTTTGATC
Found at i:1279291 original size:3 final size:3
Alignment explanation
Indices: 1279252--1279337 Score: 104
Period size: 3 Copynumber: 29.0 Consensus size: 3
1279242 ATTTGTTTTT
* * * * *
1279252 TTA TT- TTA TTT TTA CTA TTA TTT TTA TTTA TTT TTA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
1279297 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1279338 AATAATAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
2 4 0.06
3 63 0.90
4 3 0.04
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:1280736 original size:2 final size:2
Alignment explanation
Indices: 1280729--1280769 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1280719 ATCACATTAA
1280729 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
1280770 TTTTAAGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1280921 original size:2 final size:2
Alignment explanation
Indices: 1280914--1280960 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1280904 TATAAAACAT
1280914 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1280956 TA TA T
1 TA TA T
1280961 TTACTCTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1282184 original size:19 final size:20
Alignment explanation
Indices: 1282137--1282184 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1282127 TTTTATTTTA
*
1282137 TTTTATTTTATTGTTTTCTTC
1 TTTT-TTTTATTGATTTCTTC
*
1282158 TTATTTTTATTGATTTC-TC
1 TTTTTTTTATTGATTTCTTC
1282177 TTTTTTTT
1 TTTTTTTT
1282185 TCATACATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.10, C:0.08, G:0.04, T:0.77
Consensus pattern (20 bp):
TTTTTTTTATTGATTTCTTC
Found at i:1282184 original size:20 final size:18
Alignment explanation
Indices: 1282132--1282185 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
1282122 AACCATTTTA
* *
1282132 TTTTATTTTATTTTATTG
1 TTTTCTTTTTTTTTATTG
1282150 TTTTCTTCTTATTTTTATTG
1 TTTTCTT-TT-TTTTTATTG
1282170 ATTTCTCTTTTTTTTT
1 -TTT-TCTTTTTTTTT
1282186 CATACATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 6 0.20
19 2 0.07
20 13 0.43
21 5 0.17
22 4 0.13
ACGTcount: A:0.11, C:0.07, G:0.04, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTTTTTTATTG
Found at i:1282212 original size:31 final size:32
Alignment explanation
Indices: 1282160--1282230 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 32
1282150 TTTTCTTCTT
* *
1282160 ATTTT-TATTGATTTCTCTTTTTTTTTCA-TAC
1 ATTTTATATTAATTTC-CTTTTTTTTGCATTAC
1282191 ATTTTATATTAATTT-CTTTTTTTTGCATTAC
1 ATTTTATATTAATTTCCTTTTTTTTGCATTAC
1282222 A-TTTATATT
1 ATTTTATATT
1282231 GCTCAAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 19 0.53
31 9 0.25
32 8 0.22
ACGTcount: A:0.21, C:0.10, G:0.03, T:0.66
Consensus pattern (32 bp):
ATTTTATATTAATTTCCTTTTTTTTGCATTAC
Found at i:1285412 original size:52 final size:52
Alignment explanation
Indices: 1285348--1285460 Score: 174
Period size: 52 Copynumber: 2.2 Consensus size: 52
1285338 GACAACTTGA
*
1285348 AGAGAATTCCTCAAGTTACTAGACAACACTATTGTTTAGTGACACCAG-AATG
1 AGAGAATTCCTCAAGTTACTAGACAACACTACTGTTTAGTGACACC-GCAATG
* *
1285400 AGAGAATTCCTCAAGTTACTGGACAACACTACTGTTTAGTGACATCGCAATG
1 AGAGAATTCCTCAAGTTACTAGACAACACTACTGTTTAGTGACACCGCAATG
*
1285452 AGAGTATTC
1 AGAGAATTC
1285461 AAGATAAACA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
51 1 0.02
52 55 0.98
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (52 bp):
AGAGAATTCCTCAAGTTACTAGACAACACTACTGTTTAGTGACACCGCAATG
Found at i:1288610 original size:13 final size:13
Alignment explanation
Indices: 1288585--1288629 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1288575 TGAAAACTAC
1288585 ATATTGATTTTCAA
1 ATATTG-TTTTCAA
1288599 ATATTGTTTTCAA
1 ATATTGTTTTCAA
* *
1288612 AAATTTTTTTCAA
1 ATATTGTTTTCAA
1288625 A-ATTG
1 ATATTG
1288630 CCCACTAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 3 0.11
13 19 0.68
14 6 0.21
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (13 bp):
ATATTGTTTTCAA
Found at i:1290732 original size:20 final size:20
Alignment explanation
Indices: 1290707--1290744 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1290697 AGATTGCCCA
1290707 TAGGGTACCGATACCCCTCT
1 TAGGGTACCGATACCCCTCT
1290727 TAGGGTACCGATACCCCT
1 TAGGGTACCGATACCCCT
1290745 ATGCAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (20 bp):
TAGGGTACCGATACCCCTCT
Found at i:1291593 original size:27 final size:27
Alignment explanation
Indices: 1291563--1291616 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1291553 TTTATGGTAA
*
1291563 GAGCATAAATAGAAGCAGTCACAAGGG
1 GAGCATAAATAGAAGCAATCACAAGGG
*
1291590 GAGCATCAATAGAAGCAATCACAAGGG
1 GAGCATAAATAGAAGCAATCACAAGGG
1291617 TAAGAGCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.44, C:0.17, G:0.28, T:0.11
Consensus pattern (27 bp):
GAGCATAAATAGAAGCAATCACAAGGG
Found at i:1291626 original size:30 final size:30
Alignment explanation
Indices: 1291558--1291665 Score: 150
Period size: 30 Copynumber: 3.7 Consensus size: 30
1291548 AGCATTTTAT
*
1291558 GGTAAGAGCATAAATAGAAGCAGTCACAAG
1 GGTAAGAGCATCAATAGAAGCAGTCACAAG
*
1291588 GG---GAGCATCAATAGAAGCAATCACAAG
1 GGTAAGAGCATCAATAGAAGCAGTCACAAG
* * *
1291615 GGTAAGAGCATCATTAAAAGTAGTCACAAG
1 GGTAAGAGCATCAATAGAAGCAGTCACAAG
1291645 GGTAAGAGCATCAATAGAAGC
1 GGTAAGAGCATCAATAGAAGC
1291666 CCGTTTTTGG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
27 25 0.38
30 41 0.62
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (30 bp):
GGTAAGAGCATCAATAGAAGCAGTCACAAG
Found at i:1296076 original size:11 final size:11
Alignment explanation
Indices: 1296057--1296098 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
1296047 GAGTAGTGAA
*
1296057 GCAAATCATTT
1 GCAAGTCATTT
1296068 GCAAGTCATTT
1 GCAAGTCATTT
*
1296079 GCAAGTCATCT
1 GCAAGTCATTT
1296090 GCAAGTCAT
1 GCAAGTCAT
1296099 CCTCAGCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (11 bp):
GCAAGTCATTT
Found at i:1297754 original size:21 final size:21
Alignment explanation
Indices: 1297703--1297755 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
1297693 TAATAGGATT
* *
1297703 ATTAATATTAAATTAGTAATTA
1 ATTAA-ATTAAATTAATAATAA
* * *
1297725 TTTATATTAAATTAATAGTAA
1 ATTAAATTAAATTAATAATAA
1297746 ATTAAATTAA
1 ATTAAATTAA
1297756 TTACAAGTTT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
ATTAAATTAAATTAATAATAA
Found at i:1298698 original size:19 final size:19
Alignment explanation
Indices: 1298632--1298683 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1298622 TAAAATGAAT
1298632 ATCAAT-TTAAAATTAA-G
1 ATCAATATTAAAATTAACG
1298649 CATCAA-AGTTAAAATTAACG
1 -ATCAATA-TTAAAATTAACG
1298669 ATCAATATTAAAATT
1 ATCAATATTAAAATT
1298684 TACGTTCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.17
19 23 0.77
20 2 0.07
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (19 bp):
ATCAATATTAAAATTAACG
Found at i:1301520 original size:3 final size:3
Alignment explanation
Indices: 1301514--1301562 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
1301504 TAATATTTAT
* *
1301514 TAA TAA TAA -AA TAA TAA TTA TAA TTA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
1301558 TAA TA
1 TAA TA
1301563 TTTAAATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.85
4 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1301528 original size:21 final size:21
Alignment explanation
Indices: 1301501--1301562 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1301491 TTTGGGCCTG
*
1301501 TAATAATATTTATTAATAATAA
1 TAATAATAATTA-TAATAATAA
*
1301523 -AATAATAATTATAATTATAA
1 TAATAATAATTATAATAATAA
1301543 TAATAATAA-TATAAATAATA
1 TAATAATAATTAT-AATAATA
1301563 TTTAAATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 11 0.31
21 24 0.69
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAATAATAATTATAATAATAA
Found at i:1301533 original size:18 final size:18
Alignment explanation
Indices: 1301512--1301567 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 18
1301502 AATAATATTT
1301512 ATTAATAATAAAATAATA
1 ATTAATAATAAAATAATA
*
1301530 ATT-ATAAT--TATAATA
1 ATTAATAATAAAATAATA
1301545 A-TAATAATATAAATAATA
1 ATTAATAATA-AAATAATA
*
1301563 TTTAA
1 ATTAA
1301568 ATGAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
14 1 0.03
15 12 0.40
17 5 0.17
18 9 0.30
19 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTAATAATAAAATAATA
Found at i:1312520 original size:59 final size:59
Alignment explanation
Indices: 1312416--1312547 Score: 176
Period size: 59 Copynumber: 2.2 Consensus size: 59
1312406 CATCGTAATG
* * * *
1312416 CAATCCCGAGTATGACACATAAGGTCGTGTCCTCCATCTATACTAGGTATCCTTAAGTA
1 CAATCCCGAATATGACACATAAGGTCGTGTCCACCATATACACTAGGTATCCTTAAGTA
* *
1312475 CAATCCCGAATATGACACATAAGGTCGT-TCCCACCATATACACTAGGTATCCTTTAGTG
1 CAATCCCGAATATGACACATAAGGTCGTGT-CCACCATATACACTAGGTATCCTTAAGTA
* *
1312534 TATTCCCGAATATG
1 CAATCCCGAATATG
1312548 CAGCCGACTG
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 1 0.02
59 63 0.98
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (59 bp):
CAATCCCGAATATGACACATAAGGTCGTGTCCACCATATACACTAGGTATCCTTAAGTA
Found at i:1324561 original size:2 final size:2
Alignment explanation
Indices: 1324556--1324583 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1324546 CACTTAAAGC
1324556 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
1324584 TAGTTTTACA
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:1327771 original size:21 final size:22
Alignment explanation
Indices: 1327736--1327776 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1327726 ACGCCATCGT
*
1327736 CTCTCCCTCCACCTCGTCCCAC
1 CTCTCCCTCCACCTCCTCCCAC
*
1327758 CTCT-CCTCCTCCTCCTCCC
1 CTCTCCCTCCACCTCCTCCC
1327777 CTAAAATCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.05, C:0.66, G:0.02, T:0.27
Consensus pattern (22 bp):
CTCTCCCTCCACCTCCTCCCAC
Found at i:1336502 original size:10 final size:10
Alignment explanation
Indices: 1336473--1336502 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
1336463 TTTGTGCCTT
1336473 TTTTTCTTTTA
1 TTTTT-TTTTA
1336484 TTTTTTTTTA
1 TTTTTTTTTA
1336494 TTTTTTTTT
1 TTTTTTTTT
1336503 CTTACCGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.07, C:0.03, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:1339238 original size:14 final size:15
Alignment explanation
Indices: 1339216--1339250 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1339206 TCTTGCTTCA
*
1339216 TTTTATTTTC-TTTC
1 TTTTTTTTTCTTTTC
1339230 TTTTTTTTTCTTTTC
1 TTTTTTTTTCTTTTC
1339245 TTTTTT
1 TTTTTT
1339251 CTGATGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTCTTTTC
Found at i:1347814 original size:22 final size:22
Alignment explanation
Indices: 1347780--1347859 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 22
1347770 GGTGCAGAGA
*
1347780 GAATTGATACCCCCTTGAAGGG
1 GAATCGATACCCCCTTGAAGGG
* *
1347802 GAATCGATTCCCCCTTTGAAGTG
1 GAATCGATACCCCC-TTGAAGGG
**
1347825 GAGCCGATTACCCCCTT--AGGG
1 GAATCGA-TACCCCCTTGAAGGG
*
1347846 CAATCGATACCCCC
1 GAATCGATACCCCC
1347860 ACGGGTTCTG
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 7 0.15
21 7 0.15
22 12 0.26
23 14 0.30
24 6 0.13
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.23
Consensus pattern (22 bp):
GAATCGATACCCCCTTGAAGGG
Found at i:1353344 original size:20 final size:20
Alignment explanation
Indices: 1353319--1353361 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1353309 GTCTAAAGCC
1353319 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
1353339 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
1353359 CAT
1 CAT
1353362 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:1354906 original size:20 final size:18
Alignment explanation
Indices: 1354880--1354934 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 18
1354870 ACTCTACCAT
1354880 CATTCCATTTCTACATCAA
1 CATTCCATTT-TACATCAA
1354899 CTATTCCATTTTACCA-CAA
1 C-ATTCCATTTTA-CATCAA
1354918 CATTCTCATTTGTACAT
1 CATTC-CATTT-TACAT
1354935 ACCATCACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
18 4 0.13
19 14 0.45
20 13 0.42
ACGTcount: A:0.29, C:0.29, G:0.02, T:0.40
Consensus pattern (18 bp):
CATTCCATTTTACATCAA
Found at i:1355189 original size:15 final size:16
Alignment explanation
Indices: 1355168--1355212 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
1355158 CATAGCATTC
1355168 TTATTTTACTTTTTCA
1 TTATTTTACTTTTTCA
1355184 -TATTTT-CTTTTTCA
1 TTATTTTACTTTTTCA
*
1355198 TTAGCTTTACTTTTT
1 TTA-TTTTACTTTTT
1355213 ACTTTCCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 8 0.32
15 8 0.32
16 3 0.12
17 6 0.24
ACGTcount: A:0.16, C:0.13, G:0.02, T:0.69
Consensus pattern (16 bp):
TTATTTTACTTTTTCA
Found at i:1363714 original size:20 final size:20
Alignment explanation
Indices: 1363689--1363731 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1363679 TCTAAAGGCC
1363689 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
1363709 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
1363729 CAT
1 CAT
1363732 GTAGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:1365524 original size:15 final size:16
Alignment explanation
Indices: 1365504--1365537 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1365494 AAAATGTATG
*
1365504 AAAAATAA-AAATATA
1 AAAAATAAGAAAAATA
1365519 AAAAATAAGAAAAATA
1 AAAAATAAGAAAAATA
1365535 AAA
1 AAA
1365538 TGGTTAGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (16 bp):
AAAAATAAGAAAAATA
Found at i:1366968 original size:17 final size:17
Alignment explanation
Indices: 1366946--1366979 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1366936 CATTTCTTTT
*
1366946 ATATTAAAAATAAATAA
1 ATATTAAAAAGAAATAA
*
1366963 ATATTAAGAAGAAATAA
1 ATATTAAAAAGAAATAA
1366980 TAATTTTTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (17 bp):
ATATTAAAAAGAAATAA
Found at i:1367030 original size:23 final size:23
Alignment explanation
Indices: 1367004--1367049 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1366994 AATTATAAAA
1367004 ATAAAGTAA-ATATATATATATTT
1 ATAAA-TAATATATATATATATTT
*
1367027 ATAAATAATATATATATTTATTT
1 ATAAATAATATATATATATATTT
1367050 TTTAAAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATAAATAATATATATATATATTT
Found at i:1367037 original size:19 final size:18
Alignment explanation
Indices: 1367010--1367047 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
1367000 AAAAATAAAG
1367010 TAAATATATATATATTTA
1 TAAATATATATATATTTA
1367028 TAAATAATATATATATTTA
1 TAAAT-ATATATATATTTA
1367047 T
1 T
1367048 TTTTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAATATATATATATTTA
Found at i:1368141 original size:3 final size:3
Alignment explanation
Indices: 1368133--1368166 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1368123 ATGGGTCTTG
*
1368133 TAA TAA TAA T-T TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1368167 TTTTTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 27 0.96
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1374132 original size:14 final size:13
Alignment explanation
Indices: 1374099--1374123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1374089 GTAGTATTTA
1374099 ACAAAAATTTCGT
1 ACAAAAATTTCGT
1374112 ACAAAAATTTCG
1 ACAAAAATTTCG
1374124 AGTAAAAAAA
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:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (13 bp):
ACAAAAATTTCGT
Found at i:1378063 original size:17 final size:17
Alignment explanation
Indices: 1378041--1378086 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
1378031 CAACCTGACC
1378041 GTAAATTGAT-TGAGCTT
1 GTAAATTGATCTGA-CTT
1378058 GTAAA-TGATCTGACTT
1 GTAAATTGATCTGACTT
*
1378074 GT-AATTGAACTGA
1 GTAAATTGATCTGA
1378087 TATGATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 16 0.62
17 8 0.31
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.37
Consensus pattern (17 bp):
GTAAATTGATCTGACTT
Found at i:1378151 original size:42 final size:42
Alignment explanation
Indices: 1378100--1378179 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
1378090 GATATTTATC
*
1378100 TGACTTGATTTTTACCTCACTTATACCTTATAATTGATAATT
1 TGACTTGATTTTTACCTCACTTATAACTTATAATTGATAATT
* * *
1378142 TGACTTGATTTTTACTTGACTTATAAGTTATAATTGAT
1 TGACTTGATTTTTACCTCACTTATAACTTATAATTGAT
1378180 GAAAGTGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (42 bp):
TGACTTGATTTTTACCTCACTTATAACTTATAATTGATAATT
Found at i:1378944 original size:33 final size:33
Alignment explanation
Indices: 1378884--1378974 Score: 110
Period size: 33 Copynumber: 2.7 Consensus size: 33
1378874 ATACACACAC
*
1378884 ATGTATATATATATATACATACATCATACATAA
1 ATGTATATATATATATACATGCATCATACATAA
** *
1378917 ATGTATATATATATATACATGTTTCATACATAT
1 ATGTATATATATATATACATGCATCATACATAA
* * *
1378950 ATGATACATATGTACATACATGCAT
1 ATG-TATATATATATATACATGCAT
1378975 ATATAAGGAC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
33 32 0.67
34 16 0.33
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (33 bp):
ATGTATATATATATATACATGCATCATACATAA
Found at i:1379198 original size:17 final size:18
Alignment explanation
Indices: 1379166--1379222 Score: 71
Period size: 17 Copynumber: 3.2 Consensus size: 18
1379156 ACTTATGTAC
*
1379166 ATATTATATATGTATAAGT
1 ATATTATATAT-TATAACT
*
1379185 ATATTATATA-TATAATT
1 ATATTATATATTATAACT
*
1379202 ATATTACATATTATAACT
1 ATATTATATATTATAACT
1379220 ATA
1 ATA
1379223 ATGGATGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.44
18 9 0.26
19 10 0.29
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (18 bp):
ATATTATATATTATAACT
Found at i:1380699 original size:2 final size:2
Alignment explanation
Indices: 1380692--1380717 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1380682 GAAAATATTA
1380692 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
1380718 TATTAAGTTT
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:1382784 original size:30 final size:30
Alignment explanation
Indices: 1382750--1382865 Score: 76
Period size: 29 Copynumber: 4.2 Consensus size: 30
1382740 CTGTGCGTAG
1382750 GGGTGCTAATTTTGTAATTAATTTATGTTA
1 GGGTGCTAATTTTGTAATTAATTTATGTTA
*
1382780 GGGTGAT-ATTTATGT-A--AA---A--TTA
1 GGGTGCTAATTT-TGTAATTAATTTATGTTA
* * *
1382802 GGGTGTTAGTTTTGTAAAT-ATTTATAG--A
1 GGGTGCTAATTTTGTAATTAATTTAT-GTTA
*
1382830 AGGTGGCTAATTTTGTAATTAATTTATGTTA
1 GGGT-GCTAATTTTGTAATTAATTTATGTTA
1382861 GGGTG
1 GGGTG
1382866 ATATTTGTGT
Statistics
Matches: 63, Mismatches: 8, Indels: 30
0.62 0.08 0.30
Matches are distributed among these distances:
22 12 0.19
23 4 0.06
24 2 0.03
27 3 0.05
28 4 0.06
29 18 0.29
30 16 0.25
31 4 0.06
ACGTcount: A:0.28, C:0.02, G:0.24, T:0.46
Consensus pattern (30 bp):
GGGTGCTAATTTTGTAATTAATTTATGTTA
Found at i:1382805 original size:22 final size:22
Alignment explanation
Indices: 1382777--1382819 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1382767 TTAATTTATG
1382777 TTAGGGTGATA-TTTATGTAAAA
1 TTAGGGTGATAGTTT-TGTAAAA
*
1382799 TTAGGGTGTTAGTTTTGTAAA
1 TTAGGGTGATAGTTTTGTAAA
1382820 TATTTATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (22 bp):
TTAGGGTGATAGTTTTGTAAAA
Found at i:1385498 original size:24 final size:24
Alignment explanation
Indices: 1385471--1385541 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
1385461 ACATGACCTA
*
1385471 GATTCTGTTCTGATTTCTGATATG
1 GATTCTGTTCTGATATCTGATATG
*
1385495 GATTCTGTTCTGATATCTGATTTG
1 GATTCTGTTCTGATATCTGATATG
* * *
1385519 AATTCTGTTTTGAAATCTGATAT
1 GATTCTGTTCTGATATCTGATAT
1385542 CTCCGTTTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.49
Consensus pattern (24 bp):
GATTCTGTTCTGATATCTGATATG
Found at i:1405079 original size:43 final size:43
Alignment explanation
Indices: 1405016--1405098 Score: 105
Period size: 42 Copynumber: 1.9 Consensus size: 43
1405006 TTTTAAATCA
* * * *
1405016 TATTTAATTTAAAACTCTTTTAAATTAAATGATAACAAAATTAT
1 TATTTAATGTAAAACACTTTT-AAGTAAATAATAACAAAATTAT
*
1405060 TATTT-ATGTAAAACACTTTTAAGTAAATAATAATAAAAT
1 TATTTAATGTAAAACACTTTTAAGTAAATAATAACAAAAT
1405099 ATTTCTTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 16 0.47
43 13 0.38
44 5 0.15
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (43 bp):
TATTTAATGTAAAACACTTTTAAGTAAATAATAACAAAATTAT
Found at i:1409227 original size:117 final size:117
Alignment explanation
Indices: 1408982--1409230 Score: 363
Period size: 117 Copynumber: 2.1 Consensus size: 117
1408972 TGCCCAAACA
* *
1408982 AAGCAAAGCTCGGTGCCGATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAAAGCCA
1 AAGCAAAGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAAAGCCA
* * * *
1409047 TTGAAGTGTTTCCGATGTGATGGAGAACACAAGGTGCGAGAATGCACCAATG
66 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGAATGCACCAACG
** * *
1409099 AAGCAGGGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGGTAAAGAAGCGAGAGCCA
1 AAGCAAAGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAAAGCCA
* * * *
1409164 TTGAAGTGTTTCTAATGCGGTGGACAACACAAGGTGCGAGATTGCACCACCG
66 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGAATGCACCAACG
*
1409216 AAGTAAAGCTCGGTG
1 AAGCAAAGCTCGGTG
1409231 CAAAAGCCAA
Statistics
Matches: 115, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
117 115 1.00
ACGTcount: A:0.33, C:0.19, G:0.33, T:0.16
Consensus pattern (117 bp):
AAGCAAAGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAAAGCCA
TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGAATGCACCAACG
Found at i:1409259 original size:117 final size:116
Alignment explanation
Indices: 1408982--1409293 Score: 315
Period size: 117 Copynumber: 2.7 Consensus size: 116
1408972 TGCCCAAACA
* * * * * * *
1408982 AAGCAAAGCTCGGTGCCGATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAAAGCCA
1 AAGCAAAGCTCGGTGACAAAGCAAGTGGCCAAGCAAC-AAGCCGAGGGTAAAGAAGCGAGAGCCA
* * * *
1409047 TTGAAGTGTTTCCGATGTGATGGAGAACACAAGGTGCGAGAATGCACCAATG
65 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGAATGCACCAACG
** * * *
1409099 AAGCAGGGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGGTAAAGAAGCGAGAGCCA
1 AAGCAAAGCTCGGTGACAAAGCAAGTGGCCAAGCAAC-AAGCCGAGGGTAAAGAAGCGAGAGCCA
* * * *
1409164 TTGAAGTGTTTCTAATGCGGTGGACAACACAAGGTGCGAGATTGCACCACCG
65 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGAATGCACCAACG
* * *
1409216 AAGTAAAGCTCGGTG-CAAAAGCCAAG-GGCCAAGCTGAA-GAGCCGAGGGTAAATAAGCGAGAG
1 AAGCAAAGCTCGGTGAC-AAAG-CAAGTGGCCAAGC--AACAAGCCGAGGGTAAAGAAGCGAGAG
* * *
1409278 CAACTGGAGTGTTTCC
62 CCATTGAAGTGTTTCC
1409294 GGTGCAAAGG
Statistics
Matches: 165, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
116 1 0.01
117 159 0.96
118 3 0.02
119 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.32, T:0.15
Consensus pattern (116 bp):
AAGCAAAGCTCGGTGACAAAGCAAGTGGCCAAGCAACAAGCCGAGGGTAAAGAAGCGAGAGCCAT
TGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGAATGCACCAACG
Found at i:1409920 original size:15 final size:15
Alignment explanation
Indices: 1409900--1409934 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1409890 AGCAAGGCTC
1409900 TTCGAGTGAAGCTTG
1 TTCGAGTGAAGCTTG
*
1409915 TTCGAGTGAAGTTTG
1 TTCGAGTGAAGCTTG
1409930 TTCGA
1 TTCGA
1409935 ATGGTGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.37
Consensus pattern (15 bp):
TTCGAGTGAAGCTTG
Found at i:1415294 original size:48 final size:48
Alignment explanation
Indices: 1415223--1415318 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
1415213 AATTTTCACC
*
1415223 TGGTATATGTGTTGTCGCAAGCTTATGGATATGGTGAGGTTGGATTGA
1 TGGTATATGTGTTGTCGCAAGCTTATGGATATGGCGAGGTTGGATTGA
1415271 TGGTATATGTGTTGTCGCAAGCTTATGGATATGGCGAGGTTGGATTGA
1 TGGTATATGTGTTGTCGCAAGCTTATGGATATGGCGAGGTTGGATTGA
1415319 GTTAGATAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.21, C:0.07, G:0.35, T:0.36
Consensus pattern (48 bp):
TGGTATATGTGTTGTCGCAAGCTTATGGATATGGCGAGGTTGGATTGA
Found at i:1415302 original size:24 final size:24
Alignment explanation
Indices: 1415227--1415303 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
1415217 TTCACCTGGT
1415227 ATATGTGTTGTCGCAAGCTTATGG
1 ATATGTGTTGTCGCAAGCTTATGG
** * *
1415251 ATATGGTGAGGTTG---GATTGATGG
1 ATAT-GTGTTGTCGCAAGCTT-ATGG
1415274 TATATGTGTTGTCGCAAGCTTATGG
1 -ATATGTGTTGTCGCAAGCTTATGG
1415299 ATATG
1 ATATG
1415304 GCGAGGTTGG
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
22 3 0.08
23 10 0.26
24 13 0.33
25 10 0.26
26 3 0.08
ACGTcount: A:0.22, C:0.08, G:0.32, T:0.38
Consensus pattern (24 bp):
ATATGTGTTGTCGCAAGCTTATGG
Found at i:1423505 original size:27 final size:28
Alignment explanation
Indices: 1423475--1423529 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
1423465 ATTGATTGCC
* *
1423475 CTTCTTATTCCTCC-TTTAGCTCTCCCT
1 CTTCTTATTCCCCCTTTTAGCACTCCCT
1423502 CTTCTTATTCCCCCTTTTAGCACTCCCT
1 CTTCTTATTCCCCCTTTTAGCACTCCCT
1423530 TCCACACTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.09, C:0.42, G:0.04, T:0.45
Consensus pattern (28 bp):
CTTCTTATTCCCCCTTTTAGCACTCCCT
Found at i:1434504 original size:47 final size:46
Alignment explanation
Indices: 1434385--1434580 Score: 232
Period size: 46 Copynumber: 4.3 Consensus size: 46
1434375 ATTATTCTTT
* * * ** *
1434385 ATTTTTATTTATGGCATCTTTTCATGACTATAATGCACTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
*
1434431 ATTTTCATTTATGGCA-CCTTTCATGCCTATAATGCACCATTAAGC
1 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
* ** * *
1434476 GTTTTTCATTTATATCATCCTTTCATGCCTACAATGCACTATTATGC
1 -ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
** * *
1434523 ATTTTCATTTATGGCATCCTTTCATATCGATAATGCACCGTTATGC
1 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
1434569 ATTTTCATTTAT
1 ATTTTCATTTAT
1434581 TCATTCATTT
Statistics
Matches: 126, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
45 23 0.18
46 77 0.61
47 26 0.21
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.44
Consensus pattern (46 bp):
ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
Found at i:1441118 original size:46 final size:46
Alignment explanation
Indices: 1441066--1441261 Score: 220
Period size: 46 Copynumber: 4.3 Consensus size: 46
1441056 ATTATTCTTT
*
1441066 ATTTTCATTTATGGCAT-CTATTCATACCTATAATGCACTGTTATAC
1 ATTTTCATTTATGGCATCCT-TTCATGCCTATAATGCACTGTTATAC
*
1441112 ATTTTCATTTATGGCA-CCTTTCATGCCTATAATGCACCGTTA-AGC
1 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACTGTTATA-C
* * * * * * *
1441157 GTTTTTCATTTATAGAATCCTTTCATGCCTATAATGAATTATTATGC
1 -ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACTGTTATAC
* * *
1441204 ATTTTCATTTATGGCATCCTTTCATGTCGATAATGCA-TCGTTATGC
1 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACT-GTTATAC
1441250 ATTTTCATTTAT
1 ATTTTCATTTAT
1441262 TCATTCAGTT
Statistics
Matches: 127, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
44 1 0.01
45 23 0.18
46 80 0.63
47 23 0.18
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (46 bp):
ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACTGTTATAC
Found at i:1441255 original size:92 final size:92
Alignment explanation
Indices: 1441066--1441261 Score: 252
Period size: 92 Copynumber: 2.1 Consensus size: 92
1441056 ATTATTCTTT
* * * *
1441066 ATTTTCATTTATGGCATCTATTCATACCTATAATGCACTGTTATACATTTTCATTTATGGCACCT
1 ATTTTCATTTATAGAATCTATTCATACCTATAATGAACTATTATACATTTTCATTTATGGCACCT
*
1441131 TTCATGCCTATAATGCACCGTTAAGCG
66 TTCATGCCGATAATGCACCGTTAAGCG
* * * *
1441158 TTTTTCATTTATAGAATCCT-TTCATGCCTATAATGAATTATTATGCATTTTCATTTATGGCATC
1 ATTTTCATTTATAGAAT-CTATTCATACCTATAATGAACTATTATACATTTTCATTTATGGCA-C
* * *
1441222 CTTTCATGTCGATAATGCATCGTTATGC-
64 CTTTCATGCCGATAATGCACCGTTAAGCG
1441250 ATTTTCATTTAT
1 ATTTTCATTTAT
1441262 TCATTCAGTT
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
92 62 0.70
93 27 0.30
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (92 bp):
ATTTTCATTTATAGAATCTATTCATACCTATAATGAACTATTATACATTTTCATTTATGGCACCT
TTCATGCCGATAATGCACCGTTAAGCG
Found at i:1443421 original size:20 final size:21
Alignment explanation
Indices: 1443384--1443423 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1443374 AATGCATGAA
1443384 TTTATGGCCTCAATAAAAGAT
1 TTTATGGCCTCAATAAAAGAT
*
1443405 TTTATGGCTTCAA-AAAAGA
1 TTTATGGCCTCAATAAAAGA
1443424 CCTTGATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (21 bp):
TTTATGGCCTCAATAAAAGAT
Found at i:1462689 original size:44 final size:43
Alignment explanation
Indices: 1462620--1462705 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 43
1462610 CTGTCTATAT
* * *
1462620 CTATGTTGGAGCTATTACCAGCTTTTCCAACTTATTCCCTAAAG
1 CTATGTTGGAGATATTACAAACTTTTCCAACTTATT-CCTAAAG
*
1462664 CTATGTTGGAGATTTTACAAACTTTTCCAACTTATTCCTAAA
1 CTATGTTGGAGATATTACAAACTTTTCCAACTTATTCCTAAA
1462706 TTTCAGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
43 6 0.16
44 32 0.84
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (43 bp):
CTATGTTGGAGATATTACAAACTTTTCCAACTTATTCCTAAAG
Found at i:1464423 original size:23 final size:22
Alignment explanation
Indices: 1464382--1464458 Score: 111
Period size: 21 Copynumber: 3.5 Consensus size: 22
1464372 CGAAAGGAAT
* *
1464382 CGATTCCCCCCCTAGGGGGTAT
1 CGATTCCCCCCCCAGGGGGTAC
*
1464404 CGATTCCCCCCCCCATGGGGTAC
1 CGATT-CCCCCCCCAGGGGGTAC
1464427 CGATT-CCCCCCCAGGGGGTAC
1 CGATTCCCCCCCCAGGGGGTAC
1464448 CGATTCCCCCC
1 CGATTCCCCCC
1464459 TGTTTAACAG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 20 0.41
22 10 0.20
23 19 0.39
ACGTcount: A:0.13, C:0.45, G:0.23, T:0.18
Consensus pattern (22 bp):
CGATTCCCCCCCCAGGGGGTAC
Found at i:1497423 original size:30 final size:32
Alignment explanation
Indices: 1497292--1497423 Score: 81
Period size: 33 Copynumber: 4.1 Consensus size: 32
1497282 ACTATAACTT
* * * * *
1497292 AATAATTTTGTTATAATTTGTTATTGTGA-AA
1 AATAATATTGTCACAATTTTTTATTTTGACAA
* ** *
1497323 GAATATTATTTGTCACAATTTTTTATAATGAGAA
1 -AATAATA-TTGTCACAATTTTTTATTTTGACAA
* * * * **
1497357 AATAATATTTGTTATAAATTGTTATTTTGATTA
1 AATAATA-TTGTCACAATTTTTTATTTTGACAA
1497390 AATAA-A-TGTCACAATTTTTTATTTTGACAA
1 AATAATATTGTCACAATTTTTTATTTTGACAA
1497420 AATA
1 AATA
1497424 TTAGGACGAA
Statistics
Matches: 76, Mismatches: 22, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
30 22 0.29
32 6 0.08
33 46 0.61
34 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.48
Consensus pattern (32 bp):
AATAATATTGTCACAATTTTTTATTTTGACAA
Found at i:1497482 original size:170 final size:168
Alignment explanation
Indices: 1497296--1497611 Score: 467
Period size: 170 Copynumber: 1.9 Consensus size: 168
1497286 TAACTTAATA
* * * **
1497296 ATTTTGTTATAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTATAATGAGAAAATA
1 ATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTATCACAAAATTTTATAATGAGAAAATA
*
1497361 ATATTTGTTATAAATTGTTATTTTGATTAAAT-AAA-TGTCACAATTTTTT-ATTTTGACAAAAT
66 ATATTTGTTATAAATTATTATTTTGATTAAATAAAATTGTCACAATTTTTTAATTTT-ACAAAAT
1497423 ATTAGGACGAAAACTAAATTTAACGTGTTATTCTGACTAAATC
130 ATT--GAC-AAAA-TAAATTTAACGTGTTATTCTGACTAAATC
* * *
1497466 ATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTATCACAAAATTTTATGATGATAAATTA
1 ATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTATCACAAAATTTTATAATGAGAAAATA
* *
1497531 ATATTTGTTATAAATTATTATTTTGATTAAATAAAATTTTCAGAATTTTTTAATTTTACAAAATA
66 ATATTTGTTATAAATTATTATTTTGATTAAATAAAATTGTCACAATTTTTTAATTTTACAAAATA
1497596 TTGACAAAATAAATTT
131 TTGACAAAATAAATTT
1497612 GGCATAAATT
Statistics
Matches: 132, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
168 7 0.05
169 4 0.03
170 91 0.69
171 3 0.02
172 22 0.17
173 5 0.04
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (168 bp):
ATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTATCACAAAATTTTATAATGAGAAAATA
ATATTTGTTATAAATTATTATTTTGATTAAATAAAATTGTCACAATTTTTTAATTTTACAAAATA
TTGACAAAATAAATTTAACGTGTTATTCTGACTAAATC
Found at i:1499981 original size:337 final size:327
Alignment explanation
Indices: 1499342--1500005 Score: 1204
Period size: 337 Copynumber: 2.0 Consensus size: 327
1499332 AATTCAATCC
1499342 AATCAACGAAATCATGGAGTAATCAACTAAGCAGAGCGATACAACTGCCATCAAATCACAATCAG
1 AATCAACGAAATCATGGAGTAATCAACTAAGCAGAGCGATACAACTGCCATCAAATCACAATCAG
1499407 ATCCATTTTCAGACAAATTAGAAGCAGGGAGTAATAAGCAACTATGTATACAAAAGCAAAACCAT
66 ATCCATTTTCAGACAAATTAGAAGCAGGGAGTAATAAGCAACTATGTATACAAAAGCAAAACCAT
*
1499472 AACCGAAACATGATCAATTTTAAAGAAAAGGGAAAAATACAAAACAGGGGAAACAAAGGGAAAAT
131 AACCGAAACATGATCAATTTTAAAGAAAAGGGAAAAATACAAAACAAGGGAAACAAAGGGAAAAT
1499537 TTTTATTTGGGGAATTGTCTTCTTCGAAATCATAGTTGGGAGGAGAGTAAACAATGGCAGCAACC
196 TTTTATTTGGGGAATTGTCTTCTTCGAAATCATAGTTGGGAGGAGAGTAAACAATGGCAGCAACC
1499602 ATAGATCCGGGAAGCACGACGTACTTGGCTAAAGCAGCTAGTTTTGCGACCAATGGCTCT-CCTT
261 ATAGATCCGGGAAGCACGACGTACTTGGCTAAAGCAGCTAGTTTTGCGACCAATGGCTCTCCCTT
1499666 TA
326 TA
1499668 AATCAACGAAATCATGGAGTAATCAACTAAGCAGAGCGATACAACTGCCATCAAATCACAATCAG
1 AATCAACGAAATCATGGAGTAATCAACTAAGCAGAGCGATACAACTGCCATCAAATCACAATCAG
1499733 ATCCATTTTCAGACAACAATTAGAAGCCAGGGAGTAATTAAGCAACTATGTATACAAAAGCAAAA
66 ATCCATTTTCAGAC-A-AATTAGAAG-CAGGGAGTAA-TAAGCAACTATGTATACAAAAGCAAAA
*
1499798 CCATAACCGAAAACATGATCAATTTTAAAGAAAAGGGAAAAATACAAACCAAGGGAAACAAAAGG
127 CCATAACCG-AAACATGATCAATTTTAAAGAAAAGGGAAAAATACAAAACAAGGGAAAC-AAAGG
1499863 GAAAATTTTTTATTTGGGGGAATTGTCCTTCTTCGAAGAATCATAGTTGGGAGGAGAGTAAACAA
190 GAAAA-TTTTTATTT-GGGGAATTGT-CTTCTTCG-A-AATCATAGTTGGGAGGAGAGTAAACAA
1499928 TGGCAGCAACCATAGATCCGGGAAGCACGACGTACTTGGCTAAAGCAGCTAGTTTTGCGACCAAT
250 TGGCAGCAACCATAGATCCGGGAAGCACGACGTACTTGGCTAAAGCAGCTAGTTTTGCGACCAAT
1499993 GGCTCTCCCTTTA
315 GGCTCTCCCTTTA
1500006 GCAACGACAT
Statistics
Matches: 324, Mismatches: 2, Indels: 12
0.96 0.01 0.04
Matches are distributed among these distances:
326 79 0.24
327 1 0.00
328 9 0.03
329 10 0.03
330 36 0.11
331 47 0.15
332 10 0.03
333 9 0.03
334 10 0.03
335 8 0.02
336 1 0.00
337 98 0.30
338 6 0.02
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.21
Consensus pattern (327 bp):
AATCAACGAAATCATGGAGTAATCAACTAAGCAGAGCGATACAACTGCCATCAAATCACAATCAG
ATCCATTTTCAGACAAATTAGAAGCAGGGAGTAATAAGCAACTATGTATACAAAAGCAAAACCAT
AACCGAAACATGATCAATTTTAAAGAAAAGGGAAAAATACAAAACAAGGGAAACAAAGGGAAAAT
TTTTATTTGGGGAATTGTCTTCTTCGAAATCATAGTTGGGAGGAGAGTAAACAATGGCAGCAACC
ATAGATCCGGGAAGCACGACGTACTTGGCTAAAGCAGCTAGTTTTGCGACCAATGGCTCTCCCTT
TA
Done.