Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007849.1 Hibiscus syriacus cultivar Beakdansim tig00110206_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: 3141433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 12
Found at i:1102943 original size:15 final size:16
Alignment explanation
Indices: 1102911--1102944 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1102901 TTAATTAGTT
1102911 AAATTTTCAATTATTCA
1 AAATTTTCAA-TATTCA
1102928 AAATTTTCAA-ATTCA
1 AAATTTTCAATATTCA
1102943 AA
1 AA
1102945 CCGGGATCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTTTCAATATTCA
Found at i:1112300 original size:21 final size:24
Alignment explanation
Indices: 1112245--1112300 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 24
1112235 TTTATTATAA
1112245 TTTATTACATAACTTATATATTTTAT
1 TTTATTA-ATAAC-TATATATTTTAT
*
1112271 TTT-TAAATAA-TAT-TATTTT-T
1 TTTATTAATAACTATATATTTTAT
1112291 TTTATTAATA
1 TTTATTAATA
1112301 CGTTGTAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
20 4 0.15
21 11 0.41
22 3 0.11
24 4 0.15
25 2 0.07
26 3 0.11
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTATTAATAACTATATATTTTAT
Found at i:1112607 original size:18 final size:18
Alignment explanation
Indices: 1112573--1112607 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1112563 TATTACCAAA
* *
1112573 ACATACAAATATTGCACG
1 ACATACAAACATGGCACG
1112591 ACATACAAACATGGCAC
1 ACATACAAACATGGCAC
1112608 AATCTTGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.17
Consensus pattern (18 bp):
ACATACAAACATGGCACG
Found at i:1115591 original size:31 final size:31
Alignment explanation
Indices: 1115553--1115633 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
1115543 AGGGTCGAGG
1115553 GTTTACCTATGTTCTTCGGGACATATGGAAT
1 GTTTACCTATGTTCTTCGGGACATATGGAAT
* *
1115584 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGAAT
* * *
1115615 GATTACCTAAGTTATTCGG
1 GTTTACCTATGTTCTTCGG
1115634 AATCTATGGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGAAT
Found at i:1116336 original size:21 final size:21
Alignment explanation
Indices: 1116310--1116374 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1116300 GAAATTTTTG
*
1116310 TGCATCGGTGCACTGTAGCAA
1 TGCATCGATGCACTGTAGCAA
*
1116331 TGCATCGACGCACTGTAGCAA
1 TGCATCGATGCACTGTAGCAA
*
1116352 TGCATCGATGCACTGTAACAA
1 TGCATCGATGCACTGTAGCAA
1116373 TG
1 TG
1116375 TTCATGGTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (21 bp):
TGCATCGATGCACTGTAGCAA
Found at i:1119812 original size:67 final size:66
Alignment explanation
Indices: 1119705--1119839 Score: 225
Period size: 67 Copynumber: 2.0 Consensus size: 66
1119695 ATATTTCACT
* *
1119705 TGCATTCTTTCTAAATTATCCTTGAACCATTTTTATCTTGTAGAGATTATAGGATTCATGCTGAT
1 TGCATTCCTTCTAAATTATCCTTGAACCATTTTTAGCTTGTAGAGATTATAGGATTCATGCTGAT
1119770 A
66 A
* *
1119771 TGCATTCCTTCTAAAATTATTCTTGAACCATTTTTAGCTTGTAGAGATTGTAGGATTCATGCTGA
1 TGCATTCCTTCT-AAATTATCCTTGAACCATTTTTAGCTTGTAGAGATTATAGGATTCATGCTGA
1119836 TA
65 TA
1119838 TG
1 TG
1119840 TAATGTTTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 11 0.17
67 53 0.83
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.43
Consensus pattern (66 bp):
TGCATTCCTTCTAAATTATCCTTGAACCATTTTTAGCTTGTAGAGATTATAGGATTCATGCTGAT
A
Found at i:1127872 original size:16 final size:16
Alignment explanation
Indices: 1127851--1127881 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1127841 AGGAAGCATT
1127851 ATGTAAAAAAATTAAC
1 ATGTAAAAAAATTAAC
*
1127867 ATGTAAAAAATTTAA
1 ATGTAAAAAAATTAA
1127882 TAAATTGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.29
Consensus pattern (16 bp):
ATGTAAAAAAATTAAC
Found at i:1129899 original size:18 final size:18
Alignment explanation
Indices: 1129854--1129902 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1129844 AGAAAATAAG
*
1129854 GATCGAGAGAAGGAGAGG
1 GATCGAGAGAAGGAGAGA
** * *
1129872 GAAGGTGAGAAGGATAGA
1 GATCGAGAGAAGGAGAGA
1129890 GATCGAGAGAAGG
1 GATCGAGAGAAGG
1129903 GAAAGGAGAG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.04, G:0.47, T:0.08
Consensus pattern (18 bp):
GATCGAGAGAAGGAGAGA
Found at i:1130938 original size:29 final size:29
Alignment explanation
Indices: 1130899--1130955 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1130889 AACCCCCTTC
*
1130899 ATAATTGTCAGAGAGCCAAGAGGGCAATA
1 ATAATTGTCAGAGAACCAAGAGGGCAATA
*
1130928 ATAATTGTCAGAGAACCAAGGGGGCAAT
1 ATAATTGTCAGAGAACCAAGAGGGCAAT
1130956 CTAACAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.18
Consensus pattern (29 bp):
ATAATTGTCAGAGAACCAAGAGGGCAATA
Found at i:1144518 original size:98 final size:100
Alignment explanation
Indices: 1144335--1144519 Score: 266
Period size: 98 Copynumber: 1.9 Consensus size: 100
1144325 AACAAACCAC
* * * * *
1144335 TGAGAAAACAGAACAAAGACAATCTAGAAAGGCTGGCTACATTAAATCAATATGTTGCTTAACTG
1 TGAGAAAACAGAACAAAGACAATCCAGAAAGACTGACTAAATTAAATCAATATGTTGCTAAACTG
* *
1144400 TGCCATAGGCAGGACAGTAGGGACATAGAGACCTT
66 TGCCAAAGACAGGACAGTAGGGACATAGAGACCTT
* * *
1144435 TGAGAAAACA-AA-AAAGACAATCCAGAAAGACTGACTAAATTAGATCAATATGTTTCTAAATTG
1 TGAGAAAACAGAACAAAGACAATCCAGAAAGACTGACTAAATTAAATCAATATGTTGCTAAACTG
1144498 TGCCAAAGACAGGACAGTAGGG
66 TGCCAAAGACAGGACAGTAGGG
1144520 GATTTTCAGT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
98 63 0.84
99 2 0.03
100 10 0.13
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.21
Consensus pattern (100 bp):
TGAGAAAACAGAACAAAGACAATCCAGAAAGACTGACTAAATTAAATCAATATGTTGCTAAACTG
TGCCAAAGACAGGACAGTAGGGACATAGAGACCTT
Found at i:1147339 original size:7 final size:7
Alignment explanation
Indices: 1147329--1147395 Score: 80
Period size: 7 Copynumber: 9.6 Consensus size: 7
1147319 CGGAAAGTGG
1147329 CGGCGGA
1 CGGCGGA
1147336 CGGCGGA
1 CGGCGGA
* *
1147343 TGTCGGA
1 CGGCGGA
1147350 CGGCGGA
1 CGGCGGA
1147357 CGGCGGA
1 CGGCGGA
* *
1147364 TGTCGGA
1 CGGCGGA
1147371 CGGCGGA
1 CGGCGGA
1147378 CGGCGGA
1 CGGCGGA
* *
1147385 TGTCGGA
1 CGGCGGA
1147392 CGGC
1 CGGC
1147396 AAACAGCGGC
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.13, C:0.25, G:0.52, T:0.09
Consensus pattern (7 bp):
CGGCGGA
Found at i:1147404 original size:21 final size:21
Alignment explanation
Indices: 1147329--1147395 Score: 134
Period size: 21 Copynumber: 3.2 Consensus size: 21
1147319 CGGAAAGTGG
1147329 CGGCGGACGGCGGATGTCGGA
1 CGGCGGACGGCGGATGTCGGA
1147350 CGGCGGACGGCGGATGTCGGA
1 CGGCGGACGGCGGATGTCGGA
1147371 CGGCGGACGGCGGATGTCGGA
1 CGGCGGACGGCGGATGTCGGA
1147392 CGGC
1 CGGC
1147396 AAACAGCGGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.13, C:0.25, G:0.52, T:0.09
Consensus pattern (21 bp):
CGGCGGACGGCGGATGTCGGA
Found at i:1154485 original size:2 final size:2
Alignment explanation
Indices: 1154478--1154506 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1154468 TTGTCTTTAT
1154478 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1154507 TAACAAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1154899 original size:29 final size:29
Alignment explanation
Indices: 1154857--1154927 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 29
1154847 AAACATTACC
1154857 CGGAATGAGATTCCCGACCAACCAAACAT
1 CGGAATGAGATTCCCGACCAACCAAACAT
*
1154886 CGGAATGAGATTCCCGACCAATCAAACAT
1 CGGAATGAGATTCCCGACCAACCAAACAT
*
1154915 GGGAATGTAGATT
1 CGGAATG-AGATT
1154928 TCATTCCCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 34 0.87
30 5 0.13
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (29 bp):
CGGAATGAGATTCCCGACCAACCAAACAT
Found at i:1156171 original size:35 final size:34
Alignment explanation
Indices: 1156132--1156200 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
1156122 GTATATAGTT
*
1156132 TTCATACTTCTTTGATGTCTTTATTTTTAAATGTG
1 TTCATACTTCTTTGATGTCTTT-GTTTTAAATGTG
** *
1156167 TTCATGTTTCTTTGATTTCTTTGTTTTAAATGTG
1 TTCATACTTCTTTGATGTCTTTGTTTTAAATGTG
1156201 CATTTTCTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 11 0.37
35 19 0.63
ACGTcount: A:0.17, C:0.10, G:0.13, T:0.59
Consensus pattern (34 bp):
TTCATACTTCTTTGATGTCTTTGTTTTAAATGTG
Found at i:1163581 original size:3 final size:3
Alignment explanation
Indices: 1163573--1163765 Score: 386
Period size: 3 Copynumber: 64.3 Consensus size: 3
1163563 TTTATGTTCG
1163573 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1163621 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1163669 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1163717 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1163765 A
1 A
1163766 CAGTTCATAG
Statistics
Matches: 190, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 190 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1172818 original size:54 final size:54
Alignment explanation
Indices: 1172717--1172819 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
1172707 TGTTGCAAAA
* *
1172717 CCTTGGCCTATGCAAAACCTTTTTAGTCCCATCACCTGTAGGCCCTGCCTTGGG
1 CCTTGGCCTATGCAAAACCTTTTTAGTCCCATCACCGGTACGCCCTGCCTTGGG
* *
1172771 CCTTGGCCTATGCAAAACCTTTTTAGTCCTATCACCGGTACGTCCTGCC
1 CCTTGGCCTATGCAAAACCTTTTTAGTCCCATCACCGGTACGCCCTGCC
1172820 CTGGCCAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.17, C:0.34, G:0.18, T:0.30
Consensus pattern (54 bp):
CCTTGGCCTATGCAAAACCTTTTTAGTCCCATCACCGGTACGCCCTGCCTTGGG
Found at i:1176303 original size:23 final size:23
Alignment explanation
Indices: 1176277--1176321 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1176267 AAAATATGTT
1176277 ATAAAGACATAAAAAAACGTGTA
1 ATAAAGACATAAAAAAACGTGTA
* * *
1176300 ATAATGACATAATAAAATGTGT
1 ATAAAGACATAAAAAAACGTGT
1176322 CGTAAAAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (23 bp):
ATAAAGACATAAAAAAACGTGTA
Found at i:1178052 original size:16 final size:16
Alignment explanation
Indices: 1178028--1178058 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1178018 ATATATATAA
1178028 ATATAATGAATTATTT
1 ATATAATGAATTATTT
*
1178044 ATATTATGAATTATT
1 ATATAATGAATTATT
1178059 ATTTTGTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATATAATGAATTATTT
Found at i:1187568 original size:24 final size:24
Alignment explanation
Indices: 1187527--1187582 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1187517 ACTCATTTAC
* * *
1187527 AGCTCGTTTATTGGCTCATCTATA
1 AGCTCGTTGATCGACTCATCTATA
*
1187551 AGCTCGTTGATCGACTCATTTATA
1 AGCTCGTTGATCGACTCATCTATA
1187575 AGCTCGTT
1 AGCTCGTT
1187583 ACTCAATTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (24 bp):
AGCTCGTTGATCGACTCATCTATA
Found at i:1192866 original size:18 final size:18
Alignment explanation
Indices: 1192827--1192873 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
1192817 AAAAAAAAAT
**
1192827 ATTTTTTA-AAATTTTAA
1 ATTTTTTATAAATCATAA
*
1192844 TTTTTTTATAAATCATAA
1 ATTTTTTATAAATCATAA
*
1192862 ATTTTTAATAAA
1 ATTTTTTATAAA
1192874 CACATAACAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTTTATAAATCATAA
Found at i:1198322 original size:21 final size:21
Alignment explanation
Indices: 1198296--1198340 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1198286 GATTTCTGGG
* *
1198296 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1198317 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1198338 CAA
1 CAA
1198341 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1200084 original size:21 final size:22
Alignment explanation
Indices: 1200027--1200093 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
1200017 TCCTTATGGA
1200027 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
1200049 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
1200071 CAATTCTA-GGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
1200092 CA
1 CA
1200094 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 15 0.33
22 30 0.67
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
CAATTCTACGGGCACTTCGGTG
Found at i:1203216 original size:21 final size:21
Alignment explanation
Indices: 1203190--1203234 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1203180 GATTTCTGGG
* *
1203190 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1203211 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1203232 CAA
1 CAA
1203235 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1205001 original size:22 final size:22
Alignment explanation
Indices: 1204926--1204993 Score: 136
Period size: 22 Copynumber: 3.1 Consensus size: 22
1204916 TCCTTATGGA
1204926 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
1204948 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
1204970 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
1204992 CA
1 CA
1204994 TTTATACGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (22 bp):
CAATTCTACGGGCACTTCGGTG
Found at i:1209485 original size:13 final size:13
Alignment explanation
Indices: 1209467--1209493 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1209457 ATAATTATAT
1209467 ATAAAAAAATAAA
1 ATAAAAAAATAAA
1209480 ATAAAAAAATAAA
1 ATAAAAAAATAAA
1209493 A
1 A
1209494 ACTAACCGGG
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAAAATAAA
Found at i:1211099 original size:24 final size:25
Alignment explanation
Indices: 1211047--1211099 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
1211037 AAGAACCGAG
1211047 TAAACAAACTAATAAATGAGTCGAA
1 TAAACAAACTAATAAATGAGTCGAA
* * *
1211072 -AAACAAGCTTATGAATGAGTC-AA
1 TAAACAAACTAATAAATGAGTCGAA
1211095 TAAAC
1 TAAAC
1211100 GAGTTTGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (25 bp):
TAAACAAACTAATAAATGAGTCGAA
Found at i:1211496 original size:2 final size:2
Alignment explanation
Indices: 1211489--1211516 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1211479 CATAATCTTA
1211489 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
1211517 TAGAAGATGT
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:1217336 original size:16 final size:17
Alignment explanation
Indices: 1217315--1217366 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
1217305 TTTTTAATAT
1217315 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
1217331 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
1217346 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
1217363 AATT
1 AATT
1217367 TAATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:1221523 original size:30 final size:31
Alignment explanation
Indices: 1221489--1221548 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
1221479 GGAGGTCAAC
*
1221489 TTAAAACTTT-AAAATATTTAGAGG-TTTAAA
1 TTAAAACTTTCAAAAT-TTTAAAGGATTTAAA
*
1221519 TTAAAATTTTCAAAATTTTAAAGGATTTAA
1 TTAAAACTTTCAAAATTTTAAAGGATTTAA
1221549 TTTACATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (31 bp):
TTAAAACTTTCAAAATTTTAAAGGATTTAAA
Found at i:1221560 original size:31 final size:32
Alignment explanation
Indices: 1221498--1221565 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
1221488 CTTAAAACTT
*
1221498 TAAAATATTTAGAGGTTTAAATTAAAATTTTC
1 TAAAATATTTAAAGGTTTAAATTAAAATTTTC
* * *
1221530 -AAAAT-TTTAAAGGATTTAATTTACATTTTTC
1 TAAAATATTTAAAGG-TTTAAATTAAAATTTTC
1221561 TAAAA
1 TAAAA
1221566 AGTTAGAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
30 7 0.23
31 19 0.63
32 4 0.13
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (32 bp):
TAAAATATTTAAAGGTTTAAATTAAAATTTTC
Found at i:1230591 original size:35 final size:33
Alignment explanation
Indices: 1230535--1230759 Score: 173
Period size: 35 Copynumber: 6.8 Consensus size: 33
1230525 CTTATGTACA
1230535 ATATATA-AGTTTT-AAAACATTTTGAAAATTAT
1 ATATATATAGTTTTAAAAACATTTTGAAAA-TAT
* *
1230567 ATAGTATATAGTTTTGAAATCATTTTGAAAATAT
1 ATA-TATATAGTTTTAAAAACATTTTGAAAATAT
1230601 A-ATATATAGTTTTAAAAAACATTTTTTGAAAAT-T
1 ATATATATAGTTTT-AAAAACA--TTTTGAAAATAT
*
1230635 -TATATATAGTTTAAAAAAAACATTTTGGAAAACT-T
1 ATATATATAGTTT--TAAAAACATTTT-GAAAA-TAT
*
1230670 ATATA-ATA-TTTTAAAATCATTTTTGAAAACTAT
1 ATATATATAGTTTTAAAAACA-TTTTGAAAA-TAT
* * * *
1230703 ATGATATTTAGTTTTGAAAACGTTTT-TAAATA-
1 AT-ATATATAGTTTTAAAAACATTTTGAAAATAT
* * *
1230735 AAATATATAGTTTAAAAAATATTTT
1 ATATATATAGTTTTAAAAACATTTT
1230760 TTTGAAACAT
Statistics
Matches: 159, Mismatches: 17, Indels: 35
0.75 0.08 0.17
Matches are distributed among these distances:
31 18 0.11
32 28 0.18
33 23 0.14
34 36 0.23
35 42 0.26
36 12 0.08
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (33 bp):
ATATATATAGTTTTAAAAACATTTTGAAAATAT
Found at i:1230645 original size:34 final size:33
Alignment explanation
Indices: 1230535--1230698 Score: 135
Period size: 34 Copynumber: 4.9 Consensus size: 33
1230525 CTTATGTACA
1230535 ATATATAAGTTTT--AAAACA-TTTTGAAAATTATAT
1 ATATAT-AGTTTTAAAAAACATTTTTGAAAA-T-T-T
* * *
1230569 AGTATATAGTTTT-GAAATCA-TTTTGAAAATATA
1 A-TATATAGTTTTAAAAAACATTTTTGAAAAT-TT
1230602 ATATATAGTTTTAAAAAACATTTTTTGAAAATTT
1 ATATATAGTTTTAAAAAACA-TTTTTGAAAATTT
* * *
1230636 ATATATAGTTTAAAAAAAACATTTTGGAAAACTT
1 ATATATAGTTT-TAAAAAACATTTTTGAAAATTT
*
1230670 ATATAATA-TTTT-AAAATCATTTTTGAAAA
1 ATAT-ATAGTTTTAAAAAACATTTTTGAAAA
1230699 CTATATGATA
Statistics
Matches: 112, Mismatches: 11, Indels: 16
0.81 0.08 0.12
Matches are distributed among these distances:
32 26 0.23
33 6 0.05
34 40 0.36
35 40 0.36
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (33 bp):
ATATATAGTTTTAAAAAACATTTTTGAAAATTT
Found at i:1230723 original size:68 final size:62
Alignment explanation
Indices: 1230516--1230728 Score: 166
Period size: 68 Copynumber: 3.2 Consensus size: 62
1230506 TTTGAAACGT
* * *
1230516 TTTTGAAAAC-TTATGTACAATATATAA-GTTTTAAAACA-TTTTGAAAATTATATAGTATATAG
1 TTTTGAAAACATTTTG-AAAATATATAATATTTTAAAACATTTTTGAAAA-TATATA-TATATAG
*
1230578 TTTTGAAATCATTTTGAAAATATAATATATAGTTTTAAAAAACATTTTTTGAAAAT-T-TATATA
1 TTTTGAAAACATTTTGAAAATAT-ATA-ATA-TTTT--AAAACA-TTTTTGAAAATATATATATA
1230641 TAG
60 TAG
**
1230644 TTTAAAAAAAACATTTTGGAAAACTTATATAATATTTTAAAATCATTTTTGAAAACTATATGATA
1 TTT--TGAAAACATTTT-GAAAA--TATATAATATTTTAAAA-CATTTTTGAAAA-TATAT-ATA
*
1230709 TTTAG
58 TATAG
*
1230714 TTTTGAAAACGTTTT
1 TTTTGAAAACATTTT
1230729 TAAATAAAAT
Statistics
Matches: 121, Mismatches: 11, Indels: 32
0.74 0.07 0.20
Matches are distributed among these distances:
62 15 0.12
63 7 0.06
64 1 0.01
66 28 0.23
67 5 0.04
68 30 0.25
69 10 0.08
70 22 0.18
71 3 0.02
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (62 bp):
TTTTGAAAACATTTTGAAAATATATAATATTTTAAAACATTTTTGAAAATATATATATATAG
Found at i:1231912 original size:22 final size:22
Alignment explanation
Indices: 1231855--1231922 Score: 109
Period size: 22 Copynumber: 3.0 Consensus size: 22
1231845 CTCGTATAAA
1231855 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1231878 TGCAACCGAAGTGCCCGTAGAAT
1 TGC-ACCGAAGTGCCCGTAGAAT
*
1231901 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1231923 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
22 18 0.42
23 16 0.37
24 9 0.21
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1233635 original size:21 final size:21
Alignment explanation
Indices: 1233611--1233655 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1233601 TCTTGTTCGT
* *
1233611 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1233632 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1233653 TTG
1 TTG
1233656 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1235268 original size:10 final size:10
Alignment explanation
Indices: 1235244--1235276 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1235234 TTCATTTTTT
*
1235244 CTTTTATTT-
1 CTTTGATTTA
1235253 CTTTGATTTA
1 CTTTGATTTA
1235263 CTTTGATTTA
1 CTTTGATTTA
1235273 CTTT
1 CTTT
1235277 CTTAATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.15, C:0.12, G:0.06, T:0.67
Consensus pattern (10 bp):
CTTTGATTTA
Found at i:1241462 original size:186 final size:186
Alignment explanation
Indices: 1241137--1241531 Score: 641
Period size: 186 Copynumber: 2.1 Consensus size: 186
1241127 TTTTCTAATT
* * *
1241137 TATATAA-AAATTAAATATTTTATAATTCAAAAAAAACAATTTATAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTATAATTCAAAAAAAACAATTTACAATTAATTTAAATAATATAT
* *
1241201 AACTATAAAATAAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAGTTTTAAAAGTTA
66 AACTATAAAATAAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTGTAAAAGTTA
* * * *
1241266 TTGGATCTTAAATTATTAATTGGGTTTTAAATGTTTTGGGTTGAGCCCATATGTTA
131 TTGAATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
* *
1241322 TATATAATATATTTAATATTTTTTAATTC-ATAAAAACAATTTACAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTATAATTCAAAAAAAACAATTTACAATTAATTTAAATAATATAT
* *
1241386 AATTATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTGTAAAAGTT
66 AACTATAAAATAAAAA-TTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTGTAAAAGTT
1241451 ATTGAATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
130 ATTGAATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
*
1241508 TATATAATATATTTAAAATTTTAT
1 TATATAATATATTTAATATTTTAT
1241532 TTCGGTTAAT
Statistics
Matches: 193, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
185 55 0.28
186 138 0.72
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.46
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTATAATTCAAAAAAAACAATTTACAATTAATTTAAATAATATAT
AACTATAAAATAAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTGTAAAAGTTA
TTGAATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:1243451 original size:25 final size:26
Alignment explanation
Indices: 1243417--1243467 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
1243407 AAATGTTATA
*
1243417 TTCTTTATAAAATTTTAGGTT-TGAC
1 TTCTTCATAAAATTTTAGGTTGTGAC
*
1243442 TTCTTCATAACATTTTAGGTTGTGAC
1 TTCTTCATAAAATTTTAGGTTGTGAC
1243468 CGAAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (26 bp):
TTCTTCATAAAATTTTAGGTTGTGAC
Found at i:1246721 original size:2 final size:2
Alignment explanation
Indices: 1246714--1246738 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1246704 TTATAGACTC
1246714 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1246739 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1247238 original size:9 final size:9
Alignment explanation
Indices: 1247212--1247246 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
1247202 CCTCTTTTCC
1247212 AAATATTTT
1 AAATATTTT
1247221 AAA-ATTTT
1 AAATATTTT
1247229 AAATATTTT
1 AAATATTTT
*
1247238 AATTATTTT
1 AAATATTTT
1247247 TTTTCTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
AAATATTTT
Found at i:1259136 original size:71 final size:72
Alignment explanation
Indices: 1258957--1259167 Score: 347
Period size: 73 Copynumber: 2.9 Consensus size: 72
1258947 ACTTATTATG
* * * *
1258957 GGTTGTGGGCGGGTGGTGGATTGAAAAATATTAGGTGGGTATGGGGA-GGGGAGGGGGTATCCGC
1 GGTTGTGGGCGGGTGGTGGATTGAAAAATATTAGATGGGTATAGAGATGGGGAGAGGGTATCCGC
1259021 ACCCGACA
66 A-CCGACA
1259029 GGTTGTGGGCGGGGTGGTGGATTGAAAAATATTAGATGGGTATAGAGATGGGGAGAGGGTATCCG
1 GGTTGTGGGC-GGGTGGTGGATTGAAAAATATTAGATGGGTATAGAGATGGGGAGAGGGTATCCG
1259094 CACCGACA
65 CACCGACA
1259102 GG-TGTGGGCGGGTGGTGGATTGAAAAATATTAGATGGGTATAGAGAT-GGGAGAGGGTATCCGC
1 GGTTGTGGGCGGGTGGTGGATTGAAAAATATTAGATGGGTATAGAGATGGGGAGAGGGTATCCGC
1259165 ACC
66 ACC
1259168 CTAAATACAC
Statistics
Matches: 133, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
70 19 0.14
71 38 0.29
72 17 0.13
73 42 0.32
74 17 0.13
ACGTcount: A:0.24, C:0.10, G:0.44, T:0.22
Consensus pattern (72 bp):
GGTTGTGGGCGGGTGGTGGATTGAAAAATATTAGATGGGTATAGAGATGGGGAGAGGGTATCCGC
ACCGACA
Found at i:1262732 original size:16 final size:17
Alignment explanation
Indices: 1262694--1262733 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
1262684 CAAAATTGCC
1262694 TTAATAATTCATATTTT
1 TTAATAATTCATATTTT
*
1262711 TT--TAATT-TTATTTT
1 TTAATAATTCATATTTT
1262725 TTAATAATT
1 TTAATAATT
1262734 ATTGATTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
14 8 0.40
15 5 0.25
16 5 0.25
17 2 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAATAATTCATATTTT
Found at i:1276085 original size:21 final size:23
Alignment explanation
Indices: 1276026--1276086 Score: 87
Period size: 21 Copynumber: 2.9 Consensus size: 23
1276016 AAAAATAAAA
1276026 AATA-AAAATA-T-TATATAATT
1 AATATAAAATATTATATATAATT
1276046 AATATAAAATATTATATATAATT
1 AATATAAAATATTATATATAATT
1276069 -A-ATAAAATATTATATATA
1 AATATAAAATATTATATATA
1276087 TATAATCGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.11
21 23 0.61
22 2 0.05
23 9 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATAAAATATTATATATAATT
Found at i:1277377 original size:19 final size:19
Alignment explanation
Indices: 1277353--1277391 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1277343 ATATTAAGAG
1277353 TTCT-AATAAAATAACTAAT
1 TTCTAAATAAAATAA-TAAT
1277372 TTCTAAATAAAATAATAAT
1 TTCTAAATAAAATAATAAT
1277391 T
1 T
1277392 AAATAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (19 bp):
TTCTAAATAAAATAATAAT
Found at i:1284775 original size:22 final size:23
Alignment explanation
Indices: 1284740--1284787 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
1284730 CATTTAGATT
1284740 TTTAACTAATTTATAA-TTATACG
1 TTTAACTAATTTATAATTTA-ACG
*
1284763 TTTAA-TACTTTATAATTTAACG
1 TTTAACTAATTTATAATTTAACG
1284785 TTT
1 TTT
1284788 TATAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTAACTAATTTATAATTTAACG
Found at i:1284820 original size:16 final size:16
Alignment explanation
Indices: 1284799--1284829 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1284789 ATAAATTAAT
*
1284799 TTAATGATGTTCATCG
1 TTAATGATGCTCATCG
1284815 TTAATGATGCTCATC
1 TTAATGATGCTCATC
1284830 CTCACCTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (16 bp):
TTAATGATGCTCATCG
Found at i:1285117 original size:3 final size:3
Alignment explanation
Indices: 1285109--1285140 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1285099 ATGATTAATT
1285109 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1285141 CTTGATGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1291841 original size:18 final size:19
Alignment explanation
Indices: 1291800--1291841 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1291790 TATTCAATAT
*
1291800 TTAAATTTAAAATTTATTA
1 TTAATTTTAAAATTTATTA
* *
1291819 GTAATTTTAACATTT-TTA
1 TTAATTTTAAAATTTATTA
1291837 TTAAT
1 TTAAT
1291842 AATAATATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TTAATTTTAAAATTTATTA
Found at i:1294637 original size:78 final size:78
Alignment explanation
Indices: 1294508--1294655 Score: 233
Period size: 78 Copynumber: 1.9 Consensus size: 78
1294498 AAGATAATGG
** *
1294508 TATATAAAATGACTTTTGAGATGATACAATGAATATCATCTACAGATGTTACCAAGGGAATTAAT
1 TATATAAAATGAAGTTTGAGATGATACAATGAATATCATCTACAGATGTTACCAAGGCAATTAAT
1294573 GGTAGTCTCATTT
66 GGTAGTCTCATTT
* * * *
1294586 TATATTAAATGAAGTTTGAGATGATACAATGAATCTCATCTATAGCTGTTACCAAGGCAATTAAT
1 TATATAAAATGAAGTTTGAGATGATACAATGAATATCATCTACAGATGTTACCAAGGCAATTAAT
1294651 GGTAG
66 GGTAG
1294656 AGTTAGCAGC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 63 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (78 bp):
TATATAAAATGAAGTTTGAGATGATACAATGAATATCATCTACAGATGTTACCAAGGCAATTAAT
GGTAGTCTCATTT
Found at i:1297717 original size:30 final size:30
Alignment explanation
Indices: 1297681--1297753 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
1297671 TGCTCCTTGT
1297681 GTTTATCACGGGACTCCCTGGTTACAATAC
1 GTTTATCACGGGACTCCCTGGTTACAATAC
*
1297711 GTTTATCACGGGACTCCCTGGTTACAATAT
1 GTTTATCACGGGACTCCCTGGTTACAATAC
1297741 GTTTATCACGGGA
1 GTTTATCACGGGA
1297754 TTAAACTCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (30 bp):
GTTTATCACGGGACTCCCTGGTTACAATAC
Found at i:1306080 original size:15 final size:16
Alignment explanation
Indices: 1306052--1306083 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1306042 AAAATCTTTC
1306052 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
1306068 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
1306083 T
1 T
1306084 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:1306858 original size:16 final size:16
Alignment explanation
Indices: 1306834--1306867 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1306824 TATCGCCGAC
*
1306834 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1306850 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1306866 CG
1 CG
1306868 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1313163 original size:105 final size:104
Alignment explanation
Indices: 1313037--1313249 Score: 259
Period size: 105 Copynumber: 2.0 Consensus size: 104
1313027 GCCGTTTACT
* * *
1313037 AATGCATTATAGGTAATAACATTAGGCTCAATGCCTTCCTTTATCATTCTGTCAA-TGATATGCT
1 AATGCATTATAGGTAACAACATCAGGCTCAATGCCTTCCTTTATCATTCTGTCAACAG-TAT--T
*
1313101 CA-GCTTCAGAAACCATACCTTCCTTGCAATGTGCATCGATC
63 CATGCTTCAAAAACCATACCTTCCTTGCAATGTGCATCGATC
* * ** * * * *
1313142 AATGCATTATATGTGACAACATCAGGCTCAATGCCTTGTTTTCTCATTGTGTTAACAGTATTTAT
1 AATGCATTATAGGTAACAACATCAGGCTCAATGCCTTCCTTTATCATTCTGTCAACAGTATTCA-
*
1313207 TGCTTCAAAAACCATCCCTTCCTTGCAATGTGCATCGATC
65 TGCTTCAAAAACCATACCTTCCTTGCAATGTGCATCGATC
1313247 AAT
1 AAT
1313250 ATATTATACG
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
103 2 0.02
105 89 0.97
106 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (104 bp):
AATGCATTATAGGTAACAACATCAGGCTCAATGCCTTCCTTTATCATTCTGTCAACAGTATTCAT
GCTTCAAAAACCATACCTTCCTTGCAATGTGCATCGATC
Found at i:1319191 original size:6 final size:6
Alignment explanation
Indices: 1319180--1319204 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1319170 AGGAGGTTAT
1319180 TTGGCA TTGGCA TTGGCA TTGGCA T
1 TTGGCA TTGGCA TTGGCA TTGGCA T
1319205 AGGTCTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (6 bp):
TTGGCA
Found at i:1321310 original size:27 final size:27
Alignment explanation
Indices: 1321274--1321343 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
1321264 TAAACATTAT
* *
1321274 TAATTTATAAAATTAATCA-AATAATA-
1 TAATTAATAAAATTAA-AATAATAATAC
*
1321300 TATATTAATAAAAATAAAATAATAATAC
1 TA-ATTAATAAAATTAAAATAATAATAC
1321328 TAATTAA-AAAATTAAA
1 TAATTAATAAAATTAAA
1321344 CATATAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
26 11 0.30
27 24 0.65
28 2 0.05
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (27 bp):
TAATTAATAAAATTAAAATAATAATAC
Found at i:1321323 original size:24 final size:24
Alignment explanation
Indices: 1321292--1321337 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1321282 AAAATTAATC
*
1321292 AAATAATATATATTAA-TAAAAATA
1 AAATAATA-ATACTAATTAAAAATA
1321316 AAATAATAATACTAATTAAAAA
1 AAATAATAATACTAATTAAAAA
1321338 ATTAAACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATAATAATACTAATTAAAAATA
Found at i:1321378 original size:11 final size:12
Alignment explanation
Indices: 1321337--1321390 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 12
1321327 CTAATTAAAA
1321337 AATTAAACATAT
1 AATTAAACATAT
1321349 AAAATTAAA-ATAT
1 --AATTAAACATAT
*
1321362 ATTTAAACA-AT
1 AATTAAACATAT
*
1321373 AATTAAA-ATAA
1 AATTAAACATAT
1321384 AATTAAA
1 AATTAAA
1321391 ACTAAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 1 0.03
11 22 0.63
12 1 0.03
13 4 0.11
14 7 0.20
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (12 bp):
AATTAAACATAT
Found at i:1321389 original size:22 final size:24
Alignment explanation
Indices: 1321335--1321390 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
1321325 TACTAATTAA
1321335 AAAATTAAACATATAAAATTAAAAT
1 AAAATTAAACATAT-AAATTAAAAT
* *
1321360 ATATTTAAACA-AT-AATTAAAAT
1 AAAATTAAACATATAAATTAAAAT
1321382 AAAATTAAA
1 AAAATTAAA
1321391 ACTAAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 16 0.59
24 2 0.07
25 9 0.33
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAATTAAACATATAAATTAAAAT
Found at i:1323378 original size:3 final size:3
Alignment explanation
Indices: 1323372--1323449 Score: 79
Period size: 3 Copynumber: 26.3 Consensus size: 3
1323362 TTATTTTTTT
* * *
1323372 ATA ATA ATA TTTA ATA ATA TTA TTA ATA ATA A-A AT- ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
1323416 ATA ATA ATA ATA ATT TTA ATA ATA AAA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1323450 AACGAAATGA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 4 0.06
3 56 0.90
4 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:1323411 original size:25 final size:25
Alignment explanation
Indices: 1323372--1323449 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 25
1323362 TTATTTTTTT
* * * *
1323372 ATAATAATATTTAATAATATTATTA
1 ATAATAAAATATAATAATAATAATA
1323397 ATAATAAAATATAATAATAATAATA
1 ATAATAAAATATAATAATAATAATA
* * *
1323422 ATAAT-AATTTTAATAATAAAAATA
1 ATAATAAAATATAATAATAATAATA
1323446 ATAA
1 ATAA
1323450 AACGAAATGA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 20 0.43
25 26 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATAATAAAATATAATAATAATAATA
Found at i:1323707 original size:45 final size:45
Alignment explanation
Indices: 1323638--1324222 Score: 1084
Period size: 45 Copynumber: 13.0 Consensus size: 45
1323628 TCAAAAAGCT
*
1323638 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAA-GACTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTG-AAGGGCTTACAGATGA
* *
1323685 CCCGAAGGTTTTGAAAATATCATGCACTGAAGGGCTTATAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
1323730 CCCGAAGGTTTTGAAAACATCATGCACTAAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1323775 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1323820 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1323865 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1323910 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
1323955 CCCGAAAGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1324000 CCCGAAGGTTTTGAAAACATCATGCACTGAA-GGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1324044 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1324089 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1324134 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1324179 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1324223 TTTCTTACTT
Statistics
Matches: 527, Mismatches: 9, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
44 46 0.09
45 473 0.90
47 8 0.02
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:1325490 original size:54 final size:54
Alignment explanation
Indices: 1325408--1325515 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
1325398 AGAATAGCAG
**
1325408 GTTCGTAAAACATTTGACAATGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * *
1325462 GTTCGTAAAATATTTGACAACACATTCATCCTTTCCTGTGGTTTTTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1325516 TTCTCAATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:1327388 original size:176 final size:176
Alignment explanation
Indices: 1327094--1327444 Score: 702
Period size: 176 Copynumber: 2.0 Consensus size: 176
1327084 TAGTTCTTTC
1327094 TGATACCGAGGAAATCCTGAATTCTGATTCTGATGAGGAGAGTAAATTGTTATACTTGACAAAAA
1 TGATACCGAGGAAATCCTGAATTCTGATTCTGATGAGGAGAGTAAATTGTTATACTTGACAAAAA
1327159 TGAGATTCTCAGAGGCTGAGGCTTCAATAGCCATGGAGAGATGTGGTCCAGATTCATCAATTACA
66 TGAGATTCTCAGAGGCTGAGGCTTCAATAGCCATGGAGAGATGTGGTCCAGATTCATCAATTACA
1327224 GAGTTGACAGATTTTATATGTGCTGCTCAAATGGCTAAGGCTGCTT
131 GAGTTGACAGATTTTATATGTGCTGCTCAAATGGCTAAGGCTGCTT
1327270 TGATACCGAGGAAATCCTGAATTCTGATTCTGATGAGGAGAGTAAATTGTTATACTTGACAAAAA
1 TGATACCGAGGAAATCCTGAATTCTGATTCTGATGAGGAGAGTAAATTGTTATACTTGACAAAAA
1327335 TGAGATTCTCAGAGGCTGAGGCTTCAATAGCCATGGAGAGATGTGGTCCAGATTCATCAATTACA
66 TGAGATTCTCAGAGGCTGAGGCTTCAATAGCCATGGAGAGATGTGGTCCAGATTCATCAATTACA
1327400 GAGTTGACAGATTTTATATGTGCTGCTCAAATGGCTAAGGCTGCT
131 GAGTTGACAGATTTTATATGTGCTGCTCAAATGGCTAAGGCTGCT
1327445 GACGCACTTC
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 175 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (176 bp):
TGATACCGAGGAAATCCTGAATTCTGATTCTGATGAGGAGAGTAAATTGTTATACTTGACAAAAA
TGAGATTCTCAGAGGCTGAGGCTTCAATAGCCATGGAGAGATGTGGTCCAGATTCATCAATTACA
GAGTTGACAGATTTTATATGTGCTGCTCAAATGGCTAAGGCTGCTT
Found at i:1329928 original size:30 final size:30
Alignment explanation
Indices: 1329894--1329953 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1329884 CAAGCAACTG
1329894 ACTTAAACTAGATTTACTTATTTGTAAAAA
1 ACTTAAACTAGATTTACTTATTTGTAAAAA
1329924 ACTTAAACTAGATTTACTTATTTGTAAAAA
1 ACTTAAACTAGATTTACTTATTTGTAAAAA
1329954 TTATGTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (30 bp):
ACTTAAACTAGATTTACTTATTTGTAAAAA
Found at i:1331936 original size:14 final size:15
Alignment explanation
Indices: 1331919--1331951 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1331909 TAAAAGTATG
1331919 AATGCAAA-ATGAAA
1 AATGCAAAGATGAAA
*
1331933 AATGCAAAGATGCAA
1 AATGCAAAGATGAAA
1331948 AATG
1 AATG
1331952 ATAATGCATA
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:0.58, C:0.09, G:0.18, T:0.15
Consensus pattern (15 bp):
AATGCAAAGATGAAA
Found at i:1334825 original size:11 final size:12
Alignment explanation
Indices: 1334784--1334837 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 12
1334774 CTAATTAAAA
1334784 AATTAAACATAT
1 AATTAAACATAT
1334796 AAAATTAAA-ATAT
1 --AATTAAACATAT
*
1334809 ATTTAAACA-AT
1 AATTAAACATAT
*
1334820 AATTAAA-ATAA
1 AATTAAACATAT
1334831 AATTAAA
1 AATTAAA
1334838 ACTAAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 1 0.03
11 22 0.63
12 1 0.03
13 4 0.11
14 7 0.20
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (12 bp):
AATTAAACATAT
Found at i:1334836 original size:22 final size:24
Alignment explanation
Indices: 1334782--1334837 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
1334772 TACTAATTAA
1334782 AAAATTAAACATATAAAATTAAAAT
1 AAAATTAAACATAT-AAATTAAAAT
* *
1334807 ATATTTAAACA-AT-AATTAAAAT
1 AAAATTAAACATATAAATTAAAAT
1334829 AAAATTAAA
1 AAAATTAAA
1334838 ACTAAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 16 0.59
24 2 0.07
25 9 0.33
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAATTAAACATATAAATTAAAAT
Found at i:1336261 original size:3 final size:3
Alignment explanation
Indices: 1336253--1336329 Score: 75
Period size: 3 Copynumber: 25.3 Consensus size: 3
1336243 ATTATTTTTT
* * *
1336253 ATA ATA ATA TTTA ATA ATA TTA TTA ATA ATA A-A ATA TATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
* * *
1336299 ATA ATA ATA ATT TTA ATA ATA AAA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1336330 AACGAAATGA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.03
3 54 0.89
4 5 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:1336296 original size:27 final size:28
Alignment explanation
Indices: 1336253--1336329 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 28
1336243 ATTATTTTTT
* * *
1336253 ATAATAATATTTAATAATATTATTAATA
1 ATAATAATATATAATAATAATAATAATA
1336281 ATAA-AATATATAATAATAATAATAATA
1 ATAATAATATATAATAATAATAATAATA
** *
1336308 ATTTTAATA-ATAAAAATAATAA
1 ATAATAATATATAATAATAATAA
1336330 AACGAAATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 34 0.81
28 8 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
ATAATAATATATAATAATAATAATAATA
Found at i:1338433 original size:16 final size:16
Alignment explanation
Indices: 1338412--1338444 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1338402 TCCAAAATAA
1338412 AAACACATACATAATT
1 AAACACATACATAATT
1338428 AAACACATACATAATT
1 AAACACATACATAATT
1338444 A
1 A
1338445 TAAAAGTTAG
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:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (16 bp):
AAACACATACATAATT
Found at i:1338581 original size:34 final size:33
Alignment explanation
Indices: 1338486--1338621 Score: 190
Period size: 34 Copynumber: 4.2 Consensus size: 33
1338476 GTGTTTGTAT
* *
1338486 TATATAATTAATATAAAAATATAAAATA-T-TA
1 TATATAATTAATACAAAAATAAAAAATATTATA
*
1338517 TATATAATTAATAC-AAAAT-ATAAATATTATA
1 TATATAATTAATACAAAAATAAAAAATATTATA
1338548 TATATAATTAATACAAAAATACAAAAATATTATA
1 TATATAATTAATACAAAAATA-AAAAATATTATA
*
1338582 TATATAATTAATATAAAAAATAAAAAATATTATA
1 TATATAATTAATA-CAAAAATAAAAAATATTATA
1338616 TATATA
1 TATATA
1338622 TATATAATCG
Statistics
Matches: 94, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
29 5 0.05
30 6 0.06
31 29 0.31
32 5 0.05
34 42 0.45
35 7 0.07
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (33 bp):
TATATAATTAATACAAAAATAAAAAATATTATA
Found at i:1341959 original size:2 final size:2
Alignment explanation
Indices: 1341952--1342006 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
1341942 AGAAATAACA
*
1341952 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1341993 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1342007 TGTATAATAC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1346521 original size:8 final size:8
Alignment explanation
Indices: 1346508--1346545 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
1346498 CTCATTTTCA
1346508 GAGAATTT
1 GAGAATTT
1346516 GAGAATTT
1 GAGAATTT
*
1346524 -AGAGTTT
1 GAGAATTT
1346531 GAGAATTT
1 GAGAATTT
*
1346539 AAGAATT
1 GAGAATT
1346546 CGAAAGCTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1346864 original size:128 final size:126
Alignment explanation
Indices: 1346631--1347095 Score: 698
Period size: 128 Copynumber: 3.7 Consensus size: 126
1346621 TATTCACATT
* * * * *
1346631 AAGGCGCGTTCCCGGGGGCGTGTCTTCTATTTTTTTGTCAGAGAATATGTTATCATTGCCCTACT
1 AAGGCGCGTT-CCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
*
1346696 ATGTCACTCATGTCCCTCTGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
65 ATGTCACTCATGTCCCTCGGGGACACTATT-ATATCAGTACCTATTATTTCTCAGGGGACTTG
* *
1346759 AAGGTGCGTTCACGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
1 AAGGCGCGTTC-CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
1346824 ATGTCACTCATGTCCCTCGGGGACACTATTAATATCAGTACCTATTATTTCTCAGGGGACTTG
65 ATGTCACTCATGTCCCTCGGGGACACTATT-ATATCAGTACCTATTATTTCTCAGGGGACTTG
* *
1346887 AAGGCGCGTTCC-TGGGCGCGCCTT-CATTATTTTTTCAGAGAATATGTTATCATTGCCCTATTA
1 AAGGCGCGTTCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTA
*
1346950 TGTCACTCATGT-CCTCGGGGACACTA-T-TATCATTACCTATTATTTCTCAGGGGACTT-
66 TGTCACTCATGTCCCTCGGGGACACTATTATATCAGTACCTATTATTTCTCAGGGGACTTG
* *
1347007 AAGGCGCGTTCCGGGGGTGCG-C--CCATTA-TTTGTCAGAGAATATGTTTATCATTACCCTATT
1 AAGGCGCGTTCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG-TTATCATTGCCCTATT
1347068 ATGTCACTCATGTCCCTCGGGGACACTA
65 ATGTCACTCATGTCCCTCGGGGACACTA
1347096 GATGAATTGT
Statistics
Matches: 314, Mismatches: 18, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
118 15 0.05
119 33 0.11
120 27 0.09
121 35 0.11
123 1 0.00
124 14 0.04
125 50 0.16
126 10 0.03
127 2 0.01
128 127 0.40
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (126 bp):
AAGGCGCGTTCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTA
TGTCACTCATGTCCCTCGGGGACACTATTATATCAGTACCTATTATTTCTCAGGGGACTTG
Found at i:1347518 original size:34 final size:34
Alignment explanation
Indices: 1347480--1347585 Score: 149
Period size: 34 Copynumber: 3.1 Consensus size: 34
1347470 TAAGTTGAAA
* *
1347480 TTAATGTTAAATTTCGAATACTATAATTTATATT
1 TTAATTTTAAATTTCGAATAATATAATTTATATT
* *
1347514 TTAATTTTAAATTTCGAATAATATTATTTTTATT
1 TTAATTTTAAATTTCGAATAATATAATTTATATT
* * *
1347548 TTTATTTTAAATTTTGAATAATATAATTTGTATT
1 TTAATTTTAAATTTCGAATAATATAATTTATATT
1347582 TTAA
1 TTAA
1347586 AAACATTTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
TTAATTTTAAATTTCGAATAATATAATTTATATT
Found at i:1347859 original size:50 final size:50
Alignment explanation
Indices: 1347784--1347883 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
1347774 TGGTTGTTTA
1347784 TTTCGTGGAGGATTTCTTTGTGGAACTTGTTCTTCAGTCTCCTCATCTTC
1 TTTCGTGGAGGATTTCTTTGTGGAACTTGTTCTTCAGTCTCCTCATCTTC
1347834 TTTCGTGGAGGATTTCTTTGTGGAACTTGTTCTTCAGTCTCCTCATCTTC
1 TTTCGTGGAGGATTTCTTTGTGGAACTTGTTCTTCAGTCTCCTCATCTTC
1347884 ACTATCATCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (50 bp):
TTTCGTGGAGGATTTCTTTGTGGAACTTGTTCTTCAGTCTCCTCATCTTC
Found at i:1348208 original size:20 final size:20
Alignment explanation
Indices: 1348159--1348248 Score: 117
Period size: 21 Copynumber: 4.3 Consensus size: 20
1348149 GGTATAAAAC
*
1348159 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
1348179 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
* *
1348200 CATGCGGGCTCGGAATGTAA
1 CCTGCGGGCTAGGAATGTAA
*
1348220 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
1348241 CCCTGCGG
1 -CCTGCGG
1348249 AGATGGCATA
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
20 19 0.30
21 45 0.70
ACGTcount: A:0.20, C:0.26, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:1348218 original size:41 final size:41
Alignment explanation
Indices: 1348161--1348241 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
1348151 TATAAAACCC
*
1348161 TGCGGGCTAGGCATGTAA-CCTGGCGGGCTAGGAATGTAACA
1 TGCGGGCTAGGAATGTAACCCT-GCGGGCTAGGAATGTAACA
* *
1348202 TGCGGGCTCGGAATGTAACCCTGCGGGCTCGGAATGTAAC
1 TGCGGGCTAGGAATGTAACCCTGCGGGCTAGGAATGTAAC
1348242 CCTGCGGAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 33 0.92
42 3 0.08
ACGTcount: A:0.22, C:0.22, G:0.36, T:0.20
Consensus pattern (41 bp):
TGCGGGCTAGGAATGTAACCCTGCGGGCTAGGAATGTAACA
Found at i:1350067 original size:13 final size:14
Alignment explanation
Indices: 1350049--1350086 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1350039 TTTTAAAAAA
1350049 AAATATATT-ATAT
1 AAATATATTAATAT
1350062 AAATATATTAATAT
1 AAATATATTAATAT
1350076 AAA-ATA-TAATA
1 AAATATATTAATA
1350087 ACTATTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.21
13 12 0.50
14 7 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATATATTAATAT
Found at i:1351569 original size:101 final size:101
Alignment explanation
Indices: 1351430--1351621 Score: 312
Period size: 101 Copynumber: 1.9 Consensus size: 101
1351420 ACATCAGCCT
* * *
1351430 CAATGCCTTGTTTTATCATTCTGTCAACAATATTTTCAGCTTCAGAGATCGTTCCTTCCTTGCAA
1 CAATGCCTTGTTTTATCATTCTGTCAACAATATCTTCAGCTTCAGAGATCATCCCTTCCTTGCAA
* *
1351495 TGTGCATCAATCAATGCATTATATGTGAAAACATCA
66 TATGCATCAATCAATACATTATATGTGAAAACATCA
*
1351531 CAATGCCTTGTTTTATCATTGTGTCAACAATATCTTCAGCTTCAGAGATCATCCCTTCCTTGCAA
1 CAATGCCTTGTTTTATCATTCTGTCAACAATATCTTCAGCTTCAGAGATCATCCCTTCCTTGCAA
* *
1351596 TATGCATCGATCAATATATTATATGT
66 TATGCATCAATCAATACATTATATGT
1351622 TACAATATCG
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 83 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (101 bp):
CAATGCCTTGTTTTATCATTCTGTCAACAATATCTTCAGCTTCAGAGATCATCCCTTCCTTGCAA
TATGCATCAATCAATACATTATATGTGAAAACATCA
Found at i:1354957 original size:13 final size:13
Alignment explanation
Indices: 1354939--1354984 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
1354929 CAACCCGACC
*
1354939 CGACCCGTTTACT
1 CGACCCGTTGACT
1354952 CGACCCGTTGACT
1 CGACCCGTTGACT
*
1354965 CGACCCGTTGACC
1 CGACCCGTTGACT
1354978 CGACCCG
1 CGACCCG
1354985 ACCCGTTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.15, C:0.43, G:0.22, T:0.20
Consensus pattern (13 bp):
CGACCCGTTGACT
Found at i:1354999 original size:7 final size:7
Alignment explanation
Indices: 1354987--1355025 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
1354977 CCGACCCGAC
1354987 CCGTTGA
1 CCGTTGA
1354994 CCGTTGA
1 CCGTTGA
*
1355001 CCGTTAA
1 CCGTTGA
1355008 CCCGTTGA
1 -CCGTTGA
1355016 CCGTTGA
1 CCGTTGA
1355023 CCG
1 CCG
1355026 GAGTTGACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.15, C:0.33, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:1362652 original size:33 final size:33
Alignment explanation
Indices: 1362615--1362694 Score: 126
Period size: 33 Copynumber: 2.4 Consensus size: 33
1362605 GTATCAAATG
1362615 AGATATTTTTCATTAATTTAAAGTTCAGTTAAA
1 AGATATTTTTCATTAATTTAAAGTTCAGTTAAA
*
1362648 AGATATTTCTT-ATTAATTTAAAGTTCAGTTATA
1 AGATATTT-TTCATTAATTTAAAGTTCAGTTAAA
*
1362681 AGATATTTCTCATT
1 AGATATTTTTCATT
1362695 TTGTAACAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 1 0.02
33 40 0.93
34 2 0.05
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.47
Consensus pattern (33 bp):
AGATATTTTTCATTAATTTAAAGTTCAGTTAAA
Found at i:1366204 original size:32 final size:32
Alignment explanation
Indices: 1366167--1366239 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
1366157 TTAGAAAACT
1366167 TTCAAACAAATAACAAACATTGATCATACATA
1 TTCAAACAAATAACAAACATTGATCATACATA
1366199 TTCAAACAAATAACAAACATTGATCATACATA
1 TTCAAACAAATAACAAACATTGATCATACATA
1366231 TTCAAACAA
1 TTCAAACAA
1366240 GCATTTAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.25
Consensus pattern (32 bp):
TTCAAACAAATAACAAACATTGATCATACATA
Found at i:1366654 original size:24 final size:24
Alignment explanation
Indices: 1366627--1366676 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1366617 AAGCTGAAGT
* *
1366627 GGAGGATGAAGAAGAAGAGTCTGA
1 GGAGGAAGAAGAAGAAGAGCCTGA
**
1366651 GGAGGAAGTGGAAGAAGAGCCTGA
1 GGAGGAAGAAGAAGAAGAGCCTGA
1366675 GG
1 GG
1366677 TCATTACATT
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:0.38, C:0.06, G:0.46, T:0.10
Consensus pattern (24 bp):
GGAGGAAGAAGAAGAAGAGCCTGA
Found at i:1376965 original size:105 final size:105
Alignment explanation
Indices: 1376783--1376991 Score: 262
Period size: 105 Copynumber: 2.0 Consensus size: 105
1376773 CTCGATATTG
* * * *
1376783 TCACATATAATATATTGATCGATGCATATCGCAAGGAAGGGATGATCTCTGAAGCTGAAGATATT
1 TCACATATAATACATTGATCGATGCACATCGCAAGGAAGAGATGATCTCTAAAGCTGAAGATATT
* * *
1376848 GTTGACACAATGATTAAA-CAAGGCATTGAGCCTGATGTTT
66 GTTGACAAAATGA-TAAAGCAAGGCATTGAACCTAATGTTT
* * * * *
1376888 TCACATATAATGCATTGATTGATGCACATTGCAAGGAAGAGATGGT-TGCTAAAGCTG-TGCATA
1 TCACATATAATACATTGATCGATGCACATCGCAAGGAAGAGATGATCT-CTAAAGCTGAAG-ATA
1376951 TTGTTGACAAAATGATAAAGCAAGGCATTGAACCTAATGTT
64 TTGTTGACAAAATGATAAAGCAAGGCATTGAACCTAATGTT
1376992 GTTACCTATT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
104 6 0.07
105 83 0.93
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (105 bp):
TCACATATAATACATTGATCGATGCACATCGCAAGGAAGAGATGATCTCTAAAGCTGAAGATATT
GTTGACAAAATGATAAAGCAAGGCATTGAACCTAATGTTT
Found at i:1387254 original size:29 final size:28
Alignment explanation
Indices: 1387186--1387255 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
1387176 GAATATTTAA
*
1387186 AGTTTAAGTTTTTTTATAGCCTGGGTCG
1 AGTTTAAGTTTTTTTATAGCCCGGGTCG
1387214 AGTTTAAGTTTTTTTATAGCCCGGGTCG
1 AGTTTAAGTTTTTTTATAGCCCGGGTCG
1387242 AGTTTCAA-TTTTTT
1 AGTTT-AAGTTTTTT
1387256 ATTTCGAGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 38 0.95
29 2 0.05
ACGTcount: A:0.19, C:0.11, G:0.21, T:0.49
Consensus pattern (28 bp):
AGTTTAAGTTTTTTTATAGCCCGGGTCG
Found at i:1390958 original size:17 final size:17
Alignment explanation
Indices: 1390936--1390972 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1390926 CGGTCAACGT
1390936 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGTCGGG
1390953 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGTCGGG
1390970 TCA
1 TCA
1390973 GTCGGGTTGG
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:0.14, C:0.24, G:0.43, T:0.19
Consensus pattern (17 bp):
TCAACGGTCGGGTCGGG
Found at i:1398121 original size:17 final size:17
Alignment explanation
Indices: 1398101--1398139 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1398091 GGAAGTCAAC
1398101 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1398118 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1398135 GGTCA
1 GGTCA
1398140 GTCGGGTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1398166 original size:10 final size:10
Alignment explanation
Indices: 1398151--1398229 Score: 67
Period size: 10 Copynumber: 8.1 Consensus size: 10
1398141 TCGGGTTGGG
1398151 TCAGACCGGT
1 TCAGACCGGT
1398161 TCAGACCGG-
1 TCAGACCGGT
*
1398170 TCAAACCGGT
1 TCAGACCGGT
1398180 TC-GAACCGGT
1 TCAG-ACCGGT
1398190 TCAGACCGG-
1 TCAGACCGGT
* *
1398199 TCAAACCGGG
1 TCAGACCGGT
* *
1398209 TCAAACC-GA
1 TCAGACCGGT
1398218 TCAGAACCGGT
1 TCAG-ACCGGT
1398229 T
1 T
1398230 GAAAACCGGT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
9 20 0.35
10 34 0.60
11 3 0.05
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (10 bp):
TCAGACCGGT
Found at i:1398171 original size:19 final size:19
Alignment explanation
Indices: 1398149--1398199 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
1398139 AGTCGGGTTG
1398149 GGTCAGACCGGTTC-AGACC
1 GGTCAGACCGGTTCGA-ACC
*
1398168 GGTCAAACCGGTTCGAACC
1 GGTCAGACCGGTTCGAACC
1398187 GGTTCAGACCGGT
1 GG-TCAGACCGGT
1398200 CAAACCGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.22, C:0.29, G:0.31, T:0.18
Consensus pattern (19 bp):
GGTCAGACCGGTTCGAACC
Found at i:1398197 original size:29 final size:29
Alignment explanation
Indices: 1398148--1398249 Score: 118
Period size: 29 Copynumber: 3.5 Consensus size: 29
1398138 CAGTCGGGTT
*
1398148 GGGTCAGACCGGTTCAGACCGGTCAAACC
1 GGGTCAAACCGGTTCAGACCGGTCAAACC
* *
1398177 GGTTCGAACCGGTTCAGACCGGTCAAACC
1 GGGTCAAACCGGTTCAGACCGGTCAAACC
* *
1398206 GGGTCAAACC-GATCAGAACCGGTTGAAAACC
1 GGGTCAAACCGGTTCAG-ACCGG-T-CAAACC
1398237 -GGTCAAACCGGTT
1 GGGTCAAACCGGTT
1398250 TCCAGCCCTC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 5 0.08
29 39 0.64
30 10 0.16
31 7 0.11
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.16
Consensus pattern (29 bp):
GGGTCAAACCGGTTCAGACCGGTCAAACC
Found at i:1398245 original size:20 final size:19
Alignment explanation
Indices: 1398155--1398249 Score: 93
Period size: 19 Copynumber: 4.8 Consensus size: 19
1398145 GTTGGGTCAG
*
1398155 ACCGGTTCAGACCGG-TCAA
1 ACCGG-TCAAACCGGTTCAA
* *
1398174 ACCGGTTCGAACCGGTTCAG
1 ACCGG-TCAAACCGGTTCAA
*
1398194 ACCGGTCAAACCGGGTCAA
1 ACCGGTCAAACCGGTTCAA
* *
1398213 ACCGATCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGGTT-CAA
1398234 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
1398250 TCCAGCCCTC
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
19 31 0.49
20 23 0.37
21 9 0.14
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:1399495 original size:22 final size:22
Alignment explanation
Indices: 1399470--1399547 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
1399460 AGAAAATATT
1399470 AATATTAATATTTTTATTAAAA
1 AATATTAATATTTTTATTAAAA
* *
1399492 AATATTAATATTTGATATTACCTAA
1 AATATTAATATTT-TTATTA--AAA
*
1399517 AATATT-ATTTTTTTA-TAAAA
1 AATATTAATATTTTTATTAAAA
1399537 AATATTAATAT
1 AATATTAATAT
1399548 AAAAAATATT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 8 0.17
21 3 0.07
22 15 0.33
23 7 0.15
24 5 0.11
25 8 0.17
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (22 bp):
AATATTAATATTTTTATTAAAA
Found at i:1399583 original size:21 final size:19
Alignment explanation
Indices: 1399541--1399610 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 19
1399531 ATAAAAAATA
*
1399541 TTAATATAAAAAATATTCATT
1 TTAATAT-AAAAATAAT-ATT
*
1399562 TTAGATACTAAAATTAATATTT
1 TTA-ATA-TAAAAATAATA-TT
1399584 TTAATATAAAAATAATATT
1 TTAATATAAAAATAATATT
1399603 TTAA-ATAA
1 TTAATATAA
1399611 TACTCTATCA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
18 4 0.09
19 6 0.14
20 10 0.23
21 7 0.16
22 15 0.35
23 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (19 bp):
TTAATATAAAAATAATATT
Found at i:1399599 original size:20 final size:20
Alignment explanation
Indices: 1399541--1399609 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
1399531 ATAAAAAATA
*
1399541 TTAATATAAAAAATATTCA-TT
1 TTAATAT-AAAAATAAT-ATTT
*
1399562 TTAGATACTAAAATTAATATTT
1 TTA-ATA-TAAAAATAATATTT
1399584 TTAATATAAAAATAATATTT
1 TTAATATAAAAATAATATTT
*
1399604 TAAATA
1 TTAATA
1399610 ATACTCTATC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 18 0.44
21 7 0.17
22 15 0.37
23 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (20 bp):
TTAATATAAAAATAATATTT
Found at i:1435384 original size:19 final size:18
Alignment explanation
Indices: 1435347--1435399 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
1435337 ATTCAAAATT
1435347 AAATAATTGATAAAATATAAA
1 AAATAATT--TAAAATAT-AA
* *
1435368 AAATATTTTAAATTATAA
1 AAATAATTTAAAATATAA
1435386 AAATAATTTAAAAT
1 AAATAATTTAAAAT
1435400 TTCTAAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 14 0.50
19 7 0.25
21 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAATAATTTAAAATATAA
Found at i:1435400 original size:19 final size:19
Alignment explanation
Indices: 1435347--1435400 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
1435337 ATTCAAAATT
1435347 AAATAATTGATAAAA-TATAA
1 AAATAATT--TAAAATTATAA
*
1435367 AAA-ATATTTTAAATTATAA
1 AAATA-ATTTAAAATTATAA
1435386 AAATAATTTAAAATT
1 AAATAATTTAAAATT
1435401 TCTAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 4 0.14
19 18 0.62
20 7 0.24
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATAATTTAAAATTATAA
Found at i:1437552 original size:22 final size:22
Alignment explanation
Indices: 1437526--1437568 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1437516 TAATAAATTA
1437526 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1437548 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1437569 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1437577 original size:22 final size:22
Alignment explanation
Indices: 1437528--1437576 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1437518 ATAAATTATT
**
1437528 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1437550 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1437573 TAAA
1 TAAA
1437577 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1437580 original size:54 final size:54
Alignment explanation
Indices: 1437516--1437986 Score: 495
Period size: 54 Copynumber: 8.6 Consensus size: 54
1437506 ACAACTACAA
1437516 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
1437570 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** **
1437627 TTTTAAAATAAAT-CAATCCATACAAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
1437682 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
1437736 TAATAAACTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAACCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
1437790 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** **
1437847 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
1437902 TAATAAGTTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
1437956 TAATAAATTATTTAAAATAAATCAATTCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
1437987 CAACTATAAT
Statistics
Matches: 336, Mismatches: 61, Indels: 40
0.77 0.14 0.09
Matches are distributed among these distances:
54 224 0.67
55 25 0.07
56 20 0.06
57 26 0.08
58 41 0.12
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:1437586 original size:32 final size:31
Alignment explanation
Indices: 1437548--1438057 Score: 336
Period size: 32 Copynumber: 18.4 Consensus size: 31
1437538 CAATCCATAT
1437548 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
1437580 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
1437610 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
1437628 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
1437660 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
1437692 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
1437714 TTTAAAATAAATCAATCCATAATAATAAACTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
1437746 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
1437768 TTTAAAATAAATCAACCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
1437800 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
1437830 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
1437848 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
1437880 TTTAAAATAAATCAATCCATACTAATAAGTTA
1 TTTAAAATAAATCAATCCATACTAATAA-ATA
1437912 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
1437934 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
1437966 TTTAAAATAAATCAATTCATAC-AACT--ATA
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
*
1437995 ---ATAATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
1438014 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
1438046 TTTAAAATAAAT
1 TTTAAAATAAAT
1438058 TATTTGAAAA
Statistics
Matches: 386, Mismatches: 14, Indels: 156
0.69 0.03 0.28
Matches are distributed among these distances:
20 2 0.01
22 90 0.23
23 9 0.02
24 8 0.02
25 2 0.01
26 53 0.14
28 10 0.03
29 2 0.01
30 6 0.02
31 12 0.03
32 192 0.50
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:1437657 original size:22 final size:22
Alignment explanation
Indices: 1437584--1437657 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
1437574 AAATTATTTA
*
1437584 AAATAAATCAATCCATACAACTACA
1 AAATAAATCAATCCATACAA--A-T
***
1437609 ATAATAAATCAATCCATA-TTTT
1 A-AATAAATCAATCCATACAAAT
1437631 AAAATAAATCAATCCATACAAAT
1 -AAATAAATCAATCCATACAAAT
1437654 AAAT
1 AAAT
1437658 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
25 1 0.03
26 16 0.41
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAATCAATCCATACAAAT
Found at i:1437672 original size:112 final size:111
Alignment explanation
Indices: 1437548--1437932 Score: 548
Period size: 112 Copynumber: 3.5 Consensus size: 111
1437538 CAATCCATAT
1437548 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1437613 TAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTA
66 TAAATCAATCCATATTTTAAAATAAATCAATCCATAC-AATAAATTA
* **
1437660 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
** * ** * ** **
1437721 TAAATCAATCCATAATAATAAACTATTTAAAATAAAT-CAATCCA-TA
66 TAAATCAATCCAT-ATTTTAAAATAAAT-CAATCCATACAATAAATTA
*
1437767 TTTTAAAATAAATCAACCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
1 -TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
1437832 ATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
65 ATAAATCAATCCATATTTTAAAATAAATCAATCCATAC-AATAAATTA
*
1437880 TTTAAAATAAATCAATCCATACTAATAAGTTATTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1437933 TTTTAAAATA
Statistics
Matches: 234, Mismatches: 29, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
107 2 0.01
108 70 0.30
109 14 0.06
110 10 0.04
111 14 0.06
112 122 0.52
113 2 0.01
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (111 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
TAAATCAATCCATATTTTAAAATAAATCAATCCATACAATAAATTA
Found at i:1437718 original size:22 final size:22
Alignment explanation
Indices: 1437692--1437734 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1437682 TAATAAATTA
1437692 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1437714 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1437735 ATAATAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1437772 original size:22 final size:22
Alignment explanation
Indices: 1437746--1437788 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1437736 TAATAAACTA
*
1437746 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAACCCATAT
1437768 TTTAAAATAAATCAACCCATA
1 TTTAAAATAAATCAACCCATA
1437789 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (22 bp):
TTTAAAATAAATCAACCCATAT
Found at i:1437797 original size:22 final size:22
Alignment explanation
Indices: 1437748--1437796 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1437738 ATAAACTATT
* **
1437748 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAACCCATATAA
1437770 TAAAATAAATCAACCCATACTAA
1 TAAAATAAATCAACCCATA-TAA
1437793 TAAA
1 TAAA
1437797 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAACCCATATAA
Found at i:1437837 original size:166 final size:164
Alignment explanation
Indices: 1437515--1438013 Score: 602
Period size: 166 Copynumber: 3.0 Consensus size: 164
1437505 TACAACTACA
1437515 ATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
1 ATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
*** * **
1437580 TTTAAAATAAATCAATCCATACAACTACAAT-AAT-AA--AT-C-AATCCA-TATTTTAAAATAA
66 TTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAACCATACTAATAAATTA-TTTAAAATAA
*
1437638 ATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCAT
129 ATCAATCCATACAACTAAA--A--T--AATAAATCAATCCAT
* *
1437680 ACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAACT
1 A-TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATT
1437745 ATTTAAAATAAATCAATCCATATTTTAAAATAAATCAACCCATACTAATAAATTATTTAAAATAA
65 ATTTAAAATAAATCAATCCATATTTTAAAATAAATCAA-CCATACTAATAAATTATTTAAAATAA
*
1437810 ATCAATCCATACAACTACAATAATAAATCAATCCAT
129 ATCAATCCATACAACTAAAATAATAAATCAATCCAT
** * ** * ** ** *
1437846 ATTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATACTAATAAG
1 ATAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATACTAATAAA
1437909 TTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT
63 TTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAA-CCATACTAATAAATTATTTAAAAT
* *
1437974 AAATCAATTCATACAACTATAATAATAAATCAATCCAT
127 AAATCAATCCATACAACTAAAATAATAAATCAATCCAT
1438012 AT
1 AT
1438014 TTTAAAATAA
Statistics
Matches: 296, Mismatches: 26, Indels: 23
0.86 0.08 0.07
Matches are distributed among these distances:
164 5 0.02
165 16 0.05
166 235 0.79
167 2 0.01
168 1 0.00
170 3 0.01
171 1 0.00
172 31 0.10
173 2 0.01
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (164 bp):
ATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
TTTAAAATAAATCAATCCATATTTTAAAATAAATCAACCATACTAATAAATTATTTAAAATAAAT
CAATCCATACAACTAAAATAATAAATCAATCCAT
Found at i:1437852 original size:80 final size:79
Alignment explanation
Indices: 1437751--1438057 Score: 499
Period size: 80 Copynumber: 3.8 Consensus size: 79
1437741 AACTATTTAA
*
1437751 AATAAATCAATCCATATTTTAAAATAAATCAACCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1437816 CCATACAACTACAAT
66 CCATACAACTA-AAT
1437831 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1437896 CCATACTAA-TAAGTTATTT
66 CCATAC-AACTAA---A--T
1437915 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
*
1437980 ATTCATACAACTATAAT
64 ATCCATACAACTA-AAT
1437997 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1438058 TATTTGAAAA
Statistics
Matches: 215, Mismatches: 2, Indels: 20
0.91 0.01 0.08
Matches are distributed among these distances:
79 1 0.00
80 133 0.62
81 2 0.01
82 2 0.01
84 2 0.01
85 2 0.01
86 72 0.33
87 1 0.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.33
Consensus pattern (79 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTAAAT
Found at i:1437877 original size:22 final size:23
Alignment explanation
Indices: 1437802--1437876 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
1437792 ATAAATTATT
1437802 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
1437824 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
1437850 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
1437873 TAAA
1 TAAA
1437877 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:1437896 original size:220 final size:220
Alignment explanation
Indices: 1437514--1437986 Score: 892
Period size: 220 Copynumber: 2.1 Consensus size: 220
1437504 ATACAACTAC
*
1437514 AATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATT
1 AATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAACCCATACTAATAAATT
1437579 ATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAT
66 ATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAT
1437644 CCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
131 CCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
1437709 CATATTTTAAAATAAATCAATCCAT
196 CATATTTTAAAATAAATCAATCCAT
*
1437734 AATAATAAACTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAACCCATACTAATAAATT
1 AATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAACCCATACTAATAAATT
1437799 ATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAT
66 ATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAT
* *
1437864 CCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAGTTATTTAAAATAAATCAATC
131 CCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
1437929 CATATTTTAAAATAAATCAATCCAT
196 CATATTTTAAAATAAATCAATCCAT
* *
1437954 ACTAATAAATTATTTAAAATAAATCAATTCATA
1 AATAATAAATTATTTAAAATAAATCAATCCATA
1437987 CAACTATAAT
Statistics
Matches: 246, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
220 246 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (220 bp):
AATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAACCCATACTAATAAATT
ATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAT
CCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
CATATTTTAAAATAAATCAATCCAT
Found at i:1437938 original size:22 final size:22
Alignment explanation
Indices: 1437912--1437954 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1437902 TAATAAGTTA
1437912 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1437934 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1437955 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1437955 original size:134 final size:131
Alignment explanation
Indices: 1437611--1437904 Score: 394
Period size: 140 Copynumber: 2.2 Consensus size: 131
1437601 CAACTACAAT
* *
1437611 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATA-TCTAAAATAAATCAA-CAATAC-AATAAATTATTTAAAATAAATCAAT
*
1437676 CCATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAAT
63 CCATAC-AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAAT
1437740 AAACTATTTAA
121 AAACTATTTAA
* *
1437751 AATAAATCAATCCATATTTTAAAATAAATCAACCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATA-TCTAAAATAAATCAA-CAATAC-AATAAATTATTTAAAATAAATCAAT
* *
1437816 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
63 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAACTAT
1437881 TTAA
128 TTAA
1437885 AATAAATCAATCCATA-CTAA
1 AATAAATCAATCCATATCTAA
1437905 TAAGTTATTT
Statistics
Matches: 147, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
132 3 0.02
134 68 0.46
136 1 0.01
138 1 0.01
139 2 0.01
140 72 0.49
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (131 bp):
AATAAATCAATCCATATCTAAAATAAATCAACAATACAATAAATTATTTAAAATAAATCAATCCA
TACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAACTATTTA
A
Found at i:1437963 original size:22 final size:22
Alignment explanation
Indices: 1437914--1437962 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1437904 ATAAGTTATT
**
1437914 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1437936 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1437959 TAAA
1 TAAA
1437963 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1438014 original size:166 final size:166
Alignment explanation
Indices: 1437714--1438057 Score: 634
Period size: 166 Copynumber: 2.1 Consensus size: 166
1437704 CAATCCATAT
1437714 TTTAAAATAAATCAATCCATAATAATAAACTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATAATAATAAACTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1437779 TCAACCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCC
66 TCAACCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCC
1437844 ATATTTTAAAATAAATCAATCCATACTAATAAATTA
131 ATATTTTAAAATAAATCAATCCATACTAATAAATTA
* **
1437880 TTTAAAATAAATCAATCCATACTAATAAGTTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATAATAATAAACTATTTAAAATAAATCAATCCATATTTTAAAATAAA
* * *
1437945 TCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTATAATAATAAATCAATCC
66 TCAACCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCC
1438010 ATATTTTAAAATAAATCAATCCATACTAATAAATTA
131 ATATTTTAAAATAAATCAATCCATACTAATAAATTA
1438046 TTTAAAATAAAT
1 TTTAAAATAAAT
1438058 TATTTGAAAA
Statistics
Matches: 172, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
166 172 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (166 bp):
TTTAAAATAAATCAATCCATAATAATAAACTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAACCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCC
ATATTTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:1438043 original size:22 final size:21
Alignment explanation
Indices: 1437991--1438043 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1437981 TTCATACAAC
1437991 TATAAT-AATAAATCAATCCA
1 TATAATAAATAAATCAATCCA
**
1438011 TATTTTAAAATAAATCAATCCA
1 TATAAT-AAATAAATCAATCCA
1438033 TACTAATAAAT
1 TA-TAATAAAT
1438044 TATTTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 4 0.15
22 20 0.77
23 2 0.08
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (21 bp):
TATAATAAATAAATCAATCCA
Found at i:1438069 original size:15 final size:15
Alignment explanation
Indices: 1438037--1438214 Score: 223
Period size: 15 Copynumber: 11.5 Consensus size: 15
1438027 AATCCATACT
1438037 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
*
1438051 AATAAATTATTTGAA
1 AATAAATTATTTTAA
*
1438066 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
1438088 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
1438103 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
1438118 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
1438133 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1438148 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1438163 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1438178 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1438193 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1438208 AATAAAT
1 AATAAAT
1438215 AACCTTATTA
Statistics
Matches: 146, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.06
15 121 0.83
17 1 0.01
18 2 0.01
19 3 0.02
20 1 0.01
22 9 0.06
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1438131 original size:45 final size:45
Alignment explanation
Indices: 1438036--1438214 Score: 252
Period size: 45 Copynumber: 3.8 Consensus size: 45
1438026 CAATCCATAC
*
1438036 TAATAAATTA-TTTAAAATAAATTATTTGAAAATAAATCAATCCATATTTTA
1 TAATAAATTATTTTAAAATAAATTATTTTAAAAT--A--AAT---TATTTTA
* *
1438087 TAATAATTTATTTTAAAATAAATTATTTTATAATAAATTATTTTA
1 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATTATTTTA
*
1438132 TAATAAATTATTTTATAATAAATTATTTTAAAATAAATTATTTTA
1 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATTATTTTA
1438177 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAAT
1 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAAT
1438215 AACCTTATTA
Statistics
Matches: 120, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
45 86 0.72
48 3 0.03
50 1 0.01
51 9 0.08
52 21 0.17
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (45 bp):
TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATTATTTTA
Found at i:1440614 original size:173 final size:178
Alignment explanation
Indices: 1440198--1440615 Score: 480
Period size: 179 Copynumber: 2.4 Consensus size: 178
1440188 TTGTCGATTA
* * *
1440198 TCAAGATTGAAGTTCGGTTTTTTGATCTC-TCTGTGTGAATCCTCATATACCTTTGAATCACTTG
1 TCAAGATTAAAGTTCGG-TTTTTGATCTCAT-TGTGTGAATCCTCAGATACCTTTGAATCTCTTG
* * ** * * *
1440262 GATATCAATCTGGTTTCTAGTATGAAATGTTTATGTTTAATAGTTATTTAGTTGACCATAAAGTA
64 GATACCAATCTGGTTTCTAATATGAAACATATATGATTAATAGTTATTTAG-TGAACATAAAGTA
1440327 GCTCTTCAAAATGCGATTTTCATTTTCTTTAATCGACTCTTTGTGGTTGGTTT
128 GCTCTTCAAAATGCGA-TTTCATTTTCTTTAATC-ACTCTTTGTGGTTGGTTT
** * *
1440380 TCGGGATGAAAGTTC-G-TTTTGATCTCATTGTGCGAATCCTCAGATACCTTTGAATCTCTTGGA
1 TCAAGATTAAAGTTCGGTTTTTGATCTCATTGTGTGAATCCTCAGATACCTTTGAATCTCTTGGA
*
1440443 TACCAATCTGGTTTCTAATATGAAACATATATGATTACTAG-T-TTTA-TGAACATAAAGTAGCT
66 TACCAATCTGGTTTCTAATATGAAACATATATGATTAATAGTTATTTAGTGAACATAAAGTAGCT
* ** *
1440505 CTTCGAAATTTTG-TTTC-TGTTT-TTT-ATC-TTCTTTGTGGTTGGTTT
131 CTTC-AAAATGCGATTTCAT-TTTCTTTAATCACTCTTTGTGGTTGGTTT
* * * *
1440550 TCAAGATTAAAGTCCGGTTTTTCGATATCATTGTGTGAATCCTTAGATACATTTGAATCTCTTGG
1 TCAAGATTAAAGTTCGGTTTTT-GATCTCATTGTGTGAATCCTCAGATACCTTTGAATCTCTTGG
1440615 A
65 A
1440616 CATCAATTTG
Statistics
Matches: 203, Mismatches: 27, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
170 27 0.13
171 1 0.00
172 7 0.03
173 43 0.21
174 7 0.03
175 19 0.09
176 5 0.02
177 4 0.02
178 1 0.00
179 76 0.37
180 1 0.00
181 1 0.00
182 11 0.05
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (178 bp):
TCAAGATTAAAGTTCGGTTTTTGATCTCATTGTGTGAATCCTCAGATACCTTTGAATCTCTTGGA
TACCAATCTGGTTTCTAATATGAAACATATATGATTAATAGTTATTTAGTGAACATAAAGTAGCT
CTTCAAAATGCGATTTCATTTTCTTTAATCACTCTTTGTGGTTGGTTT
Done.