Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008229.1 Hibiscus syriacus cultivar Beakdansim tig00110865_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: 3634043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 17
Found at i:1107462 original size:15 final size:15
Alignment explanation
Indices: 1107442--1107486 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1107432 TTGATTAGAC
1107442 AAATCTTGTAGATCT
1 AAATCTTGTAGATCT
*
1107457 AAATCTTGTA-AGC-
1 AAATCTTGTAGATCT
*
1107470 AAATCTTGTAGTTCT
1 AAATCTTGTAGATCT
1107485 AA
1 AA
1107487 GTCTAAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 10 0.40
14 3 0.12
15 12 0.48
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (15 bp):
AAATCTTGTAGATCT
Found at i:1109352 original size:13 final size:13
Alignment explanation
Indices: 1109334--1109373 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
1109324 ATTTTGCAAT
1109334 ATAAATATTTTTA
1 ATAAATATTTTTA
1109347 ATAAATATTTTTA
1 ATAAATATTTTTA
1109360 ATAAATATTTTTA
1 ATAAATATTTTTA
1109373 A
1 A
1109374 ATTGTTGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATAAATATTTTTA
Found at i:1110072 original size:20 final size:20
Alignment explanation
Indices: 1110044--1110081 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1110034 TATATCAGTC
*
1110044 AACAGATAATTTCAAAAATT
1 AACAAATAATTTCAAAAATT
*
1110064 AACAAATAATTTTAAAAA
1 AACAAATAATTTCAAAAA
1110082 AATCTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.29
Consensus pattern (20 bp):
AACAAATAATTTCAAAAATT
Found at i:1110812 original size:46 final size:46
Alignment explanation
Indices: 1110678--1110791 Score: 183
Period size: 46 Copynumber: 2.5 Consensus size: 46
1110668 GCGGCGTTTT
1110678 TTAATAAACGCCGCAAAAGGTCGAGATATATAACAGTGTTTTTTGGA
1 TTAA-AAACGCCGCAAAAGGTCGAGATATATAACAGTGTTTTTTGGA
* * *
1110725 TTAAAAAAGCCGCAAAAGGTCGAGCTATATAACTGTGTTTTTTGGA
1 TTAAAAACGCCGCAAAAGGTCGAGATATATAACAGTGTTTTTTGGA
*
1110771 TTAAAAACGCTGCAAAAGGTC
1 TTAAAAACGCCGCAAAAGGTC
1110792 TATATCTATA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
46 58 0.94
47 4 0.06
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (46 bp):
TTAAAAACGCCGCAAAAGGTCGAGATATATAACAGTGTTTTTTGGA
Found at i:1110939 original size:87 final size:87
Alignment explanation
Indices: 1110762--1110940 Score: 202
Period size: 87 Copynumber: 2.1 Consensus size: 87
1110752 TATAACTGTG
* * * ** ***
1110762 TTTTTTGGATTAAAAACGCTGCAAAAGGTCTATATCTATAGCGGTGTTTTTAAAAATGTCGCAAA
1 TTTTTTGGATTAAAAACACCGCAAAAGCTCTATATCTATAGCGGCATTTTTAAAAACACCGCAAA
* * *
1110827 AGGTTGAGATATTTAGTGGCGT
66 AGGTTGAGATATATAGCGGCAT
*
1110849 TTTTTTGGA-TAAAAAGCACCGCAAAAGCTCTATATCTATAGCTGCATTTTTAACAAACACCGCA
1 TTTTTTGGATTAAAAA-CACCGCAAAAGCTCTATATCTATAGCGGCATTTTTAA-AAACACCGCA
1110913 AAAGGTCTG-G-TATATAGCGGCAT
64 AAAGGT-TGAGATATATAGCGGCAT
1110936 TTTTT
1 TTTTT
1110941 GATACAAACG
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
86 6 0.08
87 55 0.71
88 14 0.18
89 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (87 bp):
TTTTTTGGATTAAAAACACCGCAAAAGCTCTATATCTATAGCGGCATTTTTAAAAACACCGCAAA
AGGTTGAGATATATAGCGGCAT
Found at i:1111377 original size:21 final size:21
Alignment explanation
Indices: 1111347--1111388 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1111337 CTGCTGATAT
*
1111347 GTTGCCTCTCTCTCTCCTTCC
1 GTTGCCTCTCTCTCTACTTCC
*
1111368 GTTGCTTCTCTCTCTACTTCC
1 GTTGCCTCTCTCTCTACTTCC
1111389 CTCGCTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.02, C:0.43, G:0.10, T:0.45
Consensus pattern (21 bp):
GTTGCCTCTCTCTCTACTTCC
Found at i:1111395 original size:21 final size:21
Alignment explanation
Indices: 1111353--1111396 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1111343 ATATGTTGCC
* * *
1111353 TCTCTCTCTCCTTCCGTTGCT
1 TCTCTCTCTACTTCCCTCGCT
1111374 TCTCTCTCTACTTCCCTCGCT
1 TCTCTCTCTACTTCCCTCGCT
1111395 TC
1 TC
1111397 ATTTTCGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.45, G:0.07, T:0.45
Consensus pattern (21 bp):
TCTCTCTCTACTTCCCTCGCT
Found at i:1116886 original size:15 final size:16
Alignment explanation
Indices: 1116828--1116890 Score: 101
Period size: 16 Copynumber: 4.0 Consensus size: 16
1116818 GATTACCTTT
*
1116828 GTTTCCTGACAAATGA
1 GTTTCCTGACAAACGA
1116844 GTTTCCTGACAAACGA
1 GTTTCCTGACAAACGA
1116860 GTTTCCTGACAAACGA
1 GTTTCCTGACAAACGA
*
1116876 G-TTCCTCACAAACGA
1 GTTTCCTGACAAACGA
1116891 ATTAAATTCG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
15 13 0.29
16 32 0.71
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (16 bp):
GTTTCCTGACAAACGA
Found at i:1117141 original size:28 final size:28
Alignment explanation
Indices: 1117084--1117142 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
1117074 GGAGAACGAC
* *
1117084 ATATGTATATATATATATACACACACAT
1 ATATGCATATATATATATACACACAAAT
* *
1117112 ATATGCATATATATATATATATACAAAT
1 ATATGCATATATATATATACACACAAAT
1117140 ATA
1 ATA
1117143 AAAAAAGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.37
Consensus pattern (28 bp):
ATATGCATATATATATATACACACAAAT
Found at i:1124188 original size:42 final size:42
Alignment explanation
Indices: 1124134--1124334 Score: 276
Period size: 42 Copynumber: 4.8 Consensus size: 42
1124124 GCATTTATAT
*
1124134 TAAAAACGCCACTAAAGGACAAAACTATTACGGTGTTTATTA
1 TAAAAACGCCACTAAAGGACAAAACTATTGCGGTGTTTATTA
* * * **
1124176 TAAAAACACCACTAAGGGATAAAACTATTGCGACGTTTATTA
1 TAAAAACGCCACTAAAGGACAAAACTATTGCGGTGTTTATTA
*
1124218 TAAAAACGCCACTAAGGGACAAAACTATTGCGGTGTTTATTA
1 TAAAAACGCCACTAAAGGACAAAACTATTGCGGTGTTTATTA
* *
1124260 CAAAAACGCCACTAAGGGACAAAACTATTGCGGTGTTTATTA
1 TAAAAACGCCACTAAAGGACAAAACTATTGCGGTGTTTATTA
* * * **
1124302 CAAAAATGCCACTAAAGTACATGACTATTGCGG
1 TAAAAACGCCACTAAAGGACAAAACTATTGCGG
1124335 CATTTAAAAA
Statistics
Matches: 143, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 143 1.00
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (42 bp):
TAAAAACGCCACTAAAGGACAAAACTATTGCGGTGTTTATTA
Found at i:1124329 original size:84 final size:84
Alignment explanation
Indices: 1124135--1124398 Score: 300
Period size: 84 Copynumber: 3.2 Consensus size: 84
1124125 CATTTATATT
* * *
1124135 AAAAACGCCACTAAAGGACAAAACTATTACGGTGTTTATTATAAAAACACCACTAAGGGATAAAA
1 AAAAACGCCACTAAAGGACAAAACTATTGCGGTGTTTATTACAAAAACACCACTAAGGGACAAAA
*
1124200 CTATTGCGACGTTTATTAT
66 CTATTGCGACGTTTATTAC
* *
1124219 AAAAACGCCACTAAGGGACAAAACTATTGCGGTGTTTATTACAAAAACGCCACTAAGGGACAAAA
1 AAAAACGCCACTAAAGGACAAAACTATTGCGGTGTTTATTACAAAAACACCACTAAGGGACAAAA
**
1124284 CTATTGCGGTGTTTATTAC
66 CTATTGCGACGTTTATTAC
* * ** ** * * * **
1124303 AAAAATGCCACTAAAGTACATGACTATTGCGGCATTTA--AAAAAAACACCACTAAAGTACAAGT
1 AAAAACGCCACTAAAGGACAAAACTATTGCGGTGTTTATTACAAAAACACCACTAAGGGACAAAA
* * *
1124366 CTATAGCGGCGTTTGTT-C
66 CTATTGCGACGTTTATTAC
*
1124384 ACAAACGCCACTAAA
1 AAAAACGCCACTAAA
1124399 TTAAGAGTAT
Statistics
Matches: 154, Mismatches: 26, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
81 14 0.09
82 33 0.21
84 107 0.69
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (84 bp):
AAAAACGCCACTAAAGGACAAAACTATTGCGGTGTTTATTACAAAAACACCACTAAGGGACAAAA
CTATTGCGACGTTTATTAC
Found at i:1128103 original size:39 final size:39
Alignment explanation
Indices: 1128045--1128300 Score: 307
Period size: 39 Copynumber: 6.6 Consensus size: 39
1128035 TCTATGACTT
*
1128045 GTAAGTCCTTACCGAAGGCTCCTCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
* * * * *
1128084 GCAAGTCCTTACTGTAGGCTCCTCGGTTTTGTGCTCAAG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
* **
1128123 ATAAGTCCTTACCGCAGGCTCCTTAGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
* * *
1128162 GTAAGTCCTTACCACATGCTCCTCGGCTTGGTGCTCAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
** * * *
1128201 GTAAGTCCTTATTGCAAGCTCATTGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
* * * *
1128240 GTAAGTCCTTACCGCAGGCTCCTCTGTTTTGTGCACATG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
*
1128279 CTAAGTCCTTACCGCAGG-TCCT
1 GTAAGTCCTTACCGCAGGCTCCT
1128301 TATATTGTAT
Statistics
Matches: 181, Mismatches: 36, Indels: 1
0.83 0.17 0.00
Matches are distributed among these distances:
38 4 0.02
39 177 0.98
ACGTcount: A:0.16, C:0.28, G:0.25, T:0.31
Consensus pattern (39 bp):
GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
Found at i:1128519 original size:107 final size:107
Alignment explanation
Indices: 1128342--1128535 Score: 343
Period size: 107 Copynumber: 1.8 Consensus size: 107
1128332 TACATTTGTG
* *
1128342 TGTATGGTTCTGGGGAACCTACACATTCTGGTTATCTGATAGGGGTAGTGTTCATATTTTTAAAA
1 TGTATGGTTCTGGGGAACCTACACATTCTGGTGATCGGATAGGGGTAGTGTTCATATTTTTAAAA
*
1128407 CATGTTTAATAAATTGATTTTTTACTAAAGTATTCAGGTGGA
66 AATGTTTAATAAATTGATTTTTTACTAAAGTATTCAGGTGGA
*
1128449 TGTATGGTTCTGGGGAACCTACACATTCTGGTGATCGGATGGGGGTAGTGTTCATATTTTTAAAA
1 TGTATGGTTCTGGGGAACCTACACATTCTGGTGATCGGATAGGGGTAGTGTTCATATTTTTAAAA
*
1128514 AATGTTTGATAAATTGATTTTT
66 AATGTTTAATAAATTGATTTTT
1128536 GCTAAGGTTT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 82 1.00
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (107 bp):
TGTATGGTTCTGGGGAACCTACACATTCTGGTGATCGGATAGGGGTAGTGTTCATATTTTTAAAA
AATGTTTAATAAATTGATTTTTTACTAAAGTATTCAGGTGGA
Found at i:1132070 original size:39 final size:39
Alignment explanation
Indices: 1132000--1132244 Score: 341
Period size: 39 Copynumber: 6.3 Consensus size: 39
1131990 TCTATGACTT
* * *
1132000 GTAAGTCCTTACCGCAAGCTCTTCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
* *
1132039 GTAAGTCCTTACCGTAGGCTCCTTGGTTTTGTGCTCAGG
1 GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
** *
1132078 GTAAGTCAGTATCGTAGGCTCCTCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
* *
1132117 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTACTCAGG
1 GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
*
1132156 GTAGGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
* * *
1132195 GTAAGTCCTTA-C-TCAGACTCCTCTGCTTTGTGCACAGG
1 GTAAGTCCTTACCGT-AGGCTCCTCGGCTTTGTGCTCAGG
1132233 GTAAGTCCTTAC
1 GTAAGTCCTTAC
1132245 AACAGGTCCT
Statistics
Matches: 182, Mismatches: 22, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
37 1 0.01
38 33 0.18
39 148 0.81
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.31
Consensus pattern (39 bp):
GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
Found at i:1132478 original size:105 final size:105
Alignment explanation
Indices: 1132291--1132496 Score: 304
Period size: 105 Copynumber: 2.0 Consensus size: 105
1132281 GAGTGTACAT
* * * **
1132291 GTGGGTGTATGGTTTTAGGGAACCTACAAATTCTGGTGAACGGATGGGGTAGTGTTCATATTTTT
1 GTGGATGTATGGTTCTAGGGAACCTACAAATTATGGTGAACAAATGGGGTAGTGTTCATATTTTT
* * *
1132356 AGAACATGTTTGATAAACTGGTTTTTACTGAAGTATCCAG
66 AAAACATGTTTGATAAACTGATTTTCACTGAAGTATCCAG
** * *
1132396 GTGGATGTATGGTTCTAGGGAAGTTACACATTATGGTGATCAAATGGGGTAGTGTTCATATTTTT
1 GTGGATGTATGGTTCTAGGGAACCTACAAATTATGGTGAACAAATGGGGTAGTGTTCATATTTTT
1132461 AAAACATGTTTGATAAACTGATTTTCACTGAAGTAT
66 AAAACATGTTTGATAAACTGATTTTCACTGAAGTAT
1132497 TTTATCTGTA
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
105 89 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.37
Consensus pattern (105 bp):
GTGGATGTATGGTTCTAGGGAACCTACAAATTATGGTGAACAAATGGGGTAGTGTTCATATTTTT
AAAACATGTTTGATAAACTGATTTTCACTGAAGTATCCAG
Found at i:1133518 original size:15 final size:16
Alignment explanation
Indices: 1133498--1133527 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1133488 AAAATTAAAG
1133498 TAAAATATAA-AATAT
1 TAAAATATAATAATAT
1133513 TAAAATATAATAATA
1 TAAAATATAATAATA
1133528 ACAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATATAATAATAT
Found at i:1133527 original size:3 final size:3
Alignment explanation
Indices: 1133519--1133548 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1133509 ATATTAAAAT
*
1133519 ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1133549 TGATTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1146515 original size:41 final size:41
Alignment explanation
Indices: 1146453--1146549 Score: 176
Period size: 41 Copynumber: 2.3 Consensus size: 41
1146443 AAAAAAAATT
*
1146453 GAATGAAGTTGGAAAGTTGGTAATAGCTCTAACAATTTTAGG
1 GAAT-AAGTTGGAAAGCTGGTAATAGCTCTAACAATTTTAGG
1146495 GAATAAGTTGGAAAGCTGGTAATAGCTCTAACAATTTTAGG
1 GAATAAGTTGGAAAGCTGGTAATAGCTCTAACAATTTTAGG
1146536 GAATAAGTTGGAAA
1 GAATAAGTTGGAAA
1146550 AACGATAATA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 50 0.93
42 4 0.07
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (41 bp):
GAATAAGTTGGAAAGCTGGTAATAGCTCTAACAATTTTAGG
Found at i:1146559 original size:41 final size:41
Alignment explanation
Indices: 1146453--1146587 Score: 155
Period size: 41 Copynumber: 3.2 Consensus size: 41
1146443 AAAAAAAATT
** *
1146453 GAATGAAGTTGGAAAGTTGGTAATAGCTCTAACAATTTTAGG
1 GAAT-AAGTTGGAAAACTGATAATAGCTCTAACAATTTTAGG
* *
1146495 GAATAAGTTGGAAAGCTGGTAATAGCTCTAACAATTTTAGG
1 GAATAAGTTGGAAAACTGATAATAGCTCTAACAATTTTAGG
* *
1146536 GAATAAGTTGGAAAAAC-GATAATAGCTCCAACATAGTCTTAGG
1 GAATAAGTTGG-AAAACTGATAATAGCTCTAACA-A-TTTTAGG
*
1146579 TAATAAGTT
1 GAATAAGTT
1146588 AGTAGATTCT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
41 61 0.73
42 9 0.11
43 14 0.17
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.29
Consensus pattern (41 bp):
GAATAAGTTGGAAAACTGATAATAGCTCTAACAATTTTAGG
Found at i:1149308 original size:20 final size:20
Alignment explanation
Indices: 1149283--1149321 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1149273 AAGTAACCCA
1149283 TACCCAA-ATTAAATCCAATT
1 TACCCAATA-TAAATCCAATT
*
1149303 TACCCATTATAAATCCAAT
1 TACCCAATATAAATCCAAT
1149322 ATCCATTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.31
Consensus pattern (20 bp):
TACCCAATATAAATCCAATT
Found at i:1150903 original size:17 final size:18
Alignment explanation
Indices: 1150881--1150914 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1150871 TTAGTCCCTC
1150881 TTATTTAGG-CATTTTTT
1 TTATTTAGGTCATTTTTT
*
1150898 TTATTTTGGTCATTTTT
1 TTATTTAGGTCATTTTT
1150915 ATATTTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.68
Consensus pattern (18 bp):
TTATTTAGGTCATTTTTT
Found at i:1157699 original size:20 final size:20
Alignment explanation
Indices: 1157660--1157697 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1157650 TTTTTGGAGT
*
1157660 TTTTTTCCTTCTTTATTTTG
1 TTTTTTCCCTCTTTATTTTG
1157680 TTTTTTCCCT-TTTATTTT
1 TTTTTTCCCTCTTTATTTT
1157698 TGATGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTTTCCCTCTTTATTTTG
Found at i:1159429 original size:76 final size:75
Alignment explanation
Indices: 1159322--1159537 Score: 274
Period size: 76 Copynumber: 2.9 Consensus size: 75
1159312 ATTTTAAACA
* *
1159322 TTATATTTTATCTTTTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
* *
1159387 GGATATTATTT
66 GAATATTA-AT
* *
1159398 TTATATTTTATCTTTGTTATAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
1159463 GAATATTAAT
66 GAATATTAAT
* * * * * **
1159473 TTAAATATTA-ATTTGTTTTTAGGTATTTTAG-TTAAGTAGTTTTTAAGTGCTTTAATTAAGATT
1 TTATATTTTATCTTTG-TTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGATT
1159536 TA
64 TA
1159538 AGATGTTTTA
Statistics
Matches: 123, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
74 15 0.12
75 40 0.33
76 68 0.55
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.56
Consensus pattern (75 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
GAATATTAAT
Found at i:1159457 original size:19 final size:19
Alignment explanation
Indices: 1159429--1159473 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1159419 GGTATTTTAG
* * *
1159429 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGATTTAGAAT
1159448 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGATTTAGAAT
*
1159467 ATTAATT
1 TTTAATT
1159474 TAAATATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (19 bp):
TTTAATTAGGATTTAGAAT
Found at i:1159479 original size:12 final size:13
Alignment explanation
Indices: 1159458--1159486 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1159448 TTTAATTAGG
1159458 ATTTAGAATATTA
1 ATTTAGAATATTA
1159471 ATTTA-AATATTA
1 ATTTAGAATATTA
1159483 ATTT
1 ATTT
1159487 GTTTTTAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (13 bp):
ATTTAGAATATTA
Found at i:1160163 original size:17 final size:17
Alignment explanation
Indices: 1160138--1160171 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1160128 CTTTATCCCA
*
1160138 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
1160155 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
1160172 TTATCTCACT
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:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:1160254 original size:8 final size:8
Alignment explanation
Indices: 1160237--1160268 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
1160227 TTTTTAATTC
1160237 ATTA-TTT
1 ATTATTTT
1160244 ATTATTTT
1 ATTATTTT
1160252 ATTATTTT
1 ATTATTTT
1160260 ATTATTTT
1 ATTATTTT
1160268 A
1 A
1160269 ATTTATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
ATTATTTT
Found at i:1165506 original size:12 final size:11
Alignment explanation
Indices: 1165489--1165536 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 11
1165479 AGGCAACCCA
1165489 TTTTGTTTATAT
1 TTTTGTTT-TAT
1165501 TTTTGTTTTTAT
1 TTTTG-TTTTAT
*
1165513 TTTCGTTTTA-
1 TTTTGTTTTAT
1165523 TTTTGTTTTAT
1 TTTTGTTTTAT
1165534 TTT
1 TTT
1165537 CAGTGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 9 0.28
11 8 0.25
12 12 0.38
13 3 0.09
ACGTcount: A:0.10, C:0.02, G:0.08, T:0.79
Consensus pattern (11 bp):
TTTTGTTTTAT
Found at i:1165515 original size:11 final size:10
Alignment explanation
Indices: 1165488--1165536 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 10
1165478 GAGGCAACCC
1165488 ATTTTGTTTAT
1 ATTTTGTTT-T
1165499 ATTTTTGTTTTT
1 A-TTTTG-TTTT
1165511 ATTTTCGTTTT
1 ATTTT-GTTTT
1165522 ATTTTGTTTT
1 ATTTTGTTTT
1165532 ATTTT
1 ATTTT
1165537 CAGTGAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.29
11 14 0.40
12 8 0.23
13 3 0.09
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.78
Consensus pattern (10 bp):
ATTTTGTTTT
Found at i:1167734 original size:75 final size:76
Alignment explanation
Indices: 1167526--1167740 Score: 278
Period size: 76 Copynumber: 2.8 Consensus size: 76
1167516 TTTTAAACAT
* * * * *
1167526 TATATTTTGTTTTTGTTTTATGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAT
1 TATAATTTATTTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAT
1167591 GATATTATTTG
66 GATATTATTTG
*
1167602 TATAATTTTTTCTTTGTTTTAGGTA-TTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TATAATTTATT-TTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1167666 -GAATATTATTT-
65 TG-ATATTATTTG
* * *
1167677 TA-AATATTATTTTTGTTTAAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGAATTT
1 TATAAT-TTATTTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTT
1167740 A
64 A
1167741 AGATGTTTTA
Statistics
Matches: 125, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
74 20 0.16
75 38 0.30
76 55 0.44
77 12 0.10
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.58
Consensus pattern (76 bp):
TATAATTTATTTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAT
GATATTATTTG
Found at i:1168366 original size:17 final size:17
Alignment explanation
Indices: 1168341--1168374 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1168331 CTTTATCCCA
*
1168341 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
1168358 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
1168375 TTATCTCATT
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:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:1168455 original size:8 final size:8
Alignment explanation
Indices: 1168438--1168494 Score: 50
Period size: 7 Copynumber: 7.2 Consensus size: 8
1168428 TTTTTAATTC
1168438 ATTA-TTT
1 ATTATTTT
1168445 ATTATTTT
1 ATTATTTT
1168453 ATTATTTTT
1 ATTA-TTTT
*
1168462 ATTTTTTTT
1 A-TTATTTT
1168471 ATT-TTTT
1 ATTATTTT
1168478 AATTA-TTT
1 -ATTATTTT
1168486 ATT-TTTT
1 ATTATTTT
1168493 AT
1 AT
1168495 ACTTTTTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
7 16 0.37
8 15 0.35
9 10 0.23
10 2 0.05
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
ATTATTTT
Found at i:1168458 original size:15 final size:14
Alignment explanation
Indices: 1168438--1168494 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 14
1168428 TTTTTAATTC
1168438 ATTATTTATTATTTT
1 ATTATTTATT-TTTT
*
1168453 ATTATTT-TTATTT
1 ATTATTTATTTTTT
1168466 -TT-TTTATTTTTT
1 ATTATTTATTTTTT
1168478 AATTATTTATTTTTT
1 -ATTATTTATTTTTT
1168493 AT
1 AT
1168495 ACTTTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
11 3 0.08
12 7 0.19
13 3 0.08
14 6 0.17
15 17 0.47
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
ATTATTTATTTTTT
Found at i:1168508 original size:8 final size:8
Alignment explanation
Indices: 1168457--1168508 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
1168447 TATTTTATTA
*
1168457 TTTTTATT
1 TTTTTAAT
*
1168465 TTTTTTAT
1 TTTTTAAT
1168473 TTTTTAAT
1 TTTTTAAT
*
1168481 TATTT-AT
1 TTTTTAAT
1168488 TTTTTATACT
1 TTTTTA-A-T
1168498 TTTTTAAT
1 TTTTTAAT
1168506 TTT
1 TTT
1168509 ACCTGGAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 21 0.58
9 2 0.06
10 7 0.19
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTAAT
Found at i:1177378 original size:194 final size:191
Alignment explanation
Indices: 1176760--1177523 Score: 1455
Period size: 194 Copynumber: 4.0 Consensus size: 191
1176750 TCATCTAACA
1176760 TTTCTCTATATTTATAGGTAATTTTCCAATAAATAAACCCCAATTATCATTCCATCTTCACACGT
1 TTTCTCTATATTTATAGGTAATTTTCCAATAAATAAACCCCAATTATCATTCCATCTTCACACGT
1176825 TCACCACAATCGAAATTTGGAAGTGTGAGTGTGGGGTAACGAGCTACGAACCCAAAAAAAAAAAA
66 TCACCACAATCGAAATTTGGAAGTGTGAGTGTGGGGTAACGAGCTACGAACCC-AAAAAAAAAAA
1176890 AAATCAATTCTAACATACAAAGCACAAAAGGCAGTTCTAATATTTTTCTCAATTGAGAGTAC
130 AAATCAATTCTAACATACAAAGCACAAAAGGCAGTTCTAATATTTTTCTCAATTGAGAGTAC
1176952 TTTCTCTATA-TT-TAGGTAATTTTCCAATAAATAAACCCCAATTATCATTCCATCTTCACACGT
1 TTTCTCTATATTTATAGGTAATTTTCCAATAAATAAACCCCAATTATCATTCCATCTTCACACGT
1177015 TCACCACAATCGAAATTTGGAAGTGTGAGTGTGGGGTAACGAGCTACGAACCC--AAAAAAAAAA
66 TCACCACAATCGAAATTTGGAAGTGTGAGTGTGGGGTAACGAGCTACGAACCCAAAAAAAAAAAA
1177078 AATCAATTCTAACATACAAAGCACAAAAGGCAGTTCTAATATTTTTCTCAATTGAGAGTAC
131 AATCAATTCTAACATACAAAGCACAAAAGGCAGTTCTAATATTTTTCTCAATTGAGAGTAC
1177139 TTTCTCTATATTTATAGGTAATTTTCCAATAAATAAACCCCAATTATCATTCCATCTTCACACGT
1 TTTCTCTATATTTATAGGTAATTTTCCAATAAATAAACCCCAATTATCATTCCATCTTCACACGT
1177204 TCACCACAATCGAAATTTGGAAGTGTGAGTGTGGGGTAACGAGCTACGAACCCAAAAAAAAAAAA
66 TCACCACAATCGAAATTTGGAAGTGTGAGTGTGGGGTAACGAGCTACGAACCC---AAAAAAAAA
*
1177269 AAAAATCAATTCTAACATACAAAGCACAAAAGGAAGTTCTAATATTTTTCTCAATTGAGAGTAC
128 AAAAATCAATTCTAACATACAAAGCACAAAAGGCAGTTCTAATATTTTTCTCAATTGAGAGTAC
1177333 TTTCTCTATATTTATAGGTAATTTTCCAATAAATAAACCCCAATTATCATTCCATCTTCACACGT
1 TTTCTCTATATTTATAGGTAATTTTCCAATAAATAAACCCCAATTATCATTCCATCTTCACACGT
1177398 TCACCACAATCGAAATTTGGAAGTGTGAGTGTGGGGTAACGAGCTACGAACCCAAAAAAAAAAAA
66 TCACCACAATCGAAATTTGGAAGTGTGAGTGTGGGGTAACGAGCTACGAACCCAAAAAAAAAAAA
1177463 AATCAATTCTAACATACAAAGCACAAAAGGCAGTTCTAATATTTTTCTCAATTGAGAGTAC
131 AATCAATTCTAACATACAAAGCACAAAAGGCAGTTCTAATATTTTTCTCAATTGAGAGTAC
1177524 AAGAATAGAG
Statistics
Matches: 563, Mismatches: 2, Indels: 15
0.97 0.00 0.03
Matches are distributed among these distances:
187 81 0.14
188 2 0.00
189 104 0.18
190 104 0.18
191 74 0.13
192 10 0.02
194 188 0.33
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (191 bp):
TTTCTCTATATTTATAGGTAATTTTCCAATAAATAAACCCCAATTATCATTCCATCTTCACACGT
TCACCACAATCGAAATTTGGAAGTGTGAGTGTGGGGTAACGAGCTACGAACCCAAAAAAAAAAAA
AATCAATTCTAACATACAAAGCACAAAAGGCAGTTCTAATATTTTTCTCAATTGAGAGTAC
Found at i:1178676 original size:29 final size:29
Alignment explanation
Indices: 1178616--1178676 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1178606 TAGAATTTAG
* *
1178616 AATTTAATCATTAGTTTAGAATGTAATTT
1 AATTTAATCATAAGTTTAGAATGTAATAT
* *
1178645 AATTTAATCATAATTTTAGTAATTTAA-AT
1 AATTTAATCATAAGTTTAG-AATGTAATAT
1178674 AAT
1 AAT
1178677 CATGTATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (29 bp):
AATTTAATCATAAGTTTAGAATGTAATAT
Found at i:1196883 original size:49 final size:49
Alignment explanation
Indices: 1196811--1197277 Score: 637
Period size: 49 Copynumber: 9.5 Consensus size: 49
1196801 TCTATAATAA
* *
1196811 AAGTTAAATGCAAAATGGTGCATTTTTGGTAGAAAGGTGCCACTAATGC
1 AAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
* *
1196860 AAGTTAAATACATAATGGTGCATTTTTGGCATAAAGGTGCCACTAATGC
1 AAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
* * * * * *
1196909 AAGTTAAATGCAAAATAGTGCATTTTTTTGCACAAATGTGTCACTAATGC
1 AAGTTAAATGCATAATGGTGCA-TTTTTGGCAGAAAGGTGCCACTAATGC
* ** *
1196959 AAGTTAAATGCATAATGGTGAATTTTTGAAAGAAATGTGCCACTAATGC
1 AAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
*
1197008 AAGTTAAATGCATAATGGTGCATTTTTAGCAGAAAGGTGCCACTAATGC
1 AAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
*
1197057 AAGTTAAATGCAAAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
1 AAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
* * *
1197106 AAGTTAAATGCATAATTGTGCAATTTTGGTAGAAAGGTGCCACTAATGC
1 AAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
* ** * *
1197155 AAATTAAATGCATAATGGTTTATTTTTGGCAGAAATGTGCCACTAATAC
1 AAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
* * * * * **
1197204 AAGTTAACTGCTTAAAGGTGCAGTTTTGGTAGAAAAATGCCACTAATGC
1 AAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
*
1197253 AAGTAAAATGCATAATGGTGCATTT
1 AAGTTAAATGCATAATGGTGCATTT
1197278 CGACATAAAA
Statistics
Matches: 363, Mismatches: 54, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
49 321 0.88
50 42 0.12
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (49 bp):
AAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGC
Found at i:1202796 original size:20 final size:20
Alignment explanation
Indices: 1202771--1202820 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1202761 TGAAAATATT
* **
1202771 TAATAAAATAAAATAGTTAA
1 TAATAAAATAAAACAGAAAA
1202791 TAAT-AAATAAAACAGAAAA
1 TAATAAAATAAAACAGAAAA
1202810 TAATAAAATAA
1 TAATAAAATAA
1202821 TAAATAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
TAATAAAATAAAACAGAAAA
Found at i:1202800 original size:19 final size:19
Alignment explanation
Indices: 1202763--1202816 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
1202753 GGTAAAGTTG
*
1202763 AAAATATTTAAT-A-AAAT
1 AAAATAGTTAATAATAAAT
1202780 AAAATAGTTAATAATAAAT
1 AAAATAGTTAATAATAAAT
* **
1202799 AAAACAGAAAATAATAAA
1 AAAATAGTTAATAATAAA
1202817 ATAATAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 11 0.35
18 1 0.03
19 19 0.61
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
AAAATAGTTAATAATAAAT
Found at i:1202904 original size:17 final size:18
Alignment explanation
Indices: 1202868--1202909 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
1202858 ACTTTTTTAA
1202868 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
* *
1202886 AAATAAACGA-AATAATT
1 AAATAAAAGATAAGAATT
1202903 AAATAAA
1 AAATAAA
1202910 TAATCTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:1203721 original size:76 final size:73
Alignment explanation
Indices: 1203510--1203731 Score: 231
Period size: 76 Copynumber: 3.0 Consensus size: 73
1203500 AAAACATCTT
* **
1203510 AAATCCTAATTAAAACACTTAAAACTATTTAAACT-AAA-AC-ACCTAAAA-ATAATATTTAAAA
1 AAATCCTAATTAAAATAC-TAAAACTATTTAAACTAAAATACAAAATAAAATATAATA-TTAAAA
*
1203571 TAATATTCT-
64 TAATATCCTA
* * * *
1203580 AAATCCTAATTAAAATACAAAAACCTATTTAAACTAAAATACTTAAAACAAAGATAAAATATAAA
1 AAATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAATAC--AAAATAAA-ATATAATATTAA
1203645 AATAATATCCTA
62 AATAATATCCTA
*
1203657 AAAT-TTAATTAAAATACTAAAATCTATTTAAACTAAAATACAAAGATAAAATATAATATCTAAA
1 AAATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAATACAAA-ATAAAATATAATAT-TAAA
*
1203721 ATATTATCCTA
63 ATAATATCCTA
1203732 CATTTGAGTT
Statistics
Matches: 126, Mismatches: 15, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
69 4 0.03
70 28 0.22
71 3 0.02
72 2 0.02
74 11 0.09
75 21 0.17
76 48 0.38
77 9 0.07
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (73 bp):
AAATCCTAATTAAAATACTAAAACTATTTAAACTAAAATACAAAATAAAATATAATATTAAAATA
ATATCCTA
Found at i:1208349 original size:15 final size:15
Alignment explanation
Indices: 1208302--1208353 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
1208292 TAGAAAATGT
1208302 ATAATAAAATAAATAA
1 ATAATAAAAT-AATAA
*
1208318 TTATAA-AAAAGAA-AA
1 --ATAATAAAATAATAA
1208333 ATAATAAAATAATAA
1 ATAATAAAATAATAA
1208348 ATAATA
1 ATAATA
1208354 GTAGTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 4 0.13
14 6 0.20
15 10 0.33
16 2 0.07
17 4 0.13
18 4 0.13
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (15 bp):
ATAATAAAATAATAA
Found at i:1208429 original size:17 final size:18
Alignment explanation
Indices: 1208393--1208432 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1208383 ATTAGTTTTA
1208393 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
*
1208411 AAATAAAAGA-AATAATT
1 AAATAAAAGATAAGAATT
1208428 AAATA
1 AAATA
1208433 TTTAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:1209100 original size:71 final size:74
Alignment explanation
Indices: 1209019--1209205 Score: 238
Period size: 76 Copynumber: 2.5 Consensus size: 74
1209009 TAAAACATCT
* * * *
1209019 TAAATCCTAATTAAAACATTTAAAACTATTTAAACTAAAACACCT-AA-AAA-ATAATAT-TTAA
1 TAAATCCTAATTAAAATA-CTAAAACTATTTAAACTAAAACACCTAAACAAAGATAAAATATAAA
*
1209080 AATAATATTC
65 AATAATATCC
*
1209090 TAAATCCTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAAC-TATTTAAACTAAAACACCT-AAACAAAGATAAAATATAA
1209155 AAATAATATCC
64 AAATAATATCC
* *
1209166 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAA
1 TAAATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAA
1209206 TACAAAGATA
Statistics
Matches: 101, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
70 6 0.06
71 35 0.35
73 2 0.02
74 3 0.03
75 6 0.06
76 48 0.48
77 1 0.01
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (74 bp):
TAAATCCTAATTAAAATACTAAAACTATTTAAACTAAAACACCTAAACAAAGATAAAATATAAAA
ATAATATCC
Found at i:1209148 original size:25 final size:24
Alignment explanation
Indices: 1209101--1209148 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1209091 AAATCCTAAT
* **
1209101 TAAAATACTAAAACATATTTAAAC
1 TAAAATACTAAAACAAAGATAAAC
1209125 TAAAATACCTAAAACAAAGATAAA
1 TAAAATA-CTAAAACAAAGATAAA
1209149 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.23
Consensus pattern (24 bp):
TAAAATACTAAAACAAAGATAAAC
Found at i:1217778 original size:24 final size:23
Alignment explanation
Indices: 1217709--1217803 Score: 75
Period size: 23 Copynumber: 4.0 Consensus size: 23
1217699 GACTTGAGAT
* * *
1217709 AATAATAATAAA-ATAATAATGAC
1 AATAATAATAAACAAAATAA-AAA
*
1217732 AATAATAATTTAAACATATATAAAAA
1 AATAATAA--TAAACA-AAATAAAAA
*
1217758 AATAATAATAAAACAAAATAAAAT
1 AATAATAAT-AAACAAAATAAAAA
* *
1217782 TATAATAATAATCAAAATAAAA
1 AATAATAATAAACAAAATAAAA
1217804 GTAATTAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
23 20 0.34
24 16 0.27
25 9 0.15
26 10 0.17
27 4 0.07
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.26
Consensus pattern (23 bp):
AATAATAATAAACAAAATAAAAA
Found at i:1217809 original size:27 final size:26
Alignment explanation
Indices: 1217756--1217822 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
1217746 CATATATAAA
1217756 AAAATAATAATAAAACAAAATAAAATT
1 AAAATAATAATAAAACAAAAT-AAATT
* *
1217783 ATAATAATAATCAAAATAAAAGT-AATT
1 AAAATAATAAT-AAAACAAAA-TAAATT
1217810 AAAAGTAATAATA
1 AAAA-TAATAATA
1217823 TTAAATTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 18 0.53
28 15 0.44
29 1 0.03
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (26 bp):
AAAATAATAATAAAACAAAATAAATT
Found at i:1217825 original size:15 final size:16
Alignment explanation
Indices: 1217807--1217843 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1217797 AATAAAAGTA
1217807 ATTAAAAGT-AATAAT
1 ATTAAAAGTGAATAAT
*
1217822 ATT-AAATTGAATAAT
1 ATTAAAAGTGAATAAT
1217837 ATTAAAA
1 ATTAAAA
1217844 ATTTAGGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 4 0.21
15 12 0.63
16 3 0.16
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (16 bp):
ATTAAAAGTGAATAAT
Found at i:1217837 original size:3 final size:3
Alignment explanation
Indices: 1217707--1217822 Score: 54
Period size: 3 Copynumber: 40.0 Consensus size: 3
1217697 ATGACTTGAG
* * *
1217707 ATA ATA ATA ATA A-A ATA ATA ATG ACA ATA ATA AT- TTA A-A CATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * *
1217750 TATA A-A AAA ATA ATA ATA A-A ACA A-A ATA A-A ATT ATA ATA ATA
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1217792 ATCA A-A ATA A-A AGTA ATTA A-A AGTA ATA ATA
1 AT-A ATA ATA ATA A-TA A-TA ATA A-TA ATA ATA
1217823 TTAAATTGAA
Statistics
Matches: 88, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
2 18 0.20
3 57 0.65
4 13 0.15
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:1218179 original size:81 final size:81
Alignment explanation
Indices: 1218044--1218297 Score: 382
Period size: 81 Copynumber: 3.1 Consensus size: 81
1218034 GTTTAGGGAC
*
1218044 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTAGCATAATTGACACTTTTCTGTCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTAGCATAATTGACACTTTTCTGCCAA
*
1218109 ATGCACAGCTAGGCCA
66 ATGCACAACTAGGCCA
* ** *
1218125 TTTATCTTTTACTCAACAGTCTTTAATTGTTCATCTAACTTGCATAATTGACACTTTTCTGCCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTAGCATAATTGACACTTTTCTGCCAA
*
1218190 ATGCACAACTAGGTCA
66 ATGCACAACTAGGCCA
* * * * * * *
1218206 GTTATCTTTTACTCAACGGTCTTTAACCATTTATGTAACTAGTATAATCGACACCTTTCTGCCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTAGCATAATTGACACTTTTCTGCCAA
1218271 ATGCACAACTAGGCCA
66 ATGCACAACTAGGCCA
1218287 TTTATCTTTTA
1 TTTATCTTTTA
1218298 TTTTAAACCA
Statistics
Matches: 153, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 153 1.00
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (81 bp):
TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTAGCATAATTGACACTTTTCTGCCAA
ATGCACAACTAGGCCA
Found at i:1218629 original size:55 final size:54
Alignment explanation
Indices: 1218504--1218697 Score: 221
Period size: 55 Copynumber: 3.6 Consensus size: 54
1218494 TTTCCCATGC
* * * * *
1218504 AGAAATACATACACTTAGTATGGATTTCTT-AGTTTGCACACATAGTGCCCATACA
1 AGAAATTCATACACTTAGTATGAATTTCTTAAATTTGAACACAAAGTG-CCATA-A
* * *
1218559 A-AAATTAAAACACTTAGTATGAATTTCTTAAATTTGAACACAAAGTGTCCTTAA
1 AGAAATTCATACACTTAGTATGAATTTCTTAAATTTGAACACAAAGTG-CCATAA
** *
1218613 AGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGAACACAAAGTGCTCATAC
1 AGAAATTCATACACTTAGTATGAATTTCTTAAATTTGAACACAAAGTGC-CATAA
* *
1218668 AGAAATTCATACACTTAGTCTGGATTTCTT
1 AGAAATTCATACACTTAGTATGAATTTCTT
1218698 TAGTCTTTGC
Statistics
Matches: 119, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
54 27 0.23
55 92 0.77
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (54 bp):
AGAAATTCATACACTTAGTATGAATTTCTTAAATTTGAACACAAAGTGCCATAA
Found at i:1219101 original size:19 final size:21
Alignment explanation
Indices: 1219060--1219103 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1219050 AACCCCCACC
*
1219060 ATGGTATCGATACTACTATATT
1 ATGGTATCGATACTAC-ACATT
1219082 ATGGTATCGATACT-C-CATT
1 ATGGTATCGATACTACACATT
1219101 ATG
1 ATG
1219104 ACACCGATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
21 1 0.05
22 14 0.67
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (21 bp):
ATGGTATCGATACTACACATT
Found at i:1219782 original size:21 final size:21
Alignment explanation
Indices: 1219731--1219783 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1219721 ATTATGACTA
*
1219731 TCGCAATTCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
** *
1219752 TCGCGTTGCGTTTTTCACAA-T
1 TCGCAATGCGATTTTC-CAATT
1219773 TCGCAATGCGA
1 TCGCAATGCGA
1219784 ATAAGTAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1219816 original size:21 final size:21
Alignment explanation
Indices: 1219773--1219826 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1219763 TTTTCACAAT
*
1219773 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
*
1219793 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1219814 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1219827 ACGTGAATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.39
21 19 0.61
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1220094 original size:20 final size:19
Alignment explanation
Indices: 1220056--1220117 Score: 79
Period size: 20 Copynumber: 3.2 Consensus size: 19
1220046 TCTCCGAAGA
**
1220056 TTCCCGTTGCGATAGTCAT
1 TTCCCGTTGCGATTTTCAT
1220075 TTCCGCGTTGCGATTTTCAT
1 TTCC-CGTTGCGATTTTCAT
*
1220095 TATCTCGTTGCGATTTTCAT
1 T-TCCCGTTGCGATTTTCAT
1220115 TTC
1 TTC
1220118 AACCAAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 6 0.16
20 30 0.79
21 2 0.05
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (19 bp):
TTCCCGTTGCGATTTTCAT
Found at i:1221821 original size:81 final size:81
Alignment explanation
Indices: 1221684--1222961 Score: 1594
Period size: 81 Copynumber: 15.8 Consensus size: 81
1221674 ATGGTAGTAT
* * * * *
1221684 CGTTCATCTAACTCGCATAATTGACACTTTTCATCCAAATGCACAACTAGGCCATTTATATTTTA
1 CGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTA
1221749 CTCAACGGTCTTTAAC
66 CTCAACGGTCTTTAAC
* * * *
1221765 CGTTCATATAACT-GCTATAATTGACACATTTCTTCCAAATGCACAGCTATGACATTTATCTTTT
1 CGTTCATCTAACTGGC-ATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTT
*
1221829 ACTCAACGGTATTTAAC
65 ACTCAACGGTCTTTAAC
* * * * *
1221846 CATTCATCTAACTCGCATAATTAACACCTTTCTGCCAAATGCACAGCTAGTCCATTTATCTTTTA
1 CGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTA
* *
1221911 CACAATGGTCTTTAAC
66 CTCAACGGTCTTTAAC
* * * * *
1221927 CGTTCATCTAACTGGAAAAATTGACACCTTTATGCCAAATGCACAGCTAGGTCATTTATCTTTTA
1 CGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTA
*
1221992 CTCAACGGTCTGTAAC
66 CTCAACGGTCTTTAAC
* * * *
1222008 CGTTCATCCAACGGGCATAATTGACACATTTCTTCCAAATGCATAGCTAGGCCATTTATCTTTTA
1 CGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTA
* **
1222073 CTTAACAATCTTTAAC
66 CTCAACGGTCTTTAAC
* * * *
1222089 CGTTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGCATAGCTAGGCCATTTATATTTTA
1 CGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTA
*
1222154 CTCAACGGTCTTTGAC
66 CTCAACGGTCTTTAAC
** * *
1222170 TATTCATCTAACTGGCATAATTGACACCTTTCTCCCAAATGCACAGTTAGGCCATTTATCTTTTA
1 CGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTA
*
1222235 CTCAATGGTCTTTAAC
66 CTCAACGGTCTTTAAC
* *
1222251 CATTCATCTAACTGGCATAATTGACACATTTCTGT-CAAATGCACAGCTAGGCCATTTATCTTTT
1 CGTTCATCTAACTGGCATAATTGACACCTTTCT-TCCAAATGCACAGCTAGGCCATTTATCTTTT
* *
1222315 ATTCAACGTTCTTTAAC
65 ACTCAACGGTCTTTAAC
* * * * *
1222332 CGTTCATCTAACTGGCATAATTGACACCTTTATACCAAATACACAACTAGGTCATTTATCTTTTA
1 CGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTA
* *
1222397 CTCAACAGTCTTTAGC
66 CTCAACGGTCTTTAAC
** * * *
1222413 CGTTCATCTAACTAACATAATTGACACCTTT-TGCCAAATGCACAGCTATGCCATTTATCTTTTT
1 CGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTA
* *
1222477 CTCAATGATCTTTAAC
66 CTCAACGGTCTTTAAC
* ** *** *
1222493 CATTCATCTAACTAACATAATTGACTTATTTCTGT-CAAATGCATAGCTAGGCCATTTATCTTTT
1 CGTTCATCTAACTGGCATAATTGACACCTTTCT-TCCAAATGCACAGCTAGGCCATTTATCTTTT
1222557 ACTCAACGGTCTTTAAC
65 ACTCAACGGTCTTTAAC
* * * * *
1222574 CGTTCATCTAACTGGAATAATTAACA-CTATTCTGCCAAATGCATAGCTAGGCCATTTATCTTTA
1 CGTTCATCTAACTGGCATAATTGACACCT-TTCTTCCAAATGCACAGCTAGGCCATTTATCTTTT
1222638 ACTCAACGGTCTTTAAC
65 ACTCAACGGTCTTTAAC
* * *
1222655 CATTCATCTAACTGGAATAATTGACACCTTTTTTCCAAATGCACAGCTAGGCCATTTATCTTTTA
1 CGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTA
1222720 CTCAACGGTCTTTAAC
66 CTCAACGGTCTTTAAC
* * * * * * * * *
1222736 CGTTCATCTAACTGACACAATTGATACATTACTGCCAAATGCAAAACTATGCCATTTATCTTTTA
1 CGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTA
1222801 CTCAACGGTCTTTAAC
66 CTCAACGGTCTTTAAC
* * * * * *
1222817 TGTTCATCTAACTGACATAATTGACACTTTTTTTCCAACTGCACAACTAGGCCATTTATCTTTTA
1 CGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTA
* *
1222882 CTCAACAGTCATTAAC
66 CTCAACGGTCTTTAAC
* * * * * * * * *
1222898 CATTCATATCACTGGCATAATTGACACATTTCTGCAAAAGGCAGAGGTAGGCCATTTATCTTTT
1 CGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTT
1222962 GTTTTAGACC
Statistics
Matches: 1033, Mismatches: 155, Indels: 18
0.86 0.13 0.01
Matches are distributed among these distances:
80 69 0.07
81 960 0.93
82 4 0.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (81 bp):
CGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGCTAGGCCATTTATCTTTTA
CTCAACGGTCTTTAAC
Found at i:1223359 original size:55 final size:55
Alignment explanation
Indices: 1223162--1223368 Score: 269
Period size: 54 Copynumber: 3.8 Consensus size: 55
1223152 ACATTTATTT
* *
1223162 CCCATACAAAAATTCATACACTTAGTAT-AGATTTCTTAG-TTTGCACACATAGTG
1 CCCATACAGAAATTCATACACTTAGTATGA-ATTTCTTAGTTTTGCACACAAAGTG
* *
1223216 CCCATAC-GATAATTCATATACTTAGTATGAATTTTTTAGTTTTGCACACAAAGTG
1 CCCATACAGA-AATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTG
* *
1223271 -CCATACATAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACAAAAAGTG
1 CCCATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTG
* * * *
1223325 CCCATACGGAAATTCATACACTTAATGTGGATTTCTTACGTTTT
1 CCCATACAGAAATTCATACACTTAGTATGAATTTCTTA-GTTTT
1223369 TTCACGCTTA
Statistics
Matches: 134, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
53 1 0.01
54 80 0.60
55 48 0.36
56 5 0.04
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (55 bp):
CCCATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTG
Found at i:1228069 original size:12 final size:13
Alignment explanation
Indices: 1228052--1228084 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1228042 TATTCACCTA
1228052 AATTTGATTC-TG
1 AATTTGATTCTTG
1228064 AATTTGATTCTTG
1 AATTTGATTCTTG
1228077 -ATTTGATT
1 AATTTGATT
1228085 GTTGTCTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 18 0.90
13 2 0.10
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.55
Consensus pattern (13 bp):
AATTTGATTCTTG
Found at i:1228426 original size:20 final size:18
Alignment explanation
Indices: 1228401--1228440 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
1228391 GGATTTTGGT
1228401 AAAATGAGATTAAATAATAA
1 AAAATGA-ATTAAATAA-AA
*
1228421 AAAATGATTTAAATAAAA
1 AAAATGAATTAAATAAAA
1228439 AA
1 AA
1228441 TAAAGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 8 0.42
20 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (18 bp):
AAAATGAATTAAATAAAA
Found at i:1229346 original size:27 final size:26
Alignment explanation
Indices: 1229304--1229357 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
1229294 TTCCAGAAGG
* *
1229304 CGCTGACTAGATCTTCTAGAAAATTAT
1 CGCTGACTAGACCTTCTA-AAAACTAT
*
1229331 CGCTGACTGGACCTTCTAAAAACTAT
1 CGCTGACTAGACCTTCTAAAAACTAT
1229357 C
1 C
1229358 ACGTCAGACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (26 bp):
CGCTGACTAGACCTTCTAAAAACTAT
Found at i:1229922 original size:2 final size:2
Alignment explanation
Indices: 1229915--1229960 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1229905 AAAGTATTTG
1229915 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1229957 AT AT
1 AT AT
1229961 GTGCATGGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1230109 original size:49 final size:49
Alignment explanation
Indices: 1230015--1230287 Score: 350
Period size: 49 Copynumber: 5.5 Consensus size: 49
1230005 TCTATAATAA
* *
1230015 AAGTTAAATGGAAAATGGTGCA-TTTTTGCAGAAAGGTGCCACTAATGC
1 AAGTTAAATGCATAATGGTGCATTTTTTGCAGAAAGGTGCCACTAATGC
* *
1230063 AAGTTAAATGCATAATGGTGCATTTTTTGTAGAAAGGTGCCACTAATGAAAA
1 AAGTTAAATGCATAATGGTGCATTTTTTGCAGAAAGGTGCCACTAATG---C
* * * *
1230115 AAGTTAAATACAAAATGGTGCATTTTTTGCAAAAATGTGCCACTAATGC
1 AAGTTAAATGCATAATGGTGCATTTTTTGCAGAAAGGTGCCACTAATGC
* *
1230164 AAGTTAAATGCATAATGGTGTATTTTTTACAGAAAGGTGCCACTAATGC
1 AAGTTAAATGCATAATGGTGCATTTTTTGCAGAAAGGTGCCACTAATGC
* * * * * *
1230213 AAGTTAAACGCTTAAAGGAGCATTTTTGGCAAAAAGGTGCCACTAATGC
1 AAGTTAAATGCATAATGGTGCATTTTTTGCAGAAAGGTGCCACTAATGC
* *
1230262 AAGTTAAATGCATAACGATGCATTTT
1 AAGTTAAATGCATAATGGTGCATTTT
1230288 GACATAAAAG
Statistics
Matches: 192, Mismatches: 29, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
48 20 0.10
49 129 0.67
52 43 0.22
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (49 bp):
AAGTTAAATGCATAATGGTGCATTTTTTGCAGAAAGGTGCCACTAATGC
Found at i:1230189 original size:101 final size:99
Alignment explanation
Indices: 1230009--1230287 Score: 377
Period size: 101 Copynumber: 2.8 Consensus size: 99
1229999 AACTGCTCTA
* *
1230009 TAAT-AAAAGTTAAATGGAAAATGGTGCA-TTTTTGCAGAAAGGTGCCACTAATGCAAGTTAAAT
1 TAATGAAAAGTTAAATGCAAAATGGTGCATTTTTTGCAAAAAGGTGCCACTAATGCAAGTTAAAT
**
1230072 GCATAATGGTGCATTTTTTGTAGAAAGGTGCCAC
66 GCATAATGGTGCATTTTTTACAGAAAGGTGCCAC
* *
1230106 TAATGAAAAAAGTTAAATACAAAATGGTGCATTTTTTGCAAAAATGTGCCACTAATGCAAGTTAA
1 TAATG--AAAAGTTAAATGCAAAATGGTGCATTTTTTGCAAAAAGGTGCCACTAATGCAAGTTAA
*
1230171 ATGCATAATGGTGTATTTTTTACAGAAAGGTGCCAC
64 ATGCATAATGGTGCATTTTTTACAGAAAGGTGCCAC
* * * * *
1230207 TAATG-CAAGTTAAACGCTTAAA-GGAGCATTTTTGGCAAAAAGGTGCCACTAATGCAAGTTAAA
1 TAATGAAAAGTTAAATGC-AAAATGGTGCATTTTTTGCAAAAAGGTGCCACTAATGCAAGTTAAA
* *
1230270 TGCATAACGATGCATTTT
65 TGCATAATGGTGCATTTT
1230288 GACATAAAAG
Statistics
Matches: 160, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
97 4 0.03
98 62 0.39
99 3 0.02
100 22 0.14
101 69 0.43
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (99 bp):
TAATGAAAAGTTAAATGCAAAATGGTGCATTTTTTGCAAAAAGGTGCCACTAATGCAAGTTAAAT
GCATAATGGTGCATTTTTTACAGAAAGGTGCCAC
Found at i:1231673 original size:21 final size:20
Alignment explanation
Indices: 1231626--1231677 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 20
1231616 TTCTAGCTGA
1231626 GAGTATCGATACTACTAGGG
1 GAGTATCGATACTACTAGGG
*
1231646 GAGTATCGATACTACTGGGG
1 GAGTATCGATACTACTAGGG
1231666 GAAGTATCGATA
1 G-AGTATCGATA
1231678 TTGTCCCTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (20 bp):
GAGTATCGATACTACTAGGG
Found at i:1233622 original size:47 final size:44
Alignment explanation
Indices: 1233551--1233676 Score: 144
Period size: 47 Copynumber: 2.8 Consensus size: 44
1233541 TATAAAATCT
**
1233551 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCA-TTATTACATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1233596 CTTACCATTTAAATTACATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCA-TT--ATTACATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
1233643 CTTGCCATTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTATTACATAAGCTCGTAAGCTTATTT
1233677 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 37 0.52
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (44 bp):
CTTACCATTATTACATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1238711 original size:6 final size:6
Alignment explanation
Indices: 1238700--1238724 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1238690 ACATTTGTAT
1238700 CATGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC C
1238725 TATGGGTCTT
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:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:1240680 original size:40 final size:40
Alignment explanation
Indices: 1240636--1240717 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
1240626 ACCGTAGTGC
*
1240636 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1240676 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1240716 TA
1 TA
1240718 TAAACCTGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:1247273 original size:47 final size:44
Alignment explanation
Indices: 1247202--1247327 Score: 144
Period size: 47 Copynumber: 2.8 Consensus size: 44
1247192 TATAAAATCT
**
1247202 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCA-TTATTACATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1247247 CTTACCATTTAAATTACATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCA-TT--ATTACATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
1247294 CTTGCCATTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTATTACATAAGCTCGTAAGCTTATTT
1247328 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 37 0.52
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (44 bp):
CTTACCATTATTACATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1270533 original size:44 final size:44
Alignment explanation
Indices: 1270483--1270582 Score: 155
Period size: 44 Copynumber: 2.3 Consensus size: 44
1270473 GCAACCCAAC
* * * *
1270483 AGTATCGATACCCTTCAAGGAGTATCGATACTACTATGTGTTGT
1 AGTATCGATACCATCCAAGGAGTATCGATACTACTATGTATAGT
*
1270527 AGTATCGATACTATCCAAGGAGTATCGATACTACTATGTATAGT
1 AGTATCGATACCATCCAAGGAGTATCGATACTACTATGTATAGT
1270571 AGTATCGATACC
1 AGTATCGATACC
1270583 GAACATGGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (44 bp):
AGTATCGATACCATCCAAGGAGTATCGATACTACTATGTATAGT
Found at i:1270535 original size:24 final size:23
Alignment explanation
Indices: 1270503--1270581 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 23
1270493 CCCTTCAAGG
1270503 AGTATCGATACTACTATGTGTTGT
1 AGTATCGATACTACTATGTG-TGT
* *
1270527 AGTATCGATACTATCCA--AG-G-
1 AGTATCGATACTA-CTATGTGTGT
*
1270547 AGTATCGATACTACTATGTATAGT
1 AGTATCGATACTACTATGTGT-GT
1270571 AGTATCGATAC
1 AGTATCGATAC
1270582 CGAACATGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 1 0.02
23 2 0.05
24 24 0.55
25 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (23 bp):
AGTATCGATACTACTATGTGTGT
Found at i:1274170 original size:39 final size:39
Alignment explanation
Indices: 1274107--1274237 Score: 190
Period size: 39 Copynumber: 3.4 Consensus size: 39
1274097 GATTCATATG
* * * *
1274107 TATGCACCGTAGTGCTTAAACATAAGTTCGTGCCCATCA
1 TATGCACCGAAGTGCTTACACATAAGGTCGTGCCCACCA
* * *
1274146 TATGCACCGAAGTACTTACGCATAAGGTCATGCCCACCA
1 TATGCACCGAAGTGCTTACACATAAGGTCGTGCCCACCA
1274185 TATGCACCGAAGTGCTTACACATAAGGTCGTGCCCACCA
1 TATGCACCGAAGTGCTTACACATAAGGTCGTGCCCACCA
*
1274224 AATGCACCGAAGTG
1 TATGCACCGAAGTG
1274238 TTTAATCGAT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (39 bp):
TATGCACCGAAGTGCTTACACATAAGGTCGTGCCCACCA
Found at i:1274415 original size:22 final size:22
Alignment explanation
Indices: 1274390--1274432 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1274380 CTAAATATCA
* *
1274390 TTCATGATAAATATCGTATATG
1 TTCATGATAAACATCATATATG
1274412 TTCATGATAAACATCATATAT
1 TTCATGATAAACATCATATAT
1274433 AACGATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (22 bp):
TTCATGATAAACATCATATATG
Found at i:1280792 original size:59 final size:59
Alignment explanation
Indices: 1280700--1280820 Score: 179
Period size: 59 Copynumber: 2.1 Consensus size: 59
1280690 GTAGGGTTGG
* * * * *
1280700 TTAGAGTCATATTATCTAGTTTTCCTTTTCATTGCGACTAGGAGGGTTCGATAGGTCAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCAATAGGACAC
* *
1280759 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGTGACTATGAGGGTTCAATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCAATAGGACAC
1280818 TTA
1 TTA
1280821 TCCATCTATT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCAATAGGACAC
Found at i:1283737 original size:193 final size:193
Alignment explanation
Indices: 1283406--1283778 Score: 570
Period size: 193 Copynumber: 1.9 Consensus size: 193
1283396 GCACTATTAG
* * *
1283406 GAAGGTTCTGCAGTCCACAAATCTCCTCCTGATAATTCTTAATTCATGAACCACACTTAGAAGAA
1 GAAGGTTCTGCAGTCCAAAAATCTCCTCCCGAGAATTCTTAATTCATGAACCACACTTAGAAGAA
* *
1283471 TTAAGAGATTACTTTAACAAACTAGTTGACATGGTTTTTCAACACTCATTCTCGCCACACACTAG
66 TTAAGAGATTACTTTAACAAACCAGTTGACATGGTTTTTCAACACTCATTCTCGCCACACACAAG
* * *
1283536 TTAAACCAT-GAAGAGAATATTTGAAGCAATCATAAAGAAAGACAATAGTAACTGGCAGTCCAC
131 TCAAACCATCG-AGAGAATATATGAAGCAATCATAAAGAAAGACAACAGTAACTGGCAGTCCAC
** *
1283599 GAAGGTTCTGTGGTCTAAAAATCTCCTCCCGAGAATTCTTAATTCATGAACCACACTTAGGAA-A
1 GAAGGTTCTGCAGTCCAAAAATCTCCTCCCGAGAATTCTTAATTCATGAACCACACTTA-GAAGA
* *
1283663 CTTAAGGGATTACTTTAACAAACCAGTTGACATGGTTTTTCAACACTCATTCTCGCCACACACAA
65 ATTAAGAGATTACTTTAACAAACCAGTTGACATGGTTTTTCAACACTCATTCTCGCCACACACAA
* * *
1283728 GTCAAACCATCGAGAGAATATATGAGGTAATCATAAAGAAAGCCAACAGTA
130 GTCAAACCATCGAGAGAATATATGAAGCAATCATAAAGAAAGACAACAGTA
1283779 GCAGGCGCCA
Statistics
Matches: 162, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
193 158 0.98
194 4 0.02
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.26
Consensus pattern (193 bp):
GAAGGTTCTGCAGTCCAAAAATCTCCTCCCGAGAATTCTTAATTCATGAACCACACTTAGAAGAA
TTAAGAGATTACTTTAACAAACCAGTTGACATGGTTTTTCAACACTCATTCTCGCCACACACAAG
TCAAACCATCGAGAGAATATATGAAGCAATCATAAAGAAAGACAACAGTAACTGGCAGTCCAC
Found at i:1284509 original size:487 final size:487
Alignment explanation
Indices: 1283595--1284540 Score: 1468
Period size: 487 Copynumber: 1.9 Consensus size: 487
1283585 AACTGGCAGT
* * * * *
1283595 CCACGAAGGTTCTGTGGTCTAAAAATCTCCTCCCGAGAATTCTTAATTCATGAACCACACTTAGG
1 CCACGAAGGTTCTGTAGTCCAAAAATCTCCTCCCGAGAAATATTAATTCATGAACCACACTTAAG
* * *
1283660 AAACTTAAGGGATTACTTTAACAAACCAGTTGACATGGTTTTTCAACACTCATTCTCGCCACACA
66 AAACTTAAGGGATTACTTTAACAAACCAATCGACATGGTTTTTCAACACTCATTCTCGCCACAAA
* * * * *
1283725 CAAGTCAAACCATCGAGAGAATATATGAGGTAATCATAAAGAAAGCCAACAGTAGCAGGCGCCAT
131 CAAGTCAAACCATCAAGAGAATATATGAAGCAATCATAAAGAAAACCAACAGTAGCAGACGCCAT
* * *
1283790 GTTGAATTTCAACCTAAACATCAGATTACAAGACTTTTATGCAAAAGAGTATTTCAAGACTACAA
196 GTTGAATTTCAACCTAAACATCAGATTACAAGACTTTTATGCAAAAGAGGATTTAAAGAATACAA
* *
1283855 GAAATCAGTCCCTACAAAGAAGAAACCTCGACTAAAATGAATAAAGACACATCACATTGATCCTA
261 GAAATCAATCCCTACAAAGAAGAAACCTCGACTAAAATCAATAAAGACACATCACATTGATCCTA
* *
1283920 GTAAATGTTTCACAAGTTTTCCTTTCAACACGTCTAATTCTCTTTCTCTTATATTTTCAGATTCG
326 GTAAATGTTTCACAAGTTTTCCTTTCAACACATCTAATTCTCTTTCTCTTAGATTTTCAGATTCG
* * *
1283985 ATGAGAAATTCTTTTGAGGAGTGGGTGAATAATACATGCACTAGAGTCCATAATACATGTTTCTT
391 AGGAGAAATTCTTTTGAGGAGTGGGTGAATAATACATGCACCAGAGTCCATAATACATGCTTCTT
1284050 TGGATTTACTTTAACACTTAGATGATGCACTA
456 TGGATTTACTTTAACACTTAGATGATGCACTA
1284082 CCACGAAGGTTCTGTAGTCCAAAAATCTCCTCCC-ATGAAATATTAATTCATGAACCACACTTAA
1 CCACGAAGGTTCTGTAGTCCAAAAATCTCCTCCCGA-GAAATATTAATTCATGAACCACACTTAA
* * *
1284146 GAGACTTAAGGGATTACTTTAACAAACCAATCGACATGGTTTTTCAACACTTATTCTTGCCACAA
65 GAAACTTAAGGGATTACTTTAACAAACCAATCGACATGGTTTTTCAACACTCATTCTCGCCACAA
* * *
1284211 ACAAGTCAAACCATCAAGATAATATCTGAAGCAATCATAAAGAAAACCAACAGTAGCTGACGCCA
130 ACAAGTCAAACCATCAAGAGAATATATGAAGCAATCATAAAGAAAACCAACAGTAGCAGACGCCA
*
1284276 TGTTGAATTTCAACCTAAACATCATATTACAAGACTTTTATGCAAAAGAGGATTTAAAGAATACA
195 TGTTGAATTTCAACCTAAACATCAGATTACAAGACTTTTATGCAAAAGAGGATTTAAAGAATACA
* * *
1284341 ATAAATCAATCCGTACAAATAAGAAACCTCGACTAAAA-CACATAAAGACACATCACATTGATCC
260 AGAAATCAATCCCTACAAAGAAGAAACCTCGACTAAAATCA-ATAAAGACACATCACATTGATCC
* * * *
1284405 TGGTAAATGTTTCACAAGTTTTCCTTTCAACACATTTAATTCTCTTTCTCTTGGATTTTTAGATT
324 TAGTAAATGTTTCACAAGTTTTCCTTTCAACACATCTAATTCTCTTTCTCTTAGATTTTCAGATT
* * *
1284470 CGAGGATG-AATTCTTTTGAGGAGTGGG-GAAATGATACATGCACCAGAGTTCATAATACTTGCT
389 CGAGGA-GAAATTCTTTTGAGGAGTGGGTG-AATAATACATGCACCAGAGTCCATAATACATGCT
1284533 TCTTTGGA
452 TCTTTGGA
1284541 CTAATGTTTC
Statistics
Matches: 415, Mismatches: 40, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
486 3 0.01
487 411 0.99
488 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (487 bp):
CCACGAAGGTTCTGTAGTCCAAAAATCTCCTCCCGAGAAATATTAATTCATGAACCACACTTAAG
AAACTTAAGGGATTACTTTAACAAACCAATCGACATGGTTTTTCAACACTCATTCTCGCCACAAA
CAAGTCAAACCATCAAGAGAATATATGAAGCAATCATAAAGAAAACCAACAGTAGCAGACGCCAT
GTTGAATTTCAACCTAAACATCAGATTACAAGACTTTTATGCAAAAGAGGATTTAAAGAATACAA
GAAATCAATCCCTACAAAGAAGAAACCTCGACTAAAATCAATAAAGACACATCACATTGATCCTA
GTAAATGTTTCACAAGTTTTCCTTTCAACACATCTAATTCTCTTTCTCTTAGATTTTCAGATTCG
AGGAGAAATTCTTTTGAGGAGTGGGTGAATAATACATGCACCAGAGTCCATAATACATGCTTCTT
TGGATTTACTTTAACACTTAGATGATGCACTA
Found at i:1285490 original size:59 final size:59
Alignment explanation
Indices: 1285394--1285511 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 59
1285384 AGAGTTTTTC
* * * * * *
1285394 AGAGCCATATTATTGATTTTTCTTTTTCATTACGACTAAGAGTGTTCAATAGGATACTT
1 AGAGCCATATTATCGAGTTTGCCTTTTCATTACGACTAAGAGGGTTCAATAGGACACTT
** * *
1285453 AGAGCCATATTATCGAGTTTGCCTTTTCATTGTGACTAGGAGGGTTCGATAGGACACTT
1 AGAGCCATATTATCGAGTTTGCCTTTTCATTACGACTAAGAGGGTTCAATAGGACACTT
1285512 TTCCATCTAG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (59 bp):
AGAGCCATATTATCGAGTTTGCCTTTTCATTACGACTAAGAGGGTTCAATAGGACACTT
Found at i:1290857 original size:10 final size:10
Alignment explanation
Indices: 1290822--1290859 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1290812 TATATATTTT
1290822 AATAT-TATA
1 AATATATATA
* *
1290831 TATATACATA
1 AATATATATA
1290841 AATATATATA
1 AATATATATA
1290851 AATATATAT
1 AATATATAT
1290860 GTATGATGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATATATA
Found at i:1291944 original size:10 final size:11
Alignment explanation
Indices: 1291929--1291971 Score: 54
Period size: 10 Copynumber: 4.0 Consensus size: 11
1291919 TTATTGATTG
1291929 AAATTAAAAA-
1 AAATTAAAAAT
1291939 AAATTAAAAAT
1 AAATTAAAAAT
*
1291950 ATATTGAAAAAT
1 AAATT-AAAAAT
1291962 AAA-TAAAAAT
1 AAATTAAAAAT
1291972 TAATATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 16 0.55
11 5 0.17
12 8 0.28
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (11 bp):
AAATTAAAAAT
Found at i:1291982 original size:28 final size:28
Alignment explanation
Indices: 1291915--1291990 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
1291905 TACATATGTA
* *
1291915 TAAATTATTGATTG-AAATTAAAAAAAAT
1 TAAA-TATTTATTGAAAAATAAAAAAAAT
* *
1291943 TAAAAATATATTGAAAAATAAATAAAAAT
1 TAAATATTTATTGAAAAATAAA-AAAAAT
*
1291972 T-AATATTTATTCAAAAATA
1 TAAATATTTATTGAAAAATA
1291991 TCTTTTATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 6 0.15
28 26 0.67
29 7 0.18
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (28 bp):
TAAATATTTATTGAAAAATAAAAAAAAT
Found at i:1294523 original size:14 final size:14
Alignment explanation
Indices: 1294501--1294550 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1294491 AACCCATACT
1294501 GAGTCAACTCGTCC
1 GAGTCAACTCGTCC
*
1294515 GAGTTAACTCGTCC
1 GAGTCAACTCGTCC
* *
1294529 -ATGTCAACTCATCT
1 GA-GTCAACTCGTCC
1294543 GAGTCAAC
1 GAGTCAAC
1294551 CTGTTAACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 1 0.03
14 28 0.93
15 1 0.03
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (14 bp):
GAGTCAACTCGTCC
Found at i:1300440 original size:138 final size:138
Alignment explanation
Indices: 1300192--1300469 Score: 556
Period size: 138 Copynumber: 2.0 Consensus size: 138
1300182 CTGAAAGATT
1300192 TGAGTGGAATGACGATGATACGCTTAAAGTGTAAAAAACACAATGGATGGCTATGATAATGAAGA
1 TGAGTGGAATGACGATGATACGCTTAAAGTGTAAAAAACACAATGGATGGCTATGATAATGAAGA
1300257 CGACCTGAGAAATCTTATTTTGATCTACTTGAACCTTGGAATCATCGATTTAACATCCGGATCTA
66 CGACCTGAGAAATCTTATTTTGATCTACTTGAACCTTGGAATCATCGATTTAACATCCGGATCTA
1300322 TATTAAAA
131 TATTAAAA
1300330 TGAGTGGAATGACGATGATACGCTTAAAGTGTAAAAAACACAATGGATGGCTATGATAATGAAGA
1 TGAGTGGAATGACGATGATACGCTTAAAGTGTAAAAAACACAATGGATGGCTATGATAATGAAGA
1300395 CGACCTGAGAAATCTTATTTTGATCTACTTGAACCTTGGAATCATCGATTTAACATCCGGATCTA
66 CGACCTGAGAAATCTTATTTTGATCTACTTGAACCTTGGAATCATCGATTTAACATCCGGATCTA
1300460 TATTAAAA
131 TATTAAAA
1300468 TG
1 TG
1300470 CCCCTGAAAT
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 140 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (138 bp):
TGAGTGGAATGACGATGATACGCTTAAAGTGTAAAAAACACAATGGATGGCTATGATAATGAAGA
CGACCTGAGAAATCTTATTTTGATCTACTTGAACCTTGGAATCATCGATTTAACATCCGGATCTA
TATTAAAA
Found at i:1304592 original size:24 final size:24
Alignment explanation
Indices: 1304565--1304659 Score: 111
Period size: 24 Copynumber: 4.0 Consensus size: 24
1304555 AAACGAATAT
*
1304565 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCATAACAGAATTCAG
* * *
1304589 ATCAGATATCATAATAGAATCCAG
1 ATCAGAAATCATAACAGAATTCAG
*
1304613 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCATAACAGAATTCAG
* *
1304637 GTCATG-TATCATAACAGAATTCA
1 ATCA-GAAATCATAACAGAATTCA
1304660 AGTCGAAAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 58 0.98
25 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCATAACAGAATTCAG
Found at i:1304636 original size:48 final size:48
Alignment explanation
Indices: 1304565--1304656 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
1304555 AAACGAATAT
*
1304565 ATCAGAAATCAAAACAGAATTCAGATCA-GATATCATAATAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGATCATG-TATCATAACAGAATCCAG
* *
1304613 ATCAGAAATCAGAACAGAATTCAGGTCATGTATCATAACAGAAT
1 ATCAGAAATCAAAACAGAATTCAGATCATGTATCATAACAGAAT
1304657 TCAAGTCGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATCATGTATCATAACAGAATCCAG
Found at i:1304671 original size:24 final size:24
Alignment explanation
Indices: 1304570--1304673 Score: 70
Period size: 24 Copynumber: 4.3 Consensus size: 24
1304560 AATATATCAG
* *
1304570 AAATCAAAACAGAATTC-AGATCAG
1 AAATCATAACAGAATTCAAG-TCAT
* * * *
1304594 ATATCATAATAGAA-TCCAGATCAG
1 AAATCATAACAGAATTCAAG-TCAT
* *
1304618 AAATCAGAACAGAATTCAGGTCAT
1 AAATCATAACAGAATTCAAGTCAT
**
1304642 GTATCATAACAGAATTCAAGTCGA-
1 AAATCATAACAGAATTCAAGTC-AT
1304666 AAATCATA
1 AAATCATA
1304674 TAAAATATTT
Statistics
Matches: 62, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
23 2 0.03
24 56 0.90
25 4 0.06
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.22
Consensus pattern (24 bp):
AAATCATAACAGAATTCAAGTCAT
Found at i:1309100 original size:24 final size:24
Alignment explanation
Indices: 1309063--1309157 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
1309053 AAATGGAGAT
* *
1309063 ATCATAAATAATAACAGAATTCAG
1 ATCATAAATCAGAACAGAATTCAG
* * *
1309087 ATCATATATCATAACAGAATCCAG
1 ATCATAAATCAGAACAGAATTCAG
*
1309111 ATCA-AAAGTTAGAACAGAATTCAG
1 ATCATAAA-TCAGAACAGAATTCAG
* **
1309135 GTCATGTATCAGAACAGAATTCA
1 ATCATAAATCAGAACAGAATTCA
1309158 AGTCGAAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
23 2 0.03
24 55 0.95
25 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCATAAATCAGAACAGAATTCAG
Found at i:1309533 original size:27 final size:27
Alignment explanation
Indices: 1309495--1309553 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
1309485 TTTTATTCAT
*
1309495 AGATCATCTTCGGAATCATCACTGAAA
1 AGATCATCTTCGAAATCATCACTGAAA
* *
1309522 AGATCATCTTCGAAATCATCAGTGAAT
1 AGATCATCTTCGAAATCATCACTGAAA
1309549 AGATC
1 AGATC
1309554 TTAAGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (27 bp):
AGATCATCTTCGAAATCATCACTGAAA
Found at i:1314222 original size:18 final size:19
Alignment explanation
Indices: 1314187--1314222 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1314177 TTTCTTTAGA
*
1314187 TTAATATAATATTTTCATT
1 TTAATATAATATTGTCATT
1314206 TTAATAT-ATATTGTCAT
1 TTAATATAATATTGTCAT
1314223 ATTATGGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (19 bp):
TTAATATAATATTGTCATT
Found at i:1317096 original size:137 final size:141
Alignment explanation
Indices: 1316908--1317162 Score: 360
Period size: 137 Copynumber: 1.8 Consensus size: 141
1316898 ATTGTAAGAA
* * *
1316908 AATATATTAATTTATATATATTAATAAGATATTTATTTATTTAAAAATATCAGAAAA-GGGCTTC
1 AATATATTAATTTATATAAATTAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATC
* * * *
1316972 TAGGTGCTTTAAGACAGCTCTTTTTTTAATATTAAAAAATAAATAAAT-ATTAATAAAAATAATT
66 CAGGTGCTTTAAGACAG-TCATTTCTTAATATTAAAAAATAAAAAAATAATTAATAAAAATAATT
1317036 AAAAAATAGATT
130 AAAAAATAGATT
1317048 AATATATATAATTTATA-AAATT-A-AA-ATATTTATTTATTTAAAAATATCAGAAAATGGACAT
1 AATATAT-TAATTTATATAAATTAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACAT
* * *
1317109 CCAGTTGCTTTAAGACTGTCATTTCTTAATATTGAAAAATAAAAAAATAATTAA
65 CCAGGTGCTTTAAGACAGTCATTTCTTAATATTAAAAAATAAAAAAATAATTAA
1317163 AATATGATTA
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
137 55 0.54
138 26 0.25
139 1 0.01
140 11 0.11
141 9 0.09
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.38
Consensus pattern (141 bp):
AATATATTAATTTATATAAATTAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATC
CAGGTGCTTTAAGACAGTCATTTCTTAATATTAAAAAATAAAAAAATAATTAATAAAAATAATTA
AAAAATAGATT
Found at i:1318979 original size:123 final size:124
Alignment explanation
Indices: 1318842--1319275 Score: 463
Period size: 123 Copynumber: 3.6 Consensus size: 124
1318832 AAATTAAGGC
*
1318842 AAGGTTGAACAAATTCTTCTCATTATGAACTTCCTCTTCTTCTTTAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTTAGATGAGTTCTTCTCATTAT
* *
1318907 GAACTCTTTTTGGAAATGTTGATGTTGATCTATCT-CTTTCTGTGATAGCA-TCGA-GC-AA
66 GAACTCTTTATGGAAATGTTGATGCTGATCTATCTCCTTT-TGTGATAG-AGTC-ATGCAAA
* * * *
1318965 AAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGCTCTTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTTAGATGAGTTCTTCTCATTAT
* * *
1319030 AAACT-TCATATGGAAATGTTGGTGCTGATCTATCTCCTTTTGTGATAGAGTCATGCAAAA
66 GAACTCT-TTATGGAAATGTTGATGCTGATCTATCTCCTTTTGTGATAGAGTCATGC-AAA
** *
1319090 AAAATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTTAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTTAGATGAGTTCTTCTCATTAT
* * * * * * **
1319155 GAACACTTCTCTGGAAAAGTTGAT-CCG-TCGA---------GTGAT-GAATTCAAACAAA
66 GAACTCTT-TATGGAAATGTTGATGCTGATCTATCTCCTTTTGTGATAG-AGTCATGCAAA
* *
1319204 AA-GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTTAGATGAGTTCTTCTCATTA
1319268 TGAACTCT
65 TGAACTCT
1319276 ACCTGGTAAT
Statistics
Matches: 268, Mismatches: 33, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
113 32 0.12
114 38 0.14
115 10 0.04
122 3 0.01
123 100 0.37
124 7 0.03
125 65 0.24
126 13 0.05
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (124 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTTAGATGAGTTCTTCTCATTAT
GAACTCTTTATGGAAATGTTGATGCTGATCTATCTCCTTTTGTGATAGAGTCATGCAAA
Found at i:1319212 original size:113 final size:114
Alignment explanation
Indices: 1319094--1319957 Score: 1233
Period size: 113 Copynumber: 7.6 Consensus size: 114
1319084 GCAAAAAAAA
*
1319094 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTTAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
1319158 CACTTCTCTGGAAAAGTTGATCCGTCGAGTGATGAATTCAAACAAAAAG
66 CTCTTCTCTGGCAATGTTGATCCATCGAGTGATGAATTCAAACAAAAGG
* *
1319207 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
1319272 CTCTAC-CTGGTAATGTTGATCCATCAAATGATGAATTCAAACAAAAGG
66 CTCTTCTCTGGCAATGTTGATCCATCGAGTGATGAATTCAAACAAAAGG
* *
1319320 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATAAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
1319385 CT-TTCTCTGGCAATGCTAATCCATCGGGTGATGAATT-AAAGCAAAAGA
66 CTCTTCTCTGGCAATGTTGATCCATCGAGTGATGAATTCAAA-CAAAAGG
*
1319433 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * * *
1319498 CTCTAC-CTGGTAATATTGATCCATCAAATGATGAATTTAAACAAAAGG
66 CTCTTCTCTGGCAATGTTGATCCATCGAGTGATGAATTCAAACAAAAGG
* *
1319546 TTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
1319611 CTTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATT-AAAGCAAAAGG
66 CTCTTCTCTGGCAATGTTGATCCATCGAGTGATGAATTCAAA-CAAAAGG
*
1319660 TTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * * *
1319725 CTATAC-CTGGTAATGCTGATCCATCAAATGATGAATTCAAACAAAAGG
66 CTCTTCTCTGGCAATGTTGATCCATCGAGTGATGAATTCAAACAAAAGG
* *
1319773 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTTATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
1319838 CT-TTCTCTGGCAATGTTAATCCATCGGGTGATGAATT-AAAGCAAAAGG
66 CTCTTCTCTGGCAATGTTGATCCATCGAGTGATGAATTCAAA-CAAAAGG
* * *
1319886 TTGAACAAGATCTTCTCATTATGAACTTCTTCTTCATTCTTTAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1319951 CTCTTCT
66 CTCTTCT
1319958 GGAAATATTG
Statistics
Matches: 668, Mismatches: 72, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
112 10 0.01
113 516 0.77
114 142 0.21
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (114 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTCTTCTCTGGCAATGTTGATCCATCGAGTGATGAATTCAAACAAAAGG
Found at i:1319355 original size:226 final size:226
Alignment explanation
Indices: 1319094--1319954 Score: 1415
Period size: 226 Copynumber: 3.8 Consensus size: 226
1319084 GCAAAAAAAA
* *
1319094 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTTAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAA
* * * * * * *
1319158 CACTTCTCTGGAAAAGTTGATCCGTCGAGTGATGAATTCAAA-CAAAAAGTTGAACAAATTCTTC
66 C-TTTCTCTGGCAATGCTAATCCATCGGGTGATGAATT-AAAGCAAAAAGTTGAACAAATTCTTC
*
1319222 TCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATG
129 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATG
1319287 TTGATCCATCAAATGATGAATTCAAACAAAAGG
194 TTGATCCATCAAATGATGAATTCAAACAAAAGG
*
1319320 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATAAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAA
*
1319385 CTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATTAAAGC-AAAAGATTGAACAAGTTCTTCT
66 CTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATTAAAGCAAAAAG-TTGAACAAATTCTTCT
* *
1319449 CATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACTCTACCTGGTAATAT
130 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATGT
*
1319514 TGATCCATCAAATGATGAATTTAAACAAAAGG
195 TGATCCATCAAATGATGAATTCAAACAAAAGG
*
1319546 TTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAA
* *
1319611 CTTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAACAAGTTCTTCT
66 C-TTTCTCTGGCAATGCTAATCCATCGGGTGATGAATTAAAGCAAAAAGTTGAACAAATTCTTCT
* * *
1319676 CATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATACCTGGTAATGC
130 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATGT
1319741 TGATCCATCAAATGATGAATTCAAACAAAAGG
195 TGATCCATCAAATGATGAATTCAAACAAAAGG
*
1319773 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTTATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAA
* *
1319838 CTTTCTCTGGCAATGTTAATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAACAAGA-TCTTCT
66 CTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATTAAAGCAAAAAGTTGAACAA-ATTCTTCT
* *
1319902 CATTATGAACTTCTTCTTCATTCTTTAGATGAGTTCTTCTCATTATGAACTCT
130 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
1319955 TCTGGAAATA
Statistics
Matches: 597, Mismatches: 32, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
225 8 0.01
226 345 0.58
227 240 0.40
228 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (226 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAA
CTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATTAAAGCAAAAAGTTGAACAAATTCTTCTC
ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATGTT
GATCCATCAAATGATGAATTCAAACAAAAGG
Found at i:1319479 original size:24 final size:23
Alignment explanation
Indices: 1319444--1319488 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1319434 TGAACAAGTT
1319444 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
1319468 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
1319489 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:1319665 original size:453 final size:451
Alignment explanation
Indices: 1319097--1319968 Score: 1476
Period size: 453 Copynumber: 1.9 Consensus size: 451
1319087 AAAAAAATTG
* *
1319097 AACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTTAGATGAGTTCTTCTCATTATGAACACT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCATTATGAACACT
* * *
1319162 TCTCTGGAAAAGTTGATCCGTCGAGTGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATT
66 TCTCTGGAAAAGCTAATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATT
* * * *
1319227 ATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATGTTGAT
131 ATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATACCTGGTAATGCTGAT
*
1319292 CCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTT
196 CCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
1319357 TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATT
261 TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATT
* * *
1319422 AAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTT
326 AAAGCAAAAGATTGAACAAGATCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTT
*
1319487 CTCATTATGAACTCTACCTGGTAATATTGATCCATCAAATGATGAATTTAAACAAAAGGTTA
391 CTCATTATGAACTCT-CCTGGAAATATTGATCCATCAAATGATGAATTTAAACAAAAGGTTA
**
1319549 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCATTATGAACAC
* * * * *
1319614 TTCTCTGGCAATGCTAATCCATCGGGTGATGAATT-AAAGCAAAAGGTTGAACAAGTTCTTCTCA
65 TTCTCTGGAAAAGCTAATCCATCGAGTGATGAATTCAAA-CAAAAAGTTGAACAAATTCTTCTCA
1319678 TTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATACCTGGTAATGCTG
129 TTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATACCTGGTAATGCTG
1319743 ATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
194 ATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
* *
1319808 CTTCTTCAGATAAGTTCTTCTTATTATGAACTTTCTCTGGCAATGTTAATCCATCGGGTGATGAA
259 CTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGCAATGCTAATCCATCGGGTGATGAA
* *
1319873 TTAAAGCAAAAGGTTGAACAAGATCTTCTCATTATGAACTTCTTCTTCATTCTTTAGATGAGTTC
324 TTAAAGCAAAAGATTGAACAAGATCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTC
*
1319938 TTCTCATTATGAACTCTTCTGGAAATATTGA
389 TTCTCATTATGAACTCTCCTGGAAATATTGA
1319969 AAACATTCTA
Statistics
Matches: 392, Mismatches: 26, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
452 46 0.12
453 346 0.88
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (451 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCATTATGAACACT
TCTCTGGAAAAGCTAATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATT
ATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATACCTGGTAATGCTGAT
CCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATT
AAAGCAAAAGATTGAACAAGATCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTT
CTCATTATGAACTCTCCTGGAAATATTGATCCATCAAATGATGAATTTAAACAAAAGGTTA
Found at i:1320255 original size:73 final size:73
Alignment explanation
Indices: 1320013--1320334 Score: 477
Period size: 73 Copynumber: 4.4 Consensus size: 73
1320003 GAGGTCTTAT
* * *
1320013 CATCTTGCACTGTAGGGCTTACAGATGGCCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1320078 TTTGA-AA
66 TTTGAGAA
* *
1320085 GCATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATC-AAATGCTCCTGAAGGCT
1 -CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCT
1320149 TTTTGAGAA
65 TTTTGAGAA
1320158 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1320223 TTTGAGAA
66 TTTGAGAA
* * *
1320231 CATCATGCATTGTAGGTCTTACAGATGACCCTGAGGGTTTTGAAAACATCAAAAAGCTCCCGAAG
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGA-GGCTTT---AAGATCAAAAAGCTCCCGAAG
*
1320296 GCTTTTTGAAAA
62 GCTTTTTGAGAA
* * *
1320308 CATCCTGCACTGTAGGGCTTACGGATG
1 CATCATGCACTGTAGGTCTTACAGATG
1320335 TTGGAAATAG
Statistics
Matches: 228, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
72 67 0.29
73 102 0.45
74 5 0.02
77 54 0.24
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (73 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
TTTGAGAA
Found at i:1321012 original size:22 final size:22
Alignment explanation
Indices: 1320957--1321014 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1320947 AATAAAGCCT
* *
1320957 TCATCTTTGAAAATAGAACCTA
1 TCATCTTTGAAGAGAGAACCTA
*
1320979 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAACCTA
1321001 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
1321015 CGTAGATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAACCTA
Found at i:1328209 original size:7 final size:7
Alignment explanation
Indices: 1328199--1328229 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1328189 AAAAATGAAA
1328199 AAAATGC
1 AAAATGC
1328206 AAAATGC
1 AAAATGC
1328213 AAAATGC
1 AAAATGC
1328220 AAAATGC
1 AAAATGC
1328227 AAA
1 AAA
1328230 TTTAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAATGC
Found at i:1329926 original size:15 final size:15
Alignment explanation
Indices: 1329890--1329927 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1329880 TGAAAATAAA
*
1329890 ATAAAAA-AATATAT
1 ATAAAAATAATATAC
1329904 ATAAAAATAATATAC
1 ATAAAAATAATATAC
*
1329919 ATATAAATA
1 ATAAAAATA
1329928 TTATGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAAAAATAATATAC
Found at i:1329962 original size:28 final size:26
Alignment explanation
Indices: 1329907--1329964 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
1329897 AATATATATA
*
1329907 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
1329933 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
1329961 AAAA
1 AAAA
1329965 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:1336725 original size:2 final size:2
Alignment explanation
Indices: 1336718--1336752 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1336708 TTTGTTGCGT
1336718 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1336753 TAATGGTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1338286 original size:22 final size:22
Alignment explanation
Indices: 1338261--1338755 Score: 685
Period size: 22 Copynumber: 22.6 Consensus size: 22
1338251 ATAATAAATT
*
1338261 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
1338283 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1338305 TTTTAAAATAAATTAATCCATA
1 TTTTAAAATAAATCAATCCATA
1338327 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
1338349 TTTTAAAATAAATTTTTGCATA
1 TTTTAAAATAAATCAATCCATA
1338371 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1338393 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
1338415 TTTTAAAATAAAAT-TTTCTATA
1 TTTTAAAAT-AAATCAATCCATA
1338437 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1338459 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1338481 TTTTAAAATAAATCCATCCATA
1 TTTTAAAATAAATCAATCCATA
1338503 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
1338525 TTTTAAAATAAAT-TTTTCATA
1 TTTTAAAATAAATCAATCCATA
* *
1338546 TTTTAAAATAAAGT--TTTCATA
1 TTTTAAAATAAA-TCAATCCATA
*** *
1338567 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
1338589 TTTTAAAAATAAATCAATCCATA
1 TTTT-AAAATAAATCAATCCATA
1338612 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1338634 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
1338656 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
1338678 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* **
1338700 TTTTAAAATAAGT-TTTCCATA
1 TTTTAAAATAAATCAATCCATA
1338721 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1338743 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1338756 TTTAAAATAG
Statistics
Matches: 424, Mismatches: 42, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
20 1 0.00
21 58 0.14
22 343 0.81
23 22 0.05
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1344544 original size:21 final size:21
Alignment explanation
Indices: 1344429--1344544 Score: 58
Period size: 21 Copynumber: 5.6 Consensus size: 21
1344419 GCGAAATAAA
*
1344429 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
1344449 AATCGCAAATC-AGTTCCCAG
1 AATCGCAACGCGATTTTCCAG
* * **
1344469 AATCGCAACACGATTATGAAG
1 AATCGCAACGCGATTTTCCAG
* ** *
1344490 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
* **
1344510 AATTTGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
1344532 AATCGCAACGCGA
1 AATCGCAACGCGA
1344545 ATATGAAAAT
Statistics
Matches: 67, Mismatches: 25, Indels: 7
0.68 0.25 0.07
Matches are distributed among these distances:
19 1 0.01
20 25 0.37
21 39 0.58
22 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:1344557 original size:20 final size:20
Alignment explanation
Indices: 1344532--1344786 Score: 142
Period size: 20 Copynumber: 12.7 Consensus size: 20
1344522 GATTTTCCAG
*
1344532 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
1344552 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
1344572 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * * *
1344592 TATCGCAACGAGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
1344612 AATCGCAACGAC-AATATGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
1344633 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
1344653 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
1344673 AATCGCAACGCGTAT-CTATA
1 AATCGCAACGCGAATACGA-A
* * *
1344693 AATCGCAATGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * * *
1344713 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGAATACGAA
1344733 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
1344754 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
1344774 AATCACAACGCGA
1 AATCGCAACGCGA
1344787 TTTTTAAAGC
Statistics
Matches: 177, Mismatches: 46, Indels: 24
0.72 0.19 0.10
Matches are distributed among these distances:
19 3 0.02
20 140 0.79
21 34 0.19
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:1344614 original size:40 final size:39
Alignment explanation
Indices: 1344532--1344787 Score: 237
Period size: 40 Copynumber: 6.4 Consensus size: 39
1344522 GATTTTCCAG
* * * **
1344532 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACATATA
1 AATCGCAACGCG-ATACGTAAATCGCAACGCGTATC-CGTA
* * *
1344572 AATCGCAACGCGATTC-TGACTATCGCAACGAGTATCCGTA
1 AATCGCAACGCGATACGT-A-AATCGCAACGCGTATCCGTA
* *
1344612 AATCGCAACGACAATATGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACG-CGATACGT-AAATCGCAACGCGTATCCGTA
* **
1344653 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTATA
1 AATCGCAACGCG-ATACGTAAATCGCAACGCGTATCCGTA
* * * *
1344693 AATCGCAATGAGAATACGTAAATCGCAATGTGTATCCGTA
1 AATCGCAACGCG-ATACGTAAATCGCAACGCGTATCCGTA
*
1344733 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACG-CGATACGT-AAATCGCAACGCGTATCCGTA
*
1344774 AATCACAACGCGAT
1 AATCGCAACGCGAT
1344788 TTTTAAAGCG
Statistics
Matches: 177, Mismatches: 31, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
39 3 0.02
40 106 0.60
41 66 0.37
42 2 0.01
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (39 bp):
AATCGCAACGCGATACGTAAATCGCAACGCGTATCCGTA
Found at i:1344693 original size:121 final size:121
Alignment explanation
Indices: 1344532--1344783 Score: 348
Period size: 121 Copynumber: 2.1 Consensus size: 121
1344522 GATTTTCCAG
* * * * *
1344532 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCG-ATTC-TGACTAT
1 AATCGCAACGAGAATACGAAAATCGCAACGCGAACATATAAATCGCAACGAGAATACGT-A-AAT
*
1344595 CGCAACGAGTATCCGTAAATCGCAACGACAATATGTAAAATCGCAACGCGTATCCGTA
64 CGCAACGAGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
* * *
1344653 AATCGCAACGAGAATACGTAAATCGCAACGCGTATC-TATAAATCGCAATGAGAATACGTAAATC
1 AATCGCAACGAGAATACGAAAATCGCAACGCG-AACATATAAATCGCAACGAGAATACGTAAATC
* *
1344717 GCAATGTGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
65 GCAACGAGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
*
1344774 AATCACAACG
1 AATCGCAACG
1344784 CGATTTTTAA
Statistics
Matches: 116, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
121 109 0.94
122 6 0.05
123 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (121 bp):
AATCGCAACGAGAATACGAAAATCGCAACGCGAACATATAAATCGCAACGAGAATACGTAAATCG
CAACGAGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
Found at i:1344713 original size:101 final size:101
Alignment explanation
Indices: 1344532--1344763 Score: 231
Period size: 101 Copynumber: 2.3 Consensus size: 101
1344522 GATTTTCCAG
* * *
1344532 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCGATTCTGACTATCG
1 AATCGCAACGCGAATACGAAAATCGCAACGAGAACACATAAATCGCAACGCGATTCTGACTATCG
* *
1344597 CAACGAGTATCCGTAAATCGCAACGACAATATGTAA
66 CAACGAGAATACGTAAATCGCAACGACAATATGTAA
* * * * *
1344633 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGCG-TATCT-A-TAAA
1 AATCGCAACGCGAATACGAAAATCGCAACGAGAACACATAAATCGCAACGCGAT-TCTGACT--A
* * *** **
1344695 TCGCAATGAGAATACGTAAATCGCAATGTGTATCCGT-A
63 TCGCAACGAGAATACGTAAATCGCAACGACAATATGTAA
1344733 AATCGCAACGAC-AATACGTAAAATCGCAACG
1 AATCGCAACG-CGAATACG-AAAATCGCAACG
1344764 CGTATCCGTA
Statistics
Matches: 106, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
99 1 0.01
100 17 0.16
101 88 0.83
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (101 bp):
AATCGCAACGCGAATACGAAAATCGCAACGAGAACACATAAATCGCAACGCGATTCTGACTATCG
CAACGAGAATACGTAAATCGCAACGACAATATGTAA
Found at i:1345400 original size:33 final size:33
Alignment explanation
Indices: 1345358--1345438 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
1345348 CGCAACGAGA
1345358 GAAATGAAAATCGCAACGAGAGAATCACAACAC
1 GAAATGAAAATCGCAACGAGAGAATCACAACAC
* * *
1345391 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCACAACAC
**
1345424 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1345439 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.49, C:0.22, G:0.19, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAACAC
Found at i:1345531 original size:20 final size:19
Alignment explanation
Indices: 1345502--1345556 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1345492 TGTGATTTTC
1345502 ATTTCGCGTTGCGATAGTT
1 ATTTCGCGTTGCGATAGTT
*
1345521 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGATAGTT
*
1345541 ATTCTCTCGTTGCGAT
1 ATT-TCGCGTTGCGAT
1345557 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 4 0.12
20 27 0.84
21 1 0.03
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (19 bp):
ATTTCGCGTTGCGATAGTT
Found at i:1345562 original size:20 final size:19
Alignment explanation
Indices: 1345434--1345565 Score: 123
Period size: 19 Copynumber: 7.1 Consensus size: 19
1345424 GAAACCAAAA
*
1345434 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1345453 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
1345472 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1345486 TCTCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1345505 TCGCGTTGCGATAGTT-ATT
1 TCGCGTTGCGAT-TTTCATT
**
1345524 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
1345544 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1345564 TC
1 TC
1345566 AACCAAAAGA
Statistics
Matches: 91, Mismatches: 13, Indels: 18
0.75 0.11 0.15
Matches are distributed among these distances:
14 9 0.10
16 3 0.03
17 2 0.02
19 45 0.49
20 31 0.34
21 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1347403 original size:17 final size:17
Alignment explanation
Indices: 1347373--1347405 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1347363 GTTGCTGCCA
1347373 ATTCTGTTAAACTGTGT
1 ATTCTGTTAAACTGTGT
1347390 ATTCT-TTAACACTGTG
1 ATTCTGTTAA-ACTGTG
1347406 AAGTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (17 bp):
ATTCTGTTAAACTGTGT
Found at i:1347416 original size:94 final size:94
Alignment explanation
Indices: 1347255--1347540 Score: 502
Period size: 94 Copynumber: 3.1 Consensus size: 94
1347245 TAGATTGCTT
*
1347255 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1347320 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1347349 AGTAAATTTGTTCGGTTGCTGCCAATTCTGTTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1347414 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
1347443 AGTAAATTTGTTCGGCTGCTGCCAATTATGCTAAACTGTTTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1347508 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1347536 AGTAA
1 AGTAA
1347541 TGCAATCCAT
Statistics
Matches: 184, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
93 6 0.03
94 178 0.97
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1347668 original size:19 final size:19
Alignment explanation
Indices: 1347588--1347670 Score: 76
Period size: 19 Copynumber: 4.2 Consensus size: 19
1347578 TAGTTTACTT
*
1347588 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
* * **
1347608 TCGCAACGTGAAAAATGACTA
1 TCGCAACGCG-AAACT-AAAA
*
1347629 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
*
1347648 TCGCAACGCGAAACTATAA
1 TCGCAACGCGAAACTAAAA
1347667 TCGC
1 TCGC
1347671 GTTGCGATTT
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
19 23 0.47
20 12 0.24
21 14 0.29
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:1347730 original size:20 final size:20
Alignment explanation
Indices: 1347705--1347791 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
1347695 GGTTCTCTCG
**
1347705 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1347725 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1347745 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
1347765 TTGCGATAGTCATTTTCACG
1 TTGCGATAGTCATTTTCGCA
1347785 TTGCGAT
1 TTGCGAT
1347792 TTTAAGTTTA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1348366 original size:21 final size:21
Alignment explanation
Indices: 1348275--1348373 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
1348265 GACTCACCTG
*
1348275 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
1348297 T-ATAGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1348317 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1348338 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
*
1348359 TCATCGTTGAAGAGG
1 TCATCGTTCAAGAGG
1348374 TCCTTCCCAA
Statistics
Matches: 58, Mismatches: 18, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
20 3 0.05
21 54 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1348382 original size:42 final size:42
Alignment explanation
Indices: 1348272--1348382 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
1348262 CCCGACTCAC
* * *
1348272 CTGTCATCGTTCAAGAGG-CCTCCCCTATAGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGTCCTTCCC-ACAGTTCAAGAGGCCA
* ** * *
1348314 CTATCATCCCTCAAGA-GTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGT-CCTTCCCACAGTTCAAGAGGCCA
*
1348356 CTGTCATCGTTGAAGAGGTCCTTCCCA
1 CTGTCATCGTTCAAGAGGTCCTTCCCA
1348383 ACATTCTAGA
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
41 1 0.02
42 45 0.85
43 7 0.13
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGGTCCTTCCCACAGTTCAAGAGGCCA
Found at i:1349757 original size:14 final size:14
Alignment explanation
Indices: 1349738--1349773 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1349728 ATTGTTTAAT
1349738 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1349752 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1349766 TGATTTGT
1 TGATTTGT
1349774 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1349948 original size:14 final size:14
Alignment explanation
Indices: 1349929--1349983 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1349919 CATTTTCGCA
1349929 TTGCGATTCACTCG
1 TTGCGATTCACTCG
*
1349943 TTGCGATTTTCATTTCG
1 TTGCGA--TTCA-CTCG
1349960 CATTGCGATTCACTCG
1 --TTGCGATTCACTCG
1349976 TTGCGATT
1 TTGCGATT
1349984 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.42
Consensus pattern (14 bp):
TTGCGATTCACTCG
Found at i:1349964 original size:33 final size:33
Alignment explanation
Indices: 1349907--1350002 Score: 183
Period size: 33 Copynumber: 2.9 Consensus size: 33
1349897 CGCAATTTTG
1349907 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
1349941 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
1349974 CGTTGCGATTTTCATTTCGCATTGCGATT
1 CGTTGCGATTTTCATTTCGCATTGCGATT
1350003 TTCATTTCAC
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 48 0.77
34 14 0.23
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:1349967 original size:19 final size:19
Alignment explanation
Indices: 1349909--1350021 Score: 120
Period size: 19 Copynumber: 6.4 Consensus size: 19
1349899 CAATTTTGCG
1349909 TTGCGATTTTCATTTTCGCA
1 TTGCGATTTTCA-TTTCGCA
*
1349929 TTGCGA--TTCA-CTCG--
1 TTGCGATTTTCATTTCGCA
1349943 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1349962 TTGCGA--TTCA-CTCG--
1 TTGCGATTTTCATTTCGCA
1349976 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1349995 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCA
1350014 TTGCGATT
1 TTGCGATT
1350022 CTCTAGTTGC
Statistics
Matches: 78, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
14 12 0.15
16 14 0.18
17 10 0.13
18 4 0.05
19 32 0.41
20 6 0.08
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1350002 original size:52 final size:53
Alignment explanation
Indices: 1349943--1350074 Score: 167
Period size: 52 Copynumber: 2.5 Consensus size: 53
1349933 GATTCACTCG
* **
1349943 TTGCGATTTTCATTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTC-GCA
1 TTGCGATTTTCATTTCGCATTGCGATTCACTAGTTGCGATAGTCATTTCTGCA
* * *
1349995 TTGCGATTTTCATTTCACATTGCGATTCTCTAGTTGCGATAGTCATTTCTGCG
1 TTGCGATTTTCATTTCGCATTGCGATTCACTAGTTGCGATAGTCATTTCTGCA
** *
1350048 TTGCGATAGTCAATTCCGCATTGCGAT
1 TTGCGATTTTC-ATTTCGCATTGCGAT
1350075 AGTTATTTCC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 44 0.65
53 11 0.16
54 13 0.19
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (53 bp):
TTGCGATTTTCATTTCGCATTGCGATTCACTAGTTGCGATAGTCATTTCTGCA
Found at i:1350052 original size:20 final size:20
Alignment explanation
Indices: 1350027--1350119 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
1350017 CGATTCTCTA
*
1350027 GTTGCGATAGTCATTTCTGC
1 GTTGCGATAGTCATTTCCGC
*
1350047 GTTGCGATAGTCAATTCCGC
1 GTTGCGATAGTCATTTCCGC
* * *
1350067 ATTGCGATAGTTATTTCCGT
1 GTTGCGATAGTCATTTCCGC
1350087 GTTGCGATAGTCATATT-CGC
1 GTTGCGATAGTCAT-TTCCGC
1350107 GTTGCGATAGTCA
1 GTTGCGATAGTCA
1350120 AATGAATGTC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 61 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGC
Done.