Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008919.1 Hibiscus syriacus cultivar Beakdansim tig00112223_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: 1453011
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 5
Found at i:1080814 original size:27 final size:28
Alignment explanation
Indices: 1080753--1080814 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
1080743 AAAGAAAATC
*
1080753 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
1080781 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTCAAAAAGA
1080808 AGAAAAG
1 AGAAAAG
1080815 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.60, C:0.11, G:0.18, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:1086238 original size:11 final size:11
Alignment explanation
Indices: 1086224--1086248 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1086214 GGCGCCAAAT
1086224 TGGAGGAGTAA
1 TGGAGGAGTAA
1086235 TGGAGGAGTAA
1 TGGAGGAGTAA
1086246 TGG
1 TGG
1086249 TGATTGGCCG
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:0.32, C:0.00, G:0.48, T:0.20
Consensus pattern (11 bp):
TGGAGGAGTAA
Found at i:1088424 original size:23 final size:24
Alignment explanation
Indices: 1088396--1088454 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 24
1088386 AAAATCAGCA
1088396 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
1088419 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
1088443 AAGAAAAATAAA
1 AAG-AAAATAAA
1088455 TAAAGAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 16 0.53
24 8 0.27
25 6 0.20
ACGTcount: A:0.64, C:0.10, G:0.15, T:0.10
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:1089226 original size:24 final size:24
Alignment explanation
Indices: 1089199--1089250 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1089189 GACATGTCCT
* * *
1089199 TTGACGTTCCAACAGCTATGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
* *
1089223 TTGATGTTCAAAAAGATGTGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
1089247 TTGA
1 TTGA
1089251 AGTGGCAAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (24 bp):
TTGACGTTCAAAAAGATATGCCAC
Found at i:1095809 original size:19 final size:19
Alignment explanation
Indices: 1095756--1095805 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1095746 ATAAAGGGTA
1095756 AAAATATAAGTAATGAAAGG
1 AAAATATAAG-AATGAAAGG
*
1095776 AAAGA-ATAAGAATGAAATG
1 AAA-ATATAAGAATGAAAGG
1095795 AAAATA-AAGAA
1 AAAATATAAGAA
1095806 ATGATAGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 6 0.22
19 12 0.44
20 8 0.30
21 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (19 bp):
AAAATATAAGAATGAAAGG
Found at i:1096256 original size:19 final size:21
Alignment explanation
Indices: 1096213--1096264 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
1096203 GAAACCCCTT
1096213 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
1096234 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
1096253 TGAAGATACATG
1 TGAAAATACATG
1096265 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:1100143 original size:170 final size:168
Alignment explanation
Indices: 1099827--1100164 Score: 626
Period size: 170 Copynumber: 2.0 Consensus size: 168
1099817 AATATTTAAT
1099827 GAGAAAGAACCATTAGATAATAGGTTGTATATATGTTACATATTGAATATTAAATAACCTATAGT
1 GAGAAAGAACCATTAGATAATAGGTTGTATATATGTTACATATTGAATATTAAATAACCTATAGT
1099892 CATATTTTTATAATATACATTATATAAGTTTATATACTTAGTTTATTTTCTTATGTTATGCATGT
66 CATATTTTTATAATATACATTATATAAGTTTATATACTTAGTTTATTTTCTTATGTTATGCATGT
1099957 AGGCACATTCGCCAACACTTGGGAGCTGTATTGGAGCTAA
131 AGGCACATTCGCCAACA-TT-GGAGCTGTATTGGAGCTAA
1099997 GAGAAAGAACCATTAGATAATAGGTTGTATAATATGTTACATATTGAATATTAAATAACCTATAG
1 GAGAAAGAACCATTAGATAATAGGTTGTAT-ATATGTTACATATTGAATATTAAATAACCTATAG
1100062 TCATATTTTT-TAATATACATTATATAAGTTTATATAC-TAGTTTATTTTCTTATGTTATGCATG
65 TCATATTTTTATAATATACATTATATAAGTTTATATACTTAGTTTATTTTCTTATGTTATGCATG
1100125 TAGGCACATTCGGCCAACATTGGAGCTGTATTGGAGCTAA
130 TAGGCACATTC-GCCAACATTGGAGCTGTATTGGAGCTAA
1100165 ATGGAGCAAG
Statistics
Matches: 166, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
168 19 0.11
169 39 0.23
170 64 0.39
171 44 0.27
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (168 bp):
GAGAAAGAACCATTAGATAATAGGTTGTATATATGTTACATATTGAATATTAAATAACCTATAGT
CATATTTTTATAATATACATTATATAAGTTTATATACTTAGTTTATTTTCTTATGTTATGCATGT
AGGCACATTCGCCAACATTGGAGCTGTATTGGAGCTAA
Found at i:1105703 original size:33 final size:33
Alignment explanation
Indices: 1105659--1105727 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1105649 GATCACCATA
*
1105659 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
1105692 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
1105725 TTC
1 TTC
1105728 ATTCAACAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:1108238 original size:14 final size:15
Alignment explanation
Indices: 1108212--1108242 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1108202 TTAACGCCTA
1108212 AACAAGTTCAGAATG
1 AACAAGTTCAGAATG
1108227 AACAAG-TCAGAATG
1 AACAAGTTCAGAATG
1108241 AA
1 AA
1108243 ACAGAGTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.52, C:0.13, G:0.19, T:0.16
Consensus pattern (15 bp):
AACAAGTTCAGAATG
Found at i:1108245 original size:15 final size:16
Alignment explanation
Indices: 1108211--1108245 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1108201 TTTAACGCCT
1108211 AAACAAGTTCAGAATG
1 AAACAAGTTCAGAATG
1108227 -AACAAG-TCAGAATG
1 AAACAAGTTCAGAATG
1108241 AAACA
1 AAACA
1108246 GAGTGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.54, C:0.14, G:0.17, T:0.14
Consensus pattern (16 bp):
AAACAAGTTCAGAATG
Found at i:1110148 original size:33 final size:33
Alignment explanation
Indices: 1110104--1110172 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1110094 GATCACCATA
*
1110104 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
1110137 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
1110170 TTC
1 TTC
1110173 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:1113679 original size:321 final size:324
Alignment explanation
Indices: 1113051--1113701 Score: 1069
Period size: 321 Copynumber: 2.0 Consensus size: 324
1113041 TTTGAAGACC
*
1113051 GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCGAGTTTGAGATACAACATCACCACCATCTT
1 GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCAAGTTTGAGATACAACATCACCACCATCTT
*
1113116 CATTTCATCATCAACATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCTGCAGC
66 CA-TT-AT-AT--ACATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGCAGC
1113181 CATCTCTATTCCTATTCTTTCATTCCATTACTTATATTATTATTCAATTCTTAAACCCATTATTA
126 CATCTCTATTCCTATTCTTTCATTCCATTACTTATATTATTATTCAATTCTTAAACCCATTATTA
* *
1113246 ATCATATTTCTTTCTTATTATTTTTTTGCAGCCCAAGCTTATTAATTCAAGGGCATCAGTACTTG
191 ATCATATTTCTTTCTTATTA-TTTTTTGCAGCCCAAGCATATTAATTCAAGGACATCAGTACTTG
* *
1113311 TCAATCTTAGATCGAGACACAATAAGGCTATCTACTCTTTTATCAAAGCGTGTAGATTCGCTTTA
255 TCAATCCTAGATCGAGACACAATAAGGCTATCTACTCTTTTATCAAAGCGTGTAGATTCGCCTTA
1113376 CATCA
320 CATCA
1113381 GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCAAGTTTGAGATACAACATCACCACCATCTT
1 GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCAAGTTTGAGATACAACATCACCACCATCTT
*
1113446 CA-T-T-T-CATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGCAGTCATCT
66 CATTATATACATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGCAGCCATCT
* *
1113507 CTATTCTTATTCTTTCATTCCATTACTTATATTATTATTCATTTCTTAAACCCAATTATTAATCA
131 CTATTCCTATTCTTTCATTCCATTACTTATATTATTATTCAATTCTTAAACCC-ATTATTAATCA
* *
1113572 TATTTCTTTCTTATTA-TTTTTGCAGTCTAAGCATATTAATTCAAGGACATCAGTACTTGTCAAT
195 TATTTCTTTCTTATTATTTTTTGCAGCCCAAGCATATTAATTCAAGGACATCAGTACTTGTCAAT
* * *
1113636 CCTAGATCGGGACACAATAAGGCTATCTACTCTTTTCATCAAAGTGTGTAGATTCTCCTTACATC
260 CCTAGATCGAGACACAATAAGGCTATCTACTCTTTT-ATCAAAGCGTGTAGATTCGCCTTACATC
1113701 A
324 A
1113702 AGCGGTAATC
Statistics
Matches: 305, Mismatches: 14, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
320 78 0.26
321 131 0.43
322 27 0.09
324 1 0.00
326 1 0.00
328 1 0.00
330 66 0.22
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (324 bp):
GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCAAGTTTGAGATACAACATCACCACCATCTT
CATTATATACATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGCAGCCATCT
CTATTCCTATTCTTTCATTCCATTACTTATATTATTATTCAATTCTTAAACCCATTATTAATCAT
ATTTCTTTCTTATTATTTTTTGCAGCCCAAGCATATTAATTCAAGGACATCAGTACTTGTCAATC
CTAGATCGAGACACAATAAGGCTATCTACTCTTTTATCAAAGCGTGTAGATTCGCCTTACATCA
Found at i:1113813 original size:15 final size:15
Alignment explanation
Indices: 1113793--1113821 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1113783 ATTGGAGTGC
1113793 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
1113808 AAAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
1113822 ACCAGAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:1120655 original size:18 final size:18
Alignment explanation
Indices: 1120632--1120670 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1120622 AAAGTAGATA
1120632 CAATGTACGTCCCCTATG
1 CAATGTACGTCCCCTATG
1120650 CAATGTACGTCCCCTATG
1 CAATGTACGTCCCCTATG
1120668 CAA
1 CAA
1120671 GTTATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (18 bp):
CAATGTACGTCCCCTATG
Found at i:1121467 original size:16 final size:16
Alignment explanation
Indices: 1121446--1121477 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1121436 TCTTCCACCA
*
1121446 ATGTTAGAATGGAAAT
1 ATGTTAGAATGCAAAT
1121462 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
1121478 GAGCTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:1124934 original size:16 final size:16
Alignment explanation
Indices: 1124913--1124944 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1124903 TCTTCCACCA
*
1124913 ATGTTAGAATGGAAAT
1 ATGTTAGAATGCAAAT
1124929 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
1124945 GAGCTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:1128014 original size:19 final size:21
Alignment explanation
Indices: 1127990--1128041 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1127980 CGGCCAATAG
*
1127990 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
1128009 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
1128030 CATGTATTTTCA
1 CATGTATTTTCA
1128042 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:1130692 original size:21 final size:19
Alignment explanation
Indices: 1130666--1130718 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 19
1130656 AAAACCCCTT
1130666 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGA-TTTT-AA
1130687 TGAAAAATACATGATTTTAA
1 TG-AAAATACATGATTTTAA
*
1130707 TGAAGATACATG
1 TGAAAATACATG
1130719 CTCATGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 9 0.30
20 4 0.13
21 6 0.20
22 11 0.37
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:1132223 original size:8 final size:9
Alignment explanation
Indices: 1132210--1132266 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
1132200 AAAAGACACA
1132210 TTCTTTTC-
1 TTCTTTTCT
1132218 TTCTTTTCT
1 TTCTTTTCT
*
1132227 TTC-TTT-A
1 TTCTTTTCT
1132234 TT-TTTTCT
1 TTCTTTTCT
* *
1132242 TTATTTTTT
1 TTCTTTTCT
1132251 TTCTTTTCT
1 TTCTTTTCT
1132260 TTCTTTT
1 TTCTTTT
1132267 TGTACTCCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
7 5 0.12
8 13 0.32
9 22 0.55
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.81
Consensus pattern (9 bp):
TTCTTTTCT
Found at i:1132241 original size:15 final size:14
Alignment explanation
Indices: 1132221--1132267 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
1132211 TCTTTTCTTC
1132221 TTTTCTTTCTTTATT
1 TTTTCTTTCTTT-TT
*
1132236 TTTTCTTT-ATTTT
1 TTTTCTTTCTTTTT
1132249 TTTTCTTTTCTTTCTT
1 TTTTC-TTTCTTT-TT
1132265 TTT
1 TTT
1132268 GTACTCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 7 0.26
14 5 0.19
15 10 0.37
16 5 0.19
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTTTCTTTTT
Found at i:1132242 original size:11 final size:11
Alignment explanation
Indices: 1132213--1132250 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1132203 AGACACATTC
1132213 TTTTCTTCT-TT
1 TTTTCTT-TATT
1132224 TCTTTCTTTATT
1 T-TTTCTTTATT
1132236 TTTTCTTTATT
1 TTTTCTTTATT
1132247 TTTT
1 TTTT
1132251 TTCTTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTCTTTATT
Found at i:1134361 original size:8 final size:9
Alignment explanation
Indices: 1134348--1134404 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
1134338 AAAAGAAACA
1134348 TTCTTTTC-
1 TTCTTTTCT
1134356 TTCTTTTCT
1 TTCTTTTCT
*
1134365 TTC-TTT-A
1 TTCTTTTCT
1134372 TT-TTTTCT
1 TTCTTTTCT
* *
1134380 TTATTTTTT
1 TTCTTTTCT
1134389 TTCTTTTCT
1 TTCTTTTCT
1134398 TTCTTTT
1 TTCTTTT
1134405 TGTACTCCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
7 5 0.12
8 13 0.32
9 22 0.55
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.81
Consensus pattern (9 bp):
TTCTTTTCT
Found at i:1134379 original size:15 final size:14
Alignment explanation
Indices: 1134359--1134405 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
1134349 TCTTTTCTTC
1134359 TTTTCTTTCTTTATT
1 TTTTCTTTCTTT-TT
*
1134374 TTTTCTTT-ATTTT
1 TTTTCTTTCTTTTT
1134387 TTTTCTTTTCTTTCTT
1 TTTTC-TTTCTTT-TT
1134403 TTT
1 TTT
1134406 GTACTCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 7 0.26
14 5 0.19
15 10 0.37
16 5 0.19
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTTTCTTTTT
Found at i:1134380 original size:11 final size:11
Alignment explanation
Indices: 1134351--1134388 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1134341 AGAAACATTC
1134351 TTTTCTTCT-TT
1 TTTTCTT-TATT
1134362 TCTTTCTTTATT
1 T-TTTCTTTATT
1134374 TTTTCTTTATT
1 TTTTCTTTATT
1134385 TTTT
1 TTTT
1134389 TTCTTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTCTTTATT
Found at i:1140285 original size:33 final size:33
Alignment explanation
Indices: 1140248--1140347 Score: 78
Period size: 33 Copynumber: 2.9 Consensus size: 33
1140238 ATGAATGAAG
*
1140248 GATGAT-TTAATGGTGATGAAATGGTAATGGAAA
1 GATGATGTTAATGGCG-TGAAATGGTAATGGAAA
* * *
1140281 GATGATGTTATTGGCGTGATATGGTGATGGAATA
1 GATGATGTTAATGGCGTGAAATGGTAATGGAA-A
* * *
1140315 TGGTGATGAT-ATAGGCGTGATAATGGTGATGGA
1 -GATGATGTTAAT-GGCGTGA-AATGGTAATGGA
1140348 CTATGGTGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
33 20 0.37
34 9 0.17
35 14 0.26
36 11 0.20
ACGTcount: A:0.31, C:0.02, G:0.35, T:0.32
Consensus pattern (33 bp):
GATGATGTTAATGGCGTGAAATGGTAATGGAAA
Found at i:1140317 original size:13 final size:12
Alignment explanation
Indices: 1140298--1140362 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
1140288 TTATTGGCGT
1140298 GATATGGTGATG
1 GATATGGTGATG
1140310 GAATATGGTGAT-
1 G-ATATGGTGATG
*
1140322 GATATAGGCG-T-
1 GATAT-GGTGATG
1140333 GATAATGGTGATG
1 GAT-ATGGTGATG
1140346 GACTATGGTGAT-
1 GA-TATGGTGATG
1140358 GATAT
1 GATAT
1140363 AGGCGCGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:1140353 original size:36 final size:36
Alignment explanation
Indices: 1140267--1140395 Score: 165
Period size: 36 Copynumber: 3.7 Consensus size: 36
1140257 ATGGTGATGA
* * * *
1140267 AATGGTAATGGAA-A-GATGATGTTATTGGCGTGAT
1 AATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1140301 -ATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGGAATATGGTGATGATATAGGCGTGAT
* *
1140336 AATGGTGATGGACTATGGTGATGATATAGGCGCGAT
1 AATGGTGATGGAATATGGTGATGATATAGGCGTGAT
* *
1140372 AATGGAGATGGATTATGGTGATGA
1 AATGGTGATGGAATATGGTGATGA
1140396 AAATAGTATC
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
33 11 0.13
34 1 0.01
35 17 0.20
36 55 0.65
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
AATGGTGATGGAATATGGTGATGATATAGGCGTGAT
Found at i:1140781 original size:19 final size:20
Alignment explanation
Indices: 1140734--1140784 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1140724 GAAATCCCTT
**
1140734 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
1140754 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
1140773 TGAAGATACATG
1 TGAAAATACATG
1140785 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:1148508 original size:23 final size:19
Alignment explanation
Indices: 1148465--1148511 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
1148455 AAGTGCAAGT
1148465 GAAAGAAATAAAAAATCAA
1 GAAAGAAATAAAAAATCAA
1148484 GAAAGAAATAAAAAATC-A
1 GAAAGAAATAAAAAATCAA
1148502 GAAAAGAAAT
1 G-AAAGAAAT
1148512 TGAAGCACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.72, C:0.04, G:0.13, T:0.11
Consensus pattern (19 bp):
GAAAGAAATAAAAAATCAA
Found at i:1148546 original size:18 final size:18
Alignment explanation
Indices: 1148523--1148563 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1148513 GAAGCACTTA
1148523 AAAAGAAGAA-AAAAAAAG
1 AAAAGAA-AAGAAAAAAAG
*
1148541 AAAAGAAAAGAAAGAAAG
1 AAAAGAAAAGAAAAAAAG
1148559 AAAAG
1 AAAAG
1148564 TTGAAGCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAAAG
Found at i:1149341 original size:35 final size:36
Alignment explanation
Indices: 1149294--1149361 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
1149284 ATTTAGAAGT
1149294 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
1149329 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
1149362 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:1155001 original size:33 final size:33
Alignment explanation
Indices: 1154959--1155027 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1154949 GTTGATGAAT
*
1154959 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
1154992 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
1155025 GAA
1 GAA
1155028 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:1156916 original size:14 final size:15
Alignment explanation
Indices: 1156897--1156927 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1156887 AACACTCTGT
1156897 TTCATTCTG-ACTTG
1 TTCATTCTGAACTTG
1156911 TTCATTCTGAACTTG
1 TTCATTCTGAACTTG
1156926 TT
1 TT
1156928 TAGGCGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.16, C:0.19, G:0.13, T:0.52
Consensus pattern (15 bp):
TTCATTCTGAACTTG
Found at i:1159499 original size:33 final size:35
Alignment explanation
Indices: 1159455--1159535 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
1159445 ATGGTGATGA
* * *
1159455 AATGGTAATGGA-A-GGATGATGTTATTGGCGTGAT
1 AATGGTGATGGATATGG-TGATGATATAGGCGTGAT
1159489 -ATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGG-ATATGGTGATGATATAGGCGTGAT
1159524 AATGGTGATGGA
1 AATGGTGATGGA
1159536 CAGATTGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
33 9 0.22
34 1 0.03
35 18 0.45
36 12 0.30
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGATATGGTGATGATATAGGCGTGAT
Found at i:1163833 original size:2 final size:2
Alignment explanation
Indices: 1163822--1163850 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1163812 AAGCTGCATC
1163822 AT AT -T 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
1163851 TATTCTATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1165234 original size:15 final size:15
Alignment explanation
Indices: 1165204--1165256 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
1165194 CCTTTGATAA
1165204 CATTT-TTATCCATTT
1 CATTTCTTATCC-TTT
1165219 CATTTCTTATCCTTT
1 CATTTCTTATCCTTT
* *
1165234 CTTTTCTT-T-ATTT
1 CATTTCTTATCCTTT
1165247 CATTTCTTAT
1 CATTTCTTAT
1165257 TTCAATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 10 0.30
14 2 0.06
15 15 0.45
16 6 0.18
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (15 bp):
CATTTCTTATCCTTT
Found at i:1166156 original size:19 final size:20
Alignment explanation
Indices: 1166093--1166164 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
1166083 GAAACCCCTT
*
1166093 TGAAAATACACGATTTTTAAA
1 TGAAAATACATGA-TTTTAAA
1166114 TGAAAATACATGATTTTAAA
1 TGAAAATACATGATTTTAAA
1166134 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTAAA
*
1166153 TGAAGATACATG
1 TGAAAATACATG
1166165 CTCTTGGCCG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.27
20 24 0.49
21 12 0.24
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:1167093 original size:30 final size:32
Alignment explanation
Indices: 1167029--1167111 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 32
1167019 CATGAGCTAA
** *
1167029 TAAATGA-ATGAAAACATGTTACCATGATATC
1 TAAATGATATGAAAACATAATACAATGATATC
1167060 TAAATGATATGAAAACATAATA-AATGA-ATC
1 TAAATGATATGAAAACATAATACAATGATATC
** *
1167090 TAAAACATATGTAAACATAATA
1 TAAATGATATGAAAACATAATA
1167112 TAAAGCTAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 22 0.49
31 11 0.24
32 12 0.27
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.28
Consensus pattern (32 bp):
TAAATGATATGAAAACATAATACAATGATATC
Found at i:1169442 original size:17 final size:17
Alignment explanation
Indices: 1169390--1169461 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 17
1169380 ATTCATGCAT
*
1169390 CTAGTTCATTGAATAAAG
1 CTAGTTCATT-AATAAAA
* * *
1169408 TTAGCTCATTAATTAAA
1 CTAGTTCATTAATAAAA
*
1169425 CTAGTTCATTTATAAAA
1 CTAGTTCATTAATAAAA
* * *
1169442 CTAATTCATTTATTAAA
1 CTAGTTCATTAATAAAA
1169459 CTA
1 CTA
1169462 ACTCTTAATT
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 36 0.82
18 8 0.18
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATAAAA
Found at i:1169462 original size:17 final size:17
Alignment explanation
Indices: 1169413--1169462 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
1169403 TAAAGTTAGC
* *
1169413 TCATTAATTAAACTAGT
1 TCATTTATTAAACTAAT
*
1169430 TCATTTATAAAACTAAT
1 TCATTTATTAAACTAAT
1169447 TCATTTATTAAACTAA
1 TCATTTATTAAACTAA
1169463 CTCTTAATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (17 bp):
TCATTTATTAAACTAAT
Found at i:1169883 original size:25 final size:25
Alignment explanation
Indices: 1169855--1169906 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
1169845 AAGCATTCAA
1169855 GGCTGATTTAATCATCCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
*
1169880 GGCTGATTTAATCATTCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
1169905 GG
1 GG
1169907 TTGTTCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (25 bp):
GGCTGATTTAATCATCCAAACCAAG
Found at i:1172797 original size:17 final size:17
Alignment explanation
Indices: 1172725--1172816 Score: 62
Period size: 17 Copynumber: 5.4 Consensus size: 17
1172715 ATCATTTAGT
*
1172725 AAACTACTTCATTCATGC
1 AAACTAGTTCATTCAT-C
* *
1172743 ATA-TAGTTCATTAAAT-
1 AAACTAGTTCATT-CATC
* * *
1172759 AAAGTTAGTTCATTAATT
1 AAA-CTAGTTCATTCATC
*
1172777 AAACTAGTTTATTCATC
1 AAACTAGTTCATTCATC
* *
1172794 AAACTAGTTCATTTATT
1 AAACTAGTTCATTCATC
1172811 AAACTA
1 AAACTA
1172817 ACTCTTAATT
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
16 2 0.03
17 41 0.69
18 16 0.27
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (17 bp):
AAACTAGTTCATTCATC
Found at i:1173248 original size:25 final size:24
Alignment explanation
Indices: 1173215--1173268 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
1173205 TCAAAGCATT
*
1173215 CAAGGCTGATTTAATCATCCAGAC
1 CAAGGCTGATTTAATCATCCAAAC
*
1173239 CAAGGTCTGATTTAATCATTCAAAC
1 CAAGG-CTGATTTAATCATCCAAAC
1173264 CAAGG
1 CAAGG
1173269 GTTGTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (24 bp):
CAAGGCTGATTTAATCATCCAAAC
Found at i:1176327 original size:36 final size:36
Alignment explanation
Indices: 1176286--1176434 Score: 190
Period size: 36 Copynumber: 4.1 Consensus size: 36
1176276 ATTTATAAGT
* * * *
1176286 TGGTGATAATATGGGCGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* *
1176322 TGGTGACGATATAAGCGTGATAATGGAGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* *** *
1176358 TGGTGATGATAAAGGCGTGATAATACTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
1176394 TGGTGATGATATAGGCGTGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
1176430 TGGTG
1 TGGTG
1176435 TTGGATAGAT
Statistics
Matches: 94, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.32, C:0.05, G:0.36, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:1180015 original size:21 final size:19
Alignment explanation
Indices: 1179982--1180025 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
1179972 TGTAGGAGTC
* *
1179982 TTTTTCTTTTCTTTTTGTT
1 TTTTTCTTTTCTTGTTGCT
1180001 TTTTTCTTCTTTCTTGTTGCT
1 TTTTTC-T-TTTCTTGTTGCT
1180022 TTTT
1 TTTT
1180026 GTTGTAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 14 0.67
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTCTTGTTGCT
Found at i:1180431 original size:36 final size:36
Alignment explanation
Indices: 1180390--1180538 Score: 181
Period size: 36 Copynumber: 4.1 Consensus size: 36
1180380 ATTTATAAGT
* * *
1180390 TGGTGATAATATGGGCGTGATAATGGTGGTGGAATA
1 TGGTGATAATATAGGCGTGATAATGGAGATGGAATA
* * *
1180426 TGGTGACAATATAAGCGTGATAATGGAGATGGACTA
1 TGGTGATAATATAGGCGTGATAATGGAGATGGAATA
* * * * *
1180462 TGGTGATGATAAAGGTGTGATAATGGTGATGGACTA
1 TGGTGATAATATAGGCGTGATAATGGAGATGGAATA
* *
1180498 TGGTGATGATATAGGCGTGATAATGGAGATGGAAGA
1 TGGTGATAATATAGGCGTGATAATGGAGATGGAATA
1180534 TGGTG
1 TGGTG
1180539 TTGGACAGAT
Statistics
Matches: 96, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 96 1.00
ACGTcount: A:0.31, C:0.04, G:0.37, T:0.28
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGAGATGGAATA
Found at i:1180469 original size:13 final size:13
Alignment explanation
Indices: 1180444--1180505 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
1180434 ATATAAGCGT
*
1180444 GATAATGGAGATG
1 GATAATGGTGATG
1180457 GACT-ATGGTGAT-
1 GA-TAATGGTGATG
*
1180469 GATAAAGGTG-T-
1 GATAATGGTGATG
1180480 GATAATGGTGATG
1 GATAATGGTGATG
1180493 GACT-ATGGTGATG
1 GA-TAATGGTGATG
1180506 ATATAGGCGT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
11 11 0.27
12 8 0.20
13 20 0.49
14 2 0.05
ACGTcount: A:0.31, C:0.03, G:0.37, T:0.29
Consensus pattern (13 bp):
GATAATGGTGATG
Found at i:1190155 original size:14 final size:14
Alignment explanation
Indices: 1190112--1190146 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1190102 CTTTCATACG
1190112 CATATTTATATATA
1 CATATTTATATATA
1190126 CATATTTATATATA
1 CATATTTATATATA
1190140 CATATTT
1 CATATTT
1190147 CTTGATACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (14 bp):
CATATTTATATATA
Found at i:1195267 original size:17 final size:17
Alignment explanation
Indices: 1195226--1195297 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
1195216 ATTCATGCAT
1195226 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
* *
1195243 GTTAGTTCAATAATTAAA
1 -CTAGTTCATTAATTAAA
* *
1195261 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
1195278 CTAGTTTATTTATTAAA
1 CTAGTTCATTAATTAAA
1195295 CTA
1 CTA
1195298 ACTCTTAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 32 0.73
18 12 0.27
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:1195727 original size:25 final size:25
Alignment explanation
Indices: 1195699--1195750 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1195689 AAGCATTCAA
1195699 GGCTGATTTAATCATCCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
* *
1195724 GGCTTATTTAATCATTCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
1195749 GG
1 GG
1195751 ATGTTCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (25 bp):
GGCTGATTTAATCATCCAAACCAAG
Found at i:1199701 original size:10 final size:10
Alignment explanation
Indices: 1199686--1199710 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1199676 TCATCCATTA
1199686 ATGCATATTC
1 ATGCATATTC
1199696 ATGCATATTC
1 ATGCATATTC
1199706 ATGCA
1 ATGCA
1199711 AGAAGCCAAA
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:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (10 bp):
ATGCATATTC
Found at i:1201867 original size:21 final size:21
Alignment explanation
Indices: 1201841--1201888 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1201831 TGATGGAGTT
1201841 GAACATGCACAAATCAAACAA
1 GAACATGCACAAATCAAACAA
*
1201862 GAACATGCACAAATCAAAGAA
1 GAACATGCACAAATCAAACAA
1201883 GAACAT
1 GAACAT
1201889 TGTGAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.10
Consensus pattern (21 bp):
GAACATGCACAAATCAAACAA
Found at i:1216642 original size:19 final size:20
Alignment explanation
Indices: 1216614--1216653 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1216604 GGATAATAAT
1216614 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
1216634 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
1216653 A
1 A
1216654 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:1229636 original size:19 final size:20
Alignment explanation
Indices: 1229612--1229651 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1229602 TATCCTTTCT
1229612 TTATTTCATTTT-ATT-CTTA
1 TTATTT-ATTTTCATTACTTA
1229631 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
1229651 T
1 T
1229652 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:1231274 original size:36 final size:36
Alignment explanation
Indices: 1231220--1231310 Score: 148
Period size: 36 Copynumber: 2.6 Consensus size: 36
1231210 GTGATAATTT
1231220 AGGCGTGAT-ATGGTGATGGAATATGGCGATGATAA
1 AGGCGTGATAATGGTGATGGAATATGGCGATGATAA
* * *
1231255 AGGCGTGATAATGGTGATGGACTATGGTGATGATAT
1 AGGCGTGATAATGGTGATGGAATATGGCGATGATAA
1231291 AGGCGTGATAATGGTGATGG
1 AGGCGTGATAATGGTGATGG
1231311 GCAGTTTGTA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 9 0.17
36 43 0.83
ACGTcount: A:0.29, C:0.05, G:0.38, T:0.27
Consensus pattern (36 bp):
AGGCGTGATAATGGTGATGGAATATGGCGATGATAA
Found at i:1235353 original size:36 final size:36
Alignment explanation
Indices: 1235280--1235416 Score: 213
Period size: 36 Copynumber: 3.8 Consensus size: 36
1235270 ATTTATAAGT
* * * *
1235280 TGGTGATAATTTAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATAGACTA
*
1235315 TGGTGATGATAAAGGCGTGATAATGGTGATAGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATAGACTA
*
1235351 TGGTTATGATATAGGCGTGATAATGGTGATAGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATAGACTA
1235387 TGGTGATGATATAGGCGTGATAATGGTGAT
1 TGGTGATGATATAGGCGTGATAATGGTGAT
1235417 GGACAGTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 18 0.19
36 75 0.81
ACGTcount: A:0.30, C:0.04, G:0.34, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATAGACTA
Found at i:1235391 original size:13 final size:11
Alignment explanation
Indices: 1235297--1235417 Score: 68
Period size: 11 Copynumber: 10.2 Consensus size: 11
1235287 AATTTAGGCG
1235297 TGATATGGTGA
1 TGATATGGTGA
1235308 TGGAATATGGTGA
1 T-G-ATATGGTGA
* *
1235321 TGATAAAGGCG-
1 TGAT-ATGGTGA
1235332 TGATAATGGTGA
1 TGAT-ATGGTGA
*
1235344 TAGACTATGGTTA
1 T-GA-TATGGTGA
*
1235357 TGATATAGGCG-
1 TGATAT-GGTGA
1235368 TGATAATGGTGA
1 TGAT-ATGGTGA
1235380 TAGACTATGGTGA
1 T-GA-TATGGTGA
*
1235393 TGATATAGGCG-
1 TGATAT-GGTGA
1235404 TGATAATGGTGA
1 TGAT-ATGGTGA
1235416 TG
1 TG
1235418 GACAGTTTAT
Statistics
Matches: 86, Mismatches: 10, Indels: 27
0.70 0.08 0.22
Matches are distributed among these distances:
11 32 0.37
12 23 0.27
13 29 0.34
14 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.34, T:0.31
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:1245248 original size:23 final size:23
Alignment explanation
Indices: 1245220--1245393 Score: 98
Period size: 23 Copynumber: 7.3 Consensus size: 23
1245210 ACAATCTGTC
1245220 CATCACCATTATCA-CACCTATAT
1 CATCACCATTATCATCACC-ATAT
1245243 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
1245266 -ATCACGCCTATATCATCACCATATT
1 CATCAC-CAT-TATCATCACCATA-T
*
1245291 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
1245315 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
1245338 -ATCACGCCTATATCATCACCATATT
1 CATCAC-CAT-TATCATCACCATA-T
*
1245363 CCATCACCA-TATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
*
1245386 TATCACCA
1 CATCACCA
1245394 ACTTATAAAT
Statistics
Matches: 121, Mismatches: 8, Indels: 45
0.70 0.05 0.26
Matches are distributed among these distances:
22 21 0.17
23 44 0.36
24 22 0.18
25 21 0.17
26 3 0.02
27 10 0.08
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:1245261 original size:13 final size:11
Alignment explanation
Indices: 1245220--1245376 Score: 115
Period size: 11 Copynumber: 13.2 Consensus size: 11
1245210 ACAATCTGTC
1245220 CATCACCATTAT
1 CATCACCA-TAT
1245232 CA-CACCTATAT
1 CATCACC-ATAT
1245243 CATCACCATAGT
1 CATCACCATA-T
1245255 CCATCACCATTAT
1 -CATCACCA-TAT
*
1245268 CA-CGCCTATAT
1 CATCACC-ATAT
1245279 CATCACCATATT
1 CATCACCATA-T
1245291 CCATCACCATTAT
1 -CATCACCA-TAT
*
1245304 CA-CGCCTATAT
1 CATCACC-ATAT
1245315 CATCACCATAGT
1 CATCACCATA-T
1245327 CCATCACCATTAT
1 -CATCACCA-TAT
*
1245340 CA-CGCCTATAT
1 CATCACC-ATAT
1245351 CATCACCATATT
1 CATCACCATA-T
1245363 CCATCACCATAT
1 -CATCACCATAT
1245375 CA
1 CA
1245377 CGCCTATATT
Statistics
Matches: 120, Mismatches: 6, Indels: 39
0.73 0.04 0.24
Matches are distributed among these distances:
11 47 0.39
12 30 0.25
13 37 0.31
14 6 0.05
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1245264 original size:36 final size:36
Alignment explanation
Indices: 1245217--1245393 Score: 311
Period size: 36 Copynumber: 4.9 Consensus size: 36
1245207 GATACAATCT
*
1245217 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
1245253 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
1245289 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
1245325 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
1245361 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
1245394 ACTTATAAAT
Statistics
Matches: 136, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
35 21 0.15
36 115 0.85
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:1249361 original size:23 final size:23
Alignment explanation
Indices: 1249333--1249506 Score: 98
Period size: 23 Copynumber: 7.3 Consensus size: 23
1249323 ACAATCTGTC
1249333 CATCACCATTATCA-CACCTATAT
1 CATCACCATTATCATCACC-ATAT
1249356 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
1249379 -ATCACGCCTATATCATCACCATATT
1 CATCAC-CAT-TATCATCACCATA-T
*
1249404 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
1249428 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
1249451 -ATCACGCCTATATCATCACCATATT
1 CATCAC-CAT-TATCATCACCATA-T
*
1249476 CCATCACCA-TATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
*
1249499 TATCACCA
1 CATCACCA
1249507 ACTTATAAAT
Statistics
Matches: 121, Mismatches: 8, Indels: 45
0.70 0.05 0.26
Matches are distributed among these distances:
22 21 0.17
23 44 0.36
24 22 0.18
25 21 0.17
26 3 0.02
27 10 0.08
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:1249374 original size:13 final size:11
Alignment explanation
Indices: 1249333--1249489 Score: 115
Period size: 11 Copynumber: 13.2 Consensus size: 11
1249323 ACAATCTGTC
1249333 CATCACCATTAT
1 CATCACCA-TAT
1249345 CA-CACCTATAT
1 CATCACC-ATAT
1249356 CATCACCATAGT
1 CATCACCATA-T
1249368 CCATCACCATTAT
1 -CATCACCA-TAT
*
1249381 CA-CGCCTATAT
1 CATCACC-ATAT
1249392 CATCACCATATT
1 CATCACCATA-T
1249404 CCATCACCATTAT
1 -CATCACCA-TAT
*
1249417 CA-CGCCTATAT
1 CATCACC-ATAT
1249428 CATCACCATAGT
1 CATCACCATA-T
1249440 CCATCACCATTAT
1 -CATCACCA-TAT
*
1249453 CA-CGCCTATAT
1 CATCACC-ATAT
1249464 CATCACCATATT
1 CATCACCATA-T
1249476 CCATCACCATAT
1 -CATCACCATAT
1249488 CA
1 CA
1249490 CGCCTATATT
Statistics
Matches: 120, Mismatches: 6, Indels: 39
0.73 0.04 0.24
Matches are distributed among these distances:
11 47 0.39
12 30 0.25
13 37 0.31
14 6 0.05
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1249377 original size:36 final size:36
Alignment explanation
Indices: 1249330--1249506 Score: 311
Period size: 36 Copynumber: 4.9 Consensus size: 36
1249320 GATACAATCT
*
1249330 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
1249366 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
1249402 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
1249438 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
1249474 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
1249507 ACTTATAAAT
Statistics
Matches: 136, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
35 21 0.15
36 115 0.85
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:1251150 original size:16 final size:16
Alignment explanation
Indices: 1251116--1251149 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1251106 TTCAACTTTC
*
1251116 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTCTCT
1251132 TTTCTTTTTCTTC-CT
1 TTTCTTTTTCTTCTCT
1251147 TTT
1 TTT
1251150 TGAGTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTCTCT
Found at i:1251177 original size:23 final size:25
Alignment explanation
Indices: 1251138--1251191 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
1251128 TTCTTTTCTT
1251138 TTTCTTCCTTTTTGAGTACTTTCAA
1 TTTCTTCCTTTTTGAGTACTTTCAA
* * *
1251163 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTACTTTCAA
1251186 TTTCTT
1 TTTCTT
1251192 TGCTGGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 19 0.73
24 1 0.04
25 6 0.23
ACGTcount: A:0.11, C:0.17, G:0.11, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTACTTTCAA
Found at i:1251731 original size:20 final size:21
Alignment explanation
Indices: 1251694--1251732 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1251684 GATGGTCTTG
*
1251694 ATGAAGGATGTTGATGATGGA
1 ATGAAGGATGGTGATGATGGA
*
1251715 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
1251733 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGGA
Found at i:1252111 original size:19 final size:20
Alignment explanation
Indices: 1252070--1252120 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1252060 GAAACCCTTT
*
1252070 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
1252090 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1252109 TGAAGATACATG
1 TGAAAATACATG
1252121 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1252996 original size:30 final size:31
Alignment explanation
Indices: 1252957--1253016 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
1252947 ACATGCTGCC
**
1252957 ATGATATCTAAATGATATGCAAACAAAATAA
1 ATGATATCTAAAACATATGCAAACAAAATAA
* *
1252988 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACAAAATA
1253017 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACAAAATAA
Found at i:1255063 original size:24 final size:24
Alignment explanation
Indices: 1255034--1255087 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1255024 TTCATTTTAG
1255034 TTCTTGGATTAGAACTCTATCAGT
1 TTCTTGGATTAGAACTCTATCAGT
1255058 TTCTTGGATTAGAACTCTATCAGT
1 TTCTTGGATTAGAACTCTATCAGT
1255082 TTCTTG
1 TTCTTG
1255088 TCAGTCTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (24 bp):
TTCTTGGATTAGAACTCTATCAGT
Found at i:1255757 original size:19 final size:20
Alignment explanation
Indices: 1255733--1255773 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
1255723 ATTTATGATT
*
1255733 TTTAATGAAAATACATG-TC
1 TTTAATAAAAATACATGCTC
1255752 TTTAATAAAAATACATGCTC
1 TTTAATAAAAATACATGCTC
1255772 TT
1 TT
1255774 GGCCGAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (20 bp):
TTTAATAAAAATACATGCTC
Found at i:1262208 original size:24 final size:24
Alignment explanation
Indices: 1262172--1262221 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1262162 GTGGATCACT
* *
1262172 AAAAGTCACGTTTATTGATTCTTC
1 AAAAGACACGTTTATTGAATCTTC
* *
1262196 AAAAGACATGTTTCTTGAATCTTC
1 AAAAGACACGTTTATTGAATCTTC
1262220 AA
1 AA
1262222 CTTGAAGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (24 bp):
AAAAGACACGTTTATTGAATCTTC
Found at i:1264378 original size:17 final size:17
Alignment explanation
Indices: 1264353--1264386 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1264343 ATATAATGCA
*
1264353 TATAATATAATGATGTG
1 TATAATATAAAGATGTG
*
1264370 TATATTATAAAGATGTG
1 TATAATATAAAGATGTG
1264387 AACTATAGGT
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:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (17 bp):
TATAATATAAAGATGTG
Found at i:1266868 original size:8 final size:8
Alignment explanation
Indices: 1266855--1266900 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
1266845 GAAATTCTTT
1266855 TTTTTTTC
1 TTTTTTTC
1266863 TTTTTTTC
1 TTTTTTTC
* *
1266871 TTCTTCTC
1 TTTTTTTC
1266879 TGTTTTTTC
1 T-TTTTTTC
*
1266888 TTTCTTTC
1 TTTTTTTC
1266896 TTTTT
1 TTTTT
1266901 GTACTCCAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
8 25 0.81
9 6 0.19
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1272959 original size:20 final size:20
Alignment explanation
Indices: 1272921--1272966 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1272911 TAATGGTCTT
*
1272921 AAGAAATGAATATATAATAA
1 AAGAAATGAATATAAAATAA
1272941 AAGAAATGAA-ATAGAAATAA
1 AAGAAATGAATATA-AAATAA
*
1272961 ATGAAA
1 AAGAAA
1272967 GAGAGATGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (20 bp):
AAGAAATGAATATAAAATAA
Found at i:1273434 original size:19 final size:21
Alignment explanation
Indices: 1273391--1273440 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
1273381 GAAACCCCTT
1273391 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
1273412 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
1273431 TGAAGATACA
1 TGAAAATACA
1273441 AGCTCTTGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 11 0.39
20 4 0.14
21 13 0.46
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:1276606 original size:19 final size:19
Alignment explanation
Indices: 1276582--1276646 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 19
1276572 TCTTTTTGAA
1276582 TTTCTTTTTCTTTTCTTCT
1 TTTCTTTTTCTTTTCTTCT
1276601 TTTCTTTTTCTGAATTTTCTTCT
1 TTTCTTTTTC----TTTTCTTCT
1276624 TTT-TTTTGTCTTTTCTTTCT
1 TTTCTTTT-TCTTTTC-TTCT
1276644 TTT
1 TTT
1276647 TGTACTCCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
19 15 0.38
20 7 0.17
22 4 0.10
23 14 0.35
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTCTTTTTCTTTTCTTCT
Found at i:1276620 original size:20 final size:19
Alignment explanation
Indices: 1276597--1276647 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
1276587 TTTTCTTTTC
1276597 TTCTTTTCTTTTTCTGAATT
1 TTCTTTTCTTTTT-TGAATT
**
1276617 TTCTTCTT-TTTTTTGTCTT
1 TTCTT-TTCTTTTTTGAATT
1276636 TTC-TTTCTTTTT
1 TTCTTTTCTTTTT
1276648 GTACTCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 2 0.07
18 6 0.22
19 7 0.26
20 10 0.37
21 2 0.07
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (19 bp):
TTCTTTTCTTTTTTGAATT
Found at i:1277401 original size:19 final size:21
Alignment explanation
Indices: 1277358--1277409 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
1277348 GAAACCCCTT
1277358 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
1277379 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
1277398 TGAAGATACATG
1 TGAAAATACATG
1277410 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:1279777 original size:19 final size:20
Alignment explanation
Indices: 1279738--1279793 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
1279728 GAAATCCCTT
*
1279738 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATCTTTAA
1279758 TGAAAATACATGA-CTTTAA
1 TGAAAATACATGATCTTTAA
*
1279777 TGAAAATACATGCTCTT
1 TGAAAATACATGATCTT
1279794 GGCCGAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATCTTTAA
Found at i:1286229 original size:22 final size:21
Alignment explanation
Indices: 1286190--1286231 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1286180 AGTGAAAAAA
**
1286190 CCGGATCGATTTTTATCCGAT
1 CCGGATCGATTTAAATCCGAT
1286211 CCGGATCGGATTTAAATCCGA
1 CCGGATC-GATTTAAATCCGA
1286232 CTATGTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (21 bp):
CCGGATCGATTTAAATCCGAT
Found at i:1286499 original size:19 final size:20
Alignment explanation
Indices: 1286475--1286514 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1286465 TATCCTTTCT
1286475 TTATTTCATATCATT-CTTA
1 TTATTTCATATCATTACTTA
* *
1286494 TTATTTCTTTTCATTACTTA
1 TTATTTCATATCATTACTTA
1286514 T
1 T
1286515 ATTATTATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTCATATCATTACTTA
Found at i:1294118 original size:15 final size:15
Alignment explanation
Indices: 1294098--1294131 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1294088 TTGAATGATC
*
1294098 TTCAATATATAAATT
1 TTCAATATAGAAATT
*
1294113 TTCAATATGGAAATT
1 TTCAATATAGAAATT
1294128 TTCA
1 TTCA
1294132 CCACGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (15 bp):
TTCAATATAGAAATT
Found at i:1294356 original size:13 final size:12
Alignment explanation
Indices: 1294338--1294394 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
1294328 GAAATTTTAG
1294338 TTTTTTTTGGCT
1 TTTTTTTTGGCT
*
1294350 CTTTTTTTT-GTT
1 -TTTTTTTTGGCT
*
1294362 TTTTTTTTGCCT
1 TTTTTTTTGGCT
**
1294374 TTTTTTTTGTTT
1 TTTTTTTTGGCT
1294386 TTTTTTTTG
1 TTTTTTTTG
1294395 AAAAAATAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
11 8 0.21
12 22 0.58
13 8 0.21
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.82
Consensus pattern (12 bp):
TTTTTTTTGGCT
Found at i:1294362 original size:22 final size:22
Alignment explanation
Indices: 1294332--1294390 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
1294322 TTTTTTGAAA
*
1294332 TTTTAGTTTTTTTTGG-CTCTTT
1 TTTTTGTTTTTTTTGGCCT-TTT
*
1294354 TTTTTGTTTTTTTTTTGCCTTTT
1 TTTTTG-TTTTTTTTGGCCTTTT
1294377 TTTTTGTTTTTTTT
1 TTTTTGTTTTTTTT
1294391 TTTGAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 13 0.39
23 18 0.55
24 2 0.06
ACGTcount: A:0.02, C:0.07, G:0.10, T:0.81
Consensus pattern (22 bp):
TTTTTGTTTTTTTTGGCCTTTT
Found at i:1294365 original size:11 final size:11
Alignment explanation
Indices: 1294351--1294392 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
1294341 TTTTTGGCTC
1294351 TTTTTTTTGTT
1 TTTTTTTTGTT
*
1294362 TTTTTTTTGCCT
1 TTTTTTTTG-TT
1294374 TTTTTTTTGTT
1 TTTTTTTTGTT
1294385 TTTTTTTT
1 TTTTTTTT
1294393 TGAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:1294394 original size:24 final size:24
Alignment explanation
Indices: 1294338--1294392 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 24
1294328 GAAATTTTAG
*
1294338 TTTTTTTTGGCTCTTTTTTTTGTT
1 TTTTTTTTGCCTCTTTTTTTTGTT
1294362 TTTTTTTTGCCT-TTTTTTTTGTT
1 TTTTTTTTGCCTCTTTTTTTTGTT
1294385 TTTTTTTT
1 TTTTTTTT
1294393 TGAAAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (24 bp):
TTTTTTTTGCCTCTTTTTTTTGTT
Found at i:1300678 original size:36 final size:36
Alignment explanation
Indices: 1300626--1300738 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
1300616 GATACTATTT
*
1300626 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
1300662 TCATCACCATAGTCCATCACCATTATCACGCTTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
1300698 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
1300733 ACATCA
1 TCATCA
1300739 TCCTTCCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:1300753 original size:33 final size:33
Alignment explanation
Indices: 1300709--1300777 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1300699 CATCACCATA
*
1300709 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
1300742 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
1300775 TTC
1 TTC
1300778 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:1306418 original size:36 final size:36
Alignment explanation
Indices: 1306359--1306471 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
1306349 GATACTATTT
* *
1306359 TCATCACCATAATCTATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
1306395 TCATCACCATAGTCCATCACCATTATCACGCTTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
1306431 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
1306466 ACATCA
1 TCATCA
1306472 TCCTTCCATT
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 16 0.23
36 53 0.77
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:1314994 original size:13 final size:13
Alignment explanation
Indices: 1314972--1315001 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1314962 ACTAAACACC
1314972 TTTC-ACATACCT
1 TTTCAACATACCT
1314984 TTTCAACATACCT
1 TTTCAACATACCT
1314997 TTTCA
1 TTTCA
1315002 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:1316590 original size:16 final size:16
Alignment explanation
Indices: 1316569--1316601 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1316559 TAGTTAGCTC
1316569 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
1316585 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
1316601 A
1 A
1316602 GGTGGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:1327283 original size:13 final size:13
Alignment explanation
Indices: 1327265--1327290 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1327255 AACACCTCTC
1327265 ACATACCTTTTCA
1 ACATACCTTTTCA
1327278 ACATACCTTTTCA
1 ACATACCTTTTCA
1327291 TATTTGGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:1330051 original size:15 final size:15
Alignment explanation
Indices: 1330015--1330044 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1330005 GTGCTTCAAC
1330015 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
1330029 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
1330044 T
1 T
1330045 ATTTTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:1330077 original size:27 final size:28
Alignment explanation
Indices: 1330039--1330105 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
1330029 TTTCTTTGCT
1330039 TTTCTTATTTTT-GAATGCTGAAATTTC
1 TTTCTTATTTTTGGAATGCTGAAATTTC
* **
1330066 TTTCTT-TCTTTTGGAGTGCTTCAATTTC
1 TTTCTTAT-TTTTGGAATGCTGAAATTTC
*
1330094 TTTTCTGATTTT
1 -TTTCTTATTTT
1330106 CTTTTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 10 0.31
28 12 0.38
29 8 0.25
30 1 0.03
ACGTcount: A:0.15, C:0.13, G:0.12, T:0.60
Consensus pattern (28 bp):
TTTCTTATTTTTGGAATGCTGAAATTTC
Found at i:1331846 original size:19 final size:21
Alignment explanation
Indices: 1331797--1331849 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1331787 TGAAACCCCT
1331797 TTGAAAATACATGATTTTTAA
1 TTGAAAATACATGATTTTTAA
1331818 TTGAAAATACATGA-TTTTAA
1 TTGAAAATACATGATTTTTAA
*
1331838 -TGAAGATACATG
1 TTGAAAATACATG
1331850 CTCTTGGCCG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.35
20 6 0.19
21 14 0.45
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (21 bp):
TTGAAAATACATGATTTTTAA
Found at i:1332325 original size:19 final size:20
Alignment explanation
Indices: 1332278--1332325 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
1332268 ACCCCTTTGC
**
1332278 AAATACATGATTTTTTATGA
1 AAATACATGATTTTAAATGA
*
1332298 AAATGCATGA-TTTAAATGA
1 AAATACATGATTTTAAATGA
*
1332317 AGATACATG
1 AAATACATG
1332326 CTCTTGGCCG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (20 bp):
AAATACATGATTTTAAATGA
Found at i:1337065 original size:35 final size:36
Alignment explanation
Indices: 1337018--1337085 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
1337008 ATTTATAAGT
1337018 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
1337053 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
1337086 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:1337476 original size:19 final size:20
Alignment explanation
Indices: 1337429--1337479 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1337419 GAAACCCCTT
**
1337429 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
1337449 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
1337468 TGAAGATACATG
1 TGAAAATACATG
1337480 CTCTTGGCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:1344887 original size:29 final size:29
Alignment explanation
Indices: 1344845--1344914 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
1344835 GGCACCAATT
1344845 TGATGTCACATGGAGTGCACATGCTTGAA
1 TGATGTCACATGGAGTGCACATGCTTGAA
1344874 TGATGTCACATGGAGTGCACATGCTTGAA
1 TGATGTCACATGGAGTGCACATGCTTGAA
*
1344903 TAATG-CACATGG
1 TGATGTCACATGG
1344915 CAGCCTACTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.17
29 33 0.82
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (29 bp):
TGATGTCACATGGAGTGCACATGCTTGAA
Found at i:1364522 original size:13 final size:13
Alignment explanation
Indices: 1364504--1364530 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1364494 AAATTTTGGA
1364504 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
1364517 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
1364530 T
1 T
1364531 GCCTTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:1365999 original size:91 final size:90
Alignment explanation
Indices: 1365833--1366004 Score: 231
Period size: 91 Copynumber: 1.9 Consensus size: 90
1365823 CACATGTGCC
* *
1365833 TTGCATATGACCAGCCCCCATGTGCCTTACATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTACATATGGATCATTTAGGCGCCAAGATGAAGAGATCT
*
1365898 CTCCATATTCGGCCAAGTCATGTATT
66 ATCCA-ATTCGGCCAAGTCATGTATT
* * * *
1365924 TTGCATGTGATCAGCCCCCATGTGCCTTGCATATGGTTCATTTAGGCGCCAAGATGAATG-GCCA
1 TTGCATATGACCAGCCCCCATGTGCCTTACATATGGATCATTTAGGCGCCAAGATGAA-GAG--A
1365988 TCTATCC-ATTCGGCCAA
63 TCTATCCAATTCGGCCAA
1366005 TCACCATTAC
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
91 64 0.90
92 1 0.01
93 6 0.08
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (90 bp):
TTGCATATGACCAGCCCCCATGTGCCTTACATATGGATCATTTAGGCGCCAAGATGAAGAGATCT
ATCCAATTCGGCCAAGTCATGTATT
Found at i:1377569 original size:19 final size:21
Alignment explanation
Indices: 1377547--1377590 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1377537 AGCTTGTACC
*
1377547 TTCA-TTAAAA-TCATGTATT
1 TTCATTTAAAAGTCAAGTATT
1377566 TTCATTTAAAAGTCAAGTATT
1 TTCATTTAAAAGTCAAGTATT
1377587 TTCA
1 TTCA
1377591 AAGGGGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 6 0.27
21 12 0.55
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (21 bp):
TTCATTTAAAAGTCAAGTATT
Found at i:1381580 original size:19 final size:21
Alignment explanation
Indices: 1381552--1381601 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
1381542 GCCAAGAGCT
*
1381552 TGTATCTTCA-TTAAAA-TCA
1 TGTATTTTCATTTAAAAGTCA
1381571 TGTATTTTCATTTAAAAGTCA
1 TGTATTTTCATTTAAAAGTCA
1381592 TGTATTTTCA
1 TGTATTTTCA
1381602 AAGGGTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 9 0.32
20 6 0.21
21 13 0.46
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (21 bp):
TGTATTTTCATTTAAAAGTCA
Found at i:1384986 original size:19 final size:20
Alignment explanation
Indices: 1384962--1385002 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1384952 ATATCCTTTC
1384962 ATTATTTCA-TTTCATT-CTT
1 ATTATTT-ATTTTCATTACTT
1384981 ATTATTTATTTTCATTACTT
1 ATTATTTATTTTCATTACTT
1385001 AT
1 AT
1385003 ATTATTATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 1 0.05
19 14 0.70
20 5 0.25
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTATTTATTTTCATTACTT
Found at i:1392247 original size:19 final size:20
Alignment explanation
Indices: 1392227--1392262 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1392217 ATTTCTTTAT
1392227 TTTA-TTTCATT-CTTATTA
1 TTTATTTTCATTACTTATTA
1392245 TTTATTTTCATTACTTAT
1 TTTATTTTCATTACTTAT
1392263 ATCATTATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 7 0.44
20 5 0.31
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTTTCATTACTTATTA
Found at i:1401229 original size:19 final size:21
Alignment explanation
Indices: 1401186--1401237 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
1401176 GAAACCCCTT
1401186 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
1401207 TGAAAATAGATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
1401226 TGAAGATACATG
1 TGAAAATACATG
1401238 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:1405793 original size:35 final size:36
Alignment explanation
Indices: 1405746--1405813 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
1405736 ATTTATAAGT
1405746 TGGTGATAATATAGACAAGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGACAAGATAATGGTGATGGAATA
* * **
1405781 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGACAAGATAATGGTGATGGA
1405814 CAGATTGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 17 0.61
36 11 0.39
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.29
Consensus pattern (36 bp):
TGGTGATAATATAGACAAGATAATGGTGATGGAATA
Found at i:1408043 original size:15 final size:16
Alignment explanation
Indices: 1408012--1408052 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
1408002 AAAAGCAACA
*
1408012 AAAAGAGAAACAGAAAG
1 AAAAGA-AAACAAAAAG
1408029 AAAA-AAAACAAAAAG
1 AAAAGAAAACAAAAAG
1408044 AAAAGAAAA
1 AAAAGAAAA
1408053 AGACTCCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 13 0.59
16 5 0.23
17 4 0.18
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAGAAAACAAAAAG
Found at i:1410785 original size:35 final size:36
Alignment explanation
Indices: 1410738--1410805 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
1410728 ATTTATAAGT
1410738 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
1410773 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
1410806 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:1414758 original size:16 final size:16
Alignment explanation
Indices: 1414726--1414759 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1414716 AGTAGGAGTC
1414726 TTTTCTTTTCTTTTTG
1 TTTTCTTTTCTTTTTG
1414742 TTTT-TTTTCTTTCTTG
1 TTTTCTTTTCTTT-TTG
1414758 TT
1 TT
1414760 GGTTTTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTCTTTTTG
Found at i:1414764 original size:20 final size:20
Alignment explanation
Indices: 1414726--1414765 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1414716 AGTAGGAGTC
*
1414726 TTTTCTTTTCTTTTTGTTTT
1 TTTTCTTTTCTTTTGGTTTT
1414746 TTTTC-TTTCTTGTTGGTTTT
1 TTTTCTTTTCTT-TTGGTTTT
1414766 GTTGCAGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (20 bp):
TTTTCTTTTCTTTTGGTTTT
Found at i:1414765 original size:19 final size:20
Alignment explanation
Indices: 1414726--1414765 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1414716 AGTAGGAGTC
* *
1414726 TTTTCTTTTCTTTTTGTTTT
1 TTTTCTTTTCTTGTTGGTTT
1414746 TTTTC-TTTCTTGTTGGTTT
1 TTTTCTTTTCTTGTTGGTTT
1414765 T
1 T
1414766 GTTGCAGCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (20 bp):
TTTTCTTTTCTTGTTGGTTT
Found at i:1415178 original size:24 final size:22
Alignment explanation
Indices: 1415134--1415180 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 22
1415124 ATTTATTAGT
1415134 TGGTGATAATATAGGTGTGATA
1 TGGTGATAATATAGGTGTGATA
1415156 TGGTGATGGAATAT-GGTGATGATA
1 TGGTGAT--AATATAGGTG-TGATA
1415180 T
1 T
1415181 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 11 0.50
ACGTcount: A:0.30, C:0.00, G:0.34, T:0.36
Consensus pattern (22 bp):
TGGTGATAATATAGGTGTGATA
Found at i:1415181 original size:35 final size:36
Alignment explanation
Indices: 1415134--1415201 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
1415124 ATTTATTAGT
*
1415134 TGGTGATAATATAGGTGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
1415169 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
1415202 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.29, C:0.01, G:0.37, T:0.32
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:1423387 original size:22 final size:23
Alignment explanation
Indices: 1423341--1423387 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
1423331 TATCACGCCT
1423341 ATATCATCACTATATTCCATCACC
1 ATATCATCACTATATT-CATCACC
1423365 ATATCACTC-CTATATT-ATCACC
1 ATATCA-TCACTATATTCATCACC
1423387 A
1 A
1423388 ACTTCTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
24 13 0.59
25 2 0.09
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (23 bp):
ATATCATCACTATATTCATCACC
Found at i:1428548 original size:20 final size:22
Alignment explanation
Indices: 1428513--1428552 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1428503 CATGCTTAAT
1428513 CATTCATTTGTTAGCTCATATA
1 CATTCATTTGTTAGCTCATATA
1428535 CATTCA-TT-TTAGCTCATA
1 CATTCATTTGTTAGCTCATA
1428553 GGTCTTACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (22 bp):
CATTCATTTGTTAGCTCATATA
Found at i:1438355 original size:35 final size:37
Alignment explanation
Indices: 1438286--1438365 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
1438276 ATACTATTTC
*
1438286 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
1438323 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
1438358 CATCACCA
1 CATCACCA
1438366 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:1438774 original size:12 final size:11
Alignment explanation
Indices: 1438743--1438790 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 11
1438733 GTGCTACAAC
1438743 AAAA-AAAAAG
1 AAAAGAAAAAG
1438753 CAACAAGAAAGAAG
1 -AA-AAGAAA-AAG
1438767 AAAAGAAAAGAG
1 AAAAGAAAA-AG
1438779 AAAAGAAAAAG
1 AAAAGAAAAAG
1438790 A
1 A
1438791 CTCCTACATC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 6 0.18
12 19 0.58
13 5 0.15
14 3 0.09
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:1438846 original size:14 final size:15
Alignment explanation
Indices: 1438812--1438858 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1438802 AATTTGGAAT
1438812 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
1438827 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
1438841 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
1438858 G
1 G
1438859 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:1442250 original size:35 final size:37
Alignment explanation
Indices: 1442181--1442260 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
1442171 ATACTATTTC
*
1442181 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
1442218 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
1442253 CATCACCA
1 CATCACCA
1442261 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Done.