Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, 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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 21 of 26
Found at i:8687342 original size:25 final size:25
Alignment explanation
Indices: 8687297--8687345 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
8687287 TCAAAATATG
*
8687297 AGATGTTACTATAAGCAAAAAATCC
1 AGATGTTACTACAAGCAAAAAATCC
**
8687322 AGATGTTACTACAAGGTAAAAATC
1 AGATGTTACTACAAGCAAAAAATC
8687346 ATAAAGTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (25 bp):
AGATGTTACTACAAGCAAAAAATCC
Found at i:8690561 original size:20 final size:22
Alignment explanation
Indices: 8690527--8690571 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
8690517 AATTTTATTT
*
8690527 TTTTTATTATATTTA-ATTAAA
1 TTTTTATAATATTTATATTAAA
*
8690548 TTTTTATAAT-TTTATGTTAAA
1 TTTTTATAATATTTATATTAAA
8690569 TTT
1 TTT
8690572 AATAAGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTTATAATATTTATATTAAA
Found at i:8692938 original size:30 final size:31
Alignment explanation
Indices: 8692876--8692939 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 31
8692866 TAACACAACA
8692876 AAAGTACTCCTTTTTGTTATAGAAACAACAAT
1 AAAGTACTCCTTTTTGTTATA-AAACAACAAT
*
8692908 AAAGTTACTCTTTTTTGTTAT-AAA-AACAAT
1 AAAG-TACTCCTTTTTGTTATAAAACAACAAT
8692938 AA
1 AA
8692940 TTAATTACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 8 0.27
31 3 0.10
32 4 0.13
33 15 0.50
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (31 bp):
AAAGTACTCCTTTTTGTTATAAAACAACAAT
Found at i:8733928 original size:5 final size:5
Alignment explanation
Indices: 8733918--8733952 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
8733908 TGGTGACTCT
*
8733918 TTTTC TTTTC TTTTC TTTTC TTTTT TTCTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTT
8733953 TTTGGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:8733954 original size:11 final size:10
Alignment explanation
Indices: 8733915--8733955 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
8733905 GAGTGGTGAC
8733915 TCTTTTTCTTT
1 TCTTTTT-TTT
*
8733926 TCTTTTCTTT
1 TCTTTTTTTT
8733936 TCTTTTTTTCT
1 TCTTTTTTT-T
8733947 TCTTTTTTT
1 TCTTTTTTT
8733956 GGTATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 11 0.41
11 16 0.59
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:8743670 original size:2 final size:2
Alignment explanation
Indices: 8743665--8743694 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
8743655 GAGAAATGGG
*
8743665 GA GA GA CA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
8743695 AGGAGAAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:8747112 original size:259 final size:260
Alignment explanation
Indices: 8746638--8747112 Score: 634
Period size: 259 Copynumber: 1.8 Consensus size: 260
8746628 TTTGTCATAT
* * * * * * * *
8746638 TATCAATATAAGATAACAAGAAATGGGATGAATCTATTTTTATTTAATTGGAGAGTGGAGAGAAA
1 TATCAATATAAAATAACAAAAAATGAGATGAATCCATTTTTATATAATTGGAGAGTGAAAACAAA
* * *
8746703 ATTGAACACGATAGTTACACTTGCAAATTGCAATATGTGTTCGAACATTGCTTCGTCTCCACTAA
66 ATTAAACACGATAGTTACACTTACAAATTGCAATATGTATTCGAACATTGCTTCGTCTCCACTAA
* * *
8746768 GTCCTTGCACATGCTCAGATGGCAGCTTCGAAGCAGTCCAGATTTTGGACATATCTCATGAGTGA
131 GTCCTTGCACATGCCCAGATGGCAACTTCGAAGCAGTCCAGATTTTGGACATACCTCATGAGTGA
* *
8746833 TCATGATTTTTTCTTATTTTTGACATTTTTGATTGAATTTAATCATCCCCATATAAAATTTTGGA
196 TCATGACTTTTTCCTATTTTTGACATTTTTGATTGAATTTAATCATCCCCATATAAAATTTTGGA
**
8746898 TATC-ATATAAAATAACAAAAAATGAGATGAATCCATTTTTATATGGTTGGAGAGTGAAAACAAA
1 TATCAATATAAAATAACAAAAAATGAGATGAATCCATTTTTATATAATTGGAGAGTGAAAACAAA
*** * * * *
8746962 ATTAAATGTGATAGTTACACTTACAAATTGTAATATGTATTCGAACATTGTTTTGTCTCCA-TTA
66 ATTAAACACGATAGTTACACTTACAAATTGCAATATGTATTCGAACATTGCTTCGTCTCCACTAA
* * *
8747026 TTCCTTGCACATGCCCAGATGGCAACTTCG-AGCTAG-CCAAGATTTTGGGCTTACCTCATGAGT
131 GTCCTTGCACATGCCCAGATGGCAACTTCGAAGC-AGTCC-AGATTTTGGACATACCTCATGAGT
*
8747089 GATTATGACCTTTTTCCTATTTTT
194 GATCATGA-CTTTTTCCTATTTTT
8747113 AGTTTTTTTT
Statistics
Matches: 183, Mismatches: 29, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
257 5 0.03
258 59 0.32
259 115 0.63
260 4 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (260 bp):
TATCAATATAAAATAACAAAAAATGAGATGAATCCATTTTTATATAATTGGAGAGTGAAAACAAA
ATTAAACACGATAGTTACACTTACAAATTGCAATATGTATTCGAACATTGCTTCGTCTCCACTAA
GTCCTTGCACATGCCCAGATGGCAACTTCGAAGCAGTCCAGATTTTGGACATACCTCATGAGTGA
TCATGACTTTTTCCTATTTTTGACATTTTTGATTGAATTTAATCATCCCCATATAAAATTTTGGA
Found at i:8752194 original size:12 final size:12
Alignment explanation
Indices: 8752170--8752205 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
8752160 TTCAAACTCC
*
8752170 AAAAAA-AAGAT
1 AAAAAATAAAAT
8752181 AAAAAATAAAAT
1 AAAAAATAAAAT
8752193 AAAAAATAAAAT
1 AAAAAATAAAAT
8752205 A
1 A
8752206 CAAAGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:8752203 original size:17 final size:18
Alignment explanation
Indices: 8752183--8752216 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8752173 AAAAAGATAA
*
8752183 AAAATA-AAATAAAAAAT
1 AAAATACAAAGAAAAAAT
8752200 AAAATACAAAGAAAAAA
1 AAAATACAAAGAAAAAA
8752217 AATACCTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (18 bp):
AAAATACAAAGAAAAAAT
Found at i:8771063 original size:20 final size:21
Alignment explanation
Indices: 8771038--8771076 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
8771028 CTTGTCAAGA
8771038 CATGGATT-CAAGTGTTAAGG
1 CATGGATTACAAGTGTTAAGG
8771058 CATGGATTACAAGTGTTAA
1 CATGGATTACAAGTGTTAA
8771077 AGGAAGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (21 bp):
CATGGATTACAAGTGTTAAGG
Found at i:8771451 original size:26 final size:25
Alignment explanation
Indices: 8771413--8771467 Score: 101
Period size: 26 Copynumber: 2.2 Consensus size: 25
8771403 AGAGAACTTA
8771413 GCTGTTTTTCCGGTGAGTATACCTT
1 GCTGTTTTTCCGGTGAGTATACCTT
8771438 GCTGTTTTTTCCGGTGAGTATACCTT
1 GCTG-TTTTTCCGGTGAGTATACCTT
8771464 GCTG
1 GCTG
8771468 GAAATCATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.11, C:0.20, G:0.25, T:0.44
Consensus pattern (25 bp):
GCTGTTTTTCCGGTGAGTATACCTT
Found at i:8775476 original size:30 final size:30
Alignment explanation
Indices: 8775401--8775476 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
8775391 TAACTGGTAA
* *
8775401 TGAAAACAAGAAATTATCCACATGGTACTAAT
1 TGAAAA-AAGAAA-TATCCACAAGATACTAAT
* * *
8775433 TG-ACAAAGAAAATATCCATAAGATATTAAT
1 TGAAAAAAG-AAATATCCACAAGATACTAAT
8775463 TGAAAAAAGAAATA
1 TGAAAAAAGAAATA
8775477 CAAAATATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
30 24 0.67
31 10 0.28
32 2 0.06
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.24
Consensus pattern (30 bp):
TGAAAAAAGAAATATCCACAAGATACTAAT
Found at i:8785794 original size:27 final size:28
Alignment explanation
Indices: 8785745--8785797 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
8785735 TCTATCTTCT
*
8785745 TTAATTTCAATAAAAAAACCTCATTTTC
1 TTAATTTCAAAAAAAAAACCTCATTTTC
8785773 TTAATTT-AAAAAAAAAACCTCATTT
1 TTAATTTCAAAAAAAAAACCTCATTT
8785798 GAATATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (28 bp):
TTAATTTCAAAAAAAAAACCTCATTTTC
Found at i:8785805 original size:26 final size:27
Alignment explanation
Indices: 8785746--8785807 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
8785736 CTATCTTCTT
* ***
8785746 TAATTTCAATAAAAAAACCTCATTTTCT
1 TAATTT-AAAAAAAAAACCTCATTTGAA
8785774 TAATTTAAAAAAAAAACCTCATTTGAA
1 TAATTTAAAAAAAAAACCTCATTTGAA
8785801 T-ATTTAA
1 TAATTTAA
8785808 CTTTAAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 6 0.20
27 18 0.60
28 6 0.20
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (27 bp):
TAATTTAAAAAAAAAACCTCATTTGAA
Found at i:8810102 original size:6 final size:6
Alignment explanation
Indices: 8810093--8810117 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
8810083 GGTGGTCGTA
8810093 GTCGCG GTCGCG GTCGCG GTCGCG G
1 GTCGCG GTCGCG GTCGCG GTCGCG G
8810118 CGGTGGTGGA
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:0.00, C:0.32, G:0.52, T:0.16
Consensus pattern (6 bp):
GTCGCG
Found at i:8810298 original size:27 final size:27
Alignment explanation
Indices: 8810263--8810331 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
8810253 TTCCTCTTAC
* *
8810263 ACTCCGCCTCGTCCTCAGGTGGCTCCT
1 ACTCAGCCTCCTCCTCAGGTGGCTCCT
*
8810290 ATTCAGCCTCCTCCTCAGGTGGCTCCT
1 ACTCAGCCTCCTCCTCAGGTGGCTCCT
*
8810317 ACTCAGCCACCTCCT
1 ACTCAGCCTCCTCCT
8810332 TCTGCCCCGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.12, C:0.45, G:0.17, T:0.26
Consensus pattern (27 bp):
ACTCAGCCTCCTCCTCAGGTGGCTCCT
Found at i:8829242 original size:20 final size:20
Alignment explanation
Indices: 8829217--8829255 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
8829207 AATAATAATT
8829217 TTTAAAATGTTTTAAAATAA
1 TTTAAAATGTTTTAAAATAA
* *
8829237 TTTAAACTTTTTTAAAATA
1 TTTAAAATGTTTTAAAATA
8829256 TTATATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TTTAAAATGTTTTAAAATAA
Found at i:8830574 original size:24 final size:24
Alignment explanation
Indices: 8830542--8830592 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
8830532 AATCTTCAGT
8830542 TAATCGTTGCAATTATCATTAGCA
1 TAATCGTTGCAATTATCATTAGCA
8830566 TAATCGTTGCAATTATCATTAGCA
1 TAATCGTTGCAATTATCATTAGCA
8830590 TAA
1 TAA
8830593 AGGTGAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (24 bp):
TAATCGTTGCAATTATCATTAGCA
Found at i:8835535 original size:2 final size:2
Alignment explanation
Indices: 8835530--8835561 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8835520 ATATATATAT
8835530 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
8835562 TAGCTATAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8836080 original size:53 final size:53
Alignment explanation
Indices: 8836008--8836115 Score: 162
Period size: 53 Copynumber: 2.0 Consensus size: 53
8835998 TTTGTGGTTA
** * **
8836008 TATTGATGGATCTAATTGACTTCATCTTATAGTAGGTTACTCCAATAATTTCT
1 TATTGATCAATCTAATTGACTTCATCTAATAACAGGTTACTCCAATAATTTCT
*
8836061 TATTGATCAATCTATTTGACTTCATCTAATAACAGGTTACTCCAATAATTTCT
1 TATTGATCAATCTAATTGACTTCATCTAATAACAGGTTACTCCAATAATTTCT
8836114 TA
1 TA
8836116 CTTTGCAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.43
Consensus pattern (53 bp):
TATTGATCAATCTAATTGACTTCATCTAATAACAGGTTACTCCAATAATTTCT
Found at i:8836199 original size:14 final size:14
Alignment explanation
Indices: 8836180--8836206 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8836170 GTACTGAAAG
8836180 CTTTAAAACTTGGT
1 CTTTAAAACTTGGT
8836194 CTTTAAAACTTGG
1 CTTTAAAACTTGG
8836207 GAGGCAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (14 bp):
CTTTAAAACTTGGT
Found at i:8867591 original size:3 final size:3
Alignment explanation
Indices: 8867583--8867657 Score: 105
Period size: 3 Copynumber: 25.0 Consensus size: 3
8867573 AAGCCTCGGC
* * * *
8867583 TCT TCT TCT TCT TCT TCT TCT TCC TCC TCT TCT TCT TCA TCT TCT ACT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
8867631 TCT TCG TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
8867658 CTCTCGTCGT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.03, C:0.36, G:0.01, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:8868547 original size:15 final size:16
Alignment explanation
Indices: 8868518--8868551 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
8868508 TTTATGAGTA
*
8868518 TATATTTTTTATAATT
1 TATAATTTTTATAATT
8868534 TATAATTTTT-TAATT
1 TATAATTTTTATAATT
8868549 TAT
1 TAT
8868552 TTATTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATAATTTTTATAATT
Found at i:8872286 original size:30 final size:30
Alignment explanation
Indices: 8872230--8872286 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
8872220 TAAAATAAAA
* *
8872230 TTATTTTTTATTATATTCAATCAAATTCTT
1 TTATTTTTTATTAAATTAAATCAAATTCTT
*
8872260 TTATTTTTATTTTAAATTAAAT-AAATT
1 TTATTTTT-TATTAAATTAAATCAAATT
8872287 TTTATAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 13 0.57
31 10 0.43
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (30 bp):
TTATTTTTTATTAAATTAAATCAAATTCTT
Found at i:8872538 original size:24 final size:22
Alignment explanation
Indices: 8872484--8872538 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
8872474 TTAATTCATC
* *
8872484 ATTAATTATAAATATATATTTG
1 ATTAAATAAAAATATATATTTG
8872506 ATATAAAATAAAAATATAATGATTTG
1 AT-T-AAATAAAAATAT-AT-ATTTG
8872532 ATTAAAT
1 ATTAAAT
8872539 GTAATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 2 0.07
23 1 0.04
24 14 0.52
25 3 0.11
26 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
ATTAAATAAAAATATATATTTG
Found at i:8889285 original size:4 final size:4
Alignment explanation
Indices: 8889276--8889306 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
8889266 ATGTATAGTT
8889276 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
8889307 TCTGCACTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:8896453 original size:2 final size:2
Alignment explanation
Indices: 8896446--8896471 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8896436 TTAAACTTTA
8896446 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
8896472 CCAAAGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8909658 original size:24 final size:24
Alignment explanation
Indices: 8909630--8909681 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
8909620 CAATATCATG
*
8909630 TTCCTCTATACCCACGCTTATCCC
1 TTCCTCTATACCCACACTTATCCC
*
8909654 TTCCTCTATACCCACACTTGTCCC
1 TTCCTCTATACCCACACTTATCCC
8909678 TTCC
1 TTCC
8909682 ACCCACTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.15, C:0.46, G:0.04, T:0.35
Consensus pattern (24 bp):
TTCCTCTATACCCACACTTATCCC
Found at i:8910507 original size:23 final size:24
Alignment explanation
Indices: 8910467--8910512 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
8910457 TAGTTGAAAT
*
8910467 TTTTTGATATAATATTTTGAAAAG
1 TTTTTGATATAATATTTTAAAAAG
* *
8910491 TTTTTGA-ATTATTTTTTAAAAA
1 TTTTTGATATAATATTTTAAAAA
8910513 AATTAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (24 bp):
TTTTTGATATAATATTTTAAAAAG
Found at i:8910811 original size:30 final size:30
Alignment explanation
Indices: 8910771--8910848 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 30
8910761 AATTGTTAAT
8910771 TATAAAAATTTATTTGATTTAAAATAAAAA
1 TATAAAAATTTATTTGATTTAAAATAAAAA
* * ** *
8910801 TATAAGAATTTAATTGA-ACATAATAAAAA
1 TATAAAAATTTATTTGATTTAAAATAAAAA
*
8910830 -ATAAAAATTTATTTAATTT
1 TATAAAAATTTATTTGATTT
8910849 TTTTTAAAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
28 13 0.35
29 9 0.24
30 15 0.41
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (30 bp):
TATAAAAATTTATTTGATTTAAAATAAAAA
Found at i:8911882 original size:30 final size:31
Alignment explanation
Indices: 8911848--8911913 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
8911838 ACTATTAATA
* *
8911848 ATAAAAG-TTTATTTGGCTCAAAATAAAAAT
1 ATAAAAGACTTATTCGGCTCAAAATAAAAAT
* * *
8911878 AT-AAAGACTTATTCGGTTCAAATTTAAAAT
1 ATAAAAGACTTATTCGGCTCAAAATAAAAAT
8911908 ATAAAA
1 ATAAAA
8911914 ATGTAATTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 4 0.14
30 22 0.76
31 3 0.10
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (31 bp):
ATAAAAGACTTATTCGGCTCAAAATAAAAAT
Found at i:8915163 original size:18 final size:19
Alignment explanation
Indices: 8915140--8915176 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
8915130 ATCGATATTA
8915140 GGGTGATT-ATGATTTAAT
1 GGGTGATTCATGATTTAAT
*
8915158 GGGTGATTCGTGATTTAAT
1 GGGTGATTCATGATTTAAT
8915177 TTTTTTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.24, C:0.03, G:0.30, T:0.43
Consensus pattern (19 bp):
GGGTGATTCATGATTTAAT
Found at i:8916655 original size:22 final size:22
Alignment explanation
Indices: 8916613--8916672 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
8916603 TGTATTCACA
* *
8916613 AATTTAATATATTATTTAATTGT
1 AATTTAA-ATTTTATTTAATTAT
*
8916636 AATTTAAATTTTTTTTAATTAT
1 AATTTAAATTTTATTTAATTAT
*
8916658 ATATTAAAATTTTAT
1 A-ATTTAAATTTTAT
8916673 AAAATTTAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
AATTTAAATTTTATTTAATTAT
Found at i:8918975 original size:13 final size:13
Alignment explanation
Indices: 8918952--8918985 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
8918942 ATATAAAATA
8918952 TATATTTTTATTAT
1 TATATTTTTATT-T
8918966 TA-ATTTTTATTT
1 TATATTTTTATTT
8918978 TATATTTT
1 TATATTTT
8918986 ATAATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 14 0.74
14 2 0.11
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TATATTTTTATTT
Found at i:8927642 original size:14 final size:14
Alignment explanation
Indices: 8927622--8927661 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
8927612 CAAATAATTT
8927622 ATTTATAAAATAAA
1 ATTTATAAAATAAA
*
8927636 GTTTATAAAAGTAAA
1 ATTTATAAAA-TAAA
8927651 ATTT-TAAAATA
1 ATTTATAAAATA
8927662 GATTTAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 14 0.61
15 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (14 bp):
ATTTATAAAATAAA
Found at i:8931518 original size:39 final size:39
Alignment explanation
Indices: 8931446--8931532 Score: 95
Period size: 39 Copynumber: 2.3 Consensus size: 39
8931436 AGAGTTTTCT
* * * * *
8931446 TGAGGATAAATGAGAGTAATCAGGACAAGTAGAGCCTCC
1 TGAGGATAGATGACAGCAATCAAGACAAATAGAGCCTCC
* * *
8931485 TGAGGATAGATGACAGCAATCAAGAGAAATAGAGCTTCT
1 TGAGGATAGATGACAGCAATCAAGACAAATAGAGCCTCC
8931524 TGA-GATAGA
1 TGAGGATAGA
8931533 GAAAGAAGAG
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
38 6 0.15
39 34 0.85
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.20
Consensus pattern (39 bp):
TGAGGATAGATGACAGCAATCAAGACAAATAGAGCCTCC
Found at i:8940295 original size:2 final size:2
Alignment explanation
Indices: 8940288--8940322 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
8940278 TATAGTAGTT
8940288 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
8940323 TTATGACGGT
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:8941017 original size:3 final size:3
Alignment explanation
Indices: 8941009--8941039 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
8940999 TGTGAAAACG
8941009 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
8941040 CAATGGATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:8941064 original size:2 final size:2
Alignment explanation
Indices: 8941057--8941085 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8941047 TGGAATCCTC
8941057 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8941086 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8952753 original size:12 final size:13
Alignment explanation
Indices: 8952710--8952753 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 13
8952700 AATAGAATTG
8952710 AAAAAATATAAAT
1 AAAAAATATAAAT
8952723 AATAATAATATAAAT
1 AA-AA-AATATAAAT
8952738 -AAAAAT-TAAAT
1 AAAAAATATAAAT
8952749 AAAAA
1 AAAAA
8952754 CTTAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 5 0.18
12 7 0.25
13 4 0.14
14 3 0.11
15 9 0.32
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAAAAATATAAAT
Found at i:8952899 original size:16 final size:17
Alignment explanation
Indices: 8952875--8952908 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
8952865 GCTAGTAAGG
*
8952875 TTATTTTATTT-TTTAA
1 TTATATTATTTATTTAA
8952891 TTATATTATTTATTTAA
1 TTATATTATTTATTTAA
8952908 T
1 T
8952909 AAAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATATTATTTATTTAA
Found at i:8955903 original size:12 final size:12
Alignment explanation
Indices: 8955886--8955963 Score: 50
Period size: 12 Copynumber: 6.0 Consensus size: 12
8955876 ACAGAAAGAG
8955886 GAAGAAAAGGAA
1 GAAGAAAAGGAA
*
8955898 GAAGAAAAAGAGGAG
1 GAAG--AAA-AGGAA
*
8955913 GAAGAGAA-GAA
1 GAAGAAAAGGAA
* *
8955924 GGAAGCAAACGAA
1 -GAAGAAAAGGAA
8955937 GAAGTAAAAGAGGAA
1 GAAG--AAA-AGGAA
8955952 GAAGAAAAGGAA
1 GAAGAAAAGGAA
8955964 TCGAAAATGG
Statistics
Matches: 51, Mismatches: 7, Indels: 16
0.69 0.09 0.22
Matches are distributed among these distances:
11 2 0.04
12 20 0.39
13 8 0.16
14 5 0.10
15 16 0.31
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.01
Consensus pattern (12 bp):
GAAGAAAAGGAA
Found at i:8962797 original size:10 final size:8
Alignment explanation
Indices: 8962776--8962802 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
8962766 TTCCACTCAT
8962776 TCTCTCCG
1 TCTCTCCG
8962784 TCTCTCCG
1 TCTCTCCG
8962792 TCTCTCCG
1 TCTCTCCG
8962800 TCT
1 TCT
8962803 TCTCATCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.48, G:0.11, T:0.41
Consensus pattern (8 bp):
TCTCTCCG
Found at i:8965775 original size:21 final size:21
Alignment explanation
Indices: 8965726--8965772 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
8965716 AAAATAAATT
*
8965726 ATTATATTTTTATTATATTTA
1 ATTAAATTTTTATTATATTTA
*
8965747 ATTAAATTTTTA-TATTTTTA
1 ATTAAATTTTTATTATATTTA
*
8965767 TTTAAA
1 ATTAAA
8965773 ATTAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTAAATTTTTATTATATTTA
Found at i:8965799 original size:31 final size:30
Alignment explanation
Indices: 8965710--8965820 Score: 134
Period size: 31 Copynumber: 3.7 Consensus size: 30
8965700 ATTATTTAAA
*
8965710 AAAATTAAAATAAATTATTATATTTTTA-TT
1 AAAATT-AAATAAATTTTTATATTTTTATTT
* * *
8965740 ATATTTAATTAAATTTTTATATTTTTATTT
1 AAAATTAAATAAATTTTTATATTTTTATTT
8965770 AAAATTAAATAAATTTTTATATTTTTTATTT
1 AAAATTAAATAAATTTTTATA-TTTTTATTT
* * *
8965801 TAAATCAGATAAATTTTTAT
1 AAAATTAAATAAATTTTTAT
8965821 TATTAATGAT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 19 0.28
30 24 0.35
31 26 0.38
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (30 bp):
AAAATTAAATAAATTTTTATATTTTTATTT
Found at i:8977452 original size:90 final size:90
Alignment explanation
Indices: 8977299--8977472 Score: 287
Period size: 90 Copynumber: 1.9 Consensus size: 90
8977289 CGACTCTCAT
* *
8977299 AGACTGGAACTAATGAAATCCAAGTATGGAGAAATTGAGGAAATGGAAGTCATGTTGGATAAATT
1 AGACTGGAACAAATGAAATCCAAGTATGGAGAAATTGAGGAAATCGAAGTCATGTTGGATAAATT
8977364 CAAGAATATAGAGGCCGAGGCCAAC
66 CAAGAATATAGAGGCCGAGGCCAAC
*
8977389 AGACTGGAACAAATGAAATCCGAGTATGGAGAAATTGAGGAAATCGAA-TCCATGTTGGATAAAT
1 AGACTGGAACAAATGAAATCCAAGTATGGAGAAATTGAGGAAATCGAAGT-CATGTTGGATAAAT
* *
8977453 TCAAGAATTTGGAGGCCGAG
65 TCAAGAATATAGAGGCCGAG
8977473 TCACATAGGT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 1 0.01
90 77 0.99
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (90 bp):
AGACTGGAACAAATGAAATCCAAGTATGGAGAAATTGAGGAAATCGAAGTCATGTTGGATAAATT
CAAGAATATAGAGGCCGAGGCCAAC
Found at i:8982053 original size:20 final size:19
Alignment explanation
Indices: 8982009--8982050 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
8981999 TTCTATTTGC
8982009 TTTTCTTTCTAGTTGTGTT
1 TTTTCTTTCTAGTTGTGTT
8982028 TTTTCTTTCTAGTTGTGTT
1 TTTTCTTTCTAGTTGTGTT
8982047 TTTT
1 TTTT
8982051 TCTAGGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.05, C:0.10, G:0.14, T:0.71
Consensus pattern (19 bp):
TTTTCTTTCTAGTTGTGTT
Found at i:8982064 original size:16 final size:16
Alignment explanation
Indices: 8982025--8982067 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
8982015 TTCTAGTTGT
**
8982025 GTTTTTTCTTTCTAGTT
1 GTTTTTT-TTTCTAGGA
*
8982042 GTGTTTTTTTCTAGGA
1 GTTTTTTTTTCTAGGA
8982058 GTTTTTTTTT
1 GTTTTTTTTT
8982068 TAGCGTGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.07, C:0.07, G:0.16, T:0.70
Consensus pattern (16 bp):
GTTTTTTTTTCTAGGA
Found at i:8985900 original size:25 final size:25
Alignment explanation
Indices: 8985870--8985918 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
8985860 CCCAAACCTT
** *
8985870 TTAAACCCTTAAACCTTAAGCCCAA
1 TTAAACCCCAAAACCTTAAACCCAA
8985895 TTAAACCCCAAAACCTTAAACCCA
1 TTAAACCCCAAAACCTTAAACCCA
8985919 TGAAACCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.43, C:0.35, G:0.02, T:0.20
Consensus pattern (25 bp):
TTAAACCCCAAAACCTTAAACCCAA
Found at i:8985931 original size:24 final size:25
Alignment explanation
Indices: 8985880--8985931 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
8985870 TTAAACCCTT
* * *
8985880 AAACCTTAAGCCCAATTAAACCCCA
1 AAACCTTAAACCCAATGAAACCACA
*
8985905 AAACCTTAAACCC-ATGAAACCATA
1 AAACCTTAAACCCAATGAAACCACA
8985929 AAA
1 AAA
8985932 AACTCTTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.50, C:0.31, G:0.04, T:0.15
Consensus pattern (25 bp):
AAACCTTAAACCCAATGAAACCACA
Found at i:8986008 original size:21 final size:20
Alignment explanation
Indices: 8985979--8986017 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
8985969 TTGAACCACC
8985979 CAAACCCTA-AGCCCTAAATA
1 CAAACCCTATA-CCCTAAATA
8985999 CAAAGCCCTATACCCTAAA
1 CAAA-CCCTATACCCTAAA
8986018 CACTAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.44, C:0.36, G:0.05, T:0.15
Consensus pattern (20 bp):
CAAACCCTATACCCTAAATA
Found at i:9014218 original size:29 final size:31
Alignment explanation
Indices: 9014170--9014236 Score: 111
Period size: 29 Copynumber: 2.2 Consensus size: 31
9014160 AAATTGAGTA
*
9014170 TTTTGATTTCTTTTTAATTTATTTCTTTGTC
1 TTTTGATTTCTTTTTAATTTATTTCATTGTC
9014201 TTTTGATTT-TTTTT-ATTTATTTCATTGTC
1 TTTTGATTTCTTTTTAATTTATTTCATTGTC
9014230 TTTTGAT
1 TTTTGAT
9014237 GTGTATTTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 21 0.60
30 5 0.14
31 9 0.26
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.72
Consensus pattern (31 bp):
TTTTGATTTCTTTTTAATTTATTTCATTGTC
Found at i:9016603 original size:16 final size:16
Alignment explanation
Indices: 9016582--9016612 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9016572 TTTTGCATAA
9016582 CTGCTGGTCCATATGC
1 CTGCTGGTCCATATGC
9016598 CTGCTGGTCCATATG
1 CTGCTGGTCCATATG
9016613 ACTGATGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.29, G:0.26, T:0.32
Consensus pattern (16 bp):
CTGCTGGTCCATATGC
Found at i:9023225 original size:33 final size:30
Alignment explanation
Indices: 9023150--9023227 Score: 75
Period size: 33 Copynumber: 2.4 Consensus size: 30
9023140 ATTACATCAT
* ***
9023150 ATATTATTATTTTAAATTAAATAAATTTTT
1 ATATTATTATTATAAATTAAATAAATTAAA
9023180 ATAATTAATTATTGATAAATTATAATAAATTAAA
1 AT-ATT-ATTATT-ATAAATTA-AATAAATTAAA
9023214 ATATTATTTATTAT
1 ATATTA-TTATTAT
9023228 TTTATATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
30 2 0.05
31 3 0.08
32 9 0.23
33 15 0.38
34 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
ATATTATTATTATAAATTAAATAAATTAAA
Found at i:9035763 original size:3 final size:3
Alignment explanation
Indices: 9035755--9035787 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
9035745 CTTCGAGATT
*
9035755 TTA TTA TTA TTA TTA TTA GTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
9035788 CTAAGTGCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:9036159 original size:22 final size:23
Alignment explanation
Indices: 9036134--9036176 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
9036124 TATTTAAAAA
*
9036134 TTTTAAAT-AATTTTTTTATTAC
1 TTTTAAATAAATTTTTATATTAC
*
9036156 TTTTAATTAAATTTTTATATT
1 TTTTAAATAAATTTTTATATT
9036177 TTTATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTAAATAAATTTTTATATTAC
Found at i:9040310 original size:2 final size:2
Alignment explanation
Indices: 9040303--9040327 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9040293 ATAGCACAGA
9040303 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9040328 ATAGTTATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9043233 original size:18 final size:17
Alignment explanation
Indices: 9043205--9043238 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9043195 TTTAATTTAA
9043205 TTTTAAAAATTATTATT
1 TTTTAAAAATTATTATT
*
9043222 TTTTATAAAATTTTTAT
1 TTTTA-AAAATTATTAT
9043239 AATAACTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAAAATTATTATT
Found at i:9060936 original size:1 final size:1
Alignment explanation
Indices: 9060930--9060958 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
9060920 AAATGCGGGT
9060930 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
9060959 TTTTATTCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:9068140 original size:2 final size:2
Alignment explanation
Indices: 9068133--9068157 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9068123 TAAAGCTTTT
9068133 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
9068158 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9073549 original size:30 final size:29
Alignment explanation
Indices: 9073514--9073595 Score: 128
Period size: 30 Copynumber: 2.8 Consensus size: 29
9073504 AAGTTTAATG
9073514 AATATTAATATTTAATTAAAAATATAAAAA
1 AATATTAATATTTAATTAAAAATAT-AAAA
*
9073544 AATATTAATATTTAACTTAAAAATATTAAA
1 AATATTAATATTTAA-TTAAAAATATAAAA
*
9073574 AATATTAATATTTAACTAAAAA
1 AATATTAATATTTAATTAAAAA
9073596 CCTTTTTACT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
29 6 0.12
30 33 0.67
31 10 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AATATTAATATTTAATTAAAAATATAAAA
Found at i:9077827 original size:2 final size:2
Alignment explanation
Indices: 9077820--9077846 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9077810 ACAGTAATGA
9077820 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9077847 GGGATATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9087978 original size:15 final size:15
Alignment explanation
Indices: 9087958--9088011 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
9087948 ATTACAATGC
* *
9087958 AATGTGATTACAGGT
1 AATGTGATTGCAAGT
9087973 AATGTGATTGCAAGT
1 AATGTGATTGCAAGT
*
9087988 AATGTGATTGCAAGC
1 AATGTGATTGCAAGT
9088003 AATGTGATT
1 AATGTGATT
9088012 TGCAGGGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:9088190 original size:13 final size:15
Alignment explanation
Indices: 9088169--9088616 Score: 88
Period size: 15 Copynumber: 30.5 Consensus size: 15
9088159 GTTTAATATT
*
9088169 TATATTTTTAT-TAT
1 TATATTTTTATATAA
9088183 TA-ATTTTTATATAA
1 TATATTTTTATATAA
9088197 TATA-TTTT-TA-AA
1 TATATTTTTATATAA
9088209 TATATTTTTAATATCATA
1 TATATTTTT-ATAT-A-A
*
9088227 TATTTATTTTTAT-TTA
1 TA--TATTTTTATATAA
9088243 TATAATATTTTATAT--
1 TAT-AT-TTTTATATAA
* *
9088258 TTTATTTTAATAT-A
1 TATATTTTTATATAA
*
9088272 TTTATATTTT-T-T-A
1 TATAT-TTTTATATAA
9088285 TA-ATTTTTATA-AA
1 TATATTTTTATATAA
*
9088298 TATCATTTCTTAATATAT
1 TAT-ATTT-TT-ATATAA
* * *
9088316 TAATATATATTATTTAT
1 T-ATAT-TTTTATATAA
*
9088333 TTTATTTATTAT-T-A
1 TATATTT-TTATATAA
9088347 TA-ATATTTTATAT--
1 TATAT-TTTTATATAA
* *
9088360 TTTATTTTAATAT-A
1 TATATTTTTATATAA
* * *
9088374 TTTATATTTATATTA
1 TATATTTTTATATAA
9088389 T-TAATTTTTATATAA
1 TAT-ATTTTTATATAA
*
9088404 TATCATTTCT-TA-AA
1 TAT-ATTTTTATATAA
* *
9088418 TATATTTTTAATGTCA
1 TATATTTTT-ATATAA
9088434 TATA-TTTTAT-T--
1 TATATTTTTATATAA
9088445 T-TATTTATTAT-T-A
1 TATATTT-TTATATAA
9088458 TATA-TTTTATAT--
1 TATATTTTTATATAA
*
9088470 TTTATTTTTATAT-A
1 TATATTTTTATATAA
* * *
9088484 TTTATATTTATATTA
1 TATATTTTTATATAA
9088499 T-TAATTTTTATATAA
1 TAT-ATTTTTATATAA
*
9088514 TATCATATTT-TA-AA
1 TAT-ATTTTTATATAA
* *
9088528 TATATTTTGTCTATAT
1 TATATTTT-TATATAA
* *
9088544 TTTATTTTTATTTATTAT
1 TATATTTTTA--TA-TAA
*
9088562 TATAATTTTATATATATT
1 TAT-ATTTT-TATATA-A
* * * *
9088580 TTTTTTTTTTTTTAA
1 TATATTTTTATATAA
*
9088595 TATATTTTTATATTA
1 TATATTTTTATATAA
9088610 TATATTT
1 TATATTT
9088617 ATTTTAATTT
Statistics
Matches: 334, Mismatches: 45, Indels: 109
0.68 0.09 0.22
Matches are distributed among these distances:
10 2 0.01
11 7 0.02
12 21 0.06
13 63 0.19
14 65 0.19
15 71 0.21
16 47 0.14
17 19 0.06
18 20 0.06
19 10 0.03
20 9 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TATATTTTTATATAA
Found at i:9088200 original size:28 final size:28
Alignment explanation
Indices: 9088169--9088359 Score: 88
Period size: 26 Copynumber: 6.9 Consensus size: 28
9088159 GTTTAATATT
9088169 TATATTTTTATTATTAATTTTTATATAA
1 TATATTTTTATTATTAATTTTTATATAA
*
9088197 TATATTTTTA--AATATATTTTTA-AT-A
1 TATATTTTTATTATTA-ATTTTTATATAA
* *
9088222 TCATATATTTATT-TT--TATTTATATAA
1 T-ATATTTTTATTATTAATTTTTATATAA
* *
9088248 TAT-TTTATATT-TT-ATTTTAATAT-A
1 TATATTTTTATTATTAATTTTTATATAA
*
9088272 TTTATATTTT-TTA-TAATTTTTATA-AA
1 TATAT-TTTTATTATTAATTTTTATATAA
* *
9088298 TATCATTTCTTAATATATTAATATATATTATTTAT
1 TAT-ATTT-TT-AT-TATTAAT-T-T-TTATATAA
*
9088333 TTTATTTATTATTA-TAATATTTTATAT
1 TATATTT-TTATTATTAAT-TTTTATAT
9088360 TTTATTTTAA
Statistics
Matches: 124, Mismatches: 17, Indels: 43
0.67 0.09 0.23
Matches are distributed among these distances:
24 16 0.13
25 17 0.14
26 31 0.25
27 12 0.10
28 10 0.08
29 6 0.05
30 3 0.02
31 10 0.08
32 3 0.02
33 3 0.02
34 10 0.08
35 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
TATATTTTTATTATTAATTTTTATATAA
Found at i:9088373 original size:59 final size:59
Alignment explanation
Indices: 9088307--9088622 Score: 170
Period size: 59 Copynumber: 5.5 Consensus size: 59
9088297 ATATCATTTC
9088307 TTAATATATTAATATATATTATTTATTTTATTTATTATTATAATATTTTATATTTTATT
1 TTAATATATTAATATATATTATTTATTTTATTTATTATTATAATATTTTATATTTTATT
* * *
9088366 TTAATATATT--TATAT-TTATATTA-TTAATTT-TTA-TATAATA--TCAT-TTCTTA-A
1 TTAATATATTAATATATATTAT-TTATTTTATTTATTATTATAATATTTTATATT-TTATT
* * *
9088417 AT-ATATTTTTAATGTCATA-TATTTTATTTTATTTATTATTAT-ATATTTTATATTTTATT
1 TTAATA-TATTAATAT-ATATTA-TTTATTTTATTTATTATTATAATATTTTATATTTTATT
* * * * * * * *
9088476 TTTATATATTTATATTTATATTATTAATTTT-TATA-TAATATCATATTTTA-AATATATT
1 TTAATATA-TTA-ATATATATTATTTATTTTATTTATTATTATAATATTTTATATTTTATT
** * * * * *
9088534 TTGTCTATATT-TTAT-TTTTATTTATTATTA-TAATT-TTATATATATTTT-TTTTTTTTT
1 TT-AATATATTAATATATATTATTTATT-TTATTTATTATTATA-ATATTTTATATTTTATT
**
9088591 TTAATATATTTTTATATTATATATTTATTTTA
1 TTAATATATTAATATA-TAT-TATTTATTTTA
9088623 ATTTGTTTTA
Statistics
Matches: 194, Mismatches: 33, Indels: 60
0.68 0.11 0.21
Matches are distributed among these distances:
50 3 0.02
51 6 0.03
52 6 0.03
53 2 0.01
54 14 0.07
55 19 0.10
56 30 0.15
57 29 0.15
58 21 0.11
59 35 0.18
60 24 0.12
61 5 0.03
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (59 bp):
TTAATATATTAATATATATTATTTATTTTATTTATTATTATAATATTTTATATTTTATT
Found at i:9088460 original size:22 final size:22
Alignment explanation
Indices: 9088434--9088501 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
9088424 TTTAATGTCA
9088434 TATATTTTATTTTATTTATTAT
1 TATATTTTATTTTATTTATTAT
* * *
9088456 TATATATT-TTATATTTTATTTT
1 TATATTTTATTTTA-TTTATTAT
9088478 TATATATTTATATTTATATTATTA
1 TATAT-TTTAT-TTTAT-TTATTA
9088502 ATTTTTATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
21 4 0.11
22 19 0.54
23 2 0.06
24 2 0.06
25 8 0.23
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TATATTTTATTTTATTTATTAT
Found at i:9088472 original size:47 final size:47
Alignment explanation
Indices: 9088418--9088574 Score: 113
Period size: 46 Copynumber: 3.1 Consensus size: 47
9088408 ATTTCTTAAA
9088418 TATATTTTTAATGTCATATATTTTATTTTATTTATTATTATATATTT
1 TATATTTTTAATGTCATATATTTTATTTTATTTATTATTATATATTT
* * * * *
9088465 TATA-TTTTATTTTTATATATTTATATTTATATTATTAATTTTTATATAATAT
1 TATATTTTTAATGTCATATATTT-TATTT-TA-T-TT-ATTATTATAT-ATTT
*
9088517 CATATTTTAAATATATTTTGTC-TATATTTTATTTTTATTTATTATTATA-ATTT
1 TATATTTT---TA-A---TGTCATATATTTTA-TTTTATTTATTATTATATATTT
9088570 TATAT
1 TATAT
9088575 ATATTTTTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
46 15 0.18
47 9 0.11
48 2 0.02
49 1 0.01
50 2 0.02
51 9 0.11
52 6 0.07
53 10 0.12
55 8 0.10
56 4 0.05
57 1 0.01
58 4 0.05
59 10 0.12
60 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (47 bp):
TATATTTTTAATGTCATATATTTTATTTTATTTATTATTATATATTT
Found at i:9088476 original size:110 final size:108
Alignment explanation
Indices: 9088164--9088574 Score: 572
Period size: 110 Copynumber: 3.9 Consensus size: 108
9088154 TATAAGTTTA
*
9088164 ATATTTATATTTTTATTATTAATTTTTATATAATAT-ATTTTTAAATATATTTTTAATATCATAT
1 ATATTTATATTTATATTATTAATTTTTATATAATATCATTTTTAAATATA--TTTAATATCATAT
9088228 A-TTTATTTTTATTTA-TA-TA-ATATTTTATATTTTATTTTAAT
64 ATTTTATTTTTATTTATTATTATATATTTTATATTTTATTTTAAT
9088269 ATATTTATATTT-T-TTA-TAATTTTTATA-AATATCATTTCTT-AATATA-TTAATAT-ATAT-
1 ATATTTATATTTATATTATTAATTTTTATATAATATCATTT-TTAAATATATTTAATATCATATA
9088326 TATTTA-TTTTATTTATTATTATAATATTTTATATTTTATTTTAAT
65 T-TTTATTTTTATTTATTATTAT-ATATTTTATATTTTATTTTAAT
*
9088371 ATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATA
1 ATATTTATATTTATATTATTAATTTTTATATAATATCATTT-TTAAATATA--TTTAATATCATA
*
9088436 TATTTTA-TTTTATTTATTATTATATATTTTATATTTTATTTTTAT
63 TATTTTATTTTTATTTATTATTATATATTTTATATTTTATTTTAAT
*
9088481 ATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTT--TGTC-TATA
1 ATATTTATATTTATATTATTAATTTTTATATAATATCAT-TTTTAAATATATTTAATATCATATA
9088543 TTTTATTTTTATTTATTATTATA-ATTTTATAT
65 TTTTATTTTTATTTATTATTATATATTTTATAT
9088575 ATATTTTTTT
Statistics
Matches: 284, Mismatches: 2, Indels: 40
0.87 0.01 0.12
Matches are distributed among these distances:
98 13 0.05
99 13 0.05
100 2 0.01
101 5 0.02
102 55 0.19
103 6 0.02
104 4 0.01
105 41 0.14
106 34 0.12
107 6 0.02
108 3 0.01
110 75 0.26
111 26 0.09
112 1 0.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (108 bp):
ATATTTATATTTATATTATTAATTTTTATATAATATCATTTTTAAATATATTTAATATCATATAT
TTTATTTTTATTTATTATTATATATTTTATATTTTATTTTAAT
Found at i:9088570 original size:35 final size:35
Alignment explanation
Indices: 9088526--9088626 Score: 109
Period size: 33 Copynumber: 2.9 Consensus size: 35
9088516 TCATATTTTA
* *
9088526 AATAT-ATTTTGTCTATATTTTATTTTTATTTATT
1 AATATAATTTTATATATATTTTATTTTTATTTATT
* *
9088560 ATTATAATTTTATATATATTTT-TTTTT-TTTTTT
1 AATATAATTTTATATATATTTTATTTTTATTTATT
* *
9088593 AATATATTTTTATATTATATATTTATTTTAATTT
1 AATATAATTTTATA-TATAT-TTTATTTTTATTT
9088627 GTTTTATCTA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
33 17 0.31
34 14 0.25
35 17 0.31
36 4 0.07
37 3 0.05
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (35 bp):
AATATAATTTTATATATATTTTATTTTTATTTATT
Found at i:9088581 original size:29 final size:28
Alignment explanation
Indices: 9088442--9088728 Score: 82
Period size: 29 Copynumber: 9.6 Consensus size: 28
9088432 CATATATTTT
* *
9088442 ATTTTATTTATTATTATATATTTTATATT-TT
1 ATTTTATATA-TATT-T-TATTTTA-ATTATA
9088473 ATTTT-TATATA-TTTATATTTATATTATTA
1 ATTTTATATATATTTTAT-TTTA-ATTA-TA
** *
9088502 ATTTTTATATAATATCATATTTTAAATATA
1 A-TTTTATAT-ATATTTTATTTTAATTATA
* * *
9088532 TTTTGTCTATATTTTATTTTTATTTATTATTATA
1 -ATT-T-TATA-TATA-TTTTATTT-TAATTATA
* ** *
9088566 ATTTTATATATATTTTTTTTTTTTTTTA
1 ATTTTATATATATTTTATTTTAATTATA
* * *
9088594 ATATATT-TTTATATTATATATTT-ATTTTA
1 AT-T-TTATATATATTTTAT-TTTAATTATA
* * * * *
9088623 ATTTGTTTTATCTATATTA-TATAAATATA
1 A-TT-TTATATATATTTTATTTTAATTATA
* * *
9088652 ATTTTTTATATTTATTTTATTTTAATTTTT
1 A--TTTTATATATATTTTATTTTAATTATA
9088682 ATTCTTATATATATATTTATTTTAATTATA
1 ATT-TTATATATAT-TTTATTTTAATTATA
* *
9088712 ATATTATAAAATATTTT
1 ATTTTAT-ATATATTTT
9088729 TAATAAGATA
Statistics
Matches: 192, Mismatches: 40, Indels: 50
0.68 0.14 0.18
Matches are distributed among these distances:
26 3 0.02
27 9 0.05
28 13 0.07
29 62 0.32
30 57 0.30
31 16 0.08
32 14 0.07
33 12 0.06
34 6 0.03
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (28 bp):
ATTTTATATATATTTTATTTTAATTATA
Found at i:9092487 original size:70 final size:70
Alignment explanation
Indices: 9092404--9092600 Score: 202
Period size: 71 Copynumber: 2.8 Consensus size: 70
9092394 CCTGCATGAC
* *
9092404 GCGCACCTGCGTGCCGTGCACCCTTGTTGGGCCGGCGGCCCCGGGCCTGCGTGCCAGT-CGCCCA
1 GCGCACCTGCGTGCCGCGCACCCTTGCTGGGCCGGCGGCCCCGGGCCTGCGTGCC-GTACGCCCA
*
9092468 TGCTGT
65 TGCTCT
* * * * ** * **
9092474 GCGCACCTACGTGCTGCGCACCCCTGCTGGGTCGGCGGGCCTTGGGCTTGCGTATCGTACGCCCA
1 GCGCACCTGCGTGCCGCGCACCCTTGCTGGGCCGGC-GGCCCCGGGCCTGCGTGCCGTACGCCCA
9092539 TGCTCT
65 TGCTCT
* * *
9092545 GCGTC-CCCGCATGCCGCGCA-CCTCTGCTGGGCCGGCAGCCCCGGGCCTGCGTGCCG
1 GCG-CACCTGCGTGCCGCGCACCCT-TGCTGGGCCGGCGGCCCCGGGCCTGCGTGCCG
9092601 CGTACCCATG
Statistics
Matches: 99, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
70 48 0.48
71 50 0.51
72 1 0.01
ACGTcount: A:0.07, C:0.41, G:0.35, T:0.18
Consensus pattern (70 bp):
GCGCACCTGCGTGCCGCGCACCCTTGCTGGGCCGGCGGCCCCGGGCCTGCGTGCCGTACGCCCAT
GCTCT
Found at i:9099878 original size:21 final size:19
Alignment explanation
Indices: 9099854--9099915 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 19
9099844 AAAAAATTTT
* *
9099854 ATTTTTTTATGATTAATTAAA
1 ATTTTTTTA-AATTAAAT-AA
9099875 ATTTTATTTAAATTAAATAA
1 ATTTT-TTTAAATTAAATAA
* *
9099895 ATTTTTATAAA-TAAAAAA
1 ATTTTTTTAAATTAAATAA
9099913 ATT
1 ATT
9099916 AATTATCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 9 0.25
19 5 0.14
20 7 0.19
21 11 0.31
22 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATTTTTTTAAATTAAATAA
Found at i:9099914 original size:18 final size:20
Alignment explanation
Indices: 9099872--9099915 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
9099862 ATGATTAATT
*
9099872 AAAATTTTATTTAAATTAAA
1 AAAATTTTATATAAATTAAA
*
9099892 TAAATTTT-TATAAA-TAAA
1 AAAATTTTATATAAATTAAA
9099910 AAAATT
1 AAAATT
9099916 AATTATCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 9 0.43
19 5 0.24
20 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAATTTTATATAAATTAAA
Found at i:9100106 original size:10 final size:9
Alignment explanation
Indices: 9100090--9100118 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
9100080 TTAAAGATAA
9100090 TAAAAAAAT
1 TAAAAAAAT
9100099 TAAAAAAAT
1 TAAAAAAAT
9100108 TAAAAAAAT
1 TAAAAAAAT
9100117 TA
1 TA
9100119 GATATTATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:9106089 original size:22 final size:21
Alignment explanation
Indices: 9106047--9106097 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
9106037 TATCTGTAAA
*
9106047 TTAAAATATTATAATACAATGC
1 TTAAAA-ATTATAACACAATGC
*
9106069 TTAAAAATTAGTAACATAATGC
1 TTAAAAATTA-TAACACAATGC
9106091 TTAAAAA
1 TTAAAAA
9106098 CTATTCACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (21 bp):
TTAAAAATTATAACACAATGC
Found at i:9106110 original size:22 final size:21
Alignment explanation
Indices: 9106064--9106147 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 21
9106054 ATTATAATAC
* *
9106064 AATGCTTAAAAATTAGTAACAT
1 AATGCTTAAAAACTA-TTACAT
*
9106086 AATGCTTAAAAACTATTCACGT
1 AATGCTTAAAAACTATT-ACAT
* * *
9106108 AAT-ATTCAAAAACCAGTTACAA
1 AATGCTT-AAAAACTA-TTACAT
9106130 AATGCTTAAAAACTATTA
1 AATGCTTAAAAACTATTA
9106148 AAATTACTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
21 6 0.12
22 39 0.80
23 4 0.08
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (21 bp):
AATGCTTAAAAACTATTACAT
Found at i:9106348 original size:51 final size:52
Alignment explanation
Indices: 9106251--9106348 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 52
9106241 AATAATACTC
* * * *
9106251 AAAATGCTAAAAGGTTTTTCTTTATATATTAAAAACCATTCAAAAATACTTA
1 AAAATACTAAAAGGTTTTTCTTAATATATCAAAAACCACTCAAAAATACTTA
* * * *
9106303 AAAATACTCAAAGGTTTTT-TTAATGTATCAAAAATCACTCCAAAAT
1 AAAATACTAAAAGGTTTTTCTTAATATATCAAAAACCACTCAAAAAT
9106349 GTTCAAAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
51 21 0.55
52 17 0.45
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (52 bp):
AAAATACTAAAAGGTTTTTCTTAATATATCAAAAACCACTCAAAAATACTTA
Found at i:9106547 original size:13 final size:15
Alignment explanation
Indices: 9106498--9106548 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
9106488 TTAAACATAT
*
9106498 AAATTAATTTCATTAA
1 AAATTAATTT-ATTTA
*
9106514 AAATAAATTTATTTA
1 AAATTAATTTATTTA
9106529 AAATTAATTT-TTT-
1 AAATTAATTTATTTA
9106542 AAATTAA
1 AAATTAA
9106549 AAATAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 7 0.22
14 3 0.09
15 13 0.41
16 9 0.28
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTAATTTATTTA
Found at i:9107112 original size:27 final size:27
Alignment explanation
Indices: 9107082--9107136 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
9107072 TGAGATACAG
9107082 TAACTCGTTT-GAAAATGACAACCATCA
1 TAACTCGTTTGGAAAA-GACAACCATCA
9107109 TAACTCGTTTGGAAAAGACAACCATCA
1 TAACTCGTTTGGAAAAGACAACCATCA
9107136 T
1 T
9107137 TAAAGAAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (27 bp):
TAACTCGTTTGGAAAAGACAACCATCA
Found at i:9110095 original size:22 final size:21
Alignment explanation
Indices: 9110065--9110106 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
9110055 TTTCCAATCT
9110065 TAAATAATATTA-AATAATTTA
1 TAAATAATATTATAA-AATTTA
9110086 TAAATTAATATTATAAAATTT
1 TAAA-TAATATTATAAAATTT
9110107 CAATTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 13 0.68
23 2 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAATAATATTATAAAATTTA
Found at i:9111637 original size:21 final size:19
Alignment explanation
Indices: 9111612--9111664 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
9111602 GACGTATGTG
9111612 AATAATTTAATATATAAATAT
1 AATAATTTAATA-ATAAA-AT
*
9111633 CATAATTATAATAATAAAAT
1 AATAATT-TAATAATAAAAT
*
9111653 AATAAATTAATA
1 AATAATTTAATA
9111665 GATCATGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 5 0.18
20 7 0.25
21 11 0.39
22 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAATTTAATAATAAAAT
Found at i:9120865 original size:29 final size:30
Alignment explanation
Indices: 9120803--9120871 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
9120793 TACATTTAAT
* *
9120803 CAAA-TTTTATATTTTTATTTTAAGTCAAA
1 CAAATTTTTATATTTTTATTTCAAATCAAA
*
9120832 CAAATTTTTATA-TTTTATTTCAAATTAAA
1 CAAATTTTTATATTTTTATTTCAAATCAAA
*
9120861 TAAATTTTTAT
1 CAAATTTTTAT
9120872 GATTAATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 28 0.80
30 7 0.20
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (30 bp):
CAAATTTTTATATTTTTATTTCAAATCAAA
Found at i:9131264 original size:16 final size:15
Alignment explanation
Indices: 9131243--9131272 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
9131233 AAAAGAAACA
9131243 TCTCCTTACTTCTTCC
1 TCTCCTT-CTTCTTCC
9131259 TCTCCTTCTTCTTC
1 TCTCCTTCTTCTTC
9131273 TACTGCTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.03, C:0.43, G:0.00, T:0.53
Consensus pattern (15 bp):
TCTCCTTCTTCTTCC
Found at i:9132978 original size:19 final size:19
Alignment explanation
Indices: 9132941--9132977 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9132931 GATGTTTCAA
*
9132941 AAAATGTTTAAATTATTTT
1 AAAATATTTAAATTATTTT
9132960 AAAATATTTAAA-TATTTT
1 AAAATATTTAAATTATTTT
9132978 TTTACTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
AAAATATTTAAATTATTTT
Found at i:9133049 original size:17 final size:18
Alignment explanation
Indices: 9133029--9133075 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
9133019 AAATAAGTTT
9133029 TTATTATTAA-TAATTAA
1 TTATTATTAATTAATTAA
9133046 TTATTA-TAATTAATTAA
1 TTATTATTAATTAATTAA
* *
9133063 ATATTATTTATTA
1 TTATTATTAATTA
9133076 TTTTATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 3 0.12
17 18 0.69
18 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATTATTAATTAATTAA
Found at i:9133056 original size:13 final size:14
Alignment explanation
Indices: 9133031--9133061 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
9133021 ATAAGTTTTT
9133031 ATTATTAATAATTA
1 ATTATTAATAATTA
9133045 ATTATT-ATAATTA
1 ATTATTAATAATTA
9133058 ATTA
1 ATTA
9133062 AATATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTATTAATAATTA
Found at i:9135871 original size:28 final size:28
Alignment explanation
Indices: 9135840--9135893 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
9135830 TATGTAAAAA
* *
9135840 GTTTAAATAATTTTTTAT-TTTTTATTAT
1 GTTT-AATAAGTTTGTATATTTTTATTAT
9135868 GTTTAATAAGTTTGTATATTTTTATT
1 GTTTAATAAGTTTGTATATTTTTATT
9135894 TTAAGTTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (28 bp):
GTTTAATAAGTTTGTATATTTTTATTAT
Found at i:9136190 original size:31 final size:29
Alignment explanation
Indices: 9136154--9136226 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
9136144 ATTAATTATA
*
9136154 AAAATTTATTTAATTTAAAATAAAAAATAT
1 AAAATTTATTTAATGTAAAAT-AAAAATAT
* *
9136184 ACAAATTTAGTTAAATGTAATATAAAAATA-
1 A-AAATTTA-TTTAATGTAAAATAAAAATAT
9136214 AAAATTTATTTAA
1 AAAATTTATTTAA
9136227 AATTTCTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
28 4 0.11
29 7 0.19
30 2 0.05
31 14 0.38
32 10 0.27
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTTATTTAATGTAAAATAAAAATAT
Found at i:9137206 original size:3 final size:3
Alignment explanation
Indices: 9137198--9137225 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
9137188 GTTTTCATTT
9137198 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
9137226 ATATAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:9156347 original size:2 final size:2
Alignment explanation
Indices: 9156340--9156404 Score: 107
Period size: 2 Copynumber: 33.5 Consensus size: 2
9156330 GACTGAAGAC
9156340 GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
9156381 GA -A GA GA GA GA GA GA GG GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
9156405 GAAGGATAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9157783 original size:28 final size:28
Alignment explanation
Indices: 9157752--9157835 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 28
9157742 TTCATATGAC
* *
9157752 AATTTAGAGATTAAGATTTAAAATTTTT
1 AATTTAGAAATTAAGATTTAAGATTTTT
* *
9157780 AATTTTGAAATTACA-ATTTAAGATTTTG
1 AATTTAGAAATTA-AGATTTAAGATTTTT
*
9157808 AATTTA-AAATTTAAGAGTTAAGATTTTT
1 AATTTAGAAA-TTAAGATTTAAGATTTTT
9157836 TATTGATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 4 0.09
28 41 0.89
29 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.46
Consensus pattern (28 bp):
AATTTAGAAATTAAGATTTAAGATTTTT
Found at i:9157805 original size:21 final size:21
Alignment explanation
Indices: 9157781--9157823 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9157771 AAAATTTTTA
*
9157781 ATTTTGAAATTACAATTTAAG
1 ATTTTGAAATTAAAATTTAAG
*
9157802 ATTTTGAATTTAAAATTTAAG
1 ATTTTGAAATTAAAATTTAAG
9157823 A
1 A
9157824 GTTAAGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (21 bp):
ATTTTGAAATTAAAATTTAAG
Found at i:9178871 original size:30 final size:30
Alignment explanation
Indices: 9178813--9178874 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
9178803 ATTAATTATG
9178813 AAGATTTATTTTATTCAAAATAAAAAATAT
1 AAGATTTATTTTATTCAAAATAAAAAATAT
*
9178843 AAGAGTTTA-TTTAGTTTAAAAT-AAAAATAT
1 AAGA-TTTATTTTA-TTCAAAATAAAAAATAT
9178873 AA
1 AA
9178875 AAACATGATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (30 bp):
AAGATTTATTTTATTCAAAATAAAAAATAT
Found at i:9179192 original size:10 final size:10
Alignment explanation
Indices: 9179177--9179202 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9179167 CAAAATTTAT
9179177 GAAATTAAAA
1 GAAATTAAAA
9179187 GAAATTAAAA
1 GAAATTAAAA
9179197 GAAATT
1 GAAATT
9179203 GGTTTAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (10 bp):
GAAATTAAAA
Found at i:9187799 original size:14 final size:15
Alignment explanation
Indices: 9187780--9187809 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
9187770 AAATAATATT
9187780 TTAATTAA-TATTAA
1 TTAATTAATTATTAA
9187794 TTAATTAATTATTAA
1 TTAATTAATTATTAA
9187809 T
1 T
9187810 ATTAAAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATTAATTATTAA
Found at i:9208090 original size:19 final size:19
Alignment explanation
Indices: 9208048--9208090 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
9208038 AAAATATTTA
*
9208048 TTTAAATTTTATTCAATAG
1 TTTAAATTTTATTCAAAAG
*
9208067 TTTAAATTTT-TTTAAAAG
1 TTTAAATTTTATTCAAAAG
9208085 TATTAA
1 T-TTAA
9208091 TATAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTAAATTTTATTCAAAAG
Found at i:9234833 original size:15 final size:15
Alignment explanation
Indices: 9234813--9234847 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
9234803 ACAATAACTT
*
9234813 TAATAACTTGAAAAA
1 TAATAAATTGAAAAA
9234828 TAATAAATTGAAAAA
1 TAATAAATTGAAAAA
9234843 TAATA
1 TAATA
9234848 GAAACAAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (15 bp):
TAATAAATTGAAAAA
Found at i:9239356 original size:15 final size:15
Alignment explanation
Indices: 9239338--9239369 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
9239328 ATCAGGAATT
9239338 TTCAAATCTATAATA
1 TTCAAATCTATAATA
9239353 TTCAAATCTATAATA
1 TTCAAATCTATAATA
9239368 TT
1 TT
9239370 ATCACATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (15 bp):
TTCAAATCTATAATA
Found at i:9240889 original size:3 final size:3
Alignment explanation
Indices: 9240883--9240925 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
9240873 GATGGTGGGC
9240883 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
9240926 CCCTGAAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:9242934 original size:17 final size:18
Alignment explanation
Indices: 9242897--9242934 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9242887 AGTAAAGGGA
9242897 AAAACATGAAAAATAATT
1 AAAACATGAAAAATAATT
9242915 AAAACAT-AAGAAAT-ATT
1 AAAACATGAA-AAATAATT
9242932 AAA
1 AAA
9242935 GTAATAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAACATGAAAAATAATT
Found at i:9247014 original size:17 final size:18
Alignment explanation
Indices: 9246971--9247015 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
9246961 TGATTAGAAA
*
9246971 AAATAATTTTTAGTTTAT
1 AAATTATTTTTAGTTTAT
9246989 AATATTATTTTTA-TTTAT
1 AA-ATTATTTTTAGTTTAT
9247007 AAATTATTT
1 AAATTATTT
9247016 ATAATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 7 0.28
18 9 0.36
19 9 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
AAATTATTTTTAGTTTAT
Found at i:9253000 original size:22 final size:22
Alignment explanation
Indices: 9252970--9253031 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
9252960 TAACGTGTTG
* *
9252970 TGAACATGACGTGTAATATTTT
1 TGAAAATGACGTGTAACATTTT
9252992 TGAAAATGACGTGTAACATTTT
1 TGAAAATGACGTGTAACATTTT
*
9253014 T-ATATATGACGTGTAACA
1 TGA-AAATGACGTGTAACA
9253032 AATGATTGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
TGAAAATGACGTGTAACATTTT
Found at i:9253324 original size:31 final size:31
Alignment explanation
Indices: 9253278--9253353 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
9253268 AATGGTCGTG
* * * *
9253278 CATACCAAGTAAAATGTTATAACATGTTAAG
1 CATACCAGGTCAAATGTTATAACATGCTAAA
* * * *
9253309 CATACTAGGTCAAATGTTGTTATATGCTAAA
1 CATACCAGGTCAAATGTTATAACATGCTAAA
9253340 CATACCAGGTCAAA
1 CATACCAGGTCAAA
9253354 AGTTGTTACA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (31 bp):
CATACCAGGTCAAATGTTATAACATGCTAAA
Found at i:9254285 original size:69 final size:69
Alignment explanation
Indices: 9254155--9254286 Score: 169
Period size: 69 Copynumber: 1.9 Consensus size: 69
9254145 CACATATGCT
* * * *
9254155 CACCATGCCATGTCACACGATTCCAACATGCCTTGTCATAGATTCTCACCATGCCGTATCACACA
1 CACCATGCCATGTCACACGATTCCAACATGCCGTGTCACACATTCTCACCATGCCGCATCACACA
9254220 TTCC
66 TTCC
* **
9254224 CACCATGCCGTGTCACAC-ATTCCCATGATGCCGTGTCACACATTCTCACCAT-CCTGCATCACA
1 CACCATGCCATGTCACACGATT-CCAACATGCCGTGTCACACATTCTCACCATGCC-GCATCACA
9254287 AACTCCAAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
68 5 0.09
69 49 0.91
ACGTcount: A:0.25, C:0.38, G:0.12, T:0.25
Consensus pattern (69 bp):
CACCATGCCATGTCACACGATTCCAACATGCCGTGTCACACATTCTCACCATGCCGCATCACACA
TTCC
Found at i:9254286 original size:23 final size:23
Alignment explanation
Indices: 9254141--9254275 Score: 137
Period size: 23 Copynumber: 5.9 Consensus size: 23
9254131 AAGCCATGGT
* * *
9254141 GTGTCACATATGCTCACCATGCC
1 GTGTCACACATTCCCACCATGCC
* *
9254164 ATGTCACACGATT-CCAACATGCC
1 GTGTCACAC-ATTCCCACCATGCC
* * * *
9254187 TTGTCATAGATTCTCACCATGCC
1 GTGTCACACATTCCCACCATGCC
*
9254210 GTATCACACATTCCCACCATGCC
1 GTGTCACACATTCCCACCATGCC
**
9254233 GTGTCACACATTCCCATGATGCC
1 GTGTCACACATTCCCACCATGCC
*
9254256 GTGTCACACATTCTCACCAT
1 GTGTCACACATTCCCACCAT
9254276 CCTGCATCAC
Statistics
Matches: 89, Mismatches: 21, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
22 3 0.03
23 84 0.94
24 2 0.02
ACGTcount: A:0.24, C:0.36, G:0.13, T:0.27
Consensus pattern (23 bp):
GTGTCACACATTCCCACCATGCC
Found at i:9254442 original size:23 final size:23
Alignment explanation
Indices: 9254416--9254460 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
9254406 CATATCACAA
*
9254416 CCATGTCACATATGCTCACCATG
1 CCATCTCACATATGCTCACCATG
*
9254439 CCATCTCACATATTCTCACCAT
1 CCATCTCACATATGCTCACCAT
9254461 TGTGTGTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.38, G:0.07, T:0.29
Consensus pattern (23 bp):
CCATCTCACATATGCTCACCATG
Found at i:9254482 original size:23 final size:23
Alignment explanation
Indices: 9254418--9254492 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
9254408 TATCACAACC
* * **
9254418 ATGTCACATATGCTCACCATGCC
1 ATGTCATATATTCTCACCATGGT
* * *
9254441 ATCTCACATATTCTCACCATTGT
1 ATGTCATATATTCTCACCATGGT
*
9254464 GTGTCATATATTCAT-ACCATGGT
1 ATGTCATATATTC-TCACCATGGT
9254487 ATGTCA
1 ATGTCA
9254493 CATTCTCACA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 40 0.98
24 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (23 bp):
ATGTCATATATTCTCACCATGGT
Found at i:9254664 original size:23 final size:23
Alignment explanation
Indices: 9254634--9254701 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
9254624 TTGTGGCAAT
* *
9254634 CGTGTCACATATTCTCACCATGA
1 CGTGTCACACATTCCCACCATGA
9254657 CGTGTCACACATTCCCACCAT-A
1 CGTGTCACACATTCCCACCATGA
9254679 CAGTGTCACACATTCCCACCATG
1 C-GTGTCACACATTCCCACCATG
9254702 GCATTTCACA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.05
23 39 0.95
ACGTcount: A:0.26, C:0.37, G:0.12, T:0.25
Consensus pattern (23 bp):
CGTGTCACACATTCCCACCATGA
Found at i:9254710 original size:23 final size:23
Alignment explanation
Indices: 9254636--9254711 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
9254626 GTGGCAATCG
* * *
9254636 TGTCACATATTCTCACCATGACG
1 TGTCACACATTCCCACCATGACA
9254659 TGTCACACATTCCCACCAT-ACA
1 TGTCACACATTCCCACCATGACA
*
9254681 GTGTCACACATTCCCACCATGGCA
1 -TGTCACACATTCCCACCATGACA
*
9254705 TTTCACA
1 TGTCACA
9254712 AACTCTAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 2 0.04
23 42 0.91
24 2 0.04
ACGTcount: A:0.28, C:0.36, G:0.11, T:0.26
Consensus pattern (23 bp):
TGTCACACATTCCCACCATGACA
Found at i:9266945 original size:2 final size:2
Alignment explanation
Indices: 9266940--9266967 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9266930 GTGTGTGTGT
9266940 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
9266968 ACAAGGGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9275914 original size:72 final size:72
Alignment explanation
Indices: 9275838--9276001 Score: 170
Period size: 72 Copynumber: 2.3 Consensus size: 72
9275828 TCATAGAGAG
* * *
9275838 GAAAAGAGATCAACACGGCACAATGACAATGAATTTGAGCCTAA-TTC-GAGAGATGATCGGTAT
1 GAAAAGAGATCAACAAGGCACAATGACAATGAATTTGAGCC-AAGGTCAG-GAGAAGATCGGTAT
9275901 AGAAGGGAA
64 AGAAGGGAA
* * * * * * *
9275910 GAAAAAAGATCTAGAAGGCACAATGATAGTGACTTTGAGCCAAGGTCAGGAGAAGATCGTTATAG
1 GAAAAGAGATCAACAAGGCACAATGACAATGAATTTGAGCCAAGGTCAGGAGAAGATCGGTATAG
* *
9275975 GAGGGAT
66 AAGGGAA
* *
9275982 GAAAAGAGGTCAATAAGGCA
1 GAAAAGAGATCAACAAGGCA
9276002 TGGTGATGAT
Statistics
Matches: 74, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
71 2 0.03
72 71 0.96
73 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.29, T:0.18
Consensus pattern (72 bp):
GAAAAGAGATCAACAAGGCACAATGACAATGAATTTGAGCCAAGGTCAGGAGAAGATCGGTATAG
AAGGGAA
Found at i:9283779 original size:2 final size:2
Alignment explanation
Indices: 9283772--9283797 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9283762 AAGAAATAGA
9283772 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
9283798 CTCAACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9296376 original size:3 final size:3
Alignment explanation
Indices: 9296368--9296396 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9296358 GGAAAGCTGT
9296368 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
9296397 AATATTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:9297095 original size:2 final size:2
Alignment explanation
Indices: 9297088--9297122 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
9297078 TAATATCTAA
* *
9297088 AT AT AT AT AT AT AT AT CT GT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9297123 GACAGAACTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9297105 original size:20 final size:20
Alignment explanation
Indices: 9297080--9297122 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
9297070 CCCTTCGGTA
9297080 ATATCTAAATATATATATAT
1 ATATCTAAATATATATATAT
**
9297100 ATATCTGTATATATATATAT
1 ATATCTAAATATATATATAT
9297120 ATA
1 ATA
9297123 GACAGAACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATCTAAATATATATATAT
Found at i:9305733 original size:34 final size:34
Alignment explanation
Indices: 9305695--9305762 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
9305685 ACACCCGAAA
9305695 ACCGTCTTAACTTAAGTCTTTTGAATTCAAAGAC
1 ACCGTCTTAACTTAAGTCTTTTGAATTCAAAGAC
9305729 ACCGTCTTAACTTAAGTCTTTTGAATTCAAAGAC
1 ACCGTCTTAACTTAAGTCTTTTGAATTCAAAGAC
9305763 TTAGTTGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (34 bp):
ACCGTCTTAACTTAAGTCTTTTGAATTCAAAGAC
Found at i:9309304 original size:1 final size:1
Alignment explanation
Indices: 9309293--9309323 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
9309283 CAAATAAGGA
*
9309293 GGGGGGAGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
9309324 TGTGGAACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:9310222 original size:2 final size:2
Alignment explanation
Indices: 9310215--9310242 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9310205 TAAAAAGCAC
9310215 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9310243 TCATAGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9313280 original size:12 final size:12
Alignment explanation
Indices: 9313247--9313292 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
9313237 TGTGCTACTA
9313247 AAAATA-TTTTT
1 AAAATATTTTTT
*
9313258 AATAACATTTTTT
1 AA-AATATTTTTT
*
9313271 -TAATATTTTTT
1 AAAATATTTTTT
9313282 AAAATATTTTT
1 AAAATATTTTT
9313293 ATGAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
11 11 0.39
12 12 0.43
13 5 0.18
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (12 bp):
AAAATATTTTTT
Done.